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

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

Phylogenetic RAxML trees (GTR+G+I) with 500 bootstraps and MrBayes (GTR+G+I) 50M generations on the full data set.

<p>Posterior probabilities are given in proportions and bootstrap support as a percentage on each branch of interest. * Branch is supported by maximum posterior probability and bootstrap (1/100). <b>A:</b> Including outgroups and based on 5 partitions. <b>B:</b> Excluding outgroups and based on 4 partitions.</p

Sample information.

<p>Number of amplicons refers to the number of amplicons sequenced on the GS FLX, and does not include amplicons sequenced by Sanger sequencing. For total number of amplicons see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055950#pone.0055950.s008" target="_blank">Table S5</a>. Sh. stands for shotgun sequencing and refers to cases where no amplicons have been generated. Sh.+C refers to cases where shotgun and target capture data have been merged. C. refers to in solution MYSelect capture. The number of reads used is the number of reads that mapped successfully to the reference used. Coverage is provided as the total number of bases sequenced and aligned against the horse reference mitogenome divided by the length of the horse reference mitogenome (Cov.) or the horse reference mitogenome after excluding a region of tandem repeats (Cov$). Column mitogenome length provides the total sequence length of the mitogenome that is covered by a minimal read depth of 2 and excluding tandem repeats (see Methods).</p

Node ages as estimated from BEAST analyses given in years and with 95% HPD.

<p>Shown is the averaged results from the three analyses excluding outgroups (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055950#pone-0055950-t002" target="_blank">Table 2</a>).</p

Average node ages from BEAST.

<p>Analyses run with and without outgroups (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055950#pone.0055950.s012" target="_blank">Table S9a</a>–b). All dates are in years with 95% confidence interval given in parentheses. N/a = not applicable. Sum = Sumatran rhino; Wool = woolly rhino; Zeb = zebras; Don = Donkey; Donkey = <i>E. africanus</i> and <i>E. asinus</i>; Asses = <i>E. hemionus</i> and <i>E. kiang</i>; Ass = Asses. Node letters in parentheses as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055950#pone-0055950-g001" target="_blank">Figure 1</a>.</p