REHH of the core haplotypes on chromosome 20 and <i>GDF5</i>.

<p>REHH distributions at (A) 300 kb, (B) 500 kb, and (C) 1000 kb upstream and downstream of the core haplotypes. The two lines represent the 99% and 95% percentile rank values. Big dots are the major haplotype at the <i>GDF5</i> gene. (D) REHH of the major core haplotype at the <i>GDF5</i> gene at varying physical distances (kb).</p

Population statistics summary of exon1 region.

<p>The bolds are values significantly lower than 0 with P-value<0.05 by simulating human demographic history incorporating human best-fit model.</p>a<p>is the number of chromosomes.</p

Population statistics summary of haplotypes carrying derived allele A and ancestral allele G of SNP rs143384.

<p>Bolds are values significantly lower than 0 with P-value<0.05 detected by DnaSP v 5.0 program.</p>a<p>European population contains only one haplotype carrying derived allele of rs143384.</p

Fst distribution of SNPs across chromosome 20 gene regions.

<p>(A): Fst among the three populations vs minor allele frequencies (MAF). Big green dot and triangle represent SNPs rs143383 and rs143384. (B) Fst between East Asians and Europeans vs minor allele frequencies (MAF). (C) Fst between East Asians and Africans vs minor allele frequencies (MAF). (D) Fst between Africans and Europeans vs minor allele frequencies (MAF). (E) Sliding window analysis of Fst. Purple, black, brown and gray lines represent Fst among the three populations, Fst between East Asians and Africans, Fst between Africans and Europeans, Fst between East Asians and Europeans, respectively. The vertical line represents the position of <i>GDF5</i> gene. Black and brown horizontal lines represent the 95% percentile rank values of Fst values between East Asians and Africans and Fst between Africans and Europeans, respectively.</p

Median-joining phylogenetic network of the 16 haplotypes at at the exon 1 region.

<p>Each haplotype is represented by a circle with its area proportional to its frequency. The ancestral haplotype is outlined by a black line. The two haplotypes in the ellipse are the haplotypes that carry the derived allele at SNPs rs143383 and rs143384.</p

Evaluation of the ages of the derived alleles of SNPs rs143383 and rs143384 by linear regression of −ln(EHH) and 2r.

<p>Evaluation of the ages of the derived alleles of SNPs rs143383 and rs143384 by linear regression of −ln(EHH) and 2r.</p

Genome-Wide Scan for Bats and Dolphin to Detect Their Genetic Basis for New Locomotive Styles

<div><p>For most mammals, running is their major locomotive style, however, cetaceans and bats are two mammalian groups that have independently developed new locomotive styles (swimming and flying) from their terrestrial ancestors. In this study, we used a genome-wide comparative analysis in an attempt to identify the selective imprint of the development of new locomotive styles by cetaceans and bats to adapt to their new ecological niches. We found that an elevated proportion of mitochondrion-associated genes show evidence of adaptive evolution in cetaceans and on the common ancestral lineage leading to bats, compared to other terrestrial mammals. This result is consistent with the fact that during the independent developments of swimming and flying in these two groups, the changes of energy metabolism ratios would be among the most important factors to overcome elevated energy demands. Furthermore, genes that show evidence of sequence convergence or parallel evolution in these two lineages were overrepresented in the categories of energy metabolism, muscle contraction, heart, and glucose metabolism, genes that perform functions which are essential for locomotion. In conclusion, our analyses showed that on the dolphin and bat lineages, genes associated with locomotion not only both show a greater propensity to adaptively evolve, but also show evidence of sequence convergence, which likely reflects a response to a common requirement during their development of these two drastic locomotive styles.</p> </div

The analyses of selective pressures on energy metabolism genes.

<p>(A) Species tree that was used as the guide tree for the selection analyses. CA bat is the common ancestor of bats; (B) Proportion of energy metabolism genes with given <i>dN/dS</i> ratios for lineages leading to eight mammals and the common ancestor of bats (CA bat).</p