Phylogenetic tree for the 175 jawed vertebrate species considered in this study.

<p>Sequences were obtained from the NCBI Taxonomy Browser and edited with Figtree and hitmap for the presence of <i>PAX</i> genes. The dashed red line indicates the relationship suggested by Crawford et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073560#pone.0073560-Modesto1" target="_blank">[46]</a>.</p

Branch-site clade model D values for ω (dN/dS ratio) estimated for 2 site classes.

*<p>Degrees of freedom: 2; LRT: 2Δl = 2(l 1− l 0);</p

Evolutionary History of Chordate <i>PAX</i> Genes: Dynamics of Change in a Complex Gene Family

<div><p>Paired box (<i>PAX</i>) genes are transcription factors that play important roles in embryonic development. Although the <i>PAX</i> gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of <i>PAX</i> genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of <i>PAX</i> sequences from 188 chordates, which revealed restricted variation. The absence of <i>PAX4</i> and <i>PAX8</i> among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in <i>PAX4</i>, <i>PAX7</i>, and <i>PAX8</i>. This result indicates asymmetric evolution of <i>PAX</i> family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.</p></div

Synteny and neighborhood status for the <i>PAX4</i> and <i>PAX6</i> genes.

<p>Synteny and neighborhood status for the <i>PAX4</i> and <i>PAX6</i> genes.</p

Frequencies of the rs1815739 derived allele in autochthonous populations pooled into seven geographical groups.

<p>Frequencies of the rs1815739 derived allele in autochthonous populations pooled into seven geographical groups.</p

Differing Evolutionary Histories of the <i>ACTN3*R577X</i> Polymorphism among the Major Human Geographic Groups

<div><p>It has been proposed that the functional <i>ACTN3*R577X</i> polymorphism might have evolved due to selection in Eurasian human populations. To test this possibility we surveyed all available population-based data for this polymorphism and performed a comprehensive evolutionary analysis of its genetic diversity, in order to assess the action of adaptive and random mechanisms on its variation across human geographical distribution. The derived <i>577X</i> allele increases in frequency with distance from Africa, reaching the highest frequencies on the American continent. Positive selection, detected by an extended haplotype homozygosisty test, was consistent only with the Eurasian data, but simulations with neutral models could not fully explain the results found in the American continent. It is possible that particularities of Native American population structure could be responsible for the observed allele frequencies, which would have resulted from a complex interaction between selective and random factors.</p></div

Demographic models used for the coalescent simulations: A—population split at T₂ with two derived populations of the same size; B—population split at T₂ with two derived populations with ratio between their effective population sizes (N_EF) equal to 0.15; C—population split at T₂ with two derived populations with the ratio between their N_EFs equal to 0.06 at T₂ and 0.15 presently (T₀); D—same as model B, but with population substructure arising at T₁ in both derived populations; E—same as model C, but with population substructure arising at T₁ in both derived populations.

<p>The number of demes depicted does not correspond to the actual simulations. For further details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115449#sec002" target="_blank">methods</a> section.</p

Oxytocin and arginine vasopressin systems in the domestication process

<div><p>Abstract Domestication is of unquestionable importance to the technological revolution that has given rise to modern human societies. In this study, we analyzed the DNA and protein sequences of six genes of the oxytocin and arginine vasopressin systems (OXT-OXTR; AVP-AVPR1a, AVPR1b and AVPR2) in 40 placental mammals. These systems play an important role in the control of physiology and behavior. According to our analyses, neutrality does not explain the pattern of molecular evolution found in some of these genes. We observed specific sites under positive selection in AVPR1b (ω = 1.429, p = 0.001) and AVPR2 (ω= 1.49, p = 0.001), suggesting that they could be involved in behavior and physiological changes, including those related to the domestication process. Furthermore, AVPR1a, which plays a role in social behavior, is under relaxed selective constraint in domesticated species. These results provide new insights into the nature of the domestication process and its impact on the OXT-AVP system.</p></div

Oxytocin and arginine vasopressin systems in the domestication process

<div><p>Abstract Domestication is of unquestionable importance to the technological revolution that has given rise to modern human societies. In this study, we analyzed the DNA and protein sequences of six genes of the oxytocin and arginine vasopressin systems (OXT-OXTR; AVP-AVPR1a, AVPR1b and AVPR2) in 40 placental mammals. These systems play an important role in the control of physiology and behavior. According to our analyses, neutrality does not explain the pattern of molecular evolution found in some of these genes. We observed specific sites under positive selection in AVPR1b (ω = 1.429, p = 0.001) and AVPR2 (ω= 1.49, p = 0.001), suggesting that they could be involved in behavior and physiological changes, including those related to the domestication process. Furthermore, AVPR1a, which plays a role in social behavior, is under relaxed selective constraint in domesticated species. These results provide new insights into the nature of the domestication process and its impact on the OXT-AVP system.</p></div

Derived¹ allele frequencies and AMOVA results.

<p>¹Defined in comparison with the Chimpanzee sequence. For the loci in <b>bold</b> deviations from Hardy-Weinberg Equilibrium were detected.</p><p>²The number of individuals vary according to the investigated locus. ND: No data available.</p><p>Derived<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137823#t001fn001" target="_blank">¹</a> allele frequencies and AMOVA results.</p