151
|
Tesson SV, Okamura B, Dudaniec RY, Vyverman W, Löndahl J, Rushing C, Valentini A, Green AJ. Integrating microorganism and macroorganism dispersal: modes, techniques and challenges with particular focus on co-dispersal. ECOSCIENCE 2016. [DOI: 10.1080/11956860.2016.1148458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
152
|
Amaral KE, Palace M, O'Brien KM, Fenderson LE, Kovach AI. Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem. PLoS One 2016; 11:e0148842. [PMID: 26954014 PMCID: PMC4783018 DOI: 10.1371/journal.pone.0148842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/25/2016] [Indexed: 01/15/2023] Open
Abstract
Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists.
Collapse
Affiliation(s)
- Katrina E Amaral
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Michael Palace
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America.,Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Kathleen M O'Brien
- United States Fish and Wildlife Service, Rachel Carson National Wildlife Refuge, Wells, Maine, United States of America
| | - Lindsey E Fenderson
- United States Fish and Wildlife Service, Northeast Fishery Center, Conservation Genetics Lab, Lamar, Pennsylvania, United States of America
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America
| |
Collapse
|
153
|
Carnabuci M, Schiavon G, Bellingeri M, Fossa F, Paoli C, Vassallo P, Gnone G. Connectivity in the network macrostructure of Tursiops truncatus in the Pelagos Sanctuary (NW Mediterranean Sea): does landscape matter? POPUL ECOL 2016. [DOI: 10.1007/s10144-016-0540-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
154
|
Dudaniec RY, Worthington Wilmer J, Hanson JO, Warren M, Bell S, Rhodes JR. Dealing with uncertainty in landscape genetic resistance models: a case of three co-occurring marsupials. Mol Ecol 2016; 25:470-86. [DOI: 10.1111/mec.13482] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/08/2015] [Accepted: 11/10/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Rachael Y. Dudaniec
- Department of Biological Sciences; Macquarie University; Sydney NSW 2109 Australia
| | | | - Jeffrey O. Hanson
- School of Biological Sciences; The University of Queensland; Brisbane Qld 4072 Australia
| | - Matthew Warren
- School of Geography, Planning and Environmental Management; The University of Queensland; Brisbane Qld 4072 Australia
| | - Sarah Bell
- School of Biomedical Sciences; The University of Queensland; Brisbane Qld 4072 Australia
| | - Jonathan R. Rhodes
- School of Geography, Planning and Environmental Management; The University of Queensland; Brisbane Qld 4072 Australia
| |
Collapse
|
155
|
Wu Z, Yu D, Li X, Xu X. Influence of geography and environment on patterns of genetic differentiation in a widespread submerged macrophyte, Eurasian watermilfoil (Myriophyllum spicatum L., Haloragaceae). Ecol Evol 2016; 6:460-8. [PMID: 26843930 PMCID: PMC4729246 DOI: 10.1002/ece3.1882] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 01/16/2023] Open
Abstract
The effects of geographic and environmental variables on the pattern of genetic differentiation have been thoroughly studied, whereas empirical studies on aquatic plants are rare. We examined the spatial genetic differentiation of 58 Myriophyllum spicatum populations distributed throughout China with 12 microsatellite loci, and we analyzed its association with geographic distance, geographic barriers, and environmental dissimilarity using causal modeling and multiple matrix regression with randomization (MMRR) analysis. Two genetic clusters were identified, and their geographic distribution suggested mountain ranges as a barrier to gene flow. The causal modeling revealed that both climate and geographic barriers significantly influenced genetic divergence among M. spicatum populations and that climate had the highest regression coefficient according to the MMRR analysis. This study showed that geography and environment together played roles in shaping the genetic structure of M. spicatum and that the influence of environment was greater. Our findings emphasized the potential importance of the environment in producing population genetic differentiation in aquatic plants at a large geographic scale.
Collapse
Affiliation(s)
- Zhigang Wu
- National Field Station of Freshwater Ecosystem of Liangzi Lake College of Life Sciences Wuhan University Wuhan China
| | - Dan Yu
- National Field Station of Freshwater Ecosystem of Liangzi Lake College of Life Sciences Wuhan University Wuhan China
| | - Xing Li
- National Field Station of Freshwater Ecosystem of Liangzi Lake College of Life Sciences Wuhan University Wuhan China
| | - Xinwei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake College of Life Sciences Wuhan University Wuhan China
| |
Collapse
|
156
|
Harradine EL, Andrew ME, Thomas JW, How RA, Schmitt LH, Spencer PBS. Importance of dispersal routes that minimize open-ocean movement to the genetic structure of island populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1704-1714. [PMID: 26171679 DOI: 10.1111/cobi.12555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/23/2015] [Indexed: 06/04/2023]
Abstract
Islands present a unique scenario in conservation biology, offering refuge yet imposing limitations on insular populations. The Kimberley region of northwestern Australia has more than 2500 islands that have recently come into focus as substantial conservation resources. It is therefore of great interest for managers to understand the driving forces of genetic structure of species within these island archipelagos. We used the ubiquitous bar-shouldered skink (Ctenotus inornatus) as a model species to represent the influence of landscape factors on genetic structure across the Kimberley islands. On 41 islands and 4 mainland locations in a remote area of Australia, we genotyped individuals across 18 nuclear (microsatellite) markers. Measures of genetic differentiation and diversity were used in two complementary analyses. We used circuit theory and Mantel tests to examine the influence of the landscape matrix on population connectivity and linear regression and model selection based on Akaike's information criterion to investigate landscape controls on genetic diversity. Genetic differentiation between islands was best predicted with circuit-theory models that accounted for the large difference in resistance to dispersal between land and ocean. In contrast, straight-line distances were unrelated to either resistance distances or genetic differentiation. Instead, connectivity was determined by island-hopping routes that allow organisms to minimize the distance of difficult ocean passages. Island populations of C. inornatus retained varying degrees of genetic diversity (NA = 1.83 - 7.39), but it was greatest on islands closer to the mainland, in terms of resistance-distance units. In contrast, genetic diversity was unrelated to island size. Our results highlight the potential for islands to contribute to both theoretical and applied conservation, provide strong evidence of the driving forces of population structure within undisturbed landscapes, and identify the islands most valuable for conservation based on their contributions to gene flow and genetic diversity.
