Species-level view of population structure and gene flow for a critically endangered primate (Varecia variegata)

Terrain Ruggedness and Canopy Height Predict Short-Range Dispersal in the Critically Endangered Black-and-White Ruffed Lemur

Dispersal is a fundamental aspect of primates' lives and influences both population and community structuring, as well as species evolution. Primates disperse within an environmental context, where both local and intervening environmental factors affect all phases of dispersal. To date, research has primarily focused on how the intervening landscape influences primate dispersal, with few assessing the effects of local habitat characteristics. Here, we use a landscape genetics approach to examine between- and within-site environmental drivers of short-range black-and-white ruffed lemur (Varecia variegata) dispersal in the Ranomafana region of southeastern Madagascar. We identified the most influential drivers of short-range ruffed lemur dispersal as being between-site terrain ruggedness and canopy height, more so than any within-site habitat characteristic evaluated. Our results suggest that ruffed lemurs disperse through the least rugged terrain that enables them to remain within their preferred tall-canopied forest habitat. Furthermore, we noted a scale-dependent environmental effect when comparing our results to earlier landscape characteristics identified as driving long-range ruffed lemur dispersal. We found that forest structure drives short-range dispersal events, whereas forest presence facilitates long-range dispersal and multigenerational gene flow. Together, our findings highlight the importance of retaining high-quality forests and forest continuity to facilitate dispersal and maintain functional connectivity in ruffed lemurs.

The mitochondrial DNA diversity of captive ruffed lemurs (Varecia spp.): implications for conservation

Ruffed lemurs (Varecia variegata and Varecia rubra) are categorized as Critically Endangered on the IUCN Red List, and genetic studies are needed for assessing the conservation value of captive populations. Using 280 mitochondrial DNA (mtDNA) D-loop sequences, we studied the genetic diversity and structure of captive ruffed lemurs in Madagascar, Europe and North America. We found 10 new haplotypes: one from the European captive V. rubra population, three from captive V. variegata subcincta (one from Europe and two from Madagascar) and six from other captive V. variegata in Madagascar. We found low mtDNA genetic diversity in the European and North American captive populations of V. variegata. Several founder individuals shared the same mtDNA haplotype and therefore should not be assumed to be unrelated founders when making breeding recommendations. The captive population in Madagascar has high genetic diversity, including haplotypes not yet identified in wild populations. We determined the probable geographical provenance of founders of captive populations by comparison with previous studies; all reported haplotypes from captive ruffed lemurs were identical to or clustered with haplotypes from wild populations located north of the Mangoro River in Madagascar. Effective conservation strategies for wild populations, with potentially unidentified genetic diversity, should still be considered the priority for conserving ruffed lemurs. However, our results illustrate that the captive population in Madagascar has conservation value as a source of potential release stock for reintroduction or reinforcement projects and that cross-regional transfers within the global captive population could increase the genetic diversity and therefore the conservation value of each regional population.

Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis

Australian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.

HEALTH ASSESSMENT OF BLACK-AND-WHITE RUFFED LEMURS (VARECIA VARIEGATA) IN RANOMAFANA NATIONAL PARK, MADAGASCAR

The Anthropocene is a major threat to biodiversity worldwide. Human pressures including climate change and emerging infectious diseases are presenting new challenges to wildlife, requiring vigilance and monitoring of wild populations to ensure their persistence. In order to monitor fluctuations in health, baseline data from long-term studies are required. Clinical laboratory data on 80 black-and-white ruffed lemurs (Varecia variegata), derived from the capture of 98 individuals spanning six field seasons are presented. Serum biochemical profiles showed variation between years that remained within published reference intervals for the species, with the exception of total bilirubin in 2008, and creatine kinase and chloride in 2019. Serum trace minerals and fat-soluble vitamin values also fluctuated between years and are within ranges seen in other lemur species. These results, combined with previously published data on ectoparasite load and population genetic diversity, suggest that the Mangevo ruffed lemur population is healthy and can provide important and valuable baseline data for comparisons moving forward.

