The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion.

Gene duplication is a source of molecular innovation throughout evolution. However, even with massive amounts of genome sequence data, correlating gene duplication with speciation and other events in natural history can be difficult. This is especially true in its most interesting cases, where rapid and multiple duplications are likely to reflect adaptation to rapidly changing environments and life styles. This may be so for Class I of alcohol dehydrogenases (ADH1s), where multiple duplications occurred in primate lineages in Old and New World monkeys (OWMs and NWMs) and hominoids.To build a preferred model for the natural history of ADH1s, we determined the sequences of nine new ADH1 genes, finding for the first time multiple paralogs in various prosimians (lemurs, strepsirhines). Database mining then identified novel ADH1 paralogs in both macaque (an OWM) and marmoset (a NWM). These were used with the previously identified human paralogs to resolve controversies relating to dates of duplication and gene conversion in the ADH1 family. Central to these controversies are differences in the topologies of trees generated from exonic (coding) sequences and intronic sequences.We provide evidence that gene conversions are the primary source of difference, using molecular clock dating of duplications and analyses of microinsertions and deletions (micro-indels). The tree topology inferred from intron sequences appear to more correctly represent the natural history of ADH1s, with the ADH1 paralogs in platyrrhines (NWMs) and catarrhines (OWMs and hominoids) having arisen by duplications shortly predating the divergence of OWMs and NWMs. We also conclude that paralogs in lemurs arose independently. Finally, we identify errors in database interpretation as the source of controversies concerning gene conversion. These analyses provide a model for the natural history of ADH1s that posits four ADH1 paralogs in the ancestor of Catarrhine and Platyrrhine primates, followed by the loss of an ADH1 paralog in the human lineage

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

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

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

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

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