H. Bradley Shaffer

H. Bradley Shaffer
University of California, Los Angeles | UCLA · Department of Ecology and Evolutionary Biology

About

335
Publications
137,752
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
13,390
Citations

Publications

Publications (335)
Article
Conservation science and environmental regulation are sibling constructs of the latter half of the 20th century, part of a more general awakening to humanity’s effect on the natural world in the wake of two world wars. Efforts to understand the evolution of biodiversity using the models of population genetics and the data derived from DNA sequencin...
Article
Sculpins (Family Cottidae) are generally cold-temperate intertidal reef fishes most commonly found in the North Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Woolly Sculpin, Clinocottus analis, to establish a genomic model for understanding phylogeographic structure of inshore marine taxa al...
Article
Linanthus parryae is a widespread annual plant species found in washes and sandy open habitats across the Mojave Desert and Eastern Sierra Nevada of California. Studies in this species have played a central role in evolutionary biology, serving as the first test cases of the shifting balance theory of evolution, models of isolation by distance, and...
Article
Full-text available
A recently published macrogenetic dataset of California’s flora and fauna, CaliPopGen, comprehensively summarizes population genetic research published between 1985-2020. Integrating these genetic data into the requisite “best available science” upon which conservation professionals rely should facilitate the prioritization of populations based on...
Article
The rubber boa, Charina bottae is a semi-fossorial, cold-temperature adapted snake that ranges across the wetter and cooler ecoregions of the California Floristic Province. The rubber boa is one of two species in the family Boidae native to California and currently has two recognized subspecies, the Northern rubber boa Charina b. bottae and the Sou...
Article
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 conservatio...
Article
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in Cal...
Article
Surfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the...
Article
Full-text available
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,...
Article
Keystone species are known to play a critical role in kelp forest health, including the well-known killer whales,sea otter,sea urchin,kelp trophic cascade in the Aleutian Islands, Alaska, USA. In California, a major player in the regulation of sea urchin abundance, and in turn, the health of kelp forests ecosystems, is a large wrasse, the Californi...
Article
The mountains of southern California represent unique, isolated ecosystems that support distinct high-elevation habitats found nowhere else in the area. Analyses of several moisture-dependent species across these sky-islands indicate they exist as locally endemic lineages that are distributed across these fragmented mountains ranges. The Rubber Boa...
Article
The northwestern pond turtle, Actinemys marmorata, and its recently recognized sister species, the southwestern pond turtle, A. pallida, are the sole aquatic testudines occurring over most of western North America, and the only living representatives of the genus Actinemys. Although it historically ranged from Washington state through central Calif...
Article
Toxin evolution in animals is one of the most fascinating and complex subjects of scientific inquiry today. Gaining an understanding of toxins poses a multifaceted challenge given the diverse modes of acquisition, evolutionary adaptations, and abiotic components that affect toxin phenotypes. Here, we highlight some of the main genetic and ecologica...
Article
Full-text available
November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phas...
Preprint
Full-text available
Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 MYA, yet the genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remain largely unknown. Additionally, many populations have declined drastically due to anthropogenic...
Article
Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native eco...
Book
This is our 9th edition of an annotated checklist and atlas of all recognized taxa of the world’s modern turtle and tortoise fauna, documenting recent changes and controversies through mid-2021, and including all primary synonyms, updated from eight previous checklists. We provide an updated comprehensive listing of taxonomy and nomenclature, inclu...
Article
As genomic-scale data sets become economically feasible for most organisms, a key question for conservation biology is whether the increased resolution offered by new genomic approaches justifies repeating earlier studies based on traditional markers, rather than investing those same time and monetary resources in less-known species. Genomic studie...
Article
Full-text available
Accurate status assessments of long-lived, widely distributed taxa depend on the availability of long-term monitoring data from multiple populations. However, monitoring populations across large temporal and spatial scales is often beyond the scope of any one researcher or research group. Consequently, wildlife managers may be tasked with utilizing...
