MOESM4 of Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

Additional file 4: Figure S2. Comparison of GCG and GCTE in 29 fish species (ray-finned fish and outgroups lancelet Branchiostoma belcheri, lamprey Petromyzon marinus, shark Callorhinchus milii, and coelacanth Latimeria chalumnae) listed in the FishTEDB [36]. In only two species analysed, GCTE (orange) is lower than GCG (blue; A. anguilla and G. morhua). Based on the dataset for Fig. 1c in Additional file 2

MOESM2 of Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

Additional file 2: Table S2. Datasets used for generating Figs. 1, 2, 3, 4 and Additional files 3 and 4: Figures S1-S2

MOESM3 of Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

Additional file 3: Figure S1. Analysis of genome size vs. GCG including salmonids (for comparison with Fig. 1b)

MOESM1 of Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

Additional file 1: Table S1. Species overview and their counts

MOESM5 of Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

Additional file 5: Figure S3. Species-specific comparisons of GCTE between Class I and Class II TEs

Comparison of RE marker support for the possible positions of mousebirds within core landbirds.

<p>The seven alternative groupings are shown in descending order of support and include the mousebird topology of (A), our MPRE tree and the genome-level UCE tree of [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref004" target="_blank">4</a>], (C) the Hackett et al. tree [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref018" target="_blank">18</a>], (D) the main Jarvis et al. tree [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref004" target="_blank">4</a>], (E) two limited retrotransposon studies [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref010" target="_blank">10</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref023" target="_blank">23</a>], and (G) the main McCormack et al. tree [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref020" target="_blank">20</a>]. Blue bold numbers indicate the amount of RE insertion events that are conflict-free with each of the seven alternatives, respectively. Higher-level taxon names are shown for well-supported monophyla, such as the eagles/New World vulture clade (Accipitrimorphae [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref004" target="_blank">4</a>]), the passerine/parrot/falcon/seriema clade (Australaves [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref025" target="_blank">25</a>]), and the woodpecker/bee-eater/hornbill/trogon/cuckoo-roller clade (Coraciimorphae [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref004" target="_blank">4</a>], sensu stricto without mousebird). The bird paintings were generated by Jon Fjeldså (used with permission).</p

Longer ILS duration of a biallelic polymorphism leads to an exponential increase of hemiplasy.

<p>(A) Illustration of all the RE presence/absence patterns that are theoretically possible after ILS across two to four speciation events (extension of the examples shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.g001" target="_blank">Fig 1C–1E</a>). This permitted us to calculate the amounts of possible character distributions that are incongruent or congruent with the species tree under the observed durations of ILS across up to 17 speciation events (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s011" target="_blank">S5 Table</a>). Note that conflict-free patterns parsimoniously correspond to ILS across one or fewer speciation events. (B) The amount of species tree-congruent patterns increases linearly (2<i>n</i>) with ILS duration. (C) The amount of hemiplasy (i.e., species tree-incongruent patterns) increases exponentially (2^<i>n</i><i>–</i> 2<i>n</i>) with ILS duration. (D) The probability for the occurrence of hemiplasy in a biallelic polymorphism reaches 50% after ILS across three speciation events and 99% after ILS across eleven speciation events (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s011" target="_blank">S5 Table</a>).</p

Phylogenetic tree of rare genomic changes reveals varying degree of incomplete lineage sorting across Neoaves diversification.

<p>(A) The main whole-genome sequence tree from Jarvis et al. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref004" target="_blank">4</a>] mapped with our 2,118 retrotransposon markers (745 incongruent markers; tree length = 5,579; consistency index = 0.40; retention index = 0.64). (B) The same markers mapped on the single MPRE tree (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s002" target="_blank">S2 Data</a>) resulting from analysis of their 2,118 presence/absence patterns (720 incongruent markers; tree length = 5,377; consistency index = 0.41; retention index = 0.66) under Felsenstein’s polymorphism parsimony [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref016" target="_blank">16</a>]. Black branches indicate topological concordances between the MPRE tree and the main Jarvis et al. tree [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref004" target="_blank">4</a>], and discordances are limited to the deepest neoavian internodes (grey dashed branches) and the conflicting position of the mousebird (grey branches). The amount of ILS-free, conflict-free insertion events (blue bold numbers) was identified for each internode, and numbers within doughnut plots indicate counts of ILS-affected RE insertion events leading to the persistence of insertion polymorphisms across two (green), three (orange), or more (red parts of doughnut plots) speciation events. (C–E) Schematic illustration of the different genealogical fates of segregating presence (colored lines) or absence (black lines) alleles following RE insertion (colored circles) in an exemplary five-taxon species tree. We show one respective example for the different degrees of gene tree–species tree conflict that can be caused by incomplete lineage sorting (ILS) across two (C), three (D), or more than three (E) successive speciation events. Incongruence of RE presence/absence patterns (dashed boxes) is illustrated with REs as colored ovals, target site duplications as white squares, and orthologous genomic flanks as black lines. The bird paintings were generated by Jon Fjeldså (used with permission).</p

Dynamics of incomplete lineage sorting and RE insertion rates across the dated main Jarvis et al. tree [4].

<p>Per-branch levels of ILS (A) and RE insertion rates (B) vary considerably across the diversification of Neoaves. We derived these values from mapping our 2,118 RE markers on the main Jarvis et al. tree [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref004" target="_blank">4</a>] (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.g001" target="_blank">Fig 1A</a>). For each branch, percentages of ILS were calculated by dividing the amount of ILS-affected markers by the total amount of markers (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s008" target="_blank">S2 Table</a>). The latter value was then divided by the respective branch length to estimate the RE insertion rate per MY (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s008" target="_blank">S2 Table</a>). Notably, branch length and degree of ILS correlate negatively (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s008" target="_blank">S2 Table</a>) (C), but there is no correlation between branch length and RE insertion rate (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s008" target="_blank">S2 Table</a>) (D) or between degree of ILS and RE insertion rate (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s008" target="_blank">S2 Table</a>) (E). Orange dots denote those branches that are incongruent between the main Jarvis et al. tree [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref004" target="_blank">4</a>] and our MPRE tree (cf. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.g001" target="_blank">Fig 1A and 1B</a>).</p

Phylogenetic network of rare genomic changes reveals three adaptive radiations of Neoaves with varying complexity of genealogical incongruences.

<p>(A) Neighbor-net [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref031" target="_blank">31</a>] analysis of 2,118 RE presence/absence patterns suggests that Neoaves diversification may be more accurately visualized as a largely bifurcating tree with highly reticulate structures at the base of the core landbird radiation and across most of the initial super-radiation. Within the latter, red-brown reticulations highlight bifurcate relationships (cf. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.g001" target="_blank">Fig 1A and 1B</a>) with limited conflict if stretched boxes are longer than they are wide. In contrast, the core waterbird radiation exhibits limited conflict and appears fully bifurcating (cf. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.g001" target="_blank">Fig 1A and 1B</a>). (B–D) Distribution of frequencies of RE markers without and with ILS (i.e., persistence across ≥two speciation events) for each of the three adaptive radiations (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s009" target="_blank">S3 Table</a>). (B) Core waterbird radiation with 18% total ILS, mostly across two speciation events. (C) Core landbird radiation with 27% total ILS, most of which led to weak or moderate conflict via ILS across two to three speciation events. (D) The initial super-radiation exhibits 73% total ILS, almost exclusively with strong discordances caused by persistence of ILS across five or more speciation events.</p