An official website of the United States government
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.
more »
« less
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.
more »
« less
- 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
More Like this
-
-
Studying the historical biogeography and life history transitions from eusocial colony life to social parasitism contributes to our understanding of the evolutionary mechanisms generating biodiversity in eusocial insects. The ants in the genus Myrmecia are a well-suited system for testing evolutionary hypotheses about how their species diversity was assembled through time because the genus is endemic to Australia with the single exception of the species M. apicalis inhabiting the Pacific Island of New Caledonia, and because at least one social parasite species exists in the genus. However, the evolutionary mechanisms underlying the disjunct biogeographic distribution of M. apicalis and the life history transition(s) to social parasitism remain unexplored. To study the biogeographic origin of the isolated, oceanic species M. apicalis and to reveal the origin and evolution of social parasitism in the genus, we reconstructed a comprehensive phylogeny of the ant subfamily Myrmeciinae. We utilized Ultra Conserved Elements (UCEs) as molecular markers to generate a molecular genetic dataset consisting of 2,287 loci per taxon on average for 66 out of the 93 known Myrmecia species as well as for the sister lineage Nothomyrmecia macrops and selected outgroups. Our time-calibrated phylogeny inferred that: (i) stem Myrmeciinae originated during the Paleocene ~ 58 Ma ago; (ii) the current disjunct biogeographic distribution of M. apicalis was driven by long-distance dispersal from Australia to New Caledonia during the Miocene ~ 14 Ma ago; (iii) the single social parasite species, M. inquilina, evolved directly from one of the two known host species, M. nigriceps, in sympatry via the intraspecific route of social parasite evolution; and (iv) 5 of the 9 previously established taxonomic species groups are non-monophyletic. We suggest minor changes to reconcile the molecular phylogenetic results with the taxonomic classification. Our study enhances our understanding of the evolution and biogeography of Australian bulldog ants, contributes to our knowledge about the evolution of social parasitism in ants, and provides a solid phylogenetic foundation for future inquiries into the biology, taxonomy, and classification of Myrmeciinae.more » « less
-
Abstract Species of camel spiders in the family Eremobatidae are an important component of arthropod communities in arid ecosystems throughout North America. Recently, research demonstrated that the evolutionary history and biogeography of the family are poorly understood. Herein we explore the biogeographic history of this group of arachnids using genome-wide single nucleotide polymorphism (SNP) data, morphology, and distribution modelling to study the eremobatid genus Eremocosta , which contains exceptionally large species distributed throughout North American deserts. Relationships among sampled species were resolved with strong support and they appear to have diversified within distinct desert regions along an east-to-west progression beginning in the Chihuahuan Desert. The unexpected phylogenetic position of some samples suggests that the genus may contain additional, morphologically cryptic species. Geometric morphometric analyses reveal a largely conserved cheliceral morphology among Eremocosta spp. Phylogeographic analyses indicate that the distribution of E. titania was substantially reduced during the last glacial maximum and the species only recently colonized much of the Mojave Desert. Results from this study underscore the power of genome-wide data for unlocking the genetic potential of museum specimens, which is especially promising for organisms like camel spiders that are notoriously difficult to collect.more » « less
-
Abstract The United States of America has a diverse collection of freshwater mussels comprising 301 species distributed among 59 genera and two families (Margaritiferidae and Unionidae), each having a unique suite of traits. Mussels are among the most imperilled animals and are critical components of their ecosystems, and successful management, conservation and research requires a cohesive and widely accessible data source. Although trait-based analysis for mussels has increased, only a small proportion of traits reflecting mussel diversity in this region has been collated. Decentralized and non-standardized trait information impedes large-scale analysis. Assembling trait data in a synthetic dataset enables comparison across species and lineages and identification of data gaps. We collated data from the primary literature, books, state and federal reports, theses and dissertations, and museum collections into a centralized dataset covering information on taxonomy, morphology, reproductive ecology and life history, fish hosts, habitats, thermal tolerance, geographic distribution, available genetic information, and conservation status. By collating these traits, we aid researchers in assessing variation in mussel traits and modelling ecosystem change.more » « less
-
Parrots (Psittaciformes) are a well-studied, diverse group of birds distributed mainly in tropical and subtropical regions. Today, one-third of their species face extinction, mainly due to anthropogenic threats. Emerging tools in genetics have made major contributions to understanding basic and applied aspects of parrot biology in the wild and in captivity. In this review, we show how genetic methods have transformed the study of parrots by summarising important milestones in the advances of genetics and their implementations in research on parrots. We describe how genetics helped to further knowledge in specific research fields with a wide array of examples from the literature that address the conservation significance of (1) deeper phylogeny and historical biogeography; (2) species- and genus-level systematics and taxonomy; (3) conservation genetics and genomics; (4) behavioural ecology; (5) molecular ecology and landscape genetics; and (6) museomics and historical DNA. Finally, we highlight knowledge gaps to inform future genomic research on parrots. Our review shows that the application of genetic techniques to the study of parrot biology has far-reaching implications for addressing diverse research aims in a highly threatened and charismatic clade of birds.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1007/s10764-024-00430-w
