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Trense D, Schmidt TL, Yang Q, Chung J, Hoffmann AA, Fischer K. Anthropogenic and natural barriers affect genetic connectivity in an Alpine butterfly. Mol Ecol 2020; 30:114-130. [PMID: 33108010 DOI: 10.1111/mec.15707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/22/2022]
Abstract
Dispersal is a key biological process serving several functions including connectivity among populations. Habitat fragmentation caused by natural or anthropogenic structures may hamper dispersal, thereby disrupting genetic connectivity. Investigating factors affecting dispersal and gene flow is important in the current era of anthropogenic global change, as dispersal comprises a vital part of a species' resilience to environmental change. Using finescale landscape genomics, we investigated gene flow and genetic structure of the Sooty Copper butterfly (Lycaena tityrus) in the Alpine Ötz valley system in Austria. We found surprisingly high levels of gene flow in L. tityrus across the region. Nevertheless, ravines, forests, and roads had effects on genetic structure, while rivers did not. The latter is surprising as roads and rivers have a similar width and run largely in parallel in our study area, pointing towards a higher impact of anthropogenic compared with natural linear structures. Additionally, we detected eleven loci potentially under thermal selection, including ones related to membranes, metabolism, and immune function. This study demonstrates the usefulness of molecular approaches in obtaining estimates of dispersal and population processes in the wild. Our results suggest that, despite high gene flow in the Alpine valley system investigated, L. tityrus nevertheless seems to be vulnerable to anthropogenically-driven habitat fragmentation. With anthropogenic rather than natural linear structures affecting gene flow, this may have important consequences for the persistence of species such as the butterfly studied here in altered landscapes.
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Affiliation(s)
- Daronja Trense
- Institute for Integrated Natural Sciences, Zoology, University Koblenz-Landau, Koblenz, Germany
| | - Thomas L Schmidt
- Pest & Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, Parkville, Vic., Australia
| | - Qiong Yang
- Pest & Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, Parkville, Vic., Australia
| | - Jessica Chung
- Pest & Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, Parkville, Vic., Australia
| | - Ary A Hoffmann
- Pest & Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, Parkville, Vic., Australia
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, Zoology, University Koblenz-Landau, Koblenz, Germany
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2
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Dispersal, philopatry and population genetic structure of the mainland dibbler, Parantechinus apicalis. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01196-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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3
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Selwood KE, Clarke RH, McGeoch MA, Mac Nally R. Green Tongues into the Arid Zone: River Floodplains Extend the Distribution of Terrestrial Bird Species. Ecosystems 2016. [DOI: 10.1007/s10021-016-0059-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Effects of Range Contraction and Habitat Fragmentation on Genetic Variation in the Woodland Deer Mouse (Peromyscus maniculatus gracilis). AMERICAN MIDLAND NATURALIST 2016. [DOI: 10.1674/0003-0031-176.2.272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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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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Li Y, Lancaster ML, Cooper SJB, Taylor AC, Carthew SM. Population structure and gene flow in the endangered southern brown bandicoot (Isoodon obesulus obesulus) across a fragmented landscape. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0661-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Ćosić N, Říčanová Š, Bryja J, Penezić A, Ćirović D. Do rivers and human-induced habitat fragmentation affect genetic diversity and population structure of the European ground squirrel at the edge of its Pannonian range? CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0466-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Baguette M, Blanchet S, Legrand D, Stevens VM, Turlure C. Individual dispersal, landscape connectivity and ecological networks. Biol Rev Camb Philos Soc 2012; 88:310-26. [DOI: 10.1111/brv.12000] [Citation(s) in RCA: 385] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 10/18/2012] [Accepted: 10/25/2012] [Indexed: 11/28/2022]
Affiliation(s)
| | - Simon Blanchet
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Delphine Legrand
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Virginie M. Stevens
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Camille Turlure
- F.R.S.-FNRS; Universite Catholique de Louvain, Earth and Life Institute, Biodiversity Research Centre; Croix du Sud 4; B-1348; Louvain-la-Neuve; Belgium
