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

Joscha Beninde; Erin M. Toffelmier; Aarron Andreas; Celina Nishioka; Meryl Slay; Ashley Soto; Justin P Bueno; Germar Gonzalez; Hannah V. Pham; Molly Posta; Jordan L. Pace; H. Bradley Shaffer

doi:10.1038/s41597-022-01479-z

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

Joscha Beninde, Erin M. Toffelmier, Aarron Andreas, Celina Nishioka, Meryl Slay, Ashley Soto, Justin P Bueno, Germar Gonzalez, Hannah V. Pham, Molly Posta, Jordan L. Pace, H. Bradley Shaffer

Research output: Contribution to Journal › Article › Academic › peer-review

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.

Original language	English
Article number	380
Journal	Scientific Data
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41597-022-01479-z
Publication status	Published - 1 Dec 2022
Externally published	Yes

Funding

We thank Pauline Ordonez for her contribution to the first screening of articles. David Ackerley provided access to the unpublished Baker Seed Herbarium (BSH) Database. Many researchers helped us with their expertise: in particular, we thank Bruce Baldwin & Jason Alexander (UC Berkeley); Felipe Zapata, Lawren Sack & Nathan Kraft (UCLA); Nick Jensen (CNPS); Jeb McKay Bjerke & Kristi Lazar (CDFW). J.B., E.M.T. and H.B.S. conceptualized the study and supervised data extraction, curation, and validation, which were conducted by A.A., C.N., M.S., A.S., M.P., H.V.P., J.L.P., J.P.B., G.G. M.S. curated the animal life history dataset; M.P. curated the plant life history dataset. J.B. and E.M.T. wrote an initial draft of the manuscript, with assistance from C.N. and A.S. All authors contributed to review and editing of the manuscript, and J.B. and E.M.T. finalized the manuscript. Funding for J.B. and E.M.T. was provided by the UCLA La Kretz Center for California Conservation Science and the California Conservation Genomics Project. J.B. also received funding by the German Science Foundation (DFG: BE 6887/1-1).

Funders	Funder number
Felipe Zapata
Lawren Sack & Nathan Kraft
UCLA La Kretz Center for California Conservation Science
National Institute of General Medical Sciences	R25GM055052
California Department of Fish and Game	BE 6887/1-1
University of California, Los Angeles
Deutsche Forschungsgemeinschaft

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title = "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.",

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AU - Soto, Ashley

AU - Bueno, Justin P

AU - Gonzalez, Germar

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AU - Pace, Jordan L.

AU - Shaffer, H. Bradley

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

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