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    Using RNA-seq to characterize pollen–stigma interactions for pollination studies

    1.Garibaldi, L. A. et al. Stability of pollination services decreases with isolation from natural areas despite honey bee visits. Ecol. Lett. 14, 1062–1072. https://doi.org/10.1111/j.1461-0248.2011.01669.x (2011).Article 
    PubMed 

    Google Scholar 
    2.Klein, A. M. et al. Importance of pollinators in changing landscapes for world crops. Proc. Biol. Sci. 274, 303–313. https://doi.org/10.1098/rspb.2006.3721 (2007).Article 
    PubMed 

    Google Scholar 
    3.Kearns, C. A. & Inouye, A. D. W. Techniques for Pollination Biologists (University Press Colorado, 1993).
    Google Scholar 
    4.Rader, R. et al. Alternative pollinator taxa are equally efficient but not as effective as the honeybee in a mass flowering crop. J. Appl. Ecol. 46, 1080–1087. https://doi.org/10.1111/j.1365-2664.2009.01700.x (2009).Article 

    Google Scholar 
    5.Ne’eman, G., Jurgens, A., Newstrom-Lloyd, L., Potts, S. G. & Dafni, A. A framework for comparing pollinator performance: Effectiveness and efficiency. Biol. Rev. Camb. Philos. Soc. 85, 435–451. https://doi.org/10.1111/j.1469-185X.2009.00108.x (2010).Article 
    PubMed 

    Google Scholar 
    6.King, C., Ballantyne, G., Willmer, P. G. & Freckleton, R. Why flower visitation is a poor proxy for pollination: Measuring single-visit pollen deposition, with implications for pollination networks and conservation. Methods Ecol. Evol. 4, 811–818. https://doi.org/10.1111/2041-210x.12074 (2013).Article 

    Google Scholar 
    7.Wang, H. et al. Evaluation of pollinator effectiveness based on pollen deposition and seed production in a gynodieocious alpine plant, Cyananthus delavayi. Ecol. Evol. 7, 8156–8160. https://doi.org/10.1002/ece3.3391 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    8.Ashman, T. L., Alonso, C., Parra-Tabla, V. & Arceo-Gomez, G. Pollen on stigmas as proxies of pollinator competition and facilitation: Complexities, caveats, and future directions. Ann. Bot. https://doi.org/10.1093/aob/mcaa012 (2020).Article 
    PubMed 

    Google Scholar 
    9.Wodehouse, R. P. Pollen grains in the identification and classification of plants 1. The Ambrosiaceae. Bull. Torrey Bot. Club 55, 20 (1928).
    Google Scholar 
    10.Currie, J., Noiton, D., Lawes, S. & Bailey, D. Preliminary results of differentiating apple sports by pollen ultrastructure. Euphytica 98, 155–161. https://doi.org/10.1023/a:1003174529263 (1997).Article 

    Google Scholar 
    11.Bock, J. H. & Norris, D. O. Additional Approaches in Forensic Plant Science. 129–147. https://doi.org/10.1016/b978-0-12-801475-2.00010-5 (2016).12.Depciuch, J., Kasprzyk, I., Drzymala, E. & Parlinska-Wojtan, M. Identification of birch pollen species using FTIR spectroscopy. Aerobiologia (Bologna) 34, 525–538. https://doi.org/10.1007/s10453-018-9528-4 (2018).Article 

    Google Scholar 
    13.Galimberti, A. et al. A DNA barcoding approach to characterize pollen collected by honeybees. PLoS One 9, e109363. https://doi.org/10.1371/journal.pone.0109363 (2014).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    14.Keller, A. et al. Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples. Plant Biol. (Stuttg.) 17, 558–566. https://doi.org/10.1111/plb.12251 (2015).CAS 
    Article 

    Google Scholar 
    15.Sickel, W. et al. Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach. BMC Ecol. 15, 20. https://doi.org/10.1186/s12898-015-0051-y (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    16.Bell, K. L. et al. Pollen DNA barcoding: Current applications and future prospects. Genome 59, 629–640. https://doi.org/10.1139/gen-2015-0200 (2016).Article 
    PubMed 

    Google Scholar 
    17.Galliot, J.-N. et al. Investigating a flower-insect forager network in a mountain grassland community using pollen DNA barcoding. J. Insect. Conserv. 21, 827–837. https://doi.org/10.1007/s10841-017-0022-z (2017).Article 

    Google Scholar 
    18.Bell, K. L. et al. Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures. Mol. Ecol. 28, 431–455. https://doi.org/10.1111/mec.14840 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    19.Broderick, R. et al. RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias. BMC Plant Biol. 14, 10 (2014).Article 

    Google Scholar 
    20.Gómez, E. M., Buti, M., Sargent, D. J., Dicenta, F. & Ortega, E. Transcriptomic analysis of pollen–pistil interactions in almond (Prunus dulcis) identifies candidate genes for components of gametophytic self-incompatibility. Tree Genet Genomes https://doi.org/10.1007/s11295-019-1360-7 (2019).Article 

    Google Scholar 
    21.Zhang, C. C. et al. Transcriptome analysis reveals self-incompatibility in the tea plant (Camellia sinensis) might be under gametophytic control. BMC Genom. 17, 359. https://doi.org/10.1186/s12864-016-2703-5 (2016).CAS 
    Article 

    Google Scholar 
    22.Zhang, T. et al. Time-course transcriptome analysis of compatible and incompatible pollen-stigma interactions in Brassica napus L.. Front Plant Sci. 8, 682. https://doi.org/10.3389/fpls.2017.00682 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Li, K., Wang, Y. & Qu, H. RNA-Seq analysis of compatible and incompatible styles of Pyrus species at the beginning of pollination. Plant Mol. Biol. 102, 287–306. https://doi.org/10.1007/s11103-019-00948-1 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    24.Rutley, N. & Twell, D. A decade of pollen transcriptomics. Plant Reprod. 28, 73–89. https://doi.org/10.1007/s00497-015-0261-7 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    25.Conze, L. L., Berlin, S., Le Bail, A. & Kost, B. Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes. BMC Genom. 18, 581. https://doi.org/10.1186/s12864-017-3972-3 (2017).CAS 
    Article 

    Google Scholar 
    26.He, Y. et al. Transcriptome analysis of self- and cross-pollinated pistils revealing candidate unigenes of self-incompatibility in Camellia oleifera. J. Hortic. Sci. Biotechnol. 95, 19–31. https://doi.org/10.1080/14620316.2019.1632749 (2019).CAS 
    Article 

    Google Scholar 
    27.Pérez-de-Castro, M. et al. Application of genomic tools in plant breeding. Curr. Genom. 13, 179–195 (2012).Article 

    Google Scholar 
    28.Leydon, A. R. et al. The molecular dialog between flowering plant reproductive partners defined by SNP-informed RNA-sequencing. Plant Cell 29, 984–1006. https://doi.org/10.1105/tpc.16.00816 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    29.Shi, D. et al. Transcriptome and phytohormone analysis reveals a comprehensive phytohormone and pathogen defence response in pear self-/cross-pollination. Plant Cell Rep. 36, 1785–1799. https://doi.org/10.1007/s00299-017-2194-0 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    30.Kron, P. & Husband, B. C. The effects of pollen diversity on plant reproduction: Insights from apple. Sex. Plant Reprod. 19, 125–131. https://doi.org/10.1007/s00497-006-0028-2 (2006).CAS 
    Article 

    Google Scholar 
    31.Matsumoto, S., Soejima, J. & Maejima, T. Influence of repeated pollination on seed number and fruit shape of ‘Fuji’ apples. Sci. Hortic. 137, 131–137. https://doi.org/10.1016/j.scienta.2012.01.033 (2012).Article 

    Google Scholar 
    32.Garratt, M. P. et al. Avoiding a bad apple: Insect pollination enhances fruit quality and economic value. Agric. Ecosyst. Environ. 184, 34–40. https://doi.org/10.1016/j.agee.2013.10.032 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    33.Stavert, J. R., Bailey, C., Kirkland, L. & Rader, R. Pollen tube growth from multiple pollinator visits more accurately quantifies pollinator performance and plant reproduction. Sci. Rep. 10, 16958. https://doi.org/10.1038/s41598-020-73637-5 (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    34.Rader, R., Howlett, B. G., Cunningham, S. A., Westcott, D. A. & Edwards, W. Spatial and temporal variation in pollinator effectiveness: Do unmanaged insects provide consistent pollination services to mass flowering crops?. J. Appl. Ecol. 49, 126–134. https://doi.org/10.1111/j.1365-2664.2011.02066.x (2012).Article 

    Google Scholar 
    35.Sorin, Y. B., Mitchell, R. J., Trapnell, D. W. & Karron, J. D. Effects of pollination and postpollination processes on selfing rate in Mimulus ringens. Am. J. Bot. 103, 1524–1528. https://doi.org/10.3732/ajb.1600145 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    36.DeLong, C. N., Yoder, K. S., Combs, L., Veilleux, R. E. & Peck, G. M. Apple pollen tube growth rates are regulated by parentage and environment. J. Am. Soc. Hortic. Sci. 141, 548–554. https://doi.org/10.21273/jashs03824-16 (2016).Article 

    Google Scholar 
    37.Zhao, P., Wang, M. & Zhao, L. Dissecting stylar responses to self-pollination in wild tomato self-compatible and self-incompatible species using comparative proteomics. Plant Physiol. Biochem. 106, 177–186. https://doi.org/10.1016/j.plaphy.2016.05.001 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    38.Rao, P. et al. Dynamic transcriptomic analysis of the early response of female flowers of Populus alba x P. glandulosa to pollination. Sci. Rep. 7, 6048. https://doi.org/10.1038/s41598-017-06255-3 (2017).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    39.Tu, D. et al. Developmental, chemical and transcriptional characteristics of artificially pollinated and hormone-induced parthenocarpic fruits of Siraitia grosvenorii. RSC Adv. 7, 12419–12428. https://doi.org/10.1039/c6ra28341a (2017).ADS 
    CAS 
    Article 

    Google Scholar 
    40.Hiscock, S. J. & Allen, A. M. Diverse cell signalling pathways regulate pollen–stigma interactions: The search for consensus. New Phytol. 179, 286–317. https://doi.org/10.1111/j.1469-8137.2008.02457.x (2008).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    41.Xu, X. H., Wang, F., Chen, H., Sun, W. & Zhang, X. S. Transcript profile analyses of maize silks reveal effective activation of genes involved in microtubule-based movement, ubiquitin-dependent protein degradation, and transport in the pollination process. PLoS One 8, e53545. https://doi.org/10.1371/journal.pone.0053545 (2013).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    42.Habu, T. & Tao, R. Transcriptome analysis of self- and cross-pollinated pistils of Japanese Apricot (Prunus mume Sieb. et Zucc.). J. Jpn. Soc. Hortic. Sci. 83, 95–107. https://doi.org/10.2503/jjshs1.CH-086 (2014).CAS 
    Article 

    Google Scholar 
    43.Sun, Y. & Xiao, H. Identification of alternative splicing events by RNA sequencing in early growth tomato fruits. BMC Genom. 16, 948. https://doi.org/10.1186/s12864-015-2128-6 (2015).CAS 
    Article 

    Google Scholar 
    44.Zhao, Y., Li, D. & Liu, T. Pollination-induced transcriptome and phylogenetic analysis in Cymbidium tortisepalum (Orchidaceae). Russ. J. Plant Physiol. 66, 618–627. https://doi.org/10.1134/s1021443719040174 (2019).CAS 
    Article 

    Google Scholar 
    45.Nishida, S. et al. Pollen–pistil interactions in reproductive interference: Comparisons of heterospecific pollen tube growth from alien species between two native Taraxacum species. Funct. Ecol. 28, 450–457. https://doi.org/10.1111/1365-2435.12165 (2014).Article 

    Google Scholar 
    46.Briggs, H. M. et al. Heterospecific pollen deposition in Delphinium barbeyi: Linking stigmatic pollen loads to reproductive output in the field. Ann. Bot. 117, 341–347. https://doi.org/10.1093/aob/mcv175 (2016).Article 
    PubMed 

    Google Scholar 
    47.Richardson, R. T. et al. Quantitative multi-locus metabarcoding and waggle dance interpretation reveal honey bee spring foraging patterns in Midwest agroecosystems. Mol. Ecol. 28, 686–697. https://doi.org/10.1111/mec.14975 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    48.Peel, N. et al. Semi-quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet). Methods Ecol. Evol. 10, 1690–1701. https://doi.org/10.1111/2041-210x.13265 (2019).Article 

    Google Scholar 
    49.Baksay, S. et al. Experimental quantification of pollen with DNA metabarcoding using ITS1 and trnL. Sci. Rep. 10, 4202. https://doi.org/10.1038/s41598-020-61198-6 (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    50.Washburn, J. D. et al. Genome-guided phylo-transcriptomic methods and the nuclear phylogentic tree of the paniceae grasses. Sci. Rep. 7, 13528. https://doi.org/10.1038/s41598-017-13236-z (2017).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    51.Piñeiro Fernández, L. et al. A Phylogenomic analysis of the floral transcriptomes of sexually deceptive and rewarding European Orchids, Ophrys and Gymnadenia. Front. Plant Sci. https://doi.org/10.3389/fpls.2019.01553 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    52.Pawelkowicz, M. et al. Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination. Plant Reprod. 32, 193–216. https://doi.org/10.1007/s00497-019-00362-z (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    53.Li, X. et al. Comparative transcriptomic analysis provides insight into the domestication and improvement of pear (P. pyrifolia) fruit. Plant Physiol. 180, 435–452. https://doi.org/10.1104/pp.18.01322 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    54.Sassa, H., Kakui, H. & Minamikawa, M. Pollen-expressed F-box gene family and mechanism of S-RNase-based gametophytic self-incompatibility (GSI) in Rosaceae. Sex Plant Reprod. 23, 39–43. https://doi.org/10.1007/s00497-009-0111-6 (2010).CAS 
    Article 
    PubMed 

    Google Scholar 
    55.Ramírez, F. & Davenport, T. L. Apple pollination: A review. Sci. Hortic. 162, 188–203. https://doi.org/10.1016/j.scienta.2013.08.007 (2013).Article 

    Google Scholar 
    56.Gu, C., Wang, L., Korban, S. S. & Han, Y. Identification and characterization of S-RNasegenes andS-genotypes in Prunus and Malus species. Can. J. Plant Sci. 95, 213–225. https://doi.org/10.4141/cjps-2014-254 (2015).CAS 
    Article 

    Google Scholar 
    57.Sassa, H. Molecular mechanism of the S-RNase-based gametophytic self-incompatibility in fruit trees of Rosaceae. Breed. Sci. 66, 116–121. https://doi.org/10.1270/jsbbs.66.116 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    58.Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    59.Andrews, S. (Babraham, UK, 2010).60.Daccord, N. et al. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat. Genet. 49, 1099–1106. https://doi.org/10.1038/ng.3886 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    61.Kim, D., Langmead, B. & Salzberg, S. L. HISAT: A fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360. https://doi.org/10.1038/nmeth.3317 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    62.Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat. Protoc. 11, 1650–1667. https://doi.org/10.1038/nprot.2016.095 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    63.Williams, C. R., Baccarella, A., Parrish, J. Z. & Kim, C. C. Trimming of sequence reads alters RNA-Seq gene expression estimates. BMC Bioinform. 17, 103. https://doi.org/10.1186/s12859-016-0956-2 (2016).CAS 
    Article 

    Google Scholar 
    64.Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 13. https://doi.org/10.1186/s13059-016-0881-8 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    65.Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295. https://doi.org/10.1038/nbt.3122 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    66.Menzel, P., Ng, K. L. & Krogh, A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7, 11257. https://doi.org/10.1038/ncomms11257 (2016).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    67.Ballgown: Flexible, Isoform-Level Differential Expression Analysis v. 2.20.0. (Bioconductor, 2020).68.Tello, D. et al. NGSEP3: Accurate variant calling across species and sequencing protocols. Bioinformatics 35, 4716–4723. https://doi.org/10.1093/bioinformatics/btz275 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    69.Huson, D. H. & Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254–267. https://doi.org/10.1093/molbev/msj030 (2006).CAS 
    Article 
    PubMed 

    Google Scholar 
    70.Milne, I. et al. Flapjack–graphical genotype visualization. Bioinformatics 26, 3133–3134. https://doi.org/10.1093/bioinformatics/btq580 (2010).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    71.Duitama, J. et al. An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. Nucleic Acids Res. 42, e44. https://doi.org/10.1093/nar/gkt1381 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar  More

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    WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees

    The geographic area covered by the WOODIV database is the Euro-Mediterranean region, as defined by Médail et al.1. The northern Mediterranean region was selected following the definition of terrestrial ecoregions of the world by Olson et al.13. The study area covers all or part of the following countries and islands: Albania, Croatia, Cyprus, France, Greece, Italy, Malta, Montenegro, Portugal, Slovenia, Southern Macedonia, and Spain, including the Balearic archipelago, Corsica, Sardinia, Sicily, and Crete.We focused on the 245 tree taxa (210 species and 35 subspecies) identified in the Euro-Mediterranean checklist from Médail et al.1. These taxa belong to 33 families and 64 genera and include 46 endemics (as defined by Médail et al.1, i.e. range-restricted taxa in and outside of the study area).Observed occurrence dataWe collected tree occurrence data (at the species or subspecies level) from 23 sources: national databases and floras, regional databases, and publications (Table 1). Some records still unpublished were specifically provided at the grid level for this project by experts for southern Macedonia, Malta, Montenegro, and Sicily (four sources, Table 1).Table 1 Sources of the occurrence records, giving the name of the dataset (Source name; ined. if unpublished), the Type of data (records with geographic coordinates (records), records at the grid level (gridded records), or atlas-type (atlas) data), and the Countries/Islands covered by the source.Full size tableWhen considering the subspecies level, the WOODIV database lacks the occurrences of 11 sub-species among the 35 listed by Médail et al.1. When aggregated at the species level (to match the taxonomic resolution of the functional and phylogenetic data which are available at the species level only), the WOODIV database lacks only the occurrences of 3 of the 210 species from the Médail et al.1 checklist (n = 207; Table 2; Supplementary Table 2): Pyrus elaeagrifolia Pall., which occurs in Albania and Macedonia (and in northeastern Greece but outside the Mediterranean biome), P. syriaca Boiss. and Tamarix passerinoides Desv., which occur in Cyprus and in Sardinia, respectively.Table 2 Summary of the availability of data in the WOODIV database: total number of species among the 210 species from the Médail et al.1 checklist with (1) observed occurrences; (2) functional traits data, including the detail of the number of species with available data for 4 traits: adult plant height (Height), seed mass (SeedMass), specific leaf area (SLA) and wood density (SSD) (see “Functional data” section); and, (3) genetic data including the detail of the number of species with available data for 3 DNA-regions: matK, rbcL and psbA-trnH (see “Genetic data” section).Full size tableAlso, due to the taxonomic heterogeneity of the different data sources, we recommend aggregating the occurrences of certain tree taxa at the species’ group level (see sections Data Records and Usage Notes): i.e. to aggregate Pinus uncinata DC. and P. mugo Turra into P. mugo aggr., Juniperus deltoides R.P.Adams and J. oxycedrus L. into J. oxycedrus aggr. and Alnus lusitanica Vít, Douda & Mandák., A. rohlenae Vít, Douda & Mandák, and A. glutinosa (L.) Gaertn. into A. glutinosa aggr. The WOODIV database thus contains reliable occurrences of 200 species and three aggregated species (n = 203; Table 2; Supplementary Table 2).The raw dataset obtained from gathering occurrences from all sources included a total of 1,248,701 occurrence records distributed across the participating countries.The raw occurrence data were aggregated at a resolution of 10 × 10 km in line with an INSPIRE14 compliant 10 × 10 km grid (SCR 4258). This gridding procedure provided a way to standardize data from different sources. We selected this spatial grain because it was the finest resolution available for some countries of the study area (e.g. Slovenia, Croatia, Greece). Sources of occurrence data with a resolution coarser than 10 × 10 km (e.g. Atlas Florae Europaeae15) were not considered. The considered area includes 10,042 grid cells with at least one occurrence record (Fig. 1a). The occurrence dataset provided by the WOODIV database, i.e. aggregated records for species considered as native in the given grid cell using the 10 × 10 km grid (removal of duplicate species within a grid cell) includes 140,279 occurrences.Fig. 1Geographic scope of the WOODIV database, spatial distribution, and validation of trees occurrences. (a) Number of species within a 10 × 10 km grid cell based on modelled occurrence data for the 171 modelled species, with the addition of the occurrence data of the 21 small-range species; and, within grid cells of Atlas Flora Europaeae (AFE; 50x50km) (b) Number of species with presences recorded in AFE but not in the WOODIV dataset on the 104 species present both in the AFE and WOODIV data; and, (c) Number of species with presences recorded in the WOODIV dataset but not in AFE on the 104 species present both in the AFE and WOODIV data.Full size imageModelled occurrence dataThe WOODIV database provides modelled occurrences of the species from the Médail et al.1 checklist. From the 10 × 10 km gridded observed occurrence data, we modelled the distribution of each species across the Euro-Mediterranean area using Species Distribution Models (SDM). SDM statistically relate species occurrence records to environmental variables to predict the potential distribution of species16.Due to the extent of the study area, we only related species occurrence to climate gradients17. Bioclimatic variables were extracted from the CHELSA database V1.218 available at a resolution of 30 arc‐sec (http://chelsa‐climate.org/) and then averaged to a 10 × 10 km resolution. The selection of the environmental predictors for niche modeling is a source of uncertainty in model predictions that can be reduced with sound statistical methods and ecological knowledge of the target species19. We also focused on proximal predictors that directly influence species distribution and selected a low number of predictive variables to reduce the issues of model overfitting and multicollinearity20. We selected four bioclimatic variables that previous studies had reported to be relevant predictors of the distribution of plant species, especially in environments such as those that characterize the Mediterranean Basin21,22,23,24: “Minimum temperature of the coldest month” (Bio06, in °C) quantifies potentially lethal frost events and more generally, stress due to low temperatures; “Total annual precipitation” (Bio12, in mm) approximates average water availability; “Precipitation of the driest month” (Bio14, in mm) describes the extremes associated with drought events and stress due to low water availability, and “Temperature seasonality” (Bio04, no dimension) describes the variability of temperature during the year. All selected predictors showed VIF (variance inflation factor25) values below 5, indicating that a given predictor was not correlated with any linear combinations of the other predictors (VIF Bio04 = 1.68, VIF Bio06 = 2.06, VIF Bio12 = 1.53, and VIF Bio14 = 2.07).We related species occurrence to these four bioclimatic variables using the Random Forest algorithm26. As only presence data are archived in the WOODIV database, we randomly sampled a number of pseudo-absences equal to the number of observed occurrences27. This random selection of pseudo-absences was repeated 10 times for each species. When comparing the floras, occurrence data in the Italian Peninsula, Sardinia and/or Sicily were highly unrepresentative of the distribution of some species (n = 84; see Supplementary Table 3). To overcome this potential bias in the models, we did not include these regions in the model calibration step (Supplementary Table 3). The model was projected in these areas after having tested the similarity in the variables between the projection dataset (Italy, Sicily, and Sardinia) and the fitting dataset (the rest of the study area). Indeed, when model predictions are projected into regions not analyzed in the fitting data, it is necessary to measure the similarity between the new environments and those in the training sample28, as models are not so reliable when predicting outside their domain29. Similarity analyses computed using ExDet30 indicated that all covariables in the projected area are within the univariate range of the fitting area and that there is no change in correlation between covariables (NT1 and NT2 = 0).Each of these 10 datasets (per species) was then randomly split into two datasets to evaluate model performance on pseudo-independent data31: 70% of the data was used to calibrate models and the 30% remaining data was used to evaluate model performance using the True Skill Statistic (TSS32) and the Area Under the Curve (AUC) of the receiver-operating characteristic (ROC) plot33 metrics. This split-sample step was repeated 10 times resulting in 100 models per species.For each of the 171 modelled species, a mean model (from the 100 replicates) was then used to predict potential species distribution. Predicted probabilities of occurrence were finally converted into presence/absence using the threshold maximizing the TSS. We fitted all models under the R environment R Core team34 and the package biomod235,36.The WOODIV database provides modelled occurrences of each of the 171 species for each 10 × 10 km grid cell (Fig. 1a). Thirty-two species with less than 10 occurrence records were not modelled (Supplementary Table 3). Among these 32 species, 21 are small-ranged species whose distribution is limited to a few grid cells (Supplementary Table 3). The observed occurrence records for these 21 species can be considered as representative of their distribution and we therefore recommend using the non-modelled records for these species for analyses. The occurrences of the remaining 11 species should be considered unrepresentative of their distribution.Functional dataFour functional traits were considered in this project: adult plant height (Height), seed mass (SeedMass), specific leaf area (SLA), and wood density (StemSpecDens). These traits have been proposed to reflect a global spectrum of plant strategies37,38: height is a commonly measured proxy for individual size and reflects several aspects including resource acquisition, competitive ability, or dispersal capacity. SeedMass represents the trade-off between fecundity, seed survival, and dispersal. SLA (the ratio between leaf area and dry mass) is correlated to photosynthetic capacity and leaf life span and is an indirect measure of the return on investments in carbon gain compared to water loss. StemSpecDens is a key component of woody plant growth linked to the mechanical support of the stem and its growth rate.We compiled the values for these traits at the species level for the trees from the Médail et al.1 checklist, referring mostly to 2 databases: TRY9 and BROT 2.039. Supplementary values were obtained from more specific databases (Global Wood Density Database40, Kew Seed Information Database41) or from the scientific literature and atlas42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61. In total, 92% of the entries were extracted from TRY, 7% from BROT 2.0 and the remaining were retrieved from the other sources. The original ID of records from the TRY and BROT databases is provided in order to make it possible to refer to the complete observation if a user needs to have some contextual information.The WOODIV database lacks all traits data for only 6 of the 210 species from the checklist (Table 2, Supplementary Table 2): Alnus lusitanica Vít, Douda & Mandák, Alnus rohlenae Vít, Douda & Mandák, Malus dasyphylla Borkh., Quercus infectoria Olivier, Tamarix arborea Ehrenb. ex Bunge and, Tamarix passerinoides Del. ex Desf.Adult plant height and seed mass data were available for more than 75% of the 210 species (Table 2; Fig. 2a), whereas wood density and specific leaf area were available for only around 50%. The WOODIV database includes all four trait values for 41% of the 210 species (Fig. 2b; Supplementary Table 2), three trait values for 56% more species.Fig. 2Prevalence of traits and genetic data among the 210 species from Médail et al.1 checkist: (a) For each of the four considered functional traits (adult plant height (Height), seed mass (SeedMass), wood density (SSD) and specific leaf area (SLA)), percentage of the 210 species with existing data; (b) Percentage of the 210 species for which none to four functional traits data are available; (c) For each of the three considered DNA regions (matK, rbcL and psbA-trnH), percentage of the 210 species with existing data (in grey species with only one available sequence for the considered region, in black species with consensus sequence for that region); and, (d) Percentage of the 210 species for which none to three DNA regions data are available.Full size imageThe database provides an R script that can be used to estimate missing trait values using the taxonomic classification if needed.Genetic dataThree different DNA regions from the plastid genome corresponding to the most commonly used DNA barcode regions62,63,64 were considered in this project: the ribulose-bisphosphate/carboxylase Large-subunit gene (rbcL), the maturase-K gene (matK), and the psbA-trnH intergenic spacer (trnH).In a first step, we collected all sequences from GenBank (https://www.ncbi.nlm.nih.gov/genbank/) for the three DNA regions available for the species from the Médail et al.1 checklist at the species level: rbcL: n = 650 sequences for 146 species, matK: n = 644 sequences for 127 species, trnH: n = 493 sequences for 129 species). To fill the gaps, we obtained DNA from fresh samples collected in the field or gathered from herbarium specimens (Supplementary Table 4). DNA extraction and sequencing were performed at INRA-URFM, Avignon (France) and the National Research Council (IBBR-CNR), Florence (Italy) (rbcL: n = 233 for 125 species, matK: n = 162 for 91 species, trnH: n = 200 for 120 species). Methods used for DNA isolation and Sanger sequencing are described by Albassatneh et al.65. When more than one sequence was available for a given DNA region/species, a sequence alignment was performed to check data quality and a taxon-consensus sequence was generated. Consensus sequences were built using the IUPAC-IUB ambiguity66 code for a total of 119 (rbcL), 109 (matK), and 110 species (trnH), respectively (Fig. 2c). All newly created sequences were uploaded to GenBank.The WOODIV database lacks the DNA-region sequences data of only 6 of the 210 species from the Médail et al.1 checklist (Table 2, Fig. 2d): Alnus lusitanica Vít, Douda & Mandák, Cytisus aeolicus Guss., Celtis planchoniana K.I. Chr., Salix appendiculata Vill., Tamarix hampeana Boiss. & Heldr. and, Tamarix minoa J.L. Villar, Turland, Juan, Gaskin, M.A. Alonso & M.B. Crespo.PhylogenyThe WOODIV database provides a phylogram including the 204 species for which at least one piece of DNA-region sequence data was available (Supplementary Table 2) and phylograms including the 210 species from the Medail et al.1 list (Supplementary Fig. 1).Uneven taxon sampling focused on a single biogeographic area such as ours, can bias phylogenetic inferences67. Our goal here is to provide DNA sequence data that can be readily re-used to estimate, e.g. comparable phylogenetic diversity indices, not phylogenetic inferences per se. To illustrate our DNA-sequences data and to facilitate their use for future analyses (to calculate phylogenetic diversity for example), we constructed a molecular phylogeny encompassing the 204 Euro-Mediterranean tree species. Each gene was independently aligned using the MAFFT program68 and parsed using the program Gblocks69 to exclude the segments characterized by several variable positions or gaps from final alignments. An appropriate substitution model of sequence evolution was selected for each of the three plastid DNA regions using the Akaike Information Criterion (AIC) as implemented in the JModeltest 2 program70. The optimal substitution model identified was the same for all three sequences: GTR + I + G. We obtained a concatenated matrix with 1615 aligned bases. We used the Maximum Likelihood analysis71 as implemented in the RAxML V8 program72. The DNA sequence matrix of 1615 sites was analyzed using three partitions with the GTRGAMMAI model (GTR + Gamma substitution model + proportion of invariant sites). We searched for the optimal tree, running at least 20 independent maximum likelihood analyses; full analyses also consisted of 100 bootstrap replicates72.For users who would like to work on the complete pool of 210 tree species, we also built a 210 species phylogram including all Euro-Mediterranean trees. The six missing species for which no DNA-region sequence was available were added to the phylogenetic tree using the Simulation with Uncertainty for Phylogenetic Investigating (SUNPLIN) method73, with 100 replicates. The geometric median tree was computed from the set of 100 replicates with the medTree function from the R package treespace74. Both the median tree and the set of 100 replicates are provided in the WOODIV database, together with the molecular tree with 204 species. More

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    Impact of noise on development, physiological stress and behavioural patterns in larval zebrafish

    1.Miedema, H., Janssen, S., Rokho, K. & Brown, L. Burden of disease from environmental noise: quantification of healthy life years lost in Europe (2011).2.Peris, E. Environmental noise in Europe: 2020. Eur. Environ. Agency 1, 104 (2020).
    Google Scholar 
    3.Merchant, N. D. Underwater noise abatement: Economic factors and policy options. Environ. Sci. Policy 92, 116–123 (2019).Article 

    Google Scholar 
    4.Babisch, W. et al. Auditory and non-auditory effects of noise on health. NIH Lancet 23, 1–7 (2014).
    Google Scholar 
    5.Recio, A., Linares, C., Banegas, J. R. & Díaz, J. Road traffic noise effects on cardiovascular, respiratory, and metabolic health: an integrative model of biological mechanisms. Environ. Res. 146, 359–370 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    6.Shannon, G. et al. A synthesis of two decades of research documenting the effects of noise on wildlife. Biol. Rev. 91, 982–1005 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    7.Halfwerk, W. et al. Low-frequency songs lose their potency in noisy urban conditions. Proc. Natl. Acad. Sci. 108, 14549–14554 (2011).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Kight, C. R. & Swaddle, J. P. How and why environmental noise impacts animals: an integrative, mechanistic review. Ecol. Lett. 14, 1052–1061 (2011).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    9.Whitfield, A. K. & Becker, A. Impacts of recreational motorboats on fishes: a review. Mar. Pollut. Bull. 83, 24–31 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    10.Popper, A. N. N. & Hastings, M. C. C. The effects of anthropogenic sources of sound on fishes. J. Fish Biol. 75, 455–489 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    11.Bejder, L., Samuels, A., Whitehead, H., Finn, H. & Allen, S. Impact assessment research: use and misuse of habituation, sensitisation and tolerance in describing wildlife responses to anthropogenic stimuli. Mar. Ecol. Prog. Ser. 395, 177–185 (2009).ADS 
    Article 

    Google Scholar 
    12.Wale, M. A., Simpson, S. D. & Radford, A. N. Size-dependent physiological responses of shore crabs to single and repeated playback of ship noise. Biol. Lett. 9, 20121194 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    13.Nedelec, S. L., Simpson, S. D., Morley, E. L., Nedelec, B. & Radford, A. N. Impacts of regular and random noise on the behaviour, growth and development of larval Atlantic cod (Gadus morhua). Proc. R. Soc. B 282, 20151943 (2015).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    14.Johansson, K., Sigray, P., Backström, T. & Magnhagen, C. Stress response and habituation to motorboat noise in two coastal fish species in the Bothnian Sea. In The Effects of Noise on Aquatic Life II 273–279 (2016).15.Holmes, L. J., McWilliam, J., Ferrari, M. C. O. & McCormick, M. I. Juvenile damselfish are affected but desensitize to small motor boat noise. J. Exp. Mar. Bio. Ecol. 494, 63–68 (2017).Article 

