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Euarchontoglires Challenged by Incomplete Lineage Sorting
Euarchontoglires, once described as Supraprimates, comprise primates, colugos, tree shrews, rodents, and lagomorphs in a clade that evolved about 90 million years ago (mya) from a shared ancestor with Laurasiatheria. The rapid speciation of groups within Euarchontoglires, and the subsequent inherent...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9141288/ https://www.ncbi.nlm.nih.gov/pubmed/35627160 http://dx.doi.org/10.3390/genes13050774 |
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author | Doronina, Liliya Reising, Olga Clawson, Hiram Churakov, Gennady Schmitz, Jürgen |
author_facet | Doronina, Liliya Reising, Olga Clawson, Hiram Churakov, Gennady Schmitz, Jürgen |
author_sort | Doronina, Liliya |
collection | PubMed |
description | Euarchontoglires, once described as Supraprimates, comprise primates, colugos, tree shrews, rodents, and lagomorphs in a clade that evolved about 90 million years ago (mya) from a shared ancestor with Laurasiatheria. The rapid speciation of groups within Euarchontoglires, and the subsequent inherent incomplete marker fixation in ancestral lineages, led to challenged attempts at phylogenetic reconstructions, particularly for the phylogenetic position of tree shrews. To resolve this conundrum, we sampled genome-wide presence/absence patterns of transposed elements (TEs) from all representatives of Euarchontoglires. This specific marker system has the advantage that phylogenetic diagnostic characters can be extracted in a nearly unbiased fashion genome-wide from reference genomes. Their insertions are virtually free of homoplasy. We simultaneously employed two computational tools, the genome presence/absence compiler (GPAC) and 2-n-way, to find a maximum of diagnostic insertions from more than 3 million TE positions. From 361 extracted diagnostic TEs, 132 provide significant support for the current resolution of Primatomorpha (Primates plus Dermoptera), 94 support the union of Euarchonta (Primates, Dermoptera, plus Scandentia), and 135 marker insertion patterns support a variety of alternative phylogenetic scenarios. Thus, whole genome-level analysis and a virtually homoplasy-free marker system offer an opportunity to finally resolve the notorious phylogenetic challenges that nature produces in rapidly diversifying groups. |
format | Online Article Text |
id | pubmed-9141288 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-91412882022-05-28 Euarchontoglires Challenged by Incomplete Lineage Sorting Doronina, Liliya Reising, Olga Clawson, Hiram Churakov, Gennady Schmitz, Jürgen Genes (Basel) Article Euarchontoglires, once described as Supraprimates, comprise primates, colugos, tree shrews, rodents, and lagomorphs in a clade that evolved about 90 million years ago (mya) from a shared ancestor with Laurasiatheria. The rapid speciation of groups within Euarchontoglires, and the subsequent inherent incomplete marker fixation in ancestral lineages, led to challenged attempts at phylogenetic reconstructions, particularly for the phylogenetic position of tree shrews. To resolve this conundrum, we sampled genome-wide presence/absence patterns of transposed elements (TEs) from all representatives of Euarchontoglires. This specific marker system has the advantage that phylogenetic diagnostic characters can be extracted in a nearly unbiased fashion genome-wide from reference genomes. Their insertions are virtually free of homoplasy. We simultaneously employed two computational tools, the genome presence/absence compiler (GPAC) and 2-n-way, to find a maximum of diagnostic insertions from more than 3 million TE positions. From 361 extracted diagnostic TEs, 132 provide significant support for the current resolution of Primatomorpha (Primates plus Dermoptera), 94 support the union of Euarchonta (Primates, Dermoptera, plus Scandentia), and 135 marker insertion patterns support a variety of alternative phylogenetic scenarios. Thus, whole genome-level analysis and a virtually homoplasy-free marker system offer an opportunity to finally resolve the notorious phylogenetic challenges that nature produces in rapidly diversifying groups. MDPI 2022-04-27 /pmc/articles/PMC9141288/ /pubmed/35627160 http://dx.doi.org/10.3390/genes13050774 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Doronina, Liliya Reising, Olga Clawson, Hiram Churakov, Gennady Schmitz, Jürgen Euarchontoglires Challenged by Incomplete Lineage Sorting |
title | Euarchontoglires Challenged by Incomplete Lineage Sorting |
title_full | Euarchontoglires Challenged by Incomplete Lineage Sorting |
title_fullStr | Euarchontoglires Challenged by Incomplete Lineage Sorting |
title_full_unstemmed | Euarchontoglires Challenged by Incomplete Lineage Sorting |
title_short | Euarchontoglires Challenged by Incomplete Lineage Sorting |
title_sort | euarchontoglires challenged by incomplete lineage sorting |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9141288/ https://www.ncbi.nlm.nih.gov/pubmed/35627160 http://dx.doi.org/10.3390/genes13050774 |
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