Dataset Information

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

ABSTRACT: Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50?=?26.9?Mb, contig N50?=?36.6?kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.

SUBMITTER: Zepeda Mendoza ML

PROVIDER: S-EPMC5868727 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

Zepeda Mendoza M Lisandra ML Xiong Zijun Z Escalera-Zamudio Marina M Runge Anne Kathrine AK Thézé Julien J Streicker Daniel D Frank Hannah K HK Loza-Rubio Elizabeth E Liu Shengmao S Ryder Oliver A OA Samaniego Castruita Jose Alfredo JA Katzourakis Aris A Pacheco George G Taboada Blanca B Löber Ulrike U Pybus Oliver G OG Li Yang Y Rojas-Anaya Edith E Bohmann Kristine K Carmona Baez Aldo A Arias Carlos F CF Liu Shiping S Greenwood Alex D AD Bertelsen Mads F MF White Nicole E NE Bunce Michael M Zhang Guojie G Sicheritz-Pontén Thomas T Gilbert M P Thomas MPT

Nature ecology & evolution 20180219 4

Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous an ...[more]

PMID: 29459707

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Project description:BackgroundThe common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA) marker and two nuclear markers (RAG2 and DRB) to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat.ResultsFive reciprocally monophyletic clades were evident in the mitochondrial gene tree, and in most cases with high bootstrap support: Central America (CA), Amazon and Cerrado (AMC), Pantanal (PAN), Northern Atlantic Forest (NAF) and Southern Atlantic Forest (SAF). The Atlantic forest clades formed a monophyletic clade with high bootstrap support, creating an east/west division for this species in South America. On the one hand, all coalescent and non-coalescent estimates point to a Pleistocene time of divergence between the clades. On the other hand, the nuclear markers showed extensive sharing of haplotypes between distant localities, a result compatible with male-biased gene flow. In order to test if the disparity between the mitochondrial and nuclear markers was due to the difference in mutation rate and effective size, we performed a coalescent simulation to examine the feasibility that, given the time of separation between the observed lineages, even with a gene flow rate close to zero, there would not be reciprocal monophyly for a neutral nuclear marker. We used the observed values of theta and an estimated mutation rate for the nuclear marker gene to perform 1000 iterations of the simulation. The results of this simulation were inconclusive: the number of iterations with and without reciprocal monophyly of one or more clades are similar.ConclusionsWe therefore conclude that the pattern exhibited by the common vampire bat, with marked geographical structure for a mitochondrial marker and no phylogeographic structure for nuclear markers is compatible with a historical scenario of complete isolation of refuge-like populations during the Pleistocene. The results on demographic history on this species is compatible with the Carnaval-Moritz model of Pleistocene vicariance, with demographic expansions in the southern Atlantic forest.

Dataset Information

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

Publications

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

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