Supplement: The Role of Hybridization in Generating Biodiversity: Insights from Genomics of Madagascar's True Lemurs (Eulemur)

DESCRIPTION OF PROPOSED SUPPORT Overview of NSF grant DEB-2207198 The overarching goal of the funded NSF project (DEB-2207198) is to understand how new species evolve, particularly when reproductive barriers are not fully formed. The first objective is to investigate patterns of gene flow, selection, and genome architecture across a hybrid zone within Madagascar’s true lemurs (Eulemur). The second and third objectives explore how gene flow has shaped the deeper evolutionary history of the entire Eulemur radiation and whether there are extrinsic factors that promote hybridization. This project is illuminating the origins of species in a biodiversity hotspot and providing useful information to systematists contending with signatures of gene flow in their analyses. One of the key deliverables from this project is the generation of a de novo Eulemur whole genome. This genome is a critical component of our research, as it provides the necessary framework for our population- and clade-wide analyses. It will also be a valuable resource for future scientists, as it will be chromosome-scale, annotated, and freely available to the public. Proposed Work to be Supported by CLB Supplement During Year 1 of this grant, we completed the lab work necessary for whole-genome library preparation and DNA sequencing. Now that the sequencing reads are in-hand, a substantial amount of bioinformatic work is still needed to bring the whole genome to life: data quality assessment and control, sequence assembly, scaffolding, gene annotation, curation, and publication in a public data repository. Co-PI Dr. Kathryn Everson is leading this bioinformatic effort. However, this work is facing delays due to Dr. Everson’s impending family leave. Dr. Everson’s current institution, Oregon State University, is home to the Center for Quantitative Life Sciences (CQLS; https://cqls.oregonstate.edu/bioinformatics). Through the CQLS, faculty members can hire experienced bioinformaticians to assist with their research. The proposed CLB supplement would be used to fund one bioinformatician, Dr. Andrew Black, at 1.0 FTE for 3 months (see Budget Justification). It would also provide a small amount of funding (0.02 FTE) for the CQLS director, Dr. Andrew Kronmiller, for supervision, budget, and oversight. With bioinformatics assistance from the CQLS, Dr. Everson’s research program can be sustained while she is on a 3-month family leave. Dr. Black is well-qualified to assist with the next stages in the de novo genome assembly pipeline, as he has roughly 10 years of postgraduate experience in vertebrate genetics/genomics. He has experience assembling and annotating eukaryotic genomes, having published annotated genome assemblies for both fish (Black et al., 2021) and birds (Black et al., 2022). Dr. Black also has experience in conservation genetics (Evans et al., 2019) and conservation genomics (Black et al., 2017; Bylsma et al., 2021; DeWoody et al., 2022). He serves as a senior bioinformatics scientist, consulting on numerous projects and teaching graduate level courses on genomic approaches as OSU. Because of Dr. Black’s experience in bioinformatics, high performance computing, conservation genomics, and evolution, he is well equipped to complete this portion of the project.