Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Abstract

BackgroundThe greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution.ResultsFollowing whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19 k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~ 900,000 to one million individuals) between approximately 60,000–90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp.ConclusionsFrom our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60–90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~ 1700 km2. The decline in effective population size of 89–99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4841-4) contains supplementary material, which is available to authorized users.

Comparative genomic analysis of sifakas ( Propithecus ) reveals selection for folivory and high heterozygosity despite endangered status

“…A slow and steady population decline need not be accompanied by a reduction in heterozygosity, however, as numerous demographic and genetic factors (mutation rate, dispersal distance, overlapping generations, subpopulation connectivity, and admixture) can blur the relationship between past demographic events and genetic diversity ( 58 ). This trend of steady declines in IICR during the late Pleistocene is consistent with some demographic reconstructions of other lemur species using whole-genome sequence data ( 59 – 61 ). These declines have been attributed to a drying climate and resulting loss of prime forest habitat ( 59 , 60 , 62 ).…”

An empirical estimate of the generation time of mouse lemurs

“…Previously used generation times in this taxon vary considerably ranging from 1 year (e.g. G. L. Olivieri, Sousa, Chikhi, & Radespiel, ; Schad, Ganzhorn, & Sommer, ) approximating the age at first reproduction (Perret, ; Radespiel & Zimmermann, ; Zimmermann & Radespiel, ) to 3.0–4.5 years which was a previous rough estimate of the average length of the reproductive career in the wild (Hawkins et al, ; Yoder et al, ). Mouse lemurs ( Microcebus spp.)…”

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“…Finally, our findings are particularly relevant in the context of Madagascar where habitats are increasingly fragmented and many species have been losing genetic diversity (Craul et al 2009;Bailey et al 2016;Hawkins et al 2018;Vieilledent et al 2018). The effect of ecological disturbance on social structure in Malagasy species is not well studied.…”