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Campos PM, Lucid MK, Ehlers S, Walke JB. Low-level pathogen infection and geographic location correlate with the skin microbiomes of Columbia spotted frogs ( Rana luteiventris) in a montane landscape. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100213. [PMID: 38187998 PMCID: PMC10770434 DOI: 10.1016/j.crmicr.2023.100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
The skin microbiome of amphibians can influence host susceptibility towards the fungal pathogen Batrachochytrium dendrobatidis (Bd), while simultaneously having the potential to be altered by Bd. Severe Bd infections are known to alter the amphibian skin microbiome; however, little is known about microbiome interactions in amphibians with low infection intensity. In addition to disease dynamics, environmental factors may influence the microbiome. To test for patterns in bacterial diversity based on pathogen infection and environmental factors, 399 Columbia spotted frogs (Rana luteiventris) were sampled throughout northern Idaho and northeastern Washington across two years. Bd prevalence and intensity were measured in 376 frogs, revealing a prevalence of 69%, but generally low infection intensity (Mean = 127 Bd zoospore equivalents among infected frogs). Skin bacterial communities were characterized in 92 frogs using 16S rRNA gene amplicon sequencing. Our results indicated correlations of decreasing Shannon diversity and evenness as infection intensity increased. Latitude was correlated with bacterial richness and Faith's Phylogenetic Diversity measures, indicating increased diversity in northern locations. Beta diversity (UniFrac) analyses revealed that skin microbiomes were distinct between infected and uninfected frogs, and infection intensity had a significant effect on microbiome composition. Site explained the majority of microbiome variation (weighted UniFrac: 57.5%), suggesting a combination of local habitat conditions explain variation, as only small proportions of variation could be explained by year, month, temperature, elevation, and latitude individually. Bacterial genera with potential for Bd-inhibitory properties were found with differential relative abundance in infected and uninfected frogs, with higher Stenotrophomonas and lower Pseudomonas relative abundance observed in infected frogs. Further study may indicate if Bd inhibition by members of the skin microbiome is an influence behind the low infection intensities observed and whether low Bd infection intensities are capable of altering skin microbiome composition.
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Affiliation(s)
- Philip M. Campos
- Department of Biology, Eastern Washington University, 1175 Washington St., Cheney, WA 99004, USA
| | - Michael K. Lucid
- Idaho Department of Fish and Game, 2885 Kathleen Ave., Coeur d'Alene, ID 83815, USA
- Selkirk Wildlife Science, LLC, PO Box 733, Sandpoint, ID 83864, USA
| | - Shannon Ehlers
- Idaho Department of Fish and Game, 2885 Kathleen Ave., Coeur d'Alene, ID 83815, USA
- U.S. Fish and Wildlife Service, 287 Westside Rd., Bonners Ferry, ID 83805, USA
| | - Jenifer B. Walke
- Department of Biology, Eastern Washington University, 1175 Washington St., Cheney, WA 99004, USA
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Tornabene BJ, Hossack BR, Breuner CW. Assay validation of saliva glucocorticoids in Columbia spotted frogs and effects of handling and marking. CONSERVATION PHYSIOLOGY 2023; 11:coad078. [PMID: 38026797 PMCID: PMC10660366 DOI: 10.1093/conphys/coad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/24/2023] [Indexed: 12/01/2023]
Abstract
Non-invasive methods are important to the field of conservation physiology to reduce negative effects on organisms being studied. Glucocorticoid (GC) hormones are often used to assess health of individuals, but collection methods can be invasive. Many amphibians are imperiled worldwide, and saliva is a non- or semi-invasive matrix to measure GCs that has been partially validated for only four amphibian species. Validation ensures that assays are reliable and can detect changes in saliva corticosterone (sCORT) after exposure to stressors, but it is also necessary to ensure sCORT concentrations are correlated with plasma concentrations. To help validate the use of saliva in assessing CORT responses in amphibians, we captured uniquely marked Columbia spotted frogs (Rana luteiventris) on sequential days and collected baseline and stress-induced (after handling) samples. For a subset of individuals, we collected and quantified CORT in both saliva and blood samples, which have not been compared for amphibians. We tested several aspects of CORT responses and, by collecting across separate days, measured repeatability of CORT responses across days. We also evaluated whether methods common to amphibian conservation, such as handling alone or handling, clipping a toe and tagging elevated sCORT. Similar to previous studies, we show that sCORT is reliable concerning parallelism, recovery, precision and sensitivity. sCORT was weakly correlated with plasma CORT (R2 = 0.21), and we detected elevations in sCORT after handling, demonstrating biological validation. Toe clipping and tagging did not increase sCORT over handling alone, but repeated handling elevated sCORT for ~72 hours. However, sCORT responses were highly variable and repeatability was low within individuals and among capture sessions, contrary to previous studies with urinary and waterborne CORT. sCORT is a semi-invasive and rapid technique that could be useful to assess effects of anthropogenic change and conservation efforts, but will require careful study design and future validation.
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Affiliation(s)
- Brian J Tornabene
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 32 Campus Dr., University of Montana, Missoula, Montana, 59812, USA
- Wildlife Biology Program, W. A. Franke College of Forestry & Conservation, 32 Campus Dr., University of Montana, Missoula, Montana, 59812, USA
| | - Blake R Hossack
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 32 Campus Dr., University of Montana, Missoula, Montana, 59812, USA
- Wildlife Biology Program, W. A. Franke College of Forestry & Conservation, 32 Campus Dr., University of Montana, Missoula, Montana, 59812, USA
| | - Creagh W Breuner
- Wildlife Biology Program, W. A. Franke College of Forestry & Conservation, 32 Campus Dr., University of Montana, Missoula, Montana, 59812, USA
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Blanco-Pastor JL, Fernández-Mazuecos M, Coello AJ, Pastor J, Vargas P. Topography explains the distribution of genetic diversity in one of the most fragile European hotspots. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12836] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- José Luis Blanco-Pastor
- Real Jardín Botánico de Madrid (RJB-CSIC); Madrid Spain
- INRA; Centre Nouvelle-Aquitaine-Poitiers, UR4 (URP3F); Lusignan France
| | | | - Alberto J. Coello
- Real Jardín Botánico de Madrid (RJB-CSIC); Madrid Spain
- Universidad Rey Juan Carlos; Madrid Spain
| | - Julia Pastor
- Real Jardín Botánico de Madrid (RJB-CSIC); Madrid Spain
| | - Pablo Vargas
- Real Jardín Botánico de Madrid (RJB-CSIC); Madrid Spain
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Pilliod DS, Arkle RS, Robertson JM, Murphy MA, Funk WC. Effects of changing climate on aquatic habitat and connectivity for remnant populations of a wide-ranging frog species in an arid landscape. Ecol Evol 2015; 5:3979-94. [PMID: 26445654 PMCID: PMC4588645 DOI: 10.1002/ece3.1634] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/13/2015] [Accepted: 07/09/2015] [Indexed: 12/24/2022] Open
Abstract
Amphibian species persisting in isolated streams and wetlands in desert environments can be susceptible to low connectivity, genetic isolation, and climate changes. We evaluated the past (1900–1930), recent (1981–2010), and future (2071–2100) climate suitability of the arid Great Basin (USA) for the Columbia spotted frog (Rana luteiventris) and assessed whether changes in surface water may affect connectivity for remaining populations. We developed a predictive model of current climate suitability and used it to predict the historic and future distribution of suitable climates. We then modeled changes in surface water availability at each time period. Finally, we quantified connectivity among existing populations on the basis of hydrology and correlated it with interpopulation genetic distance. We found that the area of the Great Basin with suitable climate conditions has declined by approximately 49% over the last century and will likely continue to decline under future climate scenarios. Climate conditions at currently occupied locations have been relatively stable over the last century, which may explain persistence at these sites. However, future climates at these currently occupied locations are predicted to become warmer throughout the year and drier during the frog's activity period (May – September). Fall and winter precipitation may increase, but as rain instead of snow. Earlier runoff and lower summer base flows may reduce connectivity between neighboring populations, which is already limited. Many of these changes could have negative effects on remaining populations over the next 50–80 years, but milder winters, longer growing seasons, and wetter falls might positively affect survival and dispersal. Collectively, however, seasonal shifts in temperature, precipitation, and stream flow patterns could reduce habitat suitability and connectivity for frogs and possibly other aquatic species inhabiting streams in this arid region.
