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Sidlauskas BL, Mathur S, Aydoğan H, Monzyk FR, Black AN. Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish. BMC Ecol Evol 2024; 24:2. [PMID: 38177987 PMCID: PMC10765885 DOI: 10.1186/s12862-023-02191-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
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Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA.
| | - Samarth Mathur
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W 12th Ave, Columbus, OH, 43210, USA
| | - Hakan Aydoğan
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA
| | - Fred R Monzyk
- Oregon Department of Fish and Wildlife, Corvallis Research Lab, 28655 OR-34, Corvallis, OR, 97333, USA
| | - Andrew N Black
- Center for Quantitative Life Sciences, Oregon State University, 2750 SW Campus Way, Corvallis, OR, 97331, USA
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Mossop KD, Lemmon AR, Moriarty Lemmon E, Eytan R, Adams M, Unmack PJ, Smith Date K, Morales HE, Hammer MP, Wong BBM, Chapple DG. Phylogenomics and biogeography of arid-adapted Chlamydogobius goby fishes. Mol Phylogenet Evol 2023; 182:107757. [PMID: 36925090 DOI: 10.1016/j.ympev.2023.107757] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/01/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023]
Abstract
The progressive aridification of the Australian continent from ∼ 20 million years ago posed severe challenges for the persistence of its resident biota. A key question involves the role of refugial habitats - specifically, their ability to mediate the effects of habitat loss and fragmentation, and their potential to shape opportunities for allopatric speciation. With freshwater species, for example, the patchiness, or absence, of water will constrain distributions. However, aridity may not necessarily isolate populations if disjunct refugia experience frequent hydrological connections. To investigate this potential dichotomy, we explored the evolutionary history of the Chlamydogobius gobies (Gobiiformes: Gobiidae), an arid-adapted genus of six small, benthic fish species that exploit all types of waterbodies (i.e. desert springs, waterholes and bore-fed wetlands, coastal estuarine creeks and mangroves) across parts of central and northern Australia. We used Anchored Phylogenomics to generate a highly resolved phylogeny of the group from sequence data for 260 nuclear loci. Buttressed by companion allozyme and mtDNA datasets, our molecular findings infer the diversification of Chlamydogobius in arid Australia, and provide a phylogenetic structure that cannot be simply explained by invoking allopatric speciation events reflecting current geographic proximity. Our findings are generally consistent with the existing morphological delimitation of species, with one exception: at the shallowest nodes of phylogenetic reconstruction, the molecular data do not fully support the current dichotomous delineation of C. japalpa from C. eremius in Kati Thanda-Lake Eyre-associated waterbodies. Together these findings illustrate the ability of structural (hydrological) connections to generate patterns of connectivity and isolation for an ecologically moderate disperser in response to ongoing habitat aridification. Finally, we explore the implications of these results for the immediate management of threatened (C. gloveri) and critically endangered (C. micropterus, C. squamigenus) congeners.
