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Baini S, De Biase A. Filling knowledge gaps in insect conservation by leveraging genetic data from public archives. Database (Oxford) 2024; 2024:baae002. [PMID: 38284937 PMCID: PMC10878047 DOI: 10.1093/database/baae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/08/2023] [Accepted: 01/06/2024] [Indexed: 01/30/2024]
Abstract
Insect decline has become a growing concern in recent years, with studies showing alarming declines in populations of several taxa. Our knowledge about genetic spatial patterns and evolutionary history of insects still exhibits significant gaps hindering our ability to effectively conserve and manage insect populations and species. Genetic data may provide valuable insights into the diversity and the evolutionary relationships of insects' species and populations. Public repositories, such as GenBank and BOLD, containing vast archives of genetic data with associated metadata, offer an irreplaceable resource for researchers contributing to our understanding of species diversity, population structure and evolutionary relationships. However, there are some issues in using these data, as they are often scattered and may lack accuracy due to inconsistent sampling protocols and incomplete information. In this paper we describe a curated georeferenced database of genetic data collected in GenBank and BOLD, for insects listed in the International Union for Conservation of Nature (IUCN) Italian Red Lists (dragonflies, bees, saproxylic beetles and butterflies). After querying these repositories, we performed quality control and data standardization steps. We created a dataset containing approximately 33 000 mitochondrial sequences and associated metadata about taxonomy, collection localities, geographic coordinates and IUCN Red List status for 1466 species across the four insect lists. We describe the current state of geographical metadata in queried repositories for species listed under different conservation status in the Italian Red Lists to quantify data gaps posing barriers to prioritization of conservation actions. Our curated dataset is available for data repurposing and analysis, enabling researchers to conduct comparative studies. We emphasize the importance of filling knowledge gaps in insect diversity and distribution and highlight the potential of this dataset for promoting other research fields like phylogeography, macrogenetics and conservation strategies. Our database can be downloaded through the Zenodo repository in SQL format. Database URL: https://zenodo.org/records/8375181.
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Affiliation(s)
- Serena Baini
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, Viale dell’Università 32, Rome I-00185, Italy
| | - Alessio De Biase
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, Viale dell’Università 32, Rome I-00185, Italy
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2
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blab174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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3
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Diversification and post-glacial range expansion of giant North American camel spiders in genus Eremocosta (Solifugae: Eremobatidae). Sci Rep 2021; 11:22093. [PMID: 34764371 PMCID: PMC8586242 DOI: 10.1038/s41598-021-01555-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/29/2021] [Indexed: 11/08/2022] Open
Abstract
Species of camel spiders in the family Eremobatidae are an important component of arthropod communities in arid ecosystems throughout North America. Recently, research demonstrated that the evolutionary history and biogeography of the family are poorly understood. Herein we explore the biogeographic history of this group of arachnids using genome-wide single nucleotide polymorphism (SNP) data, morphology, and distribution modelling to study the eremobatid genus Eremocosta, which contains exceptionally large species distributed throughout North American deserts. Relationships among sampled species were resolved with strong support and they appear to have diversified within distinct desert regions along an east-to-west progression beginning in the Chihuahuan Desert. The unexpected phylogenetic position of some samples suggests that the genus may contain additional, morphologically cryptic species. Geometric morphometric analyses reveal a largely conserved cheliceral morphology among Eremocosta spp. Phylogeographic analyses indicate that the distribution of E. titania was substantially reduced during the last glacial maximum and the species only recently colonized much of the Mojave Desert. Results from this study underscore the power of genome-wide data for unlocking the genetic potential of museum specimens, which is especially promising for organisms like camel spiders that are notoriously difficult to collect.