Primate landscape genetics: A review and practical guide

Landscape genetics is an emerging field that integrates population genetics, landscape ecology, and spatial statistics to investigate how geographical and environmental features and evolutionary processes such as gene flow, genetic drift, and selection structure genetic variation at both the population and individual levels, with implications for ecology, evolution, and conservation biology. Despite being particularly well suited for primatologists, this method is currently underutilized. Here, we synthesize the current state of research on landscape genetics in primates. We begin by outlining how landscape genetics has been used to disentangle the drivers of diversity, followed by a review of how landscape genetic methods have been applied to primates. This is followed by a section highlighting special considerations when applying the methods to primates, and a practical guide to facilitate further landscape genetics studies using both existing and de novo datasets. We conclude by exploring future avenues of inquiry that could be facilitated by recent developments as well as underdeveloped applications of landscape genetics to primates.

Genetic population structure of endangered ring-tailed lemurs (Lemur catta) from nine sites in southern Madagascar

Madagascar's ring-tailed lemurs (Lemur catta) are experiencing rapid population declines due to ongoing habitat loss and fragmentation, as well as increasing exploitation for bushmeat and the illegal pet trade. Despite being the focus of extensive and ongoing behavioral studies, there is comparatively little known about the genetic population structuring of the species. Here, we present the most comprehensive population genetic analysis of ring-tailed lemurs to date from across their likely remaining geographic range. We assessed levels of genetic diversity and population genetic structure using multilocus genotypes for 106 adult individuals from nine geographically representative localities. Population structure and F ST analyses revealed moderate genetic differentiation with localities being geographically partitioned into northern, southern, western and also potentially central clusters. Overall genetic diversity, in terms of allelic richness and observed heterozygosity, was high in the species (AR = 4.74, H O = 0.811). In fact, it is the highest among all published lemur estimates to date. While these results are encouraging, ring-tailed lemurs are currently affected by ongoing habitat fragmentation and occur at lower densities in poorer quality habitats. The effects of continued isolation and fragmentation, coupled with climate-driven environmental instability, will therefore likely impede the long-term viability of the species.

Do functional traits offset the effects of fragmentation? The case of large-bodied diurnal lemur species

Primates worldwide are faced with increasing threats making them more vulnerable to extinction. Anthropogenic disturbances, such as habitat degradation and fragmentation, are among the main concerns, and in Madagascar, these issues have become widespread. As this situation continues to worsen, we sought to understand how fragmentation affects primate distribution throughout the island. Further, because species may exhibit different sensitivity to fragmentation, we also aimed to estimate the role of functional traits in mitigating their response. We collated data from 32 large-bodied lemur species ranges, consisting of species from the families Lemuridae (five genera) and Indriidae (two genera). We fitted Generalized Linear Models to determine the role of habitat fragmentation characteristics, for example, forest cover, patch size, edge density, and landscape configuration, as well as the protected area (PA) network, on the species relative probability of presence. We then assessed how the influence of functional traits (dietary guild, home range size) mitigate the response of species to these habitat metrics. Habitat area had a strong positive effect for many species, and there were significantly negative effects of fragmentation on the distribution of many lemur species. In addition, there was a positive influence of PAs on many lemur species' distribution. Functional trait classifications showed that lemurs of all dietary guilds are negatively affected by fragmentation; however, folivore-frugivores show greater flexibility/variability in terms of habitat area and landscape complexity compared to nearly exclusive folivores and frugivores. Furthermore, species of all home range sizes showed a negative response to fragmentation, while habitat area had an increasingly positive effect as home range increased in size. Overall, the general trends for the majority of lemur species are dire and point to the need for immediate actions on a multitude of fronts, most importantly landscape-level reforestation efforts.

Anthropogenic pressures drive population genetic structuring across a Critically Endangered lemur species range

In recent decades Madagascar has experienced significant habitat loss and modification, with minimal understanding of how human land use practices have impacted the evolution of its flora and fauna. In light of ongoing and intensifying anthropogenic pressures, we seek new insight into mechanisms driving genetic variability on this island, using a Critically Endangered lemur species, the black-and-white ruffed lemur (Varecia variegata), as a test case. Here, we examine the relative influence of natural and anthropogenic landscape features that we predict will impose barriers to dispersal and promote genetic structuring across the species range. Using circuit theory, we model functional connectivity among 18 sampling localities using population-based genetic distance (FST). We optimized resistance surfaces using genetic algorithms and assessed their performance using maximum-likelihood population-effects mixed models. The best supported resistance model was a composite surface that included two anthropogenic features, habitat cover and distance to villages, suggesting that rapid land cover modification by humans has driven change in the genetic structure of wild lemurs. Primary conservation priority should be placed on mitigating further forest loss and connecting regions identified as having low dispersal potential to prevent further loss of genetic diversity and promote the survival of other moist forest specialists.

