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Wishingrad V, Thomson RC. Biogeographic inferences across spatial and evolutionary scales. Mol Ecol 2023; 32:2055-2070. [PMID: 36695049 DOI: 10.1111/mec.16861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, spatial genetics processes at small geographical scales, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographical scales. Here, we evaluate the link between landscape genetics and phylogeographical methods using the western fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographical scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographical study of population structure at two evolutionary scales informed by inferences derived from landscape genetics results to identify concordance and conflict between these sets of methods. We found significant concordance in landscape genetics processes at all but the largest geographical scale. Phylogeographical results indicate major clades are restricted to distinct river drainages or distinct hydrological regions. At a more recent timescale, we find minor clades are restricted to single river canyons in the majority of cases, while the remainder of river canyons include samples from at most two clades. Overall, the broad-scale pattern implicating stream and river valleys as key features linking populations in the landscape genetics results, and high degree of clade specificity within major topographic subdivisions in the phylogeographical results, is consistent. As landscape genetics and phylogeography share many of the same objectives, synthesizing theory, models and methods between these fields will help bring about a better understanding of ecological and evolutionary processes structuring genetic variation across space and time.
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Affiliation(s)
- Van Wishingrad
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA.,Hawai'i, Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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2
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Grismer J, Scott P, Toffelmier E, Hinds B, Klabacka R, Stewart G, White V, Oaks J, Bradley Shaffer H. Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, Charina) and the critical need for enhanced conservation actions. Mol Phylogenet Evol 2022; 174:107542. [PMID: 35690376 DOI: 10.1016/j.ympev.2022.107542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
The mountains of southern California represent unique, isolated ecosystems that support distinct high-elevation habitats found nowhere else in the area. Analyses of several moisture-dependent species across these sky-islands indicate they exist as locally endemic lineages that occur across these fragmented mountains ranges. The Rubber Boa is a semi-fossorial snake species that is widely distributed in the cooler and more moist ecoregions regions of western North America, including isolated populations across southern California mountain ranges. We developed a genomic and ecological dataset to examine genetic diversity within Rubber Boas and to determine if the endemic Southern Rubber Boa represents a distinct lineage. We quantified current and future habitat suitability under a range of climate change scenarios, and discuss the possible environmental threats facing these unique montane isolates. Our results support four major lineages within Rubber Boas, with genetic breaks that are consistent with biogeographic boundaries observed in other co-distributed, cool-temperature, moisture adapted species. Our data support previous studies that the Southern Rubber Boa is an independent evolutionary unit and now includes multiple locally endemic sky-island populations, restricted to isolated mountain tops and ranges across southern California. Analyses of future habitat suitability indicate that many of these sky-island populations will lose most of their suitable habitat over the next 70 years given predicted increases in drought, rising temperatures, and wildfires. Collectively these data emphasize the critical conservation needs of these montane ecosystems in southern California under current and projected climate change conditions.
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Affiliation(s)
- Jesse Grismer
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA; Department of Biology, La Sierra University, Riverside, CA 92515, USA.
| | - Peter Scott
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, TX 79016, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Brian Hinds
- Department of Biology, La Sierra University, Riverside, CA 92515, USA
| | - Randy Klabacka
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Glenn Stewart
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Virginia White
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Jamie Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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Jockusch EL, Hansen RW, Fisher RN, Wake DB. Slender salamanders (genus Batrachoseps) reveal Southern California to be a center for the diversification, persistence, and introduction of salamander lineages. PeerJ 2020; 8:e9599. [PMID: 32864205 PMCID: PMC7430267 DOI: 10.7717/peerj.9599] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 07/02/2020] [Indexed: 11/20/2022] Open
Abstract
Background The southern California biodiversity hotspot has had a complex geological history, with both plate tectonic forces and sea level changes repeatedly reconfiguring the region, and likely driving both lineage splittings and extinctions. Here we investigate patterns of genetic divergence in two species of slender salamanders (Plethodontidae: Batrachoseps) in this region. The complex geological history in combination with several organismal traits led us to predict that these species harbor multiple ancient mitochondrial lineages endemic to southern California. These species belong to a clade characterized by fine-scale mitochondrial structure, which has been shown to track ancient splits. Both focal species, Batrachoseps major and B. nigriventris, are relatively widely distributed in southern California, and estimated to have persisted there across millions of years. Recently several extralimital populations of Batrachoseps were found in the San Joaquin Valley of California, a former desert area that has been extensively modified for agriculture. The origins of these populations are unknown, but based on morphology, they are hypothesized to result from human-mediated introductions of B. major. Methods We sequenced the mitochondrial gene cytochrome b from a geographically comprehensive sampling of the mitochondrial lineages of B. major and B. nigriventris that are endemic to southern California. We used phylogenetic analyses to characterize phylogeographic structure and identify mitochondrial contact zones. We also included the San Joaquin Valley samples to test whether they resulted from introductions. We used a bootstrap resampling approach to compare the strength of isolation-by-distance in both Batrachoseps species and four other salamander species with which they co-occur in southern California. Results The northern lineage of B. major harbors at least eight deeply differentiated, geographically cohesive mitochondrial subclades. We identify geographic contact between many of these mtDNA lineages and some biogeographic features that are concordant with lineage boundaries. Batrachoseps nigriventris also has multiple deeply differentiated clades within the region. Comparative analyses highlight the smaller spatial scales over which mitochondrial divergence accumulates in Batrachoseps relative to most other salamander species in southern California. The extralimital populations of Batrachoseps from the San Joaquin Valley are assigned to B. major and are shown to result from at least two independent introductions from different source populations. We also suggest that B. major on Catalina Island, where it is considered native, may be the result of an introduction. Some of the same traits that facilitate the build-up of deep phylogeographic structure in Batrachoseps likely also contribute to its propensity for introductions, and we anticipate that additional introduced populations will be discovered.
