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Regression commonality analyses on hierarchical genetic distances

Bibliographic reference Prunier, Jérôme G. ; Colyn, Marc ; Legendre, Xavier ; Flamand, Marie-Christine. Regression commonality analyses on hierarchical genetic distances. In: Ecography : pattern and diversity in ecology, (2017)
Permanent URL http://hdl.handle.net/2078.1/183303
  1. Allen Andrew M., Månsson Johan, Jarnemo Anders, Bunnefeld Nils, The impacts of landscape structure on the winter movements and habitat selection of female red deer, 10.1007/s10344-014-0797-0
  2. Alvarado-Serrano Diego F., Hickerson Michael J., Spatially explicit summary statistics for historical population genetic inference, 10.1111/2041-210x.12489
  3. Apollonio, Cambridge Univ. Press (2010)
  4. Baguette Michel, The classical metapopulation theory and the real, natural world: a critical appraisal, 10.1016/j.baae.2004.03.001
  5. Balkenhol Niko, Holbrook Joseph D., Onorato Dave, Zager Peter, White Craig, Waits Lisette P., A multi-method approach for analyzing hierarchical genetic structures: a case study with cougarsPuma concolor, 10.1111/j.1600-0587.2013.00462.x
  6. Barbujani Guido, Oden Neal L., Sokal Robert R., Detecting Regions of Abrupt Change in Maps of Biological Variables, 10.2307/2992403
  7. Beckstead Jason W., Isolating and Examining Sources of Suppression and Multicollinearity in Multiple Linear Regression, 10.1080/00273171.2012.658331
  8. Bouzat Juan L., Johnson Kristine, Genetic structure among closely spaced leks in a peripheral population of lesser prairie-chickens : GENETIC STRUCTURE IN PRAIRIE-CHICKEN LEKS, 10.1046/j.1365-294x.2003.02068.x
  9. Cárdenas Leyla, Castilla Juan Carlos, Viard Frédérique, Hierarchical analysis of the population genetic structure inConcholepas concholepas, a marine mollusk with a long-lived dispersive larva, 10.1111/maec.12286
  10. Chapuisat Michel, Goudet Jerome, Keller Laurent, Microsatellites Reveal High Population Viscosity and Limited Dispersal in the Ant Formica paralugubris, 10.2307/2411120
  11. CHEN CHIBIAO, DURAND ERIC, FORBES FLORENCE, FRANÇOIS OLIVIER, Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study, 10.1111/j.1471-8286.2007.01769.x
  12. Clevenger Anthony P., Waltho Nigel, Performance indices to identify attributes of highway crossing structures facilitating movement of large mammals, 10.1016/j.biocon.2004.04.025
  13. Cohen, L. Erlbaum Associates (2003)
  14. Colyn, Faune Sauvage, 307, 37 (2015)
  15. Conger Anthony J., A Revised Definition for Suppressor Variables: a Guide To Their Identification and Interpretation, 10.1177/001316447403400105
  16. COULON A., GUILLOT G., COSSON J.-F., ANGIBAULT J. M. A., AULAGNIER S., CARGNELUTTI B., GALAN M., HEWISON A. J. M., Genetic structure is influenced by landscape features: empirical evidence from a roe deer population : LANDSCAPE AFFECTS ROE DEER GENETIC STRUCTURE, 10.1111/j.1365-294x.2006.02861.x
  17. COULON A., FITZPATRICK J. W., BOWMAN R., STITH B. M., MAKAREWICH C. A., STENZLER L. M., LOVETTE I. J., Congruent population structure inferred from dispersal behaviour and intensive genetic surveys of the threatened Florida scrub-jay (Aphelocoma cœrulescens), 10.1111/j.1365-294x.2008.03705.x
  18. Courville Troy, Thompson Bruce, Use of Structure Coefficients in Published Multiple Regression Articles: β is not Enough, 10.1177/0013164401612006
  19. Creager, Am. Educ. Res. J, 8, 671 (1971)
  20. Daniels, J. Br. Deer Soc, 12, 420 (2003)
