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	<title>bioRxiv Channel: Society for Molecular Biology and Evolution #SMBE2016</title>
	<link>https://biorxiv.org</link>
	<description>
	This feed contains articles for bioRxiv Channel "Society for Molecular Biology and Evolution #SMBE2016"
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	<item rdf:about="https://biorxiv.org/cgi/content/short/008979v1?rss=1">
<title>
<![CDATA[
Evolving mutation rate advances invasion speed of sexual species 
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</title>
<link>
https://biorxiv.org/cgi/content/short/008979v1?rss=1"
</link>
<description><![CDATA[
Many species are shifting their ranges in response to global climate change. The evolution of dispersal during range expansion increases invasion speed, provided that a species can adapt sufficiently fast to novel local conditions. Mutation rates can evolve too, under conditions that favor an increased rate of adaptation. However, evolution at the mutator gene has thus far been deemed of minor importance in sexual populations due to its dependence on genetic hitchhiking with a beneficial mutation at a gene under selection, and thus its sensitivity to recombination. Here we use an individual-based model to show that the mutator gene and the gene under selection can be effectively linked at the population level during invasion. This causes the evolutionary increase of mutation rates in sexual populations, even if they are not linked at the individual level. The observed evolution of mutation rate is adaptive and clearly advances range expansion both through its effect on the evolution of dispersal rate, and the evolution of local adaptation. In addition, we observe the evolution of mutation rates in a spatially stable population under strong directional selection, but not when we add variance to the mean selection pressure. By this we extend the existing theory on the evolution of mutation rates, which is generally thought to be limited to asexual populations, with possibly far-reaching consequences concerning invasiveness and the rate at which species can adapt to novel environmental conditions as experienced under global climate change.
]]></description>
<dc:creator>Marleen M. P. Cobben</dc:creator>
<dc:creator>Alexander Kubisch</dc:creator>
<dc:creator></dc:creator>
<dc:date>2014-09-11</dc:date>
<dc:identifier>doi:10.1101/008979</dc:identifier>
<dc:title><![CDATA[Evolving mutation rate advances invasion speed of sexual species]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2014-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/cgi/content/short/047266v1?rss=1">
<title>
<![CDATA[
Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe. 
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</title>
<link>
https://biorxiv.org/cgi/content/short/047266v1?rss=1"
</link>
<description><![CDATA[
Large structural variations (SVs) in the genome are harder to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. Here we analyze the effects of SVs on gene expression, quantitative traits, and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalog of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) frequently segregate within closely related clonal populations, are weakly linked to single nucleotide polymorphisms (SNPs), and show other genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits such as cell shape, cell growth under diverse conditions, sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases.
]]></description>
<dc:creator>Daniel Charlton Jeffares</dc:creator>
<dc:creator>Clemency Jolly</dc:creator>
<dc:creator>Mimoza Hoti</dc:creator>
<dc:creator>Doug Speed</dc:creator>
<dc:creator>Charalampos Rallis</dc:creator>
<dc:creator>Liam Shaw</dc:creator>
<dc:creator>Francois Balloux</dc:creator>
<dc:creator>Christophe Dessimoz</dc:creator>
<dc:creator>Jurg Bahler</dc:creator>
<dc:creator>Fritz Sedlazeck</dc:creator>
<dc:creator></dc:creator>
<dc:date>2016-04-13</dc:date>
<dc:identifier>doi:10.1101/047266</dc:identifier>
<dc:title><![CDATA[Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2016-04-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/cgi/content/short/044941v1?rss=1">
<title>
<![CDATA[
Detection of pathways affected by positive selection in primate lineages ancestral to humans 
]]>
</title>
<link>
https://biorxiv.org/cgi/content/short/044941v1?rss=1"
</link>
<description><![CDATA[
Gene set enrichment approaches have been increasingly successful in finding signals of recent polygenic selection in the human genome. In this study, we aim at detecting biological pathways affected by positive selection in more ancient human evolutionary history. Focusing on four branches of the primate tree that lead to modern humans, we tested all available protein coding gene trees of the Primates clade for signals of adaptation in these branches, using the likelihood-based branch site test of positive selection. The results of these locus-specific tests were then used as input for a gene set enrichment test, where whole pathways are globally scored for a signal of positive selection, instead of focusing only on outlier "significant" genes. We identified signals of positive selection in several pathways that are mainly involved in immune response, sensory perception, metabolism, and energy production. These pathway-level results are highly significant, even though there is no functional enrichment when only focusing on top scoring genes. Interestingly, several gene sets are found significant at multiple levels in the phylogeny, but different genes are responsible for the selection signal in the different branches. This suggests that the same function has been optimized in different ways at different times in primate evolution.
]]></description>
<dc:creator>Josephine Daub</dc:creator>
<dc:creator>Sebastien Moretti</dc:creator>
<dc:creator>Iakov Igorevich Davydov</dc:creator>
<dc:creator>Laurent Excoffier</dc:creator>
<dc:creator>Marc Robinson-Rechavi</dc:creator>
<dc:creator></dc:creator>
<dc:date>2016-03-21</dc:date>
<dc:identifier>doi:10.1101/044941</dc:identifier>
<dc:title><![CDATA[Detection of pathways affected by positive selection in primate lineages ancestral to humans]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2016-03-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/cgi/content/short/059089v1?rss=1">
<title>
<![CDATA[
Uniparental inheritance promotes adaptive evolution in cytoplasmic genomes 
]]>
</title>
<link>
https://biorxiv.org/cgi/content/short/059089v1?rss=1"
</link>
<description><![CDATA[
1Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes--specifically their organization into host cells and their uniparental (maternal) inheritance--enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Mullers ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes--despite their asexual mode of reproduction--can readily undergo adaptive evolution.
]]></description>
<dc:creator>Joshua R Christie</dc:creator>
<dc:creator>Madeleine Beekman</dc:creator>
<dc:creator></dc:creator>
<dc:date>2016-06-15</dc:date>
<dc:identifier>doi:10.1101/059089</dc:identifier>
<dc:title><![CDATA[Uniparental inheritance promotes adaptive evolution in cytoplasmic genomes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2016-06-15</prism:publicationDate>
<prism:section></prism:section>
</item>
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