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4
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Papa Y, Le Bail PY, Covain R. Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin. Mol Ecol Resour 2021; 21:2109-2124. [PMID: 33892518 DOI: 10.1111/1755-0998.13402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/27/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomic references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomic uncertainties concerning the status of several species. We used COI sequences of 1284 fish in conjunction with morphological and biogeographical evidence to assist with species delineation and discovery in order to validate and standardize the current taxonomy. This resulted in a final DNA barcode data set of 199 fish species (125 genera, 36 families and eight orders; 68.86% of strictly freshwater fishes from the basin), among which 25 are new putative candidate species flagged as requiring taxonomic update. DNA barcoding delineation through Barcode Index Numbers (BINs) revealed further cryptic diversity (230 BINs in total). To explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese southwest (Tapanahony and Paloemeu), the Guianese southeast (Marouini, Litany, Tampok, etc.), and the river outlet in the north. This could be explained by lower levels of connectivity between these three main areas and/or the exchange of individuals between these areas and the neighbouring basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogeneous species were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.
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Affiliation(s)
- Yvan Papa
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | - Raphaël Covain
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland
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5
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Graham MR, Myers EA, Kaiser RC, Fet V. Cryptic species and co‐diversification in sand scorpions from the Karakum and Kyzylkum deserts of Central Asia. ZOOL SCR 2019. [DOI: 10.1111/zsc.12381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Matthew R. Graham
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | - Edward A. Myers
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington DC USA
| | - Ronald C. Kaiser
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | - Victor Fet
- Department of Biological Sciences Marshall University Huntington WV USA
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6
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Guan BC, Liu X, Gong X, Cai QY, Ge G. Genetic landscape and landscape connectivity of Ceratopteris thalictroides, an endangered aquatic fern. ECOL INFORM 2019. [DOI: 10.1016/j.ecoinf.2019.100973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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7
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Myers EA, Xue AT, Gehara M, Cox CL, Davis Rabosky AR, Lemos‐Espinal J, Martínez‐Gómez JE, Burbrink FT. Environmental heterogeneity and not vicariant biogeographic barriers generate community‐wide population structure in desert‐adapted snakes. Mol Ecol 2019; 28:4535-4548. [DOI: 10.1111/mec.15182] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/23/2019] [Accepted: 07/08/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology Smithsonian Institution National Museum of Natural History Washington DC USA
- Department of Herpetology The American Museum of Natural History New York NY USA
| | | | - Marcelo Gehara
- Department of Herpetology The American Museum of Natural History New York NY USA
| | - Christian L. Cox
- Department of Biology Georgia Southern University Statesboro GA USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Julio Lemos‐Espinal
- Laboratorio de Ecología, UBIPRO, FES Iztacala Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | | | - Frank T. Burbrink
- Department of Herpetology The American Museum of Natural History New York NY USA
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8
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Inman R, Fotheringham AS, Franklin J, Esque T, Edwards T, Nussear K. Local niche differences predict genotype associations in sister taxa of desert tortoise. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Richard Inman
- School of Geographical Sciences and Urban Planning Arizona State University Tempe Arizona
- U.S. Geological Survey Western Ecological Research Center Henderson Nevada
| | | | - Janet Franklin
- Department of Botany and Plant Sciences University of California – Riverside Riverside California
| | - Todd Esque
- U.S. Geological Survey Western Ecological Research Center Henderson Nevada
| | - Taylor Edwards
- University of Arizona Genetics Core, University of Arizona Tucson Arizona
| | - Kenneth Nussear
- Department of Geography University of Nevada – Reno Reno Nevada
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9
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Myers EA, Bryson RW, Hansen RW, Aardema ML, Lazcano D, Burbrink FT. Exploring Chihuahuan Desert diversification in the gray-banded kingsnake, Lampropeltis alterna (Serpentes: Colubridae). Mol Phylogenet Evol 2019; 131:211-218. [DOI: 10.1016/j.ympev.2018.10.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022]
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10
