About

H. Bradley Shaffer is a Distinguished Professor and the Director of the UCLA La Kretz Center for California Conservation Science within the Department of Ecology and Evolutionary Biology. His research focuses on conservation biology, ecology, and evolutionary biology, primarily concerning amphibians and reptiles. His recent projects have centered on conservation genomics, including leading the California Conservation Genomics Project (CCGP), which analyzes 250 species of plants and animals using genomic analysis to aid in conserving California's biodiversity. Shaffer has conducted phylogenetic analyses of turtles and tortoises, providing an evolutionary framework essential for their conservation, and has focused ecological and genetic research on endangered species such as the California tiger salamander and various frogs, toads, and salamanders. In addition to his academic appointment, he is the Director of the UCLA Stunt Ranch Reserve and serves as the campus liaison to the UC Natural Reserve System, contributing to conservation efforts and research infrastructure in California.

Research topics

• Ecology
• Biology
• Environmental resource management
• Political Science
• Zoology
• Environmental ethics
• Environmental science
• Public relations
• Geography
• Epistemology
• Genetics
• Philosophy

Selected publications

• A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, <i>Spea hammondii</i>

  Journal of Heredity · 2026-03-05

  articleSenior author

  Abstract We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

  PublisherDOI

• Chytrid fungal infections in alpine toads proliferate during winter dormancy

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-10

  preprintOpen accessSenior author

  Abstract The spread and impact of wildlife pathogens is often seasonal, and identifying the seasons of high impact is critical to biodiversity and public health management. Here, we report new evidence that winter host dormancy, a period generally neglected in terms of pathogen seasonal dynamics, promotes the spread of infection from the globally threatening amphibian fungal pathogen, Batrachochytrium dendrobatidis (Bd) . Bd surveillance of Yosemite toads ( Anaxyrus canorus ) during their first year of life showed that: (a) detectable Bd infections were nearly absent in the tadpole stage and immediately after metamorphosis, (b) Bd prevalence and intensity gradually increased during the first two months of post-metamorphic growth, and (c) Bd prevalence and intensity increased four-fold in toads during the first winter dormancy. High prevalence and intensity of Bd infections after winter dormancy was observed in yearling toads across two consecutive years and was much higher than that observed in aquatically breeding adults during the same timeframe. To our knowledge, this is the first evidence from wild amphibians that Bd proliferates during terrestrial winter dormancy. This discovery calls for a reconsideration of the seasons enabling the proliferation and persistence of Bd and identifies recently metamorphosed hosts as overwinter Bd reservoirs. More generally, the study underscores the importance of host dormancy in pathogen persistence and seasonal infection spread.

  PublisherOA PDFDOI

• Genome assembly and annotation of a deep-diving pinniped, the northern elephant seal ( <i>Mirounga angustirostris</i> )

  Journal of Heredity · 2025-10-14

  articleOpen access

  The northern elephant seal (Mirounga angustirostris) is the largest pinniped species in the northern hemisphere. The species is classified as being of least conservation concern by the IUCN-a triumph of conservation efforts despite hunting pressure that nearly led to its extinction more than a century ago. The historical range of the northern elephant seal extended from Baja California to Alaska, but overexploitation caused a severe demographic collapse and genetic bottleneck, with only an estimated 10 to 30 survivors left on Isla Guadalupe, Mexico. As part of the California Conservation Genomics Project, we generated a de novo reference genome and annotation for M. angustirostris, combining PacBio HiFi long-read sequencing data with Dovetail Omni-C chromatin conformation data. Our assembly has a primary haplotype genome length of 2,430,321,998 base pairs (2.4 Gb), with the longest contig of 144 Mb, contig N50 of 58 Mb, largest scaffold of 215 Mb, and scaffold N50 of 154 Mb. The secondary assembly haplotype consists of 422 scaffolds, spanning 2.45 Gb, with contig N50 of 61.24 Mb, scaffold N50 of 152.94 Mb, the largest contig of 204.14 Mb, and the largest scaffold of 216.16 Mb. We used the primary assembly and annotation for a preliminary investigation of repeat element content, historical demography, genome-wide heterozygosity, and loss-of-function variants. We found that M. angustirostris has one of the lowest estimates of genetic diversity of any marine mammal and a complex demographic history that may have reduced genetic diversity several times. This newly constructed genome will facilitate future in-depth explorations into the mechanisms behind resilience and recovery after a severe population bottleneck.