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Affiliation(s)
- David S Pilliod
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center 970 Lusk Street Boise Idaho 83706
| | - Robert S Arkle
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center 970 Lusk Street Boise Idaho 83706
| | - Jeanne M Robertson
- Department of Biology California State University Northridge California 91330
| | - Melanie A Murphy
- Department of Ecosystem Science and Management Program in Ecology University of Wyoming Laramie Wyoming 82071
| | - W Chris Funk
- Department of Biology Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado 80523
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5
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Arkle RS, Pilliod DS. Persistence at distributional edges: Columbia spotted frog habitat in the arid Great Basin, USA. Ecol Evol 2015; 5:3704-24. [PMID: 26380699 PMCID: PMC4567874 DOI: 10.1002/ece3.1627] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 03/31/2015] [Accepted: 07/03/2015] [Indexed: 01/20/2023] Open
Abstract
A common challenge in the conservation of broadly distributed, yet imperiled species is understanding which factors facilitate persistence at distributional edges, locations where populations are often vulnerable to extirpation due to changes in climate, land use, or distributions of other species. For Columbia spotted frogs (Rana luteiventris) in the Great Basin (USA), a genetically distinct population segment of conservation concern, we approached this problem by examining (1) landscape-scale habitat availability and distribution, (2) water body-scale habitat associations, and (3) resource management-identified threats to persistence. We found that areas with perennial aquatic habitat and suitable climate are extremely limited in the southern portion of the species’ range. Within these suitable areas, native and non-native predators (trout and American bullfrogs [Lithobates catesbeianus]) are widespread and may further limit habitat availability in upper- and lower-elevation areas, respectively. At the water body scale, spotted frog occupancy was associated with deeper sites containing abundant emergent vegetation and nontrout fish species. Streams with American beaver (Castor canadensis) frequently had these structural characteristics and were significantly more likely to be occupied than ponds, lakes, streams without beaver, or streams with inactive beaver ponds, highlighting the importance of active manipulation of stream environments by beaver. Native and non-native trout reduced the likelihood of spotted frog occupancy, especially where emergent vegetation cover was sparse. Intensive livestock grazing, low aquatic connectivity, and ephemeral hydroperiods were also negatively associated with spotted frog occupancy. We conclude that persistence of this species at the arid end of its range has been largely facilitated by habitat stability (i.e., permanent hydroperiod), connectivity, predator-free refugia, and a commensalistic interaction with an ecosystem engineer. Beaver-induced changes to habitat quality, stability, and connectivity may increase spotted frog population resistance and resilience to seasonal drought, grazing, non-native predators, and climate change, factors which threaten local or regional persistence.
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Affiliation(s)
- Robert S Arkle
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center 970 Lusk Street, Boise, ID, 83706, USA
| | - David S Pilliod
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center 970 Lusk Street, Boise, ID, 83706, USA
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Keely CC, Hale JM, Heard GW, Parris KM, Sumner J, Hamer AJ, Melville J. Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140255. [PMID: 26361543 PMCID: PMC4555848 DOI: 10.1098/rsos.140255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 07/27/2015] [Indexed: 06/05/2023]
Abstract
Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog (Litoria raniformis) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis. However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.
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Affiliation(s)
- Claire C. Keely
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
- Sciences Department, Museum Victoria, Carlton 3053, Australia
| | - Joshua M. Hale
- Sciences Department, Museum Victoria, Carlton 3053, Australia
| | - Geoffrey W. Heard
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Kirsten M. Parris
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Joanna Sumner
- Sciences Department, Museum Victoria, Carlton 3053, Australia
| | - Andrew J. Hamer
- Australian Research Centre for Urban Ecology, Royal Botanic Gardens Melbourne c/o School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Jane Melville
- Sciences Department, Museum Victoria, Carlton 3053, Australia
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7
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Contrasting Genetic Differentiation of a Poorly Dispersing Lizard in Connected and Fragmented Scrub Habitats. J HERPETOL 2012. [DOI: 10.1670/10-291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Shitova MV, Yurchenko AA, Shaykhaev EG, Zhivotovsky LA. A panel of microsatellite loci for population studies of Sakhalin taimen Parahucho perryi (Brevoort). RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412070125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Lind AJ, Spinks PQ, Fellers GM, Shaffer HB. Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0138-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Goebel AM, Ranker TA, Corn PS, Olmstead RG. Mitochondrial DNA evolution in the Anaxyrus boreas species group. Mol Phylogenet Evol 2009; 50:209-25. [DOI: 10.1016/j.ympev.2008.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/10/2008] [Accepted: 06/24/2008] [Indexed: 11/27/2022]
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12
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Beauclerc KB, Johnson B, White BN. Genetic rescue of an inbred captive population of the critically endangered Puerto Rican crested toad (Peltophryne lemur) by mixing lineages. CONSERV GENET 2009. [DOI: 10.1007/s10592-008-9782-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Geographical pattern and historical demography of Midday gerbil Meriones meridianus (Gerbillidae, Rodentia) inferred from the sequences of the mitochondrial DNA control region. RUSSIAN JOURNAL OF THERIOLOGY 2008. [DOI: 10.15298/rusjtheriol.07.1.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Silva DDME, Cruz ADD, Bastos RP, Telles MPDC, Diniz-Filho JAF. Morphometric and genetic differentiation among populations of Eupemphix nattereri (Amphibia, Anura, Leiuperidae) from central Brazil. IHERINGIA. SERIE ZOOLOGIA 2008. [DOI: 10.1590/s0073-47212008000400013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To assess genetic structure and phenotypic diversity of Eupemphix nattereri Steindachner, 1863, morphometric and molecular analyses were carried out for nine populations from the State of Goiás. A total of 11 morphometric traits were evaluated and genetic information was estimated using RAPD markers. Genetic and phenotypic distances were determined as a function of geographical origin. Correlation among genetic, morphometric, micro, and macroenviromental were analyzed by the Mantel test. Genetic data indicated high levels of genetic diversity (Φst= 0.3) among the nine populations. Mantel tests did not reveal a significant positive correlation between genetic and geographical distances, indicating that locally geographical populations were not genetically similar, even in distances smaller than 50 km. Discriminant analysis on 11 morphometric measurements showed a high divergence among the nine populations. However, a marginally significant correlation (P=0.08) between genetic and morphometric distances was found. The observed correlation was not causal in terms of the relationship between phenotype and genotype, but indicated common spatial structures. Thus, our results suggest that isolation-by-distance processes may explain population divergence in Eupemphix nattereri.
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15
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Knopp T, Merilä J. The postglacial recolonization of Northern Europe by Rana arvalis as revealed by microsatellite and mitochondrial DNA analyses. Heredity (Edinb) 2008; 102:174-81. [PMID: 18827835 DOI: 10.1038/hdy.2008.91] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The postglacial history of the moor frog (Rana arvalis) in Northern Europe was investigated with the aid of eight variable microsatellite loci and a 661 bp sequence of the mitochondrial cytochrome b gene. A division between eastern and western mitochondrial lineages was discovered, supporting two recolonization routes to Fennoscandia since the last glacial maximum. This result was corroborated by the microsatellite data, which revealed a contact zone between the two lineages in Northern Sweden. These findings add to the increasing evidence that an intraspecific genetic biodiversity founded on the existence of eastern and western clades is a common element in Fennoscandian fauna and flora.
