Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences-4

TMRCA (kyr) in generations using a mutation rate of 1% × 10per year. The tree shows the ancestral distribution of mutations and events (TMRCA, recent rapid expansion) in the population history.<p><b>Copyright information:</b></p><p>Taken from "Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences"</p><p>http://www.biomedcentral.com/1471-2148/8/201</p><p>BMC Evolutionary Biology 2008;8():201-201.</p><p>Published online 14 Jul 2008</p><p>PMCID:PMC2483725.</p><p></p

Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences-1

Te undetected intermediate haplotype states separated by one mutational step. Boxes indicate one-step to two-step nesting levels for the nested clade analysis in NCA.<p><b>Copyright information:</b></p><p>Taken from "Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences"</p><p>http://www.biomedcentral.com/1471-2148/8/201</p><p>BMC Evolutionary Biology 2008;8():201-201.</p><p>Published online 14 Jul 2008</p><p>PMCID:PMC2483725.</p><p></p

Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences-3

Er a model of sudden expansion illustrated by the overlaid curve (black dots and solid lines). -axis: number of pair-wise differences, -axis: frequency.<p><b>Copyright information:</b></p><p>Taken from "Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences"</p><p>http://www.biomedcentral.com/1471-2148/8/201</p><p>BMC Evolutionary Biology 2008;8():201-201.</p><p>Published online 14 Jul 2008</p><p>PMCID:PMC2483725.</p><p></p

Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences-0

Ch node based on maximum likelihood inference.<p><b>Copyright information:</b></p><p>Taken from "Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences"</p><p>http://www.biomedcentral.com/1471-2148/8/201</p><p>BMC Evolutionary Biology 2008;8():201-201.</p><p>Published online 14 Jul 2008</p><p>PMCID:PMC2483725.</p><p></p

Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences-2

to . Classic skyline was shown as thin line, generalized skyline as thick line, and dot line as the expected demographic history.<p><b>Copyright information:</b></p><p>Taken from "Complex population genetic and demographic history of the Salangid, , based on cytochrome b sequences"</p><p>http://www.biomedcentral.com/1471-2148/8/201</p><p>BMC Evolutionary Biology 2008;8():201-201.</p><p>Published online 14 Jul 2008</p><p>PMCID:PMC2483725.</p><p></p

Additional file 3: of Dietary specialization drives multiple independent losses and gains in the bitter taste gene repertoire of Laurasiatherian Mammals

Excel file Supplementary_Table_S2. (XLSX 19.2 kb

Additional file 1: Tables S1-S4 and Figures S1-S2. of Dietary specialization drives multiple independent losses and gains in the bitter taste gene repertoire of Laurasiatherian Mammals

Whole-genome assemblies analyzed in the present study. Table S2. Bitter taste receptor genes TAS2Rs in the genome assemblies of Laurasiatherian mammals (Please refer to the excel file Supplementary_Table_S2, Additional file 3). Pseudogenes were listed in red characters. Whales and dolphins (Tutr, Oror, Live, Phma, Baac) which have lost most of the TAS2Rs were marked in pale read shadow, pangolin (Mape) which only have 2 TAS2Rs was marked in pale blue shadow, and the common shrew (Soar) with the most number of 52 TAS2Rs was marked in yellow shadow. Figure S1. (A and B) Dotplots comparing the Brandt’s bat and the big brown bat assemblies containing the clade of TAS2R16. (C and D) Dotplots comparing the Brandt’s bat and the big brown bat assemblies containing the clade of TAS2R18. (E and F) Dotplots comparing horse and cat assemblies containing the clades of TAS2R11 and TAS2R12. (G and H) Dotplots comparing horse and cat assemblies containing the clade of TAS2R62. The minimum repeat length was 100 bp and the repeat identity was 90 %. The TAS2Rs positions are shown by dashed lines. Figure S2. Forty PIC values converted from the 41 phylogenetically correlated data. Table S3. Classification of Truncated TAS2Rs in the genome assemblies of Laurasiatherian mammals. For each species, overlapping truncated TAS2Rs with similar orthologies in the multiple alignments were regarded as being derived from different loci. In contrast, non-overlapping TAS2Rs were regarded as being derived from the same loci with gap(s). Table S4. Birth genes and death genes in each branch of Laurasiatherian mammals. (PDF 0.99 mb

Additional file 2: of Dietary specialization drives multiple independent losses and gains in the bitter taste gene repertoire of Laurasiatherian Mammals

Data set S1. Annotated sequences of TAS2Rs (Tas2rs) in the present study. The header of each FASTA sequence indicates the TAS2R name and its location in the contig, scaffold, or chromosome in the whole-genome assembly. Truncated and disrupted genes are indicated by T and P, respectively. (PDF 796 kb

Relatively Recent Evolution of Pelage Coloration in Colobinae: Phylogeny and Phylogeography of Three Closely Related Langur Species

<div><p>To understand the evolutionary processes leading to the diversity of Asian colobines, we report here on a phylogenetic, phylogeographical and population genetic analysis of three closely related langurs, <i>Trachypithecus francoisi</i>, <i>T. poliocephalus</i> and <i>T. leucocephalus</i>, which are all characterized by different pelage coloration predominantly on the head and shoulders. Therefore, we sequenced a 395 bp long fragment of the mitochondrial control region from 178 <i>T. francoisi</i>, 54 <i>T. leucocephalus</i> and 19 <i>T. poliocephalus</i> individuals, representing all extant populations of these three species. We found 29 haplotypes in <i>T. francoisi,</i> 12 haplotypes in <i>T. leucocephalus</i> and three haplotypes in <i>T. poliocephalus</i>. <i>T. leucocephalus</i> and <i>T. poliocephalus</i> form monophyletic clades, which are both nested within <i>T. francoisi</i>, and diverged from <i>T. francoisi</i> recently, 0.46-0.27 (<i>T. leucocephalus</i>) and 0.50-0.25 million years ago (<i>T. poliocephalus</i>). Thus, <i>T. francoisi</i> appears as a polyphyletic group, while <i>T. leucocephalus</i> and <i>T. poliocephalus</i> are most likely independent descendents of <i>T. francoisi</i> that are both physically separated from <i>T. francoisi</i> populations by rivers, open sea or larger habitat gaps. Since <i>T. francoisi</i> populations show no variability in pelage coloration, pelage coloration in <i>T. leucocephalus</i> and <i>T. poliocephalus</i> is most likely the result of new genetic mutations after the split from <i>T. francoisi</i> and not of the fixation of different characters derived from an ancestral polymorphism. This case study highlights that morphological changes for example in pelage coloration can occur in isolated populations in relatively short time periods and it provides a solid basis for studies in related species. Nevertheless, to fully understand the evolutionary history of these three langur species, nuclear loci should be investigated as well.</p></div

Head and shoulder coloration of François’s langur (<i>Trachypithecus francoisi</i>; left), white-headed langur (<i>T. leucocephalus</i>; middle) and golden-headed langur (<i>T. poliocephalus</i>; right).

<p>Head and shoulder coloration of François’s langur (<i>Trachypithecus francoisi</i>; left), white-headed langur (<i>T. leucocephalus</i>; middle) and golden-headed langur (<i>T. poliocephalus</i>; right).</p