Collapse
Affiliation(s)
- E L Harradine
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - M E Andrew
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - J W Thomas
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - R A How
- School of Anatomy, Physiology & Human Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - L H Schmitt
- School of Anatomy, Physiology & Human Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - P B S Spencer
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| |
Collapse
|
157
|
Ferrer ES, García-Navas V, Bueno-Enciso J, Barrientos R, Serrano-Davies E, Cáliz-Campal C, Sanz JJ, Ortego J. The influence of landscape configuration and environment on population genetic structure in a sedentary passerine: insights from loci located in different genomic regions. J Evol Biol 2015; 29:205-19. [DOI: 10.1111/jeb.12776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- E. S. Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - V. García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - J. Bueno-Enciso
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - R. Barrientos
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - E. Serrano-Davies
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - C. Cáliz-Campal
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - J. J. Sanz
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| |
Collapse
|
158
|
Murphy AL, Pavlova A, Thompson R, Davis J, Sunnucks P. Swimming through sand: connectivity of aquatic fauna in deserts. Ecol Evol 2015; 5:5252-5264. [PMID: 30151128 PMCID: PMC6102528 DOI: 10.1002/ece3.1741] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/11/2015] [Accepted: 08/22/2015] [Indexed: 01/15/2023] Open
Abstract
Freshwater ecosystems in arid regions range from highly fragmented to highly connected, and connectivity has been assumed to be a major factor in the persistence of aquatic biota in arid environments. This review sought to synthesize existing research on genetic estimation of population connectivity in desert freshwaters, identify knowledge gaps, and set priorities for future studies of connectivity in these environments. From an extensive literature search, we synthesized the approaches applied, systems studied, and conclusions about connectivity reached in population genetic research concerning desert freshwater connectivity globally. We restrict our scope to obligate aquatic fauna that disperse largely via freshwaters and exclude those with active aerial dispersal abilities. We examined 92 papers, comprising 133 studies, published from 1987 to 2014. Most described studies of fishes and invertebrates in the deserts of Australia and North America. Connectivity declined with increasing scale, but did not differ significantly among arid regions or taxonomic classes. There were significant differences in connectivity patterns between species with different dispersal abilities, and between spring and riverine habitats at local scales. Population connectivity in desert freshwaters is typically most influenced by the ecology of the species concerned and hydrological connectivity. Most studies did not assess predefined models of connectivity, but described gene flow and/or genetic structure. Climate change and anthropogenic impacts worldwide are likely to increase the incidence and impact of habitat fragmentation in already threatened desert freshwaters. To reduce this risk, biodiversity conservation and environmental management must address connectivity, but often the required information does not exist. Researchers can provide this by explicitly considering the effects of hydrology and species' ecology on connectivity, and incorporating these into connectivity models, which are vital for understanding connectivity in desert freshwaters.
Collapse
Affiliation(s)
- Ashley L Murphy
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
| | - Ross Thompson
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory 2617 Australia
| | - Jenny Davis
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory 2617 Australia
| | - Paul Sunnucks
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
| |
Collapse
|
159
|
Razgour O. Beyond species distribution modeling: A landscape genetics approach to investigating range shifts under future climate change. ECOL INFORM 2015. [DOI: 10.1016/j.ecoinf.2015.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
160
|
Wu Z, Yu D, Wang Z, Li X, Xu X. Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient. Sci Rep 2015; 5:15618. [PMID: 26494202 PMCID: PMC4616052 DOI: 10.1038/srep15618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/28/2015] [Indexed: 11/01/2022] Open
Abstract
Understanding how natural processes affect population genetic structures is an important issue in evolutionary biology. One effective method is to assess the relative importance of environmental and geographical factors in the genetic structure of populations. In this study, we examined the spatial genetic variation of thirteen Myriophyllum spicatum populations from the Qinghai-Tibetan Plateau (QTP) and adjacent highlands (Yunnan-Guizhou Plateau, YGP) by using microsatellite loci and environmental and geographical factors. Bioclim layers, hydrological properties and elevation were considered as environmental variables and reduced by principal component analysis. The genetic isolation by geographic distance (IBD) was tested by Mantel tests and the relative importance of environmental variables on population genetic differentiation was determined by a partial Mantel test and multiple matrix regression with randomization (MMRR). Two genetic clusters corresponding to the QTP and YGP were identified. Both tests and MMRR revealed a significant and strong correlation between genetic divergence and geographic isolation under the influence of environmental heterogeneity at the overall and finer spatial scales. Our findings suggested the dominant role of geography on the evolution of M. spicatum under a steep environmental gradient in the alpine landscape as a result of dispersal limitation and genetic drift.
Collapse
Affiliation(s)
- Zhigang Wu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Dan Yu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhong Wang
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xing Li
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xinwei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| |
Collapse
|
161
|
Voigt CC, Kingston T. Responses of Tropical Bats to Habitat Fragmentation, Logging, and Deforestation. BATS IN THE ANTHROPOCENE: CONSERVATION OF BATS IN A CHANGING WORLD 2015. [PMCID: PMC7124148 DOI: 10.1007/978-3-319-25220-9_4] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Land-use change is a key driver of the global biodiversity crisis and a particularly serious threat to tropical biodiversity. Throughout the tropics, the staggering pace of deforestation, logging, and conversion of forested habitat to other land uses has created highly fragmented landscapes that are increasingly dominated by human-modified habitats and degraded forests. In this chapter, we review the responses of tropical bats to a range of land-use change scenarios, focusing on the effects of habitat fragmentation, logging, and conversion of tropical forest to various forms of agricultural production. Recent landscape-scale studies have considerably advanced our understanding of how tropical bats respond to habitat fragmentation and disturbance at the population, ensemble, and assemblage level. This research emphasizes that responses of bats are often species and ensemble specific, sensitive to spatial scale, and strongly molded by the characteristics of the prevailing landscape matrix. Nonetheless, substantial knowledge gaps exist concerning other types of response by bats. Few studies have assessed responses at the genetic, behavioral, or physiological level, with regard to disease prevalence, or the extent to which human disturbance erodes the capacity of tropical bats to provide key ecosystem services. A strong geographic bias, with Asia and, most notably, Africa, being strongly understudied, precludes a comprehensive understanding of the effects of fragmentation and disturbance on tropical bats. We strongly encourage increased research in the Paleotropics and emphasize the need for long-term studies, approaches designed to integrate multiple scales, and answering questions that are key to conserving tropical bats in an era of environmental change and dominance of modified habitats (i.e., the Anthropocene).
