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Molecular phylogeography and population genetic structure of an endangered species Pachyhynobius shangchengensis (hynobiid Salamander) in a fragmented habitat of southeastern China. PLoS One 2013; 8:e78064. [PMID: 24205092 PMCID: PMC3799735 DOI: 10.1371/journal.pone.0078064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/16/2013] [Indexed: 11/26/2022] Open
Abstract
The salamander Pachyhynobius shangchengensis (Hynobiidae) is a vulnerable species restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes in the Mount Dabieshan region in southeastern China. However, molecular phylogeography and population genetic structure of P. shangchengensis remain poorly investigated. In this study, we explored the genetic structure and phylogeography of P. shangchengensis based on partial sequences of the mitochondrial DNA (mtDNA) cytochrome b and cytochrome c oxidase subunit I genes. Fifty-one haplotypes and four clades were found among 93 samples. Phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographic regions separated by complicated topography and long distances. The distinct geographic distributions of all lineages and the estimated divergence time suggest spatial and temporal separation coinciding with climatic changes during the Pleistocene. Analysis of molecular variance indicated that most of the observed genetic variation occurred among the four groups, implying long-term interruption of gene flow, and the possible separation of P. shangchengensis into four management units for conservation.
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Tobler U, Garner TWJ, Schmidt BR. Genetic attributes of midwife toad (Alytes obstetricans) populations do not correlate with degree of species decline. Ecol Evol 2013; 3:2806-19. [PMID: 24101974 PMCID: PMC3790531 DOI: 10.1002/ece3.677] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 05/27/2013] [Accepted: 06/11/2013] [Indexed: 11/10/2022] Open
Abstract
Genetic diversity is crucial for long-term population persistence. Population loss and subsequent reduction in migration rate among the most important processes that are expected to lead to a reduction in genetic diversity and an increase in genetic differentiation. While the theory behind this is well-developed, empirical evidence from wild populations is inconsistent. Using microsatellite markers, we compared the genetic structure of populations of an amphibian species, the midwife toad (Alytes obstetricans), in four Swiss regions where the species has suffered variable levels of subpopulation extirpation. We also quantified the effects of several geographic factors on genetic structure and used a model selection approach to ascertain which of the variables were important for explaining genetic variation. Although subpopulation pairwise F ST-values were highly significant even over small geographic scales, neither any of the geographic variables nor loss of subpopulations were important factors for predicting spatial genetic structure. The absence of a signature of subpopulation loss on genetic differentiation may suggest that midwife toad subpopulations function as relatively independent units.
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Affiliation(s)
- Ursina Tobler
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich Winterthurerstrasse 190, CH-8057, Zurich, Switzerland ; KARCH Passage Maximilien-de-Meuron 6, CH-2000, Neuchâtel, Switzerland
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53
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Jennings RM, Etter RJ, Ficarra L. Population differentiation and species formation in the deep sea: the potential role of environmental gradients and depth. PLoS One 2013; 8:e77594. [PMID: 24098590 PMCID: PMC3788136 DOI: 10.1371/journal.pone.0077594] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022] Open
Abstract
Ecological speciation probably plays a more prominent role in diversification than previously thought, particularly in marine ecosystems where dispersal potential is great and where few obvious barriers to gene flow exist. This may be especially true in the deep sea where allopatric speciation seems insufficient to account for the rich and largely endemic fauna. Ecologically driven population differentiation and speciation are likely to be most prevalent along environmental gradients, such as those attending changes in depth. We quantified patterns of genetic variation along a depth gradient (1600-3800m) in the western North Atlantic for a protobranch bivalve (Nuculaatacellana) to test for population divergence. Multilocus analyses indicated a sharp discontinuity across a narrow depth range, with extremely low gene flow inferred between shallow and deep populations for thousands of generations. Phylogeographical discordance occurred between nuclear and mitochondrial loci as might be expected during the early stages of species formation. Because the geographic distance between divergent populations is small and no obvious dispersal barriers exist in this region, we suggest the divergence might reflect ecologically driven selection mediated by environmental correlates of the depth gradient. As inferred for numerous shallow-water species, environmental gradients that parallel changes in depth may play a key role in the genesis and adaptive radiation of the deep-water fauna.
