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.
mtDNA_alignment_1_allPartns.nex
Mitochondrial genome alignment data set 1. White rhino outgroup. All partitions.
mtDNA_alignment_1_reducedPartns.nex
Mitochondrial genome alignment data set 1. White rhino outgroup. Reduced partitions.
mtDNA_alignment_2_allPartns.nex
Mitochondrial genome alignment data set 2. Malayan tapir outgroup. All partitions.
mtDNA_alignment_2_reducedPartns.nex
Mitochondrial genome alignment data set 2. Malayan tapir outgroup. Reduced partitions.
mtDNA_alignment_3_allPartns.nex
Mitochondrial genome alignment data set 3. Dog and ceratomorph outgroups. All partitions.
mtDNA_alignment_3_reducedPartns.nex
Mitochondrial genome alignment data set 3. Dog and ceratomorph outgroups. Reduced partitions.
mtDNA_alignment_4_allPartns.nex
Mitochondrial genome alignment data set 4. Evolutionary Placement algorithm analysis. All partitions.
mtDNA_alignment_4_reducedPartns.nex
Mitochondrial genome alignment data set 4. Evolutionary Placement algorithm analysis. Reduced partitions.
mtDNA_alignment_5_allPartns.nex
Mitochondrial genome alignment data set 5. Reduced equid data set for BEAST analyses. All partitions.
mtDNA_alignment_5_reducedPartns.nex
Mitochondrial genome alignment data set 5. Reduced equid data set for BEAST analyses. Reduced partitions.
mtDNA_alignment_6_allPartns.nex
Mitochondrial genome alignment data set 6. Full equid data set for synapomorphy analyses. All partitions.
mtDNA_alignment_6_reducedPartns.nex
Mitochondrial genome alignment data set 6. Full equid data set for synapomorphy analyses. Reduced partitions.
BEAST_mtDNAdataset5_equidsOnly_allPartns_rootConstrained_exclEovodovi
BEAST_mtDNAdataset5_equidsOnly_allPartns_rootConstrained_inclEovodovi
BEAST_mtDNAdataset5_equidsOnly_allPartns_rootNotConstrained_exclEovodovi
BEAST_mtDNAdataset5_equidsOnly_allPartns_rootNotConstrained_inclEovodovi
BEAST_mtDNAdataset5_equidsOnly_reducedPartns_rootConstrained_exclEovodovi
BEAST_mtDNAdataset5_equidsOnly_reducedPartns_rootConstrained_inclEovodovi
BEAST_mtDNAdataset5_equidsOnly_reducedPartns_rootNotConstrained_exclEovodovi
BEAST_mtDNAdataset5_equidsOnly_reducedPartns_rootNotConstrained_inclEovodovi
BEAST_mtDNADataset5_equidsOnly_allPartns_rootConstrained_exclEovodovi.mcc
BEAST_mtDNADataset5_equidsOnly_allPartns_rootConstrained_inclEovodovi.mcc
BEAST_mtDNADataset5_equidsOnly_allPartns_rootNotConstrained_exclEovodovi.mcc
BEAST_mtDNADataset5_equidsOnly_allPartns_rootNotConstrained_inclEovodovi.mcc
BEAST_mtDNADataset5_equidsOnly_reducedPartns_rootConstrained_exclEovodovi.mcc
BEAST_mtDNADataset5_equidsOnly_reducedPartns_rootConstrained_inclEovodovi.mcc
BEAST_mtDNADataset5_equidsOnly_reducedPartns_rootNotConstrained_exclEovodovi.mcc
BEAST_mtDNADataset5_equidsOnly_reducedPartns_rootNotConstrained_inclEovodovi.mcc
EPA_mtDNADataset4_allPartns_exclHippidion
EPA_mtDNADataset4_allPartns_inclHippidion
EPA_mtDNADataset4_reducedPartns_exclHippidion
EPA_mtDNADataset4_reducedPartns_inclHippidion
MrBayes_mtDNAdataset1_rhinoOut_allPartns_exclHippidion.con
MrBayes_mtDNAdataset1_rhinoOut_allPartns_inclHippidion.con
MrBayes_mtDNAdataset1_rhinoOut_reducedPartns_exclHippidion.con
MrBayes_mtDNAdataset1_rhinoOut_reducedPartns_inclHippidion.con
MrBayes_mtDNAdataset2_tapirOut_allPartns_exclHippidion.con
MrBayes_mtDNAdataset2_tapirOut_allPartns_inclHippidion.con
MrBayes_mtDNAdataset2_tapirOut_reducedPartns_exclHippidion.con
MrBayes_mtDNAdataset2_tapirOut_reducedPartns_inclHippidion.con
MrBayes_mtDNAdataset3_dogOut_allPartns_exclHippidion.con
MrBayes_mtDNAdataset3_dogOut_allPartns_inclHippidion.con
MrBayes_mtDNAdataset3_dogOut_reducedPartns_exclHippidion.con
MrBayes_mtDNAdataset3_dogOut_reducedPartns_inclHippidion.con
RAxML_mtDNAdataset1_rhinoOut_allPartns_exclHippidion
RAxML_mtDNAdataset1_rhinoOut_allPartns_inclHippidion
RAxML_mtDNAdataset1_rhinoOut_reducedPartns_exclHippidion
RAxML_mtDNAdataset1_rhinoOut_reducedPartns_inclHippidion
RAxML_mtDNAdataset2_tapirOut_allPartns_exclHippidion
RAxML_mtDNAdataset2_tapirOut_allPartns_inclHippidion
RAxML_mtDNAdataset2_tapirOut_reducedPartns_exclHippidion
RAxML_mtDNAdataset2_tapirOut_reducedPartns_inclHippidion
RAxML_mtDNAdataset3_dogOut_allPartns_exclHippidion
RAxML_mtDNAdataset3_dogOut_allPartns_inclHippidion
RAxML_mtDNAdataset3_dogOut_reducedPartns_exclHippidion
RAxML_mtDNAdataset3_dogOut_reducedPartns_inclHippidion
Morphometrics_Rscript_code
mtDNA_alignment_4_allPartns_revised.nex
Mitochondrial genome alignment data set 4. Evolutionary Placement algorithm analysis. All partitions. Revised version.
EPA_mtDNADataset4_allPartns_exclHippidion_revised
EPA_mtDNADataset4_allPartns_inclHippidion_revised