Overview of primate phylogeny.

<p>An overview of primate phylogeny is shown, with the number of <i>ADH1</i> paralogs identified within select taxon indicated by the circled numbers at the leaves of the tree. Black numbers are derived from analysis of public databases, while red numbers were determined from cDNA sequencing reported here. The “4+1” designation for the macaque taxon indicates the presence of four <i>ADH1</i> paralogous genes plus one <i>ADH1</i> pseudogene. The genome sequencing projects are not completed for any lemur, so additional <i>ADH1</i> paralogs may be present (see text).</p

Pairwise distance estimates for orthologous intronic regions in a dataset composed of non-<i>ADH1</i> genes.

<p>Pairwise distance estimates for orthologous intronic regions in a dataset composed of non-<i>ADH1</i> genes.</p

Phylogeny of primate <i>ADH1</i> paralogs.

<p>Phylogeny of primate <i>ADH1</i> paralogs inferred from (A) exonic sequence data (“exonic tree”) and (B) intronic data (“intronic tree”). Parallel black lines indicate bifurcations associated with gene duplications without speciation. <i>ADH1</i> genes from New World monkeys (represented by marmoset) form a separate clade from the hominid/OWM genes in the exonic tree (A), while they interleave with hominid/OWM genes in the intronic tree (B). The lower panels, (C) and (D), redraw the gene tree from (A) and (B) in a species tree format, highlighting where each gene duplication occurs relative to the divergence of each primate lineage. The exonic tree is rooted using multiple non-primate <i>ADH1</i> genes (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041175#pone.0041175.s002" target="_blank">Figure S2</a>). The intronic tree is unrooted (due to ambiguity, see text). The names of <i>ADH1</i> paralogs have been shortened (e.g. the marmoset (<i>Callthrix jacchus</i>) ADH1 paralog “Cal_<i>ADH1.1”</i> is simply referred to as “marmoset ADH1.1”). Numbers at nodes refer to the Bayesian posterior probability values.</p

Estimate of the ADH1 paralog duplications relative to the time of the major primate speciation events.

<p>The average pairwise distances separating the introns of the <i>ADH1</i> paralogs were compared with the average pairwise distances separating a set of introns in paired taxa. (A) This schematic illustrates the various ortholog comparisons used to estimate the relative age among the ADH1 paralogs. (B) This plot summaries the data in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041175#pone-0041175-t002" target="_blank">Table 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041175#pone-0041175-t003" target="_blank">3</a>. The distances among the <i>ADH1</i> paralogs in marmoset, macaque and human (black diamonds) are somewhat larger than those separating catarrhine and platyrrhine orthologs (green circles), implying that these <i>ADH1</i> paralogs diverged (duplicated) before the catarrhine-platyrrhine split. Conversely, distances separating the <i>ADH1</i> paralogs in marmoset, macaque and human are somewhat smaller than those separating orthologous introns among strepsirhine and haplorhine (red squares), implying that these <i>ADH1</i> paralogs diverged after the split between strepsirhine and haplorhine.</p

Average of pairwise distances for ADH1 intronic regions (shown in Table 1) among paralogs and between orthologs.

<p>Average of pairwise distances for ADH1 intronic regions (shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041175#pone-0041175-t001" target="_blank">Table 1</a>) among paralogs and between orthologs.</p

Gene duplication can generate “whole gene” and “chimeric gene” paralogs.

<p>(a) When unequal crossing-over (denoted with an “X”) occurs within the intergenic region between two paralogs, one chromosome gains an extra copy of a paralog, while the other chromosome loses one of the paralogs. This is followed by divergence of each paralog (only shown for the chromosome that gained a paralog and denoted as shift in color). A similar process can lead to the creation of the original paralog duplication, if, for example, transposons generate regions of sequence similarity on either side of a gene, thus enabling unequal crossing-over (not shown). (b) The same process can also lead to a chimeric gene duplicate if the crossing over occurs within the intragenic region (most likely within an intronic region).</p

Pairwise distance estimates of <i>ADH1</i> intronic regions.

<p>Pairwise distance among the <i>ADH1</i> paralogs for the concatenated intronic dataset were calculated using the Maximum Composite Likelihood method implemented by MEGAv4.0. Pairwise distances are shown in the lower left of the table, with variance estimates in the upper right of table.</p

Model of <i>ADH1</i> paralog duplication and subsequent evolution in haplorhines.

<p>Thin vertical black arrows indicate the direction of the chromosome while thick vertical arrows identify ADH genes in the direction of transcription, with <i>ADH1</i> paralogs in primates colored according to the intronic phylogeny in Fig. 2B. Dashed lines connect orthologs. Diagonal lines indicate the proposed phylogeny of haplorrhine <i>ADH1</i> paralogs. The root of the haplorhine <i>ADH1</i> tree is not specified because the duplication order of haplorhine <i>ADH1</i> paralogs is ambiguous (see text). Putative gene conversions are indicated with open circles connected by vertical lines (from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041175#pone-0041175-t004" target="_blank">Table 4</a>).</p

Summary of gene conversion analysis for macaque ADH1 paralogs.

<p>Exonic and intronic data sets were examined for indicators of gene conversion using similarity plots, homoplasic micro-indels, and various computational methods. (A) The figure legend displays the color schemes used in subsequent panels for illustrating pairwise similarity scores among paralogs, and the key used to summarize the results from various methods used to identify potential gene conversions. The names of <i>ADH1</i> paralogs have been shortened (e.g. the macaque (<i>Macaca mullata</i>) <i>ADH1</i> paralog “Mac_<i>ADH1.1</i>” is simply referred to as “Mac 1.1”). Pairwise similarity within a sliding window is plotted for various paralogs within (C) exonic regions (Mac_<i>ADH1.0</i> is not included), (E) intronic regions (without Mac_<i>ADH1.0</i>, the pseudogene), and (F) intronic regions including Mac_<i>ADH1.0</i>. The color of the line in the similarity plot corresponds to the identity of the paralog pair, as indicated in the figure legend (A). Similarity scores for exonic regions are calculated within a 150-nt sliding window, while that of intronic regions are calculated using a 250-nt sliding window. Colored boxes in (B) and (D) indicate putative gene conversion events identified by various computation methods. The color of the box corresponds to the computational method identifying each potential gene conversion, as indicated in the figure legend (A). Boxes with dashed borders indicate gene conversions that were not statistically significant at p-values <0.05, but were identified using p-values <0.10. The paralogs implicated in gene conversion are indicated within (or adjacent to) the colored box using the paralog suffix (e.g a gene conversion between Mac_<i>ADH1.1</i> and Mac_<i>ADH1.2</i> is indicated by “1∶2”). Homoplasic micro-indels in the intronic sequences are shown as vertical black arrows with the paralogs sharing these micro-indels indicated above each each arrow (the many homoplasic micro-indels shared by Mac_<i>ADH1.1</i> and Mac_<i>ADH1.2</i> are simply indicated with grey arrows). Boundaries between introns or exons are demarcated with dotted vertical lines. Green boxes below the similarity plots indicate large gaps in the alignment, with the affected paralog indicated within the box.</p