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Affiliation(s)
- T Knopp
- Department of Biological and Environmental Sciences, Ecological Genetics Research Unit, University of Helsinki, Helsinki, Finland.
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16
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Amphibian phylogeography: a model for understanding historical aspects of species distributions. Heredity (Edinb) 2008; 101:109-19. [DOI: 10.1038/hdy.2008.30] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Randi E, Tabarroni C, Kark S. The role of history vs. demography in shaping genetic population structure across an ecotone: chukar partridges (Alectoris chukar) as a case study. DIVERS DISTRIB 2006. [DOI: 10.1111/j.1472-4642.2006.00261.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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18
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Randi E, Tabarroni C, Kark S. The role of history vs. demography in shaping genetic population structure across an ecotone: chukar partridges (Alectoris chukar) as a case study. DIVERS DISTRIB 2006. [DOI: 10.1111/j.1366-9516.2006.00261.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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19
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Burns EL, Eldridge MDB, Crayn DM, Houlden BA. Low Phylogeographic Structure in a Wide Spread Endangered Australian Frog Litoria aurea (Anura: Hylidae). CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9143-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Qu YH, Ericson PGP, Lei FM, Li SH. Postglacial colonization of the Tibetan plateau inferred from the matrilineal genetic structure of the endemic red-necked snow finch, Pyrgilauda ruficollis. Mol Ecol 2005; 14:1767-81. [PMID: 15836648 DOI: 10.1111/j.1365-294x.2005.02528.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most phylogeographical studies of postglacial colonization focus on high latitude locations in the Northern Hemisphere. Here, we studied the phylogeographical structure of the red-necked snow finch Pyrgilauda ruficollis, an endemic species of the Tibetan plateau. We analysed 879 base pairs (bp) of the mitochondrial cytochrome b gene and 529 bp of the control region in 41 birds from four regional groups separated by mountain ranges. We detected 34 haplotypes, 31 of which occurred in a single individual and only three of which were shared among sampling sites within regional groups or among regional groups. Haplotype diversity was high (h = 0.94); nucleotide diversity was low (eth = 0.00415) and genetic differentiation was virtually non-existent. Analyses of mismatch distributions and geographically nested clades yielded results consistent with contiguous range expansion, and the expansion times were estimated as 0.07-0.19 million years ago (Ma). Our results suggest that P. ruficollis colonized the Tibetan plateau after the extensive glacial period (0.5-0.175 Ma), expanding from the eastern margin towards the inner plateau. Thus, in contrast to many of the post-glacial phylogeographical structures known at high latitudes, this colonization occurred without matrilineal population structuring. This might be due to the short glacial cycles typical of the Tibetan plateau, adaptation of P. ruficollis to cold conditions, or refugia and colonized habitat being semicontinuous and thus promoting population mixing.
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Affiliation(s)
- Yan Hua Qu
- Institute of Zoology, Chinese Academy of Sciences, 25 Beisihuanxi Road, Haidian District, Beijing 100080, People's Republic of China.
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21
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Funk WC, Blouin MS, Corn PS, Maxell BA, Pilliod DS, Amish S, Allendorf FW. Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape. Mol Ecol 2005; 14:483-96. [PMID: 15660939 DOI: 10.1111/j.1365-294x.2005.02426.x] [Citation(s) in RCA: 225] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Landscape features such as mountains, rivers, and ecological gradients may strongly affect patterns of dispersal and gene flow among populations and thereby shape population dynamics and evolutionary trajectories. The landscape may have a particularly strong effect on patterns of dispersal and gene flow in amphibians because amphibians are thought to have poor dispersal abilities. We examined genetic variation at six microsatellite loci in Columbia spotted frogs (Rana luteiventris) from 28 breeding ponds in western Montana and Idaho, USA, in order to investigate the effects of landscape structure on patterns of gene flow. We were particularly interested in addressing three questions: (i) do ridges act as barriers to gene flow? (ii) is gene flow restricted between low and high elevation ponds? (iii) does a pond equal a 'randomly mating population' (a deme)? We found that mountain ridges and elevational differences were associated with increased genetic differentiation among sites, suggesting that gene flow is restricted by ridges and elevation in this species. We also found that populations of Columbia spotted frogs generally include more than a single pond except for very isolated ponds. There was also evidence for surprisingly high levels of gene flow among low elevation sites separated by large distances. Moreover, genetic variation within populations was strongly negatively correlated with elevation, suggesting effective population sizes are much smaller at high elevation than at low elevation. Our results show that landscape features have a profound effect on patterns of genetic variation in Columbia spotted frogs.
