Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats

Abstract

Background: The New World leaf-nosed bats (Phyllostomids) exhibit a diverse spectrum of feeding habits and innovations in their nutrient acquisition and foraging mechanisms. However, the genomic signatures associated with their distinct diets are unknown.

Results: We conducted a genomic comparative analysis to study the evolutionary dynamics related to dietary diversification and specialization. We sequenced, assembled, and annotated the genomes of five Phyllostomid species: one insect feeder (Macrotus waterhousii), one fruit feeder (Artibeus jamaicensis), and three nectar feeders from the Glossophaginae subfamily (Leptonycteris yerbabuenae, Leptonycteris nivalis, and Musonycteris harrisoni), also including the previously sequenced vampire Desmodus rotundus. Our phylogenomic analysis based on 22,388 gene families displayed differences in expansion and contraction events across the Phyllostomid lineages. Independently of diet, genes relevant for feeding strategies and food intake experienced multiple expansions and signatures of positive selection. We also found adaptation signatures associated with specialized diets: the vampire exhibited traits associated with a blood diet (i.e., coagulation mechanisms), whereas the nectarivore clade shares a group of positively selected genes involved in sugar, lipid, and iron metabolism. Interestingly, in fruit-nectar-feeding Phyllostomid and Pteropodids bats, we detected positive selection in two genes: AACS and ALKBH7, which are crucial in sugar and fat metabolism. Moreover, in these two proteins we found parallel amino acid substitutions in conserved positions exclusive to the tribe Glossophagini and to Pteropodids.

Conclusions: Our findings illuminate the genomic and molecular shifts associated with the evolution of nectarivory and shed light on how nectar-feeding bats can avoid the adverse effects of diets with high glucose content.

Keywords: Adaptation; Comparative genomics; Diet; Parallel evolution; Phyllostomid; Specialization.

Figure 1:

Phyllostomid species. (a) Leptonycteris yerbabuenae, (b) Leptonycteris nivalis, (c) Musonycteris harrisoni, (d) Artibeus jamaicensis, and (e) Macrotus waterhousii. Photo credits: (a-b) Daniel Zamora-Mejías, (c) Rodrigo Medellín-Legorreta, d) Melissa E. Rodríguez, and (e) Wikimedia, public domain.

Figure 2:

Phylogenetic tree constructed with 132 single-copy genes and estimates of divergence times based on 2 fossil records (yellow stars) (see Methods). Based on 22,388 gene families we analysed the number of orthologous families expanded (plus signs, blue) and contracted (minus signs, salmon) across the phylogeny: per node (bars) and per species branch (right), with a P-value ≤ 0.01. Gray bars reflect the divergence time interval based on 95% highest posterior density. MYA: million years ago.

Figure 3:

Positive selection in genes and proteins across the phylogeny of Phyllostomid bats, in comparison to the insect-feeding bat Macrotus waterhousii. Most of the positive selected genes likely contribute to the regulation and processing of (a) muscle and bone development, (b) carbohydrates, (c) lipids, (d) nutrients and food uptake, (e) iron storage and calcium sources, and (f) blood regulation (see gene and protein abbreviations in Supplementary Table S14).

Figure 4:

A subset of genes under positive selection (in red boldface) that are involved in glucose and ketone metabolism in the frugivorous (Aja: A. jamaicensis) and nectar-pollen bats (Mha: M. harrisoni; Lni: L. nivalis; and Lye: L. yerbabuenae). The diagram also identifies adaptative signals for some genes in the vampire D. rotundus (Dro) and the insectivore M. waterhousii (Mwa). The diagram is based on the KEGG metabolic pathways database and a review of the literature (see gene and protein abbreviations in Supplementary Table S8).

Figure 5:

Parallel molecular evolution between Pteropodids (Old World) and Glossophagini (New World) bats, in three genes: AACS, ALBKH7 and UNC-45 B. (a) Phylogeny reconstruction for these three genes by maximum likelihood (using 1,827 amino acids), for 47 mammal species. (b) Ancestral sequence reconstruction (for branches and nodes) to infer parallel substitutions in conserved positions for the three genes. (c) Probability of replacement at each ancestral state node for each sequence position. Amino acid abbreviations: A: alanine (non-polar); T: threonine (polar); Q: glutamine (polar); R: arginine (basic-charged); K: lysine (basic-charged); E: glutamic acid (acidic + charged); S: serine (polar); and L: leucine (non-polar).

Figure 6:

ACCS protein structure. (a) 3D structure of ACCS protein for L. yerbabuenae. (b) In gray: ACCS 3D structure consensus (M. waterhousii and D. rotundus). In blue: α-helix structures shared only for the 3 Glossophagini nectar-pollen feeders (M. harrisoni, L. nivalis, and L. yerbabuenae). In yellow: β-strand shared only between M. harrisoni and P. alecto (Pteropodid bat). RMSD score (protein 3D superposition and alignment) between pairs of species (see Supplementary Table S10).