    Google Scholar 
    16.Reid, S. G., Bernier, N. J. & Perry, S. F. The adrenergic stress response in fish: Control of catecholamine storage and release. Comp. Biochem. Physiol. C. Pharmacol. Toxicol. Endocrinol. 120, 1–27 (1998).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    17.Rajalakshmi, R., John, N. A. & John, J. Review on noise pollution and its associated health hazards. Sch. J. Appl. Med. Sci. 4, 500–503 (2016).
    Google Scholar 
    18.Christie, K. W. & Eberl, D. F. Noise-induced hearing loss: new animal models. Curr. Opin. Otolaryngol. Head Neck Surg. 22, 374–383 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Ortega, C. P. Effects of noise pollution on birds: A brief review of our knowledge. Source Ornithol. Monogr. Ornithol. Monogr. 74, 6–22 (2012).Article 

    Google Scholar 
    20.Simmons, A. M. & Narins, P. M. Effects of anthropogenic noise on amphibians and reptiles. In Springer Handbook of Auditory Research 179–208 (Springer, 2018).21.de Soto, N. A. et al. Anthropogenic noise causes body malformations and delays development in marine larvae. Sci. Rep. 3, 2831 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    22.Soto, N. A. de. Peer-reviewed studies on the effects of anthropogenic noise on marine invertebrates: from scallop larvae to giant squid. Eff. Noise Aquat. Life II 875, 273–279 (2016).23.Brouček, J. Effect of noise on performance, stress, and behaviour of animals. Slovak J. Anim. Sci 47, 111–123 (2014).
    Google Scholar 
    24.Tennessen, J. B., Parks, S. E. & Langkilde, T. Traffic noise causes physiological stress and impairs breeding migration behaviour in frogs. Conserv. Physiol. 2, 1–8 (2014).Article 
    CAS 

    Google Scholar 
    25.Erbe, C., Dunlop, R. & Dolman, S. Effects of noise on marine mammals. In Effects of Anthropogenic Noise on Animals 277–309 (Springer, 2018).26.Kunc, H. P., McLaughlin, K. E. & Schmidt, R. Aquatic noise pollution: implications for individuals, populations, and ecosystems. Proc. R. Soc. B 283, 20160839 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    27.van der Sluijs, I. et al. Communication in troubled waters: responses of fish communication systems to changing environments. Evol. Ecol. 25, 623–640 (2011).Article 

    Google Scholar 
    28.Cox, B. S., Dux, A. M., Quist, M. C. & Guy, C. S. Use of a seismic air gun to reduce survival of nonnative lake trout embryos: a tool for conservation?. N. Am. J. Fish. Manag. 32, 292–298 (2012).Article 

    Google Scholar 
    29.Wysocki, L. E. et al. Effects of aquaculture production noise on hearing, growth, and disease resistance of rainbow trout Oncorhynchus mykiss. Aquaculture 272, 687–697 (2007).Article 

    Google Scholar 
    30.Debusschere, E. et al. Acoustic stress responses in juvenile sea bass Dicentrarchus labrax induced by offshore pile driving. Environ. Pollut. 208, 747–757 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    31.Filiciotto, F. et al. Impact of aquatic acoustic noise on oxidative status and some immune parameters in gilthead sea bream Sparus aurata (Linnaeus, 1758) juveniles. Aquac. Res. 48, 1895–1903 (2017).CAS 
    Article 

    Google Scholar 
    32.Smith, M. E., Kane, A. S. & Popper, A. N. Noise-induced stress response and hearing loss in goldfish (Carassius auratus). J. Exp. Biol. 207, 427–435 (2004).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    33.Vasconcelos, R. O., Amorim, M. C. P. & Ladich, F. Effects of ship noise on the detectability of communication signals in the Lusitanian toadfish. J. Exp. Biol. 210, 2104–2112 (2007).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    34.Hasan, M. R., Crane, A. L., Ferrari, M. C. O. & Chivers, D. P. A cross-modal effect of noise: the disappearance of the alarm reaction of a freshwater fish. Anim. Cogn. 21, 419–424 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    35.Herbert-Read, J. E., Kremer, L., Bruintjes, R., Radford, A. N. & Ioannou, C. C. Anthropogenic noise pollution from pile-driving disrupts the structure and dynamics of fish shoals. Proc. R. Soc. B Biol. Sci. 284, 1–9 (2017).
    Google Scholar 
    36.Francis, C. D. & Barber, J. R. A framework for understanding noise impacts on wildlife: an urgent conservation priority. Front. Ecol. Environ. 11, 305–313 (2013).Article 

    Google Scholar 
    37.Ladich, F. Acoustic communication and the evolution of hearing in fishes. Philos. Trans. R. Soc. B Biol. Sci. 355, 1285–1288 (2000).CAS 
    Article 

    Google Scholar 
    38.Radford, A. N., Kerridge, E. & Simpson, S. D. Acoustic communication in a noisy world: can fish compete with anthropogenic noise?. Behav. Ecol. 25, 1022–1030 (2014).Article 

    Google Scholar 
    39.Dooling, R. J. & Popper, A. N. The effects of highway noise on birds. Environ. Bioacoust. 27, 1–74 (2007).
    Google Scholar 
    40.Blom, E. L. et al. Continuous but not intermittent noise has a negative impact on mating success in a marine fish with paternal care. Sci. Rep. 9, 1–9 (2019).CAS 
    Article 

    Google Scholar 
    41.Bureš, Z., Popelář, J. & Syka, J. Noise exposure during early development impairs the processing of sound intensity in adult rats. Hear. Res. 352, 1–11 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    42.Dorado-Correa, A. M., Zollinger, S. A., Heidinger, B. & Brumm, H. Timing matters: traffic noise accelerates telomere loss rate differently across developmental stages. Front. Zool. 15, 1–8 (2018).Article 
    CAS 

    Google Scholar 
    43.Mueller, C. A. Critical Windows in Animal Development: Interactions Between Environment, Phenotype, and Time (Springer, 2018).
    Google Scholar 
    44.Gordon, T. A. C. et al. Acoustic enrichment can enhance fish community development on degraded coral reef habitat. Nat. Commun. 10, 1–7 (2019).CAS 
    Article 

    Google Scholar 
    45.Radford, A. N., Lebre, L., Lecaillon, G., Nedelec, S. L. & Simpson, S. D. Repeated exposure reduces the response to impulsive noise in European seabass. Glob. Change Biol. 22, 3349–3360 (2016).ADS 
    Article 

    Google Scholar 
    46.Banner, A. & Hyatt, M. Effects of noise on eggs and larvae of two estuarine fishes. Trans. Am. Fish. Soc. 102, 142–144 (1973).Article 

    Google Scholar 
    47.Fakan, E. P. & McCormick, M. I. Boat noise affects the early life history of two damselfishes. Mar. Pollut. Bull. 141, 493–500 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Jain-Schlaepfer, S., Fakan, E., Rummer, J. L., Simpson, S. D. & McCormick, M. I. Impact of motorboats on fish embryos depends on engine type. Conserv. Physiol. 6, 1–9 (2018).
    Google Scholar 
    49.Brittijn, S. A. et al. Zebrafish development and regeneration: new tools for biomedical research. Int. J. Dev. Biol. 53, 835–850 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    50.Magyary, I. Recent advances and future trends in zebrafish bioassays for aquatic ecotoxicology. Ecocycles 4, 12–18 (2018).Article 

    Google Scholar 
    51.Sarmah, S. & Marrs, J. A. Zebrafish as a vertebrate model system to evaluate effects of environmental toxicants on cardiac development and function. Int. J. Mol. Sci. 17, 1–16 (2016).ADS 
    Article 
    CAS 

    Google Scholar 
    52.Varshney, G. K., Pei, W. & Burgess, S. M. Using zebrafish to study human deafness and hearing regeneration. Monogr. Hum. Genet. 20, 110–131 (2016).Article 

    Google Scholar 
    53.Uribe, P. M. et al. Larval zebrafish lateral line as a model for acoustic trauma. Eneuro 5, 0206–0218 (2018).Article 

    Google Scholar 
    54.Bhandiwad, A. A., Raible, D. W., Rubel, E. W. & Sisneros, J. A. Noise-Induced hypersensitization of the acoustic startle response in larval zebrafish. JARO 19, 741–752 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    55.Lara, R. A. & Vasconcelos, R. O. Characterization of the natural soundscape of zebrafish and comparison with the captive noise conditions. Zebrafish 8, 1–13 (2018).CAS 

    Google Scholar 
    56.Lalonde, R. The neurobiological basis of spontaneous alternation. Neurosci. Biobehav. Rev. 26, 91–104 (2002).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    57.Bogli, S. Y. & Huang, M. Y. Y. Spontaneous alternation behavior in larval zebrafish. J. Exp. Biol. 220, 171–173 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    58.Bruintjes, R. & Radford, A. N. Chronic playback of boat noise does not impact hatching success or post-hatching larval growth and survival in a cichlid fish. PeerJ 2, e594 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    59.Davidson, J., Bebak, J. & Mazik, P. The effects of aquaculture production noise on the growth, condition factor, feed conversion, and survival of rainbow trout Oncorhynchus mykiss. Aquaculture 288, 337–343 (2009).Article 

    Google Scholar 
    60.Neo, Y. Y. et al. Temporal structure of sound affects behavioural recovery from noise impact in European seabass. Biol. Conserv. 178, 65–73 (2014).Article 

    Google Scholar 
    61.Craig, M. P., Gilday, S. D. & Hove, J. R. Dose-dependent effects of chemical immobilization on the heart rate of embryonic zebrafish. Lab Anim. (NY) 35, 40–47 (2006).Article 

    Google Scholar 
    62.Barrionuevo, W. R. & Burggren, W. W. O2 consumption and heart rate in developing zebrafish (Danio rerio): influence of temperature and ambient O2. Am. Physiol. Soc. 276, 505–513 (2013).
    Google Scholar 
    63.De Luca, E. et al. ZebraBeat: a flexible platform for the analysis of the cardiac rate in zebrafish embryos. Sci. Rep. 4, 1–13 (2014).
    Google Scholar 
    64.Simpson, S. D., Yan, H. Y., Wittenrich, M. L. & Meekan, M. G. Response of embryonic coral reef fishes (Pomacentridae: Amphiprion spp.) to noise. Mar. Ecol. Prog. Ser. 287, 201–208 (2005).ADS 
    Article 

    Google Scholar 
    65.Anderson, W. G. et al. Remote monitoring of heart rate as a measure of recovery in angled Atlantic salmon, Salmo salar (L.). Hydrobiologia 371–372, 233–240 (1998).Article 

    Google Scholar 
    66.Armstrong, J. D. Heart rate as an indicator of activity, metabolic rate, food intake and digestion in pike Esox lucius. J. Fish Biol. 29, 207–221 (1986).Article 

    Google Scholar 
    67.Svendsen, E. et al. Heart rate and swimming activity as stress indicators for Atlantic salmon (Salmo salar). Aquaculture 531, 735804 (2020).Article 
    CAS 

    Google Scholar 
    68.Burleson, M. L. & Silva, P. E. Cross tolerance to environmental stressors: effects of hypoxic acclimation on cardiovascular responses of channel catfish (Ictalurus punctatus) to a thermal challenge. Bone 23, 1–7 (2008).
    Google Scholar 
    69.Brown, C., Gardner, C. & Braithwaite, V. A. Differential stress responses in fish from areas of high- and low-predation pressure. J. Comp. Physiol. B Biochem. Syst. Environ. Physiol. 175, 305–312 (2005).Article 

    Google Scholar 
    70.McEwen, B. S. & Stellar, E. Stress and individual. Arch Intern. Med. 153, 2093–2101 (1993).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    71.Mccormick, M. I. Behaviorally induced maternal stress in a fish influences progeny quality by a hormonal mechanism. Ecology 79, 1873–1883 (1998).Article 

    Google Scholar 
    72.Yabu, T., Ishibashi, Y. & Yamashita, M. Stress-induced apoptosis in larval embryos of Japanese flounder. Fish. Sci. 69, 1218–1223 (2003).CAS 
    Article 

    Google Scholar 
    73.Werner, I., Linares-Casenave, J., Van Eenennaam, J. P. & Doroshov, S. I. The effect of temperature stress on development and heat-shock protein expression in larval green sturgeon (Acipenser mirostris). Environ. Biol. Fishes 79, 191–200 (2007).Article 

    Google Scholar 
    74.Shi, Z. et al. Salinity stress on embryos and early larval stages of the pomfret Pampus punctatissimus. Aquaculture 275, 306–310 (2008).CAS 
    Article 

    Google Scholar 
    75.Wilson, K. S. et al. Physiological roles of glucocorticoids during early embryonic development of the zebrafish (Danio rerio). J. Physiol. 591, 6209–6220 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    76.Tudorache, C., Ter Braake, A., Tromp, M., Slabbekoorn, H. & Schaaf, M. J. M. Behavioral and physiological indicators of stress coping styles in larval zebrafish. Stress 3890, 121–128 (2015).Article 
    CAS 

    Google Scholar 
    77.Alsop, D. & Vijayan, M. M. Development of the corticosteroid stress axis and receptor expression in zebrafish. Am. J. Physiol. Regul. Integr. Comp. Physiol. 294, 711–719 (2008).Article 
    CAS 

    Google Scholar 
    78.Bai, Y., Liu, H., Huang, B., Wagle, M. & Guo, S. Identification of environmental stressors and validation of light preference as a measure of anxiety in larval zebrafish. BMC Neurosci. 17, 1–12 (2016).CAS 
    Article 

    Google Scholar 
    79.Barton, B. A. & Zitzow, R. E. Physiological responses of juvenile walleyes to handling stress with recovery in saline water. Progress. Fish-Cult. 57, 267–276 (1995).Article 

    Google Scholar 
    80.Yao, Q., DeSmidt, A. A., Tekin, M., Liu, X. & Lu, Z. Hearing assessment in zebrafish during the first week postfertilization. Zebrafish 13, 79–86 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    81.Colwill, R. M. & Creton, R. Imaging escape and avoidance behavior in zebrafish larvae. Rev. Neurosci. 22, 63–73 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    82.Voellmy, I. K. et al. Acoustic noise reduces foraging success in two sympatric fish species via different mechanisms. Anim. Behav. 89, 191–198 (2014).Article 

    Google Scholar 
    83.Belzung, C. & Griebel, G. Measuring normal and pathological anxiety-like behaviour in mice: a review. Behav. Brain Res. 125, 141–149 (2001).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    84.Sireeni, J. et al. Profound effects of glucocorticoid resistance on anxiety-related behavior in zebrafish adults but not in larvae. Gen. Comp. Endocrinol. 292, 130–138 (2020).Article 
    CAS 

    Google Scholar 
    85.Basnet, R. M., Zizioli, D., Taweedet, S., Finazzi, D. & Memo, M. Zebrafish larvae as a behavioral model in neuropharmacology. Biomedicines 7, 1–16 (2019).Article 
    CAS 

    Google Scholar 
    86.Peng, X. et al. Anxiety-related behavioral responses of pentylenetetrazole-treated zebrafish larvae to light-dark transitions. Pharmacol. Biochem. Behav. 145, 55–65 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    87.Stewart, A. et al. Neurophenotyping of adult zebrafish using the light/dark box paradigm. NeuroMethods 51, 157–167 (2011).CAS 
    Article 

    Google Scholar 
    88.Bögli, S. Y. & Huang, M.Y.-Y. Spontaneous alternation behavior in larval zebrafish. J. Exp. Biol. 220, 171–173 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    89.Mueller, T., Dong, Z., Berberoglu, M. A. & Guo, S. The dorsal pallium in zebrafish, Danio rerio (Cyprinidae, Teleostei). Brain Res. 1381, 95–105 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    90.Fotowat, H., Lee, C., Jun, J. J. & Maler, L. Neural activity in a hippocampus-like region of the teleost pallium are associated with navigation and active sensing. bioRxiv 8, 1–25 (2018).91.Broglio, C. et al. Hallmarks of a common forebrain vertebrate plan: specialized pallial areas for spatial, temporal and emotional memory in actinopterygian fish. Brain Res. Bull. 66, 277–281 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    92.Cheng, L., Wang, S. H., Chen, Q. C. & Liao, X. M. Moderate noise induced cognition impairment of mice and its underlying mechanisms. Physiol. Behav. 104, 981–988 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    93.Jauregui-huerta, F., Garcia-estrada, J. & Gonzalez-perez, O. Early exposure to noise followed by predator stress in adulthood impairs the rat’s
    re-learning flexibility in Radial Arm Water Maze. Neuro Endocrinol. Lett. 31, 1–12 (2010).
    Google Scholar 
    94.Rodriguez, M. & Afonso, D. Ontogeny of T-maze behavioral lateralization in rats. Physiol. Behav. 54, 91–94 (1993).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    95.Nichols, T. A., Anderson, T. W. & Ana, Š. Intermittent noise induces physiological stress in a coastal marine fish. PLoS ONE 10, 1–13 (2015).CAS 

