CaliPopGen: A genetic and life history database for the fauna and flora of California

Abstract

CaliPopGen is a database of population genetic data for native and naturalized eukaryotic species in California, USA. It summarizes the published literature (1985–2020) for 5,453 unique populations with genetic data from more than 187,394 individuals and 448 species (513 species plus subspecies) across molecular markers including allozymes, RFLPs, mtDNA, microsatellites, nDNA, and SNPs. Terrestrial habitats accounted for the majority (46.4%) of the genetic data. Taxonomic groups with the greatest representation were Magnoliophyta (20.31%), Insecta (13.4%), and Actinopterygii (12.85%). CaliPopGen also reports life-history data for most included species to enable analyses of the drivers of genetic diversity across the state. The large number of populations and wide taxonomic breadth will facilitate explorations of ecological patterns and processes across the varied geography of California. CaliPopGen covers all terrestrial and marine ecoregions of California and has a greater density of species and georeferenced populations than any previously published population genetic database. It is thus uniquely suited to inform conservation management at the regional and state levels across taxonomic groups.

Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

“…As a consequence, the California Floristic Province was the only North American ecoregion to qualify for the first global assessment of 25 Biodiversity Hotspots, defined as regions that are both species rich and at greatest threat of species loss; it remains on the expanded list of 36 global hotspots (Mittermeier et al 2004). California also has a rich history of research on the genetics of natural populations (Beninde et al, 2022). However, these earlier studies, while individually useful, lack the standardized sampling, data consistency and completeness, and landscape analyses required for drawing broadly comparative conclusions that are critical for broad scale conservation.…”

“…The CCGP also will provide a platform to explore some of the more vexing questions in conservation biology, such as whether species with limited ranges should be managed or protected in the same way as widely distributed ones, whether species formerly widespread but now limited in geographic scope should be stewarded differently than species that have always had small ranges (Robinson et al 2016), and whether, and when, genome-level data are worth collecting for species that have been previously analyzed with more restricted data sets (Beninde et al 2022;Gallego-García et al 2021). With the rate of extinction in the last century estimated to be 22 times faster than the historical baseline rate (Ceballos et al 2015) rapidly gathering largescale landscape genomic datasets, complemented by highquality reference genomes, is one positive step that can and should be made, to understand biodiversity as it now exists, and doing what we can to ensure resilience in the face of a rapidly changing world.…”

“…From the early allozyme-driven heyday of the 1970s to our current emphasis on genomic data sets, our ability to improve the capacity of resource managers to protect, steward, and relocate individuals and/or populations in the face of climate change (Supple and Shapiro 2018) has been remarkable. Nowhere has this progress been more pronounced than California (Beninde et al 2022). In the last few years, the integration of remote sensing products with genomic data 1 for a complete list of all species and their categorization into these four sets of mapped species.…”

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

“…As a result, particularly in the field of conservation genetics and genomics, the bulk of conservation management actions are carried out in single species frameworks. For example, in a recent compilation of population genetics research from across the state of California, the mean number of species per publication was 1.3 (range: 1 to 33, SD = 1.7, data derived from Beninde et al 2022 ), underscoring the species-oriented approach of most genetic research over the last several decades. In addition to precluding work on broad-scale evolutionary processes for a wide range of taxonomic groups, single-species assessments may also concentrate research and management funds to well-known or well-studied species, diverting attention from lesser-known species ( Martín-López et al 2011 ).…”

“…We therefore focus on family-level metrics of diversity. We calculated several measures of the fraction of the total family-level PD in California and compared the fraction of that diversity represented by the CCGP to that captured by 35 yr of genetics- and genomics-based research in the state collected in the CaliPopGen Database, a recent compilation of virtually all population genetic research in California from 1985 to 2020 ( Beninde et al 2022 ). These efforts allowed us to place the CCGP into an appropriate phylogenetic context for the state, identify taxonomic knowledge gaps in existing California biodiversity research, and provide recommendations for future efforts to increase conservation efficacy by maximizing phylogenetic coverage, across the state and beyond.…”