Collapse
|
162
|
Clark JD, Laufenberg JS, Davidson M, Murrow JL. Connectivity among subpopulations of louisiana black bears as estimated by a step selection function. J Wildl Manage 2015. [DOI: 10.1002/jwmg.955] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joseph D. Clark
- U.S. Geological Survey; Northern Rocky Mountain Science Center; Southern Appalachian Research Branch; University of Tennessee; 274 Ellington Plant Sciences Building; Knoxville TN 37996 USA
| | - Jared S. Laufenberg
- Department of Forestry; University of Tennessee; Wildlife and Fisheries; 274 Ellington Plant Sciences Building; Knoxville TN 37996 USA
| | - Maria Davidson
- Louisiana Department of Wildlife and Fisheries; P.O. Box 98000; 2000 Quail Dr.; Baton Rouge LA 70898 USA
| | - Jennifer L. Murrow
- Department of Environmental Science and Technology; University of Maryland; 0214 Symons Hall; College Park; MD 20742 USA
| |
Collapse
|
163
|
Thomas L, Kennington WJ, Stat M, Wilkinson SP, Kool JT, Kendrick GA. Isolation by resistance across a complex coral reef seascape. Proc Biol Sci 2015; 282:20151217. [PMID: 26224707 PMCID: PMC4528533 DOI: 10.1098/rspb.2015.1217] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/29/2015] [Indexed: 01/27/2023] Open
Abstract
A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance surface to predict the spatial genetic structure of populations and explain deviations from the widely applied isolation-by-distance model. The majority of seascape approaches to date have been applied to linear coastal systems or at large spatial scales (more than 250 km), with very few applied to complex systems at regional spatial scales (less than 100 km). Here, we apply a seascape genetics approach to a peripheral population of the broadcast-spawning coral Acropora spicifera across the Houtman Abrolhos Islands, a high-latitude complex coral reef system off the central coast of Western Australia. We coupled population genetic data from a panel of microsatellite DNA markers with a biophysical dispersal model to test whether oceanographic processes could explain patterns of genetic divergence. We identified significant variation in allele frequencies over distances of less than 10 km, with significant differentiation occurring between adjacent sites but not between the most geographically distant ones. Recruitment probabilities between sites based on simulated larval dispersal were projected into a measure of resistance to connectivity that was significantly correlated with patterns of genetic divergence, demonstrating that patterns of spatial genetic structure are a function of restrictions to gene flow imposed by oceanographic currents. This study advances our understanding of the role of larval dispersal on the fine-scale genetic structure of coral populations across a complex island system and applies a methodological framework that can be tailored to suit a variety of marine organisms with a range of life-history characteristics.
Collapse
Affiliation(s)
- Luke Thomas
- The UWA Oceans Institute, School of Plant Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - W Jason Kennington
- Centre for Evolutionary Biology, School of Animal Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Johnathan T Kool
- Geoscience Australia, Symonston, Australian Capital Territory 2601, Australia
| | - Gary A Kendrick
- The UWA Oceans Institute, School of Plant Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia
| |
Collapse
|
164
|
Okada A, Ito TY, Buuveibaatar B, Lhagvasuren B, Tsunekawa A. Genetic structure in Mongolian gazelles based on mitochondrial and microsatellite markers. Mamm Biol 2015. [DOI: 10.1016/j.mambio.2015.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
165
|
Vera-Escalona I, Habit E, Ruzzante DE. Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia. Mol Ecol 2015; 24:4112-28. [PMID: 26147523 DOI: 10.1111/mec.13303] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 12/11/2022]
Abstract
Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.
Collapse
Affiliation(s)
- Iván Vera-Escalona
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, Canada
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Barrio Universitario s/n, Concepción, Chile
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, Canada
| |
Collapse
|
166
|
Francuski L, Milankov V. Assessing spatial population structure and heterogeneity in the dronefly. J Zool (1987) 2015. [DOI: 10.1111/jzo.12278] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- L. Francuski
- Faculty of Sciences Department of Biology and Ecology University of Novi Sad Novi Sad Serbia
| | - V. Milankov
- Faculty of Sciences Department of Biology and Ecology University of Novi Sad Novi Sad Serbia
| |
Collapse
|
167
|
Bani L, Pisa G, Luppi M, Spilotros G, Fabbri E, Randi E, Orioli V. Ecological connectivity assessment in a strongly structured fire salamander (Salamandra salamandra) population. Ecol Evol 2015; 5:3472-85. [PMID: 26380679 PMCID: PMC4569041 DOI: 10.1002/ece3.1617] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 11/08/2022] Open
Abstract
Small populations are more prone to extinction if the dispersal among them is not adequately maintained by ecological connections. The degree of isolation between populations could be evaluated measuring their genetic distance, which depends on the respective geographic (isolation by distance, IBD) and/or ecological (isolation by resistance, IBR) distances. The aim of this study was to assess the ecological connectivity of fire salamander Salamandra salamandra populations by means of a landscape genetic approach. The species lives in broad-leaved forest ecosystems and is particularly affected by fragmentation due to its habitat selectivity and low dispersal capability. We analyzed 477 biological samples collected in 47 sampling locations (SLs) in the mainly continuous populations of the Prealpine and Eastern foothill lowland (PEF) and 10 SLs in the fragmented populations of the Western foothill (WF) lowland of Lombardy (northern Italy). Pairwise genetic distances (Chord distance, DC) were estimated from allele frequencies of 16 microsatellites loci. Ecological distances were calculated using one of the most promising methodology in landscape genetics studies, the circuit theory, applied to habitat suitability maps. We realized two habitat suitability models: one without barriers (EcoD) and a second one accounting for the possible barrier effect of main roads (EcoDb). Mantel tests between distance matrices highlighted how the Log-DC in PEF populations was related to log-transformed geographic distance (confirming a prevalence of IBD), while it was explained by the Log-EcoD, and particularly by the Log-EcoDb, in WF populations, even when accounting for the confounding effect of geographic distance (highlighting a prevalence of IBR). Moreover, we also demonstrated how considering the overall population, the effect of Euclidean or ecological distances on genetic distances acting at the level of a single group (PEF or WF populations) could not be detected, when population are strongly structured.
