The evolution of extinction risk: past and present anthropogenic impacts on the primate communities of Madagascar

Habitat use by the island lemurs of Nosy Be, Madagascar

Madagascar's lemurs are threatened by forest loss, fragmentation, and degradation. Many species use flexible behaviors to survive in degraded habitat, but their ability to persist in very small areas may be limited. Insular lemurs, like those found on Nosy Be, an island off the northwestern coast of Madagascar, are at heightened risk of sudden population declines and extirpation. Nosy Be is home to two Critically Endangered species-the endemic Nosy Be sportive lemur (Lepilemur tymerlachsoni) and Claire's mouse lemur (Microcebus mamiratra)-as well as the Endangered black lemur (Eulemur macaco). Most of the remaining forest on Nosy Be is protected by the 862-ha Lokobe National Park. To document how Nosy Be lemurs use their restricted habitat, we conducted vegetation and reconnaissance surveys on 53 transects in and around Lokobe. We collected data on tree size, canopy cover, understory visibility, and elevation for 248 lemur sightings. We used a spatially explicit, multi-species occupancy model to investigate which forest-structure variables are important to lemurs. Our results represent some of the first data on habitat use by insular lemurs. Black lemurs preferred significantly larger trees and areas with less dense understory. They also occurred significantly less outside of Lokobe National Park, even when accounting for sampling effort and geography. The distributions of the sportive and mouse lemurs were not related to the forest structure variables we documented, but they did negatively predict each other-perhaps because their habitat requirements differ. These results also underscore the importance of the national park to protecting the black lemur population on Nosy Be and raise questions about what factors do influence the distribution of Nosy Be's smaller lemurs. Close monitoring is needed to prevent these populations and the ecosystem services they provide from disappearing, as have other island lemurs.

Social-Ecological Interactions Influencing Primate Harvest: Insights From Madagascar

Globally, non-human primates face mounting threats due to unsustainable harvest by humans. There is a need to better understand the diverse drivers of primate harvest and the complex social-ecological interactions influencing harvest in shared human-primate systems. Here, we take an interdisciplinary, systems approach to assess how complex interactions among primate biological and ecological characteristics and human social factors affect primate harvest. We apply our approach through a review and synthesis of the literature on lemur harvest in Madagascar, a country with one of the highest primate species richness in the world coupled with high rates of threatened primate species and populations in decline. We identify social and ecological factors affecting primate harvest, including the characteristics of lemurs that may make them vulnerable to harvest by humans; factors describing human motivations for (or deterrents to) harvest; and political and governance factors related to power and accessibility. We then discuss social-ecological interactions that emerge from: (1) the prevalence of informal institutions (e.g., cultural taboos), (2) adoption of human predatory strategies, (3) synergies with habitat use and habitat loss, and (4) interactions among regional- and local-scale factors (multi-level interactions). Our results illustrate that social-ecological interactions influencing lemur harvest in Madagascar are complex and context-specific, while influenced by a combination of interactions between species-specific characteristics and human social factors. These context-specific interactions may be also influenced by local-level cultural practices, land use change, and effects from regional-level social complexities such as political upheaval and food insecurity. We conclude by discussing the importance of identifying and explicitly accounting for nuances in underlying social-ecological systems and putting forth ideas for future research on primate harvest in shared human-primate systems, including research on social-ecological feedbacks and the application of Routine Activities Theory.

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.

Lemur catta in small forest fragments: Which variables best predict population viability?

