Oral Paper

         Population Genetics/Genomics

Conservation genomics of an endangered Asteraceae (Deinandra increscens subsp. villosa) native to the Central Coast of California

Presenting Author
Susan McEvoy
Description
California is one of the most biodiverse regions in the world, but more than 30% of its species are at risk of extinction. One such taxon is Deinandra increscens subsp. villosa (Gaviota tarplant), endemic to Santa Barbara County, where it exists in small and fragmented populations of the coastal and inland areas. Deinandra increscens subsp. villosa is a small, yellow, insect-pollinated, annual with disk and ray florets common to most Asteraceae. The Asteraceae family is large, comprising 10% of angiosperm species, but not well-represented in genomic studies. Deinandra increscens subsp. villosa is listed as Endangered under both the Federal and State Endangered Species Act. Since 2016, the Strauss Wind Project has been constructing a large turbine wind farm within the core of the distribution of D. increscens subsp. villosa. While this project will provide clean energy to 44,000 homes, turbine construction will directly impact some number of plants within the construction footprint and may impact ongoing biological processes (e.g., pollen transfer) through normal turbine operation. potentially eliminating sources of adaptive genetic diversity. As part of the permitting requirements, regulatory agencies require a detailed genetic study of D. increscens subsp. villosa. As such, we are applying conservation genomics approaches to understand the genetic impact of development among the Strauss population and the broader native range. This will include population genetics, landscape genetics, and time-to-extinction modeling. Samples from almost 1,000 individuals were collected from across the range over the course of three years: 384 in year 1, and 288 in years 2 and 3.  Ninety-six from each year will be sequenced at 30x with the remainder at 4x. Reference genome sequencing includes 40x of Pacific Biosciences HiFi, 60x of Oxford Nanopore Technologies PromethION, and 70x Dovetail OMNI-C for scaffolding. Initial estimates based on flow cytometry and k-mer profiling indicate that the plant is a diploid around 1.7-2.3 Gbp in length. We are currently testing assemblies with Verkko, Canu, and Flye, and this will be followed by scaffolding with 3D-DNA, and gene annotation with both de novo and homology methods. For the transcriptome, root and shoot tissue was collected from 3 seedlings plus stem and leaf from the adult reference individual. From these eight samples, we generated 150 bp PE Illumina sequencing which will be assembled using the Oyster River Protocol. We will conduct population genetics analyses to discern population structure, effective population size, and demographic history; levels of inbreeding and runs of homozygosity; and amounts of admixture and gene flow between populations. We will incorporate environmental metadata to examine the effects of landscape and climate on populations, and we will integrate genetics and life history traits to model time-to-extinction. Together, these analyses encompass a three-year plan of evaluation which will be followed by additional assessments in 10 years. Results will help inform ongoing development within the Strauss project footprint. This study will also have broader impacts on policies regarding endangered species in California by providing an exemplary study of implementing genomic analysis for conservation planning.