  PublisherDOI

• Genome assembly for the Sierra Nevada Parnassian ( <i>Parnassius behrii</i> ) and a brief review of butterfly genome sizes

  Journal of Heredity · 2025-12-16

  articleOpen accessSenior author

  The Sierra Nevada Parnassian (Parnassius behrii W. H. Edwards, 1870) (Lepidoptera: Papilionidae) is a high-elevation specialist butterfly endemic to the Sierra Nevada, California. We present a genome assembly for P. behrii, representing the first major genomic resource for the Parnassius phoebus species complex. The assembly consists of two haplotypes, 1.59 Gb and 1.46 Gb in length, with contig N50 values of 10.93 Mb and 11.84 Mb, scaffold N50 values of 52.56 Mb and 51.90 Mb, scaffold L50 values of 13 and 14, and BUSCO completeness scores of 98.7% and 94.4%, respectively. Both haplotypes are highly contiguous, with 31 chromosome-length scaffolds, including putative Z and W sex chromosomes. We annotated the genome with NCBI's EGAPx pipeline, integrating database and novel transcript alignment with Hidden Markov Model-based gene predictions, yielding 17 191 genes with a BUSCO score of 98.1%. RepeatMasker identified that 26.68% (424.97 Mb) of the genome consists of repetitive elements. We also assembled a mitochondrial genome for P. behrii (15 391 bp) containing 2 rRNAs, 22 unique transfer RNAs, and 13 protein-coding genes. We also reviewed 514 high-quality butterfly genomes available from the National Center for Biotechnology Information (NCBI). Parnassius species were observed to have the largest genomes, with P. behrii being the largest. This assembly provides a foundational resource for whole-genome research on P. behrii and the broader P. phoebus complex, enabling analyses of evolutionary differentiation, local adaptation, inbreeding, gene flow, speciation, and conservation practices.

  PublisherOA PDFDOI

• <scp>NewtCap</scp> : An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts)

  Ecology and Evolution · 2025-08-01 · 3 citations

  articleOpen access

  ABSTRACT Salamanders have large and complex genomes, hampering whole genome sequencing. However, reduced representation sequencing provides a feasible alternative to obtain genome‐wide data. We present NewtCap: a sequence capture bait set that targets c . 7 k coding regions across the genomes of all true salamanders and newts (the family Salamandridae, also known as “salamandrids”). We test the efficacy of NewtCap, originally designed for the Eurasian Triturus newts, in 30 species, belonging to 17 different genera that cover all main Salamandridae lineages. We also test NewtCap in two other salamander families. We discover that NewtCap performs well across all Salamandridae lineages (but not in the salamander families Ambystomatidae and Hynobiidae). As expected, the amount of genetic divergence from the genus Triturus correlates negatively to capture efficacy and mapping success. However, this does not impede our downstream analyses. We showcase the potential of NewtCap in the contexts of; (1) phylogenomics, by reconstructing the phylogeny of Salamandridae, (2) phylogeography, by sequencing the four closely related species comprising the genus Taricha , (3) hybrid zone analysis, by genotyping two Lissotriton species and different classes of interspecific hybrids, and (4) conservation genetics, by comparing Triturus ivanbureschi samples from several wild populations and one captive‐bred population. Overall, NewtCap has the potential to boost straightforward, reproducible, and affordable genomic studies, tackling both fundamental and applied research questions across salamandrids.

