in

Assessing the influence of the amount of reachable habitat on genetic structure using landscape and genetic graphs

  • Andersson E, Bodin Ö (2009) Practical tool for landscape planning? an empirical investigation of network-based models of habitat fragmentation. Ecography 32(1):123–132

    Google Scholar 

  • Angelone S, Kienast F, Holderegger R (2011) Where movement happens—scale-dependent landscape effects on genetic differentiation in the European tree frog. Ecography 34(5):714–722

    Google Scholar 

  • Arnaud J-F (2003) Metapopulation genetic structure and migration pathways in the land snail Helix aspersa: influence of landscape heterogeneity. Landsc Ecol 18(3):333–346

    Google Scholar 

  • Awade M, Boscolo D, Metzger JP (2012) Using binary and probabilistic habitat availability indices derived from graph theory to model bird occurrence in fragmented forests. Landsc Ecol 27(2):185–198

    Google Scholar 

  • Balkenhol N, Pardini R, Cornelius C, Fernandes F, Sommer S (2013) Landscape-level comparison of genetic diversity and differentiation in a small mammal inhabiting different fragmented landscapes of the Brazilian Atlantic Forest. Conserv Genet 14(2):355–367

    Google Scholar 

  • Baranyi G, Saura S, Podani J, Jordán F (2011) Contribution of habitat patches to network connectivity: redundancy and uniqueness of topological indices. Ecol Indic 11(5):1301–1310

    Google Scholar 

  • Barr KR, Kus BE, Preston KL, Howell S, Perkins E, Vandergast AG (2015) Habitat fragmentation in coastal southern California disrupts genetic connectivity in the Cactus Wren (Campylorhynchus brunneicapillus). Mol Ecol 24(10):2349–2363

    PubMed 

    Google Scholar 

  • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soci Series B (Methodological) 57(1):289–300

    Google Scholar 

  • Bergés L, Avon C, Bezombes L, Clauzel C, Duflot R, Foltête J-C, Gaucherand S, Girardet X, Spiegelberger T (2020) Environmental mitigation hierarchy and biodiversity offsets revisited through habitat connectivity modelling. J Environ Manag 256:1–10

    Google Scholar 

  • Bertin A, Gouin N, Baumel A, Gianoli E, Serratosa J, Osorio R, Manel S (2017) Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat. Mol Ecol 26(2):431–443

    PubMed 

    Google Scholar 

  • Bönsel AB, Sonneck A-G (2011) Habitat use and dispersal characteristic by Stethophyma grossum: the role of habitat isolation and stable habitat conditions towards low dispersal. J Insect Conserv 15(3):455–463

    Google Scholar 

  • Boulanger E, Dalongeville A, Andrello M, Mouillot D, Manel S (2020) Spatial graphs highlight how multi-generational dispersal shapes landscape genetic patterns. Ecography 15(1):1–13

    Google Scholar 

  • Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368(6470):455–457

    PubMed 

    Google Scholar 

  • Capurucho JMG, Cornelius C, Borges SH, Cohn-Haft M, Aleixo A, Metzger JP, Ribas CC (2013) Combining phylogeography and landscape genetics of Xenopipo atronitens (Aves: Pipridae), a white sand campina specialist, to understand Pleistocene landscape evolution in Amazonia. Biol J Linnean Soc 110(1):60–76

    Google Scholar 

  • Carrascal LM, Galván I, Gordo O (2009) Partial Least Squares regression as an alternative to current regression methods used in ecology. Oikos 118(5):681–690

    Google Scholar 

  • Cushman SA, Shirk A, Landguth EL (2012) Separating the effects of habitat area, fragmentation and matrix resistance on genetic differentiation in complex landscapes. Landsc Ecol 27(3):369–380

    Google Scholar 

  • Díaz SM, Settele J, Brondízio E, Ngo H, Guèze M, Agard J, Arneth A, Balvanera P, Brauman K, Butchart S, et al. (2019). The global assessment report on biodiversity and ecosystem services: summary for policy makers. Technical report, Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services

  • Didham RK, Kapos V, Ewers RM (2012) Rethinking the conceptual foundations of habitat fragmentation research. Oikos 121(2):161–170

    Google Scholar 

  • DiLeo MF, Wagner HH (2016) A landscape ecologist’s agenda for landscape genetics. Curr Landsc Ecol Rep 1(3):115–126

    Google Scholar 

  • Dyer RJ (2015) Population graphs and landscape genetics. Annu Rev Ecol, Evolut Syst 46:327–342

    Google Scholar 

  • Fahrig L (2013) Rethinking patch size and isolation effects: the habitat amount hypothesis. J Biogeogr 40(9):1649–1663

    Google Scholar 

  • Flavenot T, Fellous S, Abdelkrim J, Baguette M, Coulon A (2015) Impact of quarrying on genetic diversity: an approach across landscapes and over time. Conserv Genet 16(1):181–194

