DOI: 10.5061/dryad.8153g
title: Data from: A new genus of horse from Pleistocene North America

description: The extinct “New World stilt-legged”, or NWSL, equids constitute a
 perplexing group of Pleistocene horses endemic to North America. Their
 slender distal limb bones resemble those of Asiatic asses, such as the
 Persian onager. Previous palaeogenetic studies, however, have suggested a
 closer relationship to caballine horses than to Asiatic asses. Here, we
 report complete mitochondrial and partial nuclear genomes from NWSL equids
 from across their geographic range. Although multiple NWSL equid species
 have been named, our palaeogenomic and morphometric analyses support the
 idea that there was only a single species of middle to late Pleistocene
 NWSL equid, and demonstrate that it falls outside of crown group Equus. We
 therefore propose a new genus, Haringtonhippus, for the sole species H.
 francisci. Our combined genomic and phenomic approach to resolving the
 systematics of extinct megafauna will allow for an improved understanding
 of the full extent of the terminal Pleistocene extinction event.
description: mtDNA_alignment_1_allPartns.nexMitochondrial genome alignment data set 1. White rhino outgroup. All partitions.mtDNA_alignment_1_reducedPartns.nexMitochondrial genome alignment data set 1. White rhino outgroup. Reduced partitions.mtDNA_alignment_2_allPartns.nexMitochondrial genome alignment data set 2. Malayan tapir outgroup. All partitions.mtDNA_alignment_2_reducedPartns.nexMitochondrial genome alignment data set 2. Malayan tapir outgroup. Reduced partitions.mtDNA_alignment_3_allPartns.nexMitochondrial genome alignment data set 3. Dog and ceratomorph outgroups. All partitions.mtDNA_alignment_3_reducedPartns.nexMitochondrial genome alignment data set 3. Dog and ceratomorph outgroups. Reduced partitions.mtDNA_alignment_4_allPartns.nexMitochondrial genome alignment data set 4. Evolutionary Placement algorithm analysis. All partitions.mtDNA_alignment_4_reducedPartns.nexMitochondrial genome alignment data set 4. Evolutionary Placement algorithm analysis. Reduced partitions.mtDNA_alignment_5_allPartns.nexMitochondrial genome alignment data set 5. Reduced equid data set for BEAST analyses. All partitions.mtDNA_alignment_5_reducedPartns.nexMitochondrial genome alignment data set 5. Reduced equid data set for BEAST analyses. Reduced partitions.mtDNA_alignment_6_allPartns.nexMitochondrial genome alignment data set 6. Full equid data set for synapomorphy analyses. All partitions.mtDNA_alignment_6_reducedPartns.nexMitochondrial genome alignment data set 6. Full equid data set for synapomorphy analyses. Reduced partitions.BEAST_mtDNAdataset5_equidsOnly_allPartns_rootConstrained_exclEovodoviBEAST_mtDNAdataset5_equidsOnly_allPartns_rootConstrained_inclEovodoviBEAST_mtDNAdataset5_equidsOnly_allPartns_rootNotConstrained_exclEovodoviBEAST_mtDNAdataset5_equidsOnly_allPartns_rootNotConstrained_inclEovodoviBEAST_mtDNAdataset5_equidsOnly_reducedPartns_rootConstrained_exclEovodoviBEAST_mtDNAdataset5_equidsOnly_reducedPartns_rootConstrained_inclEovodoviBEAST_mtDNAdataset5_equidsOnly_reducedPartns_rootNotConstrained_exclEovodoviBEAST_mtDNAdataset5_equidsOnly_reducedPartns_rootNotConstrained_inclEovodoviBEAST_mtDNADataset5_equidsOnly_allPartns_rootConstrained_exclEovodovi.mccBEAST_mtDNADataset5_equidsOnly_allPartns_rootConstrained_inclEovodovi.mccBEAST_mtDNADataset5_equidsOnly_allPartns_rootNotConstrained_exclEovodovi.mccBEAST_mtDNADataset5_equidsOnly_allPartns_rootNotConstrained_inclEovodovi.mccBEAST_mtDNADataset5_equidsOnly_reducedPartns_rootConstrained_exclEovodovi.mccBEAST_mtDNADataset5_equidsOnly_reducedPartns_rootConstrained_inclEovodovi.mccBEAST_mtDNADataset5_equidsOnly_reducedPartns_rootNotConstrained_exclEovodovi.mccBEAST_mtDNADataset5_equidsOnly_reducedPartns_rootNotConstrained_inclEovodovi.mccEPA_mtDNADataset4_allPartns_exclHippidionEPA_mtDNADataset4_allPartns_inclHippidionEPA_mtDNADataset4_reducedPartns_exclHippidionEPA_mtDNADataset4_reducedPartns_inclHippidionMrBayes_mtDNAdataset1_rhinoOut_allPartns_exclHippidion.conMrBayes_mtDNAdataset1_rhinoOut_allPartns_inclHippidion.conMrBayes_mtDNAdataset1_rhinoOut_reducedPartns_exclHippidion.conMrBayes_mtDNAdataset1_rhinoOut_reducedPartns_inclHippidion.conMrBayes_mtDNAdataset2_tapirOut_allPartns_exclHippidion.conMrBayes_mtDNAdataset2_tapirOut_allPartns_inclHippidion.conMrBayes_mtDNAdataset2_tapirOut_reducedPartns_exclHippidion.conMrBayes_mtDNAdataset2_tapirOut_reducedPartns_inclHippidion.conMrBayes_mtDNAdataset3_dogOut_allPartns_exclHippidion.conMrBayes_mtDNAdataset3_dogOut_allPartns_inclHippidion.conMrBayes_mtDNAdataset3_dogOut_reducedPartns_exclHippidion.conMrBayes_mtDNAdataset3_dogOut_reducedPartns_inclHippidion.conRAxML_mtDNAdataset1_rhinoOut_allPartns_exclHippidionRAxML_mtDNAdataset1_rhinoOut_allPartns_inclHippidionRAxML_mtDNAdataset1_rhinoOut_reducedPartns_exclHippidionRAxML_mtDNAdataset1_rhinoOut_reducedPartns_inclHippidionRAxML_mtDNAdataset2_tapirOut_allPartns_exclHippidionRAxML_mtDNAdataset2_tapirOut_allPartns_inclHippidionRAxML_mtDNAdataset2_tapirOut_reducedPartns_exclHippidionRAxML_mtDNAdataset2_tapirOut_reducedPartns_inclHippidionRAxML_mtDNAdataset3_dogOut_allPartns_exclHippidionRAxML_mtDNAdataset3_dogOut_allPartns_inclHippidionRAxML_mtDNAdataset3_dogOut_reducedPartns_exclHippidionRAxML_mtDNAdataset3_dogOut_reducedPartns_inclHippidionMorphometrics_Rscript_codemtDNA_alignment_4_allPartns_revised.nexMitochondrial genome alignment data set 4. Evolutionary Placement algorithm analysis. All partitions. Revised version.EPA_mtDNADataset4_allPartns_exclHippidion_revisedEPA_mtDNADataset4_allPartns_inclHippidion_revised