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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.
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Hidden in the Dark: A Review of Galagid Systematics and Phylogenetics
An accurate representation of species diversity is critical in primatology; most of the questions in evolutionary biology, ecology, and conservation hinge on species as a fundamental unit of analysis. Galagos are among the least-known primates. Because of their cryptic morphology, broad distribution, and sampling challenges arising from elusive habits and political instability, substantial knowledge gaps about their taxonomy, evolutionary history, and biogeography remain. Despite these limitations, recent research that integrated field surveys, acoustic, morphological, and genetic analyses helped us to better understand the taxonomic diversity of this primate group. In this paper, we (1) review the current status of galagid taxonomy; (2) synthesize our current understanding of their phylogenetics, origins, and biogeography; and (3) explore current and future approaches to elucidate galagid cryptic species diversity. The onset of galago systematics dates back to the early 19th century, with taxonomic descriptions following natural history expeditions and comparative anatomy studies. Although morphology has historically dominated systematic research on galagos, the coupling of acoustic analyses with genetic data has revolutionized the field. Taxonomic rearrangements include the discovery of new species in the wild (e.g., Galagoides kumbirensis) and the description of a new genus (Paragalago). Technological advances have allowed the collection of acoustic data in remote areas, and molecular techniques have the potential to help researchers fill important geographic gaps. Improving the resolution of galago species diversity also has implications for the conservation of wild populations, as a better understanding of species boundaries and ranges can aid in the implementation of conservation strategies.
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- Award ID(s):
- 1926105
- PAR ID:
- 10510328
- Publisher / Repository:
- Springer Link
- Date Published:
- Journal Name:
- International Journal of Primatology
- ISSN:
- 0164-0291
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1007/s10764-024-00430-w
