Puckett_etal_RatPhylogeog_SNPs.tar

SNPs (l=32,127) discovered from a ddRAD-Seq project with Rattus norvegicus (n=314) and Rattus rattus (n=33) samples from around the world. SNPs are aligned to the Rattus norvegicus Rnor_6.0 genome and provided as binary PLINK files (.bed, .bim, .fam). See Tables S1 and S2 of the manuscript for locations for each sample name

Map showing the relative proportions of haplogroups sequenced from archaeologically derived remains.

<p>Each pie represents 100% of the sequences obtained and the numbers inside each pie refer to the legend which details the geographic provenience and the number of samples from each area. Each colour represents one of three distinct haplogroups. The natural range of Red Junglefowl is outlined in red and represents the area in which initial domestication events must have occurred <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039171#pone.0039171-Johnsgard1" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039171#pone.0039171-Beebe1" target="_blank">[21]</a>. The red shaded area in northern China represents an area in which <i>G. gallus</i> bones have been recovered from archaeological sites older than 5000 BC. This has led to debate about whether the natural range of Red Junglefowl in prehistory extended further north <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039171#pone.0039171-Crawford1" target="_blank">[13]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039171#pone.0039171-Crawford2" target="_blank">[22]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039171#pone.0039171-West1" target="_blank">[25]</a>.</p

A close up of the E and D branches of a Maximum Parsimony Network showing the affinities of ten of the eleven, non-continuiously numbered, ancient haplogroups detected in our 48 samples with those previously defined by Liu et al. [<b>14</b>].

<p>Ancient haplotypes are identified in red bold text and occur in haplogroups D and E. The full network showing the B branch is available as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039171#pone.0039171.s001" target="_blank">Figure S1</a>.</p

Puckett_etal_RatPhylogeog_Supplemental from Global population divergence and admixture of the brown rat (<i>Rattus norvegicus</i>)

Supplemental Methods, Supplemental Figures S1-S1