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Affiliation(s)
- Robert M. Jennings
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Ron J. Etter
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Lynn Ficarra
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
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54
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Francuski L, Ludoški J, Milankov V. Phenotypic Diversity and Landscape Genetics ofEristalis tenaxin a Spatially Heterogeneous Environment, Durmitor Mountain (Montenegro). ANN ZOOL FENN 2013. [DOI: 10.5735/085.050.0502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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55
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Genetic diversity and structure of an endemic and critically endangered stream river salamander (Caudata: Ambystoma leorae) in Mexico. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0520-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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56
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Herrera-Arroyo ML, Sork VL, González-Rodríguez A, Rocha-Ramírez V, Vega E, Oyama K. Seed-mediated connectivity among fragmented populations of Quercus castanea (Fagaceae) in a Mexican landscape. AMERICAN JOURNAL OF BOTANY 2013; 100:1663-1671. [PMID: 23942083 DOI: 10.3732/ajb.1200396] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF STUDY Anthropogenic fragmentation is an ongoing process in many forested areas that may create loss of connectivity among tree populations and constitutes a serious threat to ecological and genetic processes. We tested the central hypothesis that seed dispersal mitigates the impact of fragmentation by comparing connectivity and genetic diversity of adult vs. seedling populations in recently fragmented populations of the Mexican red oak Quercus castanea. METHODS Adult individuals, established before fragmentation, and seedlings, established after fragmentation, were sampled at 33 forest fragments of variable size (0.2 to 294 ha) within the Cuitzeo basin, Michoacán state, and genotyped using seven highly polymorphic chloroplast microsatellite markers (cpSSRs). To test whether seed dispersal retains connectivity among fragmented populations, we compared genetic diversity and connectivity networks between adults and progeny and determined the effect of fragment size on these values. KEY RESULTS Seventy haplotypes were identified, 63 in the adults and 60 in the seedlings, with average within-population diversity (hS) values of 0.624 in the adults and 0.630 in the seedlings. A positive correlation of genetic diversity values with fragment size was found in the seedling populations but not in the adult populations. The network connectivity analysis revealed lower connectivity among seedling populations than among adults. The number of connections (edges) as well as other network properties, such as betweenness centrality, node degree and closeness, were significantly lower in the seedlings network. CONCLUSIONS Habitat fragmentation in this landscape is disrupting seed-dispersal-mediated genetic connectivity among extant populations.
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Affiliation(s)
- M Luisa Herrera-Arroyo
- Centro de Investigaciones en Ecosistemas. Universidad Nacional Autónoma de México UNAM, Antigua carretera a Pátzcuaro no. 8701, Col. Ex-hacienda San José de la Huerta, Morelia 58190 Michoacán, México
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57
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Gabrielsen CG, Kovach AI, Babbitt KJ, McDowell WH. Limited effects of suburbanization on the genetic structure of an abundant vernal pool-breeding amphibian. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0497-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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58
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Muir AP, Thomas R, Biek R, Mable BK. Using genetic variation to infer associations with climate in the common frog, Rana temporaria. Mol Ecol 2013; 22:3737-51. [PMID: 23692266 DOI: 10.1111/mec.12334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 03/28/2013] [Accepted: 03/31/2013] [Indexed: 02/01/2023]
Abstract
Recent and historical species' associations with climate can be inferred using molecular markers. This knowledge of population and species-level responses to climatic variables can then be used to predict the potential consequences of ongoing climate change. The aim of this study was to predict responses of Rana temporaria to environmental change in Scotland by inferring historical and contemporary patterns of gene flow in relation to current variation in local thermal conditions. We first inferred colonization patterns within Europe following the last glacial maximum by combining new and previously published mitochondrial DNA sequences. We found that sequences from our Scottish samples were identical to (92%), or clustered with, the common haplotype previously identified from Western Europe. This clade showed very low mitochondrial variation, which did not allow inference of historical colonization routes but did allow interpretation of patterns of current fine-scale population structure without consideration of confounding historical variation. Second, we assessed fine-scale microsatellite-based patterns of genetic variation in relation to current altitudinal temperature gradients. No population structure was found within altitudinal gradients (average FST=0.02), despite a mean annual temperature difference of 4.5 °C between low- and high-altitude sites. Levels of genetic diversity were considerable and did not vary between sites. The panmictic population structure observed, even along temperature gradients, is a potentially positive sign for R. temporaria persistence in Scotland in the face of a changing climate. This study demonstrates that within taxonomic groups, thought to be at high risk from environmental change, levels of vulnerability can vary, even within species.
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Affiliation(s)
- A P Muir
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
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59
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Richmond JQ, Barr KR, Backlin AR, Vandergast AG, Fisher RN. Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog ( Rana draytonii). Evol Appl 2013; 6:808-822. [PMID: 29387167 PMCID: PMC5779129 DOI: 10.1111/eva.12067] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 02/25/2013] [Indexed: 12/01/2022] Open
Abstract
Populations forming the edge of a species range are often imperiled by isolation and low genetic diversity, with proximity to human population centers being a major determinant of edge stability in modern landscapes. Since the 1960s, the California red‐legged frog (Rana draytonii) has undergone extensive declines in heavily urbanized southern California, where the range edge has rapidly contracted northward while shifting its cardinal orientation to an east‐west trending axis. We studied the genetic structure and diversity of these frontline populations, tested for signatures of contemporary disturbance, specifically fire, and attempted to disentangle these signals from demographic events extending deeper into the past. Consistent with the genetic expectations of the ‘abundant‐center’ model, we found that diversity, admixture, and opportunity for random mating increases in populations sampled successively further away from the range boundary. Demographic simulations indicate that bottlenecks in peripheral isolates are associated with processes extending tens to a few hundred generations in the past, despite the demographic collapse of some due to recent fire‐flood events. While the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.
