A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making

Abstract

A recently published macrogenetic dataset of California’s flora and fauna, CaliPopGen, comprehensively summarizes population genetic research published between 1985-2020. Integrating these genetic data into the requisite “best available science” upon which conservation professionals rely should facilitate the prioritization of populations based on genetic health. We evaluate the extent to which the CaliPopGen Dataset provides genetic diversity estimates that are 1) unbiased, 2) sufficient in quantity, 3) cover entire species’ ranges, and 4) include potentially adaptive loci. We identified genetic diversity estimates for 4,462 spatially-referenced populations of 432 species, confirming California’s rich published history of population genetics research. Most recent studies used microsatellites markers, which have uniquely high levels of variation, and estimates of all genetic metrics varied significantly across marker types. Most studies used less than 10 loci for inferences, rendering parameter estimates potentially unreliable, and covered small spatial extents that include only a fraction of the studied species’ California distribution (median 16.3%). In contrast, the ongoing California Conservation Genomics Project (CCGP) aims to cover the full geographical and environmental breadth of each species’ occupied habitats, and uses a consistent approach based on whole-genome data. However, the CCGP will sequence only 12% of the number of individuals, and covers only about half the evolutionary diversity, of the CaliPopGen Database. There is clearly a place in the evaluation of the genetic health of California for both approaches going forward, especially if differences among studies can be minimized, and overlap emphasized. A complementary use of both datasets is warranted to inform optimal conservation decision-making.

The phylogeny of California, and how it informs setting multispecies conservation priorities

“…While the CaliPopGen Database has considerably greater taxonomic coverage than CCGP, the historical data are overwhelmingly based upon microsatellites, AFLPs, mtDNA, and single or several gene nDNA studies, and are often limited to relatively small portions of each species’ geographic range ( Beninde et al in press ). In contrast, the CCGP is generating whole genome sequencing data for individuals across the full extent of each species’ range in California ( Shaffer et al 2022 ), a dataset which delivers many benefits in applied conservation (reviewed extensively in e.g.…”

Journeying towards best practice data management in biodiversity genomics

“…Furthermore, these information-rich biodiversity datasets have immense reuse value that can only be realised if the data-generating researchers/institutions undertake careful data management (Toczydlowski et al, 2021;Crandall et al, 2023). These secondary use cases may diverge from the original purpose of data generation (Hoban et al, 2022;Leigh et al, 2021), and can provide additional valuable insights (e.g., Crandall et al, 2019), enhancing the value of these data to the research community and their potential impacts on society (e.g., Beninde et al, 2022;Exposito-Alonso et al, 2022).…”