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    Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States

    Hallegraeff, G. M. Ocean climate change, phytoplankton community responses, and harmful algal blooms: A formidable predictive challenge 1. J. Phycol. 46, 220–235 (2010).Article 
    CAS 

    Google Scholar 
    Itakura, S. & Imai, I. Economic impacts of harmful algal blooms on fisheries and aquaculture in western Japan—An overview of interannual variability and interspecies comparison. PICES Sci. Rep. 47, 17 (2014).
    Google Scholar 
    Haigh, N. & Esenkulova, S. Economic losses to the British Columbia salmon aquaculture industry due to harmful algal blooms, 2009–2012. PICES Sci. Rep. 47, 2 (2014).
    Google Scholar 
    Sharma, N. K. et al. (eds) Cyanobacteria: An Economic Perspective 245–256 (Wiley, 2014).
    Google Scholar 
    O’Neil, J. M., Davis, T. W., Burford, M. A. & Gobler, C. J. The rise of harmful cyanobacteria blooms: The potential roles of eutrophication and climate change. Harmful Algae 14, 313–334. https://doi.org/10.1016/j.hal.2011.10.027 (2012).Article 
    CAS 

    Google Scholar 
    Paerl, H. W. & Huisman, J. Climate change: A catalyst for global expansion of harmful cyanobacterial blooms. Environ. Microbiol. Rep. 1, 27–37. https://doi.org/10.1111/j.1758-2229.2008.00004.x (2009).Article 
    CAS 
    PubMed 

    Google Scholar 
    Hallegraeff, G. M. et al. Perceived global increase in algal blooms is attributable to intensified monitoring and emerging bloom impacts. Commun. Earth Environ. 2, 117. https://doi.org/10.1038/s43247-021-00178-8 (2021).Article 
    ADS 

    Google Scholar 
    Hennon, G. M. M. & Dyhrman, S. T. Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms. Harmful Algae 91, 101587. https://doi.org/10.1016/j.hal.2019.03.005 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kudela, R., Berdalet, E. & Urban, E. Harmful Algal Blooms: A Scientific Summary for Policy Makers (2015).Lezcano, M., Velázquez, D., Quesada, A. & El-Shehawy, R. Diversity and temporal shifts of the bacterial community associated with a toxic cyanobacterial bloom: An interplay between microcystin producers and degraders. Water Res. 125, 52–61. https://doi.org/10.1016/j.watres.2017.08.025 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    Scherer, P. I. et al. Temporal dynamics of the microbial community composition with a focus on toxic cyanobacteria and toxin presence during harmful algal blooms in two South German Lakes. Front. Microbiol. 8, 02387. https://doi.org/10.3389/fmicb.2017.02387 (2017).Article 

    Google Scholar 
    Woodhouse, J. N. et al. Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake. ISME J. 10, 1337–1351. https://doi.org/10.1038/ismej.2015.218 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Beaver, J. R. et al. Land use patterns, ecoregion, and microcystin relationships in U.S. lakes and reservoirs: A preliminary evaluation. Harmful Algae 36, 57–62. https://doi.org/10.1016/j.hal.2014.03.005 (2014).Article 
    CAS 

    Google Scholar 
    Loftin, K. A. et al. Cyanotoxins in inland lakes of the United States: Occurrence and potential recreational health risks in the EPA National Lakes Assessment 2007. Harmful Algae 56, 77–90. https://doi.org/10.1016/j.hal.2016.04.001 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Casero, M. C., Velázquez, D., Medina-Cobo, M., Quesada, A. & Cirés, S. Unmasking the identity of toxigenic cyanobacteria driving a multi-toxin bloom by high-throughput sequencing of cyanotoxins genes and 16S rRNA metabarcoding. Sci. Total Environ. 665, 367–378. https://doi.org/10.1016/j.scitotenv.2019.02.083 (2019).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Chaffin, J. D., Sigler, V. & Bridgeman, T. B. Connecting the blooms: Tracking and establishing the origin of the record-breaking Lake Erie Microcystis bloom of 2011 using DGGE. Aquat. Microb. Ecol. 73, 29–39 (2014).Article 

    Google Scholar 
    Stanley, E. H. & Jones, J. B. (eds) Stream Ecosystems in a Changing Environment 321–348 (Elsevier, 2016).Book 

    Google Scholar 
    Giblin, S. M. & Gerrish, G. A. Environmental factors controlling phytoplankton dynamics in a large floodplain river with emphasis on cyanobacteria. River Res. Appl. 36, 1137–1150. https://doi.org/10.1002/rra.3658 (2020).Article 

    Google Scholar 
    Graham, J. L., Ziegler, A. C., Loving, B. L. & Loftin, K. A. Fate and Transport of Cyanobacteria and Associated Toxins and Taste-and-Odor Compounds from Upstream Reservoir Releases in the Kansas River, Kansas, September and October 2011 65 (US Geological Survey, 2012).
    Google Scholar 
    Knowlton, M. F. & Jones, J. R. Seston, light, nutrients and chlorophyll in the lower Missouri River, 1994–1998. J. Freshw. Ecol. 15, 283–297. https://doi.org/10.1080/02705060.2000.9663747 (2000).Article 

    Google Scholar 
    Otten, T. G., Crosswell, J. R., Mackey, S. & Dreher, T. W. Application of molecular tools for microbial source tracking and public health risk assessment of a Microcystis bloom traversing 300 km of the Klamath River. Harmful Algae 46, 71–81 (2015).Article 

    Google Scholar 
    Preece, E. P., Hardy, F. J., Moore, B. C. & Bryan, M. A review of microcystin detections in Estuarine and Marine waters: Environmental implications and human health risk. Harmful Algae 61, 31–45. https://doi.org/10.1016/j.hal.2016.11.006 (2017).Article 
    CAS 

    Google Scholar 
    Reinl, K. L., Sterner, R. W., Lafrancois, B. M. & Brovold, S. Fluvial seeding of cyanobacterial blooms in oligotrophic Lake Superior. Harmful Algae 100, 101941. https://doi.org/10.1016/j.hal.2020.101941 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Bridgeman, T. B. et al. From River to Lake: Phosphorus partitioning and algal community compositional changes in Western Lake Erie. J. Great Lakes Res. 38, 90–97 (2012).Article 
    CAS 

    Google Scholar 
    Brown, B. L. et al. Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River. Stand Genomic Sci. 10, 65. https://doi.org/10.1186/s40793-015-0062-5 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hamner, S. et al. Metagenomic profiling of microbial pathogens in the Little Bighorn River, Montana. Int. J. Environ. Res. Public Health 16, 071097. https://doi.org/10.3390/ijerph16071097 (2019).Article 
    CAS 

    Google Scholar 
    Staley, C. et al. Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River. J. Appl. Microbiol. 115, 1147–1158. https://doi.org/10.1111/jam.12323 (2013).Article 
    CAS 
    PubMed 

    Google Scholar 
    Winter, C., Hein, T., Kavka, G., Mach, R. L. & Farnleitner, A. H. Longitudinal changes in the bacterial community composition of the Danube River: A whole-river approach. Appl. Environ. Microbiol. 73, 421–431. https://doi.org/10.1128/aem.01849-06 (2007).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Jackson, C. R., Millar, J. J., Payne, J. T., Ochs, C. A. & Wommack, K. E. Free-living and particle-associated bacterioplankton in large rivers of the Mississippi River basin demonstrate biogeographic patterns. Appl. Environ. Microbiol. 80, 7186–7195. https://doi.org/10.1128/AEM.01844-14 (2014).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Payne, J. T., Jackson, C. R., Millar, J. J. & Ochs, C. A. Timescales of variation in diversity and production of bacterioplankton assemblages in the Lower Mississippi River. PLoS ONE 15, e0230945. https://doi.org/10.1371/journal.pone.0230945 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Payne, J. T., Millar, J. J., Jackson, C. R. & Ochs, C. A. Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers. PLoS ONE 12, e0174890. https://doi.org/10.1371/journal.pone.0174890 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Read, D. S. et al. Catchment-scale biogeography of riverine bacterioplankton. ISME J. 9, 516–526. https://doi.org/10.1038/ismej.2014.166 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Reddington, K. et al. Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function. GigaScience 9, 53. https://doi.org/10.1093/gigascience/giaa053 (2020).Article 
    CAS 

    Google Scholar 
    Staley, C. et al. Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover. Front. Microbiol. 5, 414 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Staley, C. et al. Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River. Sci. Total Environ. 505, 435–445. https://doi.org/10.1016/j.scitotenv.2014.10.012 (2015).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Van Rossum, T. et al. Year-long metagenomic study of river microbiomes across land use and water quality. Front. Microbiol. 6, 1405 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Kim, K. H. et al. Application of metagenome analysis to characterize the molecular diversity and saxitoxin-producing potentials of a cyanobacterial community: A case study in the North Han River, Korea. Appl. Biol. Chem. 61, 153–161. https://doi.org/10.1007/s13765-017-0342-4 (2018).Article 
    CAS 

    Google Scholar 
    Graham, J. L. et al. Cyanotoxin occurrence in large rivers of the United States. Inland Waters 10, 109–117. https://doi.org/10.1080/20442041.2019.1700749 (2020).Article 
    CAS 

    Google Scholar 
    Zuellig, R. E., Graham, J. L., Stelzer, E. A., Loftin, K. A. & Rosen, B. H. Cyanobacteria, Cyanotoxin Synthetase Gene, and Cyanotoxin Occurrence Among Selected Large River Sites of the Conterminous United States, 2017–18 22 (US Geological Survey, 2021).
    Google Scholar 
    Kramer, B. J. et al. Nitrogen limitation, toxin synthesis potential, and toxicity of cyanobacterial populations in Lake Okeechobee and the St. Lucie River Estuary, Florida, during the 2016 state of emergency event. PLoS ONE 13, e0196278 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bouma-Gregson, K. et al. Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network. ISME J. 13, 1618–1634. https://doi.org/10.1038/s41396-019-0374-3 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tillett, D. et al. Structural organization of microcystin biosynthesis in Microcystis aeruginosa PCC7806: An integrated peptide–polyketide synthetase system. Chem. Biol. 7, 753–764 (2000).Article 
    CAS 
    PubMed 

    Google Scholar 
    Dittmann, E., Fewer, D. P. & Neilan, B. A. Cyanobacterial toxins: Biosynthetic routes and evolutionary roots. FEMS Microbiol. Rev. 37, 23–43. https://doi.org/10.1111/j.1574-6976.2012.12000.x (2013).Article 
    CAS 
    PubMed 

    Google Scholar 
    Jungblut, A. D. & Neilan, B. A. Molecular identification and evolution of the cyclic peptide hepatotoxins, microcystin and nodularin, synthetase genes in three orders of cyanobacteria. Arch. Microbiol. 185, 107–114. https://doi.org/10.1007/s00203-005-0073-5 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Meriluoto, J. et al. (eds) Handbook of Cyanobacterial Monitoring and Cyanotoxin Analysis 501–525 (Wiley, 2017).Book 

    Google Scholar 
    Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643. https://doi.org/10.1038/ismej.2017.119 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Graham, J. L., Dubrovsky, N. M., Loftin, K. A., Rosen, B. H. & Stelzer, E. A. Cyanotoxin, Chlorophyll-a, and Cyanobacterial Toxin Genetic Data for Samples Collected at Twelve Large River Sites Throughout the United States, June Through October 2019 (U.S. Geological Survey, 2022).
    Google Scholar 
    Dodds, W. K. & Smith, V. H. Nitrogen, phosphorus, and eutrophication in streams. Inland Waters 6, 155–164. https://doi.org/10.5268/IW-6.2.909 (2016).Article 
    CAS 

    Google Scholar 
    Debroas, D. et al. Overview of freshwater microbial eukaryotes diversity: A first analysis of publicly available metabarcoding data. FEMS Microbiol. Ecol. 93, 23. https://doi.org/10.1093/femsec/fix023 (2017).Article 
    CAS 

    Google Scholar 
    Henson, M. W. et al. Nutrient dynamics and stream order influence microbial community patterns along a 2914 kilometer transect of the Mississippi River. Limnol. Oceanogr. 63, 1837–1855. https://doi.org/10.1002/lno.10811 (2018).Article 
    ADS 
    CAS 

    Google Scholar 
    Ghai, R. et al. Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS ONE 6, e23785. https://doi.org/10.1371/journal.pone.0023785 (2011).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Liao, J. et al. Cyanobacteria in lakes on Yungui Plateau, China are assembled via niche processes driven by water physicochemical property, lake morphology and watershed land-use. Sci. Rep. 6, 36357. https://doi.org/10.1038/srep36357 (2016).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Monchamp, M.-E. et al. Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication. Nat. Ecol. Evol. 2, 317–324. https://doi.org/10.1038/s41559-017-0407-0 (2018).Article 
    PubMed 

    Google Scholar 
    Pessi, I. S., Maalouf, P. D. C., LaughinghouseBaurain, H. D. D. & Wilmotte, A. On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats. J. Phycol. 52, 356–368. https://doi.org/10.1111/jpy.12399 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Tanvir, R. U., Hu, Z., Zhang, Y. & Lu, J. Cyanobacterial community succession and associated cyanotoxin production in hypereutrophic and eutrophic freshwaters. Environ. Pollut. 290, 118056. https://doi.org/10.1016/j.envpol.2021.118056 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chételat, J., Pick, F. R. & Hamilton, P. B. Potamoplankton size structure and taxonomic composition: Influence of river size and nutrient concentrations. Limnol. Oceanogr. 51, 681–689 (2006).Article 
    ADS 