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Affiliation(s)
| | - Kelly R Barr
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Adam R Backlin
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Amy G Vandergast
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Robert N Fisher
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
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60
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Hossack BR, Lowe WH, Honeycutt RK, Parks SA, Corn PS. Interactive effects of wildfire, forest management, and isolation on amphibian and parasite abundance. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2013; 23:479-492. [PMID: 23634596 DOI: 10.1890/12-0316.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Projected increases in wildfire and other climate-driven disturbances will affect populations and communities worldwide, including host-parasite relationships. Research in temperate forests has shown that wildfire can negatively affect amphibians, but this research has occurred primarily outside of managed landscapes where interactions with human disturbances could result in additive or synergistic effects. Furthermore, parasites represent a large component of biodiversity and can affect host fitness and population dynamics, yet they are rarely included in studies of how vertebrate hosts respond to disturbance. To determine how wildfire affects amphibians and their parasites, and whether effects differ between protected and managed landscapes, we compared abundance of two amphibians and two nematodes relative to wildfire extent and severity around wetlands in neighboring protected and managed forests (Montana, USA). Population sizes of adult, male long-toed salamanders (Ambystoma macrodactylum) decreased with increased burn severity, with stronger negative effects on isolated populations and in managed forests. In contrast, breeding population sizes of Columbia spotted frogs (Rana luteiventris) increased with burn extent in both protected and managed protected forests. Path analysis showed that the effects of wildfire on the two species of nematodes were consistent with differences in their life history and transmission strategies and the responses of their hosts. Burn severity indirectly reduced abundance of soil-transmitted Cosmocercoides variabilis through reductions in salamander abundance. Burn severity also directly reduced C. variabilis abundance, possibly though changes in soil conditions. For the aquatically transmitted nematode Gyrinicola batrachiensis, the positive effect of burn extent on density of Columbia spotted frog larvae indirectly increased parasite abundance. Our results show that effects of wildfire on amphibians depend upon burn extent and severity, isolation, and prior land use. Through subsequent effects on the parasites, our results also reveal how changes in disturbance regimes can affect communities across trophic levels.
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Affiliation(s)
- Blake R Hossack
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Aldo Leopold Wilderness Research Institute, 790 East Beckwith Avenue, Missoula, Montana 59801, USA.
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61
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Koen EL, Bowman J, Garroway CJ, Wilson PJ. The sensitivity of genetic connectivity measures to unsampled and under-sampled sites. PLoS One 2013; 8:e56204. [PMID: 23409155 PMCID: PMC3568052 DOI: 10.1371/journal.pone.0056204] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/09/2013] [Indexed: 12/01/2022] Open
Abstract
Landscape genetic analyses assess the influence of landscape structure on genetic differentiation. It is rarely possible to collect genetic samples from all individuals on the landscape and thus it is important to assess the sensitivity of landscape genetic analyses to the effects of unsampled and under-sampled sites. Network-based measures of genetic distance, such as conditional genetic distance (cGD), might be particularly sensitive to sampling intensity because pairwise estimates are relative to the entire network. We addressed this question by subsampling microsatellite data from two empirical datasets. We found that pairwise estimates of cGD were sensitive to both unsampled and under-sampled sites, and FST, Dest, and deucl were more sensitive to under-sampled than unsampled sites. We found that the rank order of cGD was also sensitive to unsampled and under-sampled sites, but not enough to affect the outcome of Mantel tests for isolation by distance. We simulated isolation by resistance and found that although cGD estimates were sensitive to unsampled sites, by increasing the number of sites sampled the accuracy of conclusions drawn from landscape genetic analyses increased, a feature that is not possible with pairwise estimates of genetic differentiation such as FST, Dest, and deucl. We suggest that users of cGD assess the sensitivity of this measure by subsampling within their own network and use caution when making extrapolations beyond their sampled network.
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Affiliation(s)
- Erin L Koen
- Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada.
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62
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Albert EM, Fortuna MA, Godoy JA, Bascompte J. Assessing the robustness of networks of spatial genetic variation. Ecol Lett 2013; 16 Suppl 1:86-93. [PMID: 23294521 DOI: 10.1111/ele.12061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/19/2012] [Accepted: 12/01/2012] [Indexed: 11/27/2022]
Abstract
Habitat transformation is one of the leading drivers of biodiversity loss. The ecological effects of this transformation have mainly been addressed at the demographic level, for example, finding extinction thresholds. However, interpopulation genetic variability and the subsequent potential for adaptation can be eroded before effects are noticed on species abundances. To what degree this is the case has been difficult to evaluate, partly because of the lack of both spatially extended genetic data and an appropriate framework to map and analyse such data. Here, we extend recent work on the analysis of networks of spatial genetic variation to address the robustness of these networks in the face of perturbations. We illustrate the potential of this framework using the case study of an amphibian metapopulation. Our results show that while the disappearance of some spatial sites barely changes the modular structure of the genetic network, other sites have a much stronger effect. Interestingly, these consequences can not be anticipated using topological, static measures. Mapping these networks of spatial genetic variation will allow identifying significant evolutionary units and how they vanish, merge and reorganise following perturbations.