  21. Dellicour S., Frantz A. C., Colyn M., Bertouille S., Chaumont F., Flamand M. C., Population structure and genetic diversity of red deer (Cervus elaphus) in forest fragments in north-western France, 10.1007/s10592-011-0230-0
  22. Dormann Carsten F., Elith Jane, Bacher Sven, Buchmann Carsten, Carl Gudrun, Carré Gabriel, Marquéz Jaime R. García, Gruber Bernd, Lafourcade Bruno, Leitão Pedro J., Münkemüller Tamara, McClean Colin, Osborne Patrick E., Reineking Björn, Schröder Boris, Skidmore Andrew K., Zurell Damaris, Lautenbach Sven, Collinearity: a review of methods to deal with it and a simulation study evaluating their performance, 10.1111/j.1600-0587.2012.07348.x
  23. Drescher, Paper presented at the American agricultural economics association annual meeting (2001)
  24. Doyle, Focus, 12, 13 (1990)
  25. Dunning John B., Danielson Brent J., Pulliam H. Ronald, Ecological Processes That Affect Populations in Complex Landscapes, 10.2307/3544901
  26. Dupanloup I., Schneider S., Excoffier L., A simulated annealing approach to define the genetic structure of populations : DEFINING THE GENETIC STRUCTURE OF POPULATIONS, 10.1046/j.1365-294x.2002.01650.x
  27. Earl Dent A., vonHoldt Bridgett M., STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method, 10.1007/s12686-011-9548-7
  28. Epps Clinton W., Keyghobadi Nusha, Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change, 10.1111/mec.13454
  29. Epps Clinton W., Palsbøll Per J., Wehausen John D., Roderick George K., Ramey Rob R., McCullough Dale R., Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep : Highways reduce genetic diversity, 10.1111/j.1461-0248.2005.00804.x
  30. EVANNO G., REGNAUT S., GOUDET J., Detecting the number of clusters of individuals using the software structure: a simulation study, 10.1111/j.1365-294x.2005.02553.x
  31. Excoffier, Genetics, 131, 479 (1992)
  32. Fahrig Lenore, Effects of Habitat Fragmentation on Biodiversity, 10.1146/annurev.ecolsys.34.011802.132419
  33. Farrar Donald E., Glauber Robert R., Multicollinearity in Regression Analysis: The Problem Revisited, 10.2307/1937887
  34. Fischer Joern, Lindenmayer David B., Landscape modification and habitat fragmentation: a synthesis, 10.1111/j.1466-8238.2007.00287.x
  35. FRANTZ A. C., POURTOIS J. TIGEL, HEUERTZ M., SCHLEY L., FLAMAND M. C., KRIER A., BERTOUILLE S., CHAUMONT F., BURKE T., Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population : ILLEGAL TRANSLOCATION OF RED DEER, 10.1111/j.1365-294x.2006.03022.x
  36. Frantz, Ecol, 46, 493 (2009)
  37. FRANTZ A. C., BERTOUILLE S., ELOY M. C., LICOPPE A., CHAUMONT F., FLAMAND M. C., Comparative landscape genetic analyses show a Belgian motorway to be a gene flow barrier for red deer (Cervus elaphus), but not wild boars (Sus scrofa) : A BELGIAN MOTORWAY AS A BARRIER TO GENE FLOW, 10.1111/j.1365-294x.2012.05623.x
  38. GARROWAY COLIN J., BOWMAN JEFF, WILSON PAUL J., Using a genetic network to parameterize a landscape resistance surface for fishers, Martes pennanti : MODELLING LANDSCAPE RESISTANCE TO GENE FLOW, 10.1111/j.1365-294x.2011.05243.x
  39. Giles Barbara E, Lundqvist Elisabeth, Goudet Jérôme, Restricted gene flow and subpopulation differentiation in Silene dioica, 10.1046/j.1365-2540.1998.00348.x
  40. Ginson Robert, Walter Ryan P., Mandrak Nicholas E., Beneteau Courtney L., Heath Daniel D., Hierarchical analysis of genetic structure in the habitat-specialist Eastern Sand Darter (Ammocrypta pellucida), 10.1002/ece3.1392