    Google Scholar 
    Heiskary, S. & Markus, H. Establishing relationships among nutrient concentrations, phytoplankton abundance, and biochemical oxygen demand in Minnesota, USA, rivers. Lake Reserv. Manag. 17, 251–262 (2001).Article 
    CAS 

    Google Scholar 
    Smith, V. H. Eutrophication of freshwater and coastal marine ecosystems a global problem. Environ. Sci. Pollut. Res. 10, 126–139 (2003).Article 
    CAS 

    Google Scholar 
    Verspagen, J. M. et al. Rising CO2 levels will intensify phytoplankton blooms in eutrophic and hypertrophic lakes. PLoS ONE 9, e104325 (2014).Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zepernick, B. N. et al. Elevated pH conditions associated with Microcystis spp. blooms decrease viability of the cultured diatom Fragilaria crotonensis and natural diatoms in Lake Erie. Front. Microbiol. 12, 598736. https://doi.org/10.3389/fmicb.2021.598736 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Urban, L. et al. Freshwater monitoring by nanopore sequencing. Elife 10, 61504. https://doi.org/10.7554/eLife.61504 (2021).Article 

    Google Scholar 
    Lee, C. J. & Henderson, R. J. Tracking Water-Quality in U.S. Streams and Rivers: U.S. Geological Survey National Water Quality Network. https://nrtwq.usgs.gov/nwqn (2020).Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data (2010).Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257. https://doi.org/10.1186/s13059-019-1891-0 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lu, J. B. F., Thielen, P. & Salzberg, S. L. Bracken: Estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3, 104. https://doi.org/10.7717/peerj-cs.104 (2017).Article 

    Google Scholar 
    Bagley, M. et al. High-throughput environmental DNA analysis informs a biological assessment of an urban stream. Ecol. Ind. 104, 378–389. https://doi.org/10.1016/j.ecolind.2019.04.088 (2019).Article 
    CAS 

    Google Scholar 
    Magoč, T. & Salzberg, S. L. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963. https://doi.org/10.1093/bioinformatics/btr507 (2011).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857. https://doi.org/10.1038/s41587-019-0209-9 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583. https://doi.org/10.1038/nmeth.3869 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Nübel, U., Garcia-Pichel, F. & Muyzer, G. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol. 63, 3327–3332. https://doi.org/10.1128/aem.63.8.3327-3332.1997 (1997).Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Neilan, B. A. et al. rRNA sequences and evolutionary relationships among toxic and nontoxic cyanobacteria of the genus Microcystis. Int. J. Syst. Bacteriol. 47, 693–697. https://doi.org/10.1099/00207713-47-3-693 (1997).Article 
    CAS 
    PubMed 

    Google Scholar 
    Team R Core. R: A Language and Environment for Statistical Computing (2013).McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Oksanen, J. et al. Vegan: Community Ecology Package. R Package Version 2.5-2 (2018).Wickham, H. ggplot2-Elegant Graphics for Data Analysis (Springer, 2016).MATH 

    Google Scholar 
    U.S. Geological Survey. National Water Information System Database. https://doi.org/10.5066/F7P55KJN (2022). More

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    Non-lethal fungal infection could reduce aggression towards strangers in ants

    Schmid-Hempel P. Parasites in social insects. Princeton University Press (1998).Lefèvre, T. et al. The ecological significance of manipulative parasites. Trends Ecol. Evol. 24, 41–48 (2009).Article 
    PubMed 

    Google Scholar 
    Elya, C. et al. Robust manipulation of the behavior of Drosophila melanogaster by a fungal pathogen in the laboratory. Elife 7, e34414 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Herbison, R., Lagrue, C. & Poulin, R. The missing link in parasite manipulation of host behaviour. Parasites Vectors 11, 1–6 (2018).Article 

    Google Scholar 
    Csata, E., Billen, J., Barbu-Tudoran, L. & Markó, B. Inside Pandora’s box: development of the lethal myrmecopathogenic fungus Pandora formicae within its ant host. Fungal Ecol. 50, 101022 (2021).Article 

    Google Scholar 
    Trinh, T., Ouellette, R. & de Bekker, C. Getting lost: the fungal hijacking of ant foraging behaviour in space and time. Anim. Behav. 181, 165–184 (2021).Article 

    Google Scholar 
    Moore J. Parasites and the Behavior of Animals. Oxford University Press, Oxford (2002).Thomas, F., Fauchier, J. & Lafferty, K. D. Conflict of interest between a nematode and a trematode in an amphipod host: test of the “sabotage” hypothesis. Behav. Ecol. Sociobiol. 51, 296–301 (2002).Article 

    Google Scholar 
    Stroeymeyt, N. et al. Social network plasticity decreases disease transmission in a eusocial insect. Science 362, 941–945 (2018).Article 
    CAS 
    PubMed 

    Google Scholar 
    Beros, S., Foitzik, S. & Menzel, F. What are the mechanisms behind a parasite-induced decline in nestmate recognition in ants? J. Chem. Ecol. 43, 869–880 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    Hamilton, W. D. Kinship, recognition, disease, and intelligence: constraints of social evolution. In: Ito Y., Brown J. L., Kikkawa J. (eds) Animal societies: theories and facts. Jpn Sci Soc Press, Tokyo, pp 81–102 (1987).Hunt, J. H. & Richard, F. J. Intracolony vibroacoustic communication in social insects. Insect Soc. 60, 403–417 (2013).Article 

    Google Scholar 
    Wyatt, T. D. Proteins and peptides as pheromone signals and chemical signatures. Anim. Behav. 97, 273–280 (2014).Article 

    Google Scholar 
    Leonhardt, S. D., Menzel, F., Nehring, V. & Schmitt, T. Ecology and evolution of communication in social insects. Cell 164, 1277–1287 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Casacci, L. P. et al. Ant pupae employ acoustics to communicate social status in their colony’s hierarchy. Curr. Biol. 23, 323–327 (2013).Article 
    CAS 
    PubMed 

    Google Scholar 
    Schönrogge, K., Barbero, F., Casacci, L. P., Settele, J. & Thomas, J. A. Acoustic communication within ant societies and its mimicry by mutualistic and socially parasitic myrmecophiles. Anim. Behav. 134, 249–256 (2017).Article 

    Google Scholar 
    Sheehan, M. J. & Tibbetts, E. A. Specialized face learning is associated with individual recognition in paper wasps. Science 334, 1272–1275 (2011).Article 
    CAS 
    PubMed 

    Google Scholar 
    Chittka, L. & Dyer, A. Your face looks familiar. Nature 481, 154–155 (2012).Article 
    CAS 
    PubMed 

    Google Scholar 
    Billen, J. Signal variety and communication in social insects. Proc. Neht. Entomol. Soc. Meet. 17, 9 (2006).
    Google Scholar 
    Blomquist G. J. Biosynthesis of cuticular hydrocarbons. In: Blomquist, G. J., Bagnères, A.-G. (eds.): Insect hydrocarbons: biology, biochemistry and chemical ecology. Cambridge University Press (2010).Hefetz, A. The evolution of hydrocarbon pheromone parsimony in ants (Hymenoptera: Formicidae) – interplay of colony odor uniformity and odor idiosyncrasy. Myrmecol. N. 10, 59–68 (2007).
    Google Scholar 
    Bagnères A. G., Lorenzi M. C. Chemical deception/mimicry using cuticular hydrocarbons. Insect hydrocarbons: Biology, biochemistry and chemical ecology. Chemical deception/mimicry using cuticular hydrocarbons, 282–324 (2010).van Zweden, J. S. & d’Ettorre, P. Nestmate recognition in social insects and the role of hydrocarbons. Insect Hydrocarbons: Biol. Biochem. Chem. Ecol. 11, 222–243 (2010).Article 

    Google Scholar 
    Esponda, F. & Gordon, D. M. Distributed nestmate recognition in ants. Proc. R. Soc. B. 282, 20142838 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Crozier, R. & Dix, M. W. Analysis of two genetic models for the innate components of colony odor in social Hymenoptera. Behav. Ecol. Sociobiol. 4, 217–224 (1979).Article 

    Google Scholar 
    Wakonigg, G., Eveleigh, L., Arnold, G. & Crailsheim, K. Cuticular hydrocarbon profiles reveal age-related changes in honey bee drones (Apis mellifera carnica). J. Apic. Res. 39, 137–141 (2000).Article 
    CAS 

    Google Scholar 
    Cuvillier-Hot, V., Cobb, M., Malosse, C. & Peeters, C. Sex, age and ovarian activity affect cuticular hydrocarbons in Diacamma ceylonense, a queenless ant. J. Insect Physiol. 47, 485–493 (2001).Article 
    CAS 
    PubMed 

    Google Scholar 
    Greene, M. J. & Gordon, D. M. Cuticular hydrocarbons inform task decisions. Nature 423, 32–32 (2003).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kather, R., Drijfhout, F. P. & Martin, S. J. Task group differences in cuticular lipids in the honey bee Apis mellifera. J. Chem. Ecol. 37, 205–212 (2011).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kleeberg, I., Menzel, F. & Foitzik, S. The influence of slavemaking lifestyle, caste and sex on chemical profiles in Temnothorax ants: insights into the evolution of cuticular hydrocarbons. Proc. R. Soc. B. 284, 20162249 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sprenger, P. P. & Menzel, F. Cuticular hydrocarbons in ants (Hymenoptera: Formicidae) and other insects: how and why they differ among individuals, colonies, and species. Myrmecol. N. 30, 1–26 (2020).
    Google Scholar 
    Reeve, H. K. The evolution of conspecific acceptance thresholds. Am. Nat. 133, 407–435 (1989).Article 

    Google Scholar 
    Lenoir, A., D’Ettore, P. & Errard, C. Chemical ecology and social parasitism in ants. Annu. Rev. Entomol. 46, 573–599 (2001).Article 
    CAS 
    PubMed 

    Google Scholar 
    Akino, T. Chemical strategies to deal with ants: a review of mimicry, camouflage, propaganda, and phytomimesis by ants (Hymenoptera: Formicidae) and other arthropods. Myrmecol. N. 11, 173–181 (2008).
    Google Scholar 
    Akino, T., Knapp, J. J., Thomas, J. A. & Elmes, G. W. Chemical mimicry and host specificity in the butterfly Maculinea rebeli, a social parasite of Myrmica ant colonies. Proc. Roy. Soc. B. 266, 1419–1426 (1999).Article 
    CAS 

    Google Scholar 
    Nash, D. R., Als, T. D., Maile, R., Jones, G. R. & Boomsma, J. J. A mosaic of chemical coevolution in a large blue butterfly. Science 319, 88–90 (2008).Article 
    CAS 
    PubMed 

    Google Scholar 
    Johnson, C. A., Vander Meer, R. K. & Lavine, B. Changes in the cuticular hydrocarbon profile of the slave-maker ant queen, Polyergus breviceps Emery, after killing a Formica host queen (Hymenoptera: Formicidae). J. Chem. Ecol. 27, 1787–1804 (2001).Article 
    CAS 
    PubMed 

    Google Scholar 
    Lecuona, R., Riba, G., Cassier, P. & Clément, J. L. Alterations of insect epicuticular hydrocarbons during infection with Beauveria bassiana or B. brongniartii. J. Invertebr. Pathol. 58, 10–18 (1991).Article 
    CAS 

    Google Scholar 
    Trabalon, M., Plateaux, L., Péru, L., Bagnères, A. G. & Hartmann, N. Modification of morphological characters and cuticular compounds in worker ants Leptothorax nylanderi induced by endoparasites Anomotaenia brevis. J. Insect Physiol. 46, 169–178 (2000).Article 
    CAS 
    PubMed 

    Google Scholar 
    Zurek, L., Watson, D. W., Krasnoff, S. B. & Schal, C. Effect of the entomopathogenic fungus, Entomophthora muscae (Zygomycetes: Entomophthoraceae), on sex pheromone and other cuticular hydrocarbons of the house fly. Musca Domestica. J. Invertebr. Pathol. 80, 171–176 (2002).Article 
    CAS 
    PubMed 

    Google Scholar 
    Nielsen, M. L. & Holman, L. Terminal investment in multiple sexual signals: immune‐challenged males produce more attractive pheromones. Func. Ecol. 26, 20–28 (2012).Article 

    Google Scholar 
    Beros, S., Jongepier, E., Hagemeier, F. & Foitzik, S. The parasite’s long arm: a tapeworm parasite induces behavioural changes in uninfected group members of its social host. Proc. Roy. Soc. B. 282, 20151473 (2015).Article 

    Google Scholar 
    Csata, E., Erős, K. & Markó, B. Effects of the ectoparasitic fungus Rickia wasmannii on its ant host Myrmica scabrinodis: changes in host mortality and behavior. Insectes Soc. 61, 247–252 (2014).Article 

    Google Scholar 
    Markó, B. et al. Distribution of the myrmecoparasitic fungus Rickia wasmannii (Ascomycota: Laboulbeniales) across colonies, individuals, and body parts of Myrmica scabrinodis. J. Invertebr. Pathol. 136, 74–80 (2016).Article 
    PubMed 

    Google Scholar 
    Báthori, F., Csata, E. & Tartally, A. Rickia wasmannii increases the need for water in Myrmica scabrinodis (Ascomycota: Laboulbeniales; Hymenoptera: Formicidae). J. Invertebr. Pathol. 126, 7–82 (2015).Article 

