Hominids adapted to metabolize ethanol long before human-directed fermentation

Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate-ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol

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

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

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

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

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