  PublisherOA PDFDOI

• Building genomically‐informed demographic models to guide management of invasive hybrids

  Ecological Applications · 2025-10-01

  articleOpen accessSenior author

  Abstract Invasive species present one of the most challenging threats to native biodiversity, particularly when they hybridize with imperiled native taxa. In California, hybridization between the endangered California tiger salamander (“CTS,” Ambystoma californiense ) and the invasive barred tiger salamander (“BTS,” Ambystoma mavortium ) is one of the best understood examples of this management challenge. Reclusive life history and cryptic hybridization, often on private land, render eradication programs difficult or impossible. This study evaluates hydroperiod management as a tool to conserve and maintain native CTS populations threatened by hybridization. We adapt a recent, empirically informed Bayesian integral projection model (IPM) for CTS to incorporate new results that link genotype and ecology to fitness, and use this individual‐based model to evaluate alternative management scenarios. We found overwhelming support for the importance of hydrology in both native and hybrid populations, where a 10‐day increase in hydroperiod can increase population growth rate () 17% and triple the carrying‐capacity ( K ). We assess hydroperiod management as a strategy to control and contain hybrid introgression, and suggest a three‐pronged strategy. First, for native populations not at risk of hybridization, hydroperiod should be increased to &gt;120 days to support robust populations. Second, within the geographic hybrid zone, hydroperiod should be reduced to limit hybrid populations, maintain vernal pool function, and improve the efficiency of adult hybrid removal. Finally, our models indicate that managers should combine hydroperiod management with rapid field‐based genotyping and hybrid removal, focusing on ponds where hybrids are rare, typically at the leading edge of the hybrid swarm. Efforts should also prioritize high‐intensity surveys and early removal as opposed to long‐duration (10+ years), lower effort surveys. This study demonstrates the value of integrating demographic, genetic, and ecological information to evaluate strategies for endangered species management, and may serve as modeling framework for a wide variety of imperiled species.

  PublisherOA PDFDOI

• Genomic and ecological divergence support recognition of a new species of endangered Satyrium butterfly (Lepidoptera, Lycaenidae)

  ZooKeys · 2025-04-17 · 2 citations

  articleOpen access

  We describe a highly isolated population of hairstreak butterfly from Waterton Lakes National Park, Alberta, Canada, as a new species, Satyrium curiosolus sp. nov. , previously recognized as Satyrium semiluna (Half-moon Hairstreak). We propose “Curiously Isolated Hairstreak” as the common name due to its disjunct and unusual distribution. Previous whole-genome analyses revealed S. curiosolus has extremely low genomic diversity and is highly divergent from the nearest S. semiluna populations in British Columbia and Montana, more than 400 km distant. Further analysis suggested prolonged inbreeding and isolation for up to ~40,000 years BP. Ecological niche modeling indicated that S. curiosolus occupies environmental conditions that are distinct from S. semiluna , suggesting niche divergence driven by long-term geographical and ecological separation. While host plant and ant associations have not been definitively resolved, they likely differ between S. curiosolus and S. semiluna . As part of this description, we provide whole-genome consensus sequences for each individual of the type series and identify 21,985 single nucleotide polymorphisms (SNPs) that are divergently fixed between S. curiosolus and S. semiluna , including 117 unlinked SNPs distributed across the genome as putative diagnostic markers. Previously listed as Endangered in Canada as the Waterton population of S. semiluna , S. curiosolus should retain this conservation status due to its extreme isolation, small population size, and flatlined genomic diversity. We propose species recognition as a testable hypothesis under the General Lineage Concept and recommend further research to explore the taxonomy, ecological relationships, and conservation of the greater species complex, including S. curiosolus , S. semiluna , and S. fuliginosa .

