Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Abstract

Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.

Widespread introgression across a phylogeny of 155Drosophilagenomes

“…In each of these systems introgression has occurred relatively recently, as the common ancestor for each species group occurred no more than 15 million years ago. A notable exception is evidence for introgression across much deeper phylogenetic timescales among vascular plants (Pease et al, 2018) and primates (Vanderpool et al, 2020). In some species, there is also evidence that introgression has been a source of adaptive genetic variation that has helped drive adaptation (e.g., (Chen et al, 2018;Eberlein et al, 2019;Jones et al, 2018;Platt et al, 2019;Richards and Martin, 2017)).…”

“…The extent of gene exchange in nature has remained one of the most hotly debated questions in speciation genetics. Genomic data have revealed that introgression is common across taxa, having been identified in major groups such as fungi (Eberlein et al, 2019;Leducq et al, 2016;Tusso et al, 2019), vertebrates (Lamichhaney et al, 2015;Racimo et al, 2015;Schumer et al, 2018;Vanderpool et al, 2020), insects (Edelman et al, 2019;Lohse et al, 2015;, and angiosperms (Pease et al, 2018(Pease et al, , 2016. The evolutionary effects of introgression are diverse, and are determined by multiple ecological and genomic factors (Rhymer and Simberloff, 1996;Taylor and Larson, 2019).…”

Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

“…However, gene trees at individual loci can disagree with each other and with the species tree, a phenomenon known as gene tree discordance. While genomic data allow us to overcome many technical sources of discordance ( Delsuc et al, 2005 ; Dunn et al, 2008 ; Misof et al, 2014 ), discordance also has biological causes ( Degnan and Rosenberg, 2009 ), and remains a common feature of phylogenomic datasets ( Pollard et al, 2006 ; Fontaine et al, 2015 ; Pease et al, 2016 ; Novikova et al, 2016 ; Wu et al, 2018 ; Vanderpool et al, 2020 ).…”

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

“…Figure 1 displays an example of a phylogenetic workflow inspired from ( 3 ) and described in details in the Results section. The main objective of this workflow is to analyse a phylogenomic dataset to infer a species tree and compare it to a reference tree.…”