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Lecocq T, Michez D, Gérard M, Vereecken NJ, Delangre J, Rasmont P, Vray S, Dufrêne M, Mardulyn P, Dellicour S. Divergent geographic patterns of genetic diversity among wild bees: Conservation implications. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Thomas Lecocq
- Université de Lorraine; INRA; URAFPA; Nancy France
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Denis Michez
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Maxence Gérard
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Nicolas J. Vereecken
- Agroecology & Pollination; Landscape Ecology & Plant Production Systems; Université libre de Bruxelles (ULB); Brussels Belgium
| | - Jessica Delangre
- Biodiversity & Landscape; Gembloux Agro-Bio Tech; University of Liège; Gembloux Belgium
| | - Pierre Rasmont
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Sarah Vray
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
- Department of Geography; University of Namur; Namur Belgium
| | - Marc Dufrêne
- Biodiversity & Landscape; Gembloux Agro-Bio Tech; University of Liège; Gembloux Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology; Université libre de Bruxelles (ULB); Bruxelles Belgium
| | - Simon Dellicour
- KU Leuven Department of Microbiology and Immunology; Rega Institute; Laboratory for Clinical and Epidemiological Virology; Leuven Belgium
- Spatial Epidemiology Lab (SpELL); Université Libre de Bruxelles; CP160/12 50, av. FD Roosevelt; 1050 Bruxelles Belgium
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11
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Yu H, Favre A, Sui X, Chen Z, Qi W, Xie G. Mapping the genetic patterns of plants in the region of the Qinghai-Tibet Plateau: Implications for conservation strategies. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12847] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Haibin Yu
- School of Life Sciences; Guangzhou University; Guangzhou China
| | - Adrien Favre
- Senckenberg Research Institute and Natural History Museum; Frankfurt am Main Germany
| | - Xinghua Sui
- State Key Laboratory of Biocontrol; School of Life Sciences; Sun Yat-sen University; Guangzhou China
| | - Zhao Chen
- Guangdong Institute of Eco-environmental Science & Technology; Guangzhou China
| | - Wei Qi
- Institute of Polar Meteorology; Chinese Academy of Meteorological Sciences; Beijing China
| | - Guowen Xie
- School of Life Sciences; Guangzhou University; Guangzhou China
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12
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Cox CL, Davis Rabosky AR, Holmes IA, Reyes-Velasco J, Roelke CE, Smith EN, Flores-Villela O, McGuire JA, Campbell JA. Synopsis and taxonomic revision of three genera in the snake tribe Sonorini. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1449912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Christian L. Cox
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Jacobo Reyes-Velasco
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
- Evolutionary Genomics Laboratory, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Corey E. Roelke
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | - Eric N. Smith
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | | | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jonathan A. Campbell
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
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13
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Comparative phylogeography clarifies the complexity and problems of continental distribution that drove A. R. Wallace to favor islands. Proc Natl Acad Sci U S A 2017; 113:7970-7. [PMID: 27432953 DOI: 10.1073/pnas.1601072113] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Deciphering the geographic context of diversification and distributional dynamics in continental biotas has long been an interest of biogeographers, ecologists, and evolutionary biologists. Thirty years ago, the approach now known as comparative phylogeography was introduced in a landmark study of a continental biota. Here, I use a set of 455 studies to explore the current scope of continental comparative phylogeography, including geographic, conceptual, temporal, ecological, and genomic attributes. Geographically, studies are more frequent in the northern hemisphere, but the south is catching up. Most studies focus on a Quaternary timeframe, but the Neogene is well represented. As such, explanations for geographic structure and history include geological and climatic events in Earth history, and responses include vicariance, dispersal, and range contraction-expansion into and out of refugia. Focal taxa are biased toward terrestrial or semiterrestrial vertebrates, although plants and invertebrates are well represented in some regions. The use of various kinds of nuclear DNA markers is increasing, as are multiple locus studies, but use of organelle DNA is not decreasing. Species distribution models are not yet widely incorporated into studies. In the future, continental comparative phylogeographers will continue to contribute to erosion of the simple vicariance vs. dispersal paradigm, including exposure of the widespread nature of temporal pseudocongruence and its implications for models of diversification; provide new templates for addressing a variety of ecological and evolutionary traits; and develop closer working relationships with earth scientists and biologists in a variety of disciplines.
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Xue AT, Hickerson MJ. multi-dice: r package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes. Mol Ecol Resour 2017; 17:e212-e224. [PMID: 28449263 PMCID: PMC5724483 DOI: 10.1111/1755-0998.12686] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/14/2017] [Accepted: 04/14/2017] [Indexed: 01/25/2023]
Abstract
Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis. This approach has been applied to classical phylogeographic data sets such as mitochondrial barcodes as well as reduced-genome polymorphism data sets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest and composite likelihood optimization. Here, we introduce the r package multi-dice, a wrapper program that exploits existing simulation software for flexible execution of hierarchical model-based inference using the aSFS, which is derived from reduced genome data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding co-demographic pulses and specifying flexible hyperprior distributions. In sum, multi-dice provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a tool for comparative phylogeography and population genomics.
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Affiliation(s)
- Alexander T. Xue
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and BehaviorCity College and Graduate Center of City University of New YorkNew YorkNYUSA
| | - Michael J. Hickerson
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and BehaviorCity College and Graduate Center of City University of New YorkNew YorkNYUSA
- Division of Invertebrate ZoologyAmerican Museum of Natural HistoryNew YorkNYUSA
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15
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Guan BC, Liu X, Gong X, Ge G. Identification of evolutionary hotspots in the Poyang Lake Basin based on genetic data from multiple rare and endangered plant species. ECOL INFORM 2017. [DOI: 10.1016/j.ecoinf.2017.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Book Reviews. COPEIA 2017. [DOI: 10.1643/ot-17-687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Graham MR, Wood DA, Henault JA, Valois ZJ, Cushing PE. Ancient lakes, Pleistocene climates and river avulsions structure the phylogeography of a large but little-known rock scorpion from the Mojave and Sonoran deserts. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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18
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Ferguson AW, McDonough MM, Guerra GI, Rheude M, Dragoo JW, Ammerman LK, Dowler RC. Phylogeography of a widespread small carnivore, the western spotted skunk ( Spilogale gracilis) reveals temporally variable signatures of isolation across western North America. Ecol Evol 2017; 7:4229-4240. [PMID: 28649336 PMCID: PMC5478080 DOI: 10.1002/ece3.2931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/26/2016] [Accepted: 02/21/2017] [Indexed: 02/06/2023] Open
Abstract
We analyzed phylogeographic patterns in the western spotted skunk, Spilogale gracilis Merriam, 1890 (Carnivora: Mephitidae) in relation to historical events associated with Pre-Pleistocene Divergence (PPD) and Quaternary climate change (QCC) using mitochondrial DNA from 97 individuals distributed across Western North America. Divergence times were generated using BEAST to estimate when isolation in putative refugia occurred. Patterns and timing of demographic expansion was performed using Bayesian skyline plot. Putative climatic refugia resulting from Quaternary climate change were identified using paleoecological niche modeling and divergence dates compared to major vicariant events associated with Pre-Pleistocene conditions. We recovered three major mitochondrial clades corresponding to western North America (California, Baja, and across the Great Basin), east-central North America (Texas, central Mexico, New Mexico), and southwestern Arizona/northwestern Mexico. Time to most recent common ancestor for S. gracilis occurred ~1.36 Ma. Divergence times for each major clade occurred between 0.25 and 0.12 Ma, with signature of population expansion occurring 0.15 and 0.10 Ma. Ecological niche models identified three potential climatic refugia during the Last Interglacial, (1) west coast of California and Oregon, (2) northwestern Mexico, and (3) southern Texas/northeastern Mexico as well as two refugia during the Last Glacial Maximum, (1) western USA and (2) southern Texas/northeastern Mexico. This study supports PPD in shaping species-level diversity compared to QCC-driven changes at the intraspecific level for Spilogale, similar to the patterns reported for other small mammals (e.g., rodents and bats). Phylogeographic patterns also appear to have been shaped by both habitat and river vicariance, especially across the desert southwest. Further, continuing climate change during the Holocene coupled with anthropogenic modifications during the Anthropocene appears to be removing both of these barriers to current dispersal of western spotted skunks.
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Affiliation(s)
| | - Molly M. McDonough
- Division of MammalsNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Gema I. Guerra
- Department of BiologyAngelo State UniversitySan AngeloTXUSA
| | - Margaret Rheude
- United States Fish and Wildlife ServiceTwin Cities Ecological Services OfficeBloomingtonMNUSA
| | - Jerry W. Dragoo
- Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNMUSA
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Gottscho AD, Wood DA, Vandergast AG, Lemos-Espinal J, Gatesy J, Reeder TW. Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow. Mol Phylogenet Evol 2017; 106:103-117. [DOI: 10.1016/j.ympev.2016.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 07/26/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023]
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20
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Kierepka EM, Latch EK. High gene flow in the American badger overrides habitat preferences and limits broadscale genetic structure. Mol Ecol 2016; 25:6055-6076. [PMID: 27862522 DOI: 10.1111/mec.13915] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 10/13/2016] [Accepted: 11/01/2016] [Indexed: 01/05/2023]
Abstract
Habitat associations are a function of habitat preferences and dispersal capabilities, both of which can influence how species responded to Quaternary climatic changes and contemporary habitat heterogeneity. Predicting resultant genetic structure is not always straightforward, especially in species where high dispersal potential and habitat preferences yield opposing predictions. The American badger has high dispersal capabilities that predict widespread panmixia, but avoids closed-canopy forests and clay soils, which could restrict gene flow and create ecologically based population genetic structure. We used mitochondrial sequence and microsatellite data sets to characterize how these opposing forces contribute to genetic structure in badgers at a continent-wide scale. Our data revealed an overall lack of ecologically based population genetic structure, suggesting that high dispersal capabilities were sufficiently realized to overcome most habitat-based genetic structure. At a broadscale, badger gene flow is limited only by geographic distance (isolation by distance) and large water barriers (Lake Michigan and the Mississippi River). The absence of genetic structure in a species with strong avoidance of unsuitable habitats advances our understanding of when and how genetic structure emerges in widespread, highly mobile species.
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Affiliation(s)
- E M Kierepka
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - E K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
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Piry S, Chapuis M, Gauffre B, Papaïx J, Cruaud A, Berthier K. Mapping Averaged Pairwise Information (MAPI): a new exploratory tool to uncover spatial structure. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12616] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - Bertrand Gauffre
- UMR 7372, Centre d'Etudes Biologiques de Chizé CNRS – Université de La Rochelle 79360 Villiers‐en‐Bois France
- USC1339, Centre d'Etudes Biologiques de Chizé INRA 79360 Villiers‐en‐Bois France
| | - Julien Papaïx
- Biostatistique et Processus Spatiaux INRA 84914 Avignon France
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22
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Gámez N, Nihei SS, Scheinvar E, Morrone JJ. A temporally dynamic approach for cladistic biogeography and the processes underlying the biogeographic patterns of North American deserts. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Niza Gámez
- Museo de Zoología ‘Alfonso L. Herrera’; Departamento de Biología Evolutiva; Facultad de Ciencias; Universidad Nacional Autónoma de México (UNAM); Mexico City Mexico
| | - Silvio S. Nihei
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Cidade Universitária; São Paulo SP Brazil
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México (UNAM); Mexico City Mexico
| | - Juan J. Morrone
- Museo de Zoología ‘Alfonso L. Herrera’; Departamento de Biología Evolutiva; Facultad de Ciencias; Universidad Nacional Autónoma de México (UNAM); Mexico City Mexico
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23
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Schmitt T, Louy D, Zimmermann E, Habel JC. Species radiation in the Alps: multiple range shifts caused diversification in Ringlet butterflies in the European high mountains. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0282-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Conroy CJ, Patton JL, Lim MCW, Phuong MA, Parmenter B, Höhna S. Following the rivers: historical reconstruction of California volesMicrotus californicus(Rodentia: Cricetidae) in the deserts of eastern California. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Chris J. Conroy
- Museum of Vertebrate Zoology; University of California; 3101 Valley Life Sciences Building Berkeley CA 94720 USA
| | - James L. Patton
- Museum of Vertebrate Zoology; University of California; 3101 Valley Life Sciences Building Berkeley CA 94720 USA
| | - Marisa C. W. Lim
- Department of Ecology & Evolution; Stony Brook University; 650 Life Sciences Building Stony Brook NY 11794-5245 USA
| | - Mark A. Phuong
- Department of Ecology & Evolutionary Biology; University of California; 612 Charles E. Young Dr. South Los Angeles CA 90095 USA
| | - Brett Parmenter
- Department of Biology; Warren Wilson College; P.O. Box 9000 Asheville NC 28815 USA
| | - Sebastian Höhna
- Department of Integrative Biology; University of California; 1005 Valley Life Sciences Building #3140 Berkeley CA 94720 USA
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25
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Gray DA, Gutierrez NJ, Chen TL, Gonzalez C, Weissman DB, Cole JA. Species divergence in field crickets: genetics, song, ecomorphology, and pre- and postzygotic isolation. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David A. Gray
- Department of Biology; California State University Northridge; Northridge CA 91330-8303 USA
| | - Nicholas J. Gutierrez
- Department of Biology; California State University Northridge; Northridge CA 91330-8303 USA
| | - Tom L. Chen
- Department of Biology; California State University Northridge; Northridge CA 91330-8303 USA
| | - Christopher Gonzalez
- Department of Biology; California State University Northridge; Northridge CA 91330-8303 USA
| | - David B. Weissman
- Department of Entomology; California Academy of Sciences; San Francisco CA 94118 USA
| | - Jeffrey A. Cole
- Department of Biology; California State University Northridge; Northridge CA 91330-8303 USA
- Department of Biology; Pasadena City College; Pasadena CA 91106 USA
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26
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Hope AG, Waltari E, Malaney JL, Payer DC, Cook JA, Talbot SL. Arctic biodiversity: increasing richness accompanies shrinking refugia for a cold-associated tundra fauna. Ecosphere 2015. [DOI: 10.1890/es15-00104.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Pope LC, Liggins L, Keyse J, Carvalho SB, Riginos C. Not the time or the place: the missing spatio-temporal link in publicly available genetic data. Mol Ecol 2015; 24:3802-9. [DOI: 10.1111/mec.13254] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 05/07/2015] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Lisa C. Pope
- School of Biological Sciences; The University of Queensland; Brisbane Qld 4072 Australia
| | - Libby Liggins
- Allan Wilson Centre for Molecular Ecology and Evolution; New Zealand Institute for Advanced Study; Institute of Natural and Mathematical Sciences; Massey University; Auckland 0745 New Zealand
- Auckland War Memorial Museum; Tāmaki Paenga Hira; Auckland 1142 New Zealand
| | - Jude Keyse
- School of Biological Sciences; The University of Queensland; Brisbane Qld 4072 Australia
| | - Silvia B Carvalho
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Cynthia Riginos
- School of Biological Sciences; The University of Queensland; Brisbane Qld 4072 Australia
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28
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Edwards T, Berry KH, Inman RD, Esque TC, Nussear KE, Jones CA, Culver M. Testing Taxon Tenacity of Tortoises: evidence for a geographical selection gradient at a secondary contact zone. Ecol Evol 2015; 5:2095-114. [PMID: 26045959 PMCID: PMC4449762 DOI: 10.1002/ece3.1500] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022] Open
Abstract
We examined a secondary contact zone between two species of desert tortoise, Gopherus agassizii and G. morafkai. The taxa were isolated from a common ancestor during the formation of the Colorado River (4–8 mya) and are a classic example of allopatric speciation. However, an anomalous population of G. agassizii comes into secondary contact with G. morafkai east of the Colorado River in the Black Mountains of Arizona and provides an opportunity to examine reinforcement of species' boundaries under natural conditions. We sampled 234 tortoises representing G. agassizii in California (n - 103), G. morafkai in Arizona (n - 78), and 53 individuals of undetermined assignment in the contact zone including and surrounding the Black Mountains. We genotyped individuals for 25 STR loci and determined maternal lineage using mtDNA sequence data. We performed multilocus genetic clustering analyses and used multiple statistical methods to detect levels of hybridization. We tested hypotheses about habitat use between G. agassizii and G. morafkai in the region where they co-occur using habitat suitability models. Gopherus agassizii and G. morafkai maintain independent taxonomic identities likely due to ecological niche partitioning, and the maintenance of the hybrid zone is best described by a geographical selection gradient model.
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; University of Arizona Genetics Core, University of Arizona 1657 E. Helen Street, Tucson, Arizona, 85721
| | - Kristin H Berry
- Western Ecological Research Center, U.S. Geological Survey Falcon Business Park, 21803 Cactus Avenue, Suite F, Riverside, California, 92518
| | - Richard D Inman
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Todd C Esque
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Kenneth E Nussear
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Cristina A Jones
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Game and Fish Department, Nongame Wildlife Branch Phoenix, Arizona, 85086
| | - Melanie Culver
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Arizona Tucson, Arizona, 85721
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29
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Chan YL, Schanzenbach D, Hickerson MJ. Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation. Mol Biol Evol 2014; 31:2501-15. [PMID: 24925925 PMCID: PMC4137712 DOI: 10.1093/molbev/msu187] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate.
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Affiliation(s)
- Yvonne L Chan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa
| | | | - Michael J Hickerson
- Biology Department, City College of New YorkThe Graduate Center, City University of New York
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30
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Gottscho AD, Marks SB, Jennings WB. Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern. Ecol Evol 2014; 4:2546-62. [PMID: 25360285 PMCID: PMC4203297 DOI: 10.1002/ece3.1111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/20/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022] Open
Abstract
The North American deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using isolation-with-migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The likelihood ratio test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia and define this species as a single evolutionarily significant unit for conservation purposes.
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Affiliation(s)
- Andrew D Gottscho
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521 ; Department of Biology, University of California Riverside, California, 92521
| | - Sharyn B Marks
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521
| | - W Bryan Jennings
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521
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31
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Wood DA, Fisher RN, Vandergast AG. Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication. PLoS One 2014; 9:e97494. [PMID: 24848638 PMCID: PMC4029750 DOI: 10.1371/journal.pone.0097494] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/16/2014] [Indexed: 11/23/2022] Open
Abstract
Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.
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Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Robert N. Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
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Cryptic genetic diversity and complex phylogeography of the boreal North American scorpion, Paruroctonus boreus (Vaejovidae). Mol Phylogenet Evol 2013; 71:298-307. [PMID: 24269314 DOI: 10.1016/j.ympev.2013.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/25/2013] [Accepted: 11/10/2013] [Indexed: 11/22/2022]
Abstract
Diverse studies in western North America have revealed the role of topography for dynamically shaping genetic diversity within species though vicariance, dispersal and range expansion. We examined patterns of phylogeographical diversity in the widespread but poorly studied North American vaejovid scorpion, Paruroctonus boreus Girard 1854. We used mitochondrial sequence data and parsimony, likelihood, and Bayesian inference to reconstruct phylogenetic relationships across the distributional range of P. boreus, focusing on intermontane western North America. Additionally, we developed a species distribution model to predict its present and historical distributions during the Last Glacial Maximum and the Last Interglacial Maximum. Our results documented complex phylogeographic relationships within P. boreus, with multiple, well-supported crown clades that are either geographically-circumscribed or widespread and separated by short, poorly supported internodes. We also observed subtle variation in predicted habitat suitability, especially at the northern, eastern and southern edges of the predicted distributional range under past climatic conditions. The complex phylogenetic relationships of P. boreus suggests that historical isolation and expansion of populations may have occurred. Variation in the predicted distributional range over time may implicate past climatic fluctuations in generating the patterns of genetic diversity observed in P. boreus. These findings highlight both the potential for cryptic biodiversity in widespread North American scorpion species and the importance of phylogeographical studies for understanding the factors responsible for generating the biodiversity of western North America.
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