Collapse
Affiliation(s)
- Luciano Bani
- Department of Earth and Environmental Sciences, University of Milano-Bicocca Piazza della Scienza 1, I-20126, Milano, Italy
| | - Giulia Pisa
- Department of Earth and Environmental Sciences, University of Milano-Bicocca Piazza della Scienza 1, I-20126, Milano, Italy
| | - Massimiliano Luppi
- Department of Earth and Environmental Sciences, University of Milano-Bicocca Piazza della Scienza 1, I-20126, Milano, Italy
| | - Giulia Spilotros
- Department of Biology, University of Milano via Celoria 26, I-20133, Milano, Italy
| | - Elena Fabbri
- Laboratory of Genetics, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) I-40064, Ozzano Emilia, Bologna, Italy
| | - Ettore Randi
- Laboratory of Genetics, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) I-40064, Ozzano Emilia, Bologna, Italy ; Section of Biology and Environmental Science, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University Sohngaardsholmsvej 57, DK-9000, Aalborg, Denmark
| | - Valerio Orioli
- Department of Earth and Environmental Sciences, University of Milano-Bicocca Piazza della Scienza 1, I-20126, Milano, Italy
| |
Collapse
|
168
|
LaPoint S, Balkenhol N, Hale J, Sadler J, Ree R. Ecological connectivity research in urban areas. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12489] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Scott LaPoint
- Max Planck Institute for Ornithology Am Obstberg 1 78315 Radolfzell Germany
- Department of Biology University of Konstanz Universitätsstraße 10 78464 Konstanz Germany
| | - Niko Balkenhol
- Department of Wildlife Sciences Georg‐August‐University Göttingen Büsgenweg 3 37077 Göttingen Germany
| | - James Hale
- School of Geography, Earth and Environmental Sciences University of Birmingham Birmingham B15 2TT UK
| | - Jonathan Sadler
- School of Geography, Earth and Environmental Sciences University of Birmingham Birmingham B15 2TT UK
| | - Rodney Ree
- Australian Research Centre for Urban Ecology Royal Botanic Gardens Victoria School of BioSciences The University of Melbourne Parkville Vic. 3010 Australia
| |
Collapse
|
169
|
Ishiyama N, Sueyoshi M, Nakamura F. To what extent do human-altered landscapes retain population connectivity? Historical changes in gene flow of wetland fish Pungitius pungitius. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150033. [PMID: 26587264 PMCID: PMC4632577 DOI: 10.1098/rsos.150033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/08/2015] [Indexed: 06/05/2023]
Abstract
Understanding how human-altered landscapes affect population connectivity is valuable for conservation planning. Natural connectivity among wetlands, which is maintained by floods, is disappearing owing to farmland expansion. Using genetic data, we assessed historical changes in the population connectivity of the ninespine stickleback within a human-altered wetland system. We predicted that: (i) the contemporary gene flow maintained by the artificial watercourse network may be restricted to a smaller spatial scale compared with the gene flow preceding alteration, and (ii) the contemporary gene flow is dominated by the downstream direction owing to the construction of low-head barriers. We evaluated the potential source population in both timescales. Seventeen studied populations were grouped into four genetically different clusters, and we estimated the migration rates among these clusters. Contemporary migration was restricted to between neighbouring clusters, although a directional change was not detected. Furthermore, we consistently found the same potential source cluster, from past to present, characterized by large amounts of remnant habitats connected by artificial watercourses. These findings highlight that: (i) artificial connectivity can sustain the short-distance connectivity of the ninespine stickleback, which contributes to maintaining the potential source populations; however, (ii) population connectivity throughout the landscape has been prevented by agricultural developments.
Collapse
Affiliation(s)
- N. Ishiyama
- Author for correspondence: N. Ishiyama e-mail:
| | | | | |
Collapse
|
170
|
Santos AS, Cazetta E, Morante Filho JC, Baumgarten J, Faria D, Gaiotto FA. Lessons from a palm: genetic diversity and structure in anthropogenic landscapes from Atlantic Forest, Brazil. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0740-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
171
|
Ortego J, Aguirre MP, Noguerales V, Cordero PJ. Consequences of extensive habitat fragmentation in landscape-level patterns of genetic diversity and structure in the Mediterranean esparto grasshopper. Evol Appl 2015; 8:621-32. [PMID: 26136826 PMCID: PMC4479516 DOI: 10.1111/eva.12273] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/27/2015] [Indexed: 11/28/2022] Open
Abstract
Anthropogenic habitat fragmentation has altered the distribution and population sizes in many organisms worldwide. For this reason, understanding the demographic and genetic consequences of this process is necessary to predict the fate of populations and establish management practices aimed to ensure their viability. In this study, we analyse whether the spatial configuration of remnant semi-natural habitat patches within a chronically fragmented landscape has shaped the patterns of genetic diversity and structure in the habitat-specialist esparto grasshopper (Ramburiella hispanica). In particular, we predict that agricultural lands constitute barriers to gene flow and hypothesize that fragmentation has restricted interpopulation dispersal and reduced local levels of genetic diversity. Our results confirmed the expectation that isolation and habitat fragmentation have reduced the genetic diversity of local populations. Landscape genetic analyses based on circuit theory showed that agricultural land offers ∽1000 times more resistance to gene flow than semi-natural habitats, indicating that patterns of dispersal are constrained by the spatial configuration of remnant patches of suitable habitat. Overall, this study shows that semi-natural habitat patches act as corridors for interpopulation gene flow and should be preserved due to the disproportionately large ecological function that they provide considering their insignificant area within these human-modified landscapes.
Collapse
Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC) Seville, Spain
| | - María P Aguirre
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real, Spain
| | - Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real, Spain
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real, Spain
| |
Collapse
|
172
|
Berkman LK, Nielsen CK, Roy CL, Heist EJ. Comparative genetic structure of sympatric leporids in southern Illinois. J Mammal 2015. [DOI: 10.1093/jmammal/gyv060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
173
|
Koen EL, Bowman J, Wilson PJ. Node-based measures of connectivity in genetic networks. Mol Ecol Resour 2015; 16:69-79. [PMID: 25917123 DOI: 10.1111/1755-0998.12423] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 11/30/2022]
Abstract
At-site environmental conditions can have strong influences on genetic connectivity, and in particular on the immigration and settlement phases of dispersal. However, at-site processes are rarely explored in landscape genetic analyses. Networks can facilitate the study of at-site processes, where network nodes are used to model site-level effects. We used simulated genetic networks to compare and contrast the performance of 7 node-based (as opposed to edge-based) genetic connectivity metrics. We simulated increasing node connectivity by varying migration in two ways: we increased the number of migrants moving between a focal node and a set number of recipient nodes, and we increased the number of recipient nodes receiving a set number of migrants. We found that two metrics in particular, the average edge weight and the average inverse edge weight, varied linearly with simulated connectivity. Conversely, node degree was not a good measure of connectivity. We demonstrated the use of average inverse edge weight to describe the influence of at-site habitat characteristics on genetic connectivity of 653 American martens (Martes americana) in Ontario, Canada. We found that highly connected nodes had high habitat quality for marten (deep snow and high proportions of coniferous and mature forest) and were farther from the range edge. We recommend the use of node-based genetic connectivity metrics, in particular, average edge weight or average inverse edge weight, to model the influences of at-site habitat conditions on the immigration and settlement phases of dispersal.
Collapse
Affiliation(s)
- Erin L Koen
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Jeff Bowman
- Wildlife Research & Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Paul J Wilson
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| |
Collapse
|
174
|
Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm. Heredity (Edinb) 2015; 115:216-24. [PMID: 25873150 DOI: 10.1038/hdy.2015.30] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 03/03/2015] [Accepted: 03/12/2015] [Indexed: 11/08/2022] Open
Abstract
Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.