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Affiliation(s)
- Elizabeth L Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America
| | - Robert W Hansen
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America
| | - Robert N Fisher
- Western Ecological Research Center, San Diego Field Station, San Diego, CA, U.S. Geological Survey, United States of America
| | - David B Wake
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
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Lavin BR, Wogan GOU, McGuire JA, Feldman CR. Phylogeography of the Northern Alligator Lizard (Squamata, Anguidae): Hidden diversity in a western endemic. ZOOL SCR 2018. [DOI: 10.1111/zsc.12294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Brian R. Lavin
- Department of Biology; Sonoma State University; Rohnert Park California
| | - Guinevere O. U. Wogan
- Department of Environmental Science, Policy and Management and Museum of Vertebrate Zoology; University of California; Berkeley California
| | - Jimmy A. McGuire
- Department of Integrative Biology and Museum of Vertebrate Zoology; University of California; Berkeley California
| | - Chris R. Feldman
- Department of Biology and Program in Ecology, Evolution and Conservation Biology; University of Nevada; Reno Nevada
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Valdivia-Carrillo T, García-De León FJ, Blázquez MC, Gutiérrez-Flores C, González Zamorano P. Phylogeography and Ecological Niche Modeling of the Desert Iguana (Dipsosaurus dorsalis, Baird & Girard 1852) in the Baja California Peninsula. J Hered 2017; 108:640-649. [PMID: 28821185 DOI: 10.1093/jhered/esx064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/13/2017] [Indexed: 11/14/2022] Open
Abstract
Understanding the factors that explain the patterns of genetic structure or phylogeographic breaks at an intraspecific level is key to inferring the mechanisms of population differentiation in its early stages. These topics have been well studied in the Baja California region, with vicariance and the dispersal ability of individuals being the prevailing hypothesis for phylogeographic breaks. In this study, we evaluated the phylogeographic patterns in the desert iguana (Dipsosaurus dorsalis), a species with a recent history in the region and spatial variation in life history traits. We analyzed a total of 307 individuals collected throughout 19 localities across the Baja California Peninsula with 15 microsatellite DNA markers. Our data reveal the existence of 3 geographically discrete genetic populations with moderate gene flow and an isolation-by-distance pattern presumably produced by the occurrence of a refugium in the Cape region during the Pleistocene Last Glacial Maximum. Bayesian methods and ecological niche modeling were used to assess the relationship between population genetic structure and present and past climatic preferences of the desert iguana. We found that the present climatic heterogeneity of the Baja California Peninsula has a marked influence on the population genetic structure of the species, suggesting that there are alternative explanations besides vicariance. The information obtained in this study provides data allowing a better understanding of how historical population processes in the Baja California Peninsula can be understood from an ecological perspective.
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Affiliation(s)
- Tania Valdivia-Carrillo
- Laboratorio de Genética para la Conservación, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Ecología del Comportamiento, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Sistemas de Información Geográfica, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México
| | - Francisco J García-De León
- Laboratorio de Genética para la Conservación, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Ecología del Comportamiento, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Sistemas de Información Geográfica, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México
| | - Ma Carmen Blázquez
- Laboratorio de Genética para la Conservación, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Ecología del Comportamiento, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Sistemas de Información Geográfica, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México
| | - Carina Gutiérrez-Flores
- Laboratorio de Genética para la Conservación, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Ecología del Comportamiento, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Sistemas de Información Geográfica, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México
| | - Patricia González Zamorano
- Laboratorio de Genética para la Conservación, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Ecología del Comportamiento, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México; Laboratorio de Sistemas de Información Geográfica, Programa de Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México
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Greenbaum IF, Chirhart SE, Walker ML, Honeycutt RL. Molecular phylogenetics of western deer mice ( Peromyscus): Taxonomic and biogeographic implications. SOUTHWEST NAT 2017. [DOI: 10.1894/0038-4909-62.2.129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Ira F. Greenbaum
- Department of Biology, Texas A&M University, College Station, TX 77843-3258 (IFG, SEC, MLW)
| | - Scott E. Chirhart
- Department of Biology, Texas A&M University, College Station, TX 77843-3258 (IFG, SEC, MLW)
| | - Mindy L. Walker
- Department of Biology, Texas A&M University, College Station, TX 77843-3258 (IFG, SEC, MLW)
| | - Rodney L. Honeycutt
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, 77843-3258 (RLH)