    Google Scholar 
    Csata, E. et al. Lock-picks: fungal infection facilitates the intrusion of strangers into ant colonies. Sci. Rep. 7, 46323 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Csata, E., Billen, J., Bernadou, A., Heinze, J. & Markó, B. Infection-related variation in cuticle thickness in the ant Myrmica scabrinodis (Hymenoptera: Formicidae). Insectes Soc. 65, 503–506 (2018).Article 

    Google Scholar 
    Csősz, S., Rádai, Z., Tartally, A., Ballai, L. E. & Báthori, F. Ectoparasitic fungi Rickia wasmannii infection is associated with smaller body size in Myrmica ants. Sci. Rep. 11, 1–9 (2021).Article 

    Google Scholar 
    Dani, F. R., Jones, G. R., Destri, S., Spencer, S. H. & Turillazzi, S. Deciphering the recognition signature within the cuticular chemical profile of paper wasps. Anim. Behav. 62, 165–171 (2001).Article 

    Google Scholar 
    Lorenzi, M. C., Bagneres, A. G., Clément, J. L. & Turillazzi, S. Polistes biglumis bimaculatus epicuticular hydrocarbons and nestmate recognition (Hymenoptera Vespidae). Insectes Soc. 44, 123–138 (1997).Article 

    Google Scholar 
    Ruther, J., Sieben, S. & Schricker, B. Nestmate recognition in social wasps: manipulation of hydrocarbon profiles induces aggression in the European hornet. Naturwissenschaften 89, 111–114 (2002).Article 
    CAS 
    PubMed 

    Google Scholar 
    Smith, A. A., Hölldobler, B. & Liebig, J. Cuticular hydrocarbons reliably identify cheaters and allow enforcement of altruism in a social insect. Curr. Biol. 19, 78–81 (2009).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ebsen, J. R., Boomsma, J. J. & Nash, D. R. Phylogeography and cryptic speciation in the Myrmica scabrinodis Nylander, 1846 species complex (Hymenoptera: Formicidae), and their conservation implications. Insect Conserv. Divers 12, 467–480 (2019).Article 

    Google Scholar 
    Ballinger, M. J., Moore, L. D. & Perlman, S. J. Evolution and diversity of inherited Spiroplasma symbionts in Myrmica ants. Appl. Environ. Microbiol. 84, e02299–17 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Menzel, F. et al. Crematoenones – a novel substance class exhibited by ants functions as appeasement signal. Front. Zool. 10, 1–12 (2013).Article 

    Google Scholar 
    Qiu, H.-L., Qin, C.-S., Fox, E. G. P., Wang, D.-S. & He, Y.-R. Differential behavioral responses of Solenopsis invicta (Hymenoptera: Formicidae) workers toward nestmate and non-nestmate corpses. J. Ins. Sci. 20, 11 (2020).Article 

    Google Scholar 
    Martin, S. J., Vitikainen, E., Helanterä, H. & Drijfhout, F. P. Chemical basis of nest-mate discrimination in the ant Formica exsecta. Proc. R. Soc. B. 275, 1271–1278 (2008).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Guerrieri, F. J. et al. Ants recognize foes and not friends. Proc. R. Soc. B. 276, 2461–2468 (2009).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gibbs, A. & Pomonis, J. G. Physical properties of insect cuticular hydrocarbons: the effects of chain lengths, methyl branching and unsaturation. Comp. Biochem. Physiol. 112, 243–249 (1995).Article 

    Google Scholar 
    Menzel, F., Blaimer, B. B. & Schmitt, T. How do cuticular hydrocarbons evolve? Physiological constraints and climatic and biotic selection pressures act on a complex functional trait. Proc. R. Soc. B. 284, 20161727 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Breed, M. D., Leger, E. A., Pearce, A. M. & Wang, Y. J. Comb wax effects on the ontogeny of honey bee nestmate recognition. Anim. Behav. 55, 13–20 (1998).Article 
    CAS 
    PubMed 

    Google Scholar 
    Breed, M. D. & Stiller, T. M. Honey bee, Apis mellifera, nestmate discrimination: hydrocarbon effects and the evolutionary implications of comb choice. Anim. Behav. 43, 875–883 (1992).Article 

    Google Scholar 
    Akino, T., Yamamura, K., Wakamura, S. & Yamaoka, R. Direct behavioral evidence for hydrocarbons as nestmate recognition cues in Formica japonica (Hymenoptera: Formicidae). Appl. Entomol. Zool. 39, 381–387 (2004).Article 
    CAS 

    Google Scholar 
    Greene, M. J. & Gordon, D. M. Structural complexity of chemical recognition cues affects the perception of group membership in the ants Linepithema humile and Aphaenogaster cockerelli. J. Exp. Biol. 210, 897–905 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Casacci, L. P., Barbero, F., Ślipiński, P. & Witek, M. The inquiline ant Myrmica karavajevi uses both chemical and vibroacoustic deception mechanisms to integrate into its host colonies. Biology 10, 654 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bhatkar, A. & Whitcomb, W. Artificial diet for rearing various species of ants. Florid. Entomol. 53, 229–232 (1970).Article 

    Google Scholar 
    Espadaler X., Santamaria S. Ecto- and endoparasitic fungi on ants from the Holarctic region. Psyche 168478, 1–10 (2012).Csata, E. et al. Comprehensive survey of Romanian myrmecoparasitic fungi: new species, biology and distribution. North West J. Zool. 9, 23–29 (2013).
    Google Scholar 
    Witek, M., Barbero, F. & Markó, B. Myrmica ants host highly diverse parasitic communities: from social parasites to microbes. Insectes Soc. 61, 307–323 (2014).Article 

    Google Scholar 
    Tragust, S., Tartally, A., Espadaler, X. & Billen, J. Histopathology of Laboulbeniales (Ascomycota: Laboulbeniales): ectoparasitic fungi on ants (Hymenoptera: Formicidae). Myrmecol. N. 23, 81–89 (2016).
    Google Scholar 
    Czekes, Z. et al. The genus Myrmica Latreille, 1804 (Hymenoptera: Formicidae) in Romania: distribution of species and key for their identification. Entomol. Rom. 17, 29–50 (2012).
    Google Scholar 
    Buczkowski, G. & Silverman, J. Context-dependent nestmate discrimination and the effect of action thresholds on exogenous cue recognition in the Argentine ant. Anim. Behav. 69, 741–749 (2005).Article 

    Google Scholar 
    Diez, L., Moquet, L. & Detrain, C. Post-mortem changes in chemical profile and their influence on corpse removal in ants. J. Chem. Ecol. 39, 1424–1432 (2013).Article 
    CAS 
    PubMed 

    Google Scholar 
    Csata, E., Bernadou, A., Rákosy-Tican, E., Heinze, J. & Markó, B. The effects of fungal infection and physiological condition on the locomotory behaviour of the ant Myrmica scabrinodis. J. Insect Physiol. 98, 167–172 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    Moroń, D., Witek, M. & Woyciechowski, M. Division of labour among workers with different life expectancy in the ant Myrmica scabrinodis. Anim. Behav. 75, 345–350 (2008).Article 

    Google Scholar 
    Bernadou, A., Felden, A., Moreau, M., Moretto, P. & Fourcassié, V. Ergonomics of load transport in the seed harvesting ant Messor barbarus: morphology influences transportation method and efficiency. J. Exp. Biol. 219, 2920–2927 (2016).PubMed 

    Google Scholar 
    Keresztes, K. K., Csata, E., Lunka-Tekla, A. & Markó, B. Friend or foe? Differential aggression towards neighbors and strangers in the ant Liometopum microcephalum (Hymenoptera: Formicidae). Sci. Entomol. 23, 351–358 (2020).Article 

    Google Scholar 
    Ratnasingham, S. & Hebert, P. D. BOLD: The Barcode of life data system. Mol. Ecol. Notes 7, 355–364, http://www.barcodinglife.org (2007).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (URL ) (2020).Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting Linear Mixed-Effects Models Using lme4. J. Stat. Soft. 67, 1–48 (2015).Fox J., Weisberg S. Using car and effects Functions in Other Functions. Using Car Eff. Funct. Other Funct., 3, 1–5 (2020).Hothorn, T., Bretz, F. & Westfall, P. Simultaneous inference in general parametric 312 models. Biom. J. 50, 346–363 (2008).Article 
    PubMed 

    Google Scholar 
    Wickham H. ggplot2: elegant graphics for data analysis. (Springer Science & Business Media) (2009). More

  • in

    An ankylosaur larynx provides insights for bird-like vocalization in non-avian dinosaurs

    Reilly, S. M. & Lauder, G. V. The evolution of tetrapod feeding behavior: kinematic homologies in prey transport. Evolution 44, 1542–1557 (1990).Article 

    Google Scholar 
    Iwasaki, S. Evolution of the structure and function of the vertebrate tongue. J. Anat. 201, 1–13 (2002).Article 

    Google Scholar 
    Fitch, W. T. & Suthers, R. A. In Vertebrate Sound Production and Acoustic Communication (eds Suthers, R. A., Fitch, W. T., Fay, R. R., & Popper, A. N.) 1–18 (Springer, 2016).Carroll, R. L. The Palaeozoic ancestry of salamanders, frogs and caecilians. Zool. J. Linn. Soc. 150, 1–140 (2007).Article 

    Google Scholar 
    Schwenk, K. in Feeding: Form, Function and Evolution in Tetrapod Vertebrates (ed. Schwenk, K.) 175–291 (Academic Press, 2000).Schwenk, K. & Rubega, M. In Physiological and ecological adaptations to feeding in vertebrates, (eds. Starck, M. & Wang, T.) 1–41 (Science Pub. Inc., 2005).Schumacher, G. H. In Biology of the Reptilia, 4 (ed Gans, C.) 101–200 (Academic Press, 1973).Reese, A. M. The laryngeal region of Alligator mississippiensis. Anat. Rec. 92, 273–277 (1945).Article 

    Google Scholar 
    Riede, T., Li, Z., Tokuda, I. & Farmer, C. G. Functional morphology of the Alligator mississippiensis larynx with implications for vocal production. J. Exp. Biol. 218, 991–998 (2015).Article 

    Google Scholar 
    McLelland, J. In Form and Function in Birds, 4 (eds King, A. S. & McLelland, J.) 69–103 (Academic Press, 1989).Homberger, D. G. In The Biology of the Avian Respiratory System (ed Maina, J. N.) 27–97 (Springer, 2017).Fitch, W. T. In Encyclopedia of Language & Linguistics (ed Brown, K.) 115–121 (Elsevier, 2006).Clarke, J. A. et al. Fossil evidence of the avian vocal organ from the Mesozoic. Nature 538, 502–505 (2016).Article 

    Google Scholar 
    Kingsley, E. P. et al. Identity and novelty in the avian syrinx. Proc. Natl Acad. Sci. USA 115, 10209–10217 (2018).Article 
    CAS 

    Google Scholar 
    Riede, T., Thomson, S. L., Titze, I. R. & Goller, F. The evolution of the syrinx: an acoustic theory. PLoS Biol. 17, e2006507 (2019).Nowicki, S. Vocal tract resonances in oscine bird sound production: evidence from birdsongs in a helium atmosphere. Nature 325, 53–55 (1987).Article 
    CAS 

    Google Scholar 
    Hill, R. V. et al. A complex hyobranchial apparatus in a Cretaceous dinosaur and the antiquity of avian paraglossalia. Zool. J. Linn. Soc. 175, 892–909 (2015).Article 

    Google Scholar 
    Li, Z. H., Zhou, Z. H. & Clarke, J. A. Convergent evolution of a mobile bony tongue in flighted dinosaurs and pterosaurs. PLoS One 13, e0198078 (2018).Article 

    Google Scholar 
    Bonaparte, J. F., Novas, F. E. & Coria, R. A. Carnotaurus sastrei Bonaparte, the horned, lightly built carnosaur from the Middle Cretaceous of Patagonia. Contrib. in Sci. Nat. Hist. Mus. L. A. 416, 1–42 (1990).Maryanska, T. Ankylosauridae (Dinosauria) from Mongolia. Palaeontol. Pol. 37, 85–151 (1977).
    Google Scholar 
    Mori, C. A comparative anatomical study on the laryngeal cartilages and laryngeal muscles of birds, and a developmental study on the larynx of the domestic fowl. Acta Med. 27, 2629–2678 (1957).
    Google Scholar 
    Siebenrock, F. Über den Kehlkopf und die Luftröhre der Schildkröten. Sitzungsberichte Der Kais. 108, 581–595 (1899).
    Google Scholar 
    Soley, J. T., Tivane, C. & Crole, M. R. Gross morphology and topographical relationships of the hyobranchial apparatus and laryngeal cartilages in the ostrich (Struthio camelus). Acta Zool. 96, 442–451 (2015).Article 

    Google Scholar 
    Olson, S. L. & Feduccia, A. Presbyornis and the origin of the Anseriformes (Aves: Charadriomorphae). Smithson. Contrib. Zool. 323, 1–24 (1980).Soley, J. T., Tivane, C. & Crole, M. R. A Gross morphology and topographical relationships of the hyobranchial apparatus and laryngeal cartilages in the ostrich (Struthio camelus). Acta Zool. 94, 442–451 (2015).Article 

    Google Scholar 
    Hogg, D. A. Ossification of the laryngeal, tracheal and syringeal cartilages in the domestic fowl. J. Anat. 134, 57–71 (1982).CAS 

    Google Scholar 
    Gaunt, A. S., Stein, R. C. & Gaunt, S. L. Pressure and air flow during distress calls of the starling, Sturnus vulgaris (Aves; Passeriformes). J. Exp. Zool. 183, 241–261 (1973).Article 

