COLLABORATIVE RESEARCH: UNLOCKING MUSEUM COLLECTIONS FOR PHYLOGENOMIC STUDIES: A CASE STUDY IN LORISIFORM PRIMATES

Overview: Lorisiform primates represent almost 10% of the living primate species; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. Indeed, a major limitation to investigations of primate evolutionary history is the ability to obtain high quality genetic data across the entire geographic distribution of a taxon. Low quality samples, lack of geographic resolution, and access to wild populations have been some of the many limitations that have negatively impacted the field of primate phylogenetics. The main goal of this project is to use Lorisiformes as a model group to employ a novel approach aimed at obtaining high quality phylogenomic data in taxa that are highly cryptic, widely distributed, and extremely difficult to sample in the wild. The project will investigate the evolutionary history of lorisiform primates, with particular attention to testing hypotheses about: 1) alternative biogeographic models in relation to the disjointed distribution of lorisiforms; and 2) climatic and geological events that affected distribution, biodiversity, and species abundance over the past ~40 million years. To achieve these goals, a twofold approach will be implemented: a) new whole genomic sequences, representing all the genera currently recognized within the lorisiforms, will be generated, and b) several hundreds of loci will be obtained using anchored hybrid enrichment across a large number of museum specimens to achieve a full representation of the geographic diversity within this widely distributed primate group. Over 400 museum samples are currently in hand; the remaining specimens will be obtained by sampling additional museums in Europe and the US. By comparing the power of full genome sequencing and anchored phylogenomics, this project will result in one of the most comprehensive datasets for any primate group at both the taxonomic and genomic levels.   Intellectual Merit: An understanding of primate evolutionary history has been hindered either by poor taxonomic and geographic sampling or by limited phylogenetic power. This can lead to erroneous inference which can have critical implications for both systematic understanding and conservation. Hybrid enrichment is less sensitive to tissue quality and quantity, is generally more cost-efficient, and therefore allows for the potential inclusion of a vast number of primate specimens stored in museum collections. This project will address one of the main gaps in primate evolution. Lorisiform primates are among the world's least studied primates. By integrating the newly generated anchored loci data with an ongoing project using the same dataset in lemurs, this project aims at providing a complete picture of strepsirhine evolution and biogeography. The proposed holistic approach, that integrates genomic and fossil data, will also provide a powerful database to compare future findings in the paleontological record. Broader Impacts:   The project will continue the mission of UTSA and AMNH in integrating research with education by enabling the training of students from groups underrepresented in STEM. UTSA is a Hispanic-Serving Community with a population of 45% first-generation college students. Undergraduate and graduate students will be involved in the project through UTSA and CBC-AMNH's Enhancing Diversity in Conservation Science Initiative, which focuses on increasing recruitment, retention, and success of historically underrepresented groups in the conservation sciences. The research will inform development of an open access teaching module on applications of museum collections and phylogenomics to biodiversity conservation for the CBC-AMNH Network of Conservation Educators and Practitioners. At UTSA a partnership with Alamo colleges will be developed to provide community college students the opportunity to gain hands-on experience at UTSA research lab during the summer. Finally, the proposed research will inform the conservation of endangered lorisiforms, which are typically neglected in both research focus and conservation attention. The phylogenomic work will be extremely important especially for the conservation of critically endangered lorisiforms including Paragalago rondoensis and Nycticebus javanicus, which are both list on the 2018-2020 Top 25 Most Endangered Primates. The research will directly feed into ongoing conservation efforts led by CBC-AMNH on slow loris conservation, particularly in Vietnam.