Article
Full-text available
Proteins encoded by Antigen Processing Genes (APGs) provide MHC class I (MHC-I) with antigenic peptides. In mammals, polymorphic multigenic MHC-I family is served by monomorphic APGs, whereas in certain non-mammalian species both MHC-I and APGs are polymorphic and coevolve within stable haplotypes. Coevolution was suggested as an ancestral gnathost...
Article
Full-text available
Tetrodotoxin (TTX) is a potent neurotoxin that was first identified in pufferfish but has since been isolated from an array of taxa that host TTX-producing bacteria. However, determining its origin, ecosystem roles, and biomedical applications has challenged researchers for decades. Recognized as a poison and for its lethal effects on humans when i...
Article
Hansson et al . argue that our main finding could provide an overly simplistic metric for maximizing genetic rescue. They agree that translocating the most genetically diverse individuals led to a large increase in translocated tortoise survival, but recommend instead moving individuals that have low genetic load and the greatest representation of...
Article
Full-text available
Hedrick brings up several potential concerns that he feels challenge or limit our main finding. Hedrick does not comment on our empirical results, but rather argues that several factors may confound or invalidate our conclusion. Many of these concerns focus on unknown ecological aspects of the translocated tortoises, but we believe there is no reas...
Article
Full-text available
The western pond turtle (WPT) was formerly considered a single species ( Actinemys or Emys marmorata ) that ranged from southern British Columbia, Canada to Baja California, México. More recently it was divided into a northern and a southern species. WPTs are found primarily in streams that drain into the Pacific Ocean, although scattered populatio...
Article
Significance Population structure and speciation are shaped by a combination of biotic and abiotic factors. The tiger salamander complex has been considered a key group in which life history variation has led to a rapid rate of speciation, driven in large part by the evolution of obligate paedomorphosis—a condition in which adults maintain an aquat...
Article
1. Globally endangered ecosystems, such as ephemeral wetlands, are often critical habitat for multiple interacting imperilled species. To conserve this biodiversity, managers must consider both species-specific resource requirements and mechanisms for endangered species coexistence under variable habitat conditions. 2. We examined communities nati...
Article
Full-text available
As the biodiversity crisis accelerates, the stakes are higher for threatened plants and animals. Rebuilding the health of our planet will require addressing underlying threats at many scales, including habitat loss and climate change. Conservation interventions such as habitat protection, management, restoration, predator control, translocation, ge...
Article
Significance Biodiversity is unevenly distributed across the tree of life. Understanding the factors that led to this unevenness can illuminate how macroevolutionary processes have interacted with changing global environments to shape patterns of biodiversity. By developing a comprehensive phylogeny for extant turtles and analyzing the diversificat...
Article
Full-text available
The phylogeny of California Slender Salamanders (Batrachoseps attenuatus), which inhabits Northern California's Coast Ranges and Sierra Nevada foothills, was previously investigated by Martínez-Solano et al. (2007), who recovered a monophyletic species that contained five geographically cohesive major clades. However, a population isolate of B. att...
Article
Conservation planners use a variety of decision-making tools, many of which require identifying and prioritizing spatial units based on their biodiversity and levels of imperilment. Turtles are highly imperiled, but present schemes for determining global priority areas are focused mostly on broad regional scales. We conduct the first global evaluat...
Article
Hybridization between native and non‐native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance an...
Article
Survival of the most variable As more species become highly threatened because of human activity, there has been an increasing push to understand how best to reintroduce or translocate individuals from wild or captive populations. Suggestions have varied from choosing individuals from the most environmentally similar regions to choosing those that...
Article
Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii h...
Preprint
Full-text available
The North American tiger salamander species complex, including its flagship species the axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis and those able to forego metamorphosis and retain...
Preprint
Full-text available
A bstract The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis, those able to forego metamo...
Article
Turtles and tortoises (chelonians) have been integral components of global ecosystems for about 220 million years and have played important roles in human culture for at least 400,000 years. The chelonian shell is a remarkable evolutionary adaptation, facilitating success in terrestrial, freshwater and marine ecosystems. Today, more than half of th...
Article
Full-text available
The western pond turtle (WPT), recently separated into two paripatrically distributed species ( Emys pallida and Emys marmorata ), is experiencing significant reductions in its range and population size. In addition to habitat loss, two potential causes of decline are female-biased road mortality and high juvenile mortality from non-native predator...
Article
Full-text available
Climate change-induced extinctions are estimated to eliminate one in six known species by the end of the century. One major factor that will contribute to these extinctions is extreme climatic events. Here, we show the ecological impacts of recent record warm air temperatures and simultaneous peak drought conditions in California. From 2008–2016, t...
Preprint
Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their ability to outcompete the native parent. It is crucial to understand the mechanisms that drive these transgressive hybrid traits to diagnose and...
Preprint
Full-text available
The barrier effect is a restriction of gene flow between diverged populations by barrier genes. Asymmetric introgression can point to selection, hybrid zone movement, asymmetric reproductive isolation, or a combination of these. Restriction of gene flow and asymmetric introgression over multiple transects point towards influence of intrinsic (genet...
Article
Full-text available
The red-eared slider turtle (Trachemys scripta elegans; RES) is often considered one of the world's most invasive species. Results from laboratory and mesocosm experiments suggest that introduced RES outcompete native turtles for key ecological resources, but such experiments can overestimate the strength of competition. We report on the first fiel...
Preprint
Landscape genomic signatures indicate reduced gene flow and forest-associated adaptive divergence in an endangered neotropical turtle Running title: Landscape genomics of a neotropical turtle ABSTRACT Human-induced transformations of ecosystems usually result in fragmented populations subject to increased extinction risk. Fragmentation is also ofte...
Article
Genomic data increasingly are used for high resolution population genetic studies including those at the forefront of biological conservation. A key methodological challenge is determining sequence similarity clustering thresholds for RADseq data when no reference genome is available. These thresholds define the maximum permitted divergence among a...
Article
Human‐induced transformations of ecosystems usually result in fragmented populations subject to increased extinction risk. Fragmentation is also often associated with novel environmental heterogeneity, which in combination with restricted gene flow may increase the opportunity for local adaptation. To manage at‐risk populations in these landscapes,...
Article
Full-text available
Newts of the genus Triturus (marbled and crested newts) exhibit substantial variation in the number of trunk vertebrae (NTV) and a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny has thwarted resolution to date, the evolutionary history of NTV, annual aquatic period, and their potential coevolution has remai...
Article
Full-text available
We present a review and analysis of the conservation status and International Union for Conservation of Nature (IUCN) threat categories of all 360 currently recognized species of extant and recently extinct turtles and tortoises (Order Testudines). Our analysis is based on the 2018 IUCN Red List status of 251 listed species, augmented by provisiona...
Article
Urban biodiversity is an unplanned species assemblage. Although promoting native biodiversity should be the primary goal, the built environment often contains optimal habitat for non-natives. With planning and research, we could use cities as semi-natural assurance colonies for endangered species.
Article
Cryptic species are a challenge for systematics, but their elucidation also may leave critical information gaps about the distribution, conservation status, and behavior of affected species. We use the leopard frogs of the eastern U.S. as a case study of this issue. We refined the known range of the recently described Rana kauffeldi, the Atlantic C...
Article
Full-text available
Cryptic species are a challenge for systematics, but their elucidation also may leave critical information gaps about the distribution, conservation status, and behavior of affected species. We use the leopard frogs of the eastern U.S. as a case study of this issue. We refined the known range of the recently described Rana kauffeldi, the Atlantic C...
Data
Reticulum characterization with ImageJ. (DOCX)
Data
Exemplar photographs of characters used in analysis of leopard frog morphology and patterning. (DOCX)
Data
Additional genetic methods and results. (DOCX)
Data
Morphological and color characters from photographic analysis of 220 leopard frogs (Rana spp.) in the eastern U.S. Frogs were identified using genetics and designated as “pure” if they had a 90% or greater match with a single species; individuals with a species match between 10% and 90% were designated as admixed. Sample sizes for each character ar...