  PublisherOA PDFDOI

• A reference genome for Colusa grass, <i>Neostapfia colusana</i> , a threatened and endangered California vernal pool plant

  Journal of Heredity · 2025-10-04 · 2 citations

  articleOpen access

  Colusa grass, Neostapfia colusana, is a listed California endangered plant endemic to the vernal pools of California. Vernal pool habitat is highly degraded and threatened by further anthropological development, with only 10% of its historical range remaining. With only 42 confirmed extant populations, it is a major conservation concern to understand patterns of genomic diversity. Here we report the first complete genome assembly of Colusa grass. The assembly includes two haplotypes: haplotype one spans 2.13 Gb with contig N50 of 10.62 Mb, scaffold N50 of 112.31 Mb, and BUSCO completeness of 98.1%. Haplotype two spans 2.04 Gb with contig N50 of 10.05 Mb and scaffold N50 of 138.31 Mb, with a BUSCO completeness of 97.6%. This genome assembly will allow for in-depth analysis of genomic variation and gene flow in populations of this threatened grass and will be a major asset to studies supporting its conservation. This genome was assembled as part of the California Conservation Genomics Project, which contributes to a collection of resources and tools to support state-wide conservation efforts.

  PublisherDOI

• The nitrogen‐fixing fern <i>Azolla</i> has a complex microbiome characterized by varying degrees of cophylogenetic signal

  American Journal of Botany · 2025-02-22 · 6 citations

  articleOpen access

  PREMISE: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown. METHODS: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction. RESULTS: Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome. CONCLUSIONS: These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.

  PublisherOA PDFDOI

• Reference genome of the Gophersnake, <i>Pituophis catenifer</i> (Serpentes: Colubridae)

  Journal of Heredity · 2025-04-10

  articleSenior author

  The Gophersnake, Pituophis catenifer, is a habitat generalist that ranges throughout the western half of the United States and southward into México. Five of the six subspecies, P. catenifer affinis (Sonoran Gophersnake), P. catenifer annectens (San Diego Gophersnake), P. catenifer catenifer (Pacific Gophersnake), P. catenifer deserticola (Great Basin Gophersanke), and P. catenifer pumilus (Santa Cruz Island Gophersnake), occur in California and span virtually all the state's diverse terrestrial habitats. These subspecies are ecologically and morphologically distinct from one another, although existing genetic data indicate there is genetic admixture across some of their contact zones. Given that these subspecies occur in such different environments they will not all respond to climate change and anthropogenic stressors equally. Here, we report a new, chromosome-level assembly of P. catenifer as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 426 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.5 Mb, a scaffold N50 of 161 Mb, and BUSCO completeness score of 95.3%. This genome will be a foundational resource for future studies on the conservation, adaptation, biogeography, and systematics of P. catenifer.

  PublisherDOI

Recent grants

• SG: Will phylogenomics resolve the most difficult parts of the tree of life: an empirical evaluation with the turtle genus Pseudemys

  NSF · $150k · 2015–2018

• Turtles of the World: Global Systematics for an Imperiled Clade

  NSF · $254k · 2012–2014

• Collaborative Research: Gauging Introgression: Variation Across the Genome in Mode and Tempo of Natural Selection in a Tiger Salamander Hybrid Zone

  NSF · $257k · 2005–2009

• Turtles of the World: Global Systematics for an Imperiled Clade

  NSF · $577k · 2008–2012

• The Cladogenic Record for Turtles: Paleontological Dates, DNA Sequences and a Test of the Molecular Clock

  NSF · $204k · 1993–1996

Frequent coauthors

• Beth Shapiro

  763 shared

• Thomas J. Near

  Yale Peabody Museum

  755 shared

• Felipe Zapata

  752 shared

• F. Keith Barker

  Science Museum of Minnesota

  752 shared

• Joël Cracraft

  American Museum of Natural History

  752 shared

• David Bryant

  751 shared

• Hélène Morlon

  Centre National de la Recherche Scientifique

  751 shared

• Richard E. Glor

  University of Kansas

  751 shared

Education

• Ph.D., Ecology and Evolutionary Biology

  University of California, Los Angeles

  1990

• M.S., Ecology and Evolutionary Biology

  University of California, Los Angeles

  1986

• B.S., Zoology

  University of California, Los Angeles

  1983