- Present address of SEC: Department of Biology, Centenary College of Louisiana, 2911 Centenary Boulevard, Shreveport, LA 71134
- Present address of MLW: Department of Environmental Science, University of Evansville, 1800 Lincoln Avenue, Evansville, IN 47714
- Present address of RLH: Natural Science Division, Pepperdine University, Malibu, CA 90263
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Bryson RW, Savary WE, Zellmer AJ, Bury RB, McCormack JE. Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province. Mol Ecol 2016; 25:3731-51. [DOI: 10.1111/mec.13707] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/03/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Robert W. Bryson
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Box 351800 Seattle WA 98195-1800 USA
| | - Warren E. Savary
- Department of Entomology; California Academy of Sciences; 55 Music Concourse Drive, Golden Gate Park San Francisco CA 94118 USA
| | - Amanda J. Zellmer
- Department of Biology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
| | | | - John E. McCormack
- Department of Biology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
- Moore Laboratory of Zoology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
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Gottscho AD. Zoogeography of the San Andreas Fault system: Great Pacific Fracture Zones correspond with spatially concordant phylogeographic boundaries in western North America. Biol Rev Camb Philos Soc 2014; 91:235-54. [DOI: 10.1111/brv.12167] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 10/28/2014] [Accepted: 11/11/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew D. Gottscho
- Department of Biology; San Diego State University; 5500 Campanile Drive San Diego CA 92182 U.S.A
- Department of Biology; University of California; Riverside CA 92521 U.S.A
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Torstrom SM, Pangle KL, Swanson BJ. Shedding subspecies: The influence of genetics on reptile subspecies taxonomy. Mol Phylogenet Evol 2014; 76:134-43. [DOI: 10.1016/j.ympev.2014.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/08/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
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Ruane S, Bryson RW, Pyron RA, Burbrink FT. Coalescent Species Delimitation in Milksnakes (Genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses. Syst Biol 2013; 63:231-50. [DOI: 10.1093/sysbio/syt099] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Myers EA, Rodríguez-Robles JA, DeNardo DF, Staub RE, Stropoli A, Ruane S, Burbrink FT. Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province. Mol Ecol 2013; 22:5418-29. [DOI: 10.1111/mec.12478] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/23/2013] [Accepted: 07/25/2013] [Indexed: 11/30/2022]
Affiliation(s)
- E. A. Myers
- Department of Biology; The Graduate School; City University of New York; NY 10016 USA
- Department of Biology; 6S-143; College of Staten Island; 2800 Victory Boulevard Staten Island NY 10314 USA
| | - J. A. Rodríguez-Robles
- School of Life Sciences; University of Nevada; 4505 Maryland Parkway Las Vegas NV 89154-4004 USA
| | - D. F. DeNardo
- School of Life Sciences; Arizona State University; Tempe AZ 85287-4501 USA
| | | | - A. Stropoli
- Science, Math and Engineering; Staten Island Technical High School; 485 Clawson Street Staten Island New York 10306 USA
| | - S. Ruane
- Department of Biology; The Graduate School; City University of New York; NY 10016 USA
- Department of Biology; 6S-143; College of Staten Island; 2800 Victory Boulevard Staten Island NY 10314 USA
| | - F. T. Burbrink
- Department of Biology; The Graduate School; City University of New York; NY 10016 USA
- Department of Biology; 6S-143; College of Staten Island; 2800 Victory Boulevard Staten Island NY 10314 USA
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Population Stability of the Northern Desert Nightsnake (Hypsiglena chlorophaea deserticola) during the Pleistocene. J HERPETOL 2013. [DOI: 10.1670/12-104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Devitt TJ, Devitt SEC, Hollingsworth BD, McGuire JA, Moritz C. Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander. Mol Ecol 2013; 22:1650-65. [PMID: 23379992 DOI: 10.1111/mec.12196] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 11/20/2012] [Accepted: 11/26/2012] [Indexed: 11/26/2022]
Abstract
Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate-induced habitat shifts on population genetic structure in the Large-blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high-elevation conifer forest in the Transverse and Peninsular Ranges of southern California and northern Baja California. A composite SDM representing the range through time predicts two disjunct refugia, one in southern California encompassing the core of the species range and the other in the Sierra San Pedro Mártir of northern Baja California at the southern limit of the species range. Based on our spatial model, we would expect a pattern of high connectivity among populations within the northern refugium and, conversely, a pattern of isolation due to long-term persistence of the Sierra San Pedro Mártir population. Our genetic results are consistent with these predictions based on the hypothetical refugia in that (i) historical measures of population connectivity among stable areas are correlated with gene flow estimates; and (ii) there is strong geographical structure between separate refugia. These results provide evidence for the role of recent climatic change in shaping patterns of population persistence and connectivity within the Transverse and Peninsular Ranges, an evolutionary hotspot.
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Affiliation(s)
- Thomas J Devitt
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720-3160, USA.
