Research ArticlesZOOLOGY

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

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Science  12 Dec 2014:
Vol. 346, Issue 6215, 1254449
DOI: 10.1126/science.1254449
  1. Fig. 1 Rates of substitution for ultraconserved elements (UCEs) and fourfold degenerate (4D) sites.

    (A) Inferred amniote phylogeny based on maximum likelihood analysis of partitioned UCE-anchored loci using RAxML v7.3.4 (17). All branches received 100% bootstrap support. Colors indicate the estimated rates, with cooler colors corresponding to lower rates of molecular evolution. (B) Estimated rates of molecular evolution for UCE-anchored loci (left) and 4D sites (right). Red dots indicate the estimated rate for the branch ancestral to the group of interest. The UCE rate for mouse is an outlier and is indicated by a black dot.

  2. Fig. 2 Rates of substitution, micro-indels, and break-point evolution.

    (A) Rates of substitution at 4D sites, transposable elements (TEs), and, for comparison, UCE-anchored loci. Scale bar denotes substitutions per site. (B) Indel rate versus 4D substitutions per site for each extant lineage. (C) Gene synteny breakage rate versus 4D substitutions per site, each measured with respect to either alligator or chicken.

  3. Fig. 3 Relative TE numbers among amniotes.

    Shown are TE copies that predate the speciation of crocodilians and mammals in 16 amniote genomes. The figure displays 55 unrelated TE families present in all amniote genomes. The numbers of bases, on a log scale, identified in each individual genome relative to the average in all 16 genomes are identified. An asterisk indicates that two or more subfamilies were combined to form a single category. See (17) for the full analysis encompassing all 74 TE families.

  4. Fig. 4 OR expansions and contractions within archosaurs.

    Subtrees from neighbor-joining phylogenies of the intact crocodilian (A), avian (B), and testudine (C) OR repertoires. Crocodiles are represented by the gharial, American alligator, and saltwater crocodile; birds are represented by the chicken and zebra finch; and testudines are represented by softshell and green sea turtles. Note the paucity of lineage-specific (colored) clades among crocodilian ORs relative to avian and testudine ORs. Most crocodilian ORs are outparalogs (groups of paralogous genes that emerged prior to the divergence of the species analyzed), whereas the vast majority of avian and testudine ORs fall on monophyletic groups of inparalogs (groups of paralogous genes the emerged after the divergence of the species analyzed). Neighbor-joining trees were inferred using MEGA v5, a Poisson model of substitution; 1000 bootstrap iterations were performed to evaluate support. See also fig. S24.

  5. Fig. 5 Crocodilian genetic diversity and population history.

    (A) Rates of observed heterozygosity within annotated exons, intergenic sequence, and introns. (B and C) PSMC estimates of the historical crocodilian Ne inferred from each genome shown in a time span of 5 million years (B) and 1 million years (C) under the assumption of a generation time of 20 years.

  6. Fig. 6 Analyzing the archosaur assembly.

    (A) Expected base reconstruction accuracy. (B) Total archosaur bases assembled in several annotated functional classes and numbers of bases in each category from the alligator genome.