Dietary flexibility of the greater bamboo lemur (Prolemur simus), a specialized feeder, in eastern Madagascar.

The degree of dietary flexibility in primates is species specific; some incorporate a wider array of resources than others. Extreme interannual weather variability in Madagascar results in seasonal resource scarcity which has been linked to specialized behaviors in lemurs. Prolemur simus, for example, has been considered an obligate specialist on large culm bamboo with >60% of its diet composed of woody bamboos requiring morphological and physiological adaptations to process. Recent studies reported an ever-expanding list of dietary items, suggesting that this species may not be an obligate specialist. However, long-term quantitative feeding data are unavailable across this species' range. To explore the dietary flexibility of P. simus, we collected data at two northern sites, Ambalafary and Sahavola, and one southern site, Vatovavy, from September 2010 to January 2016 and May 2017 to September 2018, respectively. In total, we recorded 4022 h of behavioral data using instantaneous sampling of adult males and females from one group in Ambalafary, and two groups each in Sahavola and Vatovavy. We recorded 45 plant species eaten by P. simus over 7 years. We also observed significant differences in seasonal dietary composition between study sites. In Ambalafary, bamboo was the most frequently observed resource consumed (92.2%); however, non-bamboo resources comprised nearly one-third of the diet of P. simus in Sahavola and over 60% in Vatovavy. Consumption of all bamboo resources increased during the dry season at Ambalafary and during the wet season at Vatovavy, but never exceeded non-bamboo feeding at the latter. Culm pith feeding was only observed at Ambalafary, where it was more common during the dry season. We identify P. simus as a bamboo facultative specialist capable of adjusting its feeding behavior to its environment, indicating greater dietary flexibility than previously documented, which may enable the species to survive in increasingly degraded habitats.

Losing lemurs: Declining populations and land cover changes over space and time.

Forest loss and degradation due to land cover changes imperil biodiversity worldwide. Subtropical and tropical ecosystems experience high deforestation rates, negatively affecting species like primates. Madagascar's endemic lemurs face exceptionally high risks of population declines and extirpation. We examined how short-term land cover changes within a fragmented landscape in southeastern Madagascar impacted the density of lemur species. Using line transects, we assessed density changes in nine lemur species across five forest fragments. Diurnal surveys were conducted monthly from 2015 to 2019 on 35 transects (total effort = 1268 km). Additionally, 21 transects were surveyed nocturnally in 2015 and 2016 (total effort = 107.5 km). To quantify forest cover changes, we generated land use/land cover (LULC) maps from Sentinel-2 imagery using supervised classification for each year. For the LULC maps, we overlayed species-specific buffers around all transects and calculated the proportion of land cover classes within them. We observed declines in the annual densities of four diurnal and cathemeral lemur species between 2015 and 2019, with species-specific declines of up to 80% (Varecia variegata). While the density of two nocturnal species decreased, one increased fivefold (Cheirogaleus major) between 2015 and 2016. By 2019, Grassland was the dominant land type (50%), while Paddy Fields had the smallest coverage (1.03%). Mature Agricultural Land increased the most (63.37%), while New Agricultural Land decreased the most (-66.36%). Unexpectedly, we did not find evidence that higher forest cover supported a higher lemur population density within sampled areas, but we found support for the negative impact of degraded land cover types on three lemur species. Our study underscores the urgent need to address land-use changes and their repercussions for primate populations in tropical ecosystems. The diverse responses of lemur species to modified habitats highlight the complexity of these impacts and emphasize the importance of targeted conservation efforts.

Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi.

No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal "subfossil" remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests.

Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component of the pre-human Central Highlands vegetation. Consequently, there is now vigorous debate regarding the extent to which these grasslands have expanded due to anthropogenic pressures. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, making them a valuable indicator species. Population divergences among forest-dwelling mammals will reflect changes to their habitat, including fragmentation, whereas patterns of post-divergence gene flow can reveal formerly wooded migration corridors. To explore these patterns, we used RADseq data to infer population genetic structure, demographic models of post-divergence gene flow, and population size change through time. The results offer evidence that open habitats are an ancient component of the Central Highlands, and that widespread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may already be vulnerable from paleoclimatic conditions.

Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent.

Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we investigate mouse lemur diversity in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for two pairs of sister lineages that include three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among the two pairs of lineages. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the species-level distinction of two previously described species, M. mittermeieri and M. lehilahytsara is not supported-a result that is particularly striking when using the genealogical discordance index (gdi). Nonsister lineages occur sympatrically in two of the localities sampled for this study, despite an estimated divergence time of less than 1 Ma. This suggests rapid evolution of reproductive isolation in the focal lineages and in the mouse lemur clade generally. The divergence time estimates reported here are based on the MSC calibrated with pedigree-based mutation rates and are considerably more recent than previously published fossil-calibrated relaxed-clock estimates. We discuss the possible explanations for this discrepancy, noting that there are theoretical justifications for preferring the MSC estimates in this case. [Cryptic species; effective population size; microendemism; multispecies coalescent; speciation; species delimitation.].

The influence of seasonality, anthropogenic disturbances, and cyclonic activity on the behavior of northern sportive lemurs (Lepilemur septentrionalis) at Montagne des Français, Madagascar.

Anthropogenic tropical deforestation and degradation imminently threaten primates today. Primates living in these disturbed habitats may also be subjected to increasingly severe tropical storms such as cyclones or hurricanes. These disturbances pose an immediate risk to their livelihood and can dramatically alter their habitats, in turn potentially shifting behavioral patterns. We had the unique opportunity to study the effects of seasonality, anthropogenic disturbances, and the immediate effects of a cyclone on the behavior of the critically endangered northern sportive lemur (NSL) in an anthropogenically disturbed forest in Madagascar. Cyclone Enawo made landfall on March 7, 2017 in northeast Madagascar with sustained wind speeds of 230 km/h. We collected behavioral data on nine individual NSLs during both wet and dry seasons, before and after Cyclone Enawo, and in areas of differing human activity, using scan sampling at 5-min intervals. We ran generalized linear mixed models to test the effects of seasonality and disturbances on behavior. We found that NSLs spent more time feeding in dry months compared with wet (Z = -4.21, p < 0.001). More specifically, they spent more time-consuming leaves and vine species in the dry season (Z = -2.26, p = 0.02; Z = -2.3; p = 0.02). We also found that NSLs were observed at lower heights in trees after the cyclone (Z = -2.45; p = 0.016) and spent more time in the interior portions of trees (Z = 3.44; p < 0.001), perhaps due to extensive limb damage of emergent trees documented after the cyclone. Our analyses show that seasonality affected most aspects of NSL behavior, followed by the effects of Cyclone Enawo, with anthropogenic disturbances having little effect. Our data suggest that the behavioral flexibility of NSLs in response to predictable seasonality may enable them to respond similarly to stochastic climatic disturbances. However, their generalist diet may allow them to persist in anthropogenically disturbed landscapes without the need to greatly alter their behavior.

Locomotion of an adult female and juvenile male aye-aye (Daubentonia madagascariensis) in Torotorofotsy, Madagascar.

Aye-ayes (Daubentonia madagascariensis) locate and acquire invertebrates from within woody substrates at all levels of the rainforest; yet how their locomotion helps them accommodate this diet has not been explored in detail. We studied the locomotor behavior of an adult female (N = 1,085) and juvenile male (N = 708) aye-aye in the undisturbed forest of Torotorofotsy, Madagascar from May to December 2017. We used bout sampling to record locomotion during foraging and travel of the two radio-collared individuals. We used χ 2 tests to compare overall locomotion, travel, and foraging, as well as strata and support use. We performed a correspondence analysis to examine relationships between individual behaviors, strata, and support types. Leaping accounted for 47.9% and 50.1% of all locomotor activity in the adult female and juvenile male, respectively. Leaping was the most common behavior during travel in both individuals (59.2% and 53.9%, respectively), whereas head-first descent was most frequent during foraging (35.0% and 48.0%, respectively). For all three locomotor categories, the main canopy (40.3%-79.6%) was used most frequently and trunks were the most frequently used support type (50.7%-60.0%). There is a strong association between strata and support use overall and during travel. Quadrupedal walking was significantly associated with the main canopy, as was head-first descent with the low canopy. Our analysis demonstrates that aye-ayes use a variety of locomotor behaviors to forage for invertebrates. Aye-ayes' ability to repurpose their positional repertoire to acquire other resources in degraded forests should not obscure the importance of invertebrates to this species.

Lemur paparazzi: Arboreal camera trapping and occupancy modeling as conservation tools for monitoring threatened lemur species.

Primate species face growing risks of extinction throughout the world. To better protect their populations, effective monitoring techniques are needed. The goal of this study was to evaluate the use of arboreal camera traps and occupancy modeling as conservation tools for threatened lemur species. This project aimed to (1) estimate the occupancy and detection probabilities of lemur species, (2) investigate factors potentially affecting lemur habitat use, and (3) determine whether ground or arboreal cameras are better for surveying lemur assemblages. We conducted camera trapping research in five forest fragments (total trap nights = 1770; 900 arboreal trap nights (134 photo events); 870 ground trap nights (2 photo events)) and reforestation areas (total trap nights = 608; 1 photo event) in Kianjavato, Madagascar from May to September 2019. We used arboreal trap data from fragments to estimate occupancy for five species: the red-fronted brown lemur (Eulemur rufifrons; ψ = 0.54 ± SD 0.03), Jolly's mouse lemur (Microcebus jollyae; ψ = 0.14 ± 0.17), the greater dwarf lemur (Cheirogaleus major; ψ = 0.42 ± 0.30), the red-bellied lemur (Eulemur rubriventer; ψ = 0.24 ± 0.03), and the black-and-white ruffed lemur (Varecia variegata; ψ = 0.24 ± 0.08). Tree diameter, elevation, distance to village, and canopy connectivity were important predictors of occupancy, while camera height, canopy connectivity, fragment ID, and fragment size predicted detection. Arboreal cameras recorded significantly higher species richness compared with ground cameras. We suggest expanded application of arboreal camera traps in future research, but we recommend longer trapping periods to better sample rarer species. Overall, arboreal camera trapping combined with occupancy modeling can be a highly efficient and useful approach for monitoring and predicting the occurrence of elusive lemur species and has the potential to be effective for other arboreal primates and canopy taxa across the globe.

Possible Infanticidal Event of an Aye-Aye (Daubentonia madagascariensis) in Torotorofotsy, Madagascar.

Infanticide occurs in an array of mammalian species, especially primates. Most infanticidal events occur in polygynous societies, though they sometimes happen in nongregarious populations. We witnessed a possible infanticidal event of a 3-month-old male aye-aye, a species that exhibits a dispersed multimale social system, in Torotorofotsy, Madagascar. Though firsthand killing of the infant was not observed, physical injuries to the infant, vocalizations of the adult female, and her subsequent chase of the adult male aye-aye strongly indicates infanticide. If true, this would be the first recorded incident of an infanticidal event in a noyau primate. The evidence for three different explanations of infanticide is evaluated.

BIOMEDICAL EVALUATION OF THE GOLDEN-CROWNED SIFAKA (PROPITHECUS TATTERSALLI) IN DARAINA, MADAGASCAR.

Complete medical examinations were performed on 25 wild golden-crowned sifaka (Propithecus tattersalli) from northeastern Madagascar. Each animal received a complete physical examination and weight, body temperature, heart rate, and respiratory rate were documented. Blood samples were collected for packed cell volume, estimated total white blood cell count, serum biochemical profile, fat-soluble vitamin analysis, trace mineral analysis, and Toxoplasma gondii serology. All animals examined were adults and determined to be in good health and body condition. No ectoparasites were observed. Fecal samples were collected for endoparasite examination and bacterial culture; while no endoparasites were observed, fecal samples from two females cultured positive for Bacillus cereus. One male lemur had a positive antibody titer to Toxoplasma gondii immunoglobulin G. These baseline health data provide an important foundation for continued monitoring of this critically endangered species.

Re-assessing the applicability of the Jarman/Bell model and Kay's threshold to the insectivorous aye-aye (Daubentonia madagascariensis).

OBJECTIVES: Jarman/Bell principle and Kay's threshold suggest that large animals should not be able to sustain themselves on insects. However, animals with specialized morphological and/or behavioral adaptations violate these assumptions. Male aye-ayes were recently identified as having an insectivorous diet despite weighing 2.5 kg. We further explored this diet/body size disparity by studying behaviors of an adult female and juvenile male aye-aye. MATERIALS AND METHODS: We collected behavioral data on an adult female and juvenile male aye-aye in Torotorofotsy, Madagascar from January 2016 to December 2017. We used instantaneous sampling to determine the frequency of feeding events and continuous sampling during feeding behaviors to assess duration of feeding bouts. RESULTS: Invertebrates comprised over 88% of the diet for both animals. A Wilcoxon signed-rank test found no significant difference in the female's feeding frequencies between the hot/rainy seasons and the cold/dry seasons. DISCUSSION: Our results support earlier findings that invertebrates are the aye-aye's main resource and corroborate that aye-ayes violate assumptions of the Jarman/Bell model and Kay's threshold. We suggest that the Jarman/Bell principle and Kay's threshold be used as supporting evidence and not to repudiate findings that do not conform to these guidelines.

Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species.

Delimitation of cryptic species is increasingly based on genetic analyses but the integration of distributional, morphological, behavioral, and ecological data offers unique complementary insights into species diversification. We surveyed communities of nocturnal mouse lemurs (Microcebus spp.) in five different sites of northeastern Madagascar, measuring a variety of morphological parameters and assessing reproductive states for 123 individuals belonging to five different lineages. We documented two different non-sister lineages occurring in sympatry in two areas. In both cases, sympatric species pairs consisted of a locally restricted (M. macarthurii or M. sp. #3) and a more widespread lineage (M. mittermeieri or M. lehilahytsara). Estimated Extents of Occurrence (EOO) of these lineages differed remarkably with 560 and 1,500 km2 versus 9,250 and 50,700 km2 , respectively. Morphometric analyses distinguished unambiguously between sympatric species and detected more subtle but significant differences among sister lineages. Tail length and body size were most informative in this regard. Reproductive schedules were highly variable among lineages, most likely impacted by phylogenetic relatedness and environmental variables. While sympatric species pairs differed in their reproductive timing (M. sp. #3/M. lehilahytsara and M. macarthurii/M. mittermeieri), warmer lowland rainforests were associated with a less seasonal reproductive schedule for M. mittermeieri and M. lehilahytsara compared with populations occurring in montane forests. Distributional, morphological, and ecological data gathered in this study support the results of genomic species delimitation analyses conducted in a companion study, which identified one lineage, M. sp. #3, as meriting formal description as a new species. Consequently, a formal species description is included. Worryingly, our data also show that geographically restricted populations of M. sp. #3 and its sister species (M. macarthurii) are at high risk of local and perhaps permanent extinction from both deforestation and habitat fragmentation.

Home Range Size and Seasonal Variation in Habitat Use of Aye-Ayes (Daubentonia madagascariensis) in Torotorofotsy, Madagascar.

Madagascar's dramatic climatic fluctuations mean most lemurs adjust behaviors seasonally as resource availability fluctuates. Many lemurs will adopt one of two strategies, a resource maximizer or an area minimizer, when adjusting to seasonal shifts in resource availability. However, it is unknown if and how aye-aye (Daubentonia madagascariensis) ranging behavior is influenced by seasonality. We explored whether habitat use changed seasonally. We followed two aye-ayes, an adult male and an adult female, in the undisturbed forest of Torotorofotsy, Madagascar, from April 2012 to December 2017. We used instantaneous focal-animal sampling to collect behavioral data every 5 min and GPS locations every 20 min. We used the minimum convex polygon (MCP) to determine overall home range, and the Brownian bridge movement model (BBMM) to estimate overall and seasonal home range of the female aye-aye from November 2014 to October 2017. We used Wilcoxon signed-rank tests to determine whether there were significant differences in home range sizes between seasons across years and to examine whether there were seasonal differences in height of invertebrate foraging, generalized linear models to assess seasonal differences in travel rates and nesting locations, and χ2 tests to determine whether there were differences in forest strata use when foraging on invertebrates. The male's MCP home range was 2,586 ha, and the female's MCP home range was 765 ha. The seasonal BBMM for the female varied between 443.6 and 1,010.0 ha, though infant rearing appears to have influenced these values. There were no significant differences in seasonal home range, travel rates, nesting locations, or height of invertebrate feeding. However, canopy level invertebrate foraging occurred more often than understory or ground levels. It appears aye-ayes in this undisturbed forest were not influenced by seasonal shifts and had larger home ranges than any previously reported. These findings may indicate that aye-ayes in an undisturbed forest are resource maximizers, closely linked to invertebrate assemblages.

A massively parallel strategy for STR marker development, capture, and genotyping.

Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci-97.3-99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies.

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.

Behaviour and Ecology of Male Aye-Ayes (Daubentonia madagascariensis) in the Kianjavato Classified Forest, South-Eastern Madagascar.

Previous studies found that aye-ayes (Daubentonia madagascariensis) consume a variety of non-invertebrate resources, supporting the hypothesis that aye-ayes are too large-bodied to focus feeding efforts on insects. However, these conclusions were based on introduced populations, with little known about aye-aye behaviour and ecology in its natural habitat. This study investigates activity budgets, diet, and home range/territories of 2 male aye-ayes in the Kianjavato Classified Forest, a disturbed forest in south-eastern Madagascar, from October 2013 to October 2014. We used radiotelemetry and focal-animal sampling methods to collect behavioural data. We recorded GPS coordinates of the focal animal every 20 min, calculating the home range size for each individual. Results showed that male aye-ayes spent most of their time feeding and travelling. Their feeding time primarily focussed on larvae and adult insects from various substrates, and to a lesser extent Canarium spp. seeds. Home range sizes of the 2 males varied between individuals, overlapped greatly, and appeared to be related to the location of females. Our findings indicate that aye-aye behaviours are strongly indicative of insect-centric feeding ecology.

Novel opsin gene variation in large-bodied, diurnal lemurs.

Some primate populations include both trichromatic and dichromatic (red-green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity pattern, are hypothesized to play a role. Limited data on X-linked opsin variation in lemurs make such hypotheses difficult to evaluate. We provide the first detailed examination of X-linked opsin variation across a lemur clade (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal and largest extant lemur, Indri indri, and nine species of smaller, generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister taxon to Propithecus) lacks a polymorphism, at least eight species of diurnal indriids have two or more X-linked opsin alleles. Four rainforest-living taxa-I. indri and the three largest Propithecus species-have alleles not previously documented in lemurs. Moreover, we identified at least three opsin alleles in Indri with peak spectral sensitivities similar to some New World monkeys.

Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography.

The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species' boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.

Characterization of seasonal reproductive and stress steroid hormones in wild Radiated Tortoises, Astrochelys radiata.

The critically endangered Radiated Tortoise (Astrochelys radiata) is endemic to the southern coastlines of Madagascar. Once common, wild populations of this tortoise have undergone dramatic declines in recent years. Although there have been studies documenting reproductive activities, reproductive physiological parameters are unknown yet may be crucial in the recovery of the species. Over four research seasons in remote field locations native to A. radiata, we surveyed for, radio-tracked, and sampled wild, free ranging tortoises. We sampled and measured stress and reproductive parameters (corticosterone [CORT], testosterone [T], estradiol-17ß [E2], and progesterone [P]) in 311 plasma samples from 203 wild A. radiata, capturing their active period. Generally, hormone concentrations were associated with body condition, temperature, and humidity. There was wide variation in CORT that varied monthly and by group. Juvenile tortoises maintained more than twice the mean basal CORT concentrations than either adult sex, with the most dramatic distinctions in the middle of the wet season. For adult sex hormones, the last months of the dry season and into the wet season when ground humidities are low and just begin to rise prior to temperature declines, male T concentrations gradually increased to a peak before returning to near undetectable values into the dry season. We had limited data for T concentrations in females, but found average T concentrations were much lower than in males and positively correlated with larger female home range sizes. For female hormone cycles, E2 also peaked in the early 1/3 of the wet season along with male T, and was followed by an uptick in P which correlates to the putative ovulatory cycle. Females tracked over four years showed variation in patterns of P, indicating that number and frequency of clutches vary. Our results suggest that 1) there is high species plasticity in response to stress; 2) A. radiata reproductive cycling is somewhat dissociated with courtship timing and is instead triggered by environmental cues; and 3) individual female reproductive output is irregular. This study is oone of the first to document and describe multi-year seasonal stress and reproductive hormones in a free-ranging Malagasy chelonian. These data may be used to identify key high-production habitats for conservation, and aide in captive management and reproduction in assurance colonies for species health and survival.

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.