2018
DOI: 10.1073/pnas.1720554115
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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 tha… Show more

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Cited by 155 publications
(161 citation statements)
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“…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.…”
Section: Reticulating Histories and Extinct Lineagesmentioning
confidence: 99%
“…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.…”
Section: Reticulating Histories and Extinct Lineagesmentioning
confidence: 99%
“…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].…”
Section: Ontogeny and Age Determination Of Hippopotamuses And Elephantsmentioning
confidence: 99%
“…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).…”
Section: Data Analyses 131mentioning
confidence: 99%