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Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

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  • Andrej Kuritzin
  • Tabea Kischka
  • Jürgen Schmitz
  • Gennady Churakov

Abstract

Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p

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  • Andrej Kuritzin & Tabea Kischka & Jürgen Schmitz & Gennady Churakov, 2016. "Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data," PLOS Computational Biology, Public Library of Science, vol. 12(3), pages 1-20, March.
    • Handle: RePEc:plo:pcbi00:1004812
    DOI: 10.1371/journal.pcbi.1004812
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    References listed on IDEAS

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    1. Mitsuru Shimamura & Hiroshi Yasue & Kazuhiko Ohshima & Hideaki Abe & Hidehiro Kato & Toshiya Kishiro & Mutsuo Goto & Isao Munechika & Norihiro Okada, 1997. "Molecular evidence from retroposons that whales form a clade within even-toed ungulates," Nature, Nature, vol. 388(6643), pages 666-670, August.
    2. Meng, Chen & Kubatko, Laura Salter, 2009. "Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model," Theoretical Population Biology, Elsevier, vol. 75(1), pages 35-45.
    3. Alexander Suh & Martin Paus & Martin Kiefmann & Gennady Churakov & Franziska Anni Franke & Jürgen Brosius & Jan Ole Kriegs & Jürgen Schmitz, 2011. "Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds," Nature Communications, Nature, vol. 2(1), pages 1-7, September.
    4. Nicolas Heslot & Jessica Rutkoski & Jesse Poland & Jean-Luc Jannink & Mark E Sorrells, 2013. "Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-8, September.
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    1. Ran Tian & Yaolei Zhang & Hui Kang & Fan Zhang & Zhihong Jin & Jiahao Wang & Peijun Zhang & Xuming Zhou & Janet M. Lanyon & Helen L. Sneath & Lucy Woolford & Guangyi Fan & Songhai Li & Inge Seim, 2024. "Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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