Biology subjects

Shaffer, H. B.

Publications and source records attributed to Shaffer, H. B..

18 recordsLinked to original sources

bioRxiv2026

Can urban fence lizards identify cats?

Urban habitats can serve as wildlife refuges, or as ecological traps. As global urbanization continues to increase, native prey species may experience reduced threat from natural predators that tend to avoid human-populated areas. However, such protection often comes at the expense of susceptibility to synanthropic predators, one of the most prevalent being domestic house cats (Felis catus). While cats are a known driving force of mortalities in urban wildlife, their sublethal effects remain understudied. To better understand the behavioral effects of synanthropic predators on native urban prey, we examined responses of western fence lizards (Sceloporus occidentalis) to Artificial Intelligence (AI)-generated visual stimuli of native predators (snakes) and synanthropic predators (house cats). Visual stimuli included: California striped racers (Masticophis lateralis), a native predator; domestic cats, a synanthropic mammalian predator (Felis catus); and desert cottontails (Sylvilagus audubonii), a native mammalian non-predator. We quantified lizard responses as the change in rates of looking and locomotion during and following the video presentation. Our results revealed that lizards discriminated cats from the control by looking more within the first 90 seconds following exposure. Lizards looked more across the entire 5-minute observation period following exposure to all stimulus types compared to control conditions, indicating that AI generated visual stimuli effectively elicit behavioral responses. Together, these findings indicate that urban lizards initially detect and respond to visual cues of cats, suggesting that cat-induced mortality is not a result of inability to detect such predators. Thus, cats influence urban prey not only through direct predation risk, but also changes in behavior associated with the presence of synanthropic predators.

ecology↗

bioRxiv2025

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level reference 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 (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 reference genome, 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.

genomics↗

bioRxiv2025

Chytrid fungal infections in alpine toads proliferate during winter dormancy

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.

ecology↗

bioRxiv2025

Species distribution modeling for conservation science: new predictor layers, reproducible code, and an evaluation of California protected areas

AimOur study provides foundational resources for future SDMing: methods for generating fine-scale, equal-area predictor datasets and best-practice SDM guidelines. We also provide reproducible code to streamline their implementation. LocationSouthwestern North America MethodsUsing over 215,000 research-grade iNaturalist occurrence records for 127 species of conservation concern or scientific interest in California and surrounding area, we quantified and compared SDM performance between two predictor datasets that differ in their source of bioclimatic data, spatial resolution, and coordinate reference system: one generated using ClimateNA software (resolution = 300 x 300 m; NAD83/California Albers) and the other using existing WorldClim data (varying resolution = [~]669-797 x 926 m; WGS84). We also compared two modeling algorithms (MaxEnt vs Random Forests), and two background point selection strategies (random points vs weighted points accounting for sampling effort). As an example application, we used SDM predictions to evaluate the conservation value of different protected area types within California. ResultsClimateNA outperformed WorldClim for 94% of species, Random Forests outperformed MaxEnt for 87%, and random background points outperformed weighted background points for 100%. All differences were statistically significant. Together, the ClimateNA dataset, Random Forests, and random background points achieved highest performance for 86% of species. Using this best-performing set of models, we found that regional parks, county parks, state beaches, and open spaces in California were highest in multi-species suitability, while larger protected areas, such as national parks and national forests, generally exhibited surprisingly low suitability. Substantial spatial biases intrinsic to SDMing with unprojected predictor datasets (e.g., WGS84) are described, along with clear solutions using equal-area predictor datasets. Main conclusionsConsiderable disparity was observed among the performance of common SDM methods. This study highlights the importance of fine-scale, equal-area predictor datasets and best-practice guidelines, and demonstrates how SDMs can provide critical insights into protected area planning.

ecology↗

bioRxiv2024

Whole-genome evaluation of genetic rescue: the case of a curiously isolated and endangered butterfly

