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The availability of genetic data from wild populations limits our understanding of primate evolution and conservation, particularly for small nocturnal species such as lorisiforms (galagos, lorises, angwantibos, and pottos). Emerging methods for recovering genomic DNA from historical museum specimens have been rarely used in primate studies. We aimed to optimize extraction and bioinformatics protocols to maximize the recovery of historical DNA to fill important geographic and taxonomic gaps, improve phylogenetic resolution, and inform conservation of Lorisiform primates. First, we compared the performance of two DNA extraction methods by using 238 specimens up to a hundred years old. We then selected 96 samples with the highest DNA yields for shotgun sequencing. To evaluate the impact of phylogenetic divergence in bioinformatic read mapping, we compared coverage depths when using human and three lorisiform reference mitogenomes. Based on whole genomic data, we performed metagenomics and microbial diversity analyses to assess the composition of potentially exogenous content. Lastly, based on the most geographically and taxonomically comprehensive sampling for the West African lorisiforms to date (19/32 currently recognized species), we performed phylogenetic inference using Maximum Likelihood. The results showed that older samples yield lower DNA concentration, with an optimized phenol-chloroform protocol outperforming a commercial kit. However, both extraction methods generated DNA in sufficient amount and quality for phylogenetic inference. Our reference bias comparisons showed that higher phylogenetic proximity between focal species and reference mitogenome increases coverage depth. The metagenomic analysis found human contamination in only one of 96 samples (1%), whereas ten of 96 (11%) samples showed nonnegligible levels of other exogenous contents, among which are certain blood parasites. We inferred low support for the monophyly of Asian and African Lorisids but confirmed the monophyly and previously suggested relationships among Galagid genera. Lastly, we found evidence of cryptic species diversity within the western dwarf galagos (genus Galagoides). Taken together, these results attest to the enormous potential of museomics to advance our understanding of galago evolution, ecology, and conservation, an approach that can be extended to other primate clades. 

Improving models of species' distributions is essential for conservation, especially in light of global change. Species distribution models (SDMs) often rely on mean environmental conditions, yet species distributions are also a function of environmental heterogeneity and filtering acting at multiple spatial scales. Geodiversity, which we define as the variation of abiotic features and processes of Earth's entire geosphere (inclusive of climate), has potential to improve SDMs and conservation assessments, as they capture multiple abiotic dimensions of species niches, however they have not been sufficiently tested in SDMs. We tested a range of geodiversity variables computed at varying scales using climate and elevation data. We compared predictive performance of MaxEnt SDMs generated using CHELSA bioclimatic variables to those also including geodiversity variables for 31 mammalian species in Colombia. Results show the spatial grain of geodiversity variables affects SDM performance. Some variables consistently exhibited an increasing or decreasing trend in variable importance with spatial grain, showing slight scale-dependence and indicating that some geodiversity variables are more relevant at particular scales for some species. Incorporating geodiversity variables into SDMs, and doing so at the appropriate spatial scales, enhances the ability to model species-environment relationships, thereby contributing to the conservation and management of biodiversity. This article is part of the Theo Murphy meeting issue ‘Geodiversity for science and society’. 

Disjunct biogeographic patterns of similar species remain enigmatic within evolutionary biology. Disparate distributions typically reflect species responses to major historical events including past climate change, tectonics, dispersal, and local extinction. Paleo-ecological niche modeling (PaleoENM) has proven useful in inferring the causes of disjunct distributions within charismatic and well-studied taxa including mammals, plants, and birds, but remains under-explored in insects. The relictual Asian dragonfly genus Epiophlebia (Suborder Epiophlebioptera: Epiophlebiidae) allows us a novel opportunity to explore PaleoENM in the context of disjunct distributions due to their endemism to the Japanese islands, Himalayas, China, and North Korea. The aim of this paper is to investigate the potential causes behind the modern distribution of Epiophlebia by inferring the historical range of these species within the Last Glacial Maximum (LGM), thereby highlighting the utility of PaleoENM in the context of odonate biogeography. Our results indicate possible past routes of gene flow of Epiophlebia during the LGM due to high habitat suitability of the genus stretching from the Himalayas to Japan. Furthermore, our results predict several unsampled areas which have the potential to harbor new populations of the genus. 

Cryptic species complexes consist of geographically confluent, closely related species that were once classified as a single species. The diversification mechanisms of cryptic species complexes often are mediated by environmental factors, which in some cases lead to ecological speciation. Niche-based distribution modeling can be an important tool in characterizing the extent of ecological divergence between species that may have resulted from environmentally driven speciation scenarios. We used climatic niche modeling to examine the degree of ecological divergence within the Paragalago zanzibaricus species complex in East Africa. We expected parapatrically distributed P. cocos and P. zanzibaricus to display a significant degree of climatic niche distinction and allopatrically distributed P. zanzibaricus and P. granti to exhibit a degree of niche conservatism. The extent of niche overlap between the three species was assessed by using a Niche Similarity Analysis (NSA) on bioclimatic values. Selected models for all three species exhibited good predictive ability, although the model for P. cocos was most optimal and appeared most consistent with its known range. NSA showed that P. cocos and P. zanzibaricus were statistically more similar than predicted from null distributional values. Results for NSA between the other two species pairings appear to be within the null distribution. The extent of niche overlap between all three species is consistent with the expectations of allopatric speciation processes. Future studies should examine alternative hypotheses for speciation within this group, including the role of sensory drive, interspecific competition, and the impact of Plio-Pleistocene climatic cycles. 

Genetic analysis of historical museum collections presents an opportunity to clarify the evolutionary history of understudied primate groups, improve taxonomic inferences, and inform conservation efforts. Among the most understudied primate groups, slow and pygmy lorises (genera Nycticebus and Xanthonycticebus) are nocturnal strepsirrhines found in South and Southeast Asia. Previous molecular studies have supported five species, but studies using morphological data suggest the existence of at least nine species. We sequenced four mitochondrial loci, CO1, cytb, d-loop, and ND4, for a total of 3324 aligned characters per sample from 41 historical museum specimens for the most comprehensive geographic coverage to date for these genera. We then combined these sequences with a larger dataset composed of samples collected in Vietnam as well as previously published sequences (total sample size N = 62). We inferred phylogenetic relationships using Bayesian inference and maximum likelihood methods based on data from each locus and on concatenated sequences. We also inferred divergence dates for the most recent common ancestors of major lineages using a BEAST analysis. Consistent with previous studies, we found support for Xanthonycticebus pygmaeus as a basal taxon to the others in the group. We also confirmed the separation between lineages of X. pygmaeus from northern Vietnam/Laos/China and southern Vietnam/Cambodia and included a taxonomic revision recognizing a second taxon of pygmy loris, X. intermedius. Our results found support for multiple reciprocally monophyletic taxa within Borneo and possibly Java. The study will help inform conservation management of these trade-targeted animals as part of a genetic reference database for determining the taxonomic unit and provenance of slow and pygmy lorises confiscated from illegal wildlife trade activities.