    Google Scholar 
    96.Neo, Y. Y. et al. Sound exposure changes European seabass behaviour in a large outdoor floating pen: effects of temporal structure and a ramp-up procedure. Environ. Pollut. 214, 26–34 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    97.Celi, M. et al. Vessel noise pollution as a human threat to fish: assessment of the stress response in gilthead sea bream (Sparus aurata, Linnaeus 1758). Fish Physiol. Biochem. 42, 631–641 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    98.Erbe, C. Underwater noise of small personal watercraft (jet skis). J. Acoust. Soc. Am. 133, EL326–EL330 (2013).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    99.Department of the Environment and Water Resources. Comparative Assessment of the Environmental Performance of Small Engines Marine Outboards and Personal Watercraft. Environmental Science and Technology (2007).100.Westerfield, M. The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish (Danio rerio) 5th edn. (University of Oregon Press, Eugene, 2000).
    Google Scholar 
    101.Lu, Z. & Desmidt, A. A. Early development of hearing in zebrafish. JARO 14, 509–521 (2013).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    102.Strykowski, J. L. & Schech, J. M. Effectiveness of recommended euthanasia methods in larval zebrafish (Danio rerio). J. Am. Assoc. Lab. Anim. Sci. 54, 81–84 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    103.Amoser, S., Wysocki, L. E. & Ladich, F. Noise emission during the first powerboat race in an Alpine lake and potential impact on fish communities. J. Acoust. Soc. Am. 116, 3789–3797 (2004).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    104.Codarin, A., Wysocki, L. E., Ladich, F. & Picciulin, M. Effects of ambient and boat noise on hearing and communication in three fish species living in a marine protected area (Miramare, Italy). Mar. Pollut. Bull. 58, 1880–1887 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    105.Shafiei Sabet, S., Neo, Y. Y. & Slabbekoorn, H. The effect of temporal variation in sound exposure on swimming and foraging behaviour of captive zebrafish. Anim. Behav. 107, 49–60 (2015).Article 

    Google Scholar 
    106.Nedelec, S. L. et al. Particle motion: the missing link in underwater acoustic ecology. Methods Ecol. Evol. 7, 836–842 (2016).Article 

    Google Scholar 
    107.Chan, P. K., Lin, C. C. & Cheng, S. H. Noninvasive technique for measurement of heartbeat regularity in zebrafish (Danio rerio) embryos. BMC Biotechnol. 9, 1–10 (2009).Article 

    Google Scholar 
    108.Teixidó, E. et al. Automated morphological feature assessment for zebrafish embryo developmental toxicity screens. Toxicol. Sci. 167, 438–449 (2019).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    109.Lau, B. Y. B., Mathur, P., Gould, G. G. & Guo, S. Identification of a brain center whose activity discriminates a choice behavior in zebrafish. Proc. Natl. Acad. Sci. U. S. A. 108, 2581–2586 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    110.Bögli, S. Y., Huang, M.Y.-Y., Bogli, S. Y. & Huang, M.Y.-Y. Spontaneous alternation behavior in larval zebrafish. J. Exp. Biol. 220, 171–173 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    111.Frederickson, C. J. & Frederickson, M. H. Developmental changes in open-field behavior in the kitten. Dev. Psychobiol. 12, 623–628 (1979).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    112.Vecera, S. P., Rothbart, M. K. & Posner, M. I. Development of spontaneous alternation in infancy. J. Cogn. Neurosci. 3, 351–354 (1991).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    113.Bogli, S. Y. & Huang, M.Y.-Y. Spontaneous alternation behavior in larval zebrafish. J. Exp. Biol. 220, 171–173 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    114.Du Sert, N. P. et al. The arrive guidelines 2.0: updated guidelines for reporting animal research. PLoS Biol. 18, 1–12 (2020).
    Google Scholar  More

  • in

    Characterization of the bacterial microbiome of Rhipicephalus (Boophilus) microplus collected from Pecari tajacu “Sajino” Madre de Dios, Peru

    1.Bonnet, S. I., Binetruy, F., Hernández-Jarguín, A. M. & Duron, O. The tick microbiome: Why non-pathogenic microorganisms matter in tick biology and pathogen transmission. Front. Cell. Infect. Microbiol. 7, 236. https://doi.org/10.3389/fcimb.2017.00236 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    2.Burgdorfer, W., Hayes, S. & Mavros, A. Non-pathogenic rickettsiae in Dermacentor andersoni: A limiting factor for the distribution of Rickettsia rickettsii. In Rickettsia and Rickettsial Disease (eds Burgdorfer, A. A. & Anacker, R. L.) 585–594 (Academic, 1981).
    Google Scholar 
    3.Chauvin, A., Moreau, E., Bonnet, S., Plantard, O. & Malandrin, L. Babesia and its hosts: Adaptation to long-lasting interactions as a way to achieve efficient transmission. Vet. Res. 40, 37. https://doi.org/10.1051/vetres/2009020 (2009).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    4.Ravi, A. et al. Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus. PLoS Negl. Trop. Dis. 13(1), 1–19 (2019).CAS 
    Article 

    Google Scholar 
    5.Greay, T. L. et al. Recent insights into the tick microbiome gained through next-generation sequencing. Parasites Vectors 11(1), 1–14 (2018).Article 

    Google Scholar 
    6.Rar, V. et al. Detection and genetic characterization of a wide range of infectious agents in Ixodes pavlovskyi ticks in Western Siberia, Russia. Parasites Vectors 10(1), 1–24 (2017).Article 

    Google Scholar 
    7.Filippova, N. A. Ixodid Ticks of the Subfamily Ixodinae (Publishing House Nauka, 1977).
    Google Scholar 
    8.Bouquet, J. et al. Metagenomic-based surveillance of pacific coast tick dermacentor occidentalis identifies two novel bunyaviruses and an emerging human Ricksettsial pathogen. Sci. Rep. 7(1), 1–10. https://doi.org/10.1038/s41598-017-12047-6 (2017).CAS 
    Article 

    Google Scholar 
    9.Andreotti, R. et al. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing. BMC Microbiol. 11(6), 1–11 (2011).
    Google Scholar 
    10.Nakao, R. et al. A novel approach, based on BLSOMs (batch learning self-organizing maps), to the microbiome analysis of ticks. ISME J. 7(5), 1003–1015. https://doi.org/10.1038/ismej.2012.171 (2013).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    11.Xia, H. et al. Metagenomic profile of the viral communities in Rhipicephalus spp. ticks from Yunnan, China. PLoS ONE 10(3), 1–16. https://doi.org/10.1371/journal.pone.0121609 (2015).CAS 
    Article 

    Google Scholar 
    12.Barros-Battesti, D., Arzua, M. & Bechara, H. Carrapato de Importância Medico-Veterinaria da Região Neotropical: Um Guia Ilustrado para Identificação de Espécies (Ticks of Medical-Veterinary Importance in the Neotropical Region: An Illustrated Guide for Species Identification). 10ma edição 223 (Butantan Publicação, 2006).
    Google Scholar 
    13.QIAGEN. Gentra, Puregene (QIAGEN GROUP), 2007–2010 (accessed 9 June 2017); https://www.qiagen.com/us/shop/sample-technologies/dna/genomic-dna/gentra-puregene-tissue-kit/#orderinginformation.14.Sperling, J. L. et al. Comparison of bacterial 16S rRNA variable regions for microbiome surveys of ticks. Ticks Tick Borne Dis. 8, 453–461 (2017).Article 

    Google Scholar 
    15.Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. 108(Supplement 1), 4516–4522 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    16.Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16), 2194–2200 (2011).CAS 
    Article 

    Google Scholar 
    17.Glassing, A. et al. Changes in 16S RNA gene microbial community profiling by concentration of prokaryotic DNA. J. Microbiol. Methods 119, 239242 (2015).Article 

    Google Scholar 
    18.Bokulich, N. A. et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10(1), 57–59 (2013).CAS 
    Article 

    Google Scholar 
    19.Andersen, K. S., Kirkegaard, R. H., Karst, S. M. & Albertsen, M. ampvis2: An R package to analyse and visualise 16S rRNA amplicon data. BioRxiv. https://doi.org/10.1101/299537 (2018).Article 

    Google Scholar 
    20.McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8(4), 1–11 (2013).Article 

    Google Scholar 
    21.DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72(7), 5069–5072 (2006).CAS 
    Article 

    Google Scholar 
    22.Obregón, D., Bard, E., Abrial, D., Estrada-Peña, A. & Cabezas-Cruz, A. Sex-specific linkages between taxonomic and functional profiles of tick gut microbiomes. Front. Cell. Infect. Microbiol. 9, 298. https://doi.org/10.3389/fcimb.2019.00298 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Qiu, Y., Nakao, R., Ohnuma, A., Kawamori, F. & Sugimoto, C. Microbial population analysis of the salivary glands of ticks; a possible strategy for the surveillance of bacterial pathogens. PLoS ONE 9(8), e103961 (2014).ADS 
    Article 

    Google Scholar 
    24.Van Treuren, W. et al. Variation in the microbiota of Ixodes ticks with regard to geography, species, and sex. Appl. Environ. Microbiol. 81, 6200–6209 (2015).Article 

    Google Scholar 
    25.Carpi, G. et al. Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks. PLoS ONE 6(10), e25604 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    26.Zhang, X.-C., Yang, Z.-N., Lu, B., Ma, X.-F. & Zhang, C.-X. The composition and transmission of microbiome in hard tick, Ixodes persulcatus, during blood meal. Ticks Tick Borne Dis. 5, 864–870 (2014).Article 

    Google Scholar 
    27.Menchaca, A. C. et al. Preliminary assessment of microbiome changes following blood-feeding and survivorship in the Amblyomma americanum nymph-to-adult transition using semiconductor sequencing. PLoS ONE 8, 1–10 (2013).Article 

    Google Scholar 
    28.Clayton, K. A., Gall, C. A., Mason, K. L., Scoles, G. A. & Brayton, K. A. The characterization and manipulation of the bacterial microbiome of the Rocky Mountain wood tick, Dermacentor andersoni. Parasites Vectors 8, 1–5 (2018).CAS 

    Google Scholar 
    29.Crump, J. A., Sjölund-Karlsson, M., Gordon, M. A. & Parry, C. M. Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clin. Microbiol. Rev. 1, 901–937. https://doi.org/10.1128/CMR.00002-15 (2015).Article 

    Google Scholar 
    30.Jesser, K. J. & Noble, R. T. Vibrio ecology in the Neuse River Estuary, North Carolina, characterized by next-generation amplicon sequencing of the gene encoding heat shock protein 60 (hsp60). Appl. Environ. Microbiol. 84, 1–21. https://doi.org/10.1128/AEM.00333-18 (2018).Article 

    Google Scholar 
    31.Payne, S. M., Mey, A. R. & Wyckoff, E. E. Vibrio iron transport: Evolutionary adaptation to life in multiple environments. Microbiol. Mol. Biol. Rev. 80, 69–90. https://doi.org/10.1128/MMBR.00046-15 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    32.Boyd, E. F. et al. Post genomic analysis of the evolutionary history and innovations of the family Vibrionaceae. Microbiol. Spectr. 3(5), 1–43. https://doi.org/10.1128/microbiolspec.VE-0009-2014 (2015).ADS 
    CAS 
    Article 

    Google Scholar 
    33.Maj, A. et al. Plasmids of carotenoid-producing Paracoccus spp. (Alphaproteobacteria)—Structure, diversity and evolution. PLoS ONE 8(11), 1–27. https://doi.org/10.1371/journal.pone.0080258 (2013).CAS 
    Article 

    Google Scholar 
    34.Patro, L. P. P. & Rathinavelan, T. Targeting the sugary armor of Klebsiella species. Front. Cell. Infect. Microbiol. 9, 1–23. https://doi.org/10.3389/fcimb.2019.00367 (2019).CAS 
    Article 

    Google Scholar 
    35.Folkesson, A. et al. Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: An evolutionary perspective. Nat. Rev. Microbiol. 10, 841–851. https://doi.org/10.1038/nrmicro2907 (2019).CAS 
    Article 

    Google Scholar 
    36.Wong, J. S. J. et al. Corynebacterium accolens-associated pelvic osteomyelitis. J. Clin. Microbiol. 48(2), 654–655 (2010).Article 

    Google Scholar 
    37.Gay, N. R., Fleming, E. & Oh, J. Draft genome sequence of Cloacibacterium normanense NRS-1 isolated from municipal wastewater. Genome Announc. 4(6), 1–2. https://doi.org/10.1128/genomeA.01397-16 (2016).Article 

    Google Scholar 
    38.Kurilshikov, A. et al. Comparative metagenomic profiling of symbiotic bacterial communities associated with ixodes persulcatus, ixodes pavlovskyi and dermacentor reticulatus ticks. PLoS ONE 10(7), 1–13 (2015).CAS 
    Article 

    Google Scholar 
    39.Martínez, M. A. Retrato microbiológico. J. Microbiol. Immunol. Infect. 44(1), 289–295 (2011).
    Google Scholar 
    40.Moreno-Forero, S. K. & Van-Der-Meer, J. R. Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand. ISME J. 9(1), 150–165 (2015).CAS 
    Article 

    Google Scholar 
    41.Giron, S. Diversidad bacteriana de la garrapata Rhipicephalus (Boophilus) microplus en el ganado bovino del estado de Tamaulipas (Bacterial diversity of Rhipicephalus (Boophilus) microplus tick in cattle of the state of Tamaulipas). (2015). [Thesis]. Thesis to obtain the title of Master of Science in Genomic Biotechnology viable (accessed 14 October 2019); https://tesis.ipn.mx/handle/123456789/24552.42.Jimemez, M., Gasper, M., Carmona, M. & Terio, K. Suidae and Tayassuidae. Pathol. Wildl. Zoo Anim. 1, 207–228 (2018).
    Google Scholar 
    43.Sutherland-Smith, M. Suidae and Tayassuidae (Wild Pigs, Peccaries). Fowler’s Zoo Wild Anim. Med. 1(8), 568–584 (2015).Article 

    Google Scholar 
    44.Bermúdez, S., Meyer, N., Moreno, R. & Artavia, A. NOTAS SOBRE Pecari tajacu (L., Y Tayassu peccari (LINK, 1795) (ARTIODACTYLA: TAYASSUIDAE) COMO HOSPEDEROS DE GARRAPATAS DURAS (ACARI: IXODIDAE) EN PANAMÁ. Tecnociencia 20(1), 61–70 (2008).
    Google Scholar 
    45.Rodríguez-Vivas, R. I., Quiñones, A. F. & Fragoso, S. H. Epidemiología y control de la garrapata Boophilus en México (Epidemiology and control of Boophilus tick in Mexico). In Enfermedades de Importancia Económica en Producción Animal (Diseases of Economic Importance in Animal Production) (ed. Rodríguez-Vivas, R. I.) 571–592 (McGraw-Hill-UADY, 2005).
    Google Scholar 
    46.Duron, O. et al. Evolutionary changes in symbiont community structure in ticks. Mol. Ecol. 26, 2905–2921. https://doi.org/10.1111/mec.14094 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    47.Zhong, J., Jasinskas, A. & Barbour, A. G. Antibiotic treatment of the tick vector Amblyomma americanum reduced reproductive fitness. PLoS ONE 2, 1–7. https://doi.org/10.1371/journal.pone.0000405 (2017).CAS 
    Article 

    Google Scholar 
    48.Gottlieb, Y., Lalzar, I. & Klasson, L. Distinctive genome reduction rates revealed by genomic analyses of two Coxiella-like endosymbionts in ticks. Genome Biol. Evol. 7, 1779–1796. https://doi.org/10.1093/gbe/evv108 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    49.Gerhart, J. G., Moses, A. S. & Raghavan, R. A. Francisella-like endosymbiont in the Gulf Coast tick evolved from a mammalian pathogen. Sci. Rep. 6, 1–6. https://doi.org/10.1038/srep33670 (2016).CAS 
    Article 

    Google Scholar 
    50.Sjodin, A. et al. Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish. BMC Genomics 13, 1–13. https://doi.org/10.1186/1471-2164-13-268 (2012).Article 

    Google Scholar 
    51.Machado-Ferreira, E. et al. Coxiella symbionts are widespread into hard ticks. Parasitol. Res. 115(12), 4691–4699. https://doi.org/10.1007/s00436-016-5230-z (2016).Article 
    PubMed 