Collapse
|
175
|
Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM. Sun skink landscape genomics: assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Mol Ecol 2015; 24:1696-712. [DOI: 10.1111/mec.13151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 02/27/2015] [Accepted: 03/10/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Robert C. Thomson
- Department of Biology; University of Hawai'i at Mānoa; Honolulu HI 96822 USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA 92515 USA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| |
Collapse
|
176
|
Duarte JF, Carvalho DD, Vieira FDA. Genetic conservation of Ficus bonijesulapensis R.M. Castro in a dry forest on limestone outcrops. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
177
|
Leles B, Chaves AV, Russo P, Batista JAN, Lovato MB. Genetic structure is associated with phenotypic divergence in floral traits and reproductive investment in a high-altitude orchid from the Iron Quadrangle, southeastern Brazil. PLoS One 2015; 10:e0120645. [PMID: 25756994 PMCID: PMC4355488 DOI: 10.1371/journal.pone.0120645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/25/2015] [Indexed: 12/03/2022] Open
Abstract
Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops.
Collapse
Affiliation(s)
- Bruno Leles
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Anderson V. Chaves
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Philip Russo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - João A. N. Batista
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Maria Bernadete Lovato
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| |
Collapse
|
178
|
Eimanifar A, Van Stappen G, Wink M. Geographical distribution and evolutionary divergence times of Asian populations of the brine shrimpArtemia(Crustacea, Anostraca). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12242] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Amin Eimanifar
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center; Ghent University; Ghent Belgium
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| |
Collapse
|
179
|
Nora S, Albaladejo RG, Aparicio A. Genetic variation and structure in the Mediterranean shrubs Myrtus communis and Pistacia lentiscus in different landscape contexts. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:311-319. [PMID: 25262762 DOI: 10.1111/plb.12242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 06/25/2014] [Indexed: 06/03/2023]
Abstract
Studies concerning different habitat configurations can provide insights into the complex interactions between species' life-history traits and the environment and can help to predict patterns in population genetics. In this study, we compared patterns of genetic variation in two Mediterranean shrub species (Myrtus communis and Pistacia lentiscus) that co-occur in populations within three contrasting landscape contexts: continuous, fragmented-connected and fragmented-isolated populations. Analysing variation at microsatellites loci, our results revealed weak responses to the landscape contexts. We rather found a population-specific response in both study species. However, despite both study species sharing similar levels of genetic diversity, Myrtus displayed higher levels of homozygosity and genetic differentiation among populations, stronger patterns of within-population spatial genetic structure, lower values of mutation-scaled effective population size and stronger evidence for recent genetic bottlenecks than Pistacia. This result highlights the influence of past events (e.g. historical connectivity, fluctuations in population size) and local factors (e.g. microhabitat availability for recruitment, habitat quality, plant density, native fauna) and that the landscape configuration per se (i.e. fragment size and/or isolation) might not completely determine the species' genetic patterns.
Collapse
Affiliation(s)
- S Nora
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | | | | |
Collapse
|
180
|
Multiple-geographic-scale genetic structure of two mangrove tree species: the roles of mating system, hybridization, limited dispersal and extrinsic factors. PLoS One 2015; 10:e0118710. [PMID: 25723532 PMCID: PMC4344226 DOI: 10.1371/journal.pone.0118710] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 01/07/2015] [Indexed: 12/05/2022] Open
Abstract
Mangrove plants comprise a unique group of organisms that grow within the intertidal zones of tropical and subtropical regions and whose distributions are influenced by both biotic and abiotic factors. To understand how these extrinsic and intrinsic processes influence a more fundamental level of the biological hierarchy of mangroves, we studied the genetic diversity of two Neotropical mangrove trees, Avicenniagerminans and A. schaueriana, using microsatellites markers. As reported for other sea-dispersed species, there was a strong differentiation between A. germinans and A. schaueriana populations sampled north and south of the northeastern extremity of South America, likely due to the influence of marine superficial currents. Moreover, we observed fine-scale genetic structures even when no obvious physical barriers were present, indicating pollen and propagule dispersal limitation, which could be explained by isolation-by-distance coupled with mating system differences. We report the first evidence of ongoing hybridization between Avicennia species and that these hybrids are fertile, although this interspecific crossing has not contributed to an increase in the genetic diversity the populations where A. germinans and A. schaueriana hybridize. These findings highlight the complex interplay between intrinsic and extrinsic factors that shape the distribution of the genetic diversity in these sea-dispersed colonizer species.
Collapse
|
181
|
Anderson SJ, Kierepka EM, Swihart RK, Latch EK, Rhodes OE. Assessing the permeability of landscape features to animal movement: using genetic structure to infer functional connectivity. PLoS One 2015; 10:e0117500. [PMID: 25719366 PMCID: PMC4342345 DOI: 10.1371/journal.pone.0117500] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/26/2014] [Indexed: 11/19/2022] Open
Abstract
Human-altered environments often challenge native species with a complex spatial distribution of resources. Hostile landscape features can inhibit animal movement (i.e., genetic exchange), while other landscape attributes facilitate gene flow. The genetic attributes of organisms inhabiting such complex environments can reveal the legacy of their movements through the landscape. Thus, by evaluating landscape attributes within the context of genetic connectivity of organisms within the landscape, we can elucidate how a species has coped with the enhanced complexity of human altered environments. In this research, we utilized genetic data from eastern chipmunks (Tamias striatus) in conjunction with spatially explicit habitat attribute data to evaluate the realized permeability of various landscape elements in a fragmented agricultural ecosystem. To accomplish this we 1) used logistic regression to evaluate whether land cover attributes were most often associated with the matrix between or habitat within genetically identified populations across the landscape, and 2) utilized spatially explicit habitat attribute data to predict genetically-derived Bayesian probabilities of population membership of individual chipmunks in an agricultural ecosystem. Consistency between the results of the two approaches with regard to facilitators and inhibitors of gene flow in the landscape indicate that this is a promising new way to utilize both landscape and genetic data to gain a deeper understanding of human-altered ecosystems.
Collapse
Affiliation(s)
- Sara J. Anderson
- Biosciences Department, Minnesota State University Moorhead, 1104 7 Ave, Moorhead, MN, 56563, United States of America
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
| | - Elizabeth M. Kierepka
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI, 53024, United States of America
| | - Robert K. Swihart
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
| | - Emily K. Latch
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI, 53024, United States of America
| | - Olin E. Rhodes
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
- Savannah River Ecology Laboratory, PO Drawer E, Aiken, SC, 29802, United States of America
| |
Collapse
|
182
|
Cornille A, Feurtey A, Gélin U, Ropars J, Misvanderbrugge K, Gladieux P, Giraud T. Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples. Evol Appl 2015; 8:373-84. [PMID: 25926882 PMCID: PMC4408148 DOI: 10.1111/eva.12250] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/09/2014] [Indexed: 02/04/2023] Open
Abstract
Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M. sylvestris, by identifying five distinct genetic groups in Europe and a north–south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe.
Collapse
Affiliation(s)
- Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France ; Department of Plant Ecology and Evolution, Uppsala University Uppsala, Sweden
| | - Alice Feurtey
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France
| | - Uriel Gélin
- Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Jeanne Ropars
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France
| | | | - Pierre Gladieux
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; CNRS Orsay, France
| |
Collapse
|
183
|
Coster SS, Babbitt KJ, Cooper A, Kovach AI. Limited influence of local and landscape factors on finescale gene flow in two pond-breeding amphibians. Mol Ecol 2015; 24:742-58. [DOI: 10.1111/mec.13062] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/12/2014] [Accepted: 01/02/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Stephanie S. Coster
- Department of Natural Resources and the Environment; University of New Hampshire; 114 James Hall Durham NH 03824 USA
| | - Kimberly J. Babbitt
- Department of Natural Resources and the Environment; University of New Hampshire; 114 James Hall Durham NH 03824 USA
| | - Andrew Cooper
- School of Resource and Environmental Management; Simon Fraser University; 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment; University of New Hampshire; 114 James Hall Durham NH 03824 USA
| |
Collapse
|
184
|
Dispersal constraints for the conservation of the grassland herb Thymus pulegioides L. in a highly fragmented agricultural landscape. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0698-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
185
|
Nowakowski AJ, DeWoody JA, Fagan ME, Willoughby JR, Donnelly MA. Mechanistic insights into landscape genetic structure of two tropical amphibians using field-derived resistance surfaces. Mol Ecol 2015; 24:580-95. [DOI: 10.1111/mec.13052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/13/2014] [Accepted: 12/18/2014] [Indexed: 12/01/2022]
Affiliation(s)
- A. Justin Nowakowski
- Department of Biological Sciences; Florida International University; Miami FL 33199 USA
| | - J. Andrew DeWoody
- Department of Forestry & Natural Resources; Purdue University; West Lafayette IN 47907 USA
- Department of Biological Sciences; Purdue University; West Lafayette IN 47907 USA
| | | | - Janna R. Willoughby
- Department of Forestry & Natural Resources; Purdue University; West Lafayette IN 47907 USA
| | - Maureen A. Donnelly
- Department of Biological Sciences; Florida International University; Miami FL 33199 USA
- College of Arts and Sciences; Florida International University; Miami FL 33199 USA
| |
Collapse
|
186
|
Prunier JG, Colyn M, Legendre X, Nimon KF, Flamand MC. Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses. Mol Ecol 2015; 24:263-83. [PMID: 25495950 DOI: 10.1111/mec.13029] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 02/02/2023]
Abstract
Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance-partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses.
Collapse
Affiliation(s)
- J G Prunier
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | | | | | | | | |
Collapse
|
187
|
Kluever BM, Gese EM, Dempsey SJ. The influence of road characteristics and species on detection probabilities of carnivore faeces. WILDLIFE RESEARCH 2015. [DOI: 10.1071/wr14244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Determining reliable estimates of carnivore population size and distributions are paramount for developing informed conservation and management plans. Traditionally, invasive sampling has been employed to monitor carnivores, but non-invasive sampling has the advantage of not needing to capture the animal and is generally less expensive. Faeces sampling is a common non-invasive sampling technique and future use is forecasted to increase due to the low costs and logistical ease of sampling, and more advanced techniques in landscape and conservation genetics. For many species, faeces sampling often occurs on or alongside roads. Despite the commonality of road-based faeces sampling, detectability issues are often not addressed.
Aim
We sought to test whether faeces detection probabilities varied by species – coyote (Canis latrans) versus kit fox (Vulpes macrotis) – and to test whether road characteristics influenced faeces detection probabilities.
Methods
We placed coyote and kit fox faeces along roads, quantified road characteristics, and then subsequently conducted ‘blind’ road-based faeces detection surveys in Utah during 2012 and 2013. Technicians that surveyed the faeces deposition transects had no knowledge of the locations of the placed faeces.
Key results
Faeces detection probabilities for kit foxes and coyotes were 45% and 74%, respectively; larger faeces originated from coyotes and were more readily detected. Misidentification of placed faeces was rare and did not differ by species. The width of survey roads and the composition of a road’s surface influenced detection probabilities.
Conclusion
We identified factors that can influence faeces detection probabilities. Not accounting for variable detection probabilities of different species or not accounting for or reducing road-based variables influencing faeces detection probabilities could hamper reliable counts of mammalian faeces, and could potentially reduce precision of population estimates derived from road-based faeces deposition surveys.
Implications
We recommend that wildlife researchers acknowledge and account for imperfect faeces detection probabilities during faecal sampling. Steps can be taken during study design to improve detection probabilities, and during the analysis phase to account for variable detection probabilities.
Collapse
|
188
|
Wilson AW, Wickett NJ, Grabowski P, Fant J, Borevitz J, Mueller GM. Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology. Mycologia 2015; 107:217-26. [PMID: 25361831 PMCID: PMC4829919 DOI: 10.3852/13-278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Given the diversity and ecological importance of Fungi, there is a lack of population genetic research on these organisms. The reason for this can be explained in part by their cryptic nature and difficulty in identifying genets. In addition the difficulty (relative to plants and animals) in developing molecular markers for fungal population genetics contributes to the lack of research in this area. This study examines the ability of restriction-site associated DNA (RAD) sequencing to generate SNPs in Laccaria bicolor. Eighteen samples of morphologically identified L. bicolor from the United States and Europe were selected for this project. The RAD sequencing method produced anywhere from 290 000 to more than 3 000 000 reads. Mapping these reads to the genome of L. bicolor resulted in 84 000-940 000 unique reads from individual samples. Results indicate that incorporation of non-L. bicolor taxa into the analysis resulted in a precipitous drop in shared loci among samples, suggests the potential of these methods to identify cryptic species. F-statistics were easily calculated, although an observable "noise" was detected when using the "All Loci" treatment versus filtering loci to those present in at least 50% of the individuals. The data were analyzed with tests of Hardy-Weinburg equilibrium, population genetic statistics (FIS and FST), and population structure analysis using the program Structure. The results provide encouraging feedback regarding the potential utility of these methods and their data for population genetic analysis. We were unable to draw conclusions of life history of L. bicolor populations from this dataset, given the small sample size. The results of this study indicate the potential of these methods to address population genetics and general life history questions in the Agaricales. Further research is necessary to explore the specific application of these methods in the Agaricales or other fungal groups.
