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Fig. 3 in Molecular phylogenetics of the sucking louse genus Lemurpediculus (Insecta: Phthiraptera), ectoparasites of lemurs, with descriptions of three new species

Fig. 3. Maximum likelihood phylogenetic tree based on concatenated cytochrome C oxidase subunit I (COI), elongation factor 1α (EF1α) and internal transcribed spacer 1 (ITS1) sequences. Substitution models were TPM2u + F + I + G4 for COI, TIM2e for EF1α and F81 + F + I for ITS1. Values next to the branches indicate ultrafast bootstrap support. Tree scale is in substitutions/site. Abbreviations: L., Lemurpediculus.

Fig. 4 in Molecular phylogenetics of the sucking louse genus Lemurpediculus (Insecta: Phthiraptera), ectoparasites of lemurs, with descriptions of three new species

Fig. 4. Lemurpediculus zimmermanni, male, scanning electron micrographs: A, dorsal whole body. B, ventral whole body. Abbreviations sgp, subgenital plate; sp, spiracle; tc, tibiotarsal claw; tsp, thoracic sternal plate; vs, ventral head spike.

Fig. 1 in Molecular phylogenetics of the sucking louse genus Lemurpediculus (Insecta: Phthiraptera), ectoparasites of lemurs, with descriptions of three new species

Fig. 1. Sampling sites where cheirogaleids were trapped for collection of lice. Different colours/symbols correspond to the sampled host species/populations, with different shades of blue and green indicating different populations of M. murinus and M. gerpi, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 12 in Molecular phylogenetics of the sucking louse genus Lemurpediculus (Insecta: Phthiraptera), ectoparasites of lemurs, with descriptions of three new species

Fig. 12. Identifying morphological characters of male genitalia for previously described species of Lemurpediculus, A: Lemurpediculus petterorum Paulian, 1958. B: Lemurpediculus verruculosus (Ward, 1951). C: Lemurpediculus claytoni Durden et al., 2017. D: Lemurpediculus robbinsi Durden et al., 2017. E: Lemurpediculus madagascariensis Durden et al. (2018). Scale bar, 0.1 mm. Abbreviations: as, accessory sclerite; ba, basal apodeme; p, paramere; ndomere; ps, pseudopenis.

Fig. 11. Lemurpediculus tsinamanpesotsae, A in Molecular phylogenetics of the sucking louse genus Lemurpediculus (Insecta: Phthiraptera), ectoparasites of lemurs, with descriptions of three new species

Fig. 11. Lemurpediculus tsinamanpesotsae, A: Ventral head of male Holotype, B: Thoracic sternal plate of Holotype male, C: Genitalia of male Holotype, D: Subgenital plate of female Allotype. Abbreviations: ae, anterior endomere; aen, aedeagal endomere; ba, basal apodeme; p, paramere; pe, posterior endomere; ps, pseudopenis.

Fig. 9. Lemurpediculus gerpi, A in Molecular phylogenetics of the sucking louse genus Lemurpediculus (Insecta: Phthiraptera), ectoparasites of lemurs, with descriptions of three new species

Fig. 9. Lemurpediculus gerpi, A: Ventral head of male Holotype, B: Thoracic sternal plate of Holotype male, C: Genitalia of male Holotype. Abbreviations: ae, anterior endomere; aen, aedeagal endomere; ba, basal apodeme; p, paramere; pe, posterior endomere; ps, pseudopenis.

opencc-by-nc-sa-4.0May 2023View details →

Passive acoustic monitoring applied to black-and-white ruffed lemurs (Varecia variegata) in Ranomafana National Park, Madagascar