    Google Scholar 
    52.Duron, O. The IS1111 insertion sequence used for detection of Coxiella burnetii is widespread in Coxiella-like endosymbionts of ticks. FEMS Microbiol. Lett. 362(17), 1–8. https://doi.org/10.1093/femsle/fnv132 (2015).CAS 
    Article 

    Google Scholar  More

  • in

    Vegetation feedback causes delayed ecosystem response to East Asian Summer Monsoon Rainfall during the Holocene

    1.Walker, M. et al. Formal ratification of the subdivision of the Holocene Series/Epoch (Quaternary System/Period): two new Global Boundary Stratotype Sections and Points (GSSPs) and three new stages/subseries. Episodes [online]. https://doi.org/10.18814/epiiugs/2018/018016 (2018).2.Liu, T., Lu, Y. & Zheng, H. Loess and the Environment. (China Ocean Press, 1985).3.An, Z. et al. Asynchronous Holocene optimum of the East Asian monsoon. Quat. Sci. Rev. 19, 743–762 (2000).ADS 
    Article 

    Google Scholar 
    4.Dai, A. G. & Zhao, T. Uncertainties in historical changes and future projections of drought. Part I: estimates of historical drought changes. Clim. Chang. 144, 519–533 (2017).ADS 
    Article 

    Google Scholar 
    5.Zastrow, M. China’s tree-planting could falter in a warming world. Nature 573, 474–475 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    6.Huang, J., Yu, H., Guan, X., Wang, G. & Guo, R. Accelerated dryland expansion under climate change. Nat. Clim. Change 6, 166–172 (2016).ADS 
    Article 

    Google Scholar 
    7.Jin, G. & Liu, T. Mid-Holocene climate change in North China, and the effect on cultural development. Chin. Sci. Bull. 47, 408–413 (2002).Article 

    Google Scholar 
    8.Wang, Y. et al. The Holocene Asian monsoon: links to solar changes and North Atlantic climate. Science 308, 854–857 (2005).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    9.Cheng, H. et al. The Asian monsoon over the past 640,000 years and ice age terminations. Nature 534, 640–646 (2016).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    10.Dong, J. et al. A high-resolution stalagmite record of the Holocene East Asian monsoon from Mt Shennongjia, central China. Holocene 20, 257–264 (2010).ADS 
    Article 

    Google Scholar 
    11.Beck, J. W. et al. A 550,000-year record of East Asian monsoon rainfall from Be-10 in loess. Science 360, 877–881 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    12.Goldsmith, Y. et al. Northward extent of East Asian monsoon covaries with intensity on orbital and millennial timescales. Proc. Natl Acad. Sci. U. S. A. 114, 1817–1821 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    13.Chen, F. et al. East Asian summer monsoon precipitation variability since the last deglaciation. Sci. Rep. 5, 11186 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    14.Li, Q. et al. Reconstructed moisture evolution of the deserts in northern China since the Last Glacial Maximum and its implications for the East Asian Summer Monsoon. Glob. Planet. Change 121, 101–112 (2014).ADS 
    Article 

    Google Scholar 
    15.Xu, Z. et al. Critical transitions in Chinese dunes during the past 12,000 years. Sci. Adv. 6, eaay8020 (2020).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    16.Lu, H. et al. Late Quaternary aeolian activity in the Mu Us and Otindag dune fields (north China) and lagged response to insolation forcing. Geophys. Res. Lett. 32, L21716 (2005).ADS 
    Article 

    Google Scholar 
    17.Peterse, F. et al. Decoupled warming and monsoon precipitation in East Asia over the last deglaciation. Earth Planet. Sci. Lett. 301, 256–264 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    18.Yang, X. et al. Early-Holocene monsoon instability and climatic optimum recorded by Chinese stalagmites. Holocene 29, 1059–1067 (2019).ADS 
    Article 

    Google Scholar 
    19.Wei, Y. et al. Holocene and deglaciation hydroclimate changes in northern China as inferred from stalagmite growth frequency. Glob. Planet. Change 195, 103360 (2020).Article 

    Google Scholar 
    20.Wang, B. et al. How to measure the strength of the East Asian Summer Monsoon. J. Clim. 21, 4449–4463 (2008).ADS 
    Article 

    Google Scholar 
    21.Liu, J. et al. Holocene East Asian summer monsoon records in northern China and their inconsistency with Chinese stalagmite delta O-18 records. Earth-Sci. Rev. 148, 194–208 (2015).ADS 
    CAS 
    Article 

    Google Scholar 
    22.Kutzbach, J. E. & Street-Perrott, F. A. Milankovitch forcing of fluctuations in the level of tropical lakes from 18 to 0 kyr BP. Nature 317, 130–134 (1985).ADS 
    Article 

    Google Scholar 
    23.Liu, Z. et al. Chinese cave records and the East Asia Summer Monsoon. Quat. Sci. Rev. 83, 115–128 (2014).ADS 
    Article 

    Google Scholar 
    24.Wen, X., Liu, Z., Wang, S., Cheng, J. & Zhu, J. Correlation and anti-correlation of the East Asian summer and winter monsoons during the last 21,000 years. Nat. Commun. 7, 11999 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    25.Liu, Z. et al. Transient simulation of last deglaciation with a new mechanism for Bolling-Allerod warming. Science 325, 310–314 (2009).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    26.LeGrande, A. N. & Schmidt, G. A. Sources of Holocene variability of oxygen isotopes in paleoclimate archives. Clim. Past 5, 441–455 (2009).Article 

    Google Scholar 
    27.Zhang, H. et al. East Asian hydroclimate modulated by the position of the westerlies during Termination I. Science 362, 580–583 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    28.Chiang, J. C. H. et al. Role of seasonal transitions and westerly jets in East Asian paleoclimate. Quat. Sci. Rev. 108, 111–129 (2015).ADS 
    Article 

    Google Scholar 
    29.Waelbroeck, C. et al. Sea-level and deep water temperature changes derived from benthic foraminifera isotopic records. Quat. Sci. Rev. 21, 295–305 (2002).ADS 
    Article 

    Google Scholar 
    30.Joos, F. & Spahni, R. Rates of change in natural and anthropogenic radiative forcing over the past 20,000 years. Proc. Natl Acad. Sci. U.S.A. 105, 1425–1430 (2008).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    31.He, C. et al. The hydroclimate footprint accompanying pan-Asian monsoon water isotope evolution during the last deglaciation. Sci. Adv. 7, eabe2611 (2021).PubMed 
    Article 

    Google Scholar 
    32.Wu, D. et al. Decoupled early Holocene summer temperature and monsoon precipitation in southwest China. Quat. Sci. Rev. 193, 54–67 (2018).ADS 
    Article 

    Google Scholar 
    33.Xiao, X., Yao, A., Hillman, A., Shen, J. & Haberle, S. G. Vegetation, climate and human impact since 20 ka in central Yunnan Province based on high-resolution pollen and charcoal records from Dianchi, southwestern China. Quat. Sci. Rev. 236, 106297 (2020).Article 

    Google Scholar 
    34.Ding, Q. & Wang, B. Circumglobal teleconnection in the Northern Hemisphere summer. J. Clim. 18, 3483–3505 (2005).ADS 
    Article 

    Google Scholar 
    35.Seneviratne, S. I. et al. Investigating soil moisture-climate interactions in a changing climate: a review. Earth-Sci. Rev. 99, 125–161 (2010).ADS 
    CAS 
    Article 

    Google Scholar 
    36.Bonan, G. B., Levis, S., Sitch, S., Vertenstein, M. & Oleson, K. W. A dynamic global vegetation model for use with climate models: concepts and description of simulated vegetation dynamics. Glob. Chang. Biol. 9, 1543–1566 (2003).ADS 
    Article 

    Google Scholar 
    37.Yamazaki, T., Yabuki, H., Ishii, Y., Ohta, T. & Ohata, T. Water and energy exchanges at forests and a grassland in Eastern Siberia evaluated using a one-dimensional land surface model. J. Hydrometeor. 5, 504–515 (2004).ADS 
    Article 

    Google Scholar 
    38.Overpeck, J., Anderson, D., Trumbore, S. & Prell, W. The southwest Indian Monsoon over the last 18 000 years. Clim. Dyn. 12, 213–225 (1996).Article 

    Google Scholar 
    39.Ruddiman, W. F. What is the timing of orbital-scale monsoon changes? Quat. Sci. Rev. 25, 657–658 (2006).ADS 
    Article 

    Google Scholar 
    40.Clemens, S. C. & Prell, W. L. A 350,000 year summer-monsoon multi-proxy stack from the Owen Ridge, Northern Arabian Sea. Mar. Geol. 201, 35–51 (2003).ADS 
    Article 

    Google Scholar 
    41.Xie, P. & Arkin, P. A. Global precipitation: a 17-year monthly analysis based on gauge observations, satellite estimates, and numerical model outputs. Bull. Am. Meteorol. Soc. 78, 2539–2558 (1997).ADS 
    Article 

    Google Scholar 
    42.Xu, Q. et al. Vegetation succession and East Asian Summer Monsoon Changes since the last deglaciation inferred from high-resolution pollen record in Gonghai Lake, Shanxi Province, China. Holocene 27, 835–846 (2017).ADS 
    Article 

    Google Scholar 
    43.Xiao, J. et al. Holocene vegetation variation in the Daihai Lake region of north-central China: a direct indication of the Asian monsoon climatic history. Quat. Sci. Rev. 23, 1669–1679 (2004).ADS 
    Article 

    Google Scholar 
    44.Blaauw, M. Methods and code for ‘classical’ age-modelling of radiocarbon sequences. Quat. Geochronol. 5, 512–518 (2010).Article 

    Google Scholar 
    45.Zheng, Z. et al. East Asian pollen database: modern pollen distribution and its quantitative relationship with vegetation and climate. J. Biogeogr. 41, 1819–1832 (2014).Article 

    Google Scholar 
    46.Song, C. et al. Simulation of China Biome reconstruction based on pollen data from surface sediment samples. Acta Botanica. Sin. 43, 201–209 (2001).
    Google Scholar 
    47.Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).Article 

    Google Scholar 
    48.Overpeck, J. T., Webb, T. & Prentice, I. C. Quantitative interpretation of fossil pollen spectra: dissimilarity coefficients and the method of modern analogs. Quat. Res. 23, 87–108 (1985).Article 

    Google Scholar 
    49.Guiot, J. Methodology of the last climatic cycle reconstruction in France from pollen data. Palaeogeogr. Palaeoclimatol. Palaeoecol. 80, 49–69 (1990).Article 

    Google Scholar 
    50.Peyron, O. et al. Climatic reconstruction in Europe for 18,000 YR B.P. from pollen data. Quat. Res. 49, 183–196 (1998).Article 

    Google Scholar 
    51.Davis, A. S., Brewer, S., Stevenson, A. C. & Guiot, J. The temperature of Europe during the Holocene reconstructed from pollen data. Quat. Sci. Rev. 22, 1701–1716 (2003).ADS 
    Article 

    Google Scholar 
    52.Marsicek, J., Shuman, B. N., Bartlein, P. J., Shafer, S. L. & Brewer, S. Reconciling divergent trends and millennial variations in Holocene temperatures. Nature 554, 92–96 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    53.Juggins, S. Rioja: analysis of quaternary science data. https://cran.r-project.org/package=rioja (2017).54.Prentice, C. et al. Special paper: a global biome model based on plant physiology and dominance, soil properties and climate. J. Biogeogr. 19, 117–134 (1992).Article 

    Google Scholar 
    55.Williams, W. & Shuman, B. Obtaining accurate and precise environmental reconstructions from the modern analog technique and North American surface pollen dataset. Quat. Sci. Rev. 27, 669–687 (2008).ADS 
    Article 

    Google Scholar 
    56.Simpson, G. L. “Analogue methods in palaeolimnology” in Tracking Environmental Change Using Lake Sediments: Data Handling and Numerical Techniques, (eds Birks, H. J. B., Lotter, A. F., Juggins, S. & Smol, J. P.) 495–522 (Springer, 2012).57.Birks, H. J. B., Line, J. M., Juggins, S., Stevenson, A. C. & ter Braak, C. J. F. Diatoms and pH reconstruction. Philos. Trans. R. Soc. B 327, 263–278 (1990).ADS 

    Google Scholar 
    58.ter Braak, C. J. F. & Juggins, S. Weighted averaging partial least squares regression (WA-PLS): an improved method for reconstructing environmental variables from species assemblages. Hydrobiologia 269, 485–502 (1993).Article 

    Google Scholar 
    59.Collins, W. D. et al. The Community Climate System Model version 3 (CCSM3). J. Clim. 19, 2122–2143 (2006).ADS 
    Article 

    Google Scholar 
    60.Berger, A. Long-term variations of daily insolation and quaternary climatic changes. J. Atmos. Sci. 35, 2362–2367 (1978).ADS 
    Article 

    Google Scholar 
    61.Peltier, W. R. Global glacial isostasy and the surface of the ice-age earth: the ICE-5G (VM2) model and GRACE. Annu. Rev. Earth Planet. Sci. 32, 111–149 (2004).ADS 
    CAS 
    Article 

    Google Scholar 
    62.He, F. Simulating transient climate evolution of the last deglaciation with CCSM3. PhD thesis, University of Wisconsin-Madison (2011).63.Shakun, J. D. et al. Global warming preceded by increasing carbon dioxide concentrations during the last deglaciation. Nature 484, 49–54 (2012).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    64.He, F. et al. Northern hemisphere forcing of southern hemisphere climate during the last deglaciation. Nature 494, 81–85 (2013).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    65.Liu, Z. et al. Younger Dryas cooling and the Greenland climate response to CO2. Proc. Natl Acad. Sci. U.S.A. 109, 11101–11104 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    66.Liu, Z. et al. Evolution and forcing mechanisms of El Nino over the past 21,000 years. Nature 515, 550–553 (2014).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    67.Liu, Z. et al. The Holocene temperature conundrum. Proc. Natl Acad. Sci. U.S.A. 111, E3501–E3505 (2014).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    68.Otto-Bliesner, B. L. et al. Coherent changes of southeastern equatorial and northern African rainfall during the last deglaciation. Science 346, 1223–1227 (2014).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar  More

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    A new fossil piddock (Bivalvia: Pholadidae) may indicate estuarine to freshwater environments near Cretaceous amber-producing forests in Myanmar

