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Leigh DM, Vandergast AG, Hunter ME, Crandall ED, Funk WC, Garroway CJ, Hoban S, Oyler-McCance SJ, Rellstab C, Segelbacher G, Schmidt C, Vázquez-Domínguez E, Paz-Vinas I. Best practices for genetic and genomic data archiving. Nat Ecol Evol 2024:10.1038/s41559-024-02423-7. [PMID: 38789640 DOI: 10.1038/s41559-024-02423-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.
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Affiliation(s)
- Deborah M Leigh
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
| | - Amy G Vandergast
- US Geological Survey, Western Ecological Research Center, San Diego, CA, USA
| | - Margaret E Hunter
- US Geological Survey, Wetland & Aquatic Research Center, Gainesville, FL, USA
| | - Eric D Crandall
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean Hoban
- Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | | | | | | | - Chloé Schmidt
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Leipzig, Germany
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Ivan Paz-Vinas
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
- Universite Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, Villeurbanne, France
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2
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Maier PA, Vandergast AG, Bohonak AJ. Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression. Mol Ecol 2024; 33:e17317. [PMID: 38488670 DOI: 10.1111/mec.17317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, San Diego, California, USA
- Family TreeDNA, Gene by Gene, Houston, Texas, USA
| | - Amy G Vandergast
- Western Ecological Research Center, San Diego Field Station, U.S. Geological Survey, San Diego, California, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, San Diego, California, USA
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Dutcher KE, Nussear KE, Heaton JS, Esque TC, Vandergast AG. Move it or lose it: Predicted effects of culverts and population density on Mojave desert tortoise (Gopherus agassizii) connectivity. PLoS One 2023; 18:e0286820. [PMID: 37768995 PMCID: PMC10538755 DOI: 10.1371/journal.pone.0286820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 05/24/2023] [Indexed: 09/30/2023] Open
Abstract
Roadways and railways can reduce wildlife movements across landscapes, negatively impacting population connectivity. Connectivity may be improved by structures that allow safe passage across linear barriers, but connectivity could be adversely influenced by low population densities. The Mojave desert tortoise is threatened by habitat loss, fragmentation, and population declines. The tortoise continues to decline as disturbance increases across the Mojave Desert in the southwestern United States. While underground crossing structures, like hydrological culverts, have begun receiving attention, population density has not been considered in tortoise connectivity. Our work asks a novel question: How do culverts and population density affect connectivity and potentially drive genetic and demographic patterns? To explore the role of culverts and population density, we used agent-based spatially explicit forward-in-time simulations of gene flow. We constructed resistance surfaces with a range of barriers to movement and representative of tortoise habitat with anthropogenic disturbance. We predicted connectivity under variable population densities. Simulations were run for 200 non-overlapping generations (3400 years) with 30 replicates using 20 microsatellite loci. We evaluated population genetic structure and diversity and found that culverts would not entirely negate the effects of linear barriers, but gene flow improved. Our results also indicated that density is important for connectivity. Low densities resulted in declines regardless of the landscape barrier scenario (> 75% population census size, > 97% effective population size). Results from our simulation using current anthropogenic disturbance predicted decreased population connectivity over time. Genetic and demographic effects were detectable within five generations (85 years) following disturbance with estimated losses in effective population size of 69%. The pronounced declines in effective population size indicate this could be a useful monitoring metric. We suggest management strategies that improve connectivity, such as roadside fencing tied to culverts, conservation areas in a connected network, and development restricted to disturbed areas.
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Affiliation(s)
- Kirsten E. Dutcher
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Kenneth E. Nussear
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Jill S. Heaton
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Todd C. Esque
- United States Geological Survey, Western Ecological Research Center, Boulder City, Nevada, United States of America
| | - Amy G. Vandergast
- United States Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
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4
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Vandergast AG, Brehme CS, Iwanowicz D, Cornman RS, Adsit‐Morris D, Fisher RN. Fecal metabarcoding of the endangered Pacific pocket mouse ( Perognathus longimembris pacificus) reveals a diverse and forb rich diet that reflects local habitat availability. Ecol Evol 2023; 13:e10460. [PMID: 37745784 PMCID: PMC10514273 DOI: 10.1002/ece3.10460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
Information on diet breadth and preference can assist in understanding links between food resources and population growth and inform habitat restoration for rare herbivores. We assessed the diet of the endangered Pacific pocket mouse using metabarcoding of fecal samples and compared it to plant community composition in long-term study plots in two populations on Marine Corps Base Camp Pendleton, San Diego County, CA. Fecal samples (n = 221) were collected between spring 2016 and fall 2017 during monthly live-trap surveys. Concurrently, percent cover and plant phenology were measured in plots centered on trap locations. Fecal samples were sequenced with paired-end reads of the internal transcribed spacer 2 region of the nuclear ribosomal gene, and the resulting amplicons were matched to a regionally specific database. Seventy-three plant taxa were detected, which were mostly forbs and perennial herbs (70-90%). Diet composition differed between populations, years, seasons, and plots. Overall, diet and local habitat composition in plots were significantly correlated. However, we detected some differences in above-ground seed availability and proportion in fecal samples that indicate diet preferences for some forbs, perennial herbs, and native bunch grasses over perennial shrubs and non-native grasses. This is the first study of PPM to pair plant phenology surveys with diet metabarcoding to estimate resource selection, and results suggest that managing habitat for diverse native forb communities and reducing non-native grass cover may be beneficial for this critically endangered species.