Collapse
Affiliation(s)
- Andrew W Wilson
- Chicago Botanic Garden, Plant Conservation Science, 1000 Lake Cook Road, Glencoe, Illinois 60022
| | - Norman J Wickett
- Chicago Botanic Garden, Plant Conservation Science, 1000 Lake Cook Road, Glencoe, Illinois 60022; Northwestern University, Program in Biological Sciences, 2205 Tech Drive O.T. Hogan Hall Room 2-144, Evanston, Illinois 60208
| | - Paul Grabowski
- University of Chicago, Ecology and Evolution, 1101 E 57th Street, Chicago, Illinois 60637
| | - Jeremie Fant
- Chicago Botanic Garden, Plant Conservation Science, 1000 Lake Cook Road, Glencoe, Illinois 60022
| | - Justin Borevitz
- Australian National University, Research School of Biology, Canberra, Australia; University of Chicago, Ecology and Evolution, 1101 E 57th Street, Chicago, Illinois 60637
| | - Gregory M Mueller
- Chicago Botanic Garden, Plant Conservation Science, 1000 Lake Cook Road, Glencoe, Illinois 60022
| |
Collapse
|
189
|
van Strien MJ, Holderegger R, Van Heck HJ. Isolation-by-distance in landscapes: considerations for landscape genetics. Heredity (Edinb) 2015; 114:27-37. [PMID: 25052412 PMCID: PMC4815601 DOI: 10.1038/hdy.2014.62] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 05/13/2014] [Accepted: 05/27/2014] [Indexed: 11/08/2022] Open
Abstract
In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST-distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST-distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.
Collapse
Affiliation(s)
- M J van Strien
- Planning of Landscape and Urban Systems, ETH Zurich, Stefano-Franscini-Platz 5, Zurich, Switzerland
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, Switzerland
| | - R Holderegger
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, Switzerland
- Department of Environmental System Sciences, ETH Zurich, Universitätsstrasse 16, Zurich, Switzerland
| | - H J Van Heck
- Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, UK
- Institute of Earth Sciences, Utrecht University, Budapestlaan 4, Utrecht, The Netherlands
| |
Collapse
|
190
|
Keller D, Holderegger R, van Strien MJ, Bolliger J. How to make landscape genetics beneficial for conservation management? CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0684-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
191
|
Abstract
Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over nonmodel-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum. We devise efficient algorithms based on hidden Markov models to localize on a map the recent ancestors (e.g., grandparents) of admixed individuals, joint with assigning ancestry at each locus in the genome. We validate our methods by using empirical data from individuals with mixed European ancestry from the Population Reference Sample study and show that our approach is able to localize their recent ancestors within an average of 470 km of the reported locations of their grandparents. Furthermore, simulations from real Population Reference Sample genotype data show that our method attains high accuracy in localizing recent ancestors of admixed individuals in Europe (an average of 550 km from their true location for localization of two ancestries in Europe, four generations ago). We explore the limits of ancestry localization under our approach and find that performance decreases as the number of distinct ancestries and generations since admixture increases. Finally, we build a map of expected localization accuracy across admixed individuals according to the location of origin within Europe of their ancestors.
Collapse
|
192
|
Medley KA, Jenkins DG, Hoffman EA. Human-aided and natural dispersal drive gene flow across the range of an invasive mosquito. Mol Ecol 2014; 24:284-95. [DOI: 10.1111/mec.12925] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/09/2014] [Accepted: 09/12/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Kim A. Medley
- Department of Biology; University of Central Florida; 4000 Central Florida Blvd. Orlando FL 32816 USA
- Tyson Research Center; Washington University in St. Louis; 6750 Tyson Valley Road Eureka MO 63025 USA
| | - David G. Jenkins
- Department of Biology; University of Central Florida; 4000 Central Florida Blvd. Orlando FL 32816 USA
| | - Eric A. Hoffman
- Department of Biology; University of Central Florida; 4000 Central Florida Blvd. Orlando FL 32816 USA
| |
Collapse
|
193
|
Carrel M, Patel J, Taylor SM, Janko M, Mwandagalirwa MK, Tshefu AK, Escalante AA, McCollum A, Alam MT, Udhayakumar V, Meshnick S, Emch M. The geography of malaria genetics in the Democratic Republic of Congo: A complex and fragmented landscape. Soc Sci Med 2014; 133:233-41. [PMID: 25459204 DOI: 10.1016/j.socscimed.2014.10.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 08/27/2014] [Accepted: 10/17/2014] [Indexed: 11/28/2022]
Abstract
Understanding how malaria parasites move between populations is important, particularly given the potential for malaria to be reintroduced into areas where it was previously eliminated. We examine the distribution of malaria genetics across seven sites within the Democratic Republic of Congo (DRC) and two nearby countries, Ghana and Kenya, in order to understand how the relatedness of malaria parasites varies across space, and whether there are barriers to the flow of malaria parasites within the DRC or across borders. Parasite DNA was retrieved from dried blood spots from 7 Demographic and Health Survey sample clusters in the DRC. Malaria genetic characteristics of parasites from Ghana and Kenya were also obtained. For each of 9 geographic sites (7 DRC, 1 Ghana and 1 Kenya), a pair-wise RST statistic was calculated, indicating the genetic distance between malaria parasites found in those locations. Mapping genetics across the spatial extent of the study area indicates a complex genetic landscape, where relatedness between two proximal sites may be relatively high (RST > 0.64) or low (RST < 0.05), and where distal sites also exhibit both high and low genetic similarity. Mantel's tests suggest that malaria genetics differ as geographic distances increase. Principal Coordinate Analysis suggests that genetically related samples are not co-located. Barrier analysis reveals no significant barriers to gene flow between locations. Malaria genetics in the DRC have a complex and fragmented landscape. Limited exchange of genes across space is reflected in greater genetic distance between malaria parasites isolated at greater geographic distances. There is, however, evidence for close genetic ties between distally located sample locations, indicating that movement of malaria parasites and flow of genes is being driven by factors other than distance decay. This research demonstrates the contributions that spatial disease ecology and landscape genetics can make to understanding the evolutionary dynamics of infectious diseases.