    Altogether nine polished pieces of the lower Cenomanian Kachin amber from northern Myanmar (Figs. 1A–D, 2A–E) were examined in this study (depository: Russian Museum of Biodiversity Hotspots, N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Arkhangelsk, Russia). A brief description of each amber piece is given below.Figure 1Lower Cenomanian Kachin amber samples with specimens and borings of †Palaeolignopholas kachinensis gen. & sp. nov. from northern Myanmar used in this study. (A) RMBH biv1115 (frontal view with the holotype). (B) RMBH biv1101 (lateral view with two paratypes and a shell fragment). (C) RMBH biv1116 (frontal view with the fossilized paratype). (D) RMBH biv1100 (frontal view with borings). The red frames indicate position of the type specimens (holotype and some paratypes). The red arrows indicate bivalve borings. Scale bars = 5 mm. (Photos: Ilya V. Vikhrev).Full size imageFigure 2Lower Cenomanian Kachin amber samples with borings of †Palaeolignopholas kachinensis gen. & sp. nov. from northern Myanmar used in this study. (A) RMBH biv1102 (frontal view). (B) RMBH biv1103 (frontal view). (C) RMBH biv1114 (frontal view). (D) RMBH biv1118 (frontal view). (E) RMBH biv1117 (frontal view). The red arrows indicate bivalve borings. Scale bars = 5 mm. (Photos: Ilya V. Vikhrev).Full size imageRMBH biv1115: Size 8.5 × 5.8 × 8.1 mm (Fig. 1A). Inclusions: articulated shell of †Palaeolignopholas kachinensis gen. & sp. nov., “floating” in the resin (the holotype).RMBH biv1101: Size 15.6 × 6.4 × 11.5 mm (Fig. 1B). Inclusions: two complete articulated shells (paratypes) and a shell fragment of †Palaeolignopholas kachinensis gen. & sp. nov., “floating” in the resin.RMBH biv1116: Size 22.5 × 8.3 × 16.5 mm (Fig. 1C). Inclusions: fossilized shell of †Palaeolignopholas kachinensis gen. & sp. nov. (paratype), borings of this species (filled with fine gray sand), unidentified fly specimens (Insecta: Diptera), and unidentified organic fragments (probably, plant debris).RMBH biv1100: Size 17.5 × 4.9 × 12.0 mm (Fig. 1D). Inclusions: borings of †Palaeolignopholas kachinensis gen. & sp. nov. (filled with fine gray sand), and an unidentified caddisfly specimen (Insecta: Trichoptera).RMBH biv1102: Size 15.6 × 5.1 × 12.7 mm (Fig. 2A). Inclusions: borings of †Palaeolignopholas kachinensis gen. & sp. nov. (filled with fine gray sand), and unidentified organic fragments (probably, plant debris).RMBH biv1103: Size 19.6 × 4.7 × 14.3 mm (Fig. 2B). Inclusions: borings of †Palaeolignopholas kachinensis gen. & sp. nov. (filled with fine gray sand), an unidentified beetle specimen (Insecta: Coleoptera), and unidentified organic fragments (probably, plant debris).RMBH biv1114: Size 33.1 × 7.8 × 21.7 mm (Fig. 2C). Inclusions: multiple borings of †Palaeolignopholas kachinensis gen. & sp. nov. (filled with fine gray sand), and unidentified plant remains.RMBH biv1118: Size 25.1 × 8.4 × 14.3 mm (Fig. 2D). Inclusions: separate borings of †Palaeolignopholas kachinensis gen. & sp. nov. (filled with fine gray sand), a plant fragment with a cluster of borings around, and an unidentified insect specimen.RMBH biv1117: Size 15.5 × 3.9 × 10.7 mm (Fig. 2E). Inclusions: borings of †Palaeolignopholas kachinensis gen. & sp. nov. (filled with fine gray sand), and an unidentified insect specimen.Additionally, six amber samples containing adult and sub-adult specimens of †Palaeolignopholas kachinensis gen. & sp. nov. were examined using photographs in published works as follows: BMNH 20205 (Department of Palaeontology, Natural History Museum, London, UK)15, NIGP 169623 and NIGP 169624 (Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China)20, RS.P1450 (Ru D. A. Smith collection, Kuala Lumpur, Malaysia)19, and AMNH (Division of Invertebrates, American Museum of Natural History, New York, NY, United States of America)16.Based on morphological analyses of the fossil piddock shells, it was found to be a genus and species new to science, which is described here.Systematic paleontologyPhylum Mollusca Linnaeus, 1758Class Bivalvia Linnaeus, 1758Family Pholadidae Lamarck, 1809Subfamily Martesiinae Grant & Gale, 1931†Palaeolignopholas gen. novLSID: http://zoobank.org/urn:lsid:zoobank.org:act:1D686DCE-A5E9-41DA-9504-2EC58C93D988Type species: †Palaeolignopholas kachinensis gen. & sp. nov.Etymology. This name is derived from the prefix ‘Palaeo-’ (ancient), and ‘-lignopholas’, the name of a recent genus of estuarine and freshwater piddocks boring into wood, mudstone rocks, brickwork, laterites, etc.11,13. Masculine in gender.Diagnosis. The new monotypic genus is conchologically similar to several other piddock genera such as Lignopholas, Martesia, and Diplothyra Tryon 1862 but can be distinguished from these taxa by the following combination of characters: mesoplax relatively small, triangular, divided longitudinally, posterior slope without concentric sculpture, sculptured valve with concave parallel ridges (Martesia-like “rasping teeth”) curved anteriorly, periostracal lamellae dense, fine, hair-like. The fossil genus †Opertochasma Stephenson, 1952 shares a divided mesoplax but it clearly differs from both †Palaeolignopholas gen. nov. and Lignopholas by having two radial grooves on the shell surface21.Distribution. Kachin State, northern Myanmar; Upper Cretaceous (lower Cenomanian)15,19,22.Comments. Both †Palaeolignopholas gen. nov. and Lignopholas appear to be closely related to each other because they share a longitudinally divided mesoplax and periostracal lamellae, which are considered diagnostic features distinguishing this clade from Martesia + Diplothyra. Based on available conchological characters, we assume that †Palaeolignopholas gen. nov. might be placed on the ancestral stem lineage of the Lignopholas clade, although a possibility of homeomorphy could not entirely be excluded.†Palaeolignopholas kachinensis gen. & sp. nov = Plant Antheridia or Fungal Sporangia indet. sensu Grimaldi et al. (2002): 9, fig. 2a,b (bivalve specimens), fig. 3 (borings), fig. 5 (shell reconstruction of an immature specimen), figs. 6 and 7 (SEMs of borings surface showing rasped ornament at different magnifications)16. = Palaeoclavaria burmitis Poinar & Brown (2003): 765, figs. 1–4 (borings) [this fungal taxon was introduced using a trace fossil (boring) as the holotype]17; Poinar (2016): 2, figs. 10, 15, 16 (borings)18. = Martesiinae indet. sensu Smith & Ross (2018): 4, figs. 1a–c, 2a,b, 3a–d (borings), 4a,b, 5a–e (bivalve specimens)19. = Pholadidae indet. sensu Mao et al. (2018): 99, figs. 8a–f (borings), 8g,h (bivalve specimens)20. = Martesia sp. 2 sensu Mayoral et al. (2020): 10, figs. 4a (borings), 7b, 8a–l (bivalve specimens)15. = Pholadidae indet. sensu Balashov (2020): 623.Figures 1, 2, 3, 4, 5, 6 and 7.Figure 3Holotype and a paratype of †Palaeolignopholas kachinensis gen. & sp. nov. from lower Cenomanian Kachin amber, northern Myanmar. (A) Holotype: ventro-lateral view of articulated shell. (B) Paratype: anterio-lateral view of fossilized shell. VN ventral margin; DR dorsal margin; AN anterior margin; PS posterior margin; d disc; rs rasping surface of the valve; uvs umbonal ventral sulcus; pg pedal gape; pl periostracal lamellae. Scale bars = 500 µm. (Photos: Ilya V. Vikhrev).Full size imageFigure 4Paratypes of †Palaeolignopholas kachinensis gen. & sp. nov. from lower Cenomanian Kachin amber, northern Myanmar. (A) Paratype: dorsal view of articulated shell. Scale bar = 500 µm. (B) Paratype: dorsal view of articulated shell. The detached and deflected umbonal paired fragment of the valves is framed by red square. The blue contour indicates the lifetime position of this fragment. The blue arrows show the shell breakages. Scale bar = 200 µm. (C) Umbonal paired fragment of the holotype valves (inner view). The blue arrows show the shell breakage. Scale bar = 200 µm.  VN ventral margin; DR dorsal margin; AN anterior margin; PS posterior margin; ms longitudinally divided mesoplax (inner view); pr prora; d disc; rs rasping surface of the valve; uvs umbonal ventral sulcus; pg pedal gape; pl periostracal lamellae; sb shell breakage. (Photos: Ilya V. Vikhrev).Full size imageFigure 5Rasping surface of †Palaeolignopholas kachinensis gen. & sp. nov. shell. (A) Holotype shell. The red frame marks position of the enlarged area. (B) Undulated micro-sculpture of the rasping surface. Scale bar = 100 µm. (Photos: Ilya V. Vikhrev).Full size imageFigure 6Schematic reconstruction of †Palaeolignopholas kachinensis gen. & sp. nov. from lower Cenomanian Kachin amber, northern Myanmar based on the type series and other fossil material15,16,19,20. (A) Lateral view of adult specimen. (B) Dorsal view of adult specimen. (C) Ventral view of adult specimen (based on a paratype BMNH 2020515). (D) Anterio-ventral view of immature specimen. (E) Dorsal view of immature specimen. (F) Mesoplax of adult specimen. (G) Mesoplax of immature specimen. d disc; mt metaplax; ms mesoplax; hp hypoplax; ca callum; uvs umbonal ventral sulcus; pg pedal gape; pl periostracal lamellae. Scale bars = 1 mm (A–C). (Line graphics: Yulia E. Chapurina).Full size imageFigure 7Clavate borings of †Palaeolignopholas kachinensis gen. & sp. nov. from lower Cenomanian Kachin amber, northern Myanmar. (A) Cluster of borings. It marks drilling of immature piddocks into soft resin from the unidentified plant (wood?) fragment. (B–D) Clavate borings of adult piddocks. Scale bars = 1 mm. Abbreviation: bg a characteristic bioglyph indicating the shell rotation inside hardening resin. (Photos: Ilya V. Vikhrev).Full size imageLSID: http://zoobank.org/urn:lsid:zoobank.org:act:F6659EBF-B0A4-4B21-A99B-2C56BDB7EC9B.Common name. Kachin Amber Piddock.Holotype. RMBH biv1115, the adult shell with length 3.07 mm and width 1.13 mm “floating” in the resin (Figs. 1A, 3A, 5A,B), local collector leg., Russian Museum of Biodiversity Hotspots, N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Arkhangelsk, Russia.Paratypes. RMBH biv1116, the fossilized adult shell with length 4.05 mm and width 1.83 mm (Figs. 1C, 3B); RMBH biv1101, the immature specimen with articulated shell (width 1.86 mm) sharing a detached and deflected umbonal paired fragment of the valves due to the shell breakage (Figs. 1B, 4B,C); RMBH biv1101, the other immature specimen with shell length 2.68 mm and shell width 2.52 mm in this amber piece (Figs. 1B, 4A); BMNH 20205, adult specimen [illustrated in Mayoral et al. (2020): fig. 7B15], Department of Palaeontology, Natural History Museum, London, UK; NIGP 169623, adult specimen [illustrated in Mao et al. (2018): 100, fig. 8G20], and NIGP 169624, two adult specimens [illustrated in Mao et al. (2018): 100, fig. 8H20], Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China; RS.P1450, two sub-adult specimens [illustrated in Smith & Ross (2018): 5, fig. 4A,B19], Ru D. A. Smith collection, Kuala Lumpur, Malaysia.Type locality and strata. The Noije Bum Hill mines, Hukawng Valley, near Tanai (26.3593°N, 96.7200°E), Kachin State, northern Myanmar; Upper Cretaceous (lower Cenomanian; absolute age of youngest zircons in enclosing marine sediment: 98.79 ± 0.62 Ma)19,22.Etymology. The name of this species reflects its type locality, which is situated in the Kachin State of Myanmar.Diagnosis. As for the genus.Description. Shell small (up to 9.3 mm in length15,19,20), conical, with a rounded anterior margin, tapering posteriorly (Figs. 3A,B, 4A–C, 6A–E); its shape is similar to those in the recent Lignopholas, Martesia, and Diplothyra. Valve sculptured, with concave parallel ridges (Martesia-like “rasping teeth”) curved anteriorly (Fig. 5A,B). The ridges share a characteristic wave-like micro-sculpture (Fig. 5B). Sulcus deep (Figs. 3A, 4C, 6A–C). Mesoplax longitudinally divided, relatively small, triangular, tapering or lobed anteriorly (Fig. 3A, 6B,F), in immature specimens sometimes with lateral lobes (Figs. 4C, 6E,G). Metaplax and hypoplax long, narrow, not longitudinally divided but sometimes slightly bifurcated posteriorly (Fig. 6A–C). Periostracum densely covered by fine, hair-like lamellae (Figs. 4B,C and 6D). Umbonal reflection with large flattened ridge. Pedal gape presents in immature (Figs. 4A,B, 6D) and some adult specimens (Fig. 3A) but it is covered by callum in older specimens (Figs. 3B, 6C). Morphological details of the new species were also presented in a series of micro-CT images published Mayoral et al. (see Fig. 8 in that paper15) and in the reconstruction of Grimaldy et al. (see Fig. 5 in that work16).Figure 8Recent freshwater piddock Lignopholas fluminalis (Blanford, 1867) in the middle reaches of the Kaladan River, Rakhine State, Myanmar13. (A) Habitat of the freshwater piddock: river pool with siltstone rocks at the bottom, a possible modern analogue of the Mesozoic riverine ecosystem with †Palaeolignopholas. (B) Siltstone rock fragment with living freshwater piddocks inside their clavate borings. (C) Ethanol-preserved piddock (dorsal view). (D) Living piddock with fully developed callum (ventral view). (E) Living piddock with pedal gape (ventral view). Abbreviations: d disc; mt metaplax; ms mesoplax; ca callum; uvs umbonal ventral sulcus; pg pedal gape; pl periostracal lamellae. Scale bar = 2 mm. (Photos: Olga V. Aksenova).Full size imageBorings and corresponding ichnotaxon. The borings produced by †Palaeolignopholas kachinensis gen. & sp. nov. represent club-shaped (clavate) structures (Figs. 1C,D, 2A–E, 7A–D), sometimes with a characteristic bioglyph revealing the shell rotation in hardening resin (Fig. 7C). These borings were illustrated in detail15,16,17,19,20, and were considered belonging to Teredolites clavatus Leymerie, 184215. Initially, the trace fossils produced by the Kachin amber piddock were described as sporocarps of Palaeoclavaria burmitis Poinar & Brown, 2003, a non-gilled hymenomycete taxon17. The holotype of this taxon represents a club-shaped piddock crypt labelled as follows: “Amber from the Hukawng Valley in Burma; specimen (in piece B with accession number B-P-1) deposited in the Poinar amber collection maintained at Oregon State University (holotype)17”. Hence, Palaeoclavaria Poinar & Brown, 2003 and P. burmitis Poinar & Brown, 2003 must be considered ichnogenus and ichnospecies, respectively. New ichnotaxonomic synonymies are formally proposed here as follows: Teredolites Leymerie, 1842 (= Palaeoclavaria Poinar & Brown, 2003 syn. nov.), and Teredolites clavatus Leymerie, 1842 (= Palaeoclavaria burmitis Poinar & Brown, 2003 syn. nov.). More

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    The phylogeographic history of Krascheninnikovia reflects the development of dry steppes and semi-deserts in Eurasia

    1.Hurka, H. et al. The Eurasian steppe belt: Status quo, origin and evolutionary history. Turczaninowia 22, 5–71 (2019).
    Google Scholar 
    2.Walter, H. Die Vegetation Osteuropas (Gustav Fischer Verlag, 1974).
    Google Scholar 
    3.Walter, H. Die Vegetation der Erde in öko-physiologischer Betrachtung , Band II : Die gemäßigten und arktischen Zonen, in ökologischer Betrachtung (Gustav Fischer Verlag, 1968).
    Google Scholar 
    4.Cohen, K. M. & Gibbard, P. L. Global chronostratigraphical correlation table for the last 2.7 million years, version 2019 QI-500. Quat. Int. 500, 20–31 (2019).Article 

    Google Scholar 
    5.Frenzel, B. Grundzüge der Pleistozänen Vegetationsgeschichte Nord-Euroasiens. Geogr. J. 136, 291 (1968).
    Google Scholar 
    6.Tarasov, P. E. et al. Last glacial maximum biomes reconstructed from pollen and plant macrofossil data from northern Eurasia. J. Biogeogr. 27, 609–620 (2000).Article 

    Google Scholar 
    7.Caves Rugenstein, J., Sjostrom, D., Mix, H., Winnick, M. & Chamberlain, C. Aridification of Central Asia and uplift of the Altai and Hangay Mountains, Mongolia: Stable isotope evidence. Am. J. Sci. 314, 1171–1201 (2014).ADS 
    Article 
    CAS 

    Google Scholar 
    8.Yanina, T., Sorokin, V., Bezrodnykh, Y. & Romanyuk, B. Late Pleistocene climatic events reflected in the Caspian Sea geological history (based on drilling data). Quat. Int. 465, 130–141 (2018).Article 

    Google Scholar 
    9.Dolukhanov, P. M., Chepalyga, A. L., Shkatova, V. K. & Lavrentiev, N. V. Late Quaternary Caspian: Sea-levels, environments and human settlement. Open Geogr. J. 2, 1–15 (2009).Article 

    Google Scholar 
    10.Tudryn, A. et al. Late Quaternary Caspian Sea environment: Late Khazarian and Early Khvalynian transgressions from the lower reaches of the Volga River. Quat. Int. 292, 193–204 (2013).Article 

    Google Scholar 
    11.Dengler, J., Janišová, M., Török, P. & Wellstein, C. Biodiversity of Palaearctic grasslands: A synthesis. Agric. Ecosyst. Environ. 182, 1–14 (2014).Article 

    Google Scholar 
    12.Hejcman, M., Hejcmanová, P., Pavlů, V. & Beneš, J. Origin and history of grasslands in Central Europe—a review. Grass Forage Sci. 68, 345–363 (2013).Article 

    Google Scholar 
    13.Franzke, A. et al. Molecular signals for Late Tertiary/Early Quaternary range splits of an Eurasian steppe plant: Clausia aprica (Brassicaceae). Mol. Ecol. 13, 2789–2795 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    14.Hurka, H., Friesen, N., German, D. A., Franzke, A. & Neuffer, B. ‘Missing link’ species Capsella orientalis and Capsella thracicaelucidate evolution of model plant genus Capsella (Brassicaceae). Mol. Ecol. 21, 1223–1238 (2012).PubMed 
    Article 

    Google Scholar 
    15.Seregin, A. P., Anačkov, G. & Friesen, N. Molecular and morphological revision of the Allium saxatile group (Amaryllidaceae): Geographical isolation as the driving force of underestimated speciation. Bot. J. Linn. Soc. 178, 67–101 (2015).Article 