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Affiliation(s)
- Amy G. Vandergast
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Cheryl S. Brehme
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Deborah Iwanowicz
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Robert S. Cornman
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColoradoUSA
| | - Devin Adsit‐Morris
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Robert N. Fisher
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
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van Mantgem PJ, Milano ER, Dudney J, Nesmith JCB, Vandergast AG, Zald HSJ. Growth, drought response, and climate-associated genomic structure in whitebark pine in the Sierra Nevada of California. Ecol Evol 2023; 13:e10072. [PMID: 37206686 PMCID: PMC10191741 DOI: 10.1002/ece3.10072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/21/2023] Open
Abstract
Whitebark pine (Pinus albicaulis Engelm.) has experienced rapid population declines and is listed as threatened under the Endangered Species Act in the United States. Whitebark pine in the Sierra Nevada of California represents the southernmost end of the species' distribution and, like other portions of its range, faces threats from an introduced pathogen, native bark beetles, and a rapidly warming climate. Beyond these chronic stressors, there is also concern about how this species will respond to acute stressors, such as drought. We present patterns of stem growth from 766 large (average diameter at breast height >25 cm), disease-free whitebark pine across the Sierra Nevada before and during a recent period of drought. We contextualize growth patterns using population genomic diversity and structure from a subset of 327 trees. Sampled whitebark pine generally had positive to neutral stem growth trends from 1970 to 2011, which was positively correlated with minimum temperature and precipitation. Indices of stem growth during drought years (2012 to 2015) relative to a predrought interval were mostly positive to neutral at our sampled sites. Individual tree growth response phenotypes appeared to be linked to genotypic variation in climate-associated loci, suggesting that some genotypes can take better advantage of local climatic conditions than others. We speculate that reduced snowpack during the 2012 to 2015 drought years may have lengthened the growing season while retaining sufficient moisture to maintain growth at most study sites. Growth responses may differ under future warming, however, particularly if drought severity increases and modifies interactions with pests and pathogens.
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Affiliation(s)
| | - Elizabeth R. Milano
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
- Present address:
USDA Forest ServiceRocky Mountain Research StationMoscowIdahoUSA
| | - Joan Dudney
- Environmental Studies ProgramUC Santa BarbaraSanta BarbaraCaliforniaUSA
- Department of Environmental Science, Policy, & ManagementUC BerkeleyBerkeleyCaliforniaUSA
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Amy G. Vandergast
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Harold S. J. Zald
- USDA Forest ServicePacific Northwest Research StationCorvallisOregonUSA
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Maier PA, Vandergast AG, Bohonak AJ. Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad ( Anaxyrus canorus). Evol Appl 2023; 16:74-97. [PMID: 36699123 PMCID: PMC9850018 DOI: 10.1111/eva.13511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/05/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
An essential goal in conservation biology is delineating population units that maximize the probability of species persisting into the future and adapting to future environmental change. However, future-facing conservation concerns are often addressed using retrospective patterns that could be irrelevant. We recommend a novel landscape genomics framework for delineating future "Geminate Evolutionary Units" (GEUs) in a focal species: (1) identify loci under environmental selection, (2) model and map adaptive conservation units that may spawn future lineages, (3) forecast relative selection pressures on each future lineage, and (4) estimate their fitness and likelihood of persistence using geo-genomic simulations. Using this process, we delineated conservation units for the Yosemite toad (Anaxyrus canorus), a U.S. federally threatened species that is highly vulnerable to climate change. We used a genome-wide dataset, redundancy analysis, and Bayesian association methods to identify 24 candidate loci responding to climatic selection (R 2 ranging from 0.09 to 0.52), after controlling for demographic structure. Candidate loci included genes such as MAP3K5, involved in cellular response to environmental change. We then forecasted future genomic response to climate change using the multivariate machine learning algorithm Gradient Forests. Based on all available evidence, we found three GEUs in Yosemite National Park, reflecting contrasting adaptive optima: YF-North (high winter snowpack with moderate summer rainfall), YF-East (low to moderate snowpack with high summer rainfall), and YF-Low-Elevation (low snowpack and rainfall). Simulations under the RCP 8.5 climate change scenario suggest that the species will decline by 29% over 90 years, but the highly diverse YF-East lineage will be least impacted for two reasons: (1) geographically it will be sheltered from the largest climatic selection pressures, and (2) its standing genetic diversity will promote a faster adaptive response. Our approach provides a comprehensive strategy for protecting imperiled non-model species with genomic data alone and has wide applicability to other declining species.
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Affiliation(s)
- Paul A. Maier
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
- FamilyTreeDNAGene by GeneHoustonTexasUSA
| | - Amy G. Vandergast
- Western Ecological Research CenterU.S. Geological SurveySan DiegoCaliforniaUSA
| | - Andrew J. Bohonak
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
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7
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Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Landscape genetics of a sub-alpine toad: climate change predicted to induce upward range shifts via asymmetrical migration corridors. Heredity (Edinb) 2022; 129:257-272. [PMID: 36076071 PMCID: PMC9613655 DOI: 10.1038/s41437-022-00561-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/08/2022] Open
Abstract
Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high-elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.
- FamilyTreeDNA, Gene by Gene, 1445 N Loop W, Houston, TX, 77008, USA.
| | - Amy G Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, CA, 92101, USA
| | - Steven M Ostoja
- USDA California Climate Hub, Agricultural Research Service, John Muir Institute of the Environment, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Andres Aguilar
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Dr., Los Angeles, CA, 90032, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
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Vandergast AG, Kus BE, Smith JG, Mitelberg A. Recent declines in genetic diversity with limited dispersal among coastal cactus wren populations in San Diego County, California. Conservat Sci and Prac 2022. [DOI: 10.1111/csp2.12780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Amy G. Vandergast
- Western Ecological Research Center U.S. Geological Survey San Diego California USA
| | - Barbara E. Kus
- Western Ecological Research Center U.S. Geological Survey San Diego California USA
| | - Julia G. Smith
- Western Ecological Research Center U.S. Geological Survey San Diego California USA
| | - Anna Mitelberg
- Western Ecological Research Center U.S. Geological Survey San Diego California USA
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Wood DA, Richmond JQ, Escalona M, Marimuthu MPA, Nguyen O, Sacco S, Beraut E, Westphal M, Fisher RN, Vandergast AG, Toffelmier E, Wang IJ, Shaffer HB. Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern. J Hered 2022; 113:632-640. [PMID: 35939354 PMCID: PMC9923794 DOI: 10.1093/jhered/esac040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
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 California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis 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 technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.
