Mitochondrial Phylogenomics of Modern and Ancient Equids

Abstract

The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).

Mitogenomics of the Extinct Cave Lion, Panthera spelaea (Goldfuss, 1810), Resolve its Position within the Panthera Cats

“…The DNA extract and negative control were then built into genomic libraries using the NEB E6070 kit (New England Biolabs), following a protocol slightly modified from that by Vilstrup et al (2013). Briefly, extract (30 µL) was end-repaired and then passed through a MinElute column (Qiagen).…”

First evidence of Equus asinus L. in the Chalcolithic disputes the Phoenicians as the first to introduce donkeys into the Iberian Peninsula

“…We then built the DNA extractions into indexed blunt-end libraries using the NEBNext DNA Library Prep Master Mix set for 454 (Biolabs,ref:E6070s) and amplified the libraries as in Vilstrup et al (2013). The first 50 ml PCR amplification consisted of 8e10 cycles and included the full 25 ml DNA library, while the second consisted of four parallel PCRs consisting of 5 ml library each amplified for 10e12 cycles and purified on the same MinElute column.…”

“…The first 50 ml PCR amplification consisted of 8e10 cycles and included the full 25 ml DNA library, while the second consisted of four parallel PCRs consisting of 5 ml library each amplified for 10e12 cycles and purified on the same MinElute column. Half of the best amplified and purified libraries were directly shotgun sequenced on Illumina HiSeq2000 and the other half was capture enriched individually with a blank using BioT/B adapted baits as in Vilstrup et al (2013). Post capture, the samples were amplified by two consecutive PCRs, the first 15 cycles in a 50 ml amplification followed by 8 cycles of three parallel 25 ml PCRs in the second amplification, purified on the same column using the same PCR conditions as in Vilstrup et al (2013).…”

“…Half of the best amplified and purified libraries were directly shotgun sequenced on Illumina HiSeq2000 and the other half was capture enriched individually with a blank using BioT/B adapted baits as in Vilstrup et al (2013). Post capture, the samples were amplified by two consecutive PCRs, the first 15 cycles in a 50 ml amplification followed by 8 cycles of three parallel 25 ml PCRs in the second amplification, purified on the same column using the same PCR conditions as in Vilstrup et al (2013). The captured libraries were pooled in equimolar ratios together with other indexed samples on 1 lane on a Hiseq2000 sequencing platform (Illumina).…”

“…We trimmed our reads using a minimal read length of 25 bp in AdapterRemoval (Lindgreen, 2012) and mapped them against full mitochondrial equid genomes (Vilstrup et al, 2013) using BWA (Li and Durbin, 2009), disabling the seed and relaxing the edit distance (Schubert et al, 2012). Reads that mapped to multiple positions and which had a mapping quality score <25 were discarded using SAMtools ).…”