Data accompanying the paper: "An integrated passive acoustic monitoring and deep learning pipeline applied to black-and-white ruffed lemurs (\textit{Varecia variegata}) in Ranomafana National Park, Madagascar" Fieldwork was conducted at Mangevo (21.3833S, 47.4667E), an isolated and undisturbed forest location within Ranomafana National Park (RNP), located in southeastern Madagascar, during the period of May to July 2019. To facilitate passive acoustic monitoring, we deployed a total of two SongMeter SM4 devices (manufactured by Wildlife Acoustics) and two Swift units (provided by the Cornell Yang Center for Conservation Bioacoustics). The placement of these recorders was strategically chosen within the central regions of known subgroups, ensuring a minimum distance of 300 meters between each device. The SongMeter devices operated at a sampling rate of 48 kHz, while the Swift units operated at 32 kHz, respectively, enabling comprehensive audio data collection throughout the study period. We provide the audio data (.wav) used to train and test our neural network classifier along with the corresponding labelled text files (.data). Files provided <ul> <li>Test_Audio.zip -- contains (.wav) testing audio files</li> <li>Test_Annotations.zip -- contains (.svl) manually annotated testing files which can be read in using Sonic Visualiser or by parsing the XML file in Python or another programming language. Load in the audio file into Sonic Visualiser and then drag-and-drop the corresponding .svl file.</li> <li>Training_Audio_batch_x.zip -- several .zip files were created to simplify downloading. There are 10 batches, each is roughly 4GB. Each batch contains (.wav) training audio files</li> <li>Training_Annotations.zip -- contains (.svl) manually annotated training files which can be read in using Sonic Visualiser or by parsing the XML file in Python or another programming language. Load in the audio file into Sonic Visualiser and then drag-and-drop the corresponding .svl file.</li> <li>model_weights_tensorflow.hdf5 -- the Tensorflow model. Load the model using: model = tf.keras.models.load_model(model_filepath) note that the model expects a three channel input as explained in the research article.</li> </ul>

dryad40/100

Data from: Species-specific responses to paleoclimatic changes and landscape barriers drive contrasting phylogeography of co-distributed lemur species in northeastern Madagascar

Open the record for dataset details and reuse information.

publicDec 2025View details →

opencc-zeroJul 2020View details →

Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

Species delimitation is ever more critical for assessing biodiversity in threatened regions of the world, especially when undescribed lineages may be at risk from habitat loss. Mouse lemurs (Microcebus) are an example of a rapid radiation of morphologically cryptic species that are distributed throughout Madagascar in its rapidly vanishing forested habitats. Here, we focus on two pairs of sister lineages that occur in a region in northeastern Madagascar that shows high levels of microendemism. We revisit previous hypotheses of species diversity by filling geographic sampling gaps and by generating new genomic data for three named species, as well as an undescribed lineage previously identified to be of interest due to its highly divergent mtDNA. We analyzed RADseq data with multiple species delimitation methods based on the multispecies coalescent (MSC) model while accounting for introgression. Non-sister lineages occur sympatrically in two instances, despite an estimated divergence time of less than 1 Ma, thus suggesting rapid evolution of reproductive isolation in the mouse lemur clade. We note, however, that the divergence time estimates reported here are based on the MSC and calibrated with pedigree-based primate mutation rates. These dates are considerably more recent than previous analyses that used traditional relaxed clock methods and distant fossil calibrations. One pair of sister lineages passed all species delimitation tests while the other pair failed most, largely due to differences in Ne between the two pairs of lineages. Nevertheless, delimitation results were also supported by differences in levels of gene flow and patterns of isolation-by-distance between the two pairs. We conclude that MSC-based species delimitation methods are valuable tools for evaluating cryptic species, even though these methods can be strongly affected by variable Ne. We suggest that this result has general implications for species delimitation studies of other recently diverged lineages.

opencc-zeroOct 2020View details →

Data from: 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), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well 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 sub-tropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here we present a nuclear genome sequence (~2X coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (~85kg). To support the testing of key phylogenetic and evolutionary hypotheses we also generated new high-coverage complete nuclear genomes for two extant lemur species, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemur species and 47 non-lemur 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 extant folivorous primates (colobine monkeys) and ungulate herbivores (horses) in genes encoding protein products that function in the biodegradation of plant toxins 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.