Genetic rescue, or the translocation of individuals among populations to augment gene flow, can help ameliorate inbreeding depression and loss of adaptive potential in small and isolated populations. Genetic rescue is currently under consideration for an endangered butterfly in Canada, the half-moon hairstreak (Satyrium semiluna). A small, unique population persists in Waterton Lakes National Park, Alberta, isolated from other populations by >350km. However, whether genetic rescue would actually be helpful has not been evaluated. Here, we generate the first chromosome-level genome assembly and whole-genome resequence data for the species. We find that the Alberta populations genetic diversity is extremely low and very divergent from the nearest populations in British Columbia and Montana. Runs of homozygosity suggest this is due to a long history of inbreeding, and coalescent analyses show that the population has been small and isolated, yet stable for up to 40k years. When a population maintains its viability despite inbreeding and low genetic diversity, it has likely undergone purging of deleterious recessive alleles and could be threatened by their reintroduction via genetic rescue. Ecological niche modelling indicates that the Alberta population also exhibits environmental associations that are atypical of the species. Together, these results suggest that population crosses are likely to result in outbreeding depression. We infer that, in this case, genetic rescue has a relatively unique potential to be harmful rather than helpful at present. However, due to reduced adaptive potential, the Alberta may still benefit from future genetic rescue as climate conditions change. Proactive experimental population crosses should be completed to assess reproductive compatibility and offspring fitness.

ecology↗

bioRxiv2024

The genome assembly of the duckweed fern, Azolla caroliniana

Azolla is a genus of freshwater ferns that is economically important as a nitrogen-fixing biofertilizer, biofuel, bioremediator, and for potential carbon sequestration, but also contains weedy invasive species. In California, only two species are currently recognized but there may be up to six putative species, with the discrepancy being due to the difficulty in identifying taxa, hybridization, and the introduction of non-native species. Here, we report a new haplotype-resolved, chromosome-level assembly of Azolla caroliniana as part of the California Conservation Genomics Project (CCGP), using a combination of PacBio HiFi and Omni-C sequencing technologies. The assembly is 521 Mb in length, with a contig N50 of 1.6 Mb, and is scaffolded into 22 pseudo-chromosomes. The BUSCO completeness score is 87.5%, making it the most complete and most contiguous Azolla assembly to date. In combination with the previously published A. filiculoides genome, this A. caroliniana genome will be a powerful tool for understanding the population genetics and taxonomy of one of the most cryptic, economically important, and poorly circumscribed fern taxa, and for facilitating land plant genomics more broadly.

genomics↗

bioRxiv2024

NewtCap: an efficient target capture approach to boost genomic studies in Salamandridae (True Salamanders and Newts)

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.7k 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.

genomics↗

bioRxiv2024

The nitrogen-fixing fern Azolla has a complex microbiome characterized by multiple modes of transmission

Azolla is a floating fern that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont--Anabaena azollae--that performs nitrogen fixation in specialized Azolla leaf pockets. This cyanobac-terium has a greatly reduced genome and appears to be in the "advanced" stages of symbiosis, potentially evolving into a nitrogen-fixing organelle. However, there are also other lesser-known inhabitants of the leaf pocket whose role and mode of transmission are unknown. We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes in order to identify the common bacterial endosymbionts of the leaf pocket and assess their patterns of co-diversification. Four taxa were found across all samples, establishing that there are multiple endosymbionts that consistently inhabit the Azolla leaf pocket. We found varying degrees of co-diversification across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which implies that the endosymbiotic community is transmitted by a mix of horizontal and vertical mechanisms, and that some members of the microbiome are more facultative symbionts than others. These results show that the Azolla symbiotic community is complex, featuring 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.

ecology↗

bioRxiv2023

Reference genome of the bicolored carpenter ant, Camponotus vicinus

Carpenter ants in the genus Camponotus are large, conspicuous ants that are abundant and ecologically influential in many terrestrial ecosystems. The bicolored carpenter ant, C. vicinus Mayr, is distributed across a wide range of elevations and latitudes in western North America, where it is a prominent scavenger and predator. Here, we present a high-quality genome assembly of C. vicinus from a sample collected in Sonoma County, CA, near the type locality of the species. This genome assembly consists of 38 scaffolds spanning 302.74 Mb, with contig N50 of 15.9Mb, scaffold N50 of 19.9 Mb, and BUSCO completeness of 99.2%. This genome sequence will be a valuable resource for exploring the evolutionary ecology of C. vicinus and carpenter ants generally. It also provides an important tool for clarifying cryptic diversity within the C. vicinus species complex, a genetically diverse set of populations, some of which are quite localized and of conservation interest.

genomics↗

bioRxiv2022

Multiplex qPCR assays for detection of Anaxyrus californicus and Spea hammondii from environmental DNA