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Affiliation(s)
- Krystina D Mossop
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | | | - Ron Eytan
- Marine Biology Department, Texas A&M University at Galveston, Galveston, TX 77554, USA; Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Peter J Unmack
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, ACT 2617, Australia
| | - Katie Smith Date
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Museum Victoria, Sciences Department, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Hernán E Morales
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT 0801, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
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Epps CW, Petro VM, Creech TG, Crowhurst RS, Weldy MJ, Taylor JD. Landscape Genetics of American Beaver in Coastal Oregon. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Clinton W. Epps
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Vanessa M. Petro
- Department of Forest Ecosystems and Society Oregon State University 321 Richardson Hall Corvallis OR 97331 USA
| | - Tyler G. Creech
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Rachel S. Crowhurst
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Matthew J. Weldy
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Jimmy D. Taylor
- USDA, APHIS, National Wildlife Research Center Oregon Field Station 321 Richardson Hall Corvallis OR 97331 USA
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Different Species Requirements within a Heterogeneous Spring Complex Affects Patch Occupancy of Threatened Snails in Australian Desert Springs. WATER 2020. [DOI: 10.3390/w12102942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
(1) The distribution of organisms that inhabit patchy systems is dictated by their ability to move between patches, and the suitability of environmental conditions at patches to which they disperse. Understanding whether the species involved are identical to one another in their environmental requirements and their responses to variance in their environment is essential to understanding ecological processes in these systems, and to the management of species whose patchy and limited distributions present conservation risks. (2) Artesian springs in Australia’s arid interior are “islands” of hospitable wetland in uninhabitable “oceans” of dry land and are home to diverse and threatened assemblages of endemic species with severely restricted distributions. Many have strict environmental requirements, but the role of environmental heterogeneity amongst springs has rarely been considered alongside conventional patch characteristics (isolation and patch geometry). (3) We quantified environmental heterogeneity across springs, and the relationship between spring size, isolation (distances to neighbours) and environmental quality (depth, water chemistry), and patterns of occupancy and population persistence of six endemic spring snail species, all from different families, and with all restricted to a single <8000 ha system of springs in Australia. To do so, a survey was conducted for comparison against survey results of almost a decade before, and environmental variables of the springs were measured. Many of the snail species occupied few sites, and environmental variables strongly covaried, so an ordination-based approach was adopted to assess the relationship between environmental measures and the distribution of each species, and also whether springs that held a higher diversity of snails had specific characteristics. (4) Each snail species occupied a subset of springs (between 5% and 36% of the 85 sampled) and was associated with a particular set of conditions. Of the six species considered in further detail, most were restricted to the few springs that were large and deep. Species in family Tateidae were distinct in having colonised highly isolated springs (with >300 m to nearest neighbour). Springs with highest diversity were significantly larger, deeper and had more numerous neighbours within 300 m than those devoid of endemic snails, or those with low diversity. (5) Although spring size and isolation affect patterns of occupancy, the six snail species had significantly different environmental requirements from one another and these correlated with the distribution pattern of each. Approaches that ignore the role of environmental quality—and particularly depth in springs—are overlooking important processes outside of patch geometry that influence diversity. These organisms are highly susceptible to extinction, as most occupy less than 3 ha of habitat spread across few springs, and habitat degradation continues to compromise what little wetland area is needed for their persistence.
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Valladares MA, Méndez MA, Collado GA. Influenced but not determined by historical events: genetic, demographic and morphological differentiation in Heleobia ascotanensis from the Chilean Altiplano. PeerJ 2018; 6:e5802. [PMID: 30588392 PMCID: PMC6301281 DOI: 10.7717/peerj.5802] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 09/21/2018] [Indexed: 11/30/2022] Open
Abstract
In the present study, we focus on the phylogeographic pattern, demographic history and morphological differentiation of Heleobia ascotanensis, a freshwater gastropod restricted to the Ascotán saltpan in the Chilean Altiplano. The current distribution of the species is limited to twelve isolated or partially isolated springs that were affected by transitions between humid and arid periods during last glaciations. The genetic analysis of 322 specimens showed that H. ascotanensis is subdivided into three genetically divergent populations, with low and moderate degrees of historical gene flow among them and incipient morphological differentiation as a consequence of genetic and geographical isolation. Molecular analyses revealed different demographic histories among populations which seem to respond independently to climatic events, probably due to an environmental imposition and idiosyncratic strategies developed to cope with water availability. The results of this study and co-distributed taxa support the hypothesis that contemporary and historical events have influenced microevolutionary differentiation of these snails, although there is a need to complement further information to predict genetic or morphological divergence at microgeographic scale.
