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

Abstract

Incorporating measures of taxonomic diversity into research and management plans has long been a tenet of conservation science. Increasingly, active conservation programs are turning towards multi-species landscape and regional conservation actions, and away from single species approaches. This is both a reflection of changing trends in conservation science and advances in foundational technologies, including genomics and geospatial science. Multi-species approaches may provide more fundamental insights into evolutionary processes and equip managers with a more holistic understanding of the landscapes under their jurisdiction. Central to this approach are data generation and analyses which embrace and reflect a broad range of taxonomic diversity. Here we examine the family-level phylogenetic breadth of the California Conservation Genomics Project (CCGP) based on family-level phylogenetic diversity, family-level phylogenetic distinctness, and family richness. We place this in the context of the diversity present in California and compare it to the 35-plus years of genetic research compiled in the CaliPopGen Database. We found that the family-level phylogenetic diversity in the CCGP reflected that of California very well, slightly over-representing chordates and under-representing arthropods, and that 42% of CCGP phylogenetic diversity represented new contributions to genetic data for the state. In one focused effort, the CCGP was able to achieve roughly half the family-level phylogenetic diversity studied over the last several decades. To maximize studied phylogenetic diversity, future work should focus on arthropods, a conclusion that likely reflects the overall lack of attention to this hyper diverse clade.

A genome assembly of the Yuma myotis bat, Myotis yumanensis

“…Our Yuma bat assembly provides a high quality, near-chromosome level resource in support of these research efforts. At the level of California biodiversity, the Yuma bat genome is the first chiropteran reference genome sequenced by the CCGP, filling a major gap in our emerging phylogeny of California biodiversity ( Toffelmier et al 2022 ). It contributes a new reference genome that will help in resolving outstanding questions on both species delimitation and phylogenetic relationships for the hyperdiverse genus Myotis, including the role of hybridization in shaping contemporary genomic architecture ( Korstian et al 2022 ).…”

Reference genome of the bicolored carpenter ant, Camponotus vicinus

“…Furthermore, the bicolored carpenter ant reference genome serves as a powerful tool for both evolutionary and conservation biologists to better understand the genetic makeup of the C. vicinus species complex, which can inform taxonomic studies of this group and contribute to efforts of the California Conservation Genomics Project (CCGP) ( Shaffer et al 2022 ). It fills an important phylogenetic gap in our genomic understanding of California biodiversity ( Toffelmier et al 2022 ). Future work comparing multiple genomes of C. vicinus across California will additionally help identify regions that are associated with species resilience and biodiversity, and aid in development of effective conservation and management strategies accordingly ( Fiedler et al 2022 ).…”

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

“…The disadvantages primarily center on the number of species and populations that can be covered. The CCGP has covered roughly half of the evolutionary diversity contained in the historical database ( Toffelmier et al 2022 ), and doing so required a level of funding and coordination that has never been available previously.…”