    Google Scholar 

  • Foltête J-C, Clauzel C, Vuidel G (2012) A software tool dedicated to the modelling of landscape networks. Environ Model Softw 38:316–327

    Google Scholar 

  • Foltête J-C, Savary P, Clauzel C, Bourgeois M, Girardet X, Sahraoui Y, Vuidel G, Garnier S (2020) Coupling landscape graph modeling and biological data: a review. Landsc Ecol 35(5):1035–1052

    Google Scholar 

  • Frankham R (2005) Genetics and extinction. Biol Conserv 126(2):131–140

    Google Scholar 

  • Frankham R (2015) Genetic rescue of small inbred populations: Meta-analysis reveals large and consistent benefits of gene flow. Mol Ecol 24(11):2610–2618

    PubMed 

    Google Scholar 

  • Frankham R, Ballou JD, and Briscoe DA (2004) A primer of conservation genetics. Cambridge University Press

  • Gaggiotti OE, Foll M (2010) Quantifying population structure using the F-model. Mol Ecol Resour 10(5):821–830

    PubMed 

    Google Scholar 

  • Galpern P, Manseau M, Fall A (2011) Patch-based graphs of landscape connectivity: a guide to construction, analysis and application for conservation. Biol Conserv 144(1):44–55

    Google Scholar 

  • Greenbaum G, Fefferman NH (2017) Application of network methods for understanding evolutionary dynamics in discrete habitats. Mol Ecol 26(11):2850–2863

    PubMed 

    Google Scholar 

  • Griffioen R (1996) Over het dispersievermogen van de moerassprinkhaan. Nieuwsbrief Saltabel 15(1):39–41

    Google Scholar 

  • Hahn T, Kettle CJ, Ghazoul J, Hennig EI, Pluess AR (2013) Landscape composition has limited impact on local genetic structure in mountain clover Trifolium montanum L. J Heredity 104(6):842–852

    Google Scholar 

  • Hedrick P (2011) Genetics of populations. Jones & Bartlett Learning

  • Holzhauer SI, Ekschmitt K, Sander A-C, Dauber J, Wolters V (2006) Effect of historic landscape change on the genetic structure of the bush-cricket Metrioptera roeseli. Landsc Ecol 21(6):891–899

    Google Scholar 

  • Hutchison DW, Templeton AR (1999) Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution 53(6):1898–1914

    PubMed 

    Google Scholar 

  • Ingvarsson PK (2001) Restoration of genetic variation lost-the genetic rescue hypothesis. Trends Ecol Evol 16(2):62–63

    PubMed 

    Google Scholar 

  • Jackson ND, Fahrig L (2015) Habitat amount—not habitat configuration—best predicts population genetic structure in fragmented landscapes. Landsc Ecol 31(5):951–968

    Google Scholar 

  • Joly CA, Metzger JP, Tabarelli M (2014) Experiences from the Brazilian atlantic forest: ecological findings and conservation initiatives. New Phytol 204(3):459–473

    PubMed 

    Google Scholar 

  • Kalinowski ST (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conserv Genet 5(4):539–543

    Google Scholar 

  • Keller D, Holderegger R, Strien MJ (2013) Spatial scale affects landscape genetic analysis of a wetland grasshopper. Mol Ecol 22(9):2467–2482

    PubMed 

    Google Scholar 

  • Keyghobadi N (2007) The genetic implications of habitat fragmentation for animals. Can J Zool 85(10):1049–1064

    Google Scholar 

  • Keyghobadi N, Roland J, Matter SF, Strobeck C (2005) Among- and within-patch components of genetic diversity respond at different rates to habitat fragmentation: an empirical demonstration. Proc R Soc B 272(1562):553–560

    PubMed 
    PubMed Central 

    Google Scholar 

  • Kierepka EM, Anderson SJ, Swihart RK, Rhodes OE (2020) Differing, multiscale landscape effects on genetic diversity and differentiation in eastern chipmunks. Heredity 124(3):457–468

    PubMed 
    PubMed Central 

    Google Scholar 

  • Koen EL, Bowman J, Wilson PJ (2016) Node-based measures of connectivity in genetic networks. Mol Ecol Resour 16(1):69–79

    PubMed 

    Google Scholar 

  • Koschuh A (2004) Verbreitung, lebensräume und gefährdung der sumpfschrecke (stethophyma grossum, l., 1758)(saltatoria) in der steiermark. Joannea, Zool 6:223–246

    Google Scholar 

  • Krause S (1996) Populationsstruktur, Habitatbindung und Mobilität der Larven von Stethophyma grossum (Linné, 1758). Articulata 11(2):77–89

    Google Scholar 

  • Latta RG (2006) Integrating patterns across multiple genetic markers to infer spatial processes. Landsc Ecol21(6):809–820

