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Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework

  • 1.

    Avise, J. C. Phylogeography: retrospect and prospect. J. Biogeogr. 36, 3–15 (2009).

    Article  Google Scholar 

  • 2.

    Hewitt, G. M. Post-glacial re-colonization of European biota. Biol. J. Linn. Soc. 68, 87–112 (1999).

    Article  Google Scholar 

  • 3.

    Linder, P. H. Phylogeography. J. Biogeogr. 44, 243–244 (2017).

    Article  Google Scholar 

  • 4.

    Song, H., Buhay, J. E., Whiting, M. F. & Crandall, K. A. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc. Natl. Acad. Sci. 105, 13486–13491 (2008).

    CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

  • 5.

    Philippe, H. et al. Pitfalls in supermatrix phylogenomics. Pitfalls supermatrix phylogenomics. Eur. J. Taxon. 28, 3. https://doi.org/10.5852/ejt.2017.283 (2017).

    Article  Google Scholar 

  • 6.

    Villaverde, T. et al. Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. New Phytol. 220, 636–650 (2018).

    PubMed  Article  PubMed Central  Google Scholar 

  • 7.

    Vos, P. et al. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407–4414 (1995).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 8.

    Meudt, H. M. & Clarke, A. C. Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci. 12, 106–117 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 9.

    Paun, O. & Schönswetter, P. Amplified fragment length polymorphism: an invaluable fingerprinting technique for genomic, transcriptomic, and epigenetic studies. Methods Mol. Biol. 862, 75–87 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 10.

    Dejaco, T., Gassner, M., Arthofer, W., Schlick-Steiner, B. C. & Steiner, F. M. Taxonomist’s nightmare … evolutionist’s delight: an integrative approach resolves species limits in jumping bristletails despite widespread hybridization and parthenogenesis. Syst. Biol. 65, 947–974 (2016).

    PubMed  PubMed Central  Article  Google Scholar 

  • 11.

    Sefc, K. M. et al. Shifting barriers and phenotypic diversification by hybridisation. Ecol. Lett. 20, 651–662 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  • 12.

    Suchan, T., Malicki, M. & Ronikier, M. Relict populations and Central European glacial refugia: the case of Rhododendron ferrugineum (Ericaceae). J. Biogeogr. 46, 392–404 (2019).

    Article  Google Scholar 

  • 13.

    Schneeweiss, G. M. & Schönswetter, P. A re-appraisal of nunatak survival in arctic-alpine phylogeography. Mol. Ecol. 20, 190–192 (2011).

    PubMed  Article  PubMed Central  Google Scholar 

  • 14.

    Lemmon, A. R. & Lemmon, E. M. High-throughput identification of informative nuclear loci for shallow-scale phylogenetics and phylogeography. Syst. Biol. 61, 745–761 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 15.

    Baird, N. A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, 1–7 (2008).

    Article  CAS  Google Scholar 

  • 16.

    Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G. & Hohenlohe, P. A. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat. Rev. Genet. 17, 81–92 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 17.

    Jeffries, D. L. et al. Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius L.. Mol. Ecol. 25, 2997–3018 (2016).

    PubMed  Article  PubMed Central  Google Scholar 

  • 18.

    Bohling, J., Small, M., Von Bargen, J., Louden, A. & DeHaan, P. Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout. Conserv. Genet. 20, 329–342 (2019).

    CAS  Article  Google Scholar 

  • 19.

    Lemopoulos, A. et al. Comparing RADseq and microsatellites for estimating genetic diversity and relatedness—implications for brown trout conservation. Ecol. Evol. 9, 2106–2120 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  • 20.

    Mesak, F., Tatarenkov, A., Earley, R. L. & Avise, J. C. Hundreds of SNPs vs. dozens of SSRs: which dataset better characterizes natural clonal lineages in a self-fertilizing fish?. Front. Ecol. Evol. 2, 74 (2014).

    Article  Google Scholar 

  • 21.

    Fay, M. F., Cowan, R. S. & Leitch, I. J. The effects of nuclear DNA content (C-value) on the quality and utility of AFLP fingerprints. Ann. Bot. 95, 237–246 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 22.

    Karam, M.-J., Lefèvre, F., Dagher-Kharrat, M. B., Pinosio, S. & Vendramin, G. G. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq. Mol. Ecol. Resour. 15, 601–612 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 23.

    Etter, P. D., Bassham, S., Hohenlohe, P. A., Johnson, E. A. & Cresko, W. A. SNP Discovery and Genotyping for Evolutionary Genetics Using RAD Sequencing. Methods in Molecular Biology (Clifton, N.J.) Vol. 772, 157–178 (Springer, Berlin, 2011).

    Google Scholar 

  • 24.

    Davey, J. L. & Blaxter, M. W. RADseq: next-generation population genetics. Brief. Funct. Genomics 9, 416–423 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 25.

