Positively selected sites under branch-site model for foreground lineages Prob(w>1).

<p>Positively selected sites under branch-site model for foreground lineages Prob(w>1).</p

Functional conserved domains of poly ADP- ribosomal protein 1.

<p>Red star represents positively selected sites in different branches. Highlighted nucleotide alignments represent the positively selected amino acid. Numbers corresponded to amino acid residues at the position of Human PARP1 gene.</p

3D structural analysis for poly ADP- ribosomal protein 2.

<p>(A). Two positively selected sites in fishes for <i>PARP2</i>. (B). The folding pattern were predicted using SWISS-MODEL and electrostatic potential were calculated using the PBEQ-Solver web server. The figures were generated in PyMOL software. Numbers corresponded to positively selected amino acid sites at the position of Human <i>PARP2</i> gene.</p

Gene homologues information for 10 genes in different species.

<p>Gene homologues information for 10 genes in different species.</p

Molecular evolutionary patterns of NAD⁺/Sirtuin aging signaling pathway across taxa

<div><p>A deeper understanding of the conserved molecular mechanisms in different taxa have been made possible only because of the evolutionary conservation of crucial signaling pathways. In the present study, we explored the molecular evolutionary pattern of selection signatures in 51 species for 10 genes which are important components of NAD⁺/Sirtuin pathway and have already been directly linked to lifespan extension in worms and mice. Selection pressure analysis using PAML program revealed that <i>MRPS5</i> and <i>PPARGC1A</i> were under significant constraints because of their functional significance. <i>FOXO3a</i> also displayed strong purifying selection. All three sirtuins, which were <i>SIRT1</i>, <i>SIRT2</i> and <i>SIRT6</i>, displayed a great degree of conservation between taxa, which is consistent with the previous report. A significant evolutionary constraint is seen on the anti-oxidant gene, <i>SOD3</i>. As expected, <i>TP53</i> gene was under significant selection pressure in mammals, owing to its major role in tumor progression. Poly-ADP-ribose polymerase (<i>PARP</i>) genes displayed the most sites under positive selection. Further 3D structural analysis of <i>PARP1</i> and <i>PARP2</i> protein revealed that some of these positively selected sites caused a change in the electrostatic potential of the protein structure, which may allow a change in its interaction with other proteins and molecules ultimately leading to difference in the function. Although the functional significance of the positively selected sites could not be established in the variants databases, yet it will be interesting to see if these sites actually affect the function of <i>PARP1</i> and <i>PARP2</i>.</p></div

Positively selected sites under branch-site model for foreground lineages Prob(w>1).

<p>Positively selected sites under branch-site model for foreground lineages Prob(w>1).</p

Genetic evidence from mitochondrial DNA corroborates the origin of Tibetan chickens

<div><p>Chicken is the most common poultry species and is important to human societies. Tibetan chicken (<i>Gallus gallus domesticus</i>) is a breed endemic to China that is distributed mainly on the Qinghai-Tibet Plateau. However, its origin has not been well characterized. In the present study, we sequenced partial mitochondrial DNA (mtDNA) control region of 239 and 283 samples from Tibetan and Sichuan indigenous chickens, respectively. Incorporating 1091 published sequences, we constructed the matrilineal genealogy of Tibetan chickens to further document their domestication history. We found that the genetic structure of the mtDNA haplotypes of Tibetan chickens are dominated by seven major haplogroups (A-G). In addition, phylogenetic and network analyses showed that Tibetan chickens are not distinguishable from the indigenous chickens in surrounding areas. Furthermore, some clades of Tibetan chickens may have originated from game fowls. In summary, our results collectively indicated that Tibetan chickens may have diverged from indigenous chickens in the adjacent regions and hybridized with various chickens.</p></div

Genetic diversity indices of Tibetan and lowland fowls.

<p>Genetic diversity indices of Tibetan and lowland fowls.</p

Geographical distribution of the major clades of different populations.

<p>Geographical distribution of the major clades of different populations.</p

Maximum parsimony median-joining network of Tibetan chickens with (A) and without the chickens of adjacent regions (B).

<p>The domestic clades (A-H) are labeled. Node sizes are proportional to haplotype frequencies. The lines linking the nodes are proportional to the mutation steps. Black nodes indicate inferred steps not identified in the sampled populations. Colors within the circles represent chickens from different localities.</p