  41. Godvik Inger Maren Rivrud, Loe Leif Egil, Vik Jon Olav, Veiberg VebjØrn, Langvatn Rolf, Mysterud Atle, Temporal scales, trade-offs, and functional responses in red deer habitat selection, 10.1890/08-0576.1
  42. Goslee Sarah C., Urban Dean L., TheecodistPackage for Dissimilarity-based Analysis of Ecological Data, 10.18637/jss.v022.i07
  43. Gouskov Alexandre, Reyes Marta, Wirthner-Bitterlin Lisa, Vorburger Christoph, Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment, 10.1111/eva.12339
  44. Graves Tabitha A., Wasserman Tzeidle N., Ribeiro Milton Cezar, Landguth Erin L., Spear Stephen F., Balkenhol Niko, Higgins Colleen B., Fortin Marie-Josée, Cushman Samuel A., Waits Lisette P., The influence of landscape characteristics and home-range size on the quantification of landscape-genetics relationships, 10.1007/s10980-011-9701-4
  45. GUILLOT GILLES, LEBLOIS RAPHA��L, COULON AUR��LIE, FRANTZ ALAIN C., Statistical methods in spatial genetics, 10.1111/j.1365-294x.2009.04410.x
  46. Hamann, Bull. Mens. Natl Chasse, 260, 30 (2003)
  47. Hanski, Oxford Univ. Press (1999)
  48. HARRISON SUSAN, Local extinction in a metapopulation context: an empirical evaluation, 10.1111/j.1095-8312.1991.tb00552.x
  49. Holm, Scand. J. Stat, 6, 65 (1979)
  50. Horst, Soc. Sci. Res. Counc, 48, 431 (1941)
  51. Howell Paige E., Koen Erin L., Williams Bronwyn W., Roloff Gary J., Scribner Kim T., Contiguity of landscape features pose barriers to gene flow among American marten (Martes americana) genetic clusters in the Upper Peninsula of Michigan, 10.1007/s10980-015-0331-0
  52. Jackson Nathan D., Fahrig Lenore, Relative effects of road mortality and decreased connectivity on population genetic diversity, 10.1016/j.biocon.2011.09.010
  53. Jakobsson M., Rosenberg N. A., CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, 10.1093/bioinformatics/btm233
  54. Jarnemo Anders, Seasonal migration of male red deer (Cervus elaphus) in southern Sweden and consequences for management, 10.1007/s10344-007-0154-7
  55. Jombart T, Devillard S, Dufour A-B, Pontier D, Revealing cryptic spatial patterns in genetic variability by a new multivariate method, 10.1038/hdy.2008.34
  56. King, Paper presented at the annual meeting of the southwest educational research association (2007)
  57. Klein, Revue d'Ecol. Suppl, 5, 131 (1990)
  58. Kruuk Loeske E. B., Slate Jon, Pemberton Josephine M., Brotherstone Sue, Guinness Fiona, Clutton-Brock Tim, ANTLER SIZE IN RED DEER: HERITABILITY AND SELECTION BUT NO EVOLUTION, 10.1111/j.0014-3820.2002.tb01480.x
  59. LANDGUTH E. L., CUSHMAN S. A., SCHWARTZ M. K., McKELVEY K. S., MURPHY M., LUIKART G., Quantifying the lag time to detect barriers in landscape genetics : QUANTIFYING THE LAG TIME TO DETECT BARRIERS IN LANDSCAPE GENETICS, 10.1111/j.1365-294x.2010.04808.x
  60. Legendre, Elsevier (1998)
  61. Legendre Pierre, Anderson Marti J., DISTANCE-BASED REDUNDANCY ANALYSIS: TESTING MULTISPECIES RESPONSES IN MULTIFACTORIAL ECOLOGICAL EXPERIMENTS, 10.1890/0012-9615(1999)069[0001:dbratm]2.0.co;2
  62. Legendre Pierre, Lapointe Francois-Joseph, Casgrain Philippe, Modeling Brain Evolution from Behavior: A Permutational Regression Approach, 10.2307/2410243
  63. Lesbarrères, Evol, 27, 374 (2012)
  64. Levins, Bull. Entomol. Soc. Am, 15, 237 (1969)
  65. Lewis Jerry W., Escobar Luis A., Suppression and Enhancement in Bivariate Regression, 10.2307/2988294
  66. Malo, Ecol, 41, 701 (2004)
  67. Manel Stéphanie, Holderegger Rolf, Ten years of landscape genetics, 10.1016/j.tree.2013.05.012
  68. MAYER C., SCHIEGG K., PASINELLI G., Patchy population structure in a short-distance migrant: evidence from genetic and demographic data, 10.1111/j.1365-294x.2009.04200.x
  69. McRae Brad H., ISOLATION BY RESISTANCE, 10.1111/j.0014-3820.2006.tb00500.x
  70. McRae, The Univ. of California, Santa Barbara (2009)
  71. Mijangos Jose Luis, Pacioni Carlo, Spencer Peter B. S., Craig Michael D., Contribution of genetics to ecological restoration, 10.1111/mec.12995
  72. Monmonier Mark S., Maximum-Difference Barriers: An Alternative Numerical Regionalization Method*, 10.1111/j.1538-4632.1973.tb01011.x
  73. Mood A. M., Partitioning Variance in Multiple Regression Analyses as a Tool For Developing Learning Models, 10.3102/00028312008002191
  74. Murphy Melanie A., Evans Jeffrey S., Cushman Samuel A., Storfer Andrew, Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studies, 10.1111/j.1600-0587.2008.05428.x
  75. Newton R. G., Spurrell D. J., A Development of Multiple Regression for the Analysis of Routine Data, 10.2307/2985237
  76. Nimon, Mult. Linear Regres. Viewp, 36, 10 (2010)
  77. Nimon Kim F., Oswald Frederick L., Understanding the Results of Multiple Linear Regression : Beyond Standardized Regression Coefficients, 10.1177/1094428113493929
  78. Nimon Kim, Lewis Mitzi, Kane Richard, Haynes R. Michael, An R package to compute commonality coefficients in the multiple regression case: An introduction to the package and a practical example, 10.3758/brm.40.2.457
  79. Paulhus Delroy L., Robins Richard W., Trzesniewski Kali H., Tracy Jessica L., Two Replicable Suppressor Situations in Personality Research, 10.1207/s15327906mbr3902_7
  80. Pérez-Espona S, Pérez-Barbería F J, Goodall-Copestake W P, Jiggins C D, Gordon I J, Pemberton J M, Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey, 10.1038/hdy.2008.111
  81. Pérez-González J., Frantz A. C., Torres-Porras J., Castillo L., Carranza J., Population structure, habitat features and genetic structure of managed red deer populations, 10.1007/s10344-012-0636-0
  82. Peterman William E., Connette Grant M., Semlitsch Raymond D., Eggert Lori S., Ecological resistance surfaces predict fine-scale genetic differentiation in a terrestrial woodland salamander, 10.1111/mec.12747
  83. Pompanon François, Bonin Aurélie, Bellemain Eva, Taberlet Pierre, Genotyping errors: causes, consequences and solutions, 10.1038/nrg1707
  84. Prévot Céline, Licoppe Alain, Comparing red deer (Cervus elaphus L.) and wild boar (Sus scrofa L.) dispersal patterns in southern Belgium, 10.1007/s10344-013-0732-9
  85. Pritchard, Genetics, 155, 945 (2000)
  86. Prunier J. G., Kaufmann B., Fenet S., Picard D., Pompanon F., Joly P., Lena J. P., Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme, 10.1111/mec.12499
  87. Prunier Jérôme G., Kaufmann Bernard, Léna Jean-Paul, Fenet Serge, Pompanon François, Joly Pierre, A 40-year-old divided highway does not prevent gene flow in the alpine newt Ichthyosaura alpestris, 10.1007/s10592-013-0553-0
  88. Prunier J. G., Colyn M., Legendre X., Nimon K. F., Flamand M. C., Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses, 10.1111/mec.13029
  89. Prunier, Dryad Digital Repository (2016)
  90. Puechmaille Sebastien J., The programstructuredoes not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem, 10.1111/1755-0998.12512
  91. Ray-Mukherjee Jayanti, Nimon Kim, Mukherjee Shomen, Morris Douglas W., Slotow Rob, Hamer Michelle, Using commonality analysis in multiple regressions: a tool to decompose regression effects in the face of multicollinearity, 10.1111/2041-210x.12166