We developed a species-specific, quantitative PCR assay multiplex for the detection of two threatened and endangered anuran species, arroyo toad (Anaxyrus californicus) and western spadefoot (Spea hammondii), from environmental DNA (eDNA). Both species have experienced range wide declines over the last century, mostly as a result of habitat loss. Given these declines and their cryptic life histories, improved tools for detecting and monitoring both species are needed. Species-specificity and sensitivity of assays were empirically tested in the lab, and the multiplexed assays were validated with field-collected eDNA samples. Both assays were species-specific, sensitive, and effectively detected the target species from streams, rivers and ponds, although detection was imperfect. These assays provide an efficient and economical tool that will aid in the detection, monitoring, management, and conservation of these at-risk species.

zoology↗

bioRxiv2022

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

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 remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of non-collinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared to other reptiles, and harbor a higher genetic load compared to green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage. Statement of significanceSea turtle populations have undergone recent global declines. We analyzed de novo assembled genomes for both extant sea turtle families through the Vertebrate Genomes Project to inform their conservation and evolutionary biology. These highly conserved genomes were differentiated by localized gene-rich regions of divergence, particularly within microchromosomes, suggesting that these genomic elements play key functional roles in the evolution of sea turtles and possibly other vertebrates. We further demonstrate that dissimilar evolutionary histories impact standing genomic diversity and genetic load, and are critical to consider when using these metrics to assess adaptive potential and extinction risk. Our results also demonstrate how reference genome quality impacts inferences of comparative and conservation genomics analyses that need to be considered in their application.

genomics↗

bioRxiv2019

Allele Specific Expression and Gene Regulation Explain Transgressive Thermal Tolerance in Non-native Hybrids of the Endangered California Tiger Salamander (Ambystoma californiense)

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 develop strategies to manage hybrid populations. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 40% (6/15) able to tolerate temperatures greater than either parent. We quantified the genomic response of each individual to discover and compare thermal abatement strategies. We found that CTS and BTS have strikingly different numbers and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. We evaluated transgressive and variable phenotypes by uncovering regulatory mechanisms that give rise to these unique traits. F1 hybrids display abundant and variable degrees of allele specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms of the parental lineages. We found that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting that BTS-biased expression confers improved thermal tolerance. We discuss the implications of these findings with respect to ongoing management of CTS in the face of future climate change.

genomics↗

bioRxiv2018

Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle

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 remained unclear. To resolve the phylogeny of Triturus, we generated a c. 6,000 transcriptome-derived marker data set using a custom target enrichment probe set, and conducted phylogenetic analyses using: 1) data concatenation with RAxML, 2) gene-tree summary with ASTRAL, and 3) species-tree estimation with SNAPP. All analyses produce the same, highly supported topology, despite cladogenesis having occurred over a short timeframe, resulting in short internal branch lengths. Our new phylogenetic hypothesis is consistent with the minimal number of inferred changes in NTV count necessary to explain the diversity in NTV observed today. Although a causal relationship between NTV, body form, and aquatic ecology has yet to be experimentally established, our phylogeny indicates that these features have evolved together, and suggest that they may underlie the adaptive radiation that characterizes Triturus.

evolutionary biology↗

bioRxiv2018

Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise

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 a long-lived, threatened species for which we have an excellent understanding of range, habitat preference, and certain aspects of demography, but inadequate information on other life history components that are important for conservation management. We use an individual-based model on a discretized geographic landscape with overlapping generations and age and sex-specific dispersal, fecundity, and mortality to develop and test a method that uses genomic data to infer demographic parameters. We do this by seeking parameters that best match a set of spatial statistics of genomes, which we introduce and discuss. We find that for inferring only overall population density and mean migration distance, a simple statistical learning method performs well using simulated training data, inferring parameters to within 10% accuracy. In the process, we introduce spatial analogues of common population genetics statistics, and discuss how and why they are expected to contain signal about the geography of population dynamics that are key for ecological modeling generally and conservation of endangered taxa.

genomics↗

bioRxiv2018

Large-scale experimental removal of non-native slider turtles has unexpected consequences on basking behavior for both conspecifics and a native, threatened turtle