    Głowacka, K. et al. Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones. GCB Bioenergy 7, 386–404 (2015).

    Article  CAS  Google Scholar 

  • 26.

    Leaché, A. D., Banbury, B. L., Felsenstein, J., De Oca, A. N. M. & Stamatakis, A. Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Syst. Biol. 64, 1032–1047 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 27.

    Wu, C.-H. & Drummond, A. J. Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo. Genetics 188, 151–164 (2011).

    PubMed  PubMed Central  Article  Google Scholar 

  • 28.

    Emerson, K. J. et al. Resolving postglacial phylogeography using high-throughput sequencing. Proc. Natl. Acad. Sci. 107, 16196–16200 (2010).

    CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

  • 29.

    Sboner, A., Mu, X., Greenbaum, D., Auerbach, R. K. & Gerstein, M. B. The real cost of sequencing: higher than you think!. Genome Biol. 12, 125 (2011).

    PubMed  PubMed Central  Article  Google Scholar 

  • 30.

    Muir, P. et al. The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol. 17, 53 (2016).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 31.

    Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S. & Hoekstra, H. E. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7, e37135 (2012).

    CAS  PubMed  PubMed Central  Article  ADS  Google Scholar 

  • 32.

    Mittermeier, R. A. & Mittermeier, C. G. Megadiversity: Earth’s Biologically Wealthiest Nations. in 501 (CEMEX, 1997).

  • 33.

    Trimble, M. J. & van Aarde, R. J. Geographical and taxonomic biases in research on biodiversity in human-modified landscapes. Ecosphere 3, art119 (2012).

    Article  Google Scholar 

  • 34.

    Waldron, A. et al. Targeting global conservation funding to limit immediate biodiversity declines. Proc. Natl. Acad. Sci. USA 110, 12144–12148 (2013).

    CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

  • 35.

    Adenle, A. et al. Stakeholder visions for biodiversity conservation in developing countries. Sustainability 7, 271–293 (2014).

    Article  Google Scholar 

  • 36.

    Adenle, A. A., Stevens, C. & Bridgewater, P. Global conservation and management of biodiversity in developing countries: an opportunity for a new approach. Environ. Sci. Policy 45, 104–108 (2015).

    Article  Google Scholar 

  • 37.

    Barber, P. H. et al. Advancing biodiversity research in developing countries: the need for changing paradigms. Bull. Mar. Sci. 90, 187–210 (2014).

    Article  ADS  Google Scholar 

  • 38.

    Byrne, M. Phylogeography provides an evolutionary context for the conservation of a diverse and ancient flora. Aust. J. Bot. 55, 316 (2007).

    Article  Google Scholar 

  • 39.

    Dufresnes, C. et al. Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)?. Mol. Ecol. 22, 5669–5684 (2013).

    PubMed  Article  PubMed Central  Google Scholar 

  • 40.

    Coates, D. J., Byrne, M. & Moritz, C. Genetic diversity and conservation units: dealing with the species-population continuum in the age of genomics. Front. Ecol. Evol. 6, 165 (2018).

    Article  Google Scholar 

  • 41.

    Trimble, M. J. & van Aarde, R. J. Species inequality in scientific study. Conserv. Biol. 24, 886–890 (2010).

    PubMed  Article  PubMed Central  Google Scholar 

  • 42.

    Kirschner, P. et al. Long-term isolation of European steppe outposts boosts the biome’s conservation value. Nat. Commun. 11, 1–10 (2020).

    Article  CAS  Google Scholar 

  • 43.

    Záveská, E. et al. Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychis (Fabaceae). Mol. Phylogenet. Evol. https://doi.org/10.1016/J.YMPEV.2019.106572 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  • 44.

    Luo, M.-C. et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551, 498–502 (2017).

    CAS  PubMed  PubMed Central  Article  ADS  Google Scholar 

  • 45.

    Wang, X. X. et al. The locust genome provides insight into swarm formation and long-distance flight. Nat. Commun. 5, 2957 (2014).

    PubMed  PubMed Central  Article  ADS  CAS  Google Scholar 

  • 46.

    Hensen, I. et al. Low genetic variability and strong differentiation among isolated populations of the rare steppe grass Stipa capillata L. Central Europe. Plant Biol. 12, 526–536 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 47.

    Huang, H. & Knowles, L. L. Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences. Syst. Biol 65, 1–9 (2014).

    Google Scholar 

  • 48.

    Crotti, M., Barratt, C. D., Loader, S. P., Gower, D. J. & Streicher, J. W. Causes and analytical impacts of missing data in RADseq phylogenetics: insights from an African frog (Afrixalus). Zool. Scr. 48, 157–167 (2019).

    Article  Google Scholar 

  • 49.

    Sinclair, E. A. & Hobbs, R. J. Sample size effects on estimates of population genetic structure: implications for ecological restoration. Restor. Ecol. 17, 837–844 (2009).

    Article  Google Scholar 

  • 50.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 51.

