Zoomin1hybridprob+structure

Results of zoom-in hybrid probabilities and structure ancestry for DRC-Uganda region (Box C, Fig 1

1295structureresults

Structure results used to determine groupings for parameter estimation

1369hybridprob+structure

Global hybrid analysis giving hybrid probabilities and structure ancestr

Mondol et al. 2015- Elephant mtDNA data

Sequence alignment file with 526 bp mitochondrial partial control region sequences of both forest, savanna and hybrid elephants. This file contains sequences of pure reference African forest and savanna elephants and Asian elephants from Genbank, along with sequences generated through this study from pure (forest and savanna) and hybrid elephants. Total 125 sequences are aligned in this file

1395genotypes_updated

Genotypes of all samples used in analyses, along with location codes and sample type

regionfile

Latitude and longitude for each location code, accompanies genotype fil

Pairwise F_ST values for mitochondrial DNA.

<p>***p<0.001,</p><p>**p<0.01,</p>NS<p> = Not Significant.</p

Okapi samples used in the present study, with the colour relating to the adjacent network [30], based on 833 bp of mitochondrial DNA.

<p>For the network, TCS connected alleles with a 95% confidence limit, those that did not fall within that limit are connected with dotted lines (with numbers corresponding to the number of mutations). Haplotypes are grouped into haplogroups (number of mutations within always less than between a haplogroup) by colour. Some haplotypes contain more than one label due to different programs using missing data in different ways. Sampling locations are arbitrarily labelled 1–4 for reference in the text. Key protected areas are labelled A (Rubi-Tele Hunting Reserve), B (Okapi Faunal Reserve, RFO), C (Lomami National Park), D (Lomami River).</p

Okapi (<i>Okapia johnstoni</i>), giraffe (<i>Giraffa camelopardalis</i>), bushbuck (<i>Tragelaphus scriptus spp.</i>) and duiker (Cephalophinae <i>spp.</i>) tree drawn in BEAST v1.7.5.

<p>Posterior probabilities of >0.8 are highlighted with a single asterisk and posterior probabilities of >0.95 are highlighted with a double-asterisk. Dotted line indicates the most ancestral divergence within okapi. The shading on the tree shows when taxonomic units can be monophyletically grouped, with the different colours corresponding to different levels of inclusiveness for these groupings. For example, for bushbuck, Victoria Basin & Mt Elgon, Great Lakes & Albertine Rift and Imatong & Karamoja Highlands ecoregions could be grouped monophyletically, and are shaded red. The next monophyletic taxonomic grouping are the “scriptus” species (shaded blue), and then all bushbuck (shaded yellow).</p

Giraffidae phylogeny drawn in BEAST v1.7.5 [35], with red deer (<i>Cervus elaphus</i>) as an outgroup, using 505 bp of mtDNA.

<p>Posterior probabilities of >0.8 are highlighted with a single asterisk and posterior probabilities of >0.95 are highlighted with a double-asterisk. Haplotype labels refer to the haplotypes in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101081#pone-0101081-g001" target="_blank">Fig. 1</a>.</p