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. 2022 Jul 5;9(1):380.
doi: 10.1038/s41597-022-01479-z.

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

Joscha Beninde #  1 , Erin M Toffelmier #  2   3 , Aarron Andreas  4 , Celina Nishioka  4 , Meryl Slay  4 , Ashley Soto  4 , Justin P Bueno  4 , Germar Gonzalez  4 , Hannah V Pham  4 , Molly Posta  4 , Jordan L Pace  4 , H Bradley Shaffer  5   4
Affiliations

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

Joscha Beninde et al. Sci Data. .

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Taxonomic breakdown of species represented in the CaliPopGen database. Values in parentheses represent the total number of species as a percentage of the number of unique species in the database.
Fig. 2
Fig. 2
The six predominant marker types included in the CaliPopGen database, demonstrating different publication trends through time. The grey bars in each panel are the total number of published studies across all marker types (and are the same in each panel).
Fig. 3
Fig. 3
Maps of data contained in the CaliPopGen databases. (A) All unique sampling locations of both the population genetic (Dataset 1) and pairwise comparison (Dataset 2) data. The inset shows the location of California within the contiguous USA. (B) The number of unique populations in CaliPopGen per California ecoregion. Note the relative under-representation of inland desert regions (yellow) and over-representation of coastal ecoregions (purple-blue). (C) The number of unique populations of the populations genetic Dataset 1 per 20km raster cell. (D) The number of straight-line pairwise comparisons of Dataset 2 per 20km raster cell.
Fig. 4
Fig. 4
Flow chart of the data collection process that generated the CaliPopGen databases.
See this image and copyright information in PMC

References

    1. Dobson AP, Rodriguez JP, Roberts WM, Wilcove DS. Geographic Distribution of Endangered Species in the United States. Science (New York, N.Y.) 1997;275:550–553. doi: 10.1126/science.275.5299.550. - DOI - PubMed
    1. Griffith, G. E. et al. Ecoregions of California (poster): U.S. Geological Survey Open-File Report 2016-1021, with map, scale 1:1,100,000. Available at 10.3133/ofr20161021 (2016).
    1. Spalding MD, et al. Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas. BioScience. 2007;57:573–583. doi: 10.1641/B570707. - DOI
    1. He M, Gautam M. Variability and Trends in Precipitation, Temperature and Drought Indices in the State of California. Hydrology. 2016;3:14. doi: 10.3390/hydrology3020014. - DOI
    1. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GA, Kent J. Biodiversity hotspots for conservation priorities. Nature. 2000;403:853–858. doi: 10.1038/35002501. - DOI - PubMed

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