    Althoff, D. M., Gitzendanner, M. A. & Segraves, K. A. The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. Syst. Biol. 56, 477–484 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 52.

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 53.

    Felsenstein, J. Inferring Phylogenies (Oxford University Press Inc., Oxford, 2004).

    Google Scholar 

  • 54.

    Eaton, D. A. R., Spriggs, E. L., Park, B. & Donoghue, M. J. Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants. Syst. Biol. 66, 399–412 (2016).

    Google Scholar 

  • 55.

    Hodel, R. G. J. et al. The report of my death was an exaggeration: a review for researchers using microsatellites in the 21st century. Appl. Plant Sci. 4, 1600025 (2016).

    Article  Google Scholar 

  • 56.

    Puritz, J. B. et al. Demystifying the RAD fad. Mol. Ecol. 23, 5937–5942 (2014).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 57.

    Lowry, D. B. et al. Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol. Ecol. Resour. 17, 142–152 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 58.

    Wagner, H. C. et al. Light at the end of the tunnel: Integrative taxonomy delimits cryptic species in the Tetramorium caespitum complex (Hymenoptera: Formicidae). Myrmecol. News 25, 95–129 (2017).

    Google Scholar 

  • 59.

    Wheeler, Q. D. Taxonomic Shock and Awe. In The New Taxonomy (ed. Wheeler, Q. D.) 211–226 (CRC Press, Boca Raton, FL, 2008). https://doi.org/10.1201/9781420008562.ch10.

    Google Scholar 

  • 60.

    Holderegger, R. et al. Conservation genetics: linking science with practice. Mol. Ecol. 28, 3848–3856 (2019).

    PubMed  Article  PubMed Central  Google Scholar 

  • 61.

    Tel-Zur, N., Abbo, S., Myslabodski, D. & Mizrahi, Y. Modified CTAB procedure for DNA isolation from epiphytic cacti of the genera Hylocereus and Selenicereus (Cactaceae). Plant Mol. Biol. Rep. 17, 249–254 (1999).

    CAS  Article  Google Scholar 

  • 62.

    Wachter, G. A. et al. Pleistocene survival on central Alpine nunataks: genetic evidence from the jumping bristletail Machilis pallida. Mol. Ecol. 21, 4983–4995 (2012).

    PubMed  Article  PubMed Central  Google Scholar 

  • 63.

    Arthofer, W., Schlick-Steiner, B. C. & Steiner, F. M. optiFLP: software for automated optimization of amplified fragment length polymorphism scoring parameters. Mol. Ecol. Resour. 11, 1113–1118 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 64.

    Arthofer, W. TinyFLP and tinyCAT: software for automatic peak selection and scoring of AFLP data tables. Mol. Ecol. Resour. 10, 385–388 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 65.

    Oksanen, J., Guillaume Blanchet, F., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P.R., O’Hara, R.B., Simpson, G.L., Solymos, P., Stevens, M.H.H., Szoecs, E. & Wagner, H. Vegan: Community Ecology Package. R package. (2017).

  • 66.

    Doležel, J., Greilhuber, J. & Suda, J. Estimation of nuclear DNA content in plants using flow cytometry. Nat. Protoc. 2, 2233–2244 (2007).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  • 67.

    Davey, F. & RADseq counter. (2012). https://www.wiki.ed.ac.uk/display/RADSequencing/Home. (Accessed: 15th June 2014)

  • 68.

    Paun, O. et al. Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot. Syst. Biol. 65, 212–227 (2016).

    PubMed  Article  PubMed Central  Google Scholar 

  • 69.

    Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. & Cresko, W. A. Stacks: an analysis tool set for population genomics. Mol. Ecol. 22, 3124–3140 (2013).

    PubMed  PubMed Central  Article  Google Scholar 

  • 70.

    Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0. http://www.repeatmasker.org. (Accessed: 1st September 2016)

  • 71.

    Lunter, G. & Goodson, M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 21, 936–939 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 72.

    Felsenstein, J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376 (1981).

    CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

  • 73.

    Jakobsson, M. & Rosenberg, N. A. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 74.

    Rosenberg, N. A. DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes 4, 137–138 (2004).

    Article  Google Scholar 

  • 75.

    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).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 76.

    Huson, D. H. & Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254–267 (2006).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 77.

    Kosman, E. & Leonard, K. J. Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Mol. Ecol. 14, 415–424 (2005).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 78.

    Miclaus, K., Wolfinger, R. & Czika, W. SNP selection and multidimensional scaling to quantify population structure. Genet. Epidemiol. 33, 488–496 (2009).

    PubMed  Article  PubMed Central  Google Scholar 

  • 79.

    Clarke, K. R. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18, 117–143 (1993).

    Article  Google Scholar 

  • 80.

    Wickham, H. ggplot2 (Springer, Berlin, 2009). https://doi.org/10.1007/978-0-387-98141-3.

    Google Scholar 


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