    Google Scholar 
    Sacchi, R., Galeotti, P., Fasola, M. & Gerzeli, G. Larynx morphology and sound production in three species of Testudinidae. J. Morphol. 261, 175–183 (2004).Article 

    Google Scholar 
    Titze, I. R. The physics of small-amplitude oscillation of the vocal folds. J. Acoust. Soc. Am. 83, 1536–1552 (1988).Article 
    CAS 

    Google Scholar 
    Russell, A. P., Hood, H. A. & Bauer, A. M. Laryngotracheal and cervical muscular anatomy in the genus Uroplatus (Gekkota: Gekkonidae) in relation to distress call emission. Afr. J. Herpetol. 63, 127–151 (2014).Article 

    Google Scholar 
    Russell, A. P., Rittenhouse, D. R. & Bauer, A. M. Laryngotracheal morphology of Afro‐Madagascan Geckos: a comparative survey. J. Morphol. 245, 241–268 (2000).Article 
    CAS 

    Google Scholar 
    Gans, C. & Maderson, P. F. Sound producing mechanisms in recent reptiles: review and comment. Am. Zool. 13, 1195–1203 (1973).Article 

    Google Scholar 
    Galeotti, P., Sacchi, R., Fasola, M. & Ballasina, D. Do mounting vocalisations in tortoises have a communication function? A comparative analysis. Herpetol. J. 15, 61–71 (2005).
    Google Scholar 
    Fletcher, N. H. Bird song—a quantitative acoustic model. J. Theor. Biol. 135, 455–481 (1988).Article 

    Google Scholar 
    Vergne, A. L., Pritz, M. B. & Mathevon, N. Acoustic communication in crocodilians: from behaviour to brain. Biol. Rev. 84, 391–411 (2009).Article 
    CAS 

    Google Scholar 
    Marler, P. R. & Slabbekoorn, H. Nature’s music: The science of birdsong (Academic Press, San Diego, USA, 2004).White, S. S. In Sisson and Grossman’s The Anatomy of the Domestic Animals. 2 (ed Getty, R.) 1891–1897 (Saunders, Philadelphia, USA 975).Kirchner, J. A. The vertebrate larynx: adaptations and aberrations. Laryngoscope 103, 1197–1201 (1993).Article 
    CAS 

    Google Scholar 
    Mackelprang, R. & Goller, F. Ventilation patterns of the songbird lung/air sac system during different behaviors. J. Exp. Biol. 216, 3611–3619 (2013).
    Google Scholar 
    Brocklehurst, R. J., Schachner, E. R. & Sellers, W. I. Vertebral morphometrics and lung structure in non-avian dinosaurs. R. Soc. Open Sci. 5, 180983 (2018).Article 

    Google Scholar 
    Cerda, I. A., Salgado, L. & Powell, J. E. Extreme postcranial pneumaticity in sauropod dinosaurs from South America. Paläontol. Z. 86, 441–449 (2012).Article 

    Google Scholar 
    Sereno, P. C. et al. Evidence for avian intrathoracic air sacs in a new predatory dinosaur from Argentina. PLoS One 3, e3303 (2008).Chiari, Y., Cahais, V., Galtier, N. & Delsuc, F. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol. 10, 65 (2012).Article 

    Google Scholar  More

  • in

    Tropical biodiversity linked to polar climate

    Wallace, A. R. Tropical Nature and Other Essays (Macmillan, 1878).
    Google Scholar 
    von Humboldt, A. Ansichten der Natur: mit wissenschaftlichen Erläuterungen (Cotta, 1808).
    Google Scholar 
    Brown, J. H. J. Biogeogr. 41, 8–22 (2014).Article 
    PubMed 

    Google Scholar 
    Fenton, I. S., Aze, T., Farnsworth, A., Valdes, P. & Saupe, E. E. Nature https://doi.org/10.1038/s41586-023-05712-6 (2023).Article 

    Google Scholar 
    Woodhouse, A., Swain, A., Fagan, W. F., Fraass, A. J. & Lowery, C. M. Nature https://doi.org/10.1038/s41586-023-05694-5 (2023).Article 

    Google Scholar 
    Yasuhara, M., Tittensor, D. P., Hillebrand, H. & Worm, B. Biol. Rev. 92, 199–215 (2017).Article 
    PubMed 

    Google Scholar 
    Yasuhara, M. et al. Proc. Natl Acad. Sci. USA 117, 12891–12896 (2020).Article 
    PubMed 

    Google Scholar 
    Song, H. et al. Proc. Natl Acad. Sci. USA 117, 17578–17583 (2020).Article 
    PubMed 

    Google Scholar 
    Penn, J. L., Deutsch, C., Payne, J. L. & Sperling, E. A. Science 362, eaat1327 (2018).Article 
    PubMed 

    Google Scholar 
    Janzen, D. H. Am. Nat. 101, 233–249 (1967).Article 

    Google Scholar 
    Hahn, L. C., Armour, K. C., Zelinka, M. D., Bitz, C. M. & Donohoe, A. Front. Earth Sci. 9, 710036 (2021).Article 

    Google Scholar 
    Penn, J. L. & Deutsch, C. Science 376, 524–526 (2022).Article 
    PubMed 

    Google Scholar  More

  • in

    The interplay between spatiotemporal overlap and morphology as determinants of microstructure suggests no ‘perfect fit’ in a bat-flower network

    Study siteThe study was conducted in the Brasília National Park (PNB), Federal District, Brazil (15º39′57″ S; 47º59′38″ W), a 42.355 ha Protected Area with a typical vegetation configuration found in the Cerrado of the central highlands of Brazil, i.e., a mosaic of gallery forest patches along rivers surrounded by a matrix of savannas and grasslands34. The climate in the region falls into the Aw category in the Köppen scale, categorizing a tropical wet savanna, with marked rainy (October to March) and dry (April to September) seasons.We carried out the study in eight fixed sampling sites scattered evenly throughout the PNB and separated by at least two kilometers from one another (Supplementary Fig. S1). The sites consisted of four cerrado sensu stricto sites (bushy savanna containing low stature trees); two gallery forest edges sites (ca. 5 m from forest edges, containing a transitional community), and two gallery forest interior sites. These three types reflect the overall availability of habitat types in the reserve (excluding grasslands) and are the most appropriate foraging areas to sample interactions as bat-visited plants are either bushes, trees, or epiphytes, but rarely herbs35.Bat and interaction samplingsWe sampled bat-plant interactions using pollen loads collected from bat individuals captured in the course of one phenological year, thus configuring an animal-centered sampling. We carried out monthly field campaigns to capture bats from October 2019 to February 2020, from August to September 2020, and from March to July 2021. In each month, we carried out eight sampling nights during periods of low moonlight intensity, each associated with one of the eight sites. Each night, we set 10 mist nets (2.6 × 12 m, polyester, denier 75/2, 36 mm mesh size, Avinet NET-PTX, Japan) at ground level randomly within the site, which were opened at sunset and closed after six hours. We accumulated a total sampling effort of 552 net-hours, 28,704 m2 of net area, or 172,224 m2h sensu Straube and Bianconi36.All captured bats were sampled for pollen, irrespective of family or feeding guild. We used glycerinated and stained gelatin cubes to collect pollen grains from the external body of bats (head, torso, wings, and uropatagium). Samples were stored individually, and care was taken not to cross-contaminate samples. Pollen types were identified by light microscopy, and palynomorphs were identified to the lowest-possible taxonomical level using an extensive personal reference pollen collection from plants from the PNB (details in next section). Palynomorphs were sometimes classified to the genus or family level or grouped in entities representing more than one species. Any palynomorph numbering five or fewer grains in one sample was considered contamination, alongside any anemophilous species irrespective of pollen number.Bats were identified using a specialized key37 and four ecomorphological variables were measured for each individual. (i) Forearm length and (ii) body mass were used to calculate the body condition index (BCI), a proxy of body robustness38, where higher BCI values indicate larger and heavier bats, which are less effective in interacting with flowers in general due to a lack of hovering behavior, the incapability of interacting with delicate flowers that cannot sustain them, a lower maneuverability and higher energetic requirements39. Moreover, we measured (iii) longest skull length (distance from the edge of the occipital region to the anterior edge of the lower lip) and (iv) rostrum length (distance from the anterior edge of the eye to the anterior edge of the lower lip) to calculate the rostrum-skull ratio (RSR), a proxy of morphological specialization to nectar consumption23. Higher RSR values indicate bats with proportionally longer rostra in relation to total skull length. Longer rostra in bats are associated with a weaker bite force and thus less effective in consuming harder food items such as fruits and insects, thus suggesting a higher adaptation to towards nectar40,41. Bats were then tagged with aluminum bands for individualization and released afterward. To evaluate the sampling completeness of the bat community and of the pollen types found on bats, we employed the Chao1 asymptotic species richness estimator and an individual-based sampling effort to estimate and plot rarefaction curves, calculating sampling completeness according to Chacoff et al.42.All methods were carried out in accordance with relevant guidelines and regulations. The permits to capture, handle and collect bats were granted by the Ethical Council for the Usage of Animals (CEUA) of the University of Brasília (permit 23106.119660/2019-07) and the Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) (permit: SISBIO 70268). Vouchers of each species, when the collection was possible, were deposited in the Mammal Collection of the University of Brasília.Assessment of the plant communityIn each of the eight sampling sites, we delimited a 1000 × 10 m transect, each of which was walked monthly for one phenological year (January and February 2020, August to December 2020, and March to July 2021) to build a floristic inventory of plants of interest and to estimate their monthly abundance of flowering individuals. Plant species of interest were any potential partner for bats, which included species already known to be pollinated by bats, presenting chiropterophilous traits sensu Faegri and Van Der Pijl43, or any plant that could be accessed by and reward bats, whose flowers passes all the three following criteria:(i) Nectar or pollen is presented as the primary reward to visitors. (ii) Corolla diameter of 1 cm or more. This criterion excludes small generalist and insect-pollinated flowers where the visitation by bats is mechanically unlikely. It applies to the corolla diameter in non-tubular flowers or the diameter of the tube opening. Exceptions were small and actinomorphic flowers aggregated in one larger pollination unit (pseudanthia) where the 1 cm threshold was applied to inflorescence diameter. (iii) Reward must be promptly available for bats. This criterion excludes species with selective morphological mechanisms, such as quill-shaped bee-pollinated flowers or flowers with long and narrow calcars.All flowering individuals of interest species found in the transects were registered. A variable number of flowers/inflorescences (n = 5–18) were collected per species for morphometric analysis. For each species, we calculated floral tube length (FTL), corresponding to the distance between the base of the corolla, calyx, or hypanthium (depending on the species) to its opening, and the corolla’s outermost diameter (COD), which corresponds to the diameter of the corolla opening (tubular flowers) or simply the corolla diameter (non-tubular flowers). For pseudanthia-forming species, inflorescence width was measured. Pseudanthia and non-tubular flowers received a dummy FTL value of 0.1 mm to represent low restriction and enable later calculations. Finally, we collected reference pollen samples from all species from anthers of open flowers, which were used to identify pollen types found on bats. For plant species found in pollen loads but not in the PNB, measures were taken from plants found either on the outskirts of the site (Inga spp.) or from dried material in an online database (Ceiba pentandra, in https://specieslink.net/) using the ImageJ software44. Vouchers were deposited in the Herbarium of the Botany Department, University of Brasília.Data analysisNetwork macrostructureWe built a weighted adjacency matrix i x j, where cells corresponded to the number of individuals of bat species i that interacted with plant species or morphotype j. All edges corresponding to legitimate interactions were included. With this matrix, we calculated three structural metrics to describe the network’s macrostructure. First, weighted modularity (Qw), calculated by the DIRTLPAwb + algorithm45. A modular network comprises subgroups of species in which interactions are stronger and more frequent than species out of these subgroups10, which may reveal functional groups in the network9. Qw varies from zero to one, the latter representing a perfectly modular network.Second, complementary specialization through the H2′ metric46. It quantifies how unique, on average, are the interactions made by species in the network, considering interaction weights and correcting for network size. It varies from zero to one, the latter corresponding to a specialized network where interactions perfectly complement each other because species do not share partners.Lastly, nestedness, using the weighted WNODA metric25. Nested networks are characterized by interaction asymmetries, where peripheral species are only a subset of the pool of species with which generalists interact47. The index was normalized to vary from zero to one, with one representing a perfectly nested network. Given that the network has a modular structure, we also tested for a compound topology, i.e., the existence of distinct network patterns within network modules, by calculating intra-module WNODA and between-module WNODA36. Internally nested modules appear in networks in which consumers specialize in groups of dissimilar or clustered resources and suggest the existence of distinct functional groups of consumers25,48. Metric significance (Qw, H2′, and WNODA) was assessed using a Monte Carlo procedure based on a null model. We used the vaznull model3, where random matrices are created by preserving the connectance of the observed matrix but allowing marginal totals to vary. One thousand matrices were generated and metrics were calculated for each of them. Metric significance (p) corresponded to the number of times the null model delivered a value equal to or higher than the observed metric, divided by the number of matrices. The significance threshold was considered p ≤ 0.05.Given a modular structure, we followed the framework of Phillips et al.49 that correlates network concepts (especially modularity) with the distribution of morphological variables of pollinators to unveil patterns of niche divergence in pollination networks. Given the most parsimonious module configuration suggested by the algorithm, we compared modules in terms of the distribution of morphological variables of the bat (RCR and BCI) and plant (FTL and COD) species that composed the module. Differences between modules means were tested with one-way ANOVAs.Drivers of network microstructureThe role of different ecological variables in determining pairwise interaction frequencies was assessed using a probability matrices approach3. This framework considers that an interaction matrix Y is a product of several probability matrices of the same size as Y, with each matrix representing the probability of species interacting based on an ecological mechanism. Thus, adapting it to our objectives, we have Eq. (1):$$mathrm{Y}=mathrm{f}(mathrm{A},mathrm{ M },mathrm{P},mathrm{ S})$$
    (1)
    where Y is the observed interaction matrix, and a function of interaction probability matrices based on species relative abundances (A), representing neutrality as species interact by chance; species morphological specialization (M), phenological overlap (P), and spatial overlap (S). We built models containing each of these matrices in the following ways:Relative abundance (A): matrix cells were the products of the relative abundances of bat and plant species. The relative abundances of bats were determined through capture frequencies (each species’ capture frequency divided by all captures, excluding recaptures) and the relative abundances of plants were determined by the number of flowering individuals recorded in transections (each species’ summed abundance in all transects and all months divided by the pooled abundance of all species in the network). Cell values were normalized to sum one.Morphological specialization (M): cells were the probability of species interacting based on their matching degree of morphological specialization. Morphologically specialized bats (i.e., longer rostra and smaller size) are more likely to interact with morphologically specialized flowers (i.e., longer tubes and narrower corollas), while unspecialized bats are more likely to interact with unspecialized, accessible flowers. For this purpose, we calculated a bat specialization index (BSI) as the ratio between RCR and BCI, where higher BSI values indicate overall lower body robustness and longer snout length. Likewise, the flower specialization index (FSI) was calculated for plants as the ratio between FTL and COD, where higher values indicate smaller, narrower, long-tubed flowers that require specialized morphology and behavior from bats for visitation. BSI and FTL were normalized to range between zero and one and were averaged between individuals of each species of bat or plant. Therefore, interaction probabilities were calculated as in Eq. (2):$${P}_{i,j}=1-|{BSI}_{i}-{FSI}_{j}|$$
    (2)
    where Pi,j is the interaction probability between bat species i and plant species j and |BSIi – FSIj| is the absolute difference between bat and plant specialization indexes. Similar index values (two morphologically specialized or unspecialized species interacting) lead to a low difference in specialization and thus to a high probability of interaction (Pi,j → 1), whereas the interaction between a morphologically specialized and a morphologically unspecialized species leads to a high absolute difference and thus lower probability of interaction (Pi,j → 0). Cell values of the resulting matrix were normalized to sum one.Phenological overlap (P): cells were the probability of species interacting based on temporal synchrony, calculated as the number of months that individuals of bat species i and flowering individuals of plant species j co-occurred in the research site, pooling all capture sites/transections. Cell values were normalized to sum one.Spatial overlap (S): cells were the probability of species interacting based on their co-occurrence over small-scale distances and vegetation types, calculated as the number of individuals from a bat species i captured in sampling sites where the plant species j was registered in the transection, considering all capture months. Cell values were normalized to sum one.Because more than one ecological mechanism may simultaneously drive interactions3,9, we built an additional set of seven models resultant from the element-wise multiplication of individual probability matrices:

    SP: The spatial and temporal distribution of species work simultaneously in driving a resource turnover in the community, driving interactions.

    AS: Abundance drives interactions between bats and plants, but within spatially clustered resources in the landscape caused by a turnover in species distributions.

    AP: Abundance drives interactions between bats and plants, but within temporally clustered resources caused by a seasonal distribution of resources.

    APS: Abundance drives interactions between bats and plants, but within resource clusters that emerge by a simultaneous temporal and spatial aggregation.

    MS: Similar to AS, but morphology drives interactions within spatial clusters.

    MP: Similar to MP, but morphology drives interactions within temporal clusters.

    MPS: Similar to APS, but morphology drives interactions within spatiotemporal clusters.

    Finally, we created a benchmark null model in which all cells in the matrix had the same probability value. All the compound matrices and the null model were also normalized to sum one.To compare the fit of these probability models with the real data, we conducted a maximum likelihood analysis3,9. We calculated the likelihood of each of these models in predicting the observed interaction matrix, assuming a multinomial distribution for the probability of interaction between species12. To compare model fit, we calculated the Akaike Information Criterion (AIC) for each model and their variation in AIC (ΔAIC) in relation to the best-fitting model. The number of species used in the probability matrices was considered the number of model parameters to penalize model complexity. Intending to assess whether nectarivorous bats and non-nectarivorous bats assembly sub-networks with different assembly rules, we created two partial networks from the observed matrix. One contained nectarivores only (subfamilies Glossophaginae and Lonchophyllinae) and their interactions, and the other contained frugivore and insectivore bats and their interactions. We repeated the likelihood procedure for these two partial networks.To conduct the likelihood analysis, we excluded plant species from the network that could not have their interaction probabilities measured, such as species found in pollen samples but not registered in the park or pollen types that could not be identified to the species level. Therefore, the interaction network Y and probability matrices did not include these species (details in Supplementary Table S1).SoftwareAnalyses were performed in R 3.6.050. Network metrics and null models were generated with the bipartite package51, and the sampling completeness analysis was performed with the vegan package52. Gephi 0.9.253 was used to draw the graph. More

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    Genetic monitoring on the world’s first MSC eco-labeled common octopus (O. vulgaris) fishery in western Asturias, Spain

    FAO. El estado mundial de la pesca y la acuicultura 2020 (FAO, 2020).
    Google Scholar 
    Jackson, J. B. C. Historical overfishing and the recent collapse of coastal ecosystems. Science 293, 629–637 (2001).Article 
    CAS 
    PubMed 

    Google Scholar 
    Scheffer, M., Carpenter, S. & de Young, B. Cascading effects of overfishing marine systems. Trends Ecol. Evol. 20, 579–581 (2005).Article 
    PubMed 

    Google Scholar 
    Coll, M., Libralato, S., Tudela, S., Palomera, I. & Pranovi, F. Ecosystem overfishing in the ocean. PLoS ONE 3, e3881 (2008).Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Peterson, M. S. & Lowe, M. R. Implications of cumulative impacts to estuarine and marine habitat quality for fish and invertebrate resources. Rev. Fish. Sci. 17, 505–523 (2009).Article 

    Google Scholar 
    Claudet, J. & Fraschetti, S. Human-driven impacts on marine habitats: A regional meta-analysis in the Mediterranean Sea. Biol. Cons. 143, 2195–2206 (2010).Article 

    Google Scholar 
    Smith, V. H., Tilman, G. D. & Nekola, J. C. Eutrophication: Impacts of excess nutrient inputs on freshwater, marine, and terrestrial ecosystems. Environ. Pollut. 100, 179–196 (1999).Article 
    CAS 
    PubMed 

    Google Scholar 
    Derraik, J. G. B. The pollution of the marine environment by plastic debris: A review. Mar. Pollut. Bull. 44, 842–852 (2002).Article 
    CAS 
    PubMed 

    Google Scholar 
    Doney, S. C. et al. Climate change impacts on marine ecosystems. Ann. Rev. Mar. Sci. 4, 11–37 (2012).Article 
    PubMed 

    Google Scholar 
    Molnar, J. L., Gamboa, R. L., Revenga, C. & Spalding, M. D. Assessing the global threat of invasive species to marine biodiversity. Front. Ecol. Environ. 6, 485–492 (2008).Article 

    Google Scholar 
    Wojnarowska, M., Sołtysik, M. & Prusak, A. Impact of eco-labelling on the implementation of sustainable production and consumption. Environ. Impact Assess. Rev. 86, 106505 (2021).Article 

    Google Scholar 
    Yan, H. F. et al. Overfishing and habitat loss drive range contraction of iconic marine fishes to near extinction. Sci. Adv. 7, 6026 (2021).Article 
    ADS 

    Google Scholar 
    Bastardie, F. et al. Spatial planning for fisheries in the Northern Adriatic: Working toward viable and sustainable fishing. Ecosphere 8, e01696 (2017).Article 

    Google Scholar 
    Arkema, K. K. et al. Integrating fisheries management into sustainable development planning. Ecol. Soc. 24, 0201 (2019).Article 

    Google Scholar 
    Aguión, A. et al. Establishing a governance threshold in small-scale fisheries to achieve sustainability. Ambio. https://doi.org/10.1007/s13280-021-01606-x (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gudmundsson, E. & Wessells, C. R. Ecolabeling seafood for sustainable production: Implications for fisheries management. Mar. Resour. Econ. 15, 97–113 (2000).Article 

    Google Scholar 
    FAO. Guidelines for the Ecolabelling of Fish and Fishery Products from Marine Capture Fisheries. Revision 1 (FAO, 2009).
    Google Scholar 
    Hilborn, R. & Ovando, D. Reflections on the success of traditional fisheries management. ICES J. Mar. Sci. 71, 1040–1046 (2014).Article 

    Google Scholar 
    Casey, J., Jardim, E. & Martinsohn, J. T. H. The role of genetics in fisheries management under the E.U. common fisheries policy. J. Fish Biol. 89, 2755–2767 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    MSC. MSC Fisheries Standard v2.01. https://www.msc.org/docs/default-source/default-document-library/for-business/program-documents/fisheries-program-documents/msc-fisheries-standard-v2-01.pdf?sfvrsn=8ecb3272_9 (2018).Costello, C. et al. Status and solutions for the world’s unassessed fisheries. Science 338, 517–520 (2012).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Hilborn, R. et al. Effective fisheries management instrumental in improving fish stock status. PNAS 117, 2218–2224 (2020).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Worm, B. & Branch, T. A. The future of fish. Trends Ecol. Evol. 27, 594–599 (2012).Article 
    PubMed 

    Google Scholar 
    Palomares, M. L. D. et al. Fishery biomass trends of exploited fish populations in marine ecoregions, climatic zones and ocean basins. Estuar. Coast. Shelf Sci. 243, 106896 (2020).Article 

    Google Scholar 
    Ihssen, P. E. et al. Stock identification: Materials and methods. Can. J. Fish. Aquat. Sci. 38, 1838–1855 (1981).Article 

    Google Scholar 
    Carvalho, G. R. & Hauser, L. Molecular genetics and the stock concept in fisheries. In Molecular Genetics in Fisheries (eds Carvalho, G. R. & Pitcher, T. J.) 55–79 (Springer, 1995).Chapter 

    Google Scholar 
    Worm, B. et al. Rebuilding global fisheries. Science 325, 578–585 (2009).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Gough, C. L. A., Dewar, K. M., Godley, B. J., Zafindranosy, E. & Broderick, A. C. Evidence of overfishing in small-scale fisheries in Madagascar. Front. Mar. Sci. 7, 317 (2020).Article 

    Google Scholar 
    Widjaja, S. et al. Illegal, Unreported and Unregulated Fishing and Associated Drivers 60 (2020).Walters, C. & Martell, S. J. D. Stock assessment needs for sustainable fisheries management. Bull. Mar. Sci. 70, 629–638 (2002).
    Google Scholar 
    Moreira, A. A., Tomás, A. R. G. & Hilsdorf, A. W. S. Evidence for genetic differentiation of Octopus vulgaris (Mollusca, Cephalopoda) fishery populations from the southern coast of Brazil as revealed by microsatellites. J. Exp. Mar. Biol. Ecol. 407, 34–40 (2011).Article 

    Google Scholar 
    Allendorf, F. W., Ryman, N. & Utter, F. M. Genetics and fishery management. In Population Genetics and Fishery Management 1–19 (1987).Oosthuizen, A., Jiwaji, M. & Shaw, P. Genetic analysis of the Octopus vulgaris population on the coast of South Africa. S. Afr. J. Sci. 100, 603–607 (2004).CAS 

    Google Scholar 
    Botsford, L. W., Castilla, J. C. & Peterson, C. H. The management of fisheries and marine ecosystems. Science 277, 509–515 (1997).Article 
    CAS 

    Google Scholar 
    Hilborn, R., Orensanz, J. M. & Parma, A. M. Institutions, incentives and the future of fisheries. Philos. Trans. R. Soc. B Biol. Sci. 360, 47. https://doi.org/10.1098/rstb.2004.1569 (2005).Article 

    Google Scholar 
    Ovenden, J. R., Berry, O., Welch, D. J., Buckworth, R. C. & Dichmont, C. M. Ocean’s eleven: A critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries. Fish Fish. 16, 125–159 (2015).Article 

    Google Scholar 
    Aguirre-Sarabia, I. et al. Evidence of stock connectivity, hybridization, and misidentification in white anglerfish supports the need of a genetics-informed fisheries management framework. Evol. Appl. 14, 2221 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Grover, A. & Sharma, P. C. Development and use of molecular markers: Past and present. Crit. Rev. Biotechnol. 36, 290 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Valenzuela-Quiñonez, F. How fisheries management can benefit from genomics? Brief. Funct. Genom. 15, 352–357 (2016).Article 

    Google Scholar 
    Khoufi, W., Jabeur, C. & Bakhrouf, A. Stock assessment of the common octopus (Octopus vulgaris) in Monastir; the Mid-eastern Coast of Tunisia. Int. J. Mar. Sci. 2, 1 (2012).
    Google Scholar 
    Pita, C. et al. Fisheries for common octopus in Europe: Socioeconomic importance and management. Fish. Res. 235, 105820 (2021).Article 

    Google Scholar 
    Melis, R. et al. Genetic population structure and phylogeny of the common octopus Octopus vulgaris Cuvier, 1797 in the western Mediterranean Sea through nuclear and mitochondrial markers. Hydrobiologia 807, 277–296 (2018).Article 
    CAS 