    Google Scholar 
    16.Friesen, N. et al. Dated phylogenies and historical biogeography of Dontostemon and Clausia (Brassicaceae) mirror the palaeogeographical history of the Eurasian steppe. J. Biogeogr. 43, 738–749 (2015).Article 

    Google Scholar 
    17.Friesen, N. et al. Allium species of section Rhizomatosa, early members of the Central Asian steppe vegetation. Flora 263, 151536 (2020).Article 

    Google Scholar 
    18.Friesen, N. et al. Evolutionary history of the Eurasian steppe plant Schivereckia podolica (Brassicaceae) and its close relatives. Flora 268, 151602 (2020).Article 

    Google Scholar 
    19.Volkova, P. A., Herden, T. & Friesen, N. Genetic variation in Goniolimon speciosum (Plumbaginaceae) reveals a complex history of steppe vegetation. Bot. J. Linn. Soc. 184, 113–121 (2017).
    Google Scholar 
    20.Žerdoner Čalasan, A., Seregin, A. P., Hurka, H., Hofford, N. P. & Neuffer, B. The Eurasian steppe belt in time and space: Phylogeny and historical biogeography of the false flax (Camelina Crantz, Camelineae, Brassicaceae). Flora 260, 151477 (2019).Article 

    Google Scholar 
    21.Kirschner, P. et al. Long-term isolation of European steppe outposts boosts the biome’s conservation value. Nat. Commun. 11, 1968 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    22.Heklau, H. & von Wehrden, H. Wood anatomy reflects the distribution of Krascheninnikovia ceratoides (Chenopodiaceae). Flora Morphol. Distrib. Funct. Ecol. Plants 206, 300–309 (2011).Article 

    Google Scholar 
    23.Heklau, H. & Röser, M. Delineation, taxonomy and phylogenetic relationships of the genus Krascheninnikovia (Amaranthaceae subtribe Axyridinae). Taxon 57, 563–576 (2008).
    Google Scholar 
    24.Takhtajan, A. Floristic Regions of the World (University of California Press, 1986).
    Google Scholar 
    25.Manafzadeh, S., Staedler, Y. M. & Conti, E. Visions of the past and dreams of the future in the Orient: The Irano-Turanian region from classical botany to evolutionary studies. Biol. Rev. Camb. Philos. Soc. 92, 1365–1388 (2017).PubMed 
    Article 

    Google Scholar 
    26.Walter, H. & Breckle, S.-W. Ecological systems of the geobiosphere. 2 Tropical and subtropical zonobiomes (Springer, 1986). https://doi.org/10.1007/978-3-662-06812-0.
    Google Scholar 
    27.Hartmann, H. Zur Flora und Vegetation der Halbwüsten, Steppen und Rasengesellschaften im südöstlichen Ladakh (Indien). in Jahrbuch des Vereins zum Schutz der Bergwelt 129–188 (1997).28.Kraudzun, T., Vanselow, K. A. & Samimi, C. Realities and myths of the Teresken syndrome—An evaluation of the exploitation of dwarf shrub resources in the Eastern Pamirs of Tajikistan. J. Environ. Manag. 132, 49–59 (2014).Article 

    Google Scholar 
    29.Vanselow, K. & Samimi, C. Predictive mapping of dwarf shrub vegetation in an arid high mountain ecosystem using remote sensing and random forests. Remote Sens. 6, 6709–6726 (2014).ADS 
    Article 

    Google Scholar 
    30.Smoliak, S. & Bezeau, L. M. Chemical composition and in vitro digestibility of range forage plants of the Stipa-Bouteloua prairie. Can. J. Plant Sci. 47, 161–167 (1967).CAS 
    Article 

    Google Scholar 
    31.Waldron, B. L., Eun, J.-S., ZoBell, D. R. & Olson, K. C. Forage kochia (Kochia prostrata) for fall and winter grazing. Small Rumin. Res. 91, 47–55 (2010).Article 

    Google Scholar 
    32.Steshenko, A. P. Formation of the semi-shrub structure in the high mountains of Pamir. Trans Akad Nauk Tadzhik SSR 50, 2 (1956).
    Google Scholar 
    33.Zalenski, O. V. & Steshenko, A. P. On the special features of the main species of the vegetation of the Pamir mountains. Proc. Bot. Soc. 7, 9–12 (1957).
    Google Scholar 
    34.Barnes, M. The Effect of Plant Source Location on Restoration Success: A Reciprocal Transplant Experiment with Winterfat (Krascheninnikovia lanata) (University of New Mexico, 2009).
    Google Scholar 
    35.Seidl, A. et al. Phylogeny and biogeography of the Pleistocene Holarctic steppe and semi-desert goosefoot plant Krascheninnikovia ceratoides. Flora 262, 151504 (2020).Article 

    Google Scholar 
    36.Yang, J. Y., Fu, X. Q., Yan, G. X. & Zhang, S. Z. Analysis of three species of the genus Ceratoides. Grassl. China 1, 67–71 (1996).
    Google Scholar 
    37.Rubtsov, M., Sagimbaev, R., Shakhanov, E., Tiran, T. & Balyan, G. Natural polyploids of prostrate summer cypress and winterfat as initial material for breeding. Sov. Agric. Sci. 4, 20–24 (1989).
    Google Scholar 
    38.Yan, G., Zhang, S., Yan, J., Fu, X. & Wang, L. Chromosome numbers and geographical distribution of 68 species of forage plants. Grassl. China 4, 53–60 (1989).
    Google Scholar 
    39.Kurban, N. Karyotype analysis of three species of Ceratoides (Chenopodiaceae). J. Syst. Evol. 22, 466–468 (1984).
    Google Scholar 
    40.Zakharjeva, O. I. & Soskov, Y. D. Chromosome numbers in desert herbage plants. Bulleten VNII Rastenievod. Im. N.I. Vavilova 108, 57–60 (1981).
    Google Scholar 
    41.Domínguez, F. et al. Krascheninnikovia ceratoides (L.) Gueldenst (Chenopodiaceae) en Aragón (España): Algunos resultados para su conservación. Bol. R. Soc. Esp. Hist. Nat. (Sec. Biol.) 96, 15–26 (2001).
    Google Scholar 
    42.Zakirova, R. Chromosome numbers of some Alliaceae, Salicaceae, Polygonaceae, and Chenopodiaceae of the South Balkhash territory. Citologija 41, 1064 (1999).
    Google Scholar 
    43.Dobes, C. H., Hahn, B. & Morawetz, W. Chromosomenzahlen zur Gefässpflanzenflora Österreichs. Linzer Biol. Beitr 29, 5–43 (1997).
    Google Scholar 
    44.Sainz Ollero, H., Múgica, F. & Arias Torcal, J. Estrategias para la conservación de la flora amenazada de Aragón (Consejo de Protección de la Naturaleza de Aragón, 1996).
    Google Scholar 
    45.Lomonosova, M. N. & Krasnikov, A. A. Chromosome numbers in some members of the Chenopodiaceae. Bot. Zurn. (Moscow Leningrad) 78, 158–159 (1993).
    Google Scholar 
    46.Castroviejo, S. & Soriano, C. Krascheninnikovia ceratoides Gueldenst (Publicaciones del CSIC, 1990).
    Google Scholar 
    47.Takhtajan, A. Numeri chromosomatum magnoliophytorum florae URSS. Aceraceae–Menyanthaceae. (Academis Scientiarum Rossica, Institutum Botanicum nomine VL Komarovii;” Nauka”, 1990).48.Ghaffari, S. M., Balaei, Z., Chatrenoor, T. & Akhani, H. Cytology of SW Asian Chenopodiaceae: New data from Iran and a review of previous records and correlations with life forms and C4 photosynthesis. Plant Syst. Evol. 301, 501–521 (2014).Article 

    Google Scholar 
    49.eFloras. Published on the Internet http://www.efloras.org. (2008).50.Kadereit, G., Mavrodiev, E. V., Zacharias, E. H. & Sukhorukov, A. P. Molecular phylogeny of Atripliceae (Chenopodioideae, Chenopodiaceae): Implications for systematics, biogeography, flower and fruit evolution, and the origin of C4 photosynthesis. Am. J. Bot. 97, 1664–1687 (2010).PubMed 
    Article 

    Google Scholar 
    51.Di Vincenzo, V. et al. Evolutionary diversification of the African achyranthoid clade (Amaranthaceae) in the context of sterile flower evolution and epizoochory. Ann. Bot. 122, 69–85 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    52.Janis, C. M. Tertiary mammal evolution in the context of changing climates, vegetation, and tectonic events. Annu. Rev. Ecol. Syst. 24, 467–500 (1993).Article 

    Google Scholar 
    53.Doležel, J. & Greilhuber, J. Nuclear genome size: Are we getting closer?. Cytom. Part A 77, 635–642 (2010).Article 
    CAS 

    Google Scholar 
    54.Yokoya, K., Roberts, A. V., Mottley, J., Lewis, R. & Brandham, P. E. Nuclear DNA amounts in roses. Ann. Bot. 85, 557–561 (2000).CAS 
    Article 

    Google Scholar 
    55.Poland, J. A., Brown, P. J., Sorrells, M. E. & Jannink, J.-L. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7, e32253 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. & Cresko, W. A. Stacks: An analysis tool set for population genomics. Mol. Ecol. 22, 3124–3140 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    57.Weiß, C. L., Pais, M., Cano, L. M., Kamoun, S. & Burbano, H. A. nQuire: A statistical framework for ploidy estimation using next generation sequencing. BMC Bioinform. 19, 122 (2018).Article 
    CAS 

    Google Scholar 
    58.Corrêa, A., dos Santos, R., Goldman, G. H. & Riaño-Pachón, D. M. ploidyNGS: Visually exploring ploidy with next generation sequencing data. Bioinformatics 33, 2575–2576 (2017).Article 
    CAS 

    Google Scholar 
    59.Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    61.R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing (2013).62.Frichot, E. & François, O. LEA: An R package for landscape and ecological association studies. Methods Ecol. Evol. 6, 925–929 (2015).Article 

    Google Scholar 
    63.Jombart, T. adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    64.Gruber, B., Unmack, P. J., Berry, O. F. & Georges, A. dartr: An R package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol. Ecol. Resour. 18, 691–699 (2018).PubMed 
    Article 

    Google Scholar 
    65.Bradley, M. raxml_ascbias. GitHub https://github.com/btmartin721/raxml_ascbias (2018).66.Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    67.Minh, B. Q. et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    68.Lewis, P. O. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913–925 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    69.Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    70.Minh, B. Q., Nguyen, M. A. T. & von Haeseler, A. Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol. 30, 1188–1195 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    71.Huson, D. H. & Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254–267 (2005).PubMed 
    Article 
    CAS 

    Google Scholar 
    72.Rambaut, A. FigTree v1.3.1. (2010).73.Kalinowski, S. T. hp-rare 1.0: A computer program for performing rarefaction on measures of allelic richness. Mol. Ecol. Notes 5, 187–189 (2005).CAS 
    Article 

    Google Scholar 
    74.Brummitt, R. World geographical scheme for recording plant distributions. (2001).75.Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S. & Bremer, K. Estimating divergence times in large phylogenetic trees. Syst. Biol. 56, 741–752 (2007).PubMed 
    Article 

    Google Scholar 
    76.Matzke, N. J. BioGeoBEARS: BioGeography with Bayesian (and likelihood) evolutionary analysis with R scripts. Version 1.1. 1, published on GitHub on 6 November 2018. (2018).77.Matzke, N. J. Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades. Syst. Biol. 63, 951–970 (2014).PubMed 
    Article 

    Google Scholar 
    78.Matzke, N. J. Probabilistic historical biogeography: New models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Front. Biogeogr. 5, 2 (2013).Article 

    Google Scholar 
    79.Ronquist, F. Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography. Syst. Biol. 46, 195–203 (1997).Article 

    Google Scholar 
    80.Strömberg, C. A. E. Evolution of grasses and grassland ecosystems. Annu. Rev. Earth Planet. Sci. 39, 517–544 (2011).ADS 
    Article 
    CAS 

    Google Scholar 
    81.Linder, H. P., Lehmann, C. E. R., Archibald, S., Osborne, C. P. & Richardson, D. M. Global grass (Poaceae) success underpinned by traits facilitating colonization, persistence and habitat transformation. Biol. Rev. 93, 1125–1144 (2017).PubMed 
    Article 

    Google Scholar 
    82.Devyatkin, E. V. Meridional distribution of Pleistocene ecosystems in Asia: Basic problems. Stratigr. Geol. Correl. 1, 77–83 (1993).
    Google Scholar 
    83.Arkhipov, S. A. & Volkova, V. S. Geological history of Pleistocene landscapes and climate in West Siberia. (1994).84.Akhmetyev, M. A. et al. Chapter 8: Kazakhstan and Central Asia (plains and foothills). In Cenozoic Climatic and Environmental Changes in Russia (Geological Society of America, 2005). https://doi.org/10.1130/0-8137-2382-5.139.
    Google Scholar 
    85.Arkhipov, S. A. et al. Chapter 4: West Siberia. In Cenozoic Climatic and Environmental Changes in Russia (Geological Society of America, 2005). https://doi.org/10.1130/0-8137-2382-5.67.
    Google Scholar 
    86.Li, Q. Q. et al. Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Ann. Bot. 106, 709–733 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    87.Hais, M., Komprdová, K., Ermakov, N. & Chytrý, M. Modelling the last glacial maximum environments for a refugium of Pleistocene biota in the Russian Altai mountains Siberia. Palaeogeogr. Palaeoclimatol. Palaeoecol. 438, 135–145 (2015).Article 

    Google Scholar 
    88.Fedeneva, I. N. & Dergacheva, M. I. Paleosols as the basis of environmental reconstruction in Altai mountainous areas. Quat. Int. 106–107, 89–101 (2003).Article 

    Google Scholar 
    89.Braun-Blanquet, J. & Bolòs i Capdevila, O. de. Les groupements végétaux du bassin moyen de l’Ebre et leur dynamisme. An. la Estac. Exp. Aula Dei 5, 1–266 (1957).
    Google Scholar 
    90.Tutin, T., Webb, D., Heywood, V., Walters, S. & Moore, D. Flora Europaea (Cambridge University Press, 1993).
    Google Scholar 
    91.Heklau, H. Proposal to conserve the name Krascheninnikovia against Ceratoides (Chenopodiaceae. Taxon 55, 1044–1045 (2006).Article 

    Google Scholar 
    92.Davis, P. H. Flora of Turkey and the east Aegean islands (Edinburgh University Press, 1988).
    Google Scholar 
    93.Welsh, S., Atwood, N., Higgins, L. & Goodrich, S. A Utah Flora. Gt. Basin Nat. 9, 123 (1987).
    Google Scholar 
    94.Täckholm, V. Students’ Flora of Egypt (Cairo University Publishing, 1974).
    Google Scholar 
    95.Komarov, V. Flora of the U.R.S.S (Academiae Sciencitarum U.R.S.S, 1964).
    Google Scholar 
    96.Rechinger, K. Flora Iranica (Akademische Druck- und Verlagsanstalt, 1963).
    Google Scholar 
    97.Crawford, K. M. & Whitney, K. D. Population genetic diversity influences colonization success. Mol. Ecol. 19, 1253–1263 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    98.Hilbig, W. Vegetation of Mongolia (SPB Academic Pubishing, 1995).
    Google Scholar 
    99.Briggs, J. C. Chapter 7 Neogene. In Global Biogeography Vol. 14 (ed. Briggs, J. C.) 147–189 (Elsevier, Amsterdam, 1995).
    Google Scholar 
    100.Yurtsev, B. A. The Pleistocene ‘Tundra-steppe’ and the productivity paradox: The landscape approach. Quat. Sci. Rev. 20, 165–174 (2001).ADS 
    Article 

    Google Scholar 
    101.Stewart, J. R., Lister, A. M., Barnes, I. & Dalén, L. Refugia revisited: Individualistic responses of species in space and time. Proc. Biol. Sci. 277, 661–671 (2010).PubMed 

    Google Scholar 
    102.Varga, Z. Extra-Mediterranean refugia, post-glacial vegetation history and area dynamics in eastern Central Europe. Relict Species https://doi.org/10.1007/978-3-540-92160-8_3 (2009).Article 

    Google Scholar 
    103.Willis, K. J. & Vanandel, T. Trees or no trees? The environments of central and eastern Europe during the Last Glaciation. Quat. Sci. Rev. 23, 2369–2387 (2004).ADS 
    Article 

    Google Scholar 
    104.Tremetsberger, K. et al. Pleistocene refugia and polytopic replacement of diploids by tetraploids in the Patagonian and Subantarctic plant Hypochaeris incana (Asteraceae, Cichorieae). Mol. Ecol. 18, 3668–3682 (2009).CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    Multi-decadal trends in contingent mixing of Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic from otolith stable isotopes