opencc-zeroMar 2020View details →

Logical inferences from visual and auditory information in ruffed lemurs and sifakas

Inference by exclusion, or the ability to select a correct course of action by systematically excluding other potential alternatives, is a form of logical inference that allow individuals to solve problems without complete information. Current comparative research shows that several bird, mammal, and primate species can find hidden food through inference by exclusion. Yet there is also wide variation in how successful different species are, as well kinds of sensory information they can use to do so. An important question is therefore why some species are better at engaging in logical inference than others. Here, we investigate the evolution of logical reasoning abilities by comparing two strepsirrhine primate species that vary in dietary ecology: frugivorous ruffed lemur (Varecia spp.) and folivorous Coquerel's sifakas (Propithecus coquereli). Across two studies, we examined their abilities to locate food using direct information versus inference from exclusion and using both visual and auditory information. In Study 1, we assessed whether these lemurs could make inferences when full visual and auditory information about the two potential locations of food were provided. In Study 2, we then compared their ability to make direct inferences versus inferences by exclusion in both the visual and auditory domains. We found that both lemur species can use visual information to find food, but that only ruffed lemurs were also able to use auditory cues, mirroring differences in the complexity of their wild ecology. We further found that, unlike many anthropoid species tested to date, both strepsirrhine species failed to make inferences by exclusion. These results highlight the importance of natural history in understanding the evolution of logical inference, and help reconstruct the deeper phylogeny of primate cognition.

opencc-zeroDec 2016View details →

Data from: Genetic wealth, population health: major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta)

Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur (Lemur catta) as a model, we compared two populations under long-term study: a relatively "open," wild population (n = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003–2013) and a "closed," captive population (n = 121) derived from the Duke Lemur Center (DLC, 1980–2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.

opencc-zeroDec 2017View details →

Data from: Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar's aye-aye

In 1967 G.G. Simpson described three partial mandibles from early Miocene deposits in Kenya that he interpreted as belonging to a new strepsirrhine primate, Propotto. This interpretation was quickly challenged, with the assertion that Propotto was not a primate, but rather a pteropodid fruit bat. The latter interpretation has not been questioned for almost half a century. Here we re-evaluate the affinities of Propotto, drawing upon diverse lines of evidence to establish that this strange mammal is a strepsirrhine primate as originally suggested by Simpson. Moreover, our phylogenetic analyses support the recognition of Propotto, together with late Eocene Plesiopithecus from Egypt, as African stem chiromyiform lemurs that are exclusively related to the extant aye-aye (Daubentonia) from Madagascar. Our results challenge the long-held view that all lemurs are descended from a single ancient colonization of Madagascar, and present an intriguing alternative scenario in which two lemur lineages dispersed from Africa to Madagascar independently, possibly during the later Cenozoic.

opencc-zeroDec 2018View details →

Data from: A description of nesting behaviors, including factors impacting nest site selection, in black-and-white ruffed lemurs (Varecia variegata)

Nest site selection is at once fundamental to reproduction and a poorly understood component of many organisms' reproductive investment. This study investigates the nesting behaviors of black-and-white ruffed lemurs, Varecia variegata, a litter-bearing primate from the southeastern rainforests of Madagascar. Using a combination of behavioral, geospatial, and demographic data, I test the hypotheses that environmental and social cues influence nest site selection, and that these decisions ultimately impact maternal reproductive success. Gestating females built multiple large nests throughout their territories. Of these, females used only a fraction of the originally constructed nests, as well as several parking locations as infants aged. Nest construction was best predicted by environmental cues, including the size of the nesting tree and density of feeding trees within a 75 m radius of the nest, whereas nest use depended largely on the size and average distance to feeding trees within that same area. Microhabitat characteristics were unrelated to whether females built or used nests. Although unrelated to nest site selection, social cues, specifically the average distance to conspecifics' nest and park sites, were related to maternal reproductive success; mothers whose litters were parked in closer proximity to others' nests experienced higher infant survival than those whose nests were more isolated. This is likely because nesting proximity facilitated communal crèche use by neighboring females. Together, these results suggest a complex pattern of nesting behaviors that involves females strategically building nests in areas with high potential resource abundance, using nests in areas according to their realized productivity, and communally rearing infants within a network of nests distributed throughout the larger communal territory.