    Google Scholar 
    De Luca, D., Catanese, G., Procaccini, G. & Fiorito, G. Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic diversity and population structure. PLoS ONE 11, e0149496 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fernández-Rueda, P. & García-Flórez, L. Octopus vulgaris (Mollusca: Cephalopoda) fishery management assessment in Asturias (north-west Spain). Fish. Res. 83, 351–354 (2007).Article 

    Google Scholar 
    Gobierno del Principado de Asturias. BOPA núm. 233 de 03-XII-2021, Vol. 233 (2021).Roa-Ureta, R. H. et al. Estimation of the spawning stock and recruitment relationship of Octopus vulgaris in Asturias (Bay of Biscay) with generalized depletion models: Implications for the applicability of MSY. ICES J. Mar. Sci. https://doi.org/10.1093/icesjms/fsab113 (2021).Article 

    Google Scholar 
    González, A. F., Macho, G., de Novoa, J. & García, M. Western Asturias Octopus Traps Fishery of Artisanal Cofradías 181 (2015).Sánchez, J. L. F., Fernández Polanco, J. M. & Llorente García, I. Evidence of price premium for MSC-certified products at fishers’ level: The case of the artisanal fleet of common octopus from Asturias (Spain). Mar. Policy 119, 104098 (2020).Article 

    Google Scholar 
    Murphy, J. M., Balguerías, E., Key, L. N. & Boyle, P. R. Microsatellite DNA markers discriminate between two Octopus vulgaris (Cephalopoda: Octopoda) fisheries along the northwest African coast. Bull. Mar. Sci. 71, 545–553 (2002).
    Google Scholar 
    Cabranes, C., Fernandez-Rueda, P. & Martínez, J. L. Genetic structure of Octopus vulgaris around the Iberian Peninsula and Canary Islands as indicated by microsatellite DNA variation. ICES J. Mar. Sci. 65, 12–16 (2008).Article 

    Google Scholar 
    Quinteiro, J., Rodríguez-Castro, J., Rey-Méndez, M. & González-Henríquez, N. Phylogeography of the insular populations of common octopus, Octopus vulgaris Cuvier, 1797, in the Atlantic Macaronesia. PLoS ONE 15, e0230294 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Greatorex, E. C. et al. Microsatellite markers for investigating population structure in Octopus vulgaris (Mollusca: Cephalopoda). Mol. Ecol. 9, 641–642 (2000).Article 
    CAS 
    PubMed 

    Google Scholar 
    De Luca, D., Catanese, G., Fiorito, G. & Procaccini, G. A new set of pure microsatellite loci in the common octopus Octopus vulgaris Cuvier, 1797 for multiplex PCR assay and their cross-amplification in O. maya Voss & Solís Ramírez, 1966. Conserv. Genet. Resour. 7, 299–301 (2015).Article 

    Google Scholar 
    Zuo, Z., Zheng, X., Liu, C. & Li, Q. Development and characterization of 17 polymorphic microsatellite loci in Octopus vulgaris Cuvier, 1797. Conserv. Genet. Resour. 4, 367–369 (2012).Article 

    Google Scholar 
    Weir, B. S. & Cockerham, C. C. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358 (1984).CAS 
    PubMed 

    Google Scholar 
    Chapuis, M. P. & Estoup, A. Microsatellite null alleles and estimation of population differentiation. Mol. Biol. Evol. 24, 621–631 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Nei, M. & Takezaki, N. Estimation of Genetic Distances and Phylogenetic Trees from DNA Analysis 8 (1983).Do, C. et al. NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol. Ecol. Resour. 14, 209–214 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    Waples, R. S. Separating the wheat from the chaff: Patterns of genetic differentiation in high gene flow species. J. Hered. 89, 438–450 (1998).Article 

    Google Scholar 
    Taboada, F. G. & Anadón, R. Patterns of change in sea surface temperature in the North Atlantic during the last three decades: Beyond mean trends. Clim. Change 115, 419–431 (2012).Article 
    ADS 

    Google Scholar 
    Ellegren, H. & Galtier, N. Determinants of genetic diversity. Nat. Rev. Genet. 17, 422–433 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Sinclair, M. & Valdimarsson, G. Responsible Fisheries in the Marine Ecosystem (CABI, 2003).Book 

    Google Scholar 
    Pinsky, M. L. & Palumbi, S. R. Meta-analysis reveals lower genetic diversity in overfished populations. Mol. Ecol. 23, 29–39 (2014).Article 
    PubMed 

    Google Scholar 
    Bradbury, I. R., Laurel, B., Snelgrove, P. V. R., Bentzen, P. & Campana, S. E. Global patterns in marine dispersal estimates: The influence of geography, taxonomic category and life history. Proc. R. Soc. B Biol. Sci. 275, 1803–1809 (2008).Article 

    Google Scholar 
    Waples, R. S. Testing for Hardy-Weinberg proportions: Have we lost the plot? J. Hered. 106, 1–19 (2015).Article 
    PubMed 

    Google Scholar 
    Casu, M. et al. Genetic structure of Octopus vulgaris (Mollusca, Cephalopoda) from the Mediterranean Sea as revealed by a microsatellite locus. Ital. J. Zool. 69, 295–300 (2002).Article 

    Google Scholar 
    Fadhlaoui-Zid, K. et al. Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene. C.R. Biol. 335, 625–636 (2012).Article 
    PubMed 

    Google Scholar 
    Queiroga, H. et al. Oceanographic and behavioural processes affecting invertebrate larval dispersal and supply in the western Iberia upwelling ecosystem. Prog. Oceanogr. 74, 174–191 (2007).Article 
    ADS 

    Google Scholar 
    Mereu, M. et al. Mark–recapture investigation on Octopus vulgaris specimens in an area of the central western Mediterranean Sea. J. Mar. Biol. Assoc. U.K. 95, 131–138 (2015).Article 
    ADS 

    Google Scholar 
    Mereu, M. et al. Movement estimation of Octopus vulgaris Cuvier, 1797 from mark recapture experiment. J. Exp. Mar. Biol. Ecol. 470, 64–69 (2015).Article 

    Google Scholar 
    Roura, Á. et al. Life strategies of cephalopod paralarvae in a coastal upwelling system (NW Iberian Peninsula): Insights from zooplankton community and spatio-temporal analyses. Fish. Oceanogr. 25, 241–258 (2016).Article 

    Google Scholar 
    Moreno, A. et al. Essential habitats for pre-recruit Octopus vulgaris along the Portuguese coast. Fish. Res. 152, 74–85 (2014).Article 
    ADS 

    Google Scholar 
    Chédia, J., Widien, K. & Amina, B. Role of sea surface temperature and rainfall in determining the stock and fishery of the common octopus (Octopus vulgaris, Mollusca, Cephalopoda) in Tunisia. Mar. Ecol. 31, 431–438 (2010).Article 
    ADS 

    Google Scholar 
    Otero, J. et al. Bottom-up control of common octopus Octopus vulgaris in the Galician upwelling system, northeast Atlantic Ocean. Mar. Ecol. Prog. Ser. 362, 181–192 (2008).Article 
    ADS 

    Google Scholar 
    Hedgecock, D. & Pudovkin, A. I. A. I. Sweepstakes reproductive success in highly fecund marine fish and shellfish: A review and commentary. Bull. Mar. Sci. 87, 971–1002 (2011).Article 

    Google Scholar 
    Kalinowski, S. T. & Waples, R. S. Relationship of effective to census size in fluctuating populations. Conserv. Biol. 16, 129–136 (2002).Article 
    PubMed 

    Google Scholar 
    Sonderblohm, C. P., Pereira, J. & Erzini, K. Environmental and fishery-driven dynamics of the common octopus (Octopus vulgaris) based on time-series analyses from leeward Algarve, southern Portugal. ICES J. Mar. Sci. 71, 2231–2241 (2014).Article 

    Google Scholar 
    Sonderblohm, C. P. et al. Participatory assessment of management measures for Octopus vulgaris pot and trap fishery from southern Portugal. Mar. Policy 75, 133–142 (2017).Article 

    Google Scholar 
    Arkhipkin, A. I. et al. Stock assessment and management of cephalopods: Advances and challenges for short-lived fishery resources. ICES J. Mar. Sci. 78, 714–730 (2021).Article 

    Google Scholar 
    Franklin, I. R. Evolutionary change in small populations. In Conservation Biology: An Evolutionary-Ecological Perspective (eds Soulé, M. E. & Wilcox, B. A.) 395 (Sinauer Associates, 1980).
    Google Scholar 
    Slatkin, M. Rare alleles as indicators of gene flow. Evolution 39, 53–65 (1985).Article 
    PubMed 

    Google Scholar 
    Holleley, C. E. & Geerts, P. G. Multiplex manager 1.0: A cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46, 511–517 (2009).Article 
    CAS 
    PubMed 

    Google Scholar 
    Van Oosterhout, C., Hutchinson, W. F., Wills, D. P. M. & Shipley, P. MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4, 535–538 (2004).Article 

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

    Google Scholar 
    Paradis, E. Pegas: An R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419–420 (2010).Article 
    CAS 
    PubMed 

    Google Scholar 
    Goudet, J. HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184–186 (2005).Article 

    Google Scholar 
    Adamack, A. T. & Gruber, B. PopGenReport: Simplifying basic population genetic analyses in R. Methods Ecol. Evol. 5, 384–387 (2014).Article 

    Google Scholar 
    Goudet, J. FSTAT (Version 1.2): A computer program to calculate F-STATISTICS. J. Hered. 86, 485–486 (1995).Article 

    Google Scholar 
    Rice, W. R. Analyzing tables of statistical tests. Evolution 43, 223 (1989).Article 
    PubMed 

    Google Scholar 
    Piry, S., Luikart, G. & Cornuet, J. M. M. Bottleneck: A computer program for detecting recent reductions in the effective population size using allele frequency data. J. Hered. 90, 502–503 (1999).Article 

    Google Scholar 
    Luikart, G., Allendorf, F. W., Cornuet, J.-M.M. & Sherwin, W. B. Distortion of allele frequency distributions provides a test for recent population bottlenecks. J. Hered. https://doi.org/10.1093/jhered/89.3.238 (1998).Article 
    PubMed 

    Google Scholar 
    Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Besnier, F. & Glover, K. A. ParallelStructure: A R package to distribute parallel runs of the population genetics program STRUCTURE on multi-core computers. PLoS ONE 8, e70651 (2013).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14, 2611–2620 (2005).Article 
    CAS 
    PubMed 

    Google Scholar 
    Gilbert, K. J. et al. Recommendations for utilizing and reporting population genetic analyses: The reproducibility of genetic clustering using the program structure. Mol. Ecol. https://doi.org/10.1111/j.1365-294X.2012.05754.x (2012).Article 
    PubMed 

    Google Scholar 
    Earl, D. A. & VonHoldt, B. M. Structure harvester: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).Article 

    Google Scholar 
    Takezaki, N., Nei, M. & Tamura, K. POPTREEW: Web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities. Mol. Biol. Evol. 31, 1622–1624 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    Letunic, I. & Bork, P. Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Dray, S. & Dufour, A.-B. The ade4 package: Implementing the duality diagram for ecologists. J. Stat. Softw. 22, 1–20 (2007).Article 

    Google Scholar 
    Slatkin, M. Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47, 264–279 (1993).Article 
    PubMed 

    Google Scholar 
    Cavalli-Sforza, L. L. & Edwards, A. W. F. Phylogenetic analysis. Models and estimation procedures. Am. J. Hum. Genet. 19, 233–257 (1967).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Foll, M. & Gaggiotti, O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics 180, 977–993 (2008).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Waples, R. S. A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121, 379–391 (1989).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Katsanevakis, S. & Verriopoulos, G. Seasonal population dynamics of Octopus vulgaris in the eastern Mediterranean. ICES J. Mar. Sci. 63, 151–160 (2006).Article 

    Google Scholar 
    Jereb, P. et al. Cephalopod Biology and Fisheries in Europe: II Species Accounts 360 (ICES, 2015).
    Google Scholar  More

  • in

    Effects of moisture and density-dependent interactions on tropical tree diversity

    Gentry, A. H. Changes in plant community diversity and floristic composition on environmental and geographical gradients. Ann. Missouri Bot. Gard. 75, 1–34 (1988).Article 

    Google Scholar 
    Givnish, T. J. On the causes of gradients in tropical tree diversity. J. Ecol. 87, 193–210 (1999).Article 

    Google Scholar 
    Janzen, D. H. Herbivores and the number of tree species in tropical forests. Am. Nat. 104, 501–528 (1970).Article 

    Google Scholar 
    Connell, J. H. in Dynamics of Populations (eds Den Boer, P. J. & Gradwell, G. R.) 298–312 (PUDOC, 1971).Esquivel-Muelbert, A. et al. Seasonal drought limits tree species across the Neotropics. Ecography 40, 618–629 (2017).Article 

    Google Scholar 
    Gillett, J. B. Pest pressure, an underestimated factor in evolution. Syst. Assoc. Publ. 4, 37–46 (1962).
    Google Scholar 
    Engelbrecht, B. M. J. et al. Drought sensitivity shapes species distribution patterns in tropical forests. Nature 447, 80–82 (2007).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Condit, R., Engelbrecht, B. M. J., Pino, D., Pérez, R. & Turner, B. L. Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees. Proc. Natl Acad. Sci. USA 110, 5064–5068 (2013).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Allen, C. D. et al. A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. For. Ecol. Manage. 259, 660–684 (2010).Article 

    Google Scholar 
    Harrison, S., Spasojevic, M. J. & Li, D. Climate and plant community diversity in space and time. Proc. Natl Acad. Sci. USA 117, 4464–4470 (2020).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Milici, V. R., Dalui, D., Mickley, J. G. & Bagchi, R. Responses of plant–pathogen interactions to precipitation: Implications for tropical tree richness in a changing world. J. Ecol. 108, 1800–1809 (2020).Article 

    Google Scholar 
    Mangan, S. A. et al. Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466, 752–755 (2010).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Gripenberg, S. et al. Testing for enemy-mediated density-dependence in the mortality of seedlings: field experiments with five Neotropical tree species. Oikos 123, 185–193 (2014).Article 

    Google Scholar 
    Bagchi, R. et al. Pathogens and insect herbivores drive rainforest plant diversity and composition. Nature 506, 85–88 (2014).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Fricke, E. C., Tewksbury, J. J. & Rogers, H. S. Multiple natural enemies cause distance-dependent mortality at the seed-to-seedling transition. Ecol. Lett. 17, 593–598 (2014).Article 
    PubMed 

    Google Scholar 
    Augspurger, C. K. & Kelly, C. K. Pathogen mortality of tropical tree seedlings: experimental studies of the effects of dispersal distance, seedling density, and light conditions. Oecologia 61, 211–217 (1984).Article 
    ADS 
    PubMed 

    Google Scholar 
    Chen, L. et al. Differential soil fungus accumulation and density dependence of trees in a subtropical forest. Science 366, 124–128 (2019).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Eck, J. L., Stump, S. M., Delavaux, C. S., Mangan, S. A. & Comita, L. S. Evidence of within-species specialization by soil microbes and the implications for plant community diversity. Proc. Natl Acad. Sci. USA 116, 7371–7376 (2019).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kishimoto-Yamada, K. & Itioka, T. How much have we learned about seasonality in tropical insect abundance since Wolda (1988)? Entomol. Sci. 18, 407–419 (2015).Article 

    Google Scholar 
    Huberty, A. F. & Denno, R. F. Plant water stress and its consequences for herbivorous insects: a new synthesis. Ecology 85, 1383–1398 (2004).Article 

    Google Scholar 
    Janzen, D. H. & Hallwachs, W. To us insectometers, it is clear that insect decline in our Costa Rican tropics is real, so let’s be kind to the survivors. Proc. Natl Acad. Sci. USA 118, e2002546117 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rodríguez-Castañeda, G. The world and its shades of green: a meta-analysis on trophic cascades across temperature and precipitation gradients. Glob. Ecol. Biogeogr. 22, 118–130 (2013).Article 

    Google Scholar 
    Janzen, D. H. & Schoener, T. W. Differences in insect abundance and diversity between wetter and drier sites during a tropical dry season. Ecology 49, 96–110 (1968).Article 

    Google Scholar 
    Sturrock, R. N. et al. Climate change and forest diseases. Plant Pathol 60, 133–149 (2011).Article 

    Google Scholar 
    Desprez-Loustau, M.-L., Marçais, B., Nageleisen, L.-M., Piou, D. & Vannini, A. Interactive effects of drought and pathogens in forest trees. Ann. For. Sci. 63, 597–612 (2006).Article 

    Google Scholar 
    Swinfield, T., Lewis, O. T., Bagchi, R. & Freckleton, R. P. Consequences of changing rainfall for fungal pathogen-induced mortality in tropical tree seedlings. Ecol. Evol. 2, 1408–1413 (2012).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jactel, H. et al. Drought effects on damage by forest insects and pathogens: a meta-analysis. Glob. Chang. Biol. 18, 267–276 (2012).Article 
    ADS 

    Google Scholar 
    Maharjan, S. K. et al. Plant functional traits and the distribution of West African rain forest trees along the rainfall gradient. Biotropica 43, 552–561 (2011).Article 

    Google Scholar 
    Klironomos, J. N. Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417, 67–70 (2002).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Petermann, J. S., Fergus, A. J. F., Turnbull, L. A. & Schmid, B. Janzen–Connell effects are widespread and strong enough to maintain diversity in grasslands. Ecology 89, 2399–2406 (2008).Article 
    PubMed 

    Google Scholar 
    Chesson, P. Updates on mechanisms of maintenance of species diversity. J. Ecol. 106, 1773–1794 (2018).Article 

    Google Scholar 
    Barabás, G., Michalska-Smith, M. J. & Allesina, S. The effect of intra- and interspecific competition on coexistence in multispecies communities. Am. Nat. 188, E1–E12 (2016).Article 
    PubMed 

    Google Scholar 
    Lebrija-Trejos, E., Wright, S. J., Hernández, A. & Reich, P. B. Does relatedness matter? Phylogenetic density-dependent survival of seedlings in a tropical forest. Ecology 95, 940–951 (2014).Article 
    PubMed 

    Google Scholar 
    Lebrija-Trejos, E., Reich, P. B., Hernández, A. & Wright, S. J. Species with greater seed mass are more tolerant of conspecific neighbours: a key driver of early survival and future abundances in a tropical forest. Ecol. Lett. 19, 1071–1080 (2016).Article 
    PubMed 

    Google Scholar 
    Green, P. T., Harms, K. E. & Connell, J. H. Nonrandom, diversifying processes are disproportionately strong in the smallest size classes of a tropical forest. Proc. Natl Acad. Sci. USA 111, 18649–18654 (2014).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Comita, L. S. et al. Testing predictions of the Janzen–Connell hypothesis: a meta-analysis of experimental evidence for distance- and density-dependent seed and seedling survival. J. Ecol. 102, 845–856 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Moles, A. T. & Westoby, M. What do seedlings die from and what are the implications for evolution of seed size? Oikos 106, 193–199 (2004).Article 

    Google Scholar 
    Paine, C. E. T., Harms, K. E., Schnitzer, S. A. & Carson, W. P. Weak competition among tropical tree seedlings: implications for species coexistence. Biotropica 40, 432–440 (2008).Article 

    Google Scholar 
    Weissflog, A., Markesteijn, L., Lewis, O. T., Comita, L. S. & Engelbrecht, B. M. J. Contrasting patterns of insect herbivory and predation pressure across a tropical rainfall gradient. Biotropica 50, 302–311 (2018).Article 

    Google Scholar 
    Brenes-Arguedas, T., Coley, P. D. & Kursar, T. A. Pests vs. drought as determinants of plant distribution along a tropical rainfall gradient. Ecology 90, 1751–1761 (2009).Article 
    PubMed 

    Google Scholar 
    Gaviria, J. & Engelbrecht, B. M. J. Effects of drought, pest pressure and light availability on seedling establishment and growth: their role for distribution of tree species across a tropical rainfall gradient. PLoS ONE 10, e0143955 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Spear, E. R., Coley, P. D. & Kursar, T. A. Do pathogens limit the distributions of tropical trees across a rainfall gradient? J. Ecol. 103, 165–174 (2015).Article 

    Google Scholar 
    Clark, J. S. et al. The impacts of increasing drought on forest dynamics, structure, and biodiversity in the United States. Glob. Chang. Biol. 22, 2329–2352 (2016).Article 
    ADS 
    PubMed 

    Google Scholar 
    Riutta, T. et al. Experimental evidence for the interacting effects of forest edge, moisture and soil macrofauna on leaf litter decomposition. Soil Biol. Biochem. 49, 124–131 (2012).Article 
    CAS 

    Google Scholar 
    Lebrija-Trejos, E., Pérez-García, E. A., Meave, J. A., Poorter, L. & Bongers, F. Environmental changes during secondary succession in a tropical dry forest in Mexico. J. Trop. Ecol. 27, 477–489 (2011).Article 

    Google Scholar 
    Krishnadas, M. & Comita, L. S. Edge effects on seedling diversity are mediated by impacts of fungi and insects on seedling recruitment but not survival. Front. Glob. Chang. 2, 76 (2019).Article 

    Google Scholar 
    Garcia, R. A., Cabeza, M., Rahbek, C. & Araujo, M. B. Multiple dimensions of climate change and their implications for biodiversity. Science 344, 1247579 (2014).Article 
    PubMed 

    Google Scholar 
    Uriarte, M., Muscarella, R. & Zimmerman, J. K. Environmental heterogeneity and biotic interactions mediate climate impacts on tropical forest regeneration. Glob. Chang. Biol. 24, e692–e704 (2018).Article 
    ADS 
    PubMed 

    Google Scholar 
    Bachelot, B., Kobe, R. K. & Vriesendorp, C. Negative density-dependent mortality varies over time in a wet tropical forest, advantaging rare species, common species, or no species. Oecologia 179, 853–861 (2015).Article 
    ADS 
    PubMed 

    Google Scholar 
    Zhu, Y. et al. Density‐dependent survival varies with species life‐history strategy in a tropical forest. Ecol. Lett. 21, 506–515 (2018).Article 
    CAS 
    PubMed 

    Google Scholar 
    Wright, S. J., Calderón, O., Hernandéz, A. & Muller-Landau, H. C. Annual and spatial variation in seedfall and seedling recruitment in a neotropical forest. Ecology 86, 848–860 (2005).Article 

    Google Scholar 
    Condit, R. Tropical Forest Census Plots https://doi.org/10.1007/978-3-662-03664-8 (Springer, 1998).Kupers, S. J., Wirth, C., Engelbrecht, B. M. J. & Rüger, N. Dry season soil water potential maps of a 50 hectare tropical forest plot on Barro Colorado Island, Panama. Sci. Data 6, 63 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Garwood, N. C. in The Ecology of a Tropical Forest: Seasonal Rhythms and Long-term Changes (eds Leigh, E. G., Rand, A. S. & Windsor, D. M.) 173–185 (Smithsonian Institution Press, 1982).Jost, L. Entropy and diversity. Oikos 113, 363–375 (2006).Article 

    Google Scholar 
    Burnham, K. P. & Anderson, D. R. Model Selection and Multimodel Inference https://doi.org/10.1007/b97636 (Springer, 2004).Muller-Landau, H. C. et al. Testing metabolic ecology theory for allometric scaling of tree size, growth and mortality in tropical forests. Ecol. Lett. 9, 575–588 (2006).Article 
    PubMed 

    Google Scholar 
    Detto, M., Visser, M. D., Wright, S. J. & Pacala, S. W. Bias in the detection of negative density dependence in plant communities. Ecol. Lett. 22, 1923–1939 (2019).Article 
    PubMed 

    Google Scholar 
    Bolker, B. M. et al. Generalized linear mixed models: a practical guide for ecology and evolution. Trends Ecol. Evol. 24, 127–135 (2009).Article 
    PubMed 

    Google Scholar 
    Barr, D. J., Levy, R., Scheepers, C. & Tily, H. J. Random effects structure for confirmatory hypothesis testing: keep it maximal. J. Mem. Lang. 68, 255–278 (2013).Article 

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

    Google Scholar 
    Bates, D. et al. Package ‘lme4’ Reference Manual https://cran.r-project.org/web/packages/lme4/lme4.pdf (2021).Wilkinson, G. N. & Rogers, C. E. Symbolic description of factorial models for analysis of variance. Appl. Stat. 22, 392 (1973).Article 

    Google Scholar 
    Afshartous, D. & Preston, R. A. Key results of interaction models with centering. J. Stat. Educ. https://doi.org/10.1080/10691898.2011.11889620 (2011).Cohen, J. Statistical Power Analysis for the Behavioral Sciences https://doi.org/10.1016/C2013-0-10517-X (Elsevier, 1977).Steiger, J. H. Tests for comparing elements of a correlation matrix. Psychol. Bull. 87, 245–251 (1980).Article 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing https://www.R-project.org/ (2016).Pinheiro, J. et al. nlme: Linear and Nonlinear Mixed Effects Models https://CRAN.R-project.org/package=nlme (2020).Gelman, A. & Hill, J. Data Analysis Using Regression and Multilevel/Hierarchical Models (Cambridge Univ. Press, 2007).Hartig, F. DHARMa: Residual Diagnostics for Hierarchical (Multi-level/Mixed) Regression Models https://CRAN.R-project.org/package=DHARMa (2021).Lebrija-Trejos, E., Wright, S. J. & Hernández, A. Moisture, Density-dependent Interactions, and Tropical Tree Diversity https://figshare.com/s/a4d2dbb2a73b3eb09f9f (2022).Kupers, S. J., Wirth, C., Engelbrecht, B. M. J. & Rüger, N. Dry Season Soil Water Potential Maps of a 50 Hectare Tropical Forest Plot on Barro Colorado Island, Panama https://doi.org/10.6084/m9.figshare.7611005.v1 (2019).Paton, S. Barro Colorado Island, Lutz Catchment, Soil Moisture, Manual https://doi.org/10.25573/data.10042517.v1 (2019). More

  • in

    Late Cenozoic cooling restructured global marine plankton communities

    Jonkers, L., Hillebrand, H. & Kucera, M. Global change drives modern plankton communities away from the pre-industrial state. Nature 570, 372–375 (2019).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Barton, A. D., Irwin, A. J., Finkel, Z. V. & Stock, C. A. Anthropogenic climate change drives shift and shuffle in North Atlantic phytoplankton communities. Proc. Natl Acad. Sci. USA 113, 2964–2969 (2016).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Beaugrand, G., Reid, P. C., Ibanez, F., Lindley, J. A. & Edwards, M. Reorganization of North Atlantic marine copepod biodiversity and climate. Science 296, 1692–1694 (2002).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Cheung, W. W., Watson, R. & Pauly, D. Signature of ocean warming in global fisheries catch. Nature 497, 365–368 (2013).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Herbert-Read, J. E. et al. A global horizon scan of issues impacting marine and coastal biodiversity conservation. Nat. Ecol. Evol. 6, 1262–1270 (2022).Article 
    PubMed 