    1.Tsukamoto, K., Nakai, I. & Tesch, W.-V. Do all freshwater eels migrate?. Nature 396, 635–636 (1998).ADS 
    CAS 
    Article 

    Google Scholar 
    2.Fromentin, J.-M. & Powers, J. E. Atlantic bluefin tuna: population dynamics, ecology, fisheries and management. Fish. Fish. 6, 281–306 (2005).Article 

    Google Scholar 
    3.Kerr, L. A. & Secor, D. H. Bioenergetic trajectories underlying partial migration in Patuxent River (Chesapeake Bay) white perch (Morone americana). Can. J. Fish. Aquat. Sci. 66, 602–612 (2009).Article 

    Google Scholar 
    4.Cadrin, S. X. et al. Population structure of beaked redfish, Sebastes mentella: evidence of divergence associated with different habitats. ICES J. Mar. Sci. 67, 1617–1630 (2010).Article 

    Google Scholar 
    5.Doak, D. F. et al. The statistical inevitability of stability-diversity relationships in community ecology. Am. Nat. 151, 264–276 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    6.Tilman, D., Lehman, C. L. & Bristow, C. E. Diversity-stability relationships: statistical inevitability or ecological consequence?. Am. Nat. 151, 277–282 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    7.Secor, D. H., Kerr, L. A. & Cadrin, S. X. Connectivity effects on productivity, stability, and persistence in a herring metapopulation model. ICES J. Mar. Sci. 66, 1726–1732 (2009).Article 

    Google Scholar 
    8.Cadrin, S. X. & Secor, D. H. Accounting for spatial population structure in stock assessment: past, present, and future. In The Future of Fisheries Science in North America (eds Beamish, R. J. & Rothschild, B. J.) 405–426 (Springer, 2009).
    Google Scholar 
    9.Secor, D. H. The unit stock concept: bounded fish and fisheries. In Stock Identification Methods: Applications in Fishery Science 2nd edn (eds Cadrin, S. X. et al.) 7–28 (Elsevier, 2014).
    Google Scholar 
    10.Ricker, W. E. Maximum sustained yields from fluctuating environments and mixed stocks. J. Fish. Res. Board Can. 15, 991–1006 (1958).Article 

    Google Scholar 
    11.Kerr, L. A. et al. Lessons learned from practical approaches to reconcile mismatches between biological population structure and stock units of marine fish. ICES J. Mar. Sci. 74, 1708–1722 (2017).Article 

    Google Scholar 
    12.Kerr, L. A., Cadrin, S. X. & Kovach, A. I. Consequences of a mismatch between biological and management units on our perception of Atlantic cod off New England. ICES J. Mar. Sci. 71, 1366–1381 (2014).Article 

    Google Scholar 
    13.Goethel, D. R. & Berger, A. M. Accounting for spatial complexities in the calculation of biological reference points: effects of misdiagnosing population structure for stock status indicators. Can. J. Fish. Aquat. Sci. 74, 1878–1894 (2017).Article 

    Google Scholar 
    14.Van Beveren, E., Duplisea, D. E., Brosset, P. & Castonguay, M. Assessment modelling approaches for stocks with spawning components, seasonal and spatial dynamics, and limited resources for data collection. PLoS ONE 14, e0222472 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    15.Cadrin, S. X. Defining spatial structure for fishery stock assessment. Fish. Res. 221, 105397 (2020).Article 

    Google Scholar 
    16.Sette, O. E. Biology of the Atlantic mackerel (Scomber scombrus) of North America. Part II:migration and habits. Fish. Bull. 51, 251–358 (1950).
    Google Scholar 
    17.Moores, J. A., Winters, G. H. & Parsons, L. S. Migrations and biological characteristics of Atlantic mackerel (Scomber scombrus) occurring in Newfoundland waters. J. Fish. Res. Board Can. 32, 1347–1357 (1975).Article 

    Google Scholar 
    18.Redding, S. G., Cooper, L. W., Castonguay, M., Wiernicki, C. & Secor, D. H. Northwest Atlantic mackerel population structure evaluated using otolith δ18O composition. ICES J. Mar. Sci. 77, 2582–2589 (2020).Article 

    Google Scholar 
    19.Overholtz, W. J., Link, J. S. & Suslowicz, L. E. Consumption of important pelagic fish and squid by predatory fish in the northeastern USA shelf ecosystem with some fishery comparisons. ICES J. Mar. Sci. 57, 1147–1159 (2000).Article 

    Google Scholar 
    20.Tyrrell, M. C., Link, J. S., Moustahfid, H. & Overholtz, W. J. Evaluating the effect of predation mortality on forage species population dynamics in the Northeast US continental shelf ecosystem using multispecies virtual population analysis. ICES J. Mar. Sci. 65, 1689–1700 (2008).Article 

    Google Scholar 
    21.Jansen, T. & Gislason, H. Population structure of Atlantic mackerel (Scomber scombrus). PLoS ONE 8, e64744 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    22.Nøttestad, L. et al. Quantifying changes in abundance, biomass, and spatial distribution of Northeast Atlantic mackerel (Scomber scombrus) in the Nordic seas from 2007 to 2014. ICES J. Mar. Sci. 73, 359–373 (2016).Article 

    Google Scholar 
    23.Olafsdottir, A. H. et al. Geographical expansion of Northeast Atlantic mackerel (Scomber scombrus) in the Nordic Seas from 2007 to 2016 was primarily driven by stock size and constrained by low temperatures. Deep-Sea. Res. Part II 159, 152–168 (2019).Article 

    Google Scholar 
    24.FAO. The state of world fisheries and aquaculture 2020. Sustainability in action. 244 http://www.fao.org/documents/card/en/c/ca9229en (2020). Accessed on 23 July 2020.25.NEFSC. 64th Northeast Regional Stock Assessment Workshop (64th SAW) Assessment Report. 536 (2018).26.DFO. Assessment of the Atlantic mackerel stock for the Northwest Atlantic (Subareas 3 and 4) in 2018. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2019/035: 14 (2019).27.Secor, D. H. Specifying divergent migrations in the concept of stock: the contingent hypothesis. Fish. Res. 43, 13–34 (1999).Article 

    Google Scholar 
    28.Sette, O. E. Biology of the Atlantic mackerel (Scomber scombrus) of North America. Part I: early life history, including the growth, drift, and mortality of the egg and larval populations. Fish. Bull. 50, 149–237 (1943).
    Google Scholar 
    29.Berrien, P. L. Eggs and larvae of Scomber scombrus and Scomber japonicus in continental shelf waters between Massachusetts and Florida. Fish. Bull. 76, 95–115 (1978).
    Google Scholar 
    30.Overholtz, W. J., Hare, J. A. & Keith, C. M. Impacts of interannual environmental forcing and climate change on the distribution of Atlantic mackerel on the U.S. Northeast continental shelf. Mar. Coast. Fish. 3, 219–232 (2011).Article 

    Google Scholar 
    31.McManus, M. C., Hare, J. A., Richardson, D. E. & Collie, J. S. Tracking shifts in Atlantic mackerel (Scomber scombrus) larval habitat suitability on the Northeast U.S. Continental Shelf. Fish. Oceanogr. 27, 49–62 (2018).Article 

    Google Scholar 
    32.Richardson, D. E., Carter, L., Curti, K. L., Marancik, K. E. & Castonguay, M. Changes in the spawning distribution and biomass of Atlantic mackerel (Scomber scombrus) in the western Atlantic Ocean over 4 decades. Fish. Bull. 118, 120–134 (2020).Article 

    Google Scholar 
    33.Moura, A. et al. Population structure and dynamics of the Atlantic mackerel (Scomber scombrus) in the North Atlantic inferred from otolith chemical and shape signatures. Fish. Res. 230, 105621 (2020).Article 

    Google Scholar 
    34.Rooker, J. et al. Evidence of trans-Atlantic movement and natal homing of bluefin tuna from stable isotopes in otoliths. Mar. Ecol. Prog. Ser. 368, 231–239 (2008).ADS 
    Article 

    Google Scholar 
    35.Clarke, L. M., Munch, S. B., Thorrold, S. R. & Conover, D. O. High connectivity among locally adapted populations of a marine fish (Menidia menidia). Ecology 91, 3526–3537 (2010).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    36.Wells, R. J. D. et al. Natural tracers reveal population structure of albacore (Thunnus alalunga) in the eastern North Pacific. ICES J. Mar. Sci. 72, 2118–2127 (2015).Article 

    Google Scholar 
    37.Moreira, C. et al. Population structure of the blue jack mackerel (Trachurus picturatus) in the NE Atlantic inferred from otolith microchemistry. Fish. Res. 197, 113–122 (2018).Article 

    Google Scholar 
    38.Trueman, C. N., MacKenzie, K. M. & Palmer, M. R. Identifying migrations in marine fishes through stable-isotope analysis. J. Fish. Biol. 81, 826–847 (2012).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    39.McMahon, K. W., Hamady, L. L. & Thorrold, S. R. A review of ecogeochemistry approaches to estimating movements of marine animals. Limnol. Oceanogr. 58, 697–714 (2013).ADS 
    CAS 
    Article 

    Google Scholar 
    40.Kalish, J. M. 13C and 18O isotopic disequilibria in fish otoliths: metabolic and kinetic effects. Mar. Ecol. Prog. Ser. 75, 191–203 (1991).ADS 
    Article 

    Google Scholar 
    41.Solomon, C. T. et al. Experimental determination of the sources of otolith carbon and associated isotopic fractionation. Can. J. Fish. Aquat. Sci. 63, 79–89 (2006).CAS 
    Article 

    Google Scholar 
    42.Tohse, H. & Mugiya, Y. Sources of otolith carbonate: experimental determination of carbon incorporation rates from water and metabolic CO2, and their diel variations. Aquat. Biol. 1, 259–268 (2008).Article 

    Google Scholar 
    43.Chung, M.-T., Trueman, C. N., Godiksen, J. A., Holmstrup, M. E. & Grønkjær, P. Field metabolic rates of teleost fishes are recorded in otolith carbonate. Commun. Biol. 2, 24 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    44.Rooker, J. R. & Secor, D. H. Microchemistry: migration and ecology of Atlantic bluefin tuna. In The Future of Bluefin Tunas: Ecology, Fisheries Management, and Conservation (ed. Block, B. A.) (Johns Hopkins University Press, 2019).
    Google Scholar 
    45.Uriarte, A. et al. Spatial pattern of migration and recruitment of North East Atlantic mackerel. ICES CM 2001/O:17 (2001).46.Mendiola, D., Alvarez, P., Cotano, U. & Martínez de Murguía, A. Early development and growth of the laboratory reared north-east Atlantic mackerel (Scomber scombrus) L. J. Fish. Biol. 70, 911–933 (2007).Article 

    Google Scholar 
    47.Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

    Google Scholar 
    48.Harrison, X. A. et al. A brief introduction to mixed effects modelling and multi-model inference in ecology. PeerJ 6, e4794 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    49.Hartig, F. DHARMa: residual diagnostics for hierarchical (multi-level/mixed) regression models (2020).50.Kerr, L. A. et al. Mixed stock origin of Atlantic bluefin tuna in the U.S. rod and reel fishery (Gulf of Maine) and implications for fisheries management. Fish. Res. 224, 105461 (2020).Article 

    Google Scholar 
    51.R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).
    Google Scholar 
    52.Smith, A. D. et al. Atlantic mackerel (Scomber scombrus L.) in NAFO Subareas 3 and 4 in 2018. DFO Can. Sci. Advis. Sec. Res. Doc. 2020/013. iv + 37 p. (2020).53.Lambrey de Souza, J., Sévigny, J.-M., Chanut, J.-P., Barry, W. F. & Grégoire, F. High genetic variability in the mtDNA control region of a Northwestern Atlantic teleost, Scomber scombrus L. Can. Tech. Rep. Fish. Aquat. Sci. 2625, vi+25 (2006).
    Google Scholar 
    54.Radlinski, M. K., Sundermeyer, M. A., Bisagni, J. J. & Cadrin, S. X. Spatial and temporal distribution of Atlantic mackerel (Scomber scombrus) along the northeast coast of the United States, 1985–1999. ICES J. Mar. Sci. 70, 1151–1161 (2013).Article 

    Google Scholar 
    55.Castonguay, M., Plourde, S., Robert, D., Runge, J. A. & Fortier, L. Copepod production drives recruitment in a marine fish. Can. J. Fish. Aquat. Sci. 65, 1528–1531 (2008).Article 

    Google Scholar 
    56.McManus, M. C. Atlantic Mackerel (Scomber scombrus) Population and Habitat Trends in the Northwest Atlantic (University of Rhode Island, 2017).
    Google Scholar 
    57.Schloesser, R. W., Rooker, J. R., Louchuoarn, P., Neilson, J. D. & Secord, D. H. Interdecadal variation in seawater δ13C and δ18O recorded in fish otoliths. Limnol. Oceanogr. 54, 1665–1668 (2009).ADS 
    CAS 
    Article 

    Google Scholar 
    58.Schloesser, R. W., Neilson, J. D., Secor, D. H. & Rooker, J. R. Natal origin of Atlantic bluefin tuna (Thunnus thynnus) from Canadian waters based on otolith δ13C and δ18O. Can. J. Fish. Aquat. Sci. 67, 563–569 (2010).CAS 
    Article 

    Google Scholar 
    59.Thorrold, S. R., Campana, S. E., Jones, C. M. & Swart, P. K. Factors determining δ13C and δ18O fractionation in aragonitic otoliths of marine fish. Geochim. Cosmochim. Acta. 61, 2909–2919 (1997).ADS 
    CAS 
    Article 

    Google Scholar 
    60.Campana, S. E. Chemistry and composition of fish otoliths: pathways, mechanisms and applications. Mar. Ecol. Prog. Ser. 188, 263–297 (1999).ADS 
    CAS 
    Article 

    Google Scholar 
    61.Caesar, L., Rahmstorf, S., Robinson, A., Feulner, G. & Saba, V. Observed fingerprint of a weakening Atlantic Ocean overturning circulation. Nature 556, 191–196 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    62.Saba, V. S. et al. Enhanced warming of the Northwest Atlantic Ocean under climate change. J. Geophys. Res. Oceans 121, 118–132 (2016).ADS 
    Article 

    Google Scholar 
    63.Pershing, A. J. et al. Slow adaptation in the face of rapid warming leads to collapse of the Gulf of Maine cod fishery. Science 350, 809–812 (2015).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    64.Brickman, D., Hebert, D. & Wang, Z. Mechanism for the recent ocean warming events on the Scotian Shelf of eastern Canada. Cont. Shelf. Res. 156, 11–22 (2018).ADS 
    Article 

    Google Scholar 
    65.Thorrold, S. R., Latkoczy, C., Swart, P. K. & Jones, C. M. Natal homing in a marine fish metapopulation. Science 291, 297–299 (2001).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    66.Gillanders, B. M. Using elemental chemistry of fish otoliths to determine connectivity between estuarine and coastal habitats. Estuar. Coast. Shelf. Sci. 64, 47–57 (2005).ADS 
    Article 

    Google Scholar 
    67.Høie, H., Andersson, C., Folkvord, A. & Karlsen, Ø. Precision and accuracy of stable isotope signals in otoliths of pen-reared cod (Gadus morhua) when sampled with a high-resolution micromill. Mar. Biol. 144, 1039–1049 (2004).Article 

    Google Scholar 
    68.Martino, J. C., Doubleday, Z. A., Chung, M.-T. & Gillanders, B. M. Experimental support towards a metabolic proxy in fish using otolith carbon isotopes. J. Exp. Biol. 223, jeb217091 (2020).PubMed 
    Article 

    Google Scholar 
    69.Manel, S., Gaggiotti, O. E. & Waples, R. S. Assignment methods: matching biological questions with appropriate techniques. Trends Ecol. Evol. 20, 136–142 (2005).PubMed 
    Article 

    Google Scholar 
    70.Siskey, M. R., Wilberg, M. J., Allman, R. J., Barnett, B. K. & Secor, D. H. Forty years of fishing: changes in age structure and stock mixing in northwestern Atlantic bluefin tuna (Thunnus thynnus) associated with size-selective and long-term exploitation. ICES J. Mar. Sci. 73, 2518–2528 (2016).Article 

    Google Scholar 
    71.Kerr, L. A., Cadrin, S. X. & Secor, D. H. The role of spatial dynamics in the stability, resilience, and productivity of an estuarine fish population. Ecol. Appl. 20, 497–507 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    72.Goethel, D. R., Quinn, T. J. & Cadrin, S. X. Incorporating spatial structure in stock assessment: movement modeling in marine fish population dynamics. Rev. Fish. Sci. 19, 119–136 (2011).Article 

    Google Scholar 
    73.Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
    Google Scholar  More