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Affiliation(s)
- Moisés A Valladares
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Marco A Méndez
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Gonzalo A Collado
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Región del Bío-Bío, Chile
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Toon A, Sacre E, Fensham RJ, Cook LG. Immigrant and native? The case of the swamp foxtail Cenchrus purpurascensin Australia. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- A. Toon
- School of Biological Sciences; The University of Queensland; Brisbane Qld Australia
| | - E. Sacre
- School of Biological Sciences; The University of Queensland; Brisbane Qld Australia
| | - R. J. Fensham
- School of Biological Sciences; The University of Queensland; Brisbane Qld Australia
- Queensland Herbarium; Brisbane Qld Australia
| | - L. G. Cook
- School of Biological Sciences; The University of Queensland; Brisbane Qld Australia
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Balbi M, Ernoult A, Poli P, Madec L, Guiller A, Martin MC, Nabucet J, Beaujouan V, Petit EJ. Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum). Mol Ecol 2018; 27:1357-1370. [PMID: 29412498 DOI: 10.1111/mec.14521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 12/11/2022]
Abstract
Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multiscale analysis to determine how landscape composition, configuration and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side by side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation-by-distance and isolation-by-resistance models for this land snail, with an equal fit to least-cost paths and circuit-theory-based models. Each of the 12 landscapes analysed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavourable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results and shows how multiscale analyses provide insight into scale-dependent processes.
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Affiliation(s)
- Manon Balbi
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Aude Ernoult
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Pedro Poli
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Luc Madec
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Annie Guiller
- Edysan FRE 3498, CNRS, Université de Picardie Jules Vernes, Amiens, France
| | - Marie-Claire Martin
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Jean Nabucet
- UMR LETG, CNRS, Université de Rennes 2, Rennes Cedex, France
| | | | - Eric J Petit
- ESE, Ecology and Ecosystem Health, INRA, Rennes, France
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Creech TG, Epps CW, Landguth EL, Wehausen JD, Crowhurst RS, Holton B, Monello RJ. Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep. PLoS One 2017; 12:e0176960. [PMID: 28464013 PMCID: PMC5413035 DOI: 10.1371/journal.pone.0176960] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/19/2017] [Indexed: 11/30/2022] Open
Abstract
Landscape genetic studies based on neutral genetic markers have contributed to our understanding of the influence of landscape composition and configuration on gene flow and genetic variation. However, the potential for species to adapt to changing landscapes will depend on how natural selection influences adaptive genetic variation. We demonstrate how landscape resistance models can be combined with genetic simulations incorporating natural selection to explore how the spread of adaptive variation is affected by landscape characteristics, using desert bighorn sheep (Ovis canadensis nelsoni) in three differing regions of the southwestern United States as an example. We conducted genetic sampling and least-cost path modeling to optimize landscape resistance models independently for each region, and then simulated the spread of an adaptive allele favored by selection across each region. Optimized landscape resistance models differed between regions with respect to landscape variables included and their relationships to resistance, but the slope of terrain and the presence of water barriers and major roads had the greatest impacts on gene flow. Genetic simulations showed that differences among landscapes strongly influenced spread of adaptive genetic variation, with faster spread (1) in landscapes with more continuously distributed habitat and (2) when a pre-existing allele (i.e., standing genetic variation) rather than a novel allele (i.e., mutation) served as the source of adaptive genetic variation. The combination of landscape resistance models and genetic simulations has broad conservation applications and can facilitate comparisons of adaptive potential within and between landscapes.
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Affiliation(s)
- Tyler G. Creech
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Clinton W. Epps
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Erin L. Landguth
- Computational Ecology Laboratory, Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - John D. Wehausen
- White Mountain Research Center, University of California, Bishop, California, United States of America
| | - Rachel S. Crowhurst
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Brandon Holton
- Grand Canyon National Park, National Park Service, Grand Canyon, Arizona, United States of America
| | - Ryan J. Monello
- Biological Resources Division, National Park Service, Fort Collins, Colorado, United States of America
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Milanesi P, Holderegger R, Caniglia R, Fabbri E, Galaverni M, Randi E. Expert-based versus habitat-suitability models to develop resistance surfaces in landscape genetics. Oecologia 2016; 183:67-79. [DOI: 10.1007/s00442-016-3751-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 10/04/2016] [Indexed: 11/29/2022]
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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
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Epps CW, Keyghobadi N. Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change. Mol Ecol 2015; 24:6021-40. [DOI: 10.1111/mec.13454] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Clinton W. Epps
- Oregon State University; Nash Hall Room 104 Corvallis OR 97331 USA
| | - Nusha Keyghobadi
- Department of Biology; Western University; London ON N6A 5B7 Canada
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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.
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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
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Murphy NP, Guzik MT, Cooper SJB, Austin AD. Desert spring refugia: museums of diversity or evolutionary cradles? ZOOL SCR 2015. [DOI: 10.1111/zsc.12129] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas P. Murphy
- Department of Ecology, Environment and Evolution; La Trobe University; Bundoora Vic. 3086 Australia
| | - Michelle T. Guzik
- Australian Centre for Evolutionary Biology and Biodiversity; School of Earth and Environmental Science; The University of Adelaide; Adelaide SA 5005 Australia
| | - Steven J. B. Cooper
- Evolutionary Biology Unit; South Australian Museum; North Terrace Adelaide SA 5000 Australia
| | - Andrew D. Austin
- Australian Centre for Evolutionary Biology and Biodiversity; School of Earth and Environmental Science; The University of Adelaide; Adelaide SA 5005 Australia
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Morán-Ordóñez A, Pavlova A, Pinder AM, Sim L, Sunnucks P, Thompson RM, Davis J. Aquatic communities in arid landscapes: local conditions, dispersal traits and landscape configuration determine local biodiversity. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Alejandra Morán-Ordóñez
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
- NERP Environmental Decisions Hub; School of BioSciences (building 2); The University of Melbourne; Parkville 3010 Vic. Australia
| | - Alexandra Pavlova
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
| | - Adrian M. Pinder
- Science and Conservation Division; Department of Parks and Wildlife; Kensington 6151 WA Australia
| | - Lien Sim
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
- Science and Conservation Division; Department of Parks and Wildlife; Kensington 6151 WA Australia
| | - Paul Sunnucks
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
| | - Ross M. Thompson
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
- Institute for Applied Ecology; University of Canberra; Canberra 2617 ACT Australia
| | - Jenny Davis
- Institute for Applied Ecology; University of Canberra; Canberra 2617 ACT Australia
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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.
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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
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Rioux Paquette S, Talbot B, Garant D, Mainguy J, Pelletier F. Modelling the dispersal of the two main hosts of the raccoon rabies variant in heterogeneous environments with landscape genetics. Evol Appl 2014; 7:734-49. [PMID: 25469156 PMCID: PMC4227855 DOI: 10.1111/eva.12161] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 03/22/2014] [Indexed: 12/25/2022] Open
Abstract
Predicting the geographic spread of wildlife epidemics requires knowledge about the movement patterns of disease hosts or vectors. The field of landscape genetics provides valuable approaches to study dispersal indirectly, which in turn may be used to understand patterns of disease spread. Here, we applied landscape genetic analyses and spatially explicit models to identify the potential path of raccoon rabies spread in a mesocarnivore community. We used relatedness estimates derived from microsatellite genotypes of raccoons and striped skunks to investigate their dispersal patterns in a heterogeneous landscape composed predominantly of agricultural, forested and residential areas. Samples were collected in an area covering 22 000 km2 in southern Québec, where the raccoon rabies variant (RRV) was first detected in 2006. Multiple regressions on distance matrices revealed that genetic distance among male raccoons was strictly a function of geographic distance, while dispersal in female raccoons was significantly reduced by the presence of agricultural fields. In skunks, our results suggested that dispersal is increased in edge habitats between fields and forest fragments in both males and females. Resistance modelling allowed us to identify likely dispersal corridors used by these two rabies hosts, which may prove especially helpful for surveillance and control (e.g. oral vaccination) activities.
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Affiliation(s)
| | - Benoit Talbot
- Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada ; Canada Research Chair in Evolutionary Demography and Conservation, Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Dany Garant
- Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Julien Mainguy
- Direction générale de l'expertise sur la faune et ses habitats, Direction de la biodiversité et des maladies de la faune, Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs Québec, QC, Canada
| | - Fanie Pelletier
- Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada ; Canada Research Chair in Evolutionary Demography and Conservation, Département de biologie, Université de Sherbrooke Sherbrooke, QC, Canada
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17
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The impact of environmental factors on the diversity of gastropod communities in sinkhole ponds in a coal mining region (Silesian Upland, Southern Poland). Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0369-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Davis J, Pavlova A, Thompson R, Sunnucks P. Evolutionary refugia and ecological refuges: key concepts for conserving Australian arid zone freshwater biodiversity under climate change. GLOBAL CHANGE BIOLOGY 2013; 19:1970-1984. [PMID: 23526791 PMCID: PMC3746109 DOI: 10.1111/gcb.12203] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 05/27/2023]
Abstract
Refugia have been suggested as priority sites for conservation under climate change because of their ability to facilitate survival of biota under adverse conditions. Here, we review the likely role of refugial habitats in conserving freshwater biota in arid Australian aquatic systems where the major long-term climatic influence has been aridification. We introduce a conceptual model that characterizes evolutionary refugia and ecological refugees based on our review of the attributes of aquatic habitats and freshwater taxa (fishes and aquatic invertebrates) in arid Australia. We also identify methods of recognizing likely future refugia and approaches to assessing the vulnerability of arid-adapted freshwater biota to a warming and drying climate. Evolutionary refugia in arid areas are characterized as permanent, groundwater-dependent habitats (subterranean aquifers and springs) supporting vicariant relicts and short-range endemics. Ecological refugees can vary across space and time, depending on the dispersal abilities of aquatic taxa and the geographical proximity and hydrological connectivity of aquatic habitats. The most important are the perennial waterbodies (both groundwater and surface water fed) that support obligate aquatic organisms. These species will persist where suitable habitats are available and dispersal pathways are maintained. For very mobile species (invertebrates with an aerial dispersal phase) evolutionary refugia may also act as ecological refugees. Evolutionary refugia are likely future refugia because their water source (groundwater) is decoupled from local precipitation. However, their biota is extremely vulnerable to changes in local conditions because population extinction risks cannot be abated by the dispersal of individuals from other sites. Conservation planning must incorporate a high level of protection for aquifers that support refugial sites. Ecological refuges are vulnerable to changes in regional climate because they have little thermal or hydrological buffering. Accordingly, conservation planning must focus on maintaining meta-population processes, especially through dynamic connectivity between aquatic habitats at a landscape scale.
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Affiliation(s)
- Jenny Davis
- Australian Centre for Biodiversity, School of Biological Sciences, Monash University, Clayton, Australia.
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19
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Dudaniec RY, Rhodes JR, Worthington Wilmer J, Lyons M, Lee KE, McAlpine CA, Carrick FN. Using multilevel models to identify drivers of landscape-genetic structure among management areas. Mol Ecol 2013; 22:3752-65. [PMID: 23730800 DOI: 10.1111/mec.12359] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/02/2013] [Accepted: 04/05/2013] [Indexed: 11/26/2022]
Abstract
Landscape genetics offers a powerful approach to understanding species' dispersal patterns. However, a central obstacle is to account for ecological processes operating at multiple spatial scales, while keeping research outcomes applicable to conservation management. We address this challenge by applying a novel multilevel regression approach to model landscape drivers of genetic structure at both the resolution of individuals and at a spatial resolution relevant to management (i.e. local government management areas: LGAs) for the koala (Phascolartos cinereus) in Australia. Our approach allows for the simultaneous incorporation of drivers of landscape-genetic relationships operating at multiple spatial resolutions. Using microsatellite data for 1106 koalas, we show that, at the individual resolution, foliage projective cover (FPC) facilitates high gene flow (i.e. low resistance) until it falls below approximately 30%. Out of six additional land-cover variables, only highways and freeways further explained genetic distance after accounting for the effect of FPC. At the LGA resolution, there was significant variation in isolation-by-resistance (IBR) relationships in terms of their slopes and intercepts. This was predominantly explained by the average resistance distance among LGAs, with a weaker effect of historical forest cover. Rates of recent landscape change did not further explain variation in IBR relationships among LGAs. By using a novel multilevel model, we disentangle the effect of landscape resistance on gene flow at the fine resolution (i.e. among individuals) from effects occurring at coarser resolutions (i.e. among LGAs). This has important implications for our ability to identify appropriate scale-dependent management actions.
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Affiliation(s)
- Rachael Y Dudaniec
- School of Geography, Planning and Environmental Management, The University of Queensland, Brisbane, QLD, 4072, Australia.
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20
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Keller D, Holderegger R, van Strien MJ. Spatial scale affects landscape genetic analysis of a wetland grasshopper. Mol Ecol 2013; 22:2467-82. [DOI: 10.1111/mec.12265] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 01/15/2013] [Accepted: 01/22/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Daniela Keller
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 CH-8903 Birmensdorf Switzerland
- Department of Environmental Systems Science; ETH Zurich; Universitätsstrasse 16 CH-8092 Zurich Switzerland
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 CH-8903 Birmensdorf Switzerland
- Department of Environmental Systems Science; ETH Zurich; Universitätsstrasse 16 CH-8092 Zurich Switzerland
| | - Maarten J. van Strien
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 CH-8903 Birmensdorf Switzerland
- Department of Environmental Systems Science; ETH Zurich; Universitätsstrasse 16 CH-8092 Zurich Switzerland
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21
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Guzik MT, Adams MA, Murphy NP, Cooper SJB, Austin AD. Desert springs: deep phylogeographic structure in an ancient endemic crustacean (Phreatomerus latipes). PLoS One 2012; 7:e37642. [PMID: 22815684 PMCID: PMC3398905 DOI: 10.1371/journal.pone.0037642] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 04/26/2012] [Indexed: 12/03/2022] Open
Abstract
Desert mound springs of the Great Artesian Basin in central Australia maintain an endemic fauna that have historically been considered ubiquitous throughout all of the springs. Recent studies, however, have shown that several endemic invertebrate species are genetically highly structured and contain previously unrecognised species, suggesting that individuals may be geographically 'stranded in desert islands'. Here we further tested the generality of this hypothesis by conducting genetic analyses of the obligate aquatic phreatoicid isopod Phreatomerus latipes. Phylogenetic and phylogeographic relationships amongst P. latipes individuals were examined using a multilocus approach comprising allozymes and mtDNA sequence data. From the Lake Eyre region in South Australia we collected data for 476 individuals from 69 springs for the mtDNA gene COI; in addition, allozyme electrophoresis was conducted on 331 individuals from 19 sites for 25 putative loci. Phylogenetic and population genetic analyses showed three major clades in both allozyme and mtDNA data, with a further nine mtDNA sub-clades, largely supported by the allozymes. Generally, each of these sub-clades was concordant with a traditional geographic grouping known as spring complexes. We observed a coalescent time between ∼2-15 million years ago for haplotypes within each of the nine mtDNA sub-clades, whilst an older total time to coalescence (>15 mya) was observed for the three major clades. Overall we observed that multiple layers of phylogeographic history are exemplified by Phreatomerus, suggesting that major climate events and their impact on the landscape have shaped the observed high levels of diversity and endemism. Our results show that this genus reflects a diverse fauna that existed during the early Miocene and appears to have been regionally restricted. Subsequent aridification events have led to substantial contraction of the original habitat, possibly over repeated Pleistocene ice age cycles, with P. latipes populations becoming restricted in the distribution to desert springs.
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Affiliation(s)
- Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, The University of Adelaide, North Terrace, Adelaide, South Australia, Australia.
