Base composition bias for ancient DNA templates: AT <i>versus</i> BE libraries.

<p>Aliquots of a quagga museum specimen and an <i>Hippidion</i> bone fossil were built into AT and BE libraries. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078575#pone-0078575-g002" target="_blank">Figure 2</a> captions for further information regarding base compositions.</p

Sequence data.

<p>The number of raw sequence read pairs generated as well as the number of collapsed trimmed reads and the number of unique hits to reference genomes and passing quality filters are indicated. Endogenous DNA content was calculated by dividing the total number of unique hits passing quality filters and the total number of collapsed reads. BE: Blunt-End adapter ligation. AT: AT-overhang adapter ligation. The final concentration of adapter used for ligation is reported as standard (S) or low (L; see Material and Methods). C: Covaris sonication. B: Bioruptor sonication. N: Nebulization. While most DNA libraries were sequenced as Paired-End (2×100 cycles), one, indicated with an asterisk, was sequenced as Single-End. For this DNA library, #Collapsed refers to the numbers of reads considered post-trimming and not post-collapsing, as for other DNA libraries.</p

Nucleotide misincorporation bias for ancient DNA templates: AT <i>versus</i> BE libraries.

<p>Aliquots of a quagga museum specimen and an <i>Hippidion</i> bone fossil were built into AT and BE libraries. We report CT mismatch rates at the first 5 (positions 1 to 5) and last 5 (positions –1 to –5) nucleotide positions within sequence reads mapping with high quality a unique position of the EquCab2.0 genome. These rates are calculated using mapDamage output <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078575#pone.0078575-Ginolhac1" target="_blank">[24]</a> by summing over positions where a C (G) is found in the reference genome but a T (A) is found in sequencing reads.</p

Base composition bias: AT <i>versus</i> BE libraries.

<p>Fresh aliquots of <i>E. coli</i> DNA extracts were sheared using the Covaris E210 sonicator, size selected, and built into AT and BE libraries (adapter concentration  =  0.6 µM). We report the base composition observed at the first 10 (positions 1 to 10) and last 10 (positions N-9 to N) nucleotide positions within sequence reads mapping with high quality a unique position of the <i>E. coli</i> NC_010473 genome. The genomic composition of the 10 nucleotides located upstream (positions –10 to –1) and downstream (positions N+1 to N+10) DNA inserts are also provided.</p

PartitionFinder_files

Input & output from PartitionFinder analyses

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

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

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

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