    Google Scholar 

  • Lehnen L, Jan P-L, Besnard A-L, Fourcy D, Kerth G, Biedermann M, Nyssen P, Schorcht W, Petit E, and Puechmaille S (2021) Genetic diversity in a long-lived mammal is explained by the past’s demographic shadow and current connectivity. Mol Ecol, 00(1)

  • Long FH (2013) Multivariate analysis for metabolomics and proteomics data. In Proteomic and metabolomic approaches to biomarker discovery, pages 299–311. Elsevier

  • Malkus J (1997) Habitatpräferenzen und mobilität der sumpfschrecke (stethophyma grossum l. 1758) unter besonderer berücksichtigung der mahd. Articulata 12(1):1–18

    Google Scholar 

  • Marzelli M (1994) Ausbreitung von mecostethus grossus auf einer ausgleichs-und renaturierungsfläche. Articulata 9(1):25–32

    Google Scholar 

  • Miguet P, Fahrig L, Lavigne C (2017) How to quantify a distance-dependent landscape effect on a biological response. Methods Ecol Evol 8(12):1717–1724

    Google Scholar 

  • Millette KL, Keyghobadi N (2015) The relative influence of habitat amount and configuration on genetic structure across multiple spatial scales. Ecol Evol 5(1):73–86

    PubMed 

    Google Scholar 

  • Moilanen A, Nieminen M (2002) Simple connectivity measures in spatial ecology. Ecology 83(4):1131–1145

    Google Scholar 

  • Mony C, Abadie J, Gil-Tena A, Burel F, Ernoult A (2018) Effects of connectivity on animal-dispersed forest plant communities in agriculture-dominated landscapes. J Veg. Sci. 29(2):167–178

    Google Scholar 

  • Murphy MA, Evans JS, Storfer A (2010) Quantifying Bufo boreas connectivity in Yellowstone National Park with landscape genetics. Ecology 91(1):252–261

    PubMed 

    Google Scholar 

  • Pascual-Hortal L, Saura S (2006) Comparison and development of new graph-based landscape connectivity indices: towards the priorization of habitat patches and corridors for conservation. Landsc Ecol 21(7):959–967

    Google Scholar 

  • Pasinelli G, Meichtry-Stier K, Birrer S, Baur B, Duss M (2013) Habitat quality and geometry affect patch occupancy of two Orthopteran species. PLoS One 8(5):e65850

    PubMed 
    PubMed Central 

    Google Scholar 

  • Pérez-Rodríguez A, Khimoun A, Ollivier A, Eraud C, Faivre B, Garnier S (2018) Habitat fragmentation, not habitat loss, drives the prevalence of blood parasites in a Caribbean passerine. Ecography 41(11):1835–1849

    Google Scholar 

  • Peterman WE, Anderson TL, Ousterhout BH, Drake DL, Semlitsch RD, Eggert LS (2015) Differential dispersal shapes population structure and patterns of genetic differentiation in two sympatric pond breeding salamanders. Conserv Genet 16(1):59–69

    Google Scholar 

  • Rayfield B, Fortin M-J, Fall A (2011) Connectivity for conservation: a framework to classify network measures. Ecology 92(4):847–858

    PubMed 

    Google Scholar 

  • Reinhardt K, Köhler G, Maas S, Detzel P (2005) Low dispersal ability and habitat specificity promote extinctions in rare but not in widespread species: the Orthoptera of Germany. Ecography 28(5):593–602

    Google Scholar 

  • Roy K, Kar S, and Das RN (2015) Statistical methods in QSAR/QSPR. In A primer on QSAR/QSPR modeling, pages 37–59. Springer

  • Rozenfeld AF, Arnaud-Haond S, Hernández-Garcia E, Eguíluz VM, Serrão EA, Duarte CM (2008) Network analysis identifies weak and strong links in a metapopulation system. Proc Natl Acad Sci 105(48):18824–18829

    PubMed 
    PubMed Central 

    Google Scholar 

  • Saura S (2018) The amount of reachable habitat—jointly measuring habitat amount and connectivity in space and time. In Proceedings of international conference of ecological sciences of the French Society for Ecology and Evolution

  • Saura S (2021) The Habitat Amount Hypothesis implies negative effects of habitat fragmentation on species richness. J Biogeogr 48(1):11–22

    Google Scholar 

  • Saura S, Bodin Ö, Fortin M-J (2014) Stepping stones are crucial for species’ long-distance dispersal and range expansion through habitat networks. J Appl Ecol 51(1):171–182

    Google Scholar 

  • Saura S and de la Fuente B (2017) Connectivity as the amount of reachable habitat: conservation priorities and the roles of habitat patches in landscape networks. In Gergel, SE and Turner, MG, editors, Learning landscape ecology: a practical guide to concepts and techniques, pages 229–254. Springer