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Affiliation(s)
- W Chris Funk
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA.
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22
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Mock KE, Brim-Box JC, Miller MP, Downing ME, Hoeh WR. Genetic diversity and divergence among freshwater mussel (Anodonta) populations in the Bonneville Basin of Utah. Mol Ecol 2004; 13:1085-98. [PMID: 15078447 DOI: 10.1111/j.1365-294x.2004.02143.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Populations of the freshwater mussel genus Anodonta appear to be in a state of rapid decline in western North America, following a trend that unfortunately seems to be prevalent among these animals (Mollusca: Unionoida). Here we describe the patterns of molecular divergence and diversity among Anodonta populations in the Bonneville Basin, a large sub-basin of the Great Basin in western North America. Using amplified fragment length polymorphism (AFLP) analysis, we found a striking lack of nuclear diversity within some of these populations, along with a high degree of structuring among populations (FST = 0.61), suggesting post-Pleistocene isolation, due either to a long-term loss of hydrologic connectivity among populations or to more recent fish introductions. We also found evidence of recent hybridization in one of these populations, possibly mediated by fish-stocking practices. Using mitochondrial sequence data, we compared the Bonneville Basin populations to Anodonta in several other drainages in western North America. We found a general lack of resolution in these phylogenetic reconstructions, although there was a tendency for the Bonneville Basin Anodonta (tentatively A. californiensis) to cluster with A. oregonensis from the adjacent Lahontan Basin in Nevada. We recommend further investigation of anthropogenic factors that may be contributing to the decline of western Anodonta and a broad-scale analysis and synthesis of genetic and morphological variation among Anodonta in western North America.
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Affiliation(s)
- K E Mock
- Department of Forest, Range, and Wildlife Sciences, Utah State University, 5230 Old Main Hill, Logan, UT 84322-5230, USA.
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Babik W, Branicki W, Sandera M, Litvinchuk S, Borkin LJ, Irwin JT, Rafiński J. Mitochondrial phylogeography of the moor frog, Rana arvalis. Mol Ecol 2004; 13:1469-80. [PMID: 15140091 DOI: 10.1111/j.1365-294x.2004.02157.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The moor frog Rana arvalis is a lowland species with a broad Eurasiatic distribution, from arctic tundra through forest to the steppe zone. Its present-day range suggests that glacial refugia of this frog were located outside southern European peninsulas. We studied the species-wide phylogeographical pattern using sequence variation in a 682 base pairs fragment of mtDNA cytochrome b gene; 223 individuals from 73 localities were analysed. Two main clades, A and B, differing by c. 3.6% sequence divergence were detected. The A clade is further subdivided into two subclades, AI and AII differing by 1.0%. All three lineages are present in the Carpathian Basin (CB), whereas the rest of the species range, including huge expanses of Eurasian lowlands, are inhabited solely by the AI lineage. We infer that AII and B lineages survived several glacial cycles in the CB but did not expand, at least in the present interglacial, to the north. The geographical distribution and genealogical relationships between haplotypes from the AI lineage indicate that this group had two glacial refugia, one located in the eastern part of the CB and the other probably in southern Russia. Populations from both refugia contributed to the colonization of the western part of the range, whereas the eastern part was colonized from the eastern refugium only. The effective population size as evidenced by theta(ML) is an order of magnitude higher in the AI lineage than in the AII and B lineages. Demographic expansion was detected in all three lineages.