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Affiliation(s)
- Eva M Albert
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Américo Vespucio s/n, E-41092, Sevilla, Spain
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63
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Krueger-Hadfield SA, Roze D, Mauger S, Valero M. Intergametophytic selfing and microgeographic genetic structure shape populations of the intertidal red seaweedChondrus crispus. Mol Ecol 2013; 22:3242-60. [DOI: 10.1111/mec.12191] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 11/27/2012] [Accepted: 11/29/2012] [Indexed: 12/28/2022]
Affiliation(s)
- S. A. Krueger-Hadfield
- UPMC Univ Paris 06; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- CNRS; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- Departamento de Ecología; Facultad de Ciencias Biológicas; Center for Advanced Studies in Ecology and Biodiversity; Pontificia Universidad Católica de Chile; 6513677 Santiago Chile
| | - D. Roze
- UPMC Univ Paris 06; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- CNRS; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
| | - S. Mauger
- UPMC Univ Paris 06; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- CNRS; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
| | - M. Valero
- UPMC Univ Paris 06; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- CNRS; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
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64
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Terrestrial Movement Patterns of the Common Toad (Bufo bufo) in Central Spain Reveal Habitat of Conservation Importance. J HERPETOL 2012. [DOI: 10.1670/11-012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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65
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Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
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66
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Peterman WE, Connette GM, Spatola BN, Eggert LS, Semlitsch RD. Identification of Polymorphic Loci in Ambystoma annulatum and Review of Cross-species Microsatellite Use in the Genus Ambystoma. COPEIA 2012. [DOI: 10.1643/ch-11-001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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67
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Population structure and landscape genetics of two endangered frog species of genus Odorrana: different scenarios on two islands. Heredity (Edinb) 2012; 110:46-56. [PMID: 22990312 DOI: 10.1038/hdy.2012.59] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Isolation by distance and landscape connectivity are fundamental factors underlying speciation and evolution. To understand how landscapes affect gene flow and shape population structures, island species provide intrinsic study objects. We investigated the effects of landscapes on the population structure of the endangered frog species, Odorrana ishikawae and O. splendida, which each inhabit an island in southwest Japan. This was done by examining population structure, gene flow and demographic history of each species by analyzing 12 microsatellite loci and exploring causal environmental factors through ecological niche modeling (ENM) and the cost-distance approach. Our results revealed that the limited gene flow and multiple-population structure in O. splendida and the single-population structure in O. ishikawae were maintained after divergence of the species through ancient vicariance between islands. We found that genetic distance correlated with geographic distance between populations of both species. Our landscape genetic analysis revealed that the connectivity of suitable habitats influences gene flow and leads to the formation of specific population structures. In particular, different degrees of topographical complexity between islands are the major determining factor for shaping contrasting population structures of two species. In conclusion, our results illustrate the diversification mechanism of organisms through the interaction with space and environment. Our results also present an ENM approach for identifying the key factors affecting demographic history and population structures of target species, especially endangered species.
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68
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Messmer V, Jones GP, Munday PL, Planes S. CONCORDANCE BETWEEN GENETIC AND SPECIES DIVERSITY IN CORAL REEF FISHES ACROSS THE PACIFIC OCEAN BIODIVERSITY GRADIENT. Evolution 2012. [DOI: 10.1111/j.1558-5646.2012.01725.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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69
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Richardson JL. Divergent landscape effects on population connectivity in two co-occurring amphibian species. Mol Ecol 2012; 21:4437-51. [PMID: 22891686 DOI: 10.1111/j.1365-294x.2012.05708.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The physical and environmental attributes of landscapes often shape patterns of population connectivity by influencing dispersal and gene flow. Landscape effects on movement are typically evaluated for single species. However, inferences from multiple species are required for multi-species management strategies increasingly being applied in conservation. In this study, I compared the spatial genetic patterns of two amphibian species across the northeastern United States and estimated the influence of specific landscape features on the observed genetic structure. The spotted salamander (Ambystoma maculatum) and wood frog (Rana sylvatica) share many ecological attributes related to habitat use, phenology and site fidelity. However, I hypothesized that important differences in their movement patterns and life history would create distinct genetic patterns for each species. Using 14 microsatellite loci, I tested for differences in the level of genetic differentiation between the two species across 22 breeding ponds. The effects of eight landscape features were also estimated by evaluating 32 landscape resistance models. Spotted salamanders exhibited significantly higher genetic differentiation than wood frogs. Different landscape features were also identified as potential drivers of the genetic patterns in each species, with little overlap in model support between species. Collectively, these results provide strong evidence that these two amphibian species interact with the landscape in measurably different ways. The distinct genetic patterns observed are consistent with key differences in movement ability and life history between A. maculatum and R. sylvatica. These results highlight the importance of considering more than one species when assessing the impacts of the landscape matrix on population connectivity, even for ecologically similar species within the same habitats.
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Affiliation(s)
- Jonathan L Richardson
- School of Forestry & Environmental Studies, Yale University, New Haven, CT 06511, USA.
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70
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Oromi N, Richter-Boix A, Sanuy D, Fibla J. Genetic variability in geographic populations of the natterjack toad (Bufo calamita). Ecol Evol 2012; 2:2018-26. [PMID: 22957202 PMCID: PMC3434004 DOI: 10.1002/ece3.323] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 06/04/2012] [Accepted: 06/08/2012] [Indexed: 11/17/2022] Open
Abstract
Across altitudinal and latitudinal gradients, the proportion of suitable habitats varies, influencing the individual dispersal that ultimately can produce differentiation among populations. The natterjack toad (Bufo calamita) is distributed across a wide geographic range that qualifies the species as interesting for a geographic analysis of its genetic variability. Five populations of B. calamita in the Sierra de Gredos (Spain) were studied in an altitudinal gradient ranging from 750 to 2270 m using microsatellite markers. In addition, we analyzed the latitudinal genetic variation in B. calamita within a global European distribution using genetic diversity parameters (mean number of alleles per locus [Ma] and expected heterozygosity [HE]) obtained from our results and those published in the literature. The low level of genetic differentiation found between populations of B. calamita (Fst ranging from 0.0115 to 0.1018) and the decreases in genetic diversity with altitude (Ma from 13.6 to 8.3, HE from 0.82 to 0.74) can be interpreted by the combined effects of discontinuous habitat, produced mainly by the high slopes barriers and geographic distance. In the latitudinal gradient, genetic diversity decreases from south to north as a consequence of the colonization of the species from the Pleistocene refugium. We conclude that the genetic variability in B. calamita along its wide altitudinal and latitudinal geographic distribution mainly reflects the colonization history of the species after the last glacial period.
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71
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Dudaniec RY, Spear SF, Richardson JS, Storfer A. Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations. PLoS One 2012; 7:e36769. [PMID: 22590604 PMCID: PMC3349670 DOI: 10.1371/journal.pone.0036769] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 04/12/2012] [Indexed: 11/18/2022] Open
Abstract
With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus) in two core regions (Washington State, United States) versus the species' northern peripheral region (British Columbia, Canada) where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a ‘flat’ landscape), but at the periphery, topography (slope and elevation) had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management.
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Affiliation(s)
- Rachael Y Dudaniec
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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72
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Hether TD, Hoffman EA. Machine learning identifies specific habitats associated with genetic connectivity in Hyla squirella. J Evol Biol 2012; 25:1039-52. [PMID: 22487242 DOI: 10.1111/j.1420-9101.2012.02497.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The goal of this study was to identify and differentiate the influence of multiple habitat types that span a spectrum of suitability for Hyla squirella, a widespread frog species that occurs in a broad range of habitat types. We collected microsatellite data from 675 samples representing 20 localities from the southeastern USA and used machine-learning methodologies to identify significant habitat features associated with genetic structure. In simulation, we confirm that our machine-learning algorithm can successfully identify landscape features responsible for generating between-population genetic differentiation, suggesting that it can be a useful hypothesis-generating tool for landscape genetics. In our study system, we found that H. squirella were spatially structured and models including specific habitat types (i.e. upland oak forest and urbanization) consistently explained more variation in genetic distance (median pR(2) = 47.78) than spatial distance alone (median pR(2) = 23.81). Moreover, we estimate the relative importance that spatial distance, upland oak and urbanized habitat have in explaining genetic structure of H. squirella. We discuss how these habitat types may mechanistically facilitate dispersal in H. squirella. This study provides empirical support for the hypothesis that habitat-use can be an informative correlate of genetic differentiation, even for species that occur in a wide range of habitats.
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Affiliation(s)
- T D Hether
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA
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73
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Spear SF, Crisafulli CM, Storfer A. Genetic structure among coastal tailed frog populations at Mount St. Helens is moderated by post-disturbance management. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2012; 22:856-869. [PMID: 22645816 DOI: 10.1890/11-0627.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Catastrophic disturbances often provide "natural laboratories" that allow for greater understanding of ecological processes and response of natural populations. The 1980 eruption of the Mount St. Helens volcano in Washington, USA, provided a unique opportunity to test biotic effects of a large-scale stochastic disturbance, as well as the influence of post-disturbance management. Despite severe alteration of nearly 600 km2 of habitat, coastal tailed frogs (Ascaphus truei) were found within a portion of the blast area five years after eruption. We investigated the genetic source of recolonization within the blast area and tested whether post-eruption salvage logging and subsequent tree planting influenced tailed frog movement patterns. Our results support widespread recolonization across the blast area from multiple sources, as all sites are grouped into one genetic cluster. Landscape genetic models suggest that gene flow through the unmanaged portion of the blast area is influenced only by distance between sites and the frost-free period (r2 = 0.74). In contrast, gene flow pathways within the blast area where salvage logging and replanting occurred post-eruption are strongly limited (r2 = 0.83) by the physiologically important variables of heat load and precipitation. These data suggest that the lack of understory and coarse wood (downed and standing dead tree boles) refugia in salvaged areas may leave frogs more susceptible to desiccation and mortality than those frogs moving through the naturally regenerated area. Simulated populations based on the landscape genetic models show an increase in the inbreeding coefficient in the managed area relative to the unmanaged blast area. In sum, we show surprising resilience of an amphibian species to a catastrophic disturbance, and we suggest that, at least for this species, naturally regenerating habitat may better maintain long-term genetic diversity of populations than actively managed habitat.
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Affiliation(s)
- Stephen F Spear
- The Orianne Society, 579 Highway 441 S, Clayton, Georgia 30525, USA.
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74
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Meister B, Ursenbacher S, Baur B. Grass Snake Population Differentiation over Different Geographic Scales. HERPETOLOGICA 2012. [DOI: 10.1655/herpetologica-d-11-00036.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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75
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Latch EK, Boarman WI, Walde A, Fleischer RC. Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises. PLoS One 2011; 6:e27794. [PMID: 22132143 PMCID: PMC3221657 DOI: 10.1371/journal.pone.0027794] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 10/25/2011] [Indexed: 12/02/2022] Open
Abstract
Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately.
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Affiliation(s)
- Emily K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, United States of America.