  • Saura S, Rubio L (2010) A common currency for the different ways in which patches and links can contribute to habitat availability and connectivity in the landscape. Ecography 33(3):523–537

    Google Scholar 

  • Savary P, Foltête J-C, Moal H, Vuidel G, Garnier S (2021a) Analysing landscape effects on dispersal networks and gene flow with genetic graphs. Mol Ecol Resour 21(4):1167–1185

    PubMed 

    Google Scholar 

  • Savary P, Foltête J-C, Moal H, Vuidel G, Garnier S (2021b) graph4lg: a package for constructing and analysing graphs for landscape genetics in R. Methods Ecol Evol 12(3):539–547

    Google Scholar 

  • Schoville SD, Dalongeville A, Viennois G, Gugerli F, Taberlet P, Lequette B, Alvarez N, Manel S (2018) Preserving genetic connectivity in the European Alps protected area network. Biol Conserv 218:99–109

    Google Scholar 

  • Shirk A, Cushman S (2011) sGD: software for estimating spatially explicit indices of genetic diversity. Mol Ecol Resour 11(5):922–934

    PubMed 

    Google Scholar 

  • Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47(1):264–279

    PubMed 

    Google Scholar 

  • Sonneck A-G, Bönsel A, Matthes J (2008) Der einfluss von landnutzung auf die habitate von stethophyma grossum (linnaeus, 1758) an beispielen aus mecklenburg-vorpommern. Articulata 23:15–30

    Google Scholar 

  • Spielman D, Brook BW, Frankham R (2004) Most species are not driven to extinction before genetic factors impact them. Proc Natl Acad Sci 101(42):15261–15264

    PubMed 
    PubMed Central 

    Google Scholar 

  • Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP (2010) Landscape genetics: where are we now? Mol Ecol 19(17):3496–3514

    PubMed 

    Google Scholar 

  • Szpiech ZA, Jakobsson M, Rosenberg NA (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24(21):2498–2504

    PubMed 
    PubMed Central 

    Google Scholar 

  • Taylor Z, Hoffman S (2014) Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus). Heredity 112(6):588–595

    PubMed 
    PubMed Central 

    Google Scholar 

  • Tenenhaus M (1998) La régression PLS: théorie et pratique. Editions TECHNIP

  • Toma Y, Imanishi J, Yokogawa M, Hashimoto H, Imanishi A, Morimoto Y, Hatanaka Y, Isagi Y, Shibata S (2015) Factors affecting the genetic diversity of a perennial herb Viola grypoceras A. Gray var. grypoceras in urban fragmented forests. Landsc Ecol 30(8):1435–1447

    Google Scholar 

  • Tournant P, Afonso E, Roué S, Giraudoux P, Foltête J-C (2013) Evaluating the effect of habitat connectivity on the distribution of lesser horseshoe bat maternity roosts using landscape graphs. Biol Conserv 164:39–49

    Google Scholar 

  • Trautner J, Hermann G (2008) Die Sumpfschrecke (Stethophyma grossum L., 1758) im Aufwind-Erkenntnisse aus dem zentralen Baden-Württemberg. Articulata 23(2):37–52

    Google Scholar 

  • Urban D, Keitt T (2001) Landscape connectivity: a graph-theoretic perspective. Ecology 82(5):1205–1218

    Google Scholar 

  • van Strien MJ (2017) Consequences of population topology for studying gene flow using link-based landscape genetic methods. Ecol Evol 7(14):5070–5081

  • van Strien MJ, Keller D, Holderegger R, Ghazoul J, Kienast F, Bolliger J (2014) Landscape genetics as a tool for conservation planning: predicting the effects of landscape change on gene flow Ecol Appl 24(2):327–339

    PubMed 

    Google Scholar 

  • Varvio S-L, Chakraborty R, Nei M (1986) Genetic variation in subdivided populations and conservation genetics. Heredity 57(2):189–198

    PubMed 

    Google Scholar 

  • Villard M-A, Metzger JP (2014) Beyond the fragmentation debate: a conceptual model to predict when habitat configuration really matters. J Appl Ecol 51(2):309–318

    Google Scholar 

  • Wagner HH, Fortin M-J (2013) A conceptual framework for the spatial analysis of landscape genetic data. Conserv Genet 14(2):253–261

    Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358–1370

    PubMed 

    Google Scholar 

  • Wold S, Sjöström M, Eriksson L (2001) PLS-regression: a basic tool of chemometrics. Chemometr Intellig Lab Syst 58(2):109–130

    Google Scholar 

  • Zetterberg A, Mörtberg UM, Balfors B (2010) Making graph theory operational for landscape ecological assessments, planning, and design. Landsc Urban Plan 95(4):181–191

    Google Scholar 


  • Source: Ecology - nature.com

    Scientists build new atlas of ocean’s oxygen-starved waters

    Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution