Diet and the evolution of ADH7 across seven orders of mammals

Abstract

Dietary variation within and across species drives the eco-evolutionary responsiveness of genes necessary to metabolize nutrients and other components. Recent evidence from humans and other mammals suggests that sugar-rich diets of floral nectar and ripe fruit have favoured mutations in, and functional preservation of, the ADH7 gene, which encodes the ADH class 4 enzyme responsible for metabolizing ethanol. Here we interrogate a large, comparative dataset of ADH7 gene sequence variation, including that underlying the amino acid residue located at the key site (294) that regulates the affinity of ADH7 for ethanol. Our analyses span 171 mammal species, including 59 newly sequenced. We report extensive variation, especially among frugivorous and nectarivorous bats, with potential for functional impact. We also report widespread variation in the retention and probable pseudogenization of ADH7. However, we find little statistical evidence of an overarching impact of dietary behaviour on putative ADH7 function or presence of derived alleles at site 294 across mammals, which suggests that the evolution of ADH7 is shaped by complex factors. Our study reports extensive new diversity in a gene of longstanding ecological interest, offers new sources of variation to be explored in functional assays in future study, and advances our understanding of the processes of molecular evolution.

Keywords: alcohol dehydrogenase; comparative genetics; dietary adaptation; ethanol metabolism; mammals.

Figure 1.

Frugivory and/or nectarivory has evolved repeatedly in mammalian evolution. Images are examples of frugivorous/ nectarivorous species across six orders of mammals: (top left) Rodentia, variegated squirrel (Sciurus variegatoides), image by Amanda Melin; (top middle) Carnivora, kinkajou (Potus flavos), image by Kids Saving the Rainforest; (top right) Primates, Geoffroy's spider monkey (Ateles geoffroyi), image by Amanda Melin; (lower left) Didelphimorphia, woolly opossum (Caluromus derbianus), image by Christian Ziegler, reproduced with permission; (lower middle) Chiroptera, a Seba's short-tailed bat (Carollia perspicillata), image by Roberto Leonan Morim Novaes, reproduced with permission; (lower right) Scandentia, a pen-tailed treeshrew (Ptilocercus lowii), image shared with permission by Annette Zitzmann.

Figure 2.

Evolutionary history of ADH7 in mammals included in this study. Per cent fruit and/or nectar included in a species' diet is indicated in the first row of tip annotations. The second row indicates whether any substitutions away from the ancestral alanine are found at site 294 of ADH7 and the third row indicates whether the gene is putatively functional or pseudogenized. Red boxes with the letter psi (ψ) indicate the inferred lineage in which gene loss events occurred, based on putatively shared loss-of-function mutations. Phylogeny via TimeTree ([41]; http://timetree.org), plotted with the R package ggtree [42].

Figure 3.

Results of the phylogenetic generalized linear models used to test if a frugivorous and/or nectarivorous diet correlates with amino acid substitutions at site 294 of the ADH class IV enzyme (encoded within exon 7 of ADH7) (a) in mammals overall and (b) in bats only, and (c) if a frugivorous and/or nectarivorous diet correlates with ADH7 gene retention. For each prediction we ran two phylogenetic generalized linear models, the MPLE and the IG10 logistic regression. The slope and p-values for each method are in blue (for the MPLE method) and yellow (for the IG10 method) on each plot. Diet and genotypes of the species included are shown in black, with size of the dot indicating sample size.