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 native turtles, but such competition remains untested in the wild. Here, we experimentally removed introduced RES to test whether they compete for critical basking habitat with native, threatened western pond turtles (Emys marmorata; WPT), a species being considered for listing under the U.S. Endangered Species Act. Following removal, we found that both the remaining RES as well as WPT altered their basking distribution but in a manner inconsistent with strong interspecific competition. However, these findings suggest strong intraspecific competition for basking sites amongst RES and that interspecific competition between WPT and introduced RES likely occurs at higher RES densities. Our works suggests RES influence the behavior of native species in the wild and indicates that RES removal may be most beneficial at high RES densities. This experiment highlights the importance of considering experimental venue when evaluating competition between native and non-native species and should encourage conservation biologists to treat removal efforts as experiments.

ecology↗

bioRxiv2018

Genomic Data from an Endangered Amphibian Reveal Unforeseen Consequences of Fragmentation by Roads

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 tiger salamanders (Ambystoma tigrinum) on Long Island and quantify the impacts of roads on population fragmentation. We uncovered highly genetically structured populations over an extremely small spatial scale (approximately 40 km2) in an increasingly human-modified landscape. Geographic distance and the presence of roads between ponds are both strong predictors of genetic divergence, suggesting that both natural and anthropogenic factors are responsible for the observed patterns of genetic variation. Our study demonstrates the value of genomic approaches in molecular ecology, as these patterns did not emerge in an earlier study of the same system using microsatellite loci. Ponds supported small effective population sizes, and pond surface area showed a strong positive correlation with salamander population size. When combined with the high degree of structuring in this heavily modified landscape, our study indicates that these endangered amphibians require management at the individual pond, or pond cluster, level. Particular efforts should be made to preserve large vernal pools, which harbor the greatest genetic diversity, and their surrounding upland habitat. Contiguous upland landscapes between ponds that facilitate natural metapopulation connectivity and demographic rescue from future local extirpations should also be protected.

