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Phylogeographic breaks and how to find them: Separating vicariance from isolation by distance in a lizard with restricted dispersaluse asterix (*) to get italics
Loïs Rancilhac, Aurélien Miralles, Philippe Geniez, Daniel Mendez-Arranda, Menad Beddek, José Carlos Brito, Raphaël Leblois, Pierre-André CrochetPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
<p>Aim</p> <p>Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting.</p> <p>Location</p> <p>Morocco&nbsp;</p> <p>Taxon</p> <p>Spiny-footed lizard (Acanthodactylus erythrurus), Squamata: Lacertidae</p> <p>Methods</p> <p>Using 325 samples from 40 localities, we identified genetic discontinuities within A. erythrurus based on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks).</p> <p>Results</p> <p>A. erythrurus is characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases. &nbsp; &nbsp;</p> <p>Main conclusions</p> <p>The genetic diversity of A. erythrurus originates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations within A. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.</p> should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https:// should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://
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Acanthodactylus, Isolation by Distance, Morocco, Phylogeography, Vicariance, Admixture, Cytonuclear discordance, Phylogeographic breaks
NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).
Phylogeography & Biogeography, Population Genetics / Genomics, Speciation, Systematics / Taxonomy
Salvador Carranza, Catarina Pinho, Daniele Salvi No need for them to be recommenders of PCIEvolBiol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct
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2022-10-05 13:11:28
Eric Pante
Kevin Sánchez