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

BACKGROUND: The 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. RESULTS: Following 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. CONCLUSIONS: From 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.

Patterns of gut bacterial colonization in three primate species.

Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.

Life history traits, maternal behavior and infant development of blue-eyed black lemurs (Eulemur flavifrons).

An understanding of recruitment is important for estimating population growth and viability, and their implications for conservation. We present the first results regarding the life history, maternal behavior and infant development of the critically endangered blue-eyed black lemur (Eulemur flavifrons) of Madagascar. The species breeds seasonally, with births occurring at the end of the dry season, between late August and October. Over two successive birth seasons in 2006 and 2007, we observed a total of 13 lactating females and 22 infants from six groups. We inferred age at first reproduction as 3 years, and calculated the birth rate as 1.0 infant per female per year with a mean inter-birth interval of 358 ± 24.81 days (319-410 days). Infants spent the first 3 weeks of life constantly with their mothers; locomotor independence and ingestion of solid food began at week 10, and the infants were weaned by week 25. After week 28, infants spent less than 20% of their time in contact with their mothers. Over the study period infant mortality was 22.7%, with predation and sickness observed as causes. Our results suggest that overall recruitment is relatively slow, which has implications for the species' survival, particularly given their restricted and threatened habitat.

Life history traits and parental care in Lepilemur ruficaudatus.

In this study we investigated the importance of biparental care for the evolution and/or maintenance of pair-living in red-tailed sportive lemurs (Lepilemur ruficaudatus), a nocturnal folivorous lemur. Between 2000 and 2005, we collected data on life history traits from a total of 14 radio-collared pairs of adults and their offspring in Kirindy forest, western Madagascar. Predation rate varied between years with a minimum of 0% and a maximum of 40% per year. Patterns of parental care were quantified during simultaneous focal observations of both pair-partners in 2003 and 2004. Mating activity was limited to the months of May and June, as indicated by conspicuous changes of vulval morphology and male mate guarding behavior. After a gestation length of about 5 months, which is much longer than expected for a lemur of this body mass, single infants were born in November. Lactation lasted for about 50 days. Apart from lactation, females provided infant care by warming, grooming and transporting infants orally. Infants were parked in dense vegetation while females foraged. Males were seen only rarely in proximity to infants and we found no evidence for direct infant care provided by social fathers. We conclude that the necessity of direct infant care cannot explain the evolution and/or maintenance of pair-living in Lepilemur ruficaudatus.

Schultz's unruly rule: dental developmental sequences and schedules in small-bodied, folivorous lemurs.

Schultz's rule (as reconstructed by Smith) states that there is a relationship between the pattern (or relative order) of eruption of molar versus secondary (replacement) teeth and the overall pace (or absolute timing) of growth and maturation. Species with 'fast' life histories (rapid dental development, rapid growth, early sexual maturation, short life spans) are said to exhibit relatively early eruption of the molars and late eruption of the secondary replacement teeth (premolars, canines, incisors), whereas species with 'slow' life histories are said to exhibit relatively late eruption of the molars and early eruption of the secondary dentition. In a recent review, B.H. Smith noted that primates with tooth combs might violate this rule because tooth combs tend to erupt early, regardless of the pace of life history. We show that exceptions to Schultz's rule among lemurs are not limited to the relative timing of eruption of the tooth comb. Rather, among lemurs, some species with extremely accelerated dental development exhibit a pattern of eruption of molars and of secondary teeth in direct opposition to the expectations of Schultz's rule. We focus particularly on the pattern (order) and pace (absolute timing) of dental development and eruption in Avahi and Lepilemur - two relatively small, nocturnal folivores with rapid dental development. These taxa differ markedly in their eruption sequences (the premolars erupt after M2 and M3 in Lepilemur but not Avahi ). We offer an explanation for the failure of Schultz's rule to predict these differences. Schultz's rule presumes that eruption timing is dependent on the size of the jaw and that, therefore, molar crown formation and eruption will be delayed in species with slow-growing jaws. We show that a variety of processes (including developmental imbrication) allows the crowns of permanent teeth to form and to erupt into jaws that might appear to be too small to accommodate them.

Developmental morphology of the solum nasi in the mouse lemur (Microcebus murinus).

The solum nasi of Microcebus murinus is characterized by the presence of a zona annularis, continuity between the anterior transverse lamina and the paraseptal cartilage, a continuous paraseptal cartilage, a palatine cartilage and a posterior transverse lamina. It lacks a fibula reuniens and possibly a cartilage of the nasopalatine duct as well as a palatine papillary cartilage. The morphology in M. murinus closely resembles that seen in Tupaia and Galago. This affinity results from the retention of primitive traits. However, Galago is reported to lack a zona annularis, thus displaying a specialization not shared with M. murinus. Therefore, the zona annularis provides a useful trait for distinguishing between the ontogenies of M. murinus and Galago.