Challenges of next-generation sequencing in conservation management: Insights from long-term monitoring of corridor effects on the genetic diversity of mouse lemurs in a fragmented landscape

Long-term genetic monitoring of populations is essential for efforts aimed at preserving genetic diversity of endangered species. Here, we employ a framework of long-term genetic monitoring to evaluate the effects of fragmentation and the effectiveness of the establishment of corridors in restoring population connectivity and genetic diversity of mouse lemurs Microcebus ganzhorni. To this end, we supplement estimates of neutral genetic diversity with the assessment of adaptive genetic variability of the major histocompatibility complex (MHC). In addition, we address the challenges of long-term genetic monitoring of functional diversity by comparing the genotyping performance and estimates of MHC variability generated by single-stranded conformation polymorphism (SSCP)/Sanger sequencing with those obtained by high-throughput sequencing (next-generation sequencing [NGS], Illumina), an issue that is particularly relevant when previous work serves as a baseline for planning management strategies that aim to ensure the viability of a population. We report that SSCP greatly underestimates individual diversity and that discrepancies in estimates of MHC diversity attributable to the comparisons of traditional and NGS genotyping techniques can influence the conclusions drawn from conservation management scenarios. Evidence of migration among fragments in Mandena suggests that mouse lemurs are robust to the process of fragmentation and that the effect of corridors is masked by ongoing gene flow. Nonetheless, results based on a larger number of shared private alleles at neutral loci between fragment pairs found after the establishment of corridors in Mandena suggest that gene flow is augmented as a result of enhanced connectivity. Our data point out that despite low effective population size, M. ganzhorni maintains high individual heterozygosity at neutral loci and at MHC II DRB gene and that selection plays a predominant role in maintaining MHC diversity. These findings highlight the importance of long-term genetic monitoring in order to disentangle between the processes of drift and selection maintaining adaptive genetic diversity in small populations.

Ectoparasitism in Black-and-White Ruffed Lemurs ( Varecia variegata) in Southeastern Madagascar

We documented ectoparasites found on wild black-and-white ruffed lemurs ( Varecia variegata) in the southeastern rain forests of Madagascar and describe trends in parasitism. In this study, 235 mesostigmatid mites (1 male, 87 females, 147 nymphs) identified as Liponyssella sp., in the acarine family Macronyssidae, were collected during 87% (34/39) of lemur examinations (mean number/host=7.9). The only other ectoparasite collected was the louse fly ( Allobosca crassipes; 3 males, 8 females) in the dipteran family Hippoboscidae, which was collected during 26% (10/39) of lemur examinations (mean number/host=1.1). The lemur most heavily parasitized by mites was an adult female with 29 adult females and 17 nymphs, all collected from the face.

Sex-biased dispersal of human ancestors

Some anthropologists and primatologists have argued that, judging by extant chimpanzees and humans, which are female-biased dispersers, the common ancestors of humans and chimpanzees were also female-biased dispersers. It has been thought that sex-biased dispersal patterns have been genetically transmitted for millions of years. However, this character has changed many times with changes in environment and life-form during human evolution and historical times. I examined life-form and social organization of nonhuman primates, among them gatherers (foragers), hunter-gatherers, agriculturalists, industrialists, and modern and extant humans. I conclude that dispersal patterns changed in response to environmental conditions during primate and human evolution.

Of lemurs and louse flies: The biogeochemical and biotic effects of forest disturbance on Propithecus edwardsi and its obligate ectoparasite Allobosca crassipes in Ranomafana National Park, southeastern Madagascar

From alleles to ecosystems and landscapes, anthropogenic activity continues to affect the environment, with particularly adverse effects on biodiversity hotspots such as Madagascar. Selective logging has been proposed as a "win-win" conservation strategy, yet its effects on different components of biodiversity are still not fully understood. Here we examine biotic factors (i.e., dietary differences) that may be driving differences in biogeochemical stocks between disturbed and undisturbed forests. We present the stable nitrogen (δ¹⁵ N) and carbon (δ¹³ C) isotope composition of hair from the lemur Propithecus edwardsi and of whole bodies of its obligate ectoparasite, the louse-fly Allobosca crassipes, from sites in Ranomafana National Park (RNP) that are comparable except for the history of logging and subsequent forest regeneration. P. edwardsi and A. crassipes from the disturbed (i.e., heavily selectively logged) site are lower in ¹⁵ N and ¹³ C relative to P. edwardsi and A. crassipes from sites that were minimally selectively logged or not commercially logged at all. There is a ∼3‰ decrease in ¹⁵ N between disturbed and undisturbed sites that corresponds to a difference of nearly a full trophic level. Flowers from Bakerella clavata, a staple food source for P. edwardsi in disturbed habitats and a fallback food for P. edwardsi in primary forests, were also analyzed isotopically. B. clavata is δ¹⁵ N-depleted in both disturbed and undisturbed sites. Data from longitudinal behavioral surveys of P. edwardsi in RNP and other forests in eastern Madagascar point to significant differences in consumption patterns of B. clavata, with P. edwardsi in disturbed forests consuming almost twice as much of this plant. Depletion of ¹⁵ N in animal tissues is a complex issue, but likely the result of the interaction of physiological and ecological factors. Anthropogenic disturbance in RNP from selective logging has had both biotic and biogeochemical effects that are observable trophically.

Large-Scale Habitat Corridors for Biodiversity Conservation: A Forest Corridor in Madagascar

In biodiversity conservation, habitat corridors are assumed to increase landscape-level connectivity and to enhance the viability of otherwise isolated populations. While the role of corridors is supported by empirical evidence, studies have typically been conducted at small spatial scales. Here, we assess the quality and the functionality of a large 95-km long forest corridor connecting two large national parks (416 and 311 km²) in the southeastern escarpment of Madagascar. We analyze the occurrence of 300 species in 5 taxonomic groups in the parks and in the corridor, and combine high-resolution forest cover data with a simulation model to examine various scenarios of corridor destruction. At present, the corridor contains essentially the same communities as the national parks, reflecting its breadth which on average matches that of the parks. In the simulation model, we consider three types of dispersers: passive dispersers, which settle randomly around the source population; active dispersers, which settle only in favorable habitat; and gap-avoiding active dispersers, which avoid dispersing across non-habitat. Our results suggest that long-distance passive dispersers are most sensitive to ongoing degradation of the corridor, because increasing numbers of propagules are lost outside the forest habitat. For a wide range of dispersal parameters, the national parks are large enough to sustain stable populations until the corridor becomes severely broken, which will happen around 2065 if the current rate of forest loss continues. A significant decrease in gene flow along the corridor is expected after 2040, and this will exacerbate the adverse consequences of isolation. Our results demonstrate that simulation studies assessing the role of habitat corridors should pay close attention to the mode of dispersal and the effects of regional stochasticity.

MHC class II variation in a rare and ecological specialist mouse lemur reveals lower allelic richness and contrasting selection patterns compared to a generalist and widespread sympatric congener

The polymorphism of immunogenes of the major histocompatibility complex (MHC) is thought to influence the functional plasticity of immune responses and, consequently, the fitness of populations facing heterogeneous pathogenic pressures. Here, we evaluated MHC variation (allelic richness and divergence) and patterns of selection acting on the two highly polymorphic MHC class II loci (DRB and DQB) in the endangered primate Madame Berthe’s mouse lemur (Microcebus berthae). Using 454 pyrosequencing, we examined MHC variation in a total of 100 individuals sampled over 9 years in Kirindy Forest, Western Madagascar, and compared our findings with data obtained previously for its sympatric congener, the grey mouse lemur (Microcebus murinus). These species exhibit a contrasting ecology and demography that were expected to affect MHC variation and molecular signatures of selection. We found a lower allelic richness concordant with its low population density, but a similar level of allelic divergence and signals of historical selection in the rare feeding specialist M. berthae compared to the widespread generalist M. murinus. These findings suggest that demographic factors may exert a stronger influence than pathogen-driven selection on current levels of allelic richness in M. berthae. Despite a high sequence similarity between the two congeners, contrasting selection patterns detected at DQB suggest its potential functional divergence. This study represents a first step toward unravelling factors influencing the adaptive divergence of MHC genes between closely related but ecologically differentiated sympatric lemurs and opens new questions regarding potential functional discrepancy that would explain contrasting selection patterns detected at DQB.