Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
151
datasets available to search
ShareScore release 0.9.0
Dataset results
151 results for “Lemur”
Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats.
<p>This data set includes the R scripts (combined into one R markdown document) and input files needed to create the main text figures and major analyses for the paper "Grieneisen L, Hays A, Cook E, Blekhman R, and Tecot S. 2024. Temporal patterns of gut microbiota in lemurs (<em>Eulemur rubriventer</em>) living in intact and disturbed habitats. American Journal of Primatology." </p>
Assemblies of two Greenland wolf individuals and one Flying lemur performed by LJA,
<p>These assemblies were generated as a part of analysis performed in paper Zhu et al (2024) titled "Assessing Assembly Errors in Immunoglobulin Loci: A Comprehensive Evaluation of Long-read Genome Assemblies Across Vertebrates"</p>
Anthropogenic pressures drive population genetic structuring across a Critically Endangered lemur species range
<p>Includes initial input landscape surfaces (.acs) and final resistance surfaces (.out) generated during the current study.</p>
Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals
<p><span>Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera <i>Microcebus</i> and <i>Cheirogaleus</i>, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e., the lemurs and lorises), we find that the highly speciose and morphologically cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, </span>as might be expected if they have each evolved to respond to specific stimuli<span>. Further, a detailed syntenic comparison of mouse lemurs with mouse (genus <i>Mus</i>) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as a V1R "hotspot."</span></p>
Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
<p>Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of <i>de novo</i> mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (<i>Microcebus</i> <i>murinus</i>), we estimated the mutation rate to be 1.52 × 10<sup>–8</sup> (95% credible interval: 1.28 × 10<sup>−8</sup> to 1.78 × 10<sup>−8</sup>) mutations/site/generation, a rate among the highest calculated for a mammal. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG-sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false negative and false positive rate for our data and show that any point estimate of a <i>de novo </i>mutation rate should be considered with a large degree of uncertainty. To validate these observations, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which <i>de novo</i> mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution rate analyses for all species compared.</p>
Dataset for manuscript "Host-related and environmental factors influence long-term ectoparasite infestation dynamics of mouse lemurs in northwestern Madagascar" to be published in the American Journal of Primatology
<p>This Excel-file contains three datasets, corresponding to the initial raw dataset resulting from all ectoparasite inspections (n = 2,241), the merged dataset used for host-related and temporal modeling (n = 1940), and the even more condensed dataset with one datapoint per individual used for climatic modeling (n = 583), respectively.</p>
Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests
<p>Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The pre-human extent of these grasslands is a topic of vigorous debate, with conventional wisdom holding that they are anthropogenic in nature and emerging evidence supporting that grasslands were a component of the pre-human Central Highlands vegetation. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (<em>Microcebus lehilahytsara</em>;<em> </em>Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, which makes them a valuable indicator species. Population divergences among forest-dwelling mammals can serve as a proxy for habitat fragmentation and patterns of post-divergence gene flow can reveal potential migration corridors consistent with a wooded grassland mosiac. We used RADseq data to infer phylogenetic relationships, population structure, demographic models of post-divergence gene flow, and population size change through time. These analyses offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread 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. Notably, 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 be more vulnerable from paleoclimatic changes.</p>
Comparing effects of food mechanical properties on oral processing behaviors in two sympatric lemur species - Dataset
<p>Dataset for maximal random slope mixed models from manuscript "Comparing effects of food mechanical properties on oral processing behaviors in two sympatric lemur species". Column headers are described in the article and the key tab of the excel. </p>
Data from: Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests
<p><span>Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the formation of geographic barriers by changing water and habitat availability. The relative importance of these models for the diversification of the various forest-adapted taxa of Madagascar has yet to be understood. Here, we reconstructed the phylogeographic history of Gerp's mouse lemur (<em>Microcebus gerpi</em>) to identify relevant mechanisms and drivers of diversification in Madagascar's humid rainforests. We used restriction site associated DNA (RAD) markers and applied population genomic and coalescent-based techniques to estimate genetic diversity, population structure, gene flow and divergence times among <em>M. gerpi</em> populations and its two sister species <em>M. jollyae</em> and <em>M. marohita</em>. Genomic results were complemented with ecological niche models to better understand the relative barrier function of rivers and altitude. We show that <em>M. gerpi</em> diversified during the late Pleistocene. The inferred ecological niche, patterns of gene flow and genetic differentiation in <em>M. gerpi</em> suggest that the potential for rivers to act as biogeographic barriers depended on both size and elevation of headwaters. Populations on opposite sides of the largest river in the area with headwaters that extend far into the highlands show particularly high genetic differentiation, whereas rivers with lower elevation headwaters have weaker barrier functions, indicated by higher migration rates and admixture. We conclude that<em> M. gerpi</em> likely diversified through repeated cycles of dispersal punctuated by isolation to refugia as a result of paleoclimatic fluctuations during the Pleistocene. We argue that this diversification scenario serves as a model of diversification for other rainforest taxa that are similarly limited by geographic factors. In addition, we highlight conservation implications for this critically endangered species, which faces extreme habitat loss and fragmentation. </span></p>
Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent
Open the record for dataset details and reuse information.
Data from: Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi
Open the record for dataset details and reuse information.
Data from: The evolution of cognitive control in lemurs
Open the record for dataset details and reuse information.
Data from: A description of nesting behaviors, including factors impacting nest site selection, in black-and-white ruffed lemurs (Varecia variegata)
Open the record for dataset details and reuse information.
Data from: Temperament and cognitive flexibility across lemur species
Open the record for dataset details and reuse information.
Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
Open the record for dataset details and reuse information.
Data from: Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests
Open the record for dataset details and reuse information.
Data from: Genetic wealth, population health: major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta)
Open the record for dataset details and reuse information.
Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals
Open the record for dataset details and reuse information.
Logical inferences from visual and auditory information in ruffed lemurs and sifakas
Open the record for dataset details and reuse information.
Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar’s Central Highlands and eastern rainforests
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.