Frequency of subhaplogroup T1b among modern African cattle.

<p>Arrows are included only to illustrate the relative order in which populations were established based on radiocarbon dating of archaeological specimens, not as indicators of a specific route of travel <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071956#pone.0071956-Mitchell1" target="_blank">[28]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071956#pone.0071956-Huffman1" target="_blank">[29]</a>.</p

The frequencies of the T1 subhaplogroups found by Bonfiglio et al [13] among Egyptian, Ethiopian and European T1 cattle, tabled with the frequencies among the Southern African Nguni cattle in our dataset.

<p>The frequencies of the T1 subhaplogroups found by Bonfiglio et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071956#pone.0071956-Bonfiglio1" target="_blank">[13]</a> among Egyptian, Ethiopian and European T1 cattle, tabled with the frequencies among the Southern African Nguni cattle in our dataset.</p

The Genetic Diversity of the Nguni Breed of African Cattle (<i>Bos</i> spp.): Complete Mitochondrial Genomes of Haplogroup T1

<div><p>Domesticated cattle were commonplace in northern Africa by about 7,000 years ago. Archaeological evidence, however, suggests they were not established in southern Africa until much later, no earlier than 2,000 years ago. Genetic reconstructions have started to shed light on the movement of African cattle, but efforts have been frustrated by a lack of data south of Ethiopia and the nature of the mitochondrial haplogroup T1 which is almost fixed across the continent. We sequenced 35 complete mitochondrial genomes from a South African herd of Nguni cattle, a breed historically associated with Bantu speaking farmers who were among the first to bring cattle to southern Africa. As expected, all individuals in the study were found to be members of haplogroup T1. Only half of the sub-haplogroups of T1 (T1a-T1f) are represented in our sample and the overwhelming majority (94%) in this study belong to subhaplogroup T1b. A previous study of African cattle found frequencies of T1b of 27% in Egypt and 69% in Ethiopia. These results are consistent with serial multiple founder effects significantly shaping the gene pool as cattle were moved from north to south across the continent. Interestingly, these mitochondrial data give no indication that the impacts of the founder effects were ameliorated by gene flow from recently introduced Indian cattle breeds.</p></div

Sequence alignment of Chatham Island sea lions

Sequence alignment of Chatham Island sea lion mtDNA D-loop including all Chatham Islands individuals (NRO number, location, haplotype - C1 to 9), exemplar haplotype sequences of subantarctic individuals (SA1-3), exemplar haplotype sequences of prehistoric New Zealand individuals (NZ1-14), and outgroups (Australian sea lion, South American sea lion, New Zealand furseal). Please see Suppl. Info. Table S1 for numbers of New Zealand and subantarctic individuals for each haplotype

BEAST Dloop phylogenetic analysis with Yule speciation prior

BEAST Dloop phylogenetic analysis with Yule speciation prio

Pinniped whole mitogenome phylogenetic alignment

Pinniped whole mitogenome phylogenetic alignmen

BayeSSC .par files

BayeSSC .par file

Phylogenetic trees for each region of all available prototype EV B strains.

<p>Trees were rooted with PV1. Bootstrap values below 50 were removed. Bars indicate nucleotide substitution distance.</p

Phylogenetic trees for each genome fragment of all available prototype EV B strains.

<p>Trees were rooted with PV1. Bootstrap values below 50 were removed. Bars indicate nucleotide substitution distance.</p

Chatham Island mitogenome Ion Torrent NGS raw sequences

Chatham Island mitogenome Ion Torrent NGS raw sequence