Population connectivity across a highway in large ungulates: testing the power of redundancy analyses
Preserving nature in an urbanized modern environment proves to be rather difficult. A lot of effort is put into conserving the natural habitat. However in western Europe this natural habitat is reduced to small patches if not completely gone. Centuries of urbanization have reformed the landscape from a wild, natural environment to a more controlled, humanized creation. This shaping of the scenery has lead to a massive increase of human-induced pressure on natural populations of organisms. Large natural areas have been transformed into cities and villages in order to accommodate for the growing size of the human population. These hotspots for human activity were surrounded by vast areas of food crops and feeding grounds for domesticated animals. To be able to interact with each other and exchange goods, extensive transport networks were created. This all lead to an excessive devastation of the former natural habitat. In recent years efforts have been done to reduce the impact of human life on its environment. Nature reserves have been established and attempts have been made to reconnect fragmented habitats. However quantifying the magnitude of the impact of the transport infrastructure on animal populations, has not fully been done yet. In order to optimize nature preservation measures, a thorough understanding of the impact on the ecosystem is essential. Based on research done in 2012 on the effect of the E411 motorway in Wallonia as a barrier for gene flow in red deer (Cervus elaphus) and wild boar (Sus scrofa) populations, additional statistical analyses were performed. Using distance based redundancy analyses, a method that proved to be more accurate than the Bayesian cluster methods used in 2012, it was determined the motorway accounted for 1.7% of the total genetic structure in the red deer population. This means gene flow for red deer across the motorway is almost inexistent. The wild boar population did not show any significant impact of the motorway. This provides useful information to conservation policy makers, as the fenced motorway does not seem to have quite the same impact on different species of large ungulates. In determining which type of corridor is needed to connect fragmented patches of nature, it is essential not only to take into account which species can use it, but also which species are in need of said corridor.
Bibliografie
ANTROP, M. 2004. Landscape change and the urbanization process in Europe. Landscape
and urban planning, 67, 9-26.
BALKENHOL, N. & WAITS, L. P. 2009. Molecular road ecology: exploring the potential of
genetics for investigating transportation impacts on wildlife. Molecular Ecology, 18,
4151-4164.
BELLIER, E., MONESTIEZ, P., DURBEC, J.-P. & CANDAU, J.-N. 2007. Identifying spatial
relationships at multiple scales: principal coordinates of neighbour matrices (PCNM)
and geostatistical approaches. Ecography, 30, 385-399.
BINDER, D. A. 1978. Bayesian Cluster Analysis. Biometrika, 65, 31-38.
BLANCHET, F. G., LEGENDRE, P. & BORCARD, D. 2008. Forward selection of explanatory
variables. Ecology, 89, 2623-2632.
BORCARD, D., GILLET, F. & LEGENDRE, P. 2011. Numerical Ecology with R, New York, Springer
Science+Business Media.
BORCARD, D. & LEGENDRE, P. 2002. All-scale spatial analysis of ecological data by means of
principal coordinates of neighbour matrices. Ecological Modelling, 153, 51-68.
BORCARD, D., LEGENDRE, P., AVOIS-JACQUET, C. & TUOMISTO, H. 2004. Dissecting the
spatial structure of ecological data at multiple scales. Ecology, 85, 1826-1832.
BORCARD, D., LEGENDRE, P. & DRAPEAU, P. 1992. Partialling out the spatial component of
ecological variation. Ecology, 73, 1045-1055.
CHOW, G. C. 1960. Tests of Equality Between Sets of Coefficients in Two Linear Regressions.
Econometrica, 28, 591-605.
COFFIN, A. W. 2007. From roadkill to road