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Leaché AD, Davis HR, Feldman CR, Fujita MK, Singhal S. Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea). J Hered 2024; 115:57-71. [PMID: 37982433 PMCID: PMC10838131 DOI: 10.1093/jhered/esad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.
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Affiliation(s)
- Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, United States
| | - Hayden R Davis
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, United States
| | - Chris R Feldman
- Department of Biology and Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV, United States
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, United States
| | - Sonal Singhal
- Department of Biology, California State University - Dominguez Hills, Carson, CA, United States
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Zink RM, Klicka LB. The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.971280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.
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Multi-locus phylogeny and species delimitations of the striped-back shrew group (Eulipotyphla: Soricidae): Implications for cryptic diversity, taxonomy and multiple speciation patterns. Mol Phylogenet Evol 2022; 177:107619. [PMID: 36007821 DOI: 10.1016/j.ympev.2022.107619] [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: 11/26/2021] [Revised: 08/01/2022] [Accepted: 08/17/2022] [Indexed: 11/23/2022]
Abstract
The striped-back shrew group demonstrates remarkable variation in skull and body size, tail length, and brightness of the dorsal stripe; and karyotypic and DNA variation has been reported in recent years. In this study, we investigated the phylogenetic structure of the group, as well as speciation patterns and demographic history in Mountains of Southwestern China and adjacent mountains, including the southern Himalayas, Mts. Bashan, Wushan, and Qinling. We sequenced a total of 462 specimens from 126 localities in the known range of the group, which were sequenced and analyzed based on 6.2 kb of sequence data from two mitochondrial, six nuclear, and two Y chromosome markers. Phylogenetic analyses of the concatenated mtDNA data revealed 14 sympatric and independently evolving lineages within the striped-back shrew group, including Sorex bedfordiae, S. cylindricauda, S. excelsus, S. sinalis and several cryptic species. All concatenated data (ten genes) showed a consistent genetic structure compared to the mtDNA lineages for the group, whereas the nuclear and the Y chromosome data showed a discordant genetic structure compared to the mtDNA lineages for the striped-back shrew group. Species delimitation analyses and deep genetic distance clearly support the species status of the 14 evolving lineages. The divergence time estimation suggested that the striped-back shrew group began to diversify from the middle Pleistocene (2.34 Ma), then flourished at approximately 2.14 Ma, followed by a series of rapid diversifications through the Pleistocene. Our results also revealed multiple mechanisms of speciation in the Mountains of Southwestern China and Adjacent Mountains with complex landscapes and climate. The uplifting of the Qinghai-Tibetan Plateau, Quaternary climate oscillations, riverine barriers, ecological elevation gradients, topographical diversity, and their own low dispersal capacity may have driven the speciation, genetic structure, and phylogeographic patterns of the striped-back shrew group.
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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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Valladares-Gómez A, Celis-Diez JL, Sepúlveda-Rodríguez C, Inostroza-Michael O, Hernández CE, Palma RE. Genetic Diversity, Population Structure, and Migration Scenarios of the Marsupial "Monito del Monte" in South-Central Chile. J Hered 2020; 110:651-661. [PMID: 31420661 DOI: 10.1093/jhered/esz049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 01/11/2023] Open
Abstract
In this study, we quantified the 3 pivotal genetic processes (i.e., genetic diversity, spatial genetic structuring, and migration) necessary for a better biological understanding and management of the singular "living-fossil" and near-threatened mouse opossum marsupial Dromiciops gliroides, the "Monito del Monte," in south-central Chile. We used 11 microsatellite loci to genotype 47 individuals distributed on the mainland and northern Chiloé Island. Allelic richness, observed and expected heterozygosity, inbreeding coefficient, and levels of genetic differentiation were estimated. The genetic structure was assessed based on Bayesian clustering methods. In addition, potential migration scenarios were evaluated based on a coalescent theory framework and Bayesian approach to parameter estimations. Microsatellites revealed moderate to high levels of genetic diversity across sampled localities. Moreover, such molecular markers suggested that at least 2 consistent genetic clusters could be identified along the D. gliroides distribution ("Northern" and "Southern" cluster). However, general levels of genetic differentiation observed among localities and between the 2 genetic clusters were relatively low. Migration analyses showed that the most likely routes of migration of D. gliroides occurred 1) from the Southern cluster to the Northern cluster and 2) from the Mainland to Chiloé Island. Our results could represent critical information for future conservation programs and for a recent proposal about the taxonomic status of this unique mouse opossum marsupial.