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Hedin M, Starrett J, Hayashi C. Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae,Antrodiaetus) from California. Mol Ecol 2012. [DOI: 10.1111/mec.12130] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Marshal Hedin
- Department of Biology; San Diego State University San Diego; San Diego CA 92182-4614 USA
| | - James Starrett
- Department of Biology; University of California; Riverside CA 92521 USA
| | - Cheryl Hayashi
- Department of Biology; University of California; Riverside CA 92521 USA
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Lind AJ, Spinks PQ, Fellers GM, Shaffer HB. Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0138-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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SPINKS PHILLIPQ, THOMSON ROBERTC, BRADLEY SHAFFER H. Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle,Emys marmoratain California. Mol Ecol 2010; 19:542-56. [DOI: 10.1111/j.1365-294x.2009.04451.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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POLIHRONAKIS MAXI, CATERINO MICHAELS. Multilocus phylogeography of the flightless darkling beetle Nyctoporis carinata (Coleoptera: Tenebrionidae) in the California Floristic Province: deciphering an evolutionary mosaic. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01360.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Goebel AM, Ranker TA, Corn PS, Olmstead RG. Mitochondrial DNA evolution in the Anaxyrus boreas species group. Mol Phylogenet Evol 2009; 50:209-25. [DOI: 10.1016/j.ympev.2008.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/10/2008] [Accepted: 06/24/2008] [Indexed: 11/27/2022]
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Kuchta SR, Parks DS, Wake DB. Pronounced phylogeographic structure on a small spatial scale: Geomorphological evolution and lineage history in the salamander ring species Ensatina eschscholtzii in central coastal California. Mol Phylogenet Evol 2009; 50:240-55. [DOI: 10.1016/j.ympev.2008.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 10/05/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
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A striking lack of genetic diversity across the wide-ranging amphibian Gastrophryne carolinensis (Anura: Microhylidae). Genetica 2008; 135:169-83. [DOI: 10.1007/s10709-008-9267-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 02/20/2008] [Indexed: 11/27/2022]
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22
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Fontanella FM, Feldman CR, Siddall ME, Burbrink FT. Phylogeography of Diadophis punctatus: Extensive lineage diversity and repeated patterns of historical demography in a trans-continental snake. Mol Phylogenet Evol 2008; 46:1049-70. [DOI: 10.1016/j.ympev.2007.10.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 10/09/2007] [Accepted: 10/14/2007] [Indexed: 11/28/2022]
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Phylogeography and species boundaries of the western North American Nightsnake (Hypsiglena torquata): Revisiting the subspecies concept. Mol Phylogenet Evol 2008; 46:1095-115. [DOI: 10.1016/j.ympev.2007.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 11/26/2007] [Accepted: 12/04/2007] [Indexed: 11/21/2022]
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24
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Wood DA, Fisher RN, Reeder TW. Novel patterns of historical isolation, dispersal, and secondary contact across Baja California in the Rosy Boa (Lichanura trivirgata). Mol Phylogenet Evol 2008; 46:484-502. [DOI: 10.1016/j.ympev.2007.11.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 11/15/2007] [Accepted: 11/20/2007] [Indexed: 11/25/2022]
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25
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Chatzimanolis S, Caterino MS. TOWARD A BETTER UNDERSTANDING OF THE "TRANSVERSE RANGE BREAK": LINEAGE DIVERSIFICATION IN SOUTHERN CALIFORNIA. Evolution 2007; 61:2127-41. [PMID: 17767585 DOI: 10.1111/j.1558-5646.2007.00186.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Transverse Ranges in southern California have been identified as having a prominent phylogeographic role. Numerous studies have identified distinct north-south and/or east-west lineage breaks involving the Transverse Ranges. However, in evaluating their findings, most authors have regarded this complex system somewhat simplistically. In this study we more deeply investigate these breaks using two approaches: first we examine the phylogeographic history of Sepedophilus castaneus (Coleoptera: Staphylinidae) and then implement a comparative phylogeography approach applying Brooks parsimony analysis to the topologies of nine additional taxa. Phylogenetic analysis, nested clade analysis, and AMOVAs for S. castaneus agree that there is a major lineage break between the eastern and western Transverse Ranges, localized between the Sierra Pelona and the San Gabriel Mountains. The comparative phylogeographic analysis supports a generally strong concordance of area relationships with geographic proximity. It is notable, however, that the Transverse Ranges as a group do not show phylogenetic cohesion, but rather they are split into three main regions: an eastern region (San Gabriel, San Bernardino, and San Jacinto Mountains), a central region (central Transverse Ranges and Sierra Pelona) that is often grouped with the Tehachapi and Sierra Nevada populations, and a western region (northwestern Transverse Ranges and Santa Ynez Mountains) that is consistently grouped with coast range areas to the north. The lineage break between east and west Transverse Ranges is attributable to the presence of a marine embayment in what is now the Santa Clara River valley 5-2.5 million years ago.
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Affiliation(s)
- Stylianos Chatzimanolis
- Department of Invertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Road, Santa Barbara, California 93105, USA.
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Kuchta SR. CONTACT ZONES AND SPECIES LIMITS: HYBRIDIZATION BETWEEN LINEAGES OF THE CALIFORNIA NEWT, TARICHA TOROSA, IN THE SOUTHERN SIERRA NEVADA. HERPETOLOGICA 2007. [DOI: 10.1655/0018-0831(2007)63[332:czaslh]2.0.co;2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Waltari E, Hijmans RJ, Peterson AT, Nyári AS, Perkins SL, Guralnick RP. Locating pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS One 2007; 2:e563. [PMID: 17622339 PMCID: PMC1905943 DOI: 10.1371/journal.pone.0000563] [Citation(s) in RCA: 264] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 06/07/2007] [Indexed: 11/19/2022] Open
Abstract
Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution.
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Affiliation(s)
- Eric Waltari
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America.
