Conservation genomics and disease ecology of the Texas tortoise Gopherus berlandieri

Conservation genomics and disease ecology of the Texas tortoise Gopherus berlandieri Conservation genomics and disease ecology of the Texas tortoise, Gopherus berlandieri Genome Sequencing We will obtain the tortoise specimen for genome sequencing and send to the Yale Center for Genome Analysis for sequencing by Illumina NovaSeq S4. In addition, we will generate a long-read high-quality reference genome through PacBio sequencing and Hi-C scaffolding through a contract to Dovetail Genomics, which Drs. Dolby and Kusumi have used for the Mojave and Sonoran desert tortoise genomes. We will use our pipeline described in Tollis et al., (2017) and Dolby et al. (2020) for genome annotation. This reference genome will be used to map the population sequence data. This genome-scale data set will provide finer-scale information for the Texas tortoise than previous sequencing methods. Population Data Analysis We will perform in-house DNA extraction for 66 tortoise blood samples and send samples to the Yale Center for Genome Analysis to sequence across two lanes of Illumina NovaSeq S4. We will perform quality control on the read data, map reads, identify genomic variants based on an open source pipeline we have previously used (Dolby et al 2021). Using PCA, DAPC, and fastSTRUCTURE we will identify population structure across the range and infer demographic history of populations using PSMC and SMC++. This should reveal whether the historical demography of populations varies across regions, which is important for their appropriate management. We will perform whole genome scans calculating measures of diversity and divergence (e.g., Fst) as well as performing outlier scans (e.g., BayeScan) to determine regions across the genome that may be uniquely adapted to local conditions, and which would play a role in the survivability of populations in the context of climate change as well as the appropriateness of translocating tortoises from one region to another.