Habitat fragmentation is an increasingly serious issue affecting primates in most regions where they are found today. Populations of Lemur catta (ring-tailed lemur) in Madagascar's south-central region are increasingly restricted to small, isolated forest fragments, surrounded by grasslands or small-scale agriculture. Our aim was to evaluate the potential for population viability of L. catta in nine forest fragments of varying sizes (2-46 ha, population range: 6-210 animals) in south-central Madagascar, using a set of comparative, quantitative ecological measures. We used Poisson regression models with a log link function to examine the effects of fragment size, within-fragment food availability, and abundance of matrix resources (food and water sources) on L. catta population sizes and juvenile recruitment. We found a strong association between overall population size and (a) fragment size and (b) abundance of key food resources Melia azedarach and Ficus spp. (per 100 m along transect lines). Juvenile recruitment was also associated with fragment size and abundance of the two above-mentioned food resources. When the largest population, an outlier, was removed from the analysis, again, the model containing fragment size and abundance of M. azedarach and Ficus spp. was the best fitting, but the model that best predicted juvenile recruitment contained only fragment size. While our results are useful for predicting population presence and possible persistence in these fragments, both the potential for male dispersal and the extent of human disturbance within most fragments play crucial roles regarding the likelihood of long-term L. catta survival. While seven of the nine fragments were reasonably protected from human disturbance, only three offered the strong potential for male dispersal, thus the long-term viability of many of these populations is highly uncertain.

Effects of Environmental Stress on Primate Populations

Environmental stress on primate populations can take many forms. Abiotic factors, such as temperature and precipitation, may directly influence the behavior of primates owing to physiological demands of thermoregulation or through indirect influences on vegetation that primates rely on for food. These effects can also scale up to the macro scale, impacting primate distributions and evolution. Primates also encounter stress during interactions within and between species (i.e., biotic interactions). For example, selective pressure from male-perpetrated infanticide can drive the development of female counterstrategies and can impact life-history traits. Predation on primates can modify group size, ranging behavior, and habitat use. Finally, humans have influenced primate populations for millennia. More recently, hunting, habitat disturbance, disease, and climate change have increased in frequency and severity with detrimental impacts on primate populations worldwide. These effects and recent evidence from camera traps emphasize the importance of maintaining protected areas for conserving primate populations.

New evidence of megafaunal bone damage indicates late colonization of Madagascar

The estimated period in which human colonization of Madagascar began has expanded recently to 5000-1000 y B.P., six times its range in 1990, prompting revised thinking about early migration sources, routes, maritime capability and environmental changes. Cited evidence of colonization age includes anthropogenic palaeoecological data 2500-2000 y B.P., megafaunal butchery marks 4200-1900 y B.P. and OSL dating to 4400 y B.P. of the Lakaton'i Anja occupation site. Using large samples of newly-excavated bone from sites in which megafaunal butchery was earlier dated >2000 y B.P. we find no butchery marks until ~1200 y B.P., with associated sedimentary and palynological data of initial human impact about the same time. Close analysis of the Lakaton'i Anja chronology suggests the site dates <1500 y B.P. Diverse evidence from bone damage, palaeoecology, genomic and linguistic history, archaeology, introduced biota and seafaring capability indicate initial human colonization of Madagascar 1350-1100 y B.P.

Protected area coverage of threatened vertebrates and ecoregions in Peru: Comparison of communal, private and state reserves

Protected areas (PAs) are a conservation mainstay and arguably the most effective conservation strategy for species protection. As a 'megadiverse' country, Peru is a priority for conservation actions. Peruvian legislation allows for the creation of state PAs and private/communal PAs. Using publicly available species distribution and protected area data sets we evaluated the coverage of Threatened terrestrial vertebrate species distributions and ecoregions provided by both kinds of PA in Peru. Peru's state PA system covers 217,879 km² and private/communal PAs cover 16,588 km². Of the 462 species of Threatened and Data Deficient species we evaluated, 75% had distributions that overlapped with at least one PA but only 53% had ≥10% of their distributions within PAs, with inclusion much reduced at higher coverage targets. Of the species we evaluated, 118 species are only found in national PAs and 29 species only found in private/communal PAs. Of the 17 terrestrial ecoregions found in Peru all are represented in PAs; the national PA system included coverage of 16 and private/communal PAs protect 13. One ecoregion is only protected in private/communal PAs, whereas four are only covered in national PAs. Our results show the important role private/communal PAs can play in the protection of ecological diversity.

Does the primate pattern hold up? Testing the functional significance of infraorbital foramen size variation among marsupials

OBJECTIVES

The relative size of the infraorbital foramen (IOF) has been used to infer the ecology of extinct primates for several decades. Primates have relatively smaller IOFs than most other mammals, which may result from the fact that they pre-process and manipulate food with their hands rather than their muzzles. In primates, relative IOF area co-varies with diet, where insectivores and folivores have relatively smaller IOFs than frugivores. We wanted to determine whether the observed patterns associated with IOF variation hold across other orders.

MATERIALS AND METHODS

We examined how relative IOF area differs among marsupials occupying different ecological niches. Marsupials were chosen because they converge with primates in both ecology and morphology, but unlike primates, some marsupials approach and pre-process foods only with their muzzles. We measured IOF area and cranial lengths from 72 marsupial species, and behavioral feeding data were obtained from a subset of this sample (N = 20).

RESULTS

Relative IOF area did not vary significantly between substrate preferences. However, relative IOF area differed significantly by diet category (P < 0.001). Species that specialize in feeding on non-grassy leaves have significantly smaller relative IOF areas than species which primarily feed on grasses, insects, vertebrates, or some combination thereof. Behavioral analyses support that folivorous marsupials approach and remove food with the hands more often than marsupials from other dietary groups.

DISCUSSION

Results suggest that relatively small IOF area may reflect increased reliance on the hands while feeding, and that relative IOF size can be used as an indicator of feeding behavior.

Hunting, Exotic Carnivores, and Habitat Loss: Anthropogenic Effects on a Native Carnivore Community, Madagascar

The wide-ranging, cumulative, negative effects of anthropogenic disturbance, including habitat degradation, exotic species, and hunting, on native wildlife has been well documented across a range of habitats worldwide with carnivores potentially being the most vulnerable due to their more extinction prone characteristics. Investigating the effects of anthropogenic pressures on sympatric carnivores is needed to improve our ability to develop targeted, effective management plans for carnivore conservation worldwide. Utilizing photographic, line-transect, and habitat sampling, as well as landscape analyses and village-based bushmeat hunting surveys, we provide the first investigation of how multiple forms of habitat degradation (fragmentation, exotic carnivores, human encroachment, and hunting) affect carnivore occupancy across Madagascar's largest protected area: the Masoala-Makira landscape. We found that as degradation increased, native carnivore occupancy and encounter rates decreased while exotic carnivore occupancy and encounter rates increased. Feral cats (Felis species) and domestic dogs (Canis familiaris) had higher occupancy than half of the native carnivore species across Madagascar's largest protected landscape. Bird and small mammal encounter rates were negatively associated with exotic carnivore occupancy, but positively associated with the occupancy of four native carnivore species. Spotted fanaloka (Fossa fossana) occupancy was constrained by the presence of exotic feral cats and exotic small Indian civet (Viverricula indica). Hunting was intense across the four study sites where hunting was studied, with the highest rates for the small Indian civet (mean=90 individuals consumed/year), the ring-tailed vontsira (Galidia elegans) (mean=58 consumed/year), and the fosa (Cryptoprocta ferox) (mean=31 consumed/year). Our modeling results suggest hunters target intact forest where carnivore occupancy, abundance, and species richness, are highest. These various anthropogenic pressures and their effects on carnivore populations, especially increases in exotic carnivores and hunting, have wide-ranging, global implications and demand effective management plans to target the influx of exotic carnivores and unsustainable hunting that is affecting carnivore populations across Madagascar and worldwide.

Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar

We performed a population genomics study of the aye-aye, a highly specialized nocturnal lemur from Madagascar. Aye-ayes have low population densities and extensive range requirements that could make this flagship species particularly susceptible to extinction. Therefore, knowledge of genetic diversity and differentiation among aye-aye populations is critical for conservation planning. Such information may also advance our general understanding of Malagasy biogeography, as aye-ayes have the largest species distribution of any lemur. We generated and analyzed whole-genome sequence data for 12 aye-ayes from three regions of Madagascar (North, West, and East). We found that the North population is genetically distinct, with strong differentiation from other aye-ayes over relatively short geographic distances. For comparison, the average FST value between the North and East aye-aye populations--separated by only 248 km--is over 2.1-times greater than that observed between human Africans and Europeans. This finding is consistent with prior watershed- and climate-based hypotheses of a center of endemism in northern Madagascar. Taken together, these results suggest a strong and long-term biogeographical barrier to gene flow. Thus, the specific attention that should be directed toward preserving large, contiguous aye-aye habitats in northern Madagascar may also benefit the conservation of other distinct taxonomic units. To help facilitate future ecological- and conservation-motivated population genomic analyses by noncomputational biologists, the analytical toolkit used in this study is available on the Galaxy Web site.

Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region

The impact of climate change and anthropogenic deforestation on biodiversity is of growing concern worldwide. Disentangling how past anthropogenic and natural factors contributed to current biome distribution is thus a crucial issue to understand their complex interactions on wider time scales and to improve predictions and conservation strategies. This is particularly important in biodiversity hotspots, such as Madagascar, dominated by large open habitats whose origins are increasingly debated. Although a dominant narrative argues that Madagascar was originally entirely covered by woodlands, which were destroyed by humans, a number of recent studies have suggested that past climatic fluctuations played a major role in shaping current biome distributions well before humans arrived. Here, we address the question of the origin of open habitats in the Daraina region in northern Madagascar, using a multiproxy approach combining population genetics modeling and remote-sensing analyses. We show that (i) contrary to most regions of Madagascar, the forest cover in Daraina remained remarkably stable over the past 60 y, and (ii) the golden-crowned sifaka (Propithecus tattersalli), a forest-dwelling lemur, underwent a strong population contraction before the arrival of the first humans, hence excluding an anthropogenic cause. Prehuman Holocene droughts may have led to a significant increase of grasslands and a reduction in the species' habitat. This contradicts the prevailing narrative that land cover changes are necessarily anthropogenic in Madagascar but does not preclude the later role played by humans in other regions in which recent lemur bottlenecks have been observed.

Leaf nutritional quality as a predictor of primate biomass: further evidence of an ecological anomaly within prosimian communities in Madagascar

The correlation between the biomass of forest primates and a chemical index of the average nutritional quality of leaves in tropical forests has been repeatedly documented since 1990. We tested the role played by protein : fibre on lemur biomass in a gallery forest in southern Madagascar. Plant species abundance was determined based on transect censuses. We calculated an average ratio of protein-to-fibre in leaves and an abundance-weighted ratio, i.e. the mean weighted by the basal area of tree species, to be compared with the figures available for other forest ecosystems in Madagascar and a number of anthropoid habitats. Lemur densities were evaluated through compilation of previous studies made from prior to 1975 and up until 2011 based on strip censuses and/or identification of all groups supplemented with new censuses. A high mean ratio of protein to fibre (> 0.4) supports high folivore biomass at 390 kg km−2 (reaching 630 kg km−2 in the closed-canopy forest area) compared with primate communities in other Malagasy forests (protein : fibre: < 0.5; folivore biomass: < 440 kg km−2), as predicted. However, the data corroborate the finding that the total biomass of lemur communities as well as the biomass of folivorous lemur species are low compared with those of African and Asian primate communities for a given protein : fibre ratio. Tree diversity and leaf production do not consistently explain this pattern. In contrast, the extinction of large folivorous lemurs during the past two millennia presumably allowed too little time for smaller-sized species to evolve equally effective morphological and physiological specializations for processing a large range of fibrous foods.

Population genetics and abundance of the Endangered grey-headed lemurEulemur cinereicepsin south-east Madagascar: assessing risks for fragmented and continuous populations

Knowledge of both population size and genetic diversity is critical for assessing extinction risk but few studies include concurrent estimates of these two components of population biology. We conducted an investigation of population density and size, and genetic variation and past demographic events, of the Endangered grey-headed lemurEulemur cinereicepsin south-east Madagascar. We estimated lemur density using line-transect surveys and used satellite imagery to calculate forest fragment area in three localities. We collected tissue samples from 53 individuals and used 26 polymorphic microsatellite loci to obtain measures of population structure (divergence and diversity) across these localities. We tested the probability of past bottleneck events using three models. Contrary to expectation, there were no significant differences in population density across localities. Genetic diversity decreased, but not significantly, with decreasing habitat area and population size. We found a higher likelihood of past bottleneck events in the fragmented coastal populations. The low population size and prior decline in diversity in coastal patches are consistent with their isolation, anthropogenic disturbance, and exposure to cyclone activity. The similarities in the estimates of density between continuous and fragmented sites may indicate recent population growth in the fragments but these populations nevertheless remain at risk from reduced levels of genetic variation. These patterns should be confirmed with more extensive sampling across the limited range ofE. cinereiceps.

Evidence for dietary niche separation based on infraorbital foramen size variation among subfossil lemurs

The size of the infraorbital foramen (IOF) has been used in drawing both phylogenetic and ecological inferences regarding fossil taxa. Within the order Primates, frugivores have relatively larger IOFs than folivores or insectivores. This study uses relative IOF size in lemurs to test prior trophic inferences for subfossil lemurs and to explore the pattern of variation within and across lemur families. The IOFs of individuals belonging to 12 extinct lemur species were measured and compared to those of extant Malagasy strepsirhines. Observations matched expectations drawn from more traditional approaches (e.g. dental morphology and microwear, stable isotope analysis) remarkably well. We confirm that extinct lemurs belonging to the families Megaladapidae and Palaeopropithecidae were predominantly folivorous and that species belonging to the genus Pachylemur (Lemuridae) were frugivores. Very high values for relative IOF area in Archaeolemur support frugivory but are also consistent with omnivory, as certain omnivores use facial touch cues while feeding. These results provide additional evidence that the IOF can be used as an informative osteological feature in both phylogenetic and paleoecological interpretations of the fossil record.

Testing for a historical population bottleneck in wild Verreaux's sifaka (Propithecus verreauxi verreauxi) using microsatellite data

The degree to which historical human activities negatively impacted past and present lemur species is a long-standing question in primatology. At present, most evidence addressing this issue comes from archaeology, paleontology, and behavioral studies. Genetic data provide another source of evidence. In this study, six microsatellite loci, genotyped on more than 360 wild Verreaux's sifaka, are used in order to test the hypothesis that this population experienced a population bottleneck in the last 2000 years. Excess heterozygosity is compared with the heterozygosity expected under mutation-drift equilibrium in order to test for the genetic signature of a rapid population contraction in the past. The results indicate that the sifaka population did not experience a population bottleneck. Various methodological and conceptual implications of this result are discussed.

Biodiversity, phylogeography, biogeography and conservation: lemurs as an example

The lemurs of Madagascar represent a spectacular example of adaptive radiation among primates. Given the special setting under which they evolved (i.e. long isolation, geographical location, geological relief), they provide excellent models for study in many realms, and at different levels and scales, including diversity. At the same time, they occur in a 'hottest hot spot' region for biodiversity conservation. Although there is no single definition of biodiversity, the most commonly used units to measure biodiversity are species-species richness, species abundance and, for conservation purposes in particular, species endemism. However, what a species actually is or how, precisely, it should be defined are unresolved issues. Many species concepts have been proposed and several have been used in primatology in recent years. Nowadays, one of the more common approaches to measuring diversity, and eventually inferring species status, is to look at genetic diversity as reflected by mitochondrial DNA differences. Not enough attention has been paid, however, to the different levels at which genetic differences may occur. Lemurs provide instructive examples to highlight the questions involved in species recognition and definition. Using lemurs as examples, I will highlight the strengths and limitations of some analytical tools, including phylogeography and cladistic biogeography and, I will, in particular, emphasize the questions arising at the interface of scientific and conservation perceptions, both of which influence decisions in the field of biodiversity preservation.