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76
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Combining multiple analytical approaches for the identification of population structure and genetic delineation of two subspecies of the endemic Arabian burnet moth Reissita simonyi (Zygaenidae; Lepidoptera). CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0259-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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77
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Phillipsen IC, Funk WC, Hoffman EA, Monsen KJ, Blouin MS. Comparative analyses of effective population size within and among species: ranid frogs as a case study. Evolution 2011; 65:2927-45. [PMID: 21967433 DOI: 10.1111/j.1558-5646.2011.01356.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
It has recently become practicable to estimate the effective sizes (N(e) ) of multiple populations within species. Such efforts are valuable for estimating N(e) in evolutionary modeling and conservation planning. We used microsatellite loci to estimate N(e) of 90 populations of four ranid frog species (20-26 populations per species, mean n per population = 29). Our objectives were to determine typical values of N(e) for populations of each species, compare N(e) estimates among the species, and test for correlations between several geographic variables and N(e) within species. We used single-sample linkage disequilibrium (LD), approximate Bayesian computation (ABC), and sibship assignment (SA) methods to estimate contemporary N(e) for each population. Three of the species-Rana pretiosa, R. luteiventris, and R. cascadae- have consistently small effective population sizes (<50). N(e) in Lithobates pipiens spans a wider range, with some values in the hundreds or thousands. There is a strong east-to-west trend of decreasing N(e) in L. pipiens. The smaller effective sizes of western populations of this species may be related to habitat fragmentation and population bottlenecking.
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Affiliation(s)
- Ivan C Phillipsen
- Department of Zoology, Oregon State University, 3029 Cordley Hall, Corvallis, Oregon 97331-2914, USA.
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78
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Zhang YX, He CZ, Dudgeon D, Zhang ZY, Wang GM. Mountain Ridge and Sea: Geographic-Barrier Effects on Genetic Diversity and Differentiation of the Hong Kong Newt (Paramesotriton hongkongensis) Revealed by AFLP. ANN ZOOL FENN 2011. [DOI: 10.5735/086.048.0204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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79
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Wang IJ, Johnson JR, Johnson BB, Shaffer HB. Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, Ambystoma californiense. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0194-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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80
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RICHTER-BOIX ALEX, QUINTELA MARÍA, SEGELBACHER GERNOT, LAURILA ANSSI. Genetic analysis of differentiation among breeding ponds reveals a candidate gene for local adaptation in Rana arvalis. Mol Ecol 2011; 20:1582-600. [DOI: 10.1111/j.1365-294x.2011.05025.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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81
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Fine-Scale Spatial Genetic Structure and Genetic Diversity among Clouded Salamander (Hynobius nebulosus) Populations. CURRENT HERPETOLOGY 2010. [DOI: 10.3105/018.029.0203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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82
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Savage WK, Fremier AK, Shaffer HB. Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time. Mol Ecol 2010; 19:3301-14. [PMID: 20701683 DOI: 10.1111/j.1365-294x.2010.04718.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Quantifying the influence of the landscape on the genetic structure of natural populations remains an important empirical challenge, particularly for poorly studied, ecologically cryptic species. We conducted an extensive microsatellite analysis to examine the population genetics of the southern long-toed salamander (Ambystoma macrodactylum sigillatum) in a naturally complex landscape. Using spatially explicit modelling, we investigated the influence of the Sierra Nevada topography on potential dispersal corridors between sampled populations. Our results indicate very high-genetic divergence among populations, high within-deme relatedness, and little evidence of recent migration or population admixture. We also discovered unexpectedly high between-year genetic differentiation (F(ST)) for breeding sites, suggesting that breeding groups vary over localized space and time. While environmental factors associated with high-elevation montane habitats apparently play an important role in shaping population differentiation, additional, species-specific biological processes must also be operating to account for observed deviations from temporal, among-year panmixia. Our study emphasizes the population-level insights that can be gained from high-density sampling in space and time, and the highly substructured population biology that may characterize amphibians in extreme montane habitats.
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Affiliation(s)
- Wesley K Savage
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616-8755, USA.
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83
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Pilliod DS, Hossack BR, Bahls PF, Bull EL, Corn PS, Hokit G, Maxell BA, Munger JC, Wyrick A. Non-native salmonids affect amphibian occupancy at multiple spatial scales. DIVERS DISTRIB 2010. [DOI: 10.1111/j.1472-4642.2010.00699.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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84
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Ferchaud AL, Lyet A, Cheylan M, Arnal V, Baron JP, Montgelard C, Ursenbacher S. High Genetic Differentiation Among French Populations of the Orsini’s Viper (Vipera ursinii ursinii) Based on Mitochondrial and Microsatellite Data: Implications for Conservation Management. J Hered 2010; 102:67-78. [DOI: 10.1093/jhered/esq098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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85
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MEISTER BARBARA, HOFER ULRICH, URSENBACHER SYLVAIN, BAUR BRUNO. Spatial genetic analysis of the grass snake, Natrix natrix (Squamata: Colubridae), in an intensively used agricultural landscape. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01474.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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86
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Abstract
Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.
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Affiliation(s)
- Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
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87
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Murphy MA, Dezzani R, Pilliod DS, Storfer A. Landscape genetics of high mountain frog metapopulations. Mol Ecol 2010; 19:3634-49. [PMID: 20723055 DOI: 10.1111/j.1365-294x.2010.04723.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a powerful new modelling approach for examining a wide range of both basic and applied questions in landscape genetics.
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Affiliation(s)
- Melanie A Murphy
- Biology Department, Colorado State University, Fort Collins, CO 80523, USA.
