<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Perry, G.</style></author><author><style face="normal" font="default" size="100%">Kistler, L.</style></author><author><style face="normal" font="default" size="100%">Kelaita, M.</style></author><author><style face="normal" font="default" size="100%">Sams, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">￼Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Human Evolution</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Copy number variation</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene content variation</style></keyword><keyword><style  face="normal" font="default" size="100%">Hominin evolutionary ecology</style></keyword><keyword><style  face="normal" font="default" size="100%">Paleogenomics</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">02/2015</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/25563409</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">79</style></volume><pages><style face="normal" font="default" size="100%">55-63</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;span style=&quot;color: rgb(46, 46, 46); font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; font-size: 16px; line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach. Specifically, we infer the timing of five human gene presence/absence changes that may be related to particular hominin-specific dietary changes and discuss these results in the context of our broader reconstructions of hominin evolutionary ecology. We show that pseudogenizing (gene loss) mutations in &lt;/span&gt;&lt;span style=&quot;color: rgb(46, 46, 46); font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; font-size: 16px; line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;the&lt;/span&gt;&lt;em style=&quot;border: 0px; font-size: 16px; margin: 0px; padding: 0px; vertical-align: baseline; font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; color: rgb(46, 46, 46); line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;TAS2R62&lt;/em&gt;&lt;span style=&quot;color: rgb(46, 46, 46); font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; font-size: 16px; line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;&amp;nbsp;and&amp;nbsp;&lt;/span&gt;&lt;em style=&quot;border: 0px; font-size: 16px; margin: 0px; padding: 0px; vertical-align: baseline; font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; color: rgb(46, 46, 46); line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;TAS2R64&lt;/em&gt;&lt;span style=&quot;color: rgb(46, 46, 46); font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; font-size: 16px; line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;&amp;nbsp;bitter taste receptor genes and the&amp;nbsp;&lt;/span&gt;&lt;em style=&quot;border: 0px; font-size: 16px; margin: 0px; padding: 0px; vertical-align: baseline; font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; color: rgb(46, 46, 46); line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;MYH16&lt;/em&gt;&lt;span style=&quot;color: rgb(46, 46, 46); font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; font-size: 16px; line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;&amp;nbsp;masticatory myosin gene occurred after the hominin-chimpanzee divergence but before the divergence of the human and Neandertal/Denisovan lineages. The absence of a functional MYH16 protein may explain our relatively reduced jaw muscles; this gene loss may have followed the adoption of cooking behavior. In contrast, salivary amylase gene (&lt;/span&gt;&lt;em style=&quot;border: 0px; font-size: 16px; margin: 0px; padding: 0px; vertical-align: baseline; font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; color: rgb(46, 46, 46); line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;AMY1&lt;/em&gt;&lt;span style=&quot;color: rgb(46, 46, 46); font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; font-size: 16px; line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;) duplications were not observed in the Neandertal and Denisovan genomes, suggesting a relatively recent origin for the&amp;nbsp;&lt;/span&gt;&lt;em style=&quot;border: 0px; font-size: 16px; margin: 0px; padding: 0px; vertical-align: baseline; font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; color: rgb(46, 46, 46); line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;AMY1&lt;/em&gt;&lt;span style=&quot;color: rgb(46, 46, 46); font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; font-size: 16px; line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;&amp;nbsp;copy number gains that are observed in modern humans. Thus, if earlier hominins were consuming large quantities of starch-rich underground storage organs, as previously hypothesized, then they were likely doing so without the digestive benefits of increased salivary amylase production. Our most surprising result was the observation of a heterozygous mutation in the first codon of the&amp;nbsp;&lt;/span&gt;&lt;em style=&quot;border: 0px; font-size: 16px; margin: 0px; padding: 0px; vertical-align: baseline; font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; color: rgb(46, 46, 46); line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;TAS2R38&lt;/em&gt;&lt;span style=&quot;color: rgb(46, 46, 46); font-family: Arial, Helvetica, &#039;Lucida Sans Unicode&#039;, &#039;Microsoft Sans Serif&#039;, &#039;Segoe UI Symbol&#039;, STIXGeneral, &#039;Cambria Math&#039;, &#039;Arial Unicode MS&#039;, sans-serif; font-size: 16px; line-height: 23.68px; word-spacing: -1.24453px;&quot;&gt;&amp;nbsp;bitter taste receptor gene in the Neandertal individual, which likely would have resulted in a non-functional protein and inter-individual PTC (phenylthiocarbamide) taste sensitivity variation, as also observed in both humans and chimpanzees.&lt;/span&gt;&lt;/p&gt;
</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;http://www.sciencedirect.com/science/article/pii/S0047248414002644&lt;/p&gt;
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