Ghost lineages can invalidate or even reverse findings regarding gene flow

Abstract

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.

Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite - theLigula intestinalisspecies complex

“…10B). Ghost lineages, indicative of the existence of unsampled or extinct lineages in a species, significantly influence gene flow detection (Tricou et al, 2022). TreeMix detects introgression events based on the known lineages and branches in a tree and does not consider ghost lineages (Tricou et al, 2022).…”

A Comprehensive Overview of Baboon Phylogenetic History

“…This natural hybridization is ubiquitous across the animal kingdom, varying in extent and magnitude [ 3 , 4 ]. The evolutionary consequences of hybridization are highly variable and include “reverse speciation” [ 5 ]; reinforcement of reproductive isolation [ 6 ]; the formation of stable hybrid zones [ 7 , 8 ]; hybrid speciation [ 4 ]; (adaptive) introgression, also from so-called “ghost” lineages [ 9 , 10 , 11 ]; and mitochondrial capture or nuclear swamping [ 12 ]. All of these effects of hybridization have been documented in primates in general, and in baboons (genus Papio ) in particular, both in historic and extant populations [ 12 , 13 , 14 , 15 , 16 , 17 , 18 ].…”

Ghost introgression facilitates genomic divergence of a sympatric cryptic lineage in Cycas revoluta

“…A mounting number of studies that focused on introgression between present species, however, ignored the genetic legacy left by extinct (archaic) or unsampled lineages, also known as ghost introgressions (Beerli, 2004). However, we maintain that consideration of ghost introgression is a requisite for correctly inferring the mechanisms of macro-and micro-evolutionary processes (Hahn & Nakhleh, 2016;Herrera-Alsina et al, 2022;Tricou et al, 2022aTricou et al, , 2022b. By transferring standing genetic variations to introgressed lineages, ghost introgression is another force for accelerating adaptation and speciation (Ottenburghs, 2020).…”