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Recent speciation associated with range expansion and a shift to self-fertilization in North American Arabidopsis

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  • Coyne, J. A. & Orr, H. A. Speciation 83–178 (Sinauer, 2004).

  • Dieckmann, U., Doebeli, M., Metz, J. A. & Tautz, D. Adaptive Speciation (Cambridge University Press, 2004).

  • Butlin, R. K., Galindo, J. & Grahame, J. W. Sympatric, parapatric or allopatric: the most important way to classify speciation? Philos. T. Roy. Soc. B 363, 2997–3007 (2008).

    Article 

    Google Scholar 

  • Smadja, C. M. & Butlin, R. K. A framework for comparing processes of speciation in the presence of gene flow. Mol. Ecol. 20, 5123–5140 (2011).

    Article 

    Google Scholar 

  • Seehausen, O. et al. Genomics and the origin of species. Nat. Rev. Genet. 15, 176–192 (2014).

    Article 
    CAS 

    Google Scholar 

  • Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V. & Westram, A. M. Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers. Philos. T. Roy. Soc. B 375, 20190528 (2020).

    Article 

    Google Scholar 

  • Hofreiter, M. & Stewart, J. Ecological change, range fluctuations and population dynamics during the Pleistocene. Curr. Biol. 19, R584–R594 (2009).

    Article 
    CAS 

    Google Scholar 

  • Longman, J., Mills, B. J. W., Manners, H. R., Gernon, T. M. & Palmer, M. R. Late Ordovician climate change and extinctions driven by elevated volcanic nutrient supply. Nat. Geosci. 14, 924–929 (2021).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Thomson, R. C., Spink, P. Q. & Shaffer, H. B. A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proc. Natl Acad. Sci. USA 118, e2012215118 (2021).

    Article 
    CAS 

    Google Scholar 

  • Chaboureau, A. C., Sepulchre, P., Donnadieu, Y. & Franc, A. Tectonic-driven climate change and the diversification of angiosperms. Proc. Natl Acad. Sci. USA 111, 14066–14070 (2014).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Hewitt, G. The genetic legacy of the Quaternary ice ages. Nature 405, 907–913 (2000).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Schmitt, T. Molecular biogeography of Europe: Pleistocene cycles and postglacial trends. Front. Zool. 4, 11 (2007).

    Article 

    Google Scholar 

  • Haffer, J. Speciation in Amazonian forest birds. Science 165, 131–137 (1969).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Ebdon, S. et al. The Pleistocene species pump past its prime: evidence from European butterfly sister species. Mol. Ecol. 30, 3575–3589 (2021).

    Article 

    Google Scholar 

  • Excoffier, L., Foll, M. & Petit, R. J. Genetic consequences of range expansions. Annu. Rev. Ecol. Evol. Syst. 40, 481–501 (2009).

    Article 

    Google Scholar 

  • Baker, H. G. Self-compatibility and establishment after ‘long-distance’ dispersal. Evolution 9, 347–349 (1955).

    Google Scholar 

  • Fisher, R. The Genetical Theory of Natural Selection 125–129 (Oxford University Press, 1930).

  • Endler, J. A. Geographic Variation, Speciation, and Clines. Monographs in Population Biology Vol. 10, 53–65, 142–150 (Princeton University Press, 1977).

  • Doebeli, M. & Dieckmann, U. Speciation along environmental gradients. Nature 421, 259–264 (2003).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Ispolatov, J. & Doebeli, M. Diversification along environmental gradients in spatially structured populations. Evol. Ecol. Res. 11, 295–304 (2009).

    Google Scholar 

  • Rettelbach, A., Servedio, M. R. & Hermisson, J. Speciation in peripheral populations: effects of drift load and mating systems. J. Evol. Biol. 29, 1073–1090 (2016).

    Article 
    CAS 

    Google Scholar 

  • Wright, S. I., Kalisz, S. & Slotte, T. Evolutionary consequences of self-fertilization in plants. Proc. R. Soc. Lond. Ser. B 280, 20130133 (2013).