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Affiliation(s)
- Alejandro Valladares-Gómez
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Juan L Celis-Diez
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Casilla 4-D, Quillota, Chile
| | - Constanza Sepúlveda-Rodríguez
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Oscar Inostroza-Michael
- Laboratorio de Ecología Evolutiva y Filoinformática, Facultad de Ciencias Naturales y Ocenográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Cristián E Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática, Facultad de Ciencias Naturales y Ocenográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - R Eduardo Palma
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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Chen S, Qing J, Liu Z, Liu Y, Tang M, Murphy RW, Pu Y, Wang X, Tang K, Guo K, Jiang X, Liu S. Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China. BMC Evol Biol 2020; 20:29. [PMID: 32059644 PMCID: PMC7023792 DOI: 10.1186/s12862-020-1588-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/27/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.
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Affiliation(s)
- Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jiao Qing
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157011, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Mingkun Tang
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Robert W Murphy
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, M5S 2C6, Canada
| | - Yingting Pu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Xuming Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Keji Guo
- Central South Forest Inventory and Planning Institute of State Forestry Administration, Changsha, 410014, China
| | - Xuelong Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China.
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Camargo I, Álvarez-Castañeda ST. Rediscovery of the extinct Tule shrew (Sorex ornatus juncencis) in the San Quintin plains: a taxonomic reevaluation after 90 years without new records. MAMMALIA 2019. [DOI: 10.1515/mammalia-2017-0133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In this study, we investigate the geographic distribution of the Tule shrew (Sorex ornatus juncensis), an endemic subspecies of the San Quintin plains associated with coastal vegetation. Records on this shrew are scarce; herein, we provide knowledge about its current conservation status and report the presence of one Tule shrew specimen, something that has not happened since 1926. The distribution of the Tule shrew is associated with coastal vegetation, limited to the San Quintin plains, with scarce records. Field trips were conducted during 2013–2015 in the San Quintin plains and San Pedro Martir range of the Baja California Peninsula. The sampling effort was 3250 trap nights. One specimen of S. o. juncensis was recorded in association with coastal sage-scrub vegetation and identified following the original description, based on its narrower skull relative to Sorex ornatus ornatus. We used a mitochondrial cytochrome b gene sequence (384 bp) to confirm this identification and compare genetic distances using the Kimura’s two-parameter nucleotide substitution model vs. other populations of the ornatus group. We found a genetic divergence of less than 1.0% based on sequences from specimens collected from Sierra San Pedro Martir, El Rosario and Sierra La Laguna. In the locality of the S. o. juncensis specimen collected, the original vegetation consists of patches of coastal scrubs, which cover an area of less than 1 km2, affected by agriculture and habitat fragmentation. We reallocated the taxonomic level of the Tule shrew inhabiting the plains of San Quintin in the Baja California Peninsula to subspecies as S. o. juncensis based on geographic isolation, morphometric characteristics and coloration differences vs. S. o. ornatus. The population inhabiting San Quintin plains is subjected to strong pressure due to habitat loss.
