A comprehensive genomic history of extinct and living elephants

Abstract

Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.

Reticulate Evolutionary History of a Western Palaearctic Bat Complex Explained by Multiple mtDNA Introgressions in Secondary Contacts

“…Nowadays, there is increasing evidence showing that species within various taxonomic groups had gene flow after their divergences. For instance, big cats (Figueiró et al 2017), elephants (Palkopoulou et al 2018), and humans (Prüfer et al 2014) have reticulating phylogenetic trees rather than having simple bifurcating relationships. The patterns of mtDNA introgressions among the lineages of the M. nattereri complex suggest a similar reticulating evolutionary history.…”

Brain Changes during Phyletic Dwarfing in Elephants and Hippos

“…Both taxa are morphologically similar, and till recently, Palaeoloxodon was subsumed into the genus Elephas [Maglio, 1973;Shoshani et al, 2007]. It should be noted, however, that recent genetic studies indicate a closer phylogenetic relationship between Pa laeoloxodon and Loxodonta [Meyer et al, 2017;Palkopoulou et al, 2018].…”

Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets

“…We trimmed sequencing adapters and merged paired-end reads using SeqPrep v.1.1 132 (github.com/jstjohn/SeqPrep) with default settings (excluding reads shorter than 30bp) and a slight 133 modification of the source code to calculate the base qualities in the overlapping region 134 (Palkopoulou et al, 2015). We then mapped the merged reads to three separate reference After mapping, we removed PCR duplicates using a custom script which takes into account both 140 starting and end coordinates of the reads to be identified as duplicates (Palkopoulou et al, 2018), 141 then excluded reads with mapping quality < 30 and estimated the number of correctly unique 142 mapping reads using samtools v1.8 . We consider true endogenous sequences 143 those correctly mapping to the target species (i.e dog reference for ancient dog samples and 144 elephant reference for mammoth samples) and exogenous contaminant sequences those correctly 145 mapping to the non-target reference (i.e elephant and human references for ancient dog samples 146 and dog and human references for mammoth samples).…”