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Affiliation(s)
- W Babik
- Institute of Zoology, Jagiellonian University, Ingardena 6, 30-060 Kraków, Poland.
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Crawford AJ. Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Mol Ecol 2003; 12:2525-40. [PMID: 12969459 DOI: 10.1046/j.1365-294x.2003.01910.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Molecular genetic data were used to investigate population sizes and ages of Eleutherodactylus (Anura: Leptodactylidae), a species-rich group of small leaf-litter frogs endemic to Central America. Population genetic structure and divergence was investigated for four closely related species surveyed across nine localities in Costa Rica and Panama. DNA sequence data were collected from a mitochondrial gene (ND2) and a nuclear gene (c-myc). Phylogenetic analyses yielded concordant results between loci, with reciprocal monophyly of mitochondrial DNA haplotypes for all species and of c-myc haplotypes for three of the four species. Estimates of genetic differentiation among populations (FST) based upon mitochondrial data were always higher than nuclear-based FST estimates, even after correcting for the expected fourfold lower effective population size (Ne) of the mitochondrial genome. Comparing within-population variation and the relative mutation rates of the two genes revealed that the Ne of the mitochondrial genome was 15-fold lower than the estimate of the nuclear genome based on c-myc. Nuclear FST estimates were approximately 0 for the most proximal pairs of populations, but ranged from 0.5 to 1.0 for all other pairs, even within the same nominal species. The nuclear locus yielded estimates of Ne within localities on the order of 105. This value is two to three orders of magnitude larger than any previous Ne estimate from frogs, but is nonetheless consistent with published demographic data. Applying a molecular clock model suggested that morphologically indistinguishable populations within one species may be 107 years old. These results demonstrate that even a geologically young and dynamic region of the tropics can support very old lineages that harbour great levels of genetic diversity within populations. The association of high nucleotide diversity within populations, large divergence between populations, and high species diversity is also discussed in light of neutral community models.
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Affiliation(s)
- A J Crawford
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA.
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Veith M, Schmidtler JF, Kosuch J, Baran I, Seitz A. Palaeoclimatic changes explain Anatolian mountain frog evolution: a test for alternating vicariance and dispersal events. Mol Ecol 2003; 12:185-99. [PMID: 12492887 DOI: 10.1046/j.1365-294x.2003.01714.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Holarctic biodiversity has been influenced by climatic fluctuations since the Pliocene. Asia Minor was one of the major corridors for postglacial invasions in the Palearctic. Today this area is characterized by an extraordinarily rich fauna with close affiliation to European, Asian and Indo-African biota. However, exact scenarios of range expansion and contraction are lacking. Using a phylogeographical approach we (i). identify monophyletic lineages among Anatolian mountain frogs and (ii). derive a spatio-temporal hypothesis for the invasion process in Anatolia. We sequenced 540 bp of the mitochondrial 16S rRNA gene from 40 populations of mountain frogs from Anatolia, the Elburz Mountains and the Caucasus. Our samples comprise all known species and subspecies: Rana macrocnemis macrocnemis, R. m. tavasensis, R. m. pseudodalmatina, R. camerani and R. holtzi. They include the type localities of four of these taxa. We used a nested clade analysis (NCA) to infer historical and recurrent events that account for the observed geographical distribution of haplotypes. None of the extant species is monophyletic. Based on a molecular clock calibration using homologous sequences of Western Palearctic water frogs of the same genus, we estimated that a basic radiation into three lineages c. 2 Mya was followed by several dispersal and fragmentation events. The geographical distribution of resident and widespread haplotypes allows us to infer and date scenarios of range expansion and fragmentation that are aligned with dramatic climatic oscillations that have occurred during the last 600000 years. Consequently, Pliocene and Pleistocene climatic oscillations triggered the evolution of Anatolian mountain frogs through an interplay of vicariance and dispersal events.
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Affiliation(s)
- M Veith
- Institut für Zoologie, Universität Mainz, Saarstrasse 21, D-55099 Mainz, Germany.
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