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LADA HANIA, THOMSON JAMESR, CUNNINGHAM SHAUNC, MAC NALLY RALPH. Rainfall in prior breeding seasons influences population size of a small marsupial. AUSTRAL ECOL 2012. [DOI: 10.1111/aec.12002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- HANIA LADA
- Australian Centre for Biodiversity; School of Biological Sciences; Monash University; Clayton; Vic.; 3800; Australia
| | - JAMES R. THOMSON
- Australian Centre for Biodiversity; School of Biological Sciences; Monash University; Clayton; Vic.; 3800; Australia
| | - SHAUN C. CUNNINGHAM
- Australian Centre for Biodiversity; School of Biological Sciences; Monash University; Clayton; Vic.; 3800; Australia
| | - RALPH MAC NALLY
- Australian Centre for Biodiversity; School of Biological Sciences; Monash University; Clayton; Vic.; 3800; Australia
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Uwimana B, D'Andrea L, Felber F, Hooftman DAP, Den Nijs HCM, Smulders MJM, Visser RGF, Van De Wiel CCM. A Bayesian analysis of gene flow from crops to their wild relatives: cultivated (Lactuca sativa L.) and prickly lettuce (L. serriola L.) and the recent expansion of L. serriola in Europe. Mol Ecol 2012; 21:2640-54. [PMID: 22512715 DOI: 10.1111/j.1365-294x.2012.05489.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interspecific gene flow can lead to the formation of hybrid populations that have a competitive advantage over the parental populations, even for hybrids from a cross between crops and wild relatives. Wild prickly lettuce (Lactuca serriola) has recently expanded in Europe and hybridization with the related crop species (cultivated lettuce, L. sativa) has been hypothesized as one of the mechanisms behind this expansion. In a basically selfing species, such as lettuce, assessing hybridization in natural populations may not be straightforward. Therefore, we analysed a uniquely large data set of plants genotyped with SSR (simple sequence repeat) markers with two programs for Bayesian population genetic analysis, STRUCTURE and NewHybrids. The data set comprised 7738 plants, including a complete genebank collection, which provided a wide coverage of cultivated germplasm and a fair coverage of wild accessions, and a set of wild populations recently sampled across Europe. STRUCTURE analysis inferred the occurrence of hybrids at a level of 7% across Europe. NewHybrids indicated these hybrids to be advanced selfed generations of a hybridization event or of one backcross after such an event, which is according to expectations for a basically selfing species. These advanced selfed generations could not be detected effectively with crop-specific alleles. In the northern part of Europe, where the expansion of L. serriola took place, the fewest putative hybrids were found. Therefore, we conclude that other mechanisms than crop/wild gene flow, such as an increase in disturbed habitats and/or climate warming, are more likely explanations for this expansion.
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Amos JN, Bennett AF, Mac Nally R, Newell G, Pavlova A, Radford JQ, Thomson JR, White M, Sunnucks P. Predicting landscape-genetic consequences of habitat loss, fragmentation and mobility for multiple species of woodland birds. PLoS One 2012; 7:e30888. [PMID: 22363508 PMCID: PMC3281894 DOI: 10.1371/journal.pone.0030888] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 12/22/2011] [Indexed: 11/18/2022] Open
Abstract
Inference concerning the impact of habitat fragmentation on dispersal and gene flow is a key theme in landscape genetics. Recently, the ability of established approaches to identify reliably the differential effects of landscape structure (e.g. land-cover composition, remnant vegetation configuration and extent) on the mobility of organisms has been questioned. More explicit methods of predicting and testing for such effects must move beyond post hoc explanations for single landscapes and species. Here, we document a process for making a priori predictions, using existing spatial and ecological data and expert opinion, of the effects of landscape structure on genetic structure of multiple species across replicated landscape blocks. We compare the results of two common methods for estimating the influence of landscape structure on effective distance: least-cost path analysis and isolation-by-resistance. We present a series of alternative models of genetic connectivity in the study area, represented by different landscape resistance surfaces for calculating effective distance, and identify appropriate null models. The process is applied to ten species of sympatric woodland-dependant birds. For each species, we rank a priori the expectation of fit of genetic response to the models according to the expected response of birds to loss of structural connectivity and landscape-scale tree-cover. These rankings (our hypotheses) are presented for testing with empirical genetic data in a subsequent contribution. We propose that this replicated landscape, multi-species approach offers a robust method for identifying the likely effects of landscape fragmentation on dispersal.