  92. Renner Swen C., Suarez-Rubio Marcela, Wiesner Kerstin R., Drögemüller Cord, Gockel Sonja, Kalko Elisabeth K. V., Ayasse Manfred, Frantz Alain C., Using multiple landscape genetic approaches to test the validity of genetic clusters in a species characterized by an isolation-by-distance pattern, 10.1111/bij.12737
  93. Rice William R., Analyzing Tables of Statistical Tests, 10.2307/2409177
  94. Ricketts Taylor H., The Matrix Matters: Effective Isolation in Fragmented Landscapes, 10.1086/320863
  95. Roberts, Paper presented at the annual meeting of the southwest educational research association (2012)
  96. ROUSSET FRANÇOIS, genepop’007: a complete re-implementation of the genepop software for Windows and Linux, 10.1111/j.1471-8286.2007.01931.x
  97. Schielzeth Holger, Simple means to improve the interpretability of regression coefficients : Interpretation of regression coefficients, 10.1111/j.2041-210x.2010.00012.x
  98. Segelbacher Gernot, Cushman Samuel A., Epperson Bryan K., Fortin Marie-Josée, Francois Olivier, Hardy Olivier J., Holderegger Rolf, Taberlet Pierre, Waits Lisette P., Manel Stéphanie, Applications of landscape genetics in conservation biology: concepts and challenges, 10.1007/s10592-009-0044-5
  99. SEIBOLD DAVID R., McPHEE ROBERT D., COMMONALITY ANALYSIS: A METHOD FOR DECOMPOSING EXPLAINED VARIANCE IN MULTIPLE REGRESSION ANALYSES, 10.1111/j.1468-2958.1979.tb00649.x
  100. SELKOE KIMBERLY A., WATSON JAMES R., WHITE CROW, HORIN TAL BEN, IACCHEI MATTHEW, MITARAI SATOSHI, SIEGEL DAVID A., GAINES STEVEN D., TOONEN ROBERT J., Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species : SEASCAPE GENETICS, 10.1111/j.1365-294x.2010.04658.x
  101. Smith Adam C., Koper Nicola, Francis Charles M., Fahrig Lenore, Confronting collinearity: comparing methods for disentangling the effects of habitat loss and fragmentation, 10.1007/s10980-009-9383-3
  102. Smouse Peter E., Long Jeffrey C., Sokal Robert R., Multiple Regression and Correlation Extensions of the Mantel Test of Matrix Correspondence, 10.2307/2413122
  103. Taylor Philip D., Fahrig Lenore, Henein Kringen, Merriam Gray, Connectivity Is a Vital Element of Landscape Structure, 10.2307/3544927
  104. TER BRAAK CAJO J.F., PRENTICE I.COLIN, A Theory of Gradient Analysis, Advances in Ecological Research (2004) ISBN:9780120139347 p.235-282, 10.1016/s0065-2504(03)34003-6
  105. Tischendorf Lutz, Fahrig Lenore, On the usage and measurement of landscape connectivity, 10.1034/j.1600-0706.2000.900102.x
  106. Urban Dean L., O'Neill Robert V., Shugart, Herman H., Landscape Ecology, 10.2307/1310366
  107. VAN OOSTERHOUT COCK, HUTCHINSON WILLIAM F., WILLS DEREK P. M., SHIPLEY PETER, micro-checker: software for identifying and correcting genotyping errors in microsatellite data, 10.1111/j.1471-8286.2004.00684.x
  108. Wang Magnus, Schreiber Arnd, The impact of habitat fragmentation and social structure on the population genetics of roe deer (Capreolus capreolus L.) in Central Europe, 10.1046/j.1365-2540.2001.00889.x
  109. Wright, J. Agric. Res, 20, 557 (1921)
  110. Zachos Frank E., Frantz Alain C., Kuehn Ralph, Bertouille Sabine, Colyn Marc, Niedziałkowska Magdalena, Pérez-González Javier, Skog Anna, Sprĕm Nikica, Flamand Marie-Christine, Genetic Structure and Effective Population Sizes in European Red Deer (Cervus elaphus) at a Continental Scale: Insights from Microsatellite DNA, 10.1093/jhered/esw011