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88
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Murphy MA, Evans JS, Storfer A. Quantifying Bufo boreas connectivity in Yellowstone National Park with landscape genetics. Ecology 2010; 91:252-61. [PMID: 20380214 DOI: 10.1890/08-0879.1] [Citation(s) in RCA: 314] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A major objective of ecology is to understand how ecological processes limit population connectivity and species' distributions. By spatially quantifying ecological components driving functional connectivity, we can understand why some locally suitable habitats are unoccupied, resulting in observed discontinuities in distribution. However, estimating connectivity may be difficult due to population stochasticity and violations of assumptions of parametric statistics. To address these issues, we present a novel application of Random Forests to landscape genetic data. We address the effects of three key ecological components on Bufo boreas connectivity in Yellowstone National Park: ecological process, scale, and hierarchical organization. Habitat permeability, topographic morphology, and temperature-moisture regime are all significant ecological processes associated with B. boreas connectivity. Connectivity was influenced by growing-season precipitation, 1988 Yellowstone fires, cover, temperature, impervious surfaces (roads and development), and topographic complexity (56% variation explained). We found that habitat permeability generally operates on fine scales, while topographic morphology and temperature-moisture regime operate across multiple scales, thus demonstrating the importance of cross-scale analysis for ecological interpretation. In a hierarchical analysis, we were able to explain more variation within genetic clusters as identified using Structure (a Bayesian algorithm) (74%; dispersal cover, growing-season precipitation, impervious surfaces) as opposed to between genetic clusters (45%; ridgelines, hot, dry slopes, length of hot season, and annual precipitation). Finally, the analytical methods we developed are powerful and can be applied to any species or system with appropriate landscape and genetic data.
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Affiliation(s)
- Melanie A Murphy
- School of Biology, Colorado State University, Fort Collins, Colorado 80524, USA.
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89
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Development and characterization of 13 polymorphic microsatellite DNA markers for the pond green frog (Rana nigromaculata). J Genet 2010. [DOI: 10.1007/s12041-011-0004-y] [Citation(s) in RCA: 2] [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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90
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Inference of population history by coupling exploratory and model-driven phylogeographic analyses. Int J Mol Sci 2010; 11:1190-227. [PMID: 20480016 PMCID: PMC2871112 DOI: 10.3390/ijms11041190] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 11/16/2022] Open
Abstract
Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.
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91
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Chambers JL, Garant D. Determinants of Population Genetic Structure in Eastern Chipmunks (Tamias striatus): The Role of Landscape Barriers and Sex-Biased Dispersal. J Hered 2010; 101:413-22. [DOI: 10.1093/jhered/esq029] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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92
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Dubey S, Shine R. Restricted dispersal and genetic diversity in populations of an endangered montane lizard (Eulamprus leuraensis, Scincidae). Mol Ecol 2010; 19:886-97. [PMID: 20149087 DOI: 10.1111/j.1365-294x.2010.04539.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Many alpine species are under threat from global climate change, as their geographic ranges become increasingly fragmented and unsuitable. Understanding rates and determinants of gene flow among such fragmented populations, over historical as well as recent timescales, can help to identify populations under threat. It is also important to clarify the degree to which loss of local populations reduces overall genetic diversity within the taxon. The endangered Blue Mountains Water Skink (Eulamprus leuraensis) is restricted to <40 small swamps in montane south-eastern Australia. Our analyses of seven microsatellite loci of 241 animals from 13 populations show strong geographic structure, with major genetic divergence even between populations separated by <0.5 km. Dispersal between populations is scarce, and appears to involve mostly males. Our analyses suggest potential recent bottleneck events in all the identified populations, and lower genetic diversity and population size parameter at lower-elevation sites than at higher-elevation sites. Management of this endangered taxon thus needs to treat most populations separately, because of their genetic distinctiveness and low rates of genetic exchange.
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Affiliation(s)
- S Dubey
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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93
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GOLDBERG CARENS, WAITS LISETTEP. Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure. Mol Ecol Resour 2010; 10:304-13. [DOI: 10.1111/j.1755-0998.2009.02755.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- CAREN S. GOLDBERG
- Department of Fish and Wildlife Resources, University of Idaho, Moscow, ID 83844‐1136, USA
| | - LISETTE P. WAITS
- Department of Fish and Wildlife Resources, University of Idaho, Moscow, ID 83844‐1136, USA
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94
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WANG IANJ, SUMMERS KYLE. Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog. Mol Ecol 2010; 19:447-58. [DOI: 10.1111/j.1365-294x.2009.04465.x] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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95
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Pearson KJ, Goater CP. Effects of predaceous and nonpredaceous introduced fish on the survival, growth, and antipredation behaviours of long-toed salamanders. CAN J ZOOL 2009. [DOI: 10.1139/z09-084] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Simultaneous introduction of complex suites of exotic organisms into indigenous populations have poorly known magnitudes and consequences. We compared the effects of introduced piscivorous rainbow trout ( Oncorhynchus mykiss (Walbaum, 1792)) and nonpiscivorous fathead minnows ( Pimephales promelas Rafinesque, 1820) on growth, survival, susceptibility to predation, and antipredator behaviours of naïve long-toed salamanders ( Ambystoma macrodactylum Baird, 1850). Trout reduced salamander hatchling and larvae survival to nearly zero in predation trials and caused a 39% reduction in salamander survival within outdoor mesocosms. Salamander larvae did not increase their refuge use or alter activity patterns in the presence of trout. These results imply that allotopic distributions of trout and salamanders observed in several field surveys likely result from the inability of larvae to recognize introduced predators as a threat. Minnows also caused significant reductions in salamander survival (41%) and growth (37%) in mesocosms, and exposure to minnow cues caused larvae to spend more time within a refuge. Reduced salamander survivorship and growth in the mesocosms was likely due to competition for limiting zooplankton and (or) cannibalism. These results indicate that introductions of small-bodied, nonpiscivorous fishes can reduce amphibian survival and growth to at least the same extent as introduced trout.