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Affiliation(s)
- J Nevil Amos
- School of Biological Sciences and Australian Centre for Biodiversity, Monash University, Melbourne, Victoria, Australia.
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12
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WANG IANJ. Choosing appropriate genetic markers and analytical methods for testing landscape genetic hypotheses. Mol Ecol 2011. [DOI: 10.1111/j.1365-294x.2011.05123.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Levy E, Kennington WJ, Tomkins JL, Lebas NR. Land clearing reduces gene flow in the granite outcrop-dwelling lizard, Ctenophorus ornatus. Mol Ecol 2010; 19:4192-203. [PMID: 20831643 DOI: 10.1111/j.1365-294x.2010.04810.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An important question for the conservation of species dwelling in fragmented habitats is whether changes to the intervening landscape create a barrier to gene flow. Here, we make use of the spatial distribution of the granite outcrop-dwelling lizard, Ctenophorus ornatus, to compare inferred levels of gene flow between outcrops in a nature reserve with that between outcrops in the adjacent agricultural land. Genetic variation, relatedness and subdivision were compared within groups of individuals from different outcrops similar in size and distance apart at each site. In the agricultural land, we found significantly lower genetic variation within outcrops and greater genetic differentiation between outcrops than in the reserve. Further, the rate at which genetic divergence between outcrops increased over geographical distance was significantly greater in the agricultural land than in the reserve. We also found that individuals were more closely related within outcrops but more distantly related between outcrops in the cleared land. These effects occur over a small spatial scale with an average distance between outcrops of less than five kilometres. Thus, even though land clearing around the outcrops leaves outcrop size unchanged, it restricts gene flow, reducing genetic variation and increasing population structure, with potentially negative consequences for the long-term persistence of the lizards on these outcrops.
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Affiliation(s)
- Esther Levy
- Centre for Evolutionary Biology, School of Animal Biology, The University of Western Australia, M092, 35 Stirling Hwy, Crawley, WA 6009, Australia
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14
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Inference of population history by coupling exploratory and model-driven phylogeographic analyses. Int J Mol Sci 2010; 11:1190-227. [PMID: 20480016 PMCID: PMC2871112 DOI: 10.3390/ijms11041190] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 11/16/2022] Open
Abstract
Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.
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Braaker S, Heckel G. Transalpine colonisation and partial phylogeographic erosion by dispersal in the common vole (Microtus arvalis). Mol Ecol 2009; 18:2518-31. [PMID: 19389166 DOI: 10.1111/j.1365-294x.2009.04189.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The colonisation history and genetic structure of the common vole (Microtus arvalis) was investigated in the region of the Alps by analysing the mitochondrial cytochrome b gene (mtDNA) and 19 microsatellite loci (nucDNA) for 137 voles from 52 localities. mtDNA data provided a much refined distribution of three highly divergent evolutionary lineages in the region compared to previous studies. Although high mountain ranges are widely accepted to be barriers for colonisation processes for many organisms and especially small terrestrial mammals, our phylogeographic analyses showed clear evidence of four transalpine colonisation events by the common vole. Individual-based phylogenetic analyses of nucDNA and two alternative Bayesian-clustering approaches revealed a deep genetic structure analogous to mtDNA. Incongruence between nucDNA and mtDNA at the individual level was restricted to the regions of contact between the lineages. mtDNA patterns and strong female philopatry in M. arvalis suggest that the crossings of the Alps occurred during the colonisation of the region when it was free from ice after the last glaciation. nucDNA patterns suggest that some of the transalpine elements of this phylogeographic pattern were subsequently eroded by male-biased gene flow. We conclude that the combination of phylogeography and landscape genetics at the individual level can provide very detailed insights into colonisation events and may even allow differentiation between historical and more recent processes.