Collapse
Affiliation(s)
- Margaret Carrel
- Department of Geographical & Sustainability Sciences, University of Iowa, Iowa City, IA, USA.
| | - Jaymin Patel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina- Chapel Hill Chapel Hill, NC, USA
| | - Steve M Taylor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina- Chapel Hill Chapel Hill, NC, USA; Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, NC, USA; Duke Global Health Institute, Durham, NC, USA
| | - Mark Janko
- Department of Geography, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Melchior Kashamuka Mwandagalirwa
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina- Chapel Hill Chapel Hill, NC, USA
| | - Antoinette K Tshefu
- Ecole de Sante Publique, Faculte de Medecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Ananias A Escalante
- Center for Evolutionary Medicine & Informatics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Andrea McCollum
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Md Tauqeer Alam
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Steven Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina- Chapel Hill Chapel Hill, NC, USA
| | - Michael Emch
- Department of Geography, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
194
|
Wang IJ, Bradburd GS. Isolation by environment. Mol Ecol 2014; 23:5649-62. [DOI: 10.1111/mec.12938] [Citation(s) in RCA: 505] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/07/2014] [Accepted: 09/21/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Ian J. Wang
- Department of Environmental Science, Policy, and Management; University of California; 130 Mulford Hall #3114 Berkeley CA 94705 USA
| | - Gideon S. Bradburd
- Center for Population Biology; Department of Evolution and Ecology; University of California; 2320 Storer Hall 1 Shields Ave Davis CA 95616 USA
| |
Collapse
|
195
|
Blair C, Jiménez Arcos VH, de la Cruz FRM, Murphy RW. Historical and contemporary demography of leaf-toed geckos (Phyllodactylidae: Phyllodactylus tuberculosus saxatilis) in the Mexican dry forest. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0668-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
196
|
Zancolli G, Rödel MO, Steffan-Dewenter I, Storfer A. Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro. Mol Ecol 2014; 23:4989-5002. [DOI: 10.1111/mec.12921] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 09/07/2014] [Accepted: 09/10/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Giulia Zancolli
- Department of Animal Ecology and Tropical Biology; Biocentre; University of Würzburg; Am Hubland 97074 Würzburg Germany
- School of Biological Sciences; Washington State University; Pullman WA 99164 USA
| | - Mark-Oliver Rödel
- Museum für Naturkunde; Leibniz Institute for Evolution and Biodiversity Science; Invalidenstr. 43 10115 Berlin Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB); Berlin Germany
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology; Biocentre; University of Würzburg; Am Hubland 97074 Würzburg Germany
| | - Andrew Storfer
- School of Biological Sciences; Washington State University; Pullman WA 99164 USA
| |
Collapse
|
197
|
Falahati-Anbaran M, Lundemo S, Ansell SW, Stenøien HK. Contrasting patterns of genetic structuring in natural populations of Arabidopsis lyrata Subsp. petraea across different regions in northern Europe. PLoS One 2014; 9:e107479. [PMID: 25226024 PMCID: PMC4166467 DOI: 10.1371/journal.pone.0107479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/11/2014] [Indexed: 01/08/2023] Open
Abstract
Level and partitioning of genetic diversity is expected to vary between contrasting habitats, reflecting differences in strength of ecological and evolutionary processes. Therefore, it is necessary to consider processes acting on different time scales when trying to explain diversity patterns in different parts of species' distributions. To explore how historical and contemporary factors jointly may influence patterns of genetic diversity and population differentiation, we compared genetic composition in the perennial herb Arabidopsis lyrata ssp. petraea from the northernmost parts of its distribution range on Iceland to that previously documented in Scandinavia. Leaf tissue and soil were sampled from ten Icelandic populations of A. lyrata. Seedlings were grown from soil samples, and tissue from above-ground and seed bank individuals were genotyped with 21 microsatellite markers. Seed bank density in Icelandic populations was low but not significantly different from that observed in Norwegian populations. While within-population genetic diversity was relatively high on Iceland (H(E) = 0.35), among-population differentiation was low (F(ST) = 0.10) compared to Norwegian and Swedish populations. Population differentiation was positively associated with geographical distance in both Iceland and Scandinavia, but the strength of this relationship varied between regions. Although topography and a larger distribution range may explain the higher differentiation between mountainous Norwegian relative to lowland populations in Sweden, these factors cannot explain the lower differentiation in Icelandic compared to Swedish populations. We propose that low genetic differentiation among Icelandic populations is not caused by differences in connectivity, but is rather due to large historical effective population sizes. Thus, rather than contemporary processes, historical factors such as survival of Icelandic lineages in northern refugia during the last glacial period may have contributed to the observed pattern.
Collapse
Affiliation(s)
- Mohsen Falahati-Anbaran
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway; School of Biology and Center of Excellence in Phylogeny of Living Organisms, University of Tehran, Tehran, Iran
| | - Sverre Lundemo
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Stephen W Ansell
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
198
|
Emel SL, Storfer A. Landscape genetics and genetic structure of the southern torrent salamander, Rhyacotriton variegatus. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0653-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
199
|
Davis DJ, Wieman AC, Berendzen PB. The influence of historical and contemporary landscape variables on the spatial genetic structure of the rainbow darter (Etheostoma caeruleum) in tributaries of the upper Mississippi River. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0649-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
200
|
Rhodes MK, Fant JB, Skogen KA. Local topography shapes fine-scale spatial genetic structure in the Arkansas Valley evening primrose, Oenothera harringtonii (Onagraceae). J Hered 2014; 105:806-15. [PMID: 25189774 DOI: 10.1093/jhered/esu051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Identifying factors that shape the spatial distribution of genetic variation is crucial to understanding many population- and landscape-level processes. In this study, we explore fine-scale spatial genetic structure in Oenothera harringtonii (Onagraceae), an insect-pollinated, gravity-dispersed herb endemic to the grasslands of south-central and southeastern Colorado, USA. We genotyped 315 individuals with 11 microsatellite markers and utilized a combination of spatial autocorrelation analyses and landscape genetic models to relate life history traits and landscape features to dispersal processes. Spatial genetic structure was consistent with theoretical expectations of isolation by distance, but this pattern was weak (Sp = 0.00374). Anisotropic analyses indicated that spatial genetic structure was markedly directional, in this case consistent with increased dispersal along prominent slopes. Landscape genetic models subsequently confirmed that spatial genetic variation was significantly influenced by local topographic heterogeneity, specifically that geographic distance, elevation and aspect were important predictors of spatial genetic structure. Among these variables, geographic distance was ~68% more important than elevation in describing spatial genetic variation, and elevation was ~42% more important than aspect after removing the effect of geographic distance. From these results, we infer a mechanism of hydrochorous seed dispersal along major drainages aided by seasonal monsoon rains. Our findings suggest that landscape features may shape microevolutionary processes at much finer spatial scales than typically considered, and stress the importance of considering how particular dispersal vectors are influenced by their environmental context.
Collapse
Affiliation(s)
- Matthew K Rhodes
- From the Division of Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA (Rhodes, Fant, and Skogen); and the Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, O.T. Hogan Hall, Room 2-144, Evanston, IL 60208, USA (Rhodes).
| | - Jeremie B Fant
- From the Division of Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA (Rhodes, Fant, and Skogen); and the Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, O.T. Hogan Hall, Room 2-144, Evanston, IL 60208, USA (Rhodes)
| | - Krissa A Skogen
- From the Division of Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA (Rhodes, Fant, and Skogen); and the Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, O.T. Hogan Hall, Room 2-144, Evanston, IL 60208, USA (Rhodes)
| |
Collapse
|