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Bertin A, Ruíz VH, Figueroa R, Gouin N. The role of spatial processes and environmental determinants in microgeographic shell variation of the freshwater snail Chilina dombeyana (Bruguière, 1789). Naturwissenschaften 2012; 99:225-32. [DOI: 10.1007/s00114-012-0890-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/26/2012] [Accepted: 01/31/2012] [Indexed: 10/14/2022]
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Catastrophic floods may pave the way for increased genetic diversity in endemic artesian spring snail populations. PLoS One 2011; 6:e28645. [PMID: 22205959 PMCID: PMC3243680 DOI: 10.1371/journal.pone.0028645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 11/11/2011] [Indexed: 11/25/2022] Open
Abstract
The role of disturbance in the promotion of biological heterogeneity is widely recognised and occurs at a variety of ecological and evolutionary scales. However, within species, the impact of disturbances that decimate populations are neither predicted nor known to result in conditions that promote genetic diversity. Directly examining the population genetic consequences of catastrophic disturbances however, is rarely possible, as it requires both longitudinal genetic data sets and serendipitous timing. Our long-term study of the endemic aquatic invertebrates of the artesian spring ecosystem of arid central Australia has presented such an opportunity. Here we show a catastrophic flood event, which caused a near total population crash in an aquatic snail species (Fonscochlea accepta) endemic to this ecosystem, may have led to enhanced levels of within species genetic diversity. Analyses of individuals sampled and genotyped from the same springs sampled both pre (1988–1990) and post (1995, 2002–2006) a devastating flood event in 1992, revealed significantly higher allelic richness, reduced temporal population structuring and greater effective population sizes in nearly all post flood populations. Our results suggest that the response of individual species to disturbance and severe population bottlenecks is likely to be highly idiosyncratic and may depend on both their ecology (whether they are resilient or resistant to disturbance) and the stability of the environmental conditions (i.e. frequency and intensity of disturbances) in which they have evolved.
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Bronnenhuber JE, Dufour BA, Higgs DM, Heath DD. Dispersal strategies, secondary range expansion and invasion genetics of the nonindigenous round goby, Neogobius melanostomus, in Great Lakes tributaries. Mol Ecol 2011; 20:1845-59. [PMID: 21492265 DOI: 10.1111/j.1365-294x.2011.05030.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dispersal strategies are important mechanisms underlying the spatial distribution and colonizing ability of all mobile species. In the current study, we use highly polymorphic microsatellite markers to evaluate local dispersal and colonization dynamics of the round goby (Neogobius melanostomus), an aquatic invader expanding its range from lake to river environments in its introduced North American range. Genetic structure, genotype assignment and genetic diversity were compared among 1262 round gobies from 20 river and four lake sites in three Great Lakes tributaries. Our results indicate that a combination of short-distance diffusion and long-distance dispersal, collectively referred to as 'stratified dispersal', is facilitating river colonization. Colonization proceeded upstream yearly (approximately 500 m/year; 2005-2009) in one of two temporal replicates while genetic structure was temporally stable. Contiguous dispersal from the lake was observed in all three rivers with a substantial portion of river fish (7.3%) identified as migrants. Genotype assignment indicated a separate introduction occurred upstream of the invasion front in one river. Genetic diversity was similar and relatively high among lake and recently colonized river populations, indicating that founder effects are mitigated through a dual-dispersal strategy. The remarkable success of round goby as an aquatic invader stresses the need for better diffusion models of secondary range expansion for presumably sessile invasive species.
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Affiliation(s)
- Jennifer E Bronnenhuber
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave. Windsor, ON N9B 3P4, Canada
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Abstract
Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.
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Affiliation(s)
- Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
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Mehner T, Pohlmann K, Elkin C, Monaghan MT, Freyhof J. Genetic mixing from enhancement stocking in commercially exploited vendace populations. J Appl Ecol 2009. [DOI: 10.1111/j.1365-2664.2009.01733.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Environmental and social influences on the genetic structure of bottlenose dolphins (Tursiops aduncus) in Southeastern Australia. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9968-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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