    Google Scholar 

  • Hu, X.-S. Mating system as a barrier to gene flow. Evolution 69, 1158–1177 (2015).

    Article 
    CAS 

    Google Scholar 

  • Glémin, S. How are deleterious mutations purged? Drift versus nonrandom mating. Evolution 57, 2678–2687 (2003).

    Google Scholar 

  • Warwick, S. I., Francis, A. & Al-Shehbaz, I. A. Brassicaceae: species checklist and database on CD-Rom. Plant Syst. Evol. 259, 249–258 (2006).

    Article 

    Google Scholar 

  • Warwick, S. I., Al-Shehbaz, I. A. & Sauder, C. A. Phylogenetic position of Arabis arenicola and generic limits of Aphragmus and Eutrema (Brassicaceae) based on sequences of nuclear ribosomal DNA. Can. J. Bot. 84, 269–281 (2006).

    Article 
    CAS 

    Google Scholar 

  • Hohmann, N. et al. Taming the wild: resolving the gene pools of non-model Arabidopsis lineages. BMC Evol. Biol. 14, e224 (2014).

    Article 

    Google Scholar 

  • Novikova, P. Y. et al. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat. Genet. 48, 1077–1082 (2016).

    Article 
    CAS 

    Google Scholar 

  • Perrier, A. & Willi, Y. Intraspecific variation in reproductive barriers between two recently-diverged, allopatric Arabidopsis species. J. Evol. Biol. https://doi.org/10.1111/jeb.14122 (2022). (in press).

  • Griffin, P. C. & Willi, Y. Evolutionary shifts to self-fertilisation restricted to geographic range margins in North American Arabidopsis lyrata. Ecol. Lett. 17, 484–490 (2014).

    Article 
    CAS 

    Google Scholar 

  • Willi, Y., Fracassetti, M., Zoller, S. & Van Buskirk, J. Accumulation of mutational load at the edges of a species range. Mol. Biol. Evol. 35, 781–791 (2018).

    Article 
    CAS 

    Google Scholar 

  • Schmickl, R., Jørgensen, M. H., Brysting, A. K. & Koch, M. A. The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the Amphi-Beringian area closes a large distribution gap and builds up a genetic barrier. BMC Evol. Biol. 10, e98 (2010).

    Article 

    Google Scholar 

  • Pyhäjärvi, T., Aalto, E. & Savolainen, O. Time scales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae). Am. J. Bot. 99, 1314–1322 (2012).

    Article 

    Google Scholar 

  • Dyke, A. S. in Quaternary Glaciations – Extent and Chronology, Part II: North America (Elsevier, Amsterdam, 2004).

  • Kirkpatrick, M. & Ravigné, V. Speciation by natural and sexual selection: models and experiments. Am. Nat. 159, S22–S35 (2002).

    Article 

    Google Scholar 

  • Igic, B., Lande, R. & Kohn, J. R. Loss of self‐incompatibility and its evolutionary consequences. Int. J. Plant Sci. 169, 93–104 (2008).

    Article 

    Google Scholar 

  • Willi, Y. & Määttänen, K. Evolutionary dynamics of mating system shifts in Arabidopsis lyrata. J. Evol. Biol. 23, 2123–2131 (2010).

    Article 
    CAS 

    Google Scholar 

  • Lucek, K. & Willi, Y. Drivers of linkage disequilibrium across a species’ geographic range. PLoS Genet. 17, e1009477 (2021).

    Article 
    CAS 

    Google Scholar 

  • Pironon, S. et al. Geographic variation in genetic and demographic performance: new insights from an old biogeographical paradigm: the centre-periphery hypothesis. Biol. Rev. 92, 1877–1909 (2017).

    Article 

    Google Scholar 

  • Encinas-Viso, F., Young, A. G. & Pannell, J. R. The loss of self-incompatibility in a range expansion. J. Evol. Biol. 33, 1235–1244 (2020).

    Article 

    Google Scholar 

  • Jarne, P. & Auld, J. R. Animals mix it up too: the distribution of self-fertilization among hermaphroditic animals. Evolution 60, 1816–1824 (2006).

    Google Scholar 

  • Foxe, J. P. et al. Reconstructing origins of loss of self-incompatibility and selfing in North American Arabidopsis lyrata: a population genetic context. Evolution 64, 3495–3510 (2010).

    Article 

    Google Scholar 

  • Koski, M. H., Layman, N. C., Prior, C. J., Busch, J. W. & Galloway, L. F. Selfing ability and drift load evolve with range expansion. Evol. Lett. 3, 500–512 (2019).

    Article 

    Google Scholar 

  • Prior, C. J. & Busch, J. W. Selfing rate variation within species is unrelated to life‐history traits or geographic range position. Am. J. Bot. 108, 2294–2308 (2021).

    Article 

    Google Scholar 

  • Skeels, A. & Cardillo, M. Reconstructing the geography of speciation from contemporary biodiversity data. Am. Nat. 193, 240–254 (2019).

    Article 

    Google Scholar 

  • Sánchez-Castro, D., Perrier, A. & Willi, Y. Reduced climate adaptation at range edges in North American Arabidopsis lyrata. Glob. Ecol. Biogeogr. 31, 1066–1077 (2022).

    Article 

    Google Scholar 

  • Roessler, K. et al. The genome-wide dynamics of purging during selfing in maize. Nat. Plants 5, 980–990 (2019).

    Article 
    CAS 

    Google Scholar 

  • Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).

  • Hu, T. T. et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476–481 (2011).

    Article 

    Google Scholar 

  • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 

    Google Scholar 

  • McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    Article 
    CAS 

    Google Scholar 

  • Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92 (2012).

    Article 
    CAS 

    Google Scholar 

  • Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).

    Article 
    CAS 

    Google Scholar 

  • Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    Article 
    CAS 

    Google Scholar 

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

    Article 
    CAS 

    Google Scholar 

  • Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).

    Article 
    CAS 

    Google Scholar 

  • Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C. & Foll, M. Robust demographic inference from genomic and SNP data. PLoS Genet. 9, e1003905 (2013).

    Article 

    Google Scholar 

  • Marchi, N. et al. The genomic origins of the world’s first farmers. Cell 185, 1842–1859 (2022).

    Article 
    CAS 

    Google Scholar 

  • Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011).

    Article 
    CAS 

    Google Scholar 

  • Genete, M., Castric, V. & Vekemans, X. Genotyping and de novo discovery of allelic variants at the Brassicaceae self-incompatibility locus from short-read sequencing data. Mol. Biol. Evol. 7, 1193–1201 (2020).

    Article 

    Google Scholar 

  • Lynch, M. et al. Genome-wide linkage-disequilibrium profiles from single individuals. Genetics 198, 269–281 (2014).

    Article 

    Google Scholar 

  • R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2021).

  • Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).

    Article 
    CAS 

    Google Scholar 

  • Nychka, D., Furrer, R., Paige, J. & Sain, S. fields: tools for spatial data. R package version 14.1 https://github.com/dnychka/fieldsRPackage (2021).

  • Asquith, W. lmomco—L-moments, censored L-moments, trimmed L-moments, L-comoments, and many distributions. R package version 2.4.7 (2022).

  • Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).

    Article 

    Google Scholar 

  • Lemon, J. Plotrix: a package in the red light district of R. R. N. 6, 8–12 (2006).

    Google Scholar 

  • Pebesma, E. J. & Bivand, R. S. Classes and methods for spatial data in R. R. N. 5, 9–13 (2005).

    Google Scholar 

  • Bivand, R. S., Pebesma, E. & Gomez-Rubio, V. Applied Spatial Data Analysis with R Second edition (Springer, 2013).


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