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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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10
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Valladares-Gómez A, Celis-Diez JL, Palma RE, Manríquez GS. Cranial morphological variation of Dromiciops gliroides (Microbiotheria) along its geographical distribution in south-central Chile: A three-dimensional analysis. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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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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Jacquet F, Denys C, Verheyen E, Bryja J, Hutterer R, Kerbis Peterhans JC, Stanley WT, Goodman SM, Couloux A, Colyn M, Nicolas V. Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa. BMC Evol Biol 2015; 15:71. [PMID: 25900417 PMCID: PMC4422046 DOI: 10.1186/s12862-015-0344-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/30/2015] [Indexed: 12/18/2022] Open
Abstract
Background This study aims to reconstruct the evolutionary history of African shrews referred to the Crocidura olivieri complex. We tested the respective role of forest retraction/expansion during the Pleistocene, rivers (allopatric models), ecological gradients (parapatric model) and anthropogenic factors in explaining the distribution and diversification within this species complex. We sequenced three mitochondrial and four nuclear markers from 565 specimens encompassing the known distribution of the complex, i.e. from Morocco to Egypt and south to Mozambique. We used Bayesian phylogenetic inference, genetic structure analyses and divergence time estimates to assess the phylogenetic relationships and evolutionary history of these animals. Results The C. olivieri complex (currently composed of C. olivieri, C. fulvastra, C. viaria and C. goliath) can be segregated into eight principal geographical clades, most exhibiting parapatric distributions. A decrease in genetic diversity was observed between central and western African clades and a marked signal of population expansion was detected for a broadly distributed clade occurring across central and eastern Africa and portions of Egypt (clade IV). The main cladogenesis events occurred within the complex between 1.37 and 0.48 Ma. Crocidura olivieri sensu stricto appears polyphyletic and C. viaria and C. fulvastra were not found to be monophyletic. Conclusions Climatic oscillations over the Pleistocene probably played a major role in shaping the genetic diversity within this species complex. Different factors can explain their diversification, including Pleistocene forest refuges, riverine barriers and differentiation along environmental gradients. The earliest postulated members of the complex originated in central/eastern Africa and the first radiations took place in rain forests of the Congo Basin. A dramatic shift in the ecological requirements in early members of the complex, in association with changing environments, took place sometime after 1.13 Ma. Some lineages then colonized a substantial portion of the African continent, including a variety of savannah and forest habitats. The low genetic divergence of certain populations, some in isolated localities, can be explained by their synanthropic habits. This study underlines the need to revise the taxonomy of the C. olivieri complex. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0344-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- François Jacquet
- Institut de Systématique, Évolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 51, 75005, Paris, France.
| | - Christiane Denys
- Institut de Systématique, Évolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 51, 75005, Paris, France.
| | - Erik Verheyen
- Royal Belgian Institute of Natural Sciences, Operational Direction Taxonomy and Phylogeny, Molecular Laboratory, Vautierstraat 29, 1000, Brussels, Belgium. .,Biology Department, University of Antwerpen, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020, Antwerpen, Belgium.
| | - Josef Bryja
- Institute of Vertebrate Biology ASCR, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic. .,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Rainer Hutterer
- Zoologisches Forschungmuseum Alexander Koenig, Adenauerallee 160, D-53113, Bonn, Germany.
| | - Julian C Kerbis Peterhans
- College of Professional Studies, Roosevelt University, 430 S Michigan Avenue, Chicago, IL, 60605, USA. .,Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - William T Stanley
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - Steven M Goodman
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA. .,Association Vahatra, BP 3972, Antananarivo, 101, Madagascar.
| | - Arnaud Couloux
- Génoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057, Evry Cedex, France.
| | - Marc Colyn
- Université de Rennes 1, CNRS, UMR 6553 Ecobio, Station Biologique, 35380, Paimpont, France.
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 51, 75005, Paris, France.
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13
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Ceríaco LM, Marques MP, Jacquet F, Nicolas V, Colyn M, Denys C, Sardinha PC, Bastos-Silveira C. Description of a new endemic species of shrew (Mammalia, Soricomorpha) from PrÍncipe Island (Gulf of Guinea). MAMMALIA 2015. [DOI: 10.1515/mammalia-2014-0056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
AbstractSão Tomé and Príncipe are unique islands off the Gulf of Guinea on account of the high degree of endemism in these areas due to isolation. These islands are known to harbor, among others, two species of shrews of the genus
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14
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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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Baumsteiger J, Kinziger AP, Reid SB, Aguilar A. Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus). Mol Ecol 2014; 23:2602-18. [PMID: 24750456 DOI: 10.1111/mec.12758] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/11/2014] [Accepted: 04/13/2014] [Indexed: 11/29/2022]
Abstract
Species ranges that span different geographic landscapes frequently contain cryptic species- or population-level structure. Identifying these possible diversification factors can often be accomplished under a comparative phylogeographic framework. However, comparisons suffer if previous studies are limited to a particular group or habitat type. In California, a complex landscape has led to several phylogeographic breaks, primarily in terrestrial species. However, two sister taxa of freshwater fish, riffle sculpin (Cottus gulosus) and Pit sculpin (Cottus pitensis), display ranges based on morphological identifications that do not coincide with these breaks. Using a comprehensive sampling and nuclear, mitochondrial and microsatellite markers, we hypothesized that proposed species ranges are erroneous based on potential hybridization/gene flow between species. Results identified a phylogeographic signature consistent with this hypothesis, with breaks at the Coast Range Mountains and Sacramento/San Joaquin River confluence. Coastal locations of C. gulosus represent a unique lineage, and 'true' C. gulosus were limited to the San Joaquin basin, both regions under strong anthropogenic influence and potential conservation targets. C. pitensis limits extended historically throughout the Sacramento/Pit River basin but currently are restricted to the Pit River. Interestingly, locations in the Sacramento River contained low levels of ancestral hybridization and gene flow from C. gulosus but now appear to be a distinct population. The remaining population structure was strongly correlated with Sierra Nevada presence (high) or absence (low). This study stresses the importance of testing phylogeographic breaks across multiple taxa/habitats before conservation decisions are made, but also the potential impact of different geographic landscapes on evolutionary diversification.
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Affiliation(s)
- Jason Baumsteiger
- School of Natural Sciences & Sierra Nevada Research Institute, University of California Merced, 5200 N. Lake Rd., Merced, CA, 95343, USA
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16
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Cryptic population structuring and the role of the Isthmus of Tehuantepec as a gene flow barrier in the critically endangered Central American River Turtle. PLoS One 2013; 8:e71668. [PMID: 24086253 PMCID: PMC3783458 DOI: 10.1371/journal.pone.0071668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 07/05/2013] [Indexed: 11/25/2022] Open
Abstract
The critically endangered Central American River Turtle (Dermatemys mawii) is the only remaining member of the Dermatemydidae family, yet little is known about its population structuring. In a previous study of mitochondrial (mt) DNA in the species, three main lineages were described. One lineage (Central) was dominant across most of the range, while two other lineages were restricted to Papaloapan (PAP; isolated by the Isthmus of Tehuantepec and the Sierra de Santa Marta) or the south-eastern part of the range (1D). Here we provide data from seven polymorphic microsatellite loci and the R35 intron to re-evaluate these findings using DNA from the nuclear genome. Based on a slightly expanded data set of a total of 253 samples from the same localities, we find that mtDNA and nuclear DNA markers yield a highly congruent picture of the evolutionary history and population structuring of D. mawii. While resolution provided by the R35 intron (sequenced for a subset of the samples) was very limited, the microsatellite data revealed pronounced population structuring. Within the Grijalva-Usumacinta drainage basin, however, many populations separated by more than 300 kilometers showed signals of high gene flow. Across the entire range, neither mitochondrial nor nuclear DNA show a significant isolation-by-distance pattern, but both genomes highlight that the D. mawii population in the Papaloapan basin is genetically distinctive. Further, both marker systems detect unique genomic signals in four individuals with mtDNA clade 1D sampled on the southeast edge of the Grijalva-Usumacinta basin. These individuals may represent a separate cryptic taxon that is likely impacted by recent admixture.
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17
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Jacquet F, Nicolas V, Colyn M, Kadjo B, Hutterer R, Decher J, Akpatou B, Cruaud C, Denys C. Forest refugia and riverine barriers promote diversification in the West African pygmy shrew (Crocidura obscuriorcomplex, Soricomorpha). ZOOL SCR 2013. [DOI: 10.1111/zsc.12039] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- François Jacquet
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
| | - Violaine Nicolas
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
| | - Marc Colyn
- Université de Rennes 1, CNRS, Ecobio UMR 6553, Station Biologique; 35380 Paimpont France
| | - Blaise Kadjo
- Université de Cocody-Abidjan-UFR Biosciences, Systématique, Biologie et Ecologie des Mammifères; 22 BP 582 Abidjan 22 Côte d'Ivoire
| | - Rainer Hutterer
- Zoologisches Forschungsmuseum A. Koenig, Section of Mammals; Adenauerallee 160 D-53113 Bonn Germany
| | - Jan Decher
- Zoologisches Forschungsmuseum A. Koenig, Section of Mammals; Adenauerallee 160 D-53113 Bonn Germany
| | - Bertin Akpatou
- Université de Cocody-Abidjan-UFR Biosciences, Systématique, Biologie et Ecologie des Mammifères; 22 BP 582 Abidjan 22 Côte d'Ivoire
| | - Corinne Cruaud
- Génoscope, Centre National de Séquençage; 2 rue Gaston Crémieux CP5706 91057 Evry Cedex France
| | - Christiane Denys
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
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18
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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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19
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Matocq MD, Kelly PA, Phillips SE, Maldonado JE. Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California. Mol Ecol 2012; 21:5918-33. [PMID: 23106496 DOI: 10.1111/mec.12079] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 07/13/2012] [Accepted: 07/20/2012] [Indexed: 11/26/2022]
Abstract
Identifying historic patterns of population genetic diversity and connectivity is a primary challenge in efforts to re-establish the processes that have generated and maintained genetic variation across natural landscapes. The challenge of reconstructing pattern and process is even greater in highly altered landscapes where population extinctions and dramatic demographic fluctuations in remnant populations may have substantially altered, if not eliminated, historic patterns. Here, we seek to reconstruct historic patterns of diversity and connectivity in an endangered subspecies of woodrat that now occupies only 1-2 remnant locations within the highly altered landscape of the Great Central Valley of California. We examine patterns of diversity and connectivity using 14 microsatellite loci and sequence data from a mitochondrial locus and a nuclear intron. We reconstruct temporal change in habitat availability to establish several historical scenarios that could have led to contemporary patterns of diversity, and use an approximate Bayesian computation approach to test which of these scenarios is most consistent with our observed data. We find that the Central Valley populations harbour unique genetic variation coupled with a history of admixture between two well-differentiated species of woodrats that are currently restricted to the woodlands flanking the Valley. Our simulations also show that certain commonly used analytical approaches may fail to recover a history of admixture when populations experience severe bottlenecks subsequent to hybridization. Overall our study shows the strength of combining empirical and simulation analyses to recover the history of populations occupying highly altered landscapes.
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Affiliation(s)
- Marjorie D Matocq
- Department of Natural Resources and Environmental Science, Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Reno, NV 89557, USA
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20
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Woodman N. Taxonomic status and relationships of Sorex obscurus parvidens, from California. J Mammal 2012. [DOI: 10.1644/11-mamm-a-354.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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21
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Patterns of genetic diversity in the critically endangered Central American river turtle: human influence since the Mayan age? CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0225-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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He K, Li YJ, Brandley MC, Lin LK, Wang YX, Zhang YP, Jiang XL. A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution. Mol Phylogenet Evol 2010; 56:734-46. [PMID: 20363345 DOI: 10.1016/j.ympev.2010.03.039] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 03/24/2010] [Accepted: 03/30/2010] [Indexed: 11/16/2022]
Abstract
Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale+Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution.
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Affiliation(s)
- Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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23
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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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24
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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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25
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Aguilar A, Jones WJ. Nuclear and mitochondrial diversification in two native California minnows: insights into taxonomic identity and regional phylogeography. Mol Phylogenet Evol 2009; 51:373-81. [PMID: 19405200 DOI: 10.1016/j.ympev.2008.11.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Diversification of the California icthyofauna has been greatly influenced by a complex geomorphological history and past fluctuations in climate regimes. This complex history has resulted in areas of high endemism for a number of taxa. Here we present data on the two species in the genus Lavinia, the California roach (Lavinia symmetricus) and hitch (Lavinia exilicauda), that are widespread throughout the region. Individuals were sequenced at two mitochondrial DNA fragments and genotyped at eight microsatellite loci. Mitochondrial DNA indicated the presence to two highly divergent clades representing roach from the Gualala and Pit Rivers, which diverged from all other Lavinia approximately 3-6 MYA. Support was also foundfor roach from the Navarro River, Tomales Bay region, the Red Hills region, and the Russian River-Clear Lake basin. We found no evidence for any geographical groupings of mtDNA haplotypes for roach and hitch from the Monterey Bay region and the Sacramento-San Joaquin River drainages. Additionally roach and hitch from these two areas could not be readily distinguished by mtDNA data. Analysis of microsatellite DNA recovered all groupings found in the mtDNA analysis and was able to separate out roach, hitch, and all currently recognized subspecies of each species. These results indicate that hybridization may obscure the phylogenetic/phylogeographic informativeness of mtDNA in this group. Additionally, these results suggest that differentiation in this group occurs at the river basin level and that the described genetic entities constitute distinct units and should be conserved as such.
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Affiliation(s)
- Andres Aguilar
- School of Natural Sciences & Sierra Nevada Research Institute, University of California, Merced, CA 95344, USA.
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26
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PEASE KATHERINEM, FREEDMAN ADAMH, POLLINGER JOHNP, MCCORMACK JOHNE, BUERMANN WOLFGANG, RODZEN JEFF, BANKS JIM, MEREDITH ERIN, BLEICH VERNONC, SCHAEFER ROBERTJ, JONES KEN, WAYNE ROBERTK. Landscape genetics of California mule deer (Odocoileus hemionus): the roles of ecological and historical factors in generating differentiation. Mol Ecol 2009; 18:1848-62. [DOI: 10.1111/j.1365-294x.2009.04112.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Sacks BN, Bannasch DL, Chomel BB, Ernest HB. Coyotes demonstrate how habitat specialization by individuals of a generalist species can diversify populations in a heterogeneous ecoregion. Mol Biol Evol 2008; 25:1384-94. [PMID: 18391065 DOI: 10.1093/molbev/msn082] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The tendency for individuals to disperse into habitat similar to their natal habitat has been observed in a wide range of species, although its population genetic consequences have received little study. Such behavior could lead to discrete habitat-specific population subdivisions even in the absence of physical dispersal barriers or habitat gaps. Previous studies of coyotes have supported this hypothesis in a small region of California, but its evolutionary significance ultimately depends on the extent and magnitude of habitat-specific subdivision. Here, we investigated these questions using autosomal, Y chromosome, and mitochondrial markers and >2,000 coyotes from a broad region, including 2 adjacent ecoregions with contrasting levels of habitat heterogeneity--the California Floristic Province (CFP) (heterogeneous landscape) and the Desert-Prairie ecoregion (DPE) (homogeneous landscape). Consistent with predictions, we found a close correspondence between population genetic structure and habitat subdivisions throughout the CFP and virtual panmixia over the larger DPE. Conversely, although genetic diversity was similar in these 2 ecoregions overall, it was lower within sites of the CFP, as would be the expected consequence of greater genetic drift within subregions. The magnitude of habitat-specific genetic subdivisions (i.e., genetic distance) in the CFP varied considerably, indicating complexity (e.g., asymmetric gene flow or extinction/recolonization), but, in general, was higher than that due to geographic distance or recent human-related barriers. Because habitat-specific structure can enhance a species' adaptive potential and resilience to changing environments, these findings suggest the CFP may constitute an evolutionarily important portion of the range for coyotes and sympatric species exhibiting habitat-specific population structure.
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Affiliation(s)
- Benjamin N Sacks
- Veterinary Genetics Laboratory, University of California, Davis, CA, USA.
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28
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Álvarez-Castañeda ST. Systematics of the Antelope Ground Squirrel (Ammospermophilus) from Islands Adjacent to the Baja California Peninsula. J Mammal 2007. [DOI: 10.1644/06-mamm-a-065r3.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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29
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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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30
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Dubey S, Salamin N, Ohdachi SD, Barrière P, Vogel P. Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations. Mol Phylogenet Evol 2007; 44:126-37. [DOI: 10.1016/j.ympev.2006.12.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 11/08/2006] [Accepted: 12/07/2006] [Indexed: 10/23/2022]
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31
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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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32
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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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33
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Yuan SL, Lin LK, Oshida T. Phylogeography of the mole-shrew (Anourosorex yamashinai) in Taiwan: implications of interglacial refugia in a high-elevation small mammal. Mol Ecol 2006; 15:2119-30. [PMID: 16780429 DOI: 10.1111/j.1365-294x.2006.02875.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To test the Pleistocene interglacial refugia hypothesis with a high-elevation mammal, we studied the phylogeography of the mole-shrew (Anourosorex yamashinai) using partial mitochondrial cytochrome b gene sequences (737 bases). This shrew is endemic to Taiwan. It is mainly distributed in the highlands from 1000 to 2500 m in elevation. We examined 103 specimens from 24 localities in three mountain ranges of Taiwan and found 36 haplotypes. These haplotypes separated into two major phylogroups (Northern and Southern) plus a minor phylogroup (Houhuan) of only one haplotype. This demonstrated strong association with geography. The formation of these three phylogroups may be the result of interglacial refugia during the middle Pleistocene. Distinct sublineages were not found within each major phylogroup, suggesting that the populations (phylogroups) explosively expanded from the interglacial refugia of ancestral founder haplotypes. The present distribution pattern of haplotypes suggests that Mount Houhuan is an effective refugium in central Taiwan. It was not possible to specify the refugia for the Northern and Southern phylogroups.
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Affiliation(s)
- Shou-Li Yuan
- Laboratory of Wildlife Ecology, Department of Life Science, Tunghai University, Taichung, Taiwan 407, ROC
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34
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Oshida T, Lee JK, Lin LK, Chen YJ. PHYLOGEOGRAPHY OF PALLAS'S SQUIRREL IN TAIWAN: GEOGRAPHICAL ISOLATION IN AN ARBOREAL SMALL MAMMAL. J Mammal 2006. [DOI: 10.1644/05-mamm-a-123r1.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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35
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Paquin MM, Wylie GD, Routman EJ. Population Structure of the Giant Garter Snake, Thamnophis gigas. CONSERV GENET 2006. [DOI: 10.1007/s10592-005-7439-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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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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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: 107] [Impact Index Per Article: 5.6] [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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Hewitt GM. The structure of biodiversity - insights from molecular phylogeography. Front Zool 2004; 1:4. [PMID: 15679920 PMCID: PMC544936 DOI: 10.1186/1742-9994-1-4] [Citation(s) in RCA: 228] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2004] [Accepted: 10/26/2004] [Indexed: 11/23/2022] Open
Abstract
DNA techniques, analytical methods and palaeoclimatic studies are greatly advancing our knowledge of the global distribution of genetic diversity, and how it evolved. Such phylogeographic studies are reviewed from Arctic, Temperate and Tropical regions, seeking commonalities of cause in the resulting genetic patterns. The genetic diversity is differently patterned within and among regions and biomes, and is related to their histories of climatic changes. This has major implications for conservation science.
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Maldonado JE, Hertel F, Vilà C. DISCORDANT PATTERNS OF MORPHOLOGICAL VARIATION IN GENETICALLY DIVERGENT POPULATIONS OF ORNATE SHREWS (SOREX ORNATUS). J Mammal 2004. [DOI: 10.1644/1545-1542(2004)085<0886:dpomvi>2.0.co;2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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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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Hewitt GM. Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc Lond B Biol Sci 2004; 359:183-95; discussion 195. [PMID: 15101575 PMCID: PMC1693318 DOI: 10.1098/rstb.2003.1388] [Citation(s) in RCA: 1827] [Impact Index Per Article: 91.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An appreciation of the scale and frequency of climatic oscillations in the past few million years is modifying our views on how evolution proceeds. Such major events caused extinction and repeated changes in the ranges of those taxa that survived. Their spatial effects depend on latitude and topography, with extensive extinction and recolonization in higher latitudes and altitudinal shifts and complex refugia nearer the tropics. The associated population dynamics varied with life history and geography, and the present genetic constitution of the populations and species carry attenuated signals of these past dynamics. Phylogeographic studies with DNA have burgeoned recently and studies are reviewed from the arctic, temperate and tropical regions, seeking commonalities of cause in the resulting genetic patterns. Arctic species show distinct shallow genetic clades with common geographical boundaries. Thus Beringia is distinct phylogeographically, but its role as a refugial source is complex. Arctic taxa do not show the common genetic pattern of southern richness and northern purity in north-temperate species. Temperate refugial regions in Europe and North America show relatively deep DNA divergence for many taxa, indicating their presence over several Ice Ages, and suggesting a mode of speciation by repeated allopatry. DNA evidence indicates temperate species in Europe had different patterns of postglacial colonization across the same area and different ones in previous oscillations, whereas the northwest region of North America was colonized from the north, east and south. Tropical montane regions contain deeply diverged lineages, often in a relatively small geographical area, suggesting their survival there from the Pliocene. Our poor understanding of refugial biodiversity would benefit from further combined fossil and genetic studies.
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Affiliation(s)
- G M Hewitt
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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Rhymer JM, Barbay JM, Givens HL. TAXONOMIC RELATIONSHIP BETWEEN SOREX DISPAR AND S. GASPENSIS: INFERENCES FROM MITOCHONDRIAL DNA SEQUENCES. J Mammal 2004. [DOI: 10.1644/ber-003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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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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Calsbeek R, Thompson JN, Richardson JE. Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province. Mol Ecol 2003; 12:1021-9. [PMID: 12753220 DOI: 10.1046/j.1365-294x.2003.01794.x] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The California Floristic Province harbours more endemic plant and animal taxa and more identifiable subspecies than any other area of comparable size in North America. We present evidence that physical historical processes have resulted in congruent patterns of genetic diversity over the past 2-10 million years. Using a molecular clock approach we show that diversification and establishment of spatial genetic structure across six taxonomic groups coincide with the putative age of California's mountain ranges and aridification in the region. Our results demonstrate the importance of geographical barriers and climatological events to species diversification and the overall geographical structure of biodiversity. These results should facilitate conservation efforts in this biodiversity hotspot for taxa whose population genetic structure is still unknown and may suggest the potential utility of this approach in regional conservation planning efforts.
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Affiliation(s)
- Ryan Calsbeek
- Center for Tropical Research, 1609 Hershey Hall, University of California, Los Angeles, CA 90095, USA.
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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: 10.1111/j.1095-8312.2002.tb01703.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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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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48
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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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49
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Laakkonen J, Fisher RN, Case TJ. Effect of land cover, habitat fragmentation and ant colonies on the distribution and abundance of shrews in southern California. J Anim Ecol 2001. [DOI: 10.1046/j.0021-8790.2001.00542.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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