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Affiliation(s)
- Dustin A Wood
- Address correspondence to D.A. Wood at the address above, or e-mail:
| | - Jonathan Q Richmond
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael Westphal
- U.S. Bureau of Land Management—Central Coast Field Office, Marina, CA 93933, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Amy G Vandergast
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA,Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
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Vandergast AG, Kus BE, Wood DA, Milano ER, Preston KL. Subspecies differentiation and range‐wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation. Evol Appl 2022; 15:1201-1217. [PMID: 35899257 PMCID: PMC9309440 DOI: 10.1111/eva.13429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 12/21/2022] Open
Abstract
Understanding genetic structure and diversity within species can uncover associations with environmental and geographic attributes that highlight adaptive potential and inform conservation and management. The California gnatcatcher, Polioptila californica, is a small songbird found in desert and coastal scrub habitats from the southern end of Baja California Sur to Ventura County, California. Lack of congruence among morphological subspecies hypotheses and lack of measurable genetic structure found in a few genetic markers led to questions about the validity of subspecies within P. californica and the listing status of the coastal California gnatcatcher, P. c. californica. As a U.S. federally threatened subspecies, P. c. californica is recognized as a flagship for coastal sage scrub conservation throughout southern California. We used restriction site‐associated DNA sequencing to develop a genomic dataset for the California gnatcatcher. We sampled throughout the species' range, examined genetic structure, gene–environment associations, and demographic history, and tested for concordance between genetic structure and morphological subspecies groups. Our data support two distinct genetic groups with evidence of restricted movement and gene flow near the U.S.‐ Mexico international border. We found that climate‐associated outlier loci were more strongly differentiated than climate neutral loci, suggesting that local climate adaptation may have helped to drive differentiation after Holocene range expansions. Patterns of habitat loss and fragmentation are also concordant with genetic substructure throughout the southern California portion of the range. Finally, our genetic data supported the morphologically defined P. c. californica as a distinct group, but there was little evidence of genetic differentiation among other previously hypothesized subspecies in Baja California. Our data suggest that retaining and restoring connectivity, and protecting populations, particularly at the northern range edge, could help preserve existing adaptive potential to allow for future range expansion and long‐term persistence of the California gnatcatcher.
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Affiliation(s)
- Amy G. Vandergast
- U.S. Geological Survey Western Ecological Research Center San Diego California USA
| | - Barbara E. Kus
- U.S. Geological Survey Western Ecological Research Center San Diego California USA
| | - Dustin A. Wood
- U.S. Geological Survey Western Ecological Research Center San Diego California USA
| | - Elizabeth R. Milano
- U.S. Geological Survey Western Ecological Research Center San Diego California USA
| | - Kristine L. Preston
- U.S. Geological Survey Western Ecological Research Center San Diego California USA
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Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Gene Pool Boundaries for the Yosemite Toad (Anaxyrus canorus) Reveal Asymmetrical Migration Within Meadow Neighborhoods. Front Conserv Sci 2022. [DOI: 10.3389/fcosc.2022.851676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Yosemite toad (Anaxyrus [Bufo] canorus) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well-documented, and is reputed to remain in low abundance throughout its range. Recent phylogeographic work has demonstrated that Pleistocene toad lineages diverged and then admixed to differing extents across an elevational gradient. Although lineage divisions may have significant effects on evolutionary trajectories over large spatial and temporal scales, present-day population dynamics must be delineated in order to manage and conserve the species effectively. In this study, we used a double-digest RADseq dataset to address three primary questions: (1) Are single meadows or neighborhoods of nearby meadows most correlated with population boundaries? (2) Does asymmetrical migration occur among neighborhoods of nearby meadows? (3) What topographic or hydrological variables predict such asymmetrical migration in these meadow neighborhoods? Hierarchical STRUCTURE and AMOVA analyses suggested that populations are typically circumscribed by a single meadow, although 84% of meadows exist in neighborhoods of at least two meadows connected by low levels of migration, and over half (53%) of neighborhoods examined display strong asymmetrical migration. Meadow neighborhoods often contain one or more large and flat “hub” meadows that experience net immigration, surrounded by smaller and topographically rugged “satellite” meadows with net emigration. Hubs tend to contain more genetic diversity and could be prioritized for conservation and habitat management and as potential sources for reestablishment efforts.
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Gutiérrez-Rodríguez J, Zaldívar-Riverón A, Weissman DB, Vandergast AG. <i>Corrigendum to:</i> Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus <i>Stenopelmatus</i> (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data. INVERTEBR SYST 2022. [DOI: 10.1071/is21022_co] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American <i>Ammopelmatus</i>, and the Mexican, and central and northern South American <i>Stenopelmatus</i>. The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of <i>Stenopelmatus</i> is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of <i>Stenopelmatus</i>, with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within <i>Stenopelmatus</i>. Based on our results, we propose the existence of four species-groups within the genus (the <i>faulkneri</i>, <i>talpa</i>, Central America and <i>piceiventris</i> species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on <i>Stenopelmatus</i> to clarify its actual species richness and evolutionary history in Mesoamerica.
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Gutiérrez-Rodríguez J, Zaldívar-Riverón A, Weissman DB, Vandergast AG. Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data. INVERTEBR SYST 2022. [DOI: 10.1071/is21022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American Ammopelmatus, and the Mexican, and central and northern South American Stenopelmatus. The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of Stenopelmatus is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of Stenopelmatus, with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within Stenopelmatus. Based on our results, we propose the existence of four species-groups within the genus (the faulkneri, talpa, Central America and piceiventris species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on Stenopelmatus to clarify its actual species richness and evolutionary history in Mesoamerica.
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Mitchell CI, Shoemaker KT, Esque TC, Vandergast AG, Hromada SJ, Dutcher KE, Heaton JS, Nussear KE. Integrating telemetry data at several scales with spatial capture–recapture to improve density estimates. Ecosphere 2021. [DOI: 10.1002/ecs2.3689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Corey I. Mitchell
- Department of Geography University of Nevada, Reno 1664 North Virginia Street Reno Nevada 89557 USA
| | - Kevin T. Shoemaker
- Department of Natural Resources and Environmental Science University of Nevada, Reno 1664 North Virginia Street Reno Nevada 89557 USA
| | - Todd C. Esque
- U.S. Geological Survey, Western Ecological Research Center 160 North Stephanie Street Henderson Nevada 89074 USA
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center 4165 Spruance Road Suite 200 San Diego California 92101 USA
| | - Steven J. Hromada
- Department of Geography University of Nevada, Reno 1664 North Virginia Street Reno Nevada 89557 USA
| | - Kirsten E. Dutcher
- Department of Geography University of Nevada, Reno 1664 North Virginia Street Reno Nevada 89557 USA
| | - Jill S. Heaton
- Department of Geography University of Nevada, Reno 1664 North Virginia Street Reno Nevada 89557 USA
| | - Kenneth E. Nussear
- Department of Geography University of Nevada, Reno 1664 North Virginia Street Reno Nevada 89557 USA
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Weissman DB, Vandergast AG, Song H, Shin S, McKenna DD, Ueshima N. Generic relationships of New World Jerusalem crickets (Orthoptera: Stenopelmatoidea:Stenopelmatinae), including all known species of Stenopelmatus. Zootaxa 2021; 4917:zootaxa.4917.1.1. [PMID: 33756684 DOI: 10.11646/zootaxa.4917.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Indexed: 11/04/2022]
Abstract
The New World Jerusalem crickets currently consist of 4 genera: Stenopelmatus Burmeister, 1838, with 33 named entities; Ammopelmatus Tinkham, 1965, with 2 described species; Viscainopelmatus Tinkham, 1970, with 1 described species, and Stenopelmatopterus Gorochov, 1988, with 3 described species. We redefine the generic boundaries of these 4 genera, synonymize Stenopelmatopterus under Stenopelmatus, and synonymize Viscainopelmatus under Ammopelmatus. We then discuss, and illustrate, all the types of the species of Stenopelmatus, all of which only occur south of the United States' border. We recognize as valid the following 5 described Mexican and Central American species: S. ater, S. piceiventris, S. sartorianus, S. talpa, and S. typhlops. We declare the following 13 described Mexican and Central American Stenopelmatus taxa as nomen dubium: S. calcaratus, S. erythromelus, S. guatemalae, S. histrio, S. lessonae, S. lycosoides, S. mexicanus, S. minor, S. nieti, S. sallei, S. sumichrasti, S. toltecus, and S. vicinus. We designate a neotype for S. talpa and lectotypes for S. ater, S. guatemalae, S. histrio, S. lessonae, S. mexicanus, S. minor, S. nieti, S. sallei, S. sumichrasti, and S. toltecus. We assign a type locality for S. piceiventris. We concur with the previous synonymy of S. politus under S. sartorianus. We describe 14 new species of Stenopelmatus from Mexico, Honduras and Ecuador, based on a combination of adult morphology, DNA, calling song drumming pattern, distribution, and karyotype: S. chiapas sp. nov., S. cusuco sp. nov., S. diezmilpies sp. nov., S. durango sp. nov., S. ecuadorensis sp. nov., S. faulkneri sp. nov., S. honduras sp. nov., S. hondurasito sp. nov., S. mineraldelmonte sp. nov., S. nuevoleon sp. nov., S. perote sp. nov., S. saltillo sp. nov., S. sanfelipe sp. nov., and S. zimapan sp. nov. We transfer the following 16 described United States taxa, plus S. cephalotes from the "west coast of North America", from Stenopelmatus to Ammopelmatus: A. cahuilaensis, A. californicus, A. cephalotes, A. fasciatus, A. fuscus, A. hydrocephalus, A. intermedius, A. irregularis, A. longispinus, A. mescaleroensis, A. monahansensis, A. navajo, A. nigrocapitatus, A. oculatus, A. pictus, and A. terrenus, along with the Mexican taxon A. comanchus: these species will be discussed in a subsequent paper (Weissman et al. in prep). We believe that all new Jerusalem cricket species descriptions should include, at a minimum, calling drum (most important) and DNA information.
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Affiliation(s)
- David B Weissman
- Department of Entomology, California Academy of Sciences, Golden Gate Park, San Francisco, CA 94118, USA..
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Hromada SJ, Esque TC, Vandergast AG, Dutcher KE, Mitchell CI, Gray ME, Chang T, Dickson BG, Nussear KE. Using movement to inform conservation corridor design for Mojave desert tortoise. Mov Ecol 2020; 8:38. [PMID: 33042548 PMCID: PMC7541175 DOI: 10.1186/s40462-020-00224-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/14/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Preserving corridors for movement and gene flow among populations can assist in the recovery of threatened and endangered species. As human activity continues to fragment habitats, characterizing natural corridors is important in establishing and maintaining connectivity corridors within the anthropogenic development matrix. The Mojave desert tortoise (Gopherus agassizii) is a threatened species occupying a variety of habitats in the Mojave and Colorado Deserts. Desert tortoises have been referred to as corridor-dwellers, and understanding how they move within suitable habitat can be crucial to defining corridors that will sustain sufficient gene flow to maintain connections among populations amidst the increases in human development. METHODS To elucidate how tortoises traverse available habitat and interact with potentially inhospitable terrain and human infrastructure, we used GPS dataloggers to document fine-scale movement of individuals and estimate home ranges at ten study sites along the California/Nevada border. Our sites encompass a variety of habitats, including mountain passes that serve as important natural corridors connecting neighboring valleys, and are impacted by a variety of linear anthropogenic features. We used path selection functions to quantify tortoise movements and develop resistance surfaces based on landscape characteristics including natural features, anthropogenic alterations, and estimated home ranges with autocorrelated kernel density methods. Using the best supported path selection models and estimated home ranges, we determined characteristics of known natural corridors and compared them to mitigation corridors (remnant habitat patches) that have been integrated into land management decisions in the Ivanpah Valley. RESULTS Tortoises avoided areas of high slope and low perennial vegetation cover, avoided moving near low-density roads, and traveled along linear barriers (fences and flood control berms). CONCLUSIONS We found that mitigation corridors designated between solar facilities should be wide enough to retain home ranges and maintain function. Differences in home range size and movement resistance between our two natural mountain pass corridors align with differences in genetic connectivity, suggesting that not all natural corridors provide the same functionality. Furthermore, creation of mitigation corridors with fences may have unintended consequences and may function differently than natural corridors. Understanding characteristics of corridors with different functionality will help future managers ensure that connectivity is maintained among Mojave desert tortoise populations.
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Affiliation(s)
- Steven J. Hromada
- Program in Ecology, Evolution and Conservation Biology, University of Nevada, 1664 N. Virginia St, Reno, NV 89557 USA
- Department of Geography, University of Nevada, 1664 N. Virginia St, Reno, NV 89557 USA
| | - Todd C. Esque
- U.S. Geological Survey, Western Ecological Research Center, 160 N Stephanie St, Henderson, NV 89074 USA
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, 4165 Spruance Road Suite 200, San Diego, CA 92101 USA
| | - Kirsten E. Dutcher
- Department of Geography, University of Nevada, 1664 N. Virginia St, Reno, NV 89557 USA
| | - Corey I. Mitchell
- Department of Geography, University of Nevada, 1664 N. Virginia St, Reno, NV 89557 USA
| | - Miranda E. Gray
- Conservation Science Partners, 11050 Pioneer Trail, Suite 202, Truckee, CA 96161 USA
| | - Tony Chang
- Conservation Science Partners, 11050 Pioneer Trail, Suite 202, Truckee, CA 96161 USA
| | - Brett G. Dickson
- Conservation Science Partners, 11050 Pioneer Trail, Suite 202, Truckee, CA 96161 USA
- Landscape Conservation Initiative, Northern Arizona University, P.O. Box 5694, Flagstaff, AZ 86011 USA
| | - Kenneth E. Nussear
- Department of Geography, University of Nevada, 1664 N. Virginia St, Reno, NV 89557 USA
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Wood DA, Rose JP, Halstead BJ, Stoelting RE, Swaim KE, Vandergast AG. Combining genetic and demographic monitoring better informs conservation of an endangered urban snake. PLoS One 2020; 15:e0231744. [PMID: 32369486 PMCID: PMC7200000 DOI: 10.1371/journal.pone.0231744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/05/2020] [Indexed: 11/24/2022] Open
Abstract
Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species' ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia), a species affected by alteration and isolation of wetland habitats throughout its distribution. The primary goals were to determine the population structure and degree of genetic isolation among T. s. tetrataenia populations and estimate effective size and population abundance within sites to better understand the present and future importance of genetic drift. We also used temporally sampled datasets to examine the magnitude of genetic change over time. We found moderate population genetic structure throughout the San Francisco Peninsula that partitions sites into northern and southern regional clusters. Point estimates of both effective size and population abundance were generally small (≤ 100) for a majority of the sites, and estimates were particularly low in the northern populations. Genetic analyses of temporal datasets indicated an increase in genetic differentiation, especially for the most geographically isolated sites, and decreased genetic diversity over time in at least one site (Pacifica). Our results suggest that drift-mediated processes as a function of small population size and reduced connectivity from neighboring populations may decrease diversity and increase differentiation. Improving genetic diversity and connectivity among T. s. tetrataenia populations could promote persistence of this endangered snake.
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Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Jonathan P. Rose
- U.S. Geological Survey, Western Ecological Research Center, Santa Cruz Field Station, Santa Cruz, California, United States of America
| | - Brian J. Halstead
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, United States of America
| | - Ricka E. Stoelting
- Swaim Biological Incorporated, Livermore, California, United States of America
| | - Karen E. Swaim
- Swaim Biological Incorporated, Livermore, California, United States of America
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
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Milano ER, Mulligan MR, Rebman JP, Vandergast AG. High-throughput sequencing reveals distinct regional genetic structure among remaining populations of an endangered salt marsh plant in California. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01269-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Mitelberg A, Vandergast AG, Nussear KE, Dutcher K, Esque TC. Development of a Genotyping Protocol for Mojave Desert Tortoise Scat. Chelonian Conservation and Biology 2019. [DOI: 10.2744/ccb-1394.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anna Mitelberg
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
| | - Amy G. Vandergast
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
| | - Ken E. Nussear
- University of Nevada, Department of Geography, Mackay Science Hall, 1664 North Virginia Street, Reno, Nevada 89557 USA [; ]
| | - Kirsten Dutcher
- University of Nevada, Department of Geography, Mackay Science Hall, 1664 North Virginia Street, Reno, Nevada 89557 USA [; ]
| | - Todd C. Esque
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
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Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (
Anaxyrus canorus
). Evolution 2019; 73:2476-2496. [DOI: 10.1111/evo.13868] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/18/2019] [Accepted: 10/14/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Paul A. Maier
- Department of BiologySan Diego State University 5500 Campanile Dr. San Diego CA 92182
- FamilyTreeDNA Gene by Gene, 1445 N Loop W Houston TX 77008
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research CenterSan Diego Field Station 4165 Spruance Road, Suite 200 San Diego CA 92101
| | - Steven M. Ostoja
- USDA California Climate Hub, Agricultural Research Service, John Muir Institute of the EnvironmentUniversity of California, Davis 1 Shields Ave. Davis CA 95616
| | - Andres Aguilar
- Department of Biological SciencesCalifornia State University, Los Angeles 5151 State University Dr Los Angeles CA 90032
| | - Andrew J. Bohonak
- Department of BiologySan Diego State University 5500 Campanile Dr. San Diego CA 92182
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Tracey JA, Rochester CJ, Hathaway SA, Preston KL, Syphard AD, Vandergast AG, Diffendorfer JE, Franklin J, MacKenzie JB, Oberbauer TA, Tremor S, Winchell CS, Fisher RN. Prioritizing conserved areas threatened by wildfire and fragmentation for monitoring and management. PLoS One 2018; 13:e0200203. [PMID: 30192760 PMCID: PMC6128460 DOI: 10.1371/journal.pone.0200203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 06/21/2018] [Indexed: 11/24/2022] Open
Abstract
In many parts of the world, the combined effects of habitat fragmentation and altered disturbance regimes pose a significant threat to biodiversity. This is particularly true in Mediterranean-type ecosystems (MTEs), which tend to be fire-prone, species rich, and heavily impacted by human land use. Given the spatial complexity of overlapping threats and species’ vulnerability along with limited conservation budgets, methods are needed for prioritizing areas for monitoring and management in these regions. We developed a multi-criteria Pareto ranking methodology for prioritizing spatial units for conservation and applied it to fire threat, habitat fragmentation threat, species richness, and genetic biodiversity criteria in San Diego County, California, USA. We summarized the criteria and Pareto ranking results (from west to east) within the maritime, coastal, transitional, inland climate zones within San Diego County. Fire threat increased from the maritime zone eastward to the transitional zone, then decreased in the mountainous inland climate zone. Number of fires and fire return interval departure were strongly negatively correlated. Fragmentation threats, particularly road density and development density, were highest in the maritime climate zone, declined towards the east, and were positively correlated. Species richness criteria showed distributions among climate zones similar to those of the fire threat variables. When using species richness and fire threat criteria, most lower-ranked (higher conservation priority) units occurred in the coastal and transitional zones. When considering genetic biodiversity, lower-ranked units occurred more often in the mountainous inland zone. With Pareto ranking, there is no need to select criteria weights as part of the decision-making process. However, negative correlations and larger numbers of criteria can result in more units assigned to the same rank. Pareto ranking is broadly applicable and can be used as a standalone decision analysis method or in conjunction with other methods.
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Affiliation(s)
- Jeff A. Tracey
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
- * E-mail:
| | - Carlton J. Rochester
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| | - Stacie A. Hathaway
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| | - Kristine L. Preston
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
- San Diego Management and Monitoring Program, San Diego, California, United States of America
| | | | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| | - Jay E. Diffendorfer
- Geosciences and Environmental Change Science Center, U.S. Geological Survey, Denver, Colorado, United States of America
| | - Janet Franklin
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Jason B. MacKenzie
- Environment and Planning Directorate, ACT Government, Canberra, Australia
| | | | - Scott Tremor
- San Diego Natural History Museum, San Diego, California, United States of America
| | - Clark S. Winchell
- U.S. Fish & Wildlife Service, Carlsbad, California, United States of America
| | - Robert N. Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
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Richmond JQ, Wood DA, Westphal MF, Vandergast AG, Leaché AD, Saslaw LR, Butterfield HS, Fisher RN. Persistence of historical population structure in an endangered species despite near‐complete biome conversion in California's San Joaquin Desert. Mol Ecol 2017; 26:3618-3635. [DOI: 10.1111/mec.14125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 01/24/2017] [Accepted: 03/13/2017] [Indexed: 01/06/2023]
Affiliation(s)
| | | | | | | | - Adam D. Leaché
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Seattle WA USA
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Gottscho AD, Wood DA, Vandergast AG, Lemos-Espinal J, Gatesy J, Reeder TW. Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow. Mol Phylogenet Evol 2017; 106:103-117. [DOI: 10.1016/j.ympev.2016.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 07/26/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023]
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Iwanowicz DD, Vandergast AG, Cornman RS, Adams CR, Kohn JR, Fisher RN, Brehme CS. Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse. PLoS One 2016; 11:e0165366. [PMID: 27851756 PMCID: PMC5112926 DOI: 10.1371/journal.pone.0165366] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/11/2016] [Indexed: 11/24/2022] Open
Abstract
Understanding the diet of an endangered species illuminates the animal’s ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4–14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.
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Affiliation(s)
- Deborah D. Iwanowicz
- U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, United States of America
- * E-mail:
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| | - Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Cynthia R. Adams
- U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, United States of America
| | - Joshua R. Kohn
- University of California San Diego, Division of Biological Sciences, La Jolla, California, United States of America
| | - Robert N. Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| | - Cheryl S. Brehme
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
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Wood DA, Bui TVD, Overton CT, Vandergast AG, Casazza ML, Hull JM, Takekawa JY. A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (Rallus obsoletus obsoletus). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0888-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Richmond JQ, Wood DA, Swaim KE, Fisher RN, Vandergast AG. Historical Habitat Barriers Prevent Ring-like Genetic Continuity Throughout the Distribution of Threatened Alameda Striped Racers (Coluber lateralis euryxanthus). HERPETOLOGICA 2016. [DOI: 10.1655/herpetologica-d-15-00046.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jonathan Q. Richmond
- US Geological Survey, Western Ecological Research Center, 4165 Spruance Road, Suite 200, San Diego, CA 92106, USA
| | - Dustin A. Wood
- US Geological Survey, Western Ecological Research Center, 4165 Spruance Road, Suite 200, San Diego, CA 92106, USA
| | - Karen E. Swaim
- Swaim Biological Incorporated, 4435 First Street PMB 312, Livermore, CA 94551, USA
| | - Robert N. Fisher
- US Geological Survey, Western Ecological Research Center, 4165 Spruance Road, Suite 200, San Diego, CA 92106, USA
| | - Amy G. Vandergast
- US Geological Survey, Western Ecological Research Center, 4165 Spruance Road, Suite 200, San Diego, CA 92106, USA
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Richmond JQ, Wood DA, Swaim KE, Fisher RN, Vandergast AG. Historical Habitat Barriers Prevent Ring-like Genetic Continuity Throughout the Distribution of Threatened Alameda Striped Racers (Coluber lateralis euryxanthus). HERPETOLOGICA 2016. [DOI: 10.1655/herpetologica-d-15-00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Vandergast AG, Wood DA, Thompson AR, Fisher M, Barrows CW, Grant TJ. Drifting to oblivion? Rapid genetic differentiation in an endangered lizard following habitat fragmentation and drought. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Amy G. Vandergast
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station. 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Dustin A. Wood
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station. 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Andrew R. Thompson
- Fisheries Resources Division; Southwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; La Jolla CA 92037 USA
| | - Mark Fisher
- Natural Reserve System; P.L. Boyd Deep Canyon Desert Research Center; University of California; 54900 Desert Research Tr. Indian Wells CA 92210 USA
| | - Cameron W. Barrows
- Center for Conservation Biology; University of California Riverside; Riverside CA 92251 USA
| | - Tyler J. Grant
- Department of Natural Resource Ecology and Management; Iowa State University; 339 Science II Ames IA 50011 USA
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Barr KR, Kus BE, Preston KL, Howell S, Perkins E, Vandergast AG. Habitat fragmentation in coastal southern California disrupts genetic connectivity in the cactus wren (Campylorhynchus brunneicapillus). Mol Ecol 2015; 24:2349-63. [DOI: 10.1111/mec.13176] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Kelly R. Barr
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Barbara E. Kus
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Kristine L. Preston
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Scarlett Howell
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Emily Perkins
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Amy G. Vandergast
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
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Wood DA, Halstead BJ, Casazza ML, Hansen EC, Wylie GD, Vandergast AG. Defining population structure and genetic signatures of decline in the giant gartersnake (Thamnophis gigas): implications for conserving threatened species within highly altered landscapes. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0720-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wood DA, Fisher RN, Vandergast AG. Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication. PLoS One 2014; 9:e97494. [PMID: 24848638 PMCID: PMC4029750 DOI: 10.1371/journal.pone.0097494] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/16/2014] [Indexed: 11/23/2022] Open
Abstract
Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.
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Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Robert N. Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
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Richmond JQ, Barr KR, Backlin AR, Vandergast AG, Fisher RN. Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog ( Rana draytonii). Evol Appl 2013; 6:808-822. [PMID: 29387167 PMCID: PMC5779129 DOI: 10.1111/eva.12067] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 02/25/2013] [Indexed: 12/01/2022] Open
Abstract
Populations forming the edge of a species range are often imperiled by isolation and low genetic diversity, with proximity to human population centers being a major determinant of edge stability in modern landscapes. Since the 1960s, the California red‐legged frog (Rana draytonii) has undergone extensive declines in heavily urbanized southern California, where the range edge has rapidly contracted northward while shifting its cardinal orientation to an east‐west trending axis. We studied the genetic structure and diversity of these frontline populations, tested for signatures of contemporary disturbance, specifically fire, and attempted to disentangle these signals from demographic events extending deeper into the past. Consistent with the genetic expectations of the ‘abundant‐center’ model, we found that diversity, admixture, and opportunity for random mating increases in populations sampled successively further away from the range boundary. Demographic simulations indicate that bottlenecks in peripheral isolates are associated with processes extending tens to a few hundred generations in the past, despite the demographic collapse of some due to recent fire‐flood events. While the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.
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Affiliation(s)
| | - Kelly R Barr
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Adam R Backlin
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Amy G Vandergast
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Robert N Fisher
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
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Inman RD, Esque TC, Nussear KE, Leitner P, Matocq MD, Weisberg PJ, Dilts TE, Vandergast AG. Is there room for all of us? Renewable energy and Xerospermophilus mohavensis. ENDANGER SPECIES RES 2013. [DOI: 10.3354/esr00487] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Wood DA, Vandergast AG, Barr KR, Inman RD, Esque TC, Nussear KE, Fisher RN. Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the
M
ojave and
S
onoran Deserts. DIVERS DISTRIB 2012. [DOI: 10.1111/ddi.12022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey Western Ecological Research Center San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Amy G. Vandergast
- U.S. Geological Survey Western Ecological Research Center San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Kelly R. Barr
- U.S. Geological Survey Western Ecological Research Center San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Rich D. Inman
- U.S. Geological Survey Western Ecological Research Center Las Vegas Field Station, 160 North Stephanie Street Henderson NV 89074 USA
| | - Todd C. Esque
- U.S. Geological Survey Western Ecological Research Center Las Vegas Field Station, 160 North Stephanie Street Henderson NV 89074 USA
| | - Kenneth E. Nussear
- U.S. Geological Survey Western Ecological Research Center Las Vegas Field Station, 160 North Stephanie Street Henderson NV 89074 USA
| | - Robert N. Fisher
- U.S. Geological Survey Western Ecological Research Center San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
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Roderick GK, Croucher PJP, Vandergast AG, Gillespie RG. Species Differentiation on a Dynamic Landscape: Shifts in Metapopulation Genetic Structure Using the Chronology of the Hawaiian Archipelago. Evol Biol 2012; 39:192-206. [PMID: 22707805 PMCID: PMC3364410 DOI: 10.1007/s11692-012-9184-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 04/06/2012] [Indexed: 11/20/2022]
Abstract
Species formation during adaptive radiation often occurs in the context of a changing environment. The establishment and arrangement of populations, in space and time, sets up ecological and genetic processes that dictate the rate and pattern of differentiation. Here, we focus on how a dynamic habitat can affect genetic structure, and ultimately, differentiation among populations. We make use of the chronology and geographical history provided by the Hawaiian archipelago to examine the initial stages of population establishment and genetic divergence. We use data from a set of 6 spider lineages that differ in habitat affinities, some preferring low elevation habitats with a longer history of connection, others being more specialized for high elevation and/or wet forest, some with more general habitat affinities. We show that habitat preferences associated with lineages are important in ecological and genetic structuring. Lineages that have more restricted habitat preferences are subject to repeated episodes of isolation and fragmentation as a result of lava flows and vegetation succession. The initial dynamic set up by the landscape translates over time into discrete lineages. Further work is needed to understand how genetic changes interact with a changing set of ecological interactions amongst a shifting mosaic of landscapes to achieve species formation.
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Affiliation(s)
- George K. Roderick
- Department of Environmental Science, Policy, and Management, University of California, 130 Mulford Hall, Berkeley, CA 94720-3114 USA
| | - Peter J. P. Croucher
- Department of Environmental Science, Policy, and Management, University of California, 130 Mulford Hall, Berkeley, CA 94720-3114 USA
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road, Suite 200, San Diego, CA 92101 USA
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy, and Management, University of California, 130 Mulford Hall, Berkeley, CA 94720-3114 USA
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Wood DA, Vandergast AG, Lemos Espinal JA, Fisher RN, Holycross AT. Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data. Mol Ecol 2011; 20:3856-78. [PMID: 21851436 DOI: 10.1111/j.1365-294x.2011.05211.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Glacial-interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.
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Affiliation(s)
- Dustin A Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road, Suite 200, San Diego, CA 92101, USA.
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Vandergast AG, Wood DA, Simovich M, Bohonak AJ. Identification of co-occurring Branchinecta fairy shrimp species from encysted embryos using multiplex polymerase chain reaction. Mol Ecol Resour 2009; 9:767-70. [PMID: 21564739 DOI: 10.1111/j.1755-0998.2009.02522.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Morphological identification of many fairy shrimp species is difficult because distinguishing characters are restricted to adults. We developed two multiplex polymerase chain reaction assays that differentiate among three Branchinecta fairy shrimp with distributional overlap in southern California vernal pools. Two of the species are federally listed as threatened. Molecular identification of Branchinecta from cysts allows for species surveys to be conducted during the dry season, expanding the timeframe for population assessment and providing a less intrusive method of sampling sensitive vernal pool habitats.
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Affiliation(s)
- A G Vandergast
- US Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road, Suite 200, San Diego, CA 92101, USA University of San Diego, Department of Biology, 5998 Alacala Park, San Diego, CA 92110, USA San Diego State University, Department of Biology, 5500 Campanile Drive, San Diego, CA 92182-4614, USA
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Vandergast AG, Bohonak AJ, Weissman DB, Fisher RN. Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus). Mol Ecol 2006; 16:977-92. [PMID: 17305855 DOI: 10.1111/j.1365-294x.2006.03216.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species.
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Affiliation(s)
- Amy G Vandergast
- US Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road Suite 200, San Diego, CA 92101, USA.
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Vandergast AG, Gillespie RG, Roderick GK. Influence of volcanic activity on the population genetic structure of Hawaiian Tetragnatha spiders: fragmentation, rapid population growth and the potential for accelerated evolution. Mol Ecol 2005; 13:1729-43. [PMID: 15189199 DOI: 10.1111/j.1365-294x.2004.02179.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Volcanic activity on the island of Hawaii results in a cyclical pattern of habitat destruction and fragmentation by lava, followed by habitat regeneration on newly formed substrates. While this pattern has been hypothesized to promote the diversification of Hawaiian lineages, there have been few attempts to link geological processes to measurable changes in population structure. We investigated the genetic structure of three species of Hawaiian spiders in forests fragmented by a 150-year-old lava flow on Mauna Loa Volcano, island of Hawaii: Tetragnatha quasimodo (forest and lava flow generalist), T. anuenue and T. brevignatha (forest specialists). To estimate fragmentation effects on population subdivision in each species, we examined variation in mitochondrial and nuclear genomes (DNA sequences and allozymes, respectively). Population subdivision was higher for forest specialists than for the generalist in fragments separated by lava. Patterns of mtDNA sequence evolution also revealed that forest specialists have undergone rapid expansion, while the generalist has experienced more gradual population growth. Results confirm that patterns of neutral genetic variation reflect patterns of volcanic activity in some Tetragnatha species. Our study further suggests that population subdivision and expansion can occur across small spatial and temporal scales, which may facilitate the rapid spread of new character states, leading to speciation as hypothesized by H. L. Carson 30 years ago.
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Affiliation(s)
- Amy G Vandergast
- USGS Western Ecological Research Center, San Diego Field Station, 5745 Kearny Villa Road, Suite M, San Diego CA 92123, USA.
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Vandergast AG, Roderick GK. Erratum to “Mermithid parasitism of Hawaiian Tetragnatha spiders in a fragmented landscape” [J. Invertebr. Pathol. 84 (2003) 128–136]. J Invertebr Pathol 2004. [DOI: 10.1016/j.jip.2004.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
Hawaiian Tetragnatha spiders inhabiting small forest fragments on the Big Island of Hawaii are parasitized by mermithid nematodes. This is the first report of mermithid nematodes infecting spiders in Hawaii, and an initial attempt to characterize this host-parasite interaction. Because immature mermithids were not morphologically identifiable, a molecular identification was performed. A phylogenetic analysis based on 18S small ribosomal subunit nuclear gene sequences suggested that Hawaiian spider mermithids are more closely related to a mainland presumptive Aranimemis species that infects spiders, than to an insect-infecting mermithid collected on Oahu, HI, or to Mermis nigrescens, also a parasite of insects. Measured infection prevalence was low (ranging from 0 to 4%) but differed significantly among forest fragments. Infection prevalence was associated significantly with fragment area, but not with spider density nor spider species richness. Results suggest that mermithid populations are sensitive to habitat fragmentation, but that changes in infection prevalence do not appear to affect spider community structure.
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Affiliation(s)
- Amy G Vandergast
- USGS Western Ecological Research Center, San Diego Field Station, 5745 Kearny Villa Road, Suite M, San Diego, CA 92123, USA.
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