    Google Scholar 
    Yasuhara, M. & Deutsch, C. A. Paleobiology provides glimpses of future ocean. Science 375, 25–26 (2022).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Fenton, I. S. et al. Triton, a new species-level database of Cenozoic planktonic foraminiferal occurrences. Sci. Data 8, 160 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Strack, A., Jonkers, L., Rillo, M. C., Hillebrand, H. & Kucera, M. Plankton response to global warming is characterized by non-uniform shifts in assemblage composition since the last ice age. Nat. Ecol. Evol. 6, 1871–1880 (2022).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Barnosky, A. D. et al. Has the Earth’s sixth mass extinction already arrived? Nature 471, 51–57 (2011).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Mokany, K. & Ferrier, S. Predicting impacts of climate change on biodiversity: a role for semi‐mechanistic community‐level modelling. Divers. Distrib. 17, 374–380 (2011).Article 

    Google Scholar 
    Pörtner, H.-O. et al. eds IPCC: Climate Change 2022: Impacts, Adaptation, and Vulnerability. Contribution of Working Group II to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (Cambridge Univ. Press, 2022).Pontarp, M. et al. The latitudinal diversity gradient: novel understanding through mechanistic eco-evolutionary models. Trends Ecol. Evol. 34, 211–223 (2019).Article 
    PubMed 

    Google Scholar 
    Schumm, M. et al. Common latitudinal gradients in functional richness and functional evenness across marine and terrestrial systems. Proc. R. Soc. B 286, 20190745 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rutherford, S., D’Hondt, S. & Prell, W. Environmental controls on the geographic distribution of zooplankton diversity. Nature 400, 749–753 (1999).Article 
    ADS 
    CAS 

    Google Scholar 
    Worm, B., Lotze, H. K. & Myers, R. A. Predator diversity hotspots in the blue ocean. Proc. Natl Acad. Sci. USA 100, 9884–9888 (2003).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tittensor, D. P. et al. Global patterns and predictors of marine biodiversity across taxa. Nature 466, 1098–1101 (2010).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Fenton, I. S., Pearson, P. N., Dunkley Jones, T. & Purvis, A. Environmental predictors of diversity in recent planktonic foraminifera as recorded in marine sediments. PLoS ONE 11, e0165522 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chaudhary, C., Saeedi, H. & Costello, M. J. Bimodality of latitudinal gradients in marine species richness. Trends Ecol. Evol. 31, 670–676 (2016).Article 
    PubMed 

    Google Scholar 
    Chaudhary, C., Richardson, A. J., Schoeman, D. S. & Costello, M. J. Global warming is causing a more pronounced dip in marine species richness around the equator. Proc. Natl Acad. Sci. USA 118, e2015094118 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rillo, M. C., Miller, C. G., Kučera, M. & Ezard, T. H. G. Intraspecific size variation in planktonic foraminifera cannot be consistently predicted by the environment. Ecol. Evol. 10, 11579–11590 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Yasuhara, M. et al. Past and future decline of tropical pelagic biodiversity. Proc. Natl Acad. Sci. USA 117, 12891–12896 (2020).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Thomas, E. Descent into the icehouse. Geology 36, 191–192 (2008).Article 
    ADS 

    Google Scholar 
    Fenton, I. S. et al. The impact of Cenozoic cooling on assemblage diversity in planktonic foraminifera. Phil. Trans. R. Soc. B 371, 20150224 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Crame, J. A. Early Cenozoic evolution of the latitudinal diversity gradient. Earth Sci. Rev. 202, 103090 (2020).Article 

    Google Scholar 
    Yasuhara, M. et al. Time machine biology. Oceanography 33, 16–28 (2020).Article 

    Google Scholar 
    Alegret, L., Arreguín-Rodríguez, G. J., Trasviña-Moreno, C. A. & Thomas, E. Turnover and stability in the deep sea: benthic foraminifera as tracers of Paleogene global change. Global Planet. Change 196, 103372 (2021).Article 

    Google Scholar 
    Gaskell, D. E. et al. The latitudinal temperature gradient and its climate dependence as inferred from foraminiferal δ18O over the past 95 million years. Proc. Natl Acad. Sci. USA 119, e2111332119 (2022).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mannion, P. D., Upchurch, P., Benson, R. B. & Goswami, A. The latitudinal biodiversity gradient through deep time. Trends Ecol. Evol. 29, 42–50 (2014).Article 
    PubMed 

    Google Scholar 
    Raja, N. B. & Kiessling, W. Out of the extratropics: the evolution of the latitudinal diversity gradient of Cenozoic marine plankton. Proc. R. Soc. B 288, 20210545 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Herbert, T. D. et al. Late Miocene global cooling and the rise of modern ecosystems. Nat. Geosci. 9, 843–847 (2016).Article 
    ADS 
    CAS 

    Google Scholar 
    Steinthorsdottir, M. et al. The Miocene: the future of the past. Paleoceanogr. Paleoclimatology 36, e2020PA004037 (2021).Article 

    Google Scholar 
    Brown, R. M., Chalk, T. B., Crocker, A. J., Wilson, P. A. & Foster, G. L. Late Miocene cooling coupled to carbon dioxide with Pleistocene-like climate sensitivity. Nat. Geosci. 15, 664–670 (2022).Article 
    ADS 
    CAS 

    Google Scholar 
    Guillermic, M., Misra, S., Eagle, R. & Tripati, A. Atmospheric CO2 estimates for the Miocene to Pleistocene based on foraminiferal δ11B at Ocean Drilling Program Sites 806 and 807 in the Western Equatorial Pacific. Clim. Past 18, 183–207 (2022).Article 

    Google Scholar 
    Jablonski, D., Roy, K. & Valentine, J. W. Out of the tropics: evolutionary dynamics of the latitudinal diversity gradient. Science 314, 102–106 (2006).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Yasuhara, M., Hunt, G., Dowsett, H. J., Robinson, M. M. & Stoll, D. K. Latitudinal species diversity gradient of marine zooplankton for the last three million years. Ecol. Lett. 15, 1174–1179 (2012).Article 
    PubMed 

    Google Scholar 
    Ezard, T. H. G., Aze, T., Pearson, P. N. & Purvis, A. Interplay between changing climate and species’ ecology drives macroevolutionary dynamics. Science 332, 349–351 (2011).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Peters, S. E., Kelly, D. C. & Fraass, A. J. Oceanographic controls on the diversity and extinction of planktonic foraminifera. Nature 493, 398–401 (2013).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Woodhouse, A. et al. Adaptive ecological niche migration does not negate extinction susceptibility. Sci. Rep. 11, 15411 (2021).Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Yasuhara, M., Tittensor, D. P., Hillebrand, H. & Worm, B. Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model. Biol. Rev. 92, 199–215 (2017).Article 
    PubMed 

    Google Scholar 
    Bindoff, N. L. in IPCC Special Report on the Ocean and Cryosphere in a Changing Climate (eds Pörtner, H.-O. et al.) (IPCC, Cambridge Univ. Press, 2019).Aze, T. et al. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biol. Rev. 86, 900–927 (2011).Article 
    PubMed 

    Google Scholar 
    Delmas, E. et al. Analysing ecological networks of species interactions. Biol. Rev. 94, 16–36 (2019).Article 
    PubMed 

    Google Scholar 
    Rojas, A., Calatayud, J., Kowalewski, M., Neuman, M. & Rosvall, M. A multiscale view of the Phanerozoic fossil record reveals the three major biotic transitions. Commun. Biol. 4, 309 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Swain, A., Devereux, M. & Fagan, W. F. Deciphering trophic interactions in a mid-Cambrian assemblage. iScience 24, 102271 (2021).Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Shaw, J. O. et al. Disentangling ecological and taphonomic signals in ancient food webs. Paleobiology 47, 385–401 (2021).Article 

    Google Scholar 
    Swain, A., Maccracken, S., Fagan, W. & Labandeira, C. Understanding the ecology of host plant–insect herbivore interactions in the fossil record through bipartite networks. Paleobiology 48, 239–260 (2022).Article 

    Google Scholar 
    Poisot, T., Canard, E., Mouquet, N. & Hochberg, M. E. A comparative study of ecological specialization estimators. Methods Ecol. Evol. 3, 537–544 (2012).Article 

    Google Scholar 
    Westerhold, T. et al. An astronomically dated record of Earth’s climate and its predictability over the last 66 million years. Science 369, 1383–1387 (2020).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Boscolo-Galazzo, F. and Crichton, K.A. et al. Temperature controls carbon cycling and biological evolution in the ocean twilight zone. Science 371, 1148–1152 (2021).Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 
    Boscolo-Galazzo, F. et al. Late Neogene evolution of modern deep-dwelling plankton. Biogeosciences 19, 743–762 (2022).Article 
    ADS 

    Google Scholar 
    Keller, G. in The Miocene Ocean: Paleoceanography and Biogeography Vol. 163, 177–196 (Geological Society of America, 1985).Holbourn, A. E. et al. Late Miocene climate cooling and intensification of southeast Asian winter monsoon. Nat. Commun. 9, 1584 (2018).Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Willeit, M., Ganopolski, A., Calov, R., Robinson, A. & Maslin, M. The role of CO2 decline for the onset of Northern Hemisphere glaciation. Quat. Sci. Rev. 119, 22–34 (2015).Article 
    ADS 

    Google Scholar 
    Hayashi, T. et al. Latest Pliocene Northern Hemisphere glaciation amplified by intensified Atlantic meridional overturning circulation. Commun. Earth Environ. 1, 25–10 (2020).Article 
    ADS 

    Google Scholar 
    Lam, A. R., Crundwell, M. P., Leckie, R. M., Albanese, J. & Uzel, J. P. Diachroneity rules the mid-latitudes: a test case using late Neogene planktic foraminifera across the Western Pacific. Geosciences 12, 190 (2022).Article 
    ADS 

    Google Scholar 
    Lowery, C. M., Bown, P. R., Fraass, A. J. & Hull, P. M. Ecological response of plankton to environmental change: thresholds for extinction. Annu. Rev. Earth Planet. Sci. 48, 403–429 (2020).Article 
    ADS 
    CAS 

    Google Scholar 
    Rillo, M. C. et al. On the mismatch in the strength of competition among fossil and modern species of planktonic Foraminifera. Global Ecol. Biogeogr. 28, 1866–1878 (2019).Article 

    Google Scholar 
    Poloczanska, E. S. et al. Global imprint of climate change on marine life. Nat. Clim. Change 3, 919–925 (2013).Article 
    ADS 

    Google Scholar 
    Monllor-Hurtado, A., Pennino, M. G. & Sanchez-Lizaso, J. L. Shift in tuna catches due to ocean warming. PLoS ONE 12, e0178196 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Brook, B. W., Sodhi, N. S. & Bradshaw, C. J. Synergies among extinction drivers under global change. Trends Ecol. Evol. 23, 453–460 (2008).Article 
    PubMed 

    Google Scholar 
    Mora, C. et al. Biotic and human vulnerability to projected changes in ocean biogeochemistry over the 21st century. PLoS Biol. 11, e1001682 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Renaudie, J., Lazarus, D.B. & Diver, P. NSB (Neptune Sandbox Berlin): an expanded and improved database of marine planktonic microfossil data and deep-sea stratigraphy. Palaeontol. Electron. 23, p.a11 (2020).
    Google Scholar 
    Pearson, P. N. in Atlas of Oligocene Planktonic Foraminifera (eds Wade, B. S. et al) 415–428 (Cushman Foundation of Foraminiferal Research, 2018).Liow, L. H., Skaug, H. J., Ergon, T. & Schweder, T. Global occurrence trajectories of microfossils: environmental volatility and the rise and fall of individual species. Paleobiology 36, 224–252 (2010).Article 

    Google Scholar 
    Lazarus, D., Weinkauf, M. & Diver, P. Pacman profiling: a simple procedure to identify stratigraphic outliers in high-density deep-sea microfossil data. Paleobiology 38, 144–161 (2012).Article 

    Google Scholar 
    Woodhouse, A. et al. Paleoecology and evolutionary response of planktonic foraminifera to the Plio-Pleistocene intensification of Northern Hemisphere glaciations. Preprint at EGUsphere https://doi.org/10.5194/egusphere-2022-844 (2022).Woodhouse, A. et al. Paleoecology and evolutionary response of planktonic foraminifera to the mid-Pliocene Warm Period and Plio-Pleistocene bipolar ice sheet expansion. Biogeosciences 20, 121–139 (2023).Article 
    ADS 

    Google Scholar 
    Dormann, C. F., Fründ, J., Blüthgen, N. & Gruber, B. Indices, graphs and null models: analyzing bipartite ecological networks. Op. Ecol. J. 2, 7–24 (2009).Article 

    Google Scholar 
    Swain, A. et al. Sampling bias and the robustness of ecological metrics for plant-damage-type association networks. Ecology https://doi.org/10.1002/ecy.3922 (2022).Julliard, R., Clavel, J., Devictor, V., Jiguet, F. & Couvet, D. Spatial segregation of specialists and generalists in bird communities. Ecol. Lett. 9, 1237–1244 (2006).Article 
    PubMed 

    Google Scholar 
    Vaughan, I. P. et al. econullnetr: an R package using null models to analyse the structure of ecological networks and identify resource selection. Methods Ecol. Evol. 9, 728–733 (2018).Article 
    MathSciNet 

    Google Scholar  More