barcodePrimerFiles

Text files containing the barcodes and primers used in the study

DRYAD_dataflow

Excel spreadsheet showing a sample dataflow

perlScripts

Perl scripts used in the study

finalOTUseeds

Fasta formatted text files with the seed sequence for each OTU used in the study

readidLineageMap

Tab delimited text files containing the readID for each OTU seed, taxonomic lineage, and OTU abundance

Provenance of Bone Samples Extracted and Sequenced for This Study

<p>Details of each sample are given in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030241#st002" target="_blank">Table S2</a>.</p

Diagrammatic Representation of North and South American Equid Taxonomy Superimposed on a Time Scale according to Paleontological (A, B) and Molecular Data (C)

<p>(A) represents MacFadden's [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030241#pbio-0030241-b13" target="_blank">13</a>] view of hippidiform origins from a pliohippine, diversifying into two genera, <i>Hippidion</i> and <i>Onohippidium,</i> in North America during the Miocene. (B) shows Alberdi and Prado's [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030241#pbio-0030241-b14" target="_blank">14</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030241#pbio-0030241-b15" target="_blank">15</a>] view of hippidiforms as descendants of a pliohippine during the Miocene; the single genus, <i>Hippidion</i>, originates only after dispersal into South America (they do not recognize the genus <i>Onohippidium</i> as valid [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030241#pbio-0030241-b15" target="_blank">15</a>]). (C) represents the results of the molecular data presented in the present study; it shows <i>Hippidion</i> as originating during the Pliocene, c. 3-3.5 Ma ago. The NWSL is possibly a sister species of <i>Hippidion</i>.</p

Metatarsal Shape and Size in Pleistocene and Extant Equids

<div><p>(A) Bivariate plot showing metatarsal shape and size in extant and extinct horses. Modern asses: kiang <i>(E. kiang)</i> = light blue circles; onager <i>(E. hemionus onager)</i> = dark blue; kulan <i>(E. hemionus kulan)</i> = purple. Pleistocene equids: stilt-legged from Alaska and the Yukon = black; <i>E. lambei</i> (Alaska) = red; stilt-legged from Natural Trap Cave (Wyoming) = yellow; caballines from Natural Trap Cave = orange; caballines from Alberta = green; <i>H. saldiasi</i> from southern Patagonia = grey. “A” and “B” above/beside points of caballine horses denote the phylogenetic clade to which the specimens belong (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030241#pbio-0030241-g005" target="_blank">Figure 5</a>). Not all of the specimens were genetically analyzed.</p> <p>(B) Metatarsal shape in Pleistocene horses. From left to right: <i>H. saldiasi</i> (southern Patagonia); <i>E. lambei</i> (Yukon); NWSL (Yukon). Scale bar is 10 cm.</p></div

Maximum Likelihood Phylogenetic Tree of Recent, Historic, and Pleistocene Caballine Horses Based on 364 bp of the Mitochondrial Control Region (HVR1)

<p>Posterior probabilities/bootstrap values are presented above or beside the main nodes only if either is > 50%. Labels of prehistoric specimens are followed by their age, if available, in thousands of years (k).</p

Phylogeny of Recent and Pleistocene Equids

<p>The maximum likelihood tree was constructed with two fragments of the mitochondrial control region (583 bp and 133 bp in the HVR1 and HVR2 regions, respectively). Bayesian analysis produced a similar topology. The general time-reversible substitution model was used in both techniques. Black numbers above/beside nodes are posterior probabilities and bootstrap values, respectively (only values > 50% are shown). White numbers on black background are divergence times as calculated from the molecular data. Numbers/letters in bold at the beginning of each specimen's name are sample numbers or GenBank accession numbers. Labels of prehistoric specimens are followed by their age, if available, in thousands of years. The outgroup <i>(Rhinoceros</i> and <i>Ceratotherium)</i> is not shown.</p