Article
Understanding the evolutionary history of diversifying lineages and the delineation of evolutionarily significant units and species remain major challenges for evolutionary biology. Low cost representational sampling of the genome for single nucleotide polymorphisms (SNPs) shows great potential at the temporal scales that are typically the focus of...
Preprint
Full-text available
Understanding the course of eco-morphological evolution in adaptive radiations is challenging as the phylogenetic relationships among the species involved are typically difficult to resolve. Newts of the genus Triturus (marbled and crested newts) are a well-studied case: they exhibit substantial variation in the number of trunk vertebrae (NTV) and...
Article
A critical consideration when using molecular ecological methods to detect trends and parameterize models at very fine spatial and temporal scales has always been the technical limits of resolution. Key landscape features, including most anthropogenic modifications, can cause biologically important, but very recent changes in gene flow that require...
Article
The introductions of non‐native predators often reduce biodiversity and affect natural predator‐prey relationships. However, non‐native predators may increase the abundance of potential disease vectors (e.g. mosquitoes) indirectly through competition or predation cascades. The Santa Monica Mountains, situated in a global biodiversity hotspot, is an...
Article
Full-text available
Full text (view only): https://link.springer.com/epdf/10.1007/s10592-018-1066-7?author_access_token=HfoE1PYQ58ad3IILmWG5Sve4RwlQNchNByi7wbcMAY5WPDazG4fjRJwgbxCirivb4Yh6pC4Ku6FPuVgKbley1bTaHBPZUeuDaO365I5vHOi1xP1yy4sm0-ED3lRIaHqJlwPeASPmohoJg1YlEqDNAQ%3D%3D The western spadefoot (Spea hammondii) is a Species of Special Concern in California and is...
Article
Genomic data have the potential to inform high resolution landscape genetic and biological conservation studies that go far beyond recent mitochondrial and microsatellite analyses. We characterize the relationships of populations of the foothill yellow-legged frog, Rana boylii, a declining, “sentinel” species for stream ecosystems throughout its ra...
Preprint
Full-text available
In this paper, we study the general problem of extracting information from spatially explicit genomic data to inform inference of ecologically and geographically realistic population models. We describe methods and apply them to simulations motivated by the demography of the Mojave desert tortoise (Gopherus agassizii). The tortoise is an example of...
Preprint
Full-text available
The red-eared slider turtle (Trachemys scripta elegans; RES) is one of the worlds most invasive species. Native to the central United States, RES are now widely established in freshwater habitats across the globe, largely due to release of unwanted pets. Laboratory and mesocosm experiments suggest that introduced RES are competitively dominant to n...
Preprint
Full-text available
Roads fragment landscapes and can cause the loss of metapopulation dynamics in threatened species, but as relatively new landscape features, few studies have had the statistical power to genetically examine road effects. We used DNA sequence data from thousands of nuclear loci to characterize the population structure of New York-endangered Eastern...
Article
Full-text available
Chytridiomycosis is caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd) and is regarded as one of the most significant threats to global amphibian populations. In México, Bd was first reported in 2003 and has now been documented in 13 states. We visited 33 localities and swabbed 199 wild-caught anurans from 7 species (5 native, 2 exot...
Article
Full-text available
Inducible phenotypic responses to environmental variation are ubiquitous across the tree of life, but it remains an open question whether amphibian chemical defense phenotypes are inducible. Tetrodotoxin (TTX) is a key chemical defense trait in North American and Eurasian newts (Salamandridae). We tested if TTX can be induced by exposing population...
Article
The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well...
Preprint
Full-text available
Genomic data are useful for attaining high resolution in population genetic studies and have become increasingly available for answering questions in biological conservation. We analyzed RADseq data for the protected foothill yellow-legged frog ( Rana boylii ) throughout its native range in California and Oregon, including many of the same localiti...
Book
Full-text available
This is our 8th edition of an annotated checklist of all recognized and named taxa of the world’s modern chelonian fauna, documenting recent changes and controversies in nomenclature through early 2017, and including all primary synonyms, updated from 7 previous checklists (Turtle Taxonomy Working Group 2007b, 2009, 2010, 2011, 2012, 2014; Rhodin e...
Article
Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency...