Ghost lineages can invalidate or even reverse findings regarding gene flow

Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch leng...

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Vydané v:PLoS biology Ročník 20; číslo 9; s. e3001776
Hlavní autori: Tricou, Théo, Tannier, Eric, de Vienne, Damien M.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Public Library of Science 14.09.2022
Public Library of Science (PLoS)
Predmet:
Bioinformatics
Biological Evolution
Biology and Life Sciences
Computer and Information Sciences
Computer Science
Discovery Report
Endangered & extinct species
Evolutionary genetics
Gene Flow
Gene transfer
Genes
Genetic research
Genome
Genomes
Ghosts
Malaria
Phylogenetics
Phylogeny
Statistical analysis
Statistical tests
Taxonomy
Trees
Vector-borne diseases
Vectors
France
ISSN:1545-7885, 1544-9173, 1545-7885
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Popis
Shrnutí:Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
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The authors have declared that no competing interests exist.
ISSN:1545-7885
1544-9173
1545-7885
DOI:10.1371/journal.pbio.3001776