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Affiliation(s)
- Sonja Braaker
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
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Smith AL, Gardner MG, Fenner AL, Bull CM. Restricted gene flow in the endangered pygmy bluetongue lizard (Tiliqua adelaidensis) in a fragmented agricultural landscape. WILDLIFE RESEARCH 2009. [DOI: 10.1071/wr08171] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Habitat fragmentation can have several adverse genetic impacts on populations. Assessing the extent of these threatening processes is essential in conservation management. In the present study, we investigated the genetic population structure of the endangered pygmy bluetongue lizard, Tiliqua adelaidensis, which is now restricted to a few small fragments of its previously more extensive grassland habitat. The aim of our study was to investigate genetic diversity and gene flow both among and within sample sites. The information will assist in making recommendations for habitat conservation and translocation programs. We collected DNA from 229 individuals from six isolated sample sites and genotyped them for 16 polymorphic microsatellite loci. Across all six sample sites, observed heterozygosity ranged from 0.75 to 0.82. There was no evidence of population bottlenecks and little evidence of inbreeding due to consanguineous mating. Genetic differentiation was low to moderate although significant for all pairs of sample sites (FST = 0.021–0.091). Results from Bayesian clustering analyses revealed distinct clusters in the overall sample and suggested restricted gene flow between sample sites separated by distances ranging from 1.7 to 71.6 km. By using spatial autocorrelation, we also found a significant genetic structure within sample sites at distances up to 30 m, suggesting restricted gene flow even in small patches of continuous habitat. It will be important to preserve this finely clustered population structure in captive breeding and translocation programs. Increasing opportunities for gene flow through habitat corridors or population augmentation may help maintain genetic diversity and prevent an increase in differentiation. Although endangered species do not always present model systems for studying fragmentation, our approach shows how important genetic information can be acquired to aid conservation in highly fragmented ecosystems.
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Lada H, Thomson JR, Mac Nally R, Taylor AC. Impacts of massive landscape change on a carnivorous marsupial in south-eastern Australia: inferences from landscape genetics analysis. J Appl Ecol 2008. [DOI: 10.1111/j.1365-2664.2008.01563.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Guillot G. Inference of structure in subdivided populations at low levels of genetic differentiation--the correlated allele frequencies model revisited. ACTA ACUST UNITED AC 2008; 24:2222-8. [PMID: 18710873 DOI: 10.1093/bioinformatics/btn419] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION This article considers the problem of estimating population genetic subdivision from multilocus genotype data. A model is considered to make use of genotypes and possibly of spatial coordinates of sampled individuals. A particular attention is paid to the case of low genetic differentiation with the help of a previously described Bayesian clustering model where allele frequencies are assumed to be a priori correlated. Under this model, various problems of inference are considered, in particular the common and difficult, but still unaddressed, situation where the number of populations is unknown. RESULTS A Markov chain Monte Carlo algorithm and a new post-processing scheme are proposed. It is shown that they significantly improve the accuracy of previously existing algorithms in terms of estimated number of populations and estimated population membership. This is illustrated numerically with data simulated from the prior-likelihood model used in inference and also with data simulated from a Wright-Fisher model. Improvements are also illustrated on a real dataset of eighty-eight wolverines (Gulo gulo) genotyped at 10 microsatellites loci. The interest of the solutions presented here are not specific to any clustering model and are hence relevant to many settings in populations genetics where weakly differentiated populations are assumed or sought. AVAILABILITY The improvements implemented will be made available in version 3.0.0 of the R package Geneland. Informations on how to get and use the software are available from http://folk.uio.no/gillesg/Geneland.html. SUPPLEMENTARY INFORMATION http://folk.uio.no/gillesg/CFM/SuppMat.pdf.
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Affiliation(s)
- Gilles Guillot
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, P.O Box 1066 Blindern, 0316 Oslo, Norway.
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Lada H, Mac Nally R. Decline and potential recovery of Yellow-footed Antechinus in parts of south-eastern Australia: A perspective with implications for management. ECOLOGICAL MANAGEMENT & RESTORATION 2008. [DOI: 10.1111/j.1442-8903.2008.00403.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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