evolutionary biology↗

bioRxiv2017

Desert Tortoises in the Genomic Age: Population Genetics and the Landscape

The California Department of Fish and Wildlife (CDFW) provided research funds to study the conservation genomics and landscape genomics of the Mojave desert tortoise, Gopherus agassizii, in response to the Desert Renewable Energy Conservation Plan (DRECP). To do this, we consolidated tissue samples of the desert tortoise from across the species range within California and southern Nevada, generated a DNA dataset consisting of full genomes of 270 tortoises, and analyzed the way in which the environment of the desert tortoise has determined modern patterns of relatedness and genetic diversity across the landscape. Here we present the implications of these results for the conservation and landscape genomics of the desert tortoise. Our work strongly indicates that several well-defined genetic groups exist within the species, including a primary north-south genetic discontinuity at the Ivanpah Valley and another separating western from eastern Mojave samples. We also use existing desert tortoise habitat modeling data with a novel extension of genetic \"resistance distance\" using geographic maps of continuous space to predict the relative impacts of five proposed development alternatives within the DRECP and rank them with respect to their likely impacts on desert tortoise gene flow and connectivity in the Mojave. Finally, we analyzed the impacts of each of the 214 distinct proposed development area \"chunks,\" derived from the proposed development polygons, and ranked each chunk in terms of its range-wide impacts on desert tortoise gene flow.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC=\"FIGDIR/small/195743_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (147K):\norg.highwire.dtl.DTLVardef@b60416org.highwire.dtl.DTLVardef@1c649f2org.highwire.dtl.DTLVardef@120e625org.highwire.dtl.DTLVardef@e59b34_HPS_FORMAT_FIGEXP M_FIG C_FIG PrefaceO_ST_ABSContextC_ST_ABSThe following document is a report that was submitted to the California Department of Fish and Wildlife, describing a series of analyses to help understand the impacts of several alternative spatial configurations of renewable energy development on gene flow of the federally threatened Mojave desert tortoise. These development alternatives were the centerpiece of the Desert Renewable Energy Conservation Plan (DRECP), a landscape-level land use planning initiative undertaken by the Bureau of Land Management (BLM), U.S. Fish and Wildlife Service (USFWS), California Energy Commission (CEC), and the California Department of Fish and Wildlife (CDFW). We were tasked by the California Department of Fish and Wildlife with providing a detailed analysis of these alternative plans on desert tortoise gene flow, and submitted the report for the public comment period for the initial implementation of the DRECP.\n\nFuture PlansO_ST_ABSCurrent state of landscape-level planning for the Mojave desert tortoiseC_ST_ABSThe five proposed land use configuration alternatives analyzed in the subsequent report include public and private lands spread across several counties in California. Shortly after the end of the DRECPs public comment period, the government agencies that developed the DRECP announced that they would be splitting its implementation into two phases: one that deals with land use decisions on BLM-controlled lands and one that deals with non-BLM areas (Sahagun 2015).\n\nPhase I of the DRECP was approved by the Bureau of Land Management on September 14, 2016 (U.S. Bureau of Land Management 2016). This phase includes land use planning decisions for BLM-administered lands. Specifically, 388,000 acres of public lands were designated as development focus areas (DFAs). In applications for leasing lands for renewable energy development, DFAs will not require the same degree of environmental evaluation prior to permitting, as theyve already been evaluated in the context of the DRECP. The application process for renewable energy development within DFAs will be streamlined to encourage development in these areas. Phase I also designated a total of 6,527,000 acres for natural resource conservation. This includes California Desert National Conservation Lands, Areas of Critical Environmental Concern, and Wildlife Allocations. A further 2,691,000 acres were designated for recreation under Phase I. Phase II of the DRECP is currently under development in conjunction with county-level governments to extend this landscape-level planning beyond BLM-administered lands.\n\nAuthor ContributionsThis was a collaborative report. Evan McCartney-Melstad performed the simulations of the low-coverage full genome approach (see Figure 2); conducted all of the laboratory work to generate the genome sequences; performed all of the bioinformatic analyses to bring the raw sequence data to the various stages required for different analyses; wrote the software to quickly estimate pairwise genetic relationships between individuals using read count data in low coverage sequence data (www.github.com/atcg/cPWP); performed some of the population genetic analyses; and wrote and edited several sections of the report.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC=\"FIGDIR/small/195743_fig2.gif\" ALT=\"Figure 2\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@30a49forg.highwire.dtl.DTLVardef@187c3d8org.highwire.dtl.DTLVardef@4abe98org.highwire.dtl.DTLVardef@126febe_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Comparison of two different sequencing approaches in their ability to differentiate very slightly differentiated populations (Fst=0.001)\n\nC_FIG Peter Ralph (in collaboration with Gideon Bradburd and Erik Lundgren) invented and implemented the random walk-based gene flow model that we used to estimate reductions in gene flow due to development, and also developed the theory behind the read-based pairwise pi and genetic covariance estimation used here, in addition to writing and editing several sections of the report. Gideon Bradburd also performed some of the population genetic analyses and wrote and edited several sections of the report. Jannet Vu collected and curated the spatial environmental data and generated the maps that are included in the report (Figures 10, A10-A13), and also wrote Appendices I and IV. Bridgette Hagerty, Fran Sandmeier, Chava Weitzman, and C. Richard Tracy contributed approximately 1,000 desert tortoise blood samples that they collected (at great effort), in addition to knowledge of tortoise ecology and conservation, as well as the results of previous microsatellite-based genetic analyses and editing of the report. H. Bradley Shaffer wrote and edited several sections of the report, and is listed as the lead author for his role in conceiving of and obtaining funding support for the project.\n\nO_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC=\"FIGDIR/small/195743_fig10.gif\" ALT=\"Figure 10\">\nView larger version (82K):\norg.highwire.dtl.DTLVardef@11e99acorg.highwire.dtl.DTLVardef@1faf2f5org.highwire.dtl.DTLVardef@64c440org.highwire.dtl.DTLVardef@1907837_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 10.C_FLOATNO Spatial configuration of the proposed development chunks (see Appendix 4).\n\nC_FIG

evolutionary biology↗

bioRxiv2017

Population Genomics of the Foothill Yellow-Legged Frog (Rana boylii) and RADseq Parameter Choice for Large-Genome Organisms

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 localities included in an earlier study based on mitochondrial DNA. We recovered five primary clades that correspond to geographic regions within California and Oregon, with better resolution and more spatially consistent patterns than the previous study, confirming the increased resolving power of genomic approaches compared to single-locus analyses. Bayesian clustering, PCA and population differentiation with admixture analyses all indicated that approximately half the range of R. boylii consists of a single, relatively uniform population, while regions in the Sierra Nevada and Central Coast Range of California are deeply differentiated genetically. Additionally, a major methodological challenge for large genome organisms, including many amphibians, is deciding on sequence similarity clustering thresholds for population genetic analyses using RADseq data, and we develop a novel set of metrics that allow researchers to set a sequence similarity threshold that maximizes the separation of paralogous regions while minimizing the oversplitting of naturally occurring allelic variation within loci.

evolutionary biology↗