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Affiliation(s)
- K. J. Pearson
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - C. P. Goater
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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96
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Richards-Zawacki CL. Effects of slope and riparian habitat connectivity on gene flow in an endangered Panamanian frog,Atelopus varius. DIVERS DISTRIB 2009. [DOI: 10.1111/j.1472-4642.2009.00582.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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97
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FUNK WC, CANNATELLA DC, RYAN MJ. Genetic divergence is more tightly related to call variation than landscape features in the Amazonian frogsPhysalaemus petersiandP. freibergi. J Evol Biol 2009; 22:1839-53. [DOI: 10.1111/j.1420-9101.2009.01795.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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98
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Chan LM, Zamudio KR. Population differentiation of temperate amphibians in unpredictable environments. Mol Ecol 2009; 18:3185-200. [PMID: 19573030 DOI: 10.1111/j.1365-294x.2009.04273.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Amphibians are a globally distributed and diverse lineage, but much of our current understanding of their population genetic structure comes from studies in mesic temperate habitats. We characterize the population genetic structure of two sympatric explosive breeding amphibians in the southwestern deserts of the United States: the Great Plains toad (Anaxyrus cognatus) and Couch's spadefoot toad (Scaphiopus couchii). For both species, we find limited genetic differentiation even between populations in adjacent valleys separated by dispersal barriers such as mountainous habitats. To understand how population genetic patterns in these two arid-adapted species compare to taxa in more mesic environments, we computed a standardized measure of population differentiation for A. cognatus, S. couchii, and for pond-breeding amphibians that inhabit mesic temperate environments. Our results indicate that the arid-adapted species have lower population genetic structure at fine and moderate scales than most other amphibian species we surveyed. We hypothesize that stochasticity in the availability of appropriate breeding sites as well as landscape homogeneity may result in increased population connectivity in desert-adapted frogs. Future work examining fine-scale population structure in amphibians from a diversity of habitats will test the generality of our findings. Intraspecific comparisons among localities with varied seasonality and habitats will be particularly useful for investigating the interaction between species-typical population dynamics and environmental characteristics as determinants of population connectivity in pond-breeding amphibians.
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Affiliation(s)
- Lauren M Chan
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY 14853-2701, USA.
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99
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Wang IJ, Savage WK, Shaffer HB. Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense). Mol Ecol 2009; 18:1365-74. [PMID: 19368644 DOI: 10.1111/j.1365-294x.2009.04122.x] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A major goal of landscape genetics is to understand how landscapes structure genetic variation in natural populations. However, landscape genetics still lacks a framework for quantifying the effects of landscape features, such as habitat type, on realized gene flow. Here, we present a methodology for identifying the costs of dispersal through different habitats for the California tiger salamander (Ambystoma californiense), an endangered species restricted to grassland/vernal pool habitat mosaics. We sampled larvae from all 16 breeding ponds in a geographically restricted area of vernal pool habitat at the Fort Ord Natural Reserve, Monterey County, California. We estimated between-pond gene flow using 13 polymorphic microsatellite loci and constructed GIS data layers of habitat types in our study area. We then used least-cost path analysis to determine the relative costs of movement through each habitat that best match rates of gene flow measured by our genetic data. We identified four measurable rates of gene flow between pairs of ponds, with between 10.5% and 19.9% of larvae having immigrant ancestry. Although A. californiense is typically associated with breeding ponds in grassland habitat, we found that dispersal through grassland is nearly twice as costly as dispersal through chaparral and that oak woodland is by far the most costly habitat to traverse. With the increasing availability of molecular resources and GIS data, we anticipate that these methods could be applied to a broad range of study systems, particularly those with cryptic life histories that make direct observation of movement challenging.
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Affiliation(s)
- Ian J Wang
- Department of Evolution and Ecology and Center for Population Biology, 1 Shields Avenue, University of California, Davis, CA 95616, USA.
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100
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Trénel P, Hansen MM, Normand S, Borchsenius F. Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae). Mol Ecol 2009; 17:3528-40. [PMID: 19160480 DOI: 10.1111/j.1365-294x.2008.03853.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow bands of montane forests on each side of the Andes in Ecuador and northeastern Peru. First, we tested the hypothesis of C. echinulatum being a geographic cline species crossing the Andes in the Amotape-Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross-Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio-genetic patterns. Individual-based Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron-Paute deflection. F-statistics derived from BC suggested an east-to-west dispersal history. Population-based analyses revealed strong genetic structuring at both small and large geographic scales. Interpopulation relationships and Mantel tests strongly supported the cline model with cross-Andean dispersal in the AHZ. Along the cline, gene flow measured as F(ST) was mainly limited by distance, with less but significant impact of climatic friction. Coalescent analysis revealed that cross-Andean divergence took place during the Quaternary. Significant historical isolation (R(ST) > F(ST)) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance and historical isolation on patterns of Andean diversity and distribution.
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Affiliation(s)
- Philipp Trénel
- Department of Biological Sciences, University of Aarhus, Ny Munkegade, Building 1540, DK-8000 Aarhus C, Denmark
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