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28
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Vredenburg VT, Bingham R, Knapp R, Morgan JAT, Moritz C, Wake D. Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow-legged frog. J Zool (1987) 2007. [DOI: 10.1111/j.1469-7998.2006.00258.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Chatzimanolis S, Caterino MS. Limited phylogeographic structure in the flightless ground beetle,Calathus ruficollis, in southern California. DIVERS DISTRIB 2007. [DOI: 10.1111/j.1472-4642.2007.00352.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
| | - Michael S. Caterino
- Department of Invertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Road, Santa Barbara, California 93105, USA
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30
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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] [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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31
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Feldman CR, Spicer GS. Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion. Mol Ecol 2006; 15:2201-22. [PMID: 16780435 DOI: 10.1111/j.1365-294x.2006.02930.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ultimate goal of comparative phylogeographical analyses is to infer processes of diversification from contemporary geographical patterns of genetic diversity. When such studies are employed across diverse groups in an array of communities, it may be difficult to discover common evolutionary and ecological processes associated with diversification. In order to identify taxa that have responded in a similar fashion to historical events, we conducted comparative phylogeographical analyses on a phylogenetically and ecologically limited set of taxa. Here, we focus on a group of squamate reptiles (snakes and lizards) that share similar ecological requirements and generally occupy the same communities in the western USA. At a gross level, deep genetic division in Contia tenuis, Diadophis punctatus, Elgaria multicarinata, the Charina bottae complex, and Lampropeltis zonata are often concordant in the Transverse Ranges, the Monterey Bay and Sacramento-San Joaquin Delta region, and the southern Sierra Nevada in California. Molecular clock estimates suggest that major phyletic breaks within many of these taxa roughly coincide temporally, and may correspond to important geological events. Furthermore, significant congruence between the phylogeographies of E. multicarinata and L. zonata suggests that the succession of vicariance and dispersal events in these species progressed in concert. Such congruence suggests that E. multicarinata and L. zonata have occupied the same communities through time. However, across our entire multi-taxon data set, the sequence of branching events rarely match between sympatric taxa, indicating the importance of subtle differences in life history features as well as random processes in creating unique genetic patterns. Lastly, coalescent and noncoalescent estimates of population expansion suggest that populations in the more southerly distributed clades of C. tenuis, D. punctatus, E. multicarinata, and L. zonata have been stable, while populations in more northerly clades appear to have recently expanded. This concerted demographic response is consistent with palaeontological data and previous phylogeographical work that suggests that woodland habitat has become more restricted in southern California, but more widespread in the North during Holocene warming. Future phylogeographical work focusing on allied and ecologically associated taxa may add insight into the ecological and evolutionary processes that yield current patterns of genetic diversity.
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Affiliation(s)
- Chris R Feldman
- Department of Biology, Utah State University, Logan, Utah 84322-5305, USA.
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32
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McKay JK, Christian CE, Harrison S, Rice KJ. "How Local Is Local?"-A Review of Practical and Conceptual Issues in the Genetics of Restoration. Restor Ecol 2005. [DOI: 10.1111/j.1526-100x.2005.00058.x] [Citation(s) in RCA: 541] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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33
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Burns KJ, Barhoum DN. Population-level history of the wrentit (Chamaea fasciata): implications for comparative phylogeography in the California Floristic Province. Mol Phylogenet Evol 2005; 38:117-29. [PMID: 16129629 DOI: 10.1016/j.ympev.2005.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2005] [Revised: 07/02/2005] [Accepted: 07/05/2005] [Indexed: 11/17/2022]
Abstract
The phylogeography of a variety of species has been studied within the California Floristic Province; however, few studies have examined genetic variation in bird species across the entire region. This study uses mitochondrial DNA data to investigate the phylogeography of the wrentit (Chamaea fasciata), a sedentary bird native to scrub and chaparral habitats of this region. Analysis of molecular variance shows geographic structure, and maximum likelihood, Bayesian, and parsimony analyses consistently identify six main clades that are each restricted geographically. Nested clade phylogeographic analyses infer an overall range expansion for the entire cladogram, and a range expansion is also inferred from the mismatch distribution. Thus, our results suggest that the wrentit was isolated into southern refugia during the Pleistocene and has undergone a recent range expansion. Southern refugia and a range expansion were also identified in a previous study of the California thrasher (Toxostoma redivivum). The wrentit did not show marked divergence between northern and southern California defined by the Transverse Ranges, a pattern seen in a variety of other taxa within this region, including some birds.
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Affiliation(s)
- Kevin J Burns
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
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34
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Spinks PQ, Shaffer HB. Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications. Mol Ecol 2005; 14:2047-64. [PMID: 15910326 DOI: 10.1111/j.1365-294x.2005.02564.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas, E. marmorata contains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspecies Emys marmorata marmorata (Washington-central California). However, no clade is congruent with the distribution of the southern subspecies Emys marmorata pallida from central California-Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Our amova and phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation.
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Affiliation(s)
- Phillip Q Spinks
- Section of Evolution and Ecology, University of California, Davis, California 95616, USA
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35
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Lapointe FJ, Rissler LJ. Congruence, Consensus, and the Comparative Phylogeography of Codistributed Species in California. Am Nat 2005; 166:290-9. [PMID: 16032580 DOI: 10.1086/431283] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 04/13/2005] [Indexed: 11/03/2022]
Abstract
Comparative phylogeography has emerged as a means of understanding the spatial patterns of genetic divergence of codistributed species. However, researchers are often frustrated because of the lack of appropriate statistical tests to assess concordancy of multiple phylogeographic trees. We develop a method for testing congruence across multiple species and synthesizing the data into a regional supertree. Nine phylogeographic data sets of species with different life histories and ecologies were statistically compared using maximum agreement subtrees (MAST) and showed a high degree of concordancy. A supertree combining the different phylogeographic trees was then computed using matrix representation with parsimony, and the groups defined by this supertree were tested against climatic data to investigate a potential mechanism driving divergence. Our data suggest that species and genetic lineages in California are shaped by climatic regimes. The supertree method in combination with MAST represents a new approach to test congruence hypotheses and detect common geographic signals in comparative phylogeography.
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Affiliation(s)
- Francois-Joseph Lapointe
- Departement de sciences biologiques, Universite de Montreal, C.P. 6128, Succursale Centre-ville, Montreal, Quebec H3C 3J7, Canada.
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36
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Forister ML, Fordyce JA, Shapiro AM. Geological barriers and restricted gene flow in the holarctic skipper Hesperia comma (Hesperiidae). Mol Ecol 2005; 13:3489-99. [PMID: 15488006 DOI: 10.1111/j.1365-294x.2004.02349.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Patterns of genetic variation within a species may be a consequence of historical factors, such as past fragmentation, as well as current barriers to gene flow. Using sequence data from the mitochondrial cytochrome oxidase subunit II region (COII) and the nuclear gene wingless, we conducted a phylogeographical study of the holarctic skipper Hesperia comma to elucidate patterns of genetic diversity and to infer historical and contemporary processes maintaining genetic variation. One hundred and fifty-one individuals were sampled from throughout North America and Eurasia, focusing on California and adjacent regions in the western United States where morphological diversity is highest compared to the rest of the range. Analyses of sequence data obtained from both genes revealed a well-supported division between the Old and New World. Within western North America, wingless shows little geographical structure, while a hierarchical analysis of genetic diversity of COII sequences indicates three major clades: a western clade in Oregon and Northern California, an eastern clade including the Great Basin, Rocky Mountains and British Columbia, and a third clade in southern California. The Sierra Nevada and the Transverse Ranges appear to be the major barriers to gene flow for H. comma in the western United States. Relatively reduced haplotype diversity in Eurasia compared to North America suggests that populations on the two continents have been affected by different historical processes.
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Affiliation(s)
- M L Forister
- Section of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA.
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37
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Shaffer HB, Pauly GB, Oliver JC, Trenham PC. The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense. Mol Ecol 2004; 13:3033-49. [PMID: 15367118 DOI: 10.1111/j.1365-294x.2004.02317.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range-wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well-supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74-0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander.
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Affiliation(s)
- H Bradley Shaffer
- Section of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616, USA.
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38
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Shaffer HB, Fellers GM, Voss SR, Oliver JC, Pauly GB. Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex. Mol Ecol 2004; 13:2667-77. [PMID: 15315679 DOI: 10.1111/j.1365-294x.2004.02285.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The red-legged frog, Rana aurora, has been recognized as both a single, polytypic species and as two distinct species since its original description 150 years ago. It is currently recognized as one species with two geographically contiguous subspecies, aurora and draytonii; the latter is protected under the US Endangered Species Act. We present the results of a survey of 50 populations of red-legged frogs from across their range plus four outgroup species for variation in a phylogenetically informative, approximately 400 base pairs (bp) fragment of the mitochondrial cytochrome b gene. Our mtDNA analysis points to several major results. (1) In accord with several other lines of independent evidence, aurora and draytonii are each diagnosably distinct, evolutionary lineages; the mtDNA data indicate that they do not constitute a monophyletic group, but rather that aurora and R. cascadae from the Pacific northwest are sister taxa; (2) the range of the draytonii mtDNA clade extends about 100 km further north in coastal California than was previously suspected, and corresponds closely with the range limits or phylogeographical breaks of several codistributed taxa; (3) a narrow zone of overlap exists in southern Mendocino County between aurora and draytonii haplotypes, rather than a broad intergradation zone; and (4) the critically endangered population of draytonii in Riverside County, CA forms a distinct clade with frogs from Baja California, Mexico. The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California.
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Affiliation(s)
- H Bradley Shaffer
- Section of Evolution and Ecology, and Center for Population Biology, University of California, Davis 95616, USA.
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39
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Pfrender ME, Hicks J, Lynch M. Biogeographic patterns and current distribution of molecular-genetic variation among populations of speckled dace, Rhinichthys osculus (Girard). Mol Phylogenet Evol 2004; 30:490-502. [PMID: 15012934 DOI: 10.1016/s1055-7903(03)00242-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2002] [Revised: 06/12/2003] [Indexed: 10/27/2022]
Abstract
We examined genetic diversity within- and among-populations of speckled dace (Rhinichthys osculus) in five major drainage systems in the state of Oregon in western North America. Analysis of sequence variation in a 670-bp segment of the mitochondrial cytochrome b gene revealed deep divergence among basins and high genetic diversity within basins. Application of a molecular clock indicated that the divergence time among basins reflects vicariant events during the late Miocene to early Pliocene. The high levels of genetic diversity observed within basins is likely due to large historic population sizes, in particular, within the Klamath Basin. Two highly divergent mtDNA lineages were found to co-occur in populations in the Klamath Basin. This result may be indicative of a complex history of isolation and reconnection in this basin and/or multiple colonization events. Based on the observed level of mtDNA divergence these lineages may represent two reproductively isolated sympatric taxa. We recommend that major basins be regarded as distinct ESUs based on high levels of subdivision, deep divergences, and reciprocal monophyly among basins.
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Affiliation(s)
- Michael E Pfrender
- Department of Biology, Utah State University, 5305 Old Main Hill Road, Logan, UT 84322-5305, USA.
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40
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Greene HW, RodrÍguez-Robles JA. Feeding Ecology of the California Mountain Kingsnake, Lampropeltis zonata (Colubridae). COPEIA 2003. [DOI: 10.1643/0045-8511(2003)003[0308:feotcm]2.0.co;2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Sgariglia EA, Burns KJ. Phylogeography of the California Thrasher (Toxostoma Redivivum) Based on Nested-Clade Analysis of Mitochondrial-DNA Variation. ACTA ACUST UNITED AC 2003. [DOI: 10.1093/auk/120.2.346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractDistribution of genealogical lineages within a species is likely the result of a complicated series of ecological and historical events. Nested-clade analysis is specifically designed as an objective phylogeographic approach for inferring evolutionary processes on a spatial and temporal scale for small subclades within a larger set of intraspecific relationships. Here, we use nested-clade analysis as well as other phylogeographic methods to investigate the evolutionary history of California Thrasher (Toxostoma redivivum) populations. Inferences resulting from nested clade analysis suggest a history that includes past fragmentation, range expansion, and isolation-by-distance. Along with root information, those inferences enable the construction of a biogeographic scenario for this species involving general southern ancestry, an early north–south division, northward range expansion, and a southward back-expansion into an already populated southern region. Isolation-by-distance is also identified, particularly in southern California, indicating that gene flow between localities does occur but is restricted. Many conclusions drawn from this study are concordant with geologic data as well as phylogeographic scenarios drawn for other codistributed California taxa.
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Affiliation(s)
- Erik A. Sgariglia
- Department of Biology, San Diego State University, San Diego, California 92182-4614
| | - Kevin J. Burns
- Department of Biology, San Diego State University, San Diego, California 92182-4614
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43
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Janzen FJ, Krenz JG, Haselkorn TS, Brodie ED, Brodie ED. Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces. Mol Ecol 2002; 11:1739-51. [PMID: 12207724 DOI: 10.1046/j.1365-294x.2002.01571.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well-supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences.
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Affiliation(s)
- Fredric J Janzen
- Department of Zoology and Genetics, Program in Ecology and Evolutionary Biology, Iowa State University, Ames, IA 50011-3223, USA.
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Abstract
Phylogenetic studies of asexual lineages and their sexual progenitors are useful for inferring the causes of geographical parthenogenesis and testing hypotheses regarding the evolution of sex. With five known parthenogens and well-studied ecology, Timema walking-sticks are a useful system for studying these questions. Timema are mainly endemic to California and they exhibit the common pattern of geographical parthenogenesis, with asexuals exhibiting more-northerly distributions. Neighbour-joining and maximum-parsimony analyses of 416 bp of mitochondrial cytochrome oxidase I (COI) from 168 individuals were used to infer general phylogenetic relationships, resulting in three major phylogeographical subdivisions: a Northern clade; a Santa Barbara clade; and a Southern clade. A nested cladistic analysis, comparing intra- and interspecific haplotypic variation on a geographical scale, revealed that the overall pattern of geographical parthenogenesis in Timema could be attributed to historical range expansion. These results suggest that geographical parthenogenesis is the result of more-extensive northerly dispersal of asexuals than sexuals.
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Affiliation(s)
- Jennifer H Law
- Department of Biosciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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JOCKUSCH ELIZABETHL, WAKE DAVIDB. Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West. Biol J Linn Soc Lond 2002. [DOI: 10.1046/j.1095-8312.2002.00071.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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46
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Abstract
The dusky-footed woodrat, Neotoma fuscipes, is a medium-sized rodent that inhabits low elevation woodland habitats along the Pacific coast of North America from Oregon, throughout California and into Baja California. Analyses of mitochondrial sequence variation throughout the distribution reveal substantial phylogeographical structure within N. fuscipes. The major mitochondrial lineages are largely concordant with previously identified morphological subdivisions within the taxon. The geographical distribution of distinct clades suggests that a combination of topographic barriers and the expansion and contraction of suitable habitat during the past 2 million years, especially along particular mountain ranges, have played a major role in the diversification of N. fuscipes. Furthermore, relatively low levels of genetic variation across the northern half of the distribution suggest that dusky-footed woodrats may have only recently expanded into this region.
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Affiliation(s)
- Marjorie D Matocq
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, California 94720-3160, USA.
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Ashton KG, de Queiroz A. Molecular systematics of the western rattlesnake, Crotalus viridis (Viperidae), with comments on the utility of the D-loop in phylogenetic studies of snakes. Mol Phylogenet Evol 2001; 21:176-89. [PMID: 11697914 DOI: 10.1006/mpev.2001.1013] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Crotalus viridis, the western rattlesnake, ranges throughout western North America and has been divided into at least eight subspecies. However, the validity of and relationships among these subspecies and the monophyly of C. viridis as a whole are questionable. We used mitochondrial DNA sequence data from the D-loop region and ND2 gene to examine the relationships among 26 populations of C. viridis and to test the monophyly of this species. These data were analyzed separately and combined using maximum-likelihood and maximum-parsimony. The C. viridis group was monophyletic in all combined analyses, consisting of two strongly divergent clades. We recommend that these clades be recognized as two distinct evolutionary species: C. viridis and C. oreganus. Crotalus viridis should be restricted to the subspecies viridis and nuntius and the remaining subspecies be assigned to the species C. oreganus. Our data do not allow strong evaluation of the validity of the subspecies. We found that the ND2 gene had greater sequence divergences among closely related individuals than the D-loop region, but this relationship reversed at higher levels of divergence. This pattern is apparently due to: (1) ND2 third positions evolving faster than the D-loop but becoming saturated at higher levels of divergence, and (2) the D-loop evolving faster than ND2 second (and possibly first) positions. Our results suggest that the ND2 gene is preferable for examining intraspecific relationships and the D-loop may better resolve relationships between species of snakes. The latter result is contrary to the common perception of the phylogenetic utility of the D-loop. Another unusual result is that the 145 bp spacer region, adjacent to the 5' end of the light strand of the D-loop, provides greater phylogenetic resolution than the 1030 bp D-loop.
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Affiliation(s)
- K G Ashton
- Department of Environmental, Population, and Organismic Biology, University of Colorado, Boulder, Colorado 80309, USA.
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Macey JR, Strasburg JL, Brisson JA, Vredenburg VT, Jennings M, Larson A. Molecular phylogenetics of western North American frogs of the Rana boylii species group. Mol Phylogenet Evol 2001; 19:131-43. [PMID: 11286498 DOI: 10.1006/mpev.2000.0908] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phylogenetic relationships among frogs of the genus Rana from western North America are investigated using 2013 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase), plus the origin for light-strand replication (O(L)) between the tRNA(Asn) and tRNA(Cys) genes. The aligned sequences contain 401 phylogenetically informative characters. A well-resolved phylogenetic hypothesis in which the Rana boylii species group (R. aurora, R. boylii, R. cascadae, R. muscosa, and R. pretiosa) is monophyletic is obtained. Molecular sequence divergence suggests that the R. boylii species group is approximately 8 million years old. The traditional hypothesis showing monophyly of the yellow-legged frogs (R. boylii and R. muscosa) is statistically rejected in favor of a hypothesis in which R. aurora, R. cascadae, and R. muscosa form a clade. Reanalyses of published nuclear ribosomal DNA restriction-site data and allozymic data support a monophyletic R. boylii group, but do not effectively resolve relationships among species within this group. Eight populations of R. muscosa form two major clades separated by a biogeographic break in the Sierra Nevada of California. This biogeographic break is broadly concordant with breaks found in four other amphibian and reptilian taxa. The two major clades within R. muscosa are estimated to have diverged approximately 2.2 million years before present. Each of these major clades contains two subgroups showing approximately 1.5 million years divergence, implicating climatic effects of Pleistocene glaciation in vicariance. The four distinct subgroups of R. muscosa separated by at least 1.4 million years of evolutionary divergence are suggested as potential units for conservation.
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Affiliation(s)
- J R Macey
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
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Rodríguez-Robles JA, Stewart GR, Papenfuss TJ. Mitochondrial DNA-Based phylogeography of North American rubber boas, Charina bottae (Serpentes: Boidae). Mol Phylogenet Evol 2001; 18:227-37. [PMID: 11161758 DOI: 10.1006/mpev.2000.0886] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We used 783 bp of mitochondrial DNA sequences to study the phylogeography of Charina bottae (rubber boa) in western North America, with an emphasis on populations from California (U.S.A.). Maximum-parsimony and maximum-likelihood methods identified a basal divergence within C. bottae that corresponds to southern and northern segments of its current distribution. These clades coincide with the ranges of the two recognized subspecies, C. b. umbratica in the south and C. b. bottae to the north. A subsequent cladogenetic event in the C. b. bottae clade resulted in two groupings, which we refer to as the Sierra Nevada and the Northwestern subclades, based on the geographic distribution of their constituent populations. The two subclades have completely allopatric distributions, with a genetic break in the vicinity of Lassen Volcanic National Park in northeastern California, an area that was subjected to glaciation during the Pleistocene and that has been volcanically active in the past 100 years. An earlier genetic study documented fixed differences between populations of bottae and umbratica in four of seven allozymes surveyed, and despite noticeable variation and overlap in the characters that define C. b. bottae and C. b. umbratica, the two forms still can be separated in most cases using a suite of morphological traits. All available evidence thus indicates that C. b. umbratica is a genetically cohesive, allopatric taxon that is morphologically diagnosable, and we conclude that it is an independent evolutionary unit that should be recognized as a distinct species, Charina umbratica.
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Affiliation(s)
- J A Rodríguez-Robles
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720-3160, USA.
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50
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Abstract
We examined cytochrome b sequence variation in 251 ornate shrews (Sorex ornatus) from 20 localities distributed throughout their geographical range. Additionally, vagrant (S. vagrans) and montane (S. monticolus) shrews from four localities were used as outgroups. We found 24 haplotypes in ornate shrews from California (USA) and Baja California (Mexico) that differed by 1-31 substitutions in 392 bp of mitochondrial DNA (mtDNA) sequence. In a subset of individuals, we sequenced 699 bp of cytochrome b to better resolve the phylogeographic relationships of populations. The ornate shrew is phylogeographically structured into three haplotype clades representing southern, central and northern localities. Analysis of allozyme variation reveals a similar pattern of variation. Several other small California vertebrates have a similar tripartite pattern of genetic subdivision. We suggest that topographic barriers and expansion and contraction of wetland habitats in the central valley during Pleistocene glacial cycles account for these patterns of genetic variation. Remarkably, the northern ornate shrew clade is phylogenetically clustered with another species of shrew suggesting that it may be a unique lowland form of the vagrant shrew that evolved in parallel to their southern California counterparts.
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Affiliation(s)
- J E Maldonado
- Department of Organismic Biology, Ecology and Evolution, University of California, Los Angeles 90095-1606, USA.
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