opencc-zeroDec 2023View details →

Hyper-specialized bamboo lemurs possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes

Subfamilies of cytochrome P450 proteins have been strongly linked to the metabolism of physiologically disruptive compounds such as alkaloids, terpenoids, and other xenobiotics. Consistent with this function, these genes have adaptively evolved in response to environmental pressures exerted on animals, such as herbivores, that consume elevated amounts of toxic xenobiotics or plant secondary metabolites (PSMs). Theory on evolutionary tradeoffs predicts that highly specialized herbivores should exhibit a relatively narrow toolkit of adaptations to accommodate the concomitantly narrow arrays of PSMs in their diets. The bamboo lemurs of Madagascar (genera Prolemur and Hapalemur) represent an interesting test case for this theory because of their dietary hyper-specialization, as these lemurs consume bamboo and grasses at rates otherwise unseen in the order Primates. To test whether the hyper-specialized folivory of these primates is reflected in a similarly specialized and narrow P450 gene suite, we assembled a dataset of confidently assembled CYP1-3 genes for two species of bamboo lemur and 13 additional lemur species. With this dataset, we tested the predictions that bamboo lemurs would exhibit, first, greater rates of gene loss for xenobiotic-metabolizing P450s and, second, relaxed selection on xenobiotic-metabolizing P450 subfamilies relative to lemurs without such dietary hyper-specialization. We found support for the prediction of gene loss in the CYP2B, CYP2C, CYP2D, CYP2J, and CYP3A subfamilies, all of which encode xenobiotic metabolizers. We inferred relaxation of selection for the CYP1A and CYP2D subfamilies. The CYP2F subfamily exhibited a signal of significant intensification of selection in the bamboo-lemur lineage. The evolution of the P450 genes in bamboo lemurs provides support for the evolutionary tradeoff hypothesis, and we further hypothesize that, rather than adapting to a general array of PSMs, bamboo lemurs have instead adapted to the primary toxin in their diet, the highly potent poison cyanide.

opencc-zeroDec 2023View details →

Ancient introgression in mouse lemurs (Microcebus:Cheirogaleidae) explains 20 years of phylogenetic uncertainty

Mouse lemurs (genus Microcebus) are a clade of approximately 26 named species of small, nocturnal primates endemic to Madagascar. The genus radiated one and ten million years ago and is morphologically cryptic, with most species having been named within the past 20 years largely based on phylogenetic analysis of short fragments of mitochondrial data. More recent work has been focused on revisiting species designations with autosomal nuclear data using more sophisticated statistical approaches. The order of speciation events in Microcebus remains contentious, particularly with regard to the placement of the M. ravelobensis clade. We investigated support for previous phylogenetic hypotheses based on available whole-genome assemblies from six species and an outgroup. We recovered over 4,000 one-to-one orthologs from these assemblies and used concatenation and coalescent species tree methods to evaluate if differences between previous studies were due to methodological differences or to limitations from too few loci. Observed gene tree discordance was high with patterns inconsistent with incomplete lineage sorting alone. Therefore, we estimated phylogenetic networks to investigate ancient introgression events that may explain observed gene tree distributions and previous phylogenetic conflicts. A network model, invoking some role for introgressive hybridization in the early evolution of Microcebus, better characterizes phylogenetic relationships than does any binary species tree. Our results provide insights into the biogeographic history of a threatened and diverse group of primates while also highlighting an important role for phylogenetic network methods in resolving cases of phylogenetic uncertainty.

opencc-zeroFeb 2024View details →

Lemur population density in Sahamalaza-Iles Radama National Park, Madagascar

The clearing and fragmentation of tropical forest is the single biggest threat to primate populations who depend on this habitat for survival. In contrast to primates that live in continuous, undisturbed forests, primate communities of fragmented forests need to adapt to decreased food availability and increased inter- and intraspecific competition typical of these degraded and anthropogenically disturbed habitats. Some primate species are highly sensitive to habitat fragmentation, whilst other species can adapt and even thrive in fragmented and degraded forests. Here, we assessed how forest fragmentation and associated edge-effects impact the population density of four species of nocturnal lemur in the Sahamalaza-Iles Radama National Park, North West Madagascar. We conducted 118 transect walks over a three-year period covering a total distance of 107 km to collect encounter rate (N/km) and population density (N/Ha) data for each species, which we then compared between the edge and core areas of a continuous forest and a fragmented forest. Our results were highly species-specific, with the population densities of two species (Lepilemur sahamalaza and Microcebus sambiranensis) increasing in edge and fragmented habitat, whilst we observed the opposite for Cheirogaleus medius. Mirza zaza density appeared consistent between the continuous and fragmented forest and in both edge and core areas. We also found evidence of species-specific population density relationships with fragment size, core area, and fragment shape; however, further work is needed to support these findings. This study demonstrates that some nocturnal lemurs can adapt to degraded habitats and thrive within fragmented forests, whilst other species are less capable of doing so.

opencc-zeroFeb 2022View details →

Hair phenotype diversity across Indriidae lemurs

Objectives: Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution—serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun). Materials and Methods: Our analyses considers multiple phylogenetic scales (family-level, genus-level) and hypotheses (e.g., Gloger's rule, the body cooling hypotheses). We obtain hair color and density from museum and/or wild animals, opsin genotypes from wild animals, and climate data from WorldClim. To analyze our data, we use phylogenetic generalized linear mixed models (PGLMM) using Markov chain Monte Carlo algorithms. Results: Our results show that across the Indriidae family, darker hair is typical in wetter regions. However, within Propithecus, dark black hair is common in colder forest regions. Results also show pelage redness increases in populations exhibiting enhanced color vision. Lastly, we find follicle density on the crown and limbs increases in dry and open environments. Discussion: This study highlights how different selective pressures across distinct phylogenetic scales have likely acted on primate hair evolution. Specifically, our data across Propithecus may implicate thermoregulation and is the first empirical evidence of Bogert's rule in mammals. Our study also provides rare empirical evidence supporting an early hypothesis on hominin hair evolution.

zenodo36/100

Black-and-white ruffed lemur (Varecia variegata) calls for passive acoustic monitoring

Data accompanying the paper: "Passive Acoustic Monitoring and Transfer Learning" Please cite this dataset as: <blockquote> Dufourq, Emmanuel and Batist, Carly and Foquet, Ruben and Durbach, Ian. (2022). Passive Acoustic Monitoring and Transfer Learning. BioRxiv doi:  </blockquote> This dataset contains approximately 60 hours of audio that contained calls of the critically endangered Black-and-white ruffed lemur (Varecia variegata). The audio data was collected in a sub-humid rainforest site (Mangevo) in the southeast of Ranomafana National Park in Madagascar using 2 Swift recorders (Cornell Center for Conservation Bioacoustics). The sampling rate was set to 48,000Hz and the recordings were collected intermittently between May 2019 and November 2020. A larger dataset exists and further recordings will be released. The annotations files are in (.svl) format which is compatible with SonicVisualiser (https://www.sonicvisualiser.org/). Each audio file has a corresponding .svl file. Each .svl has segments of audio that were manually annotated as either ''thyolo-alethe" (presence class) or "noise" (absence class) -- this dataset can be used to train a binary classification model. The audio files are provided in "Audio.zip" and the manually verified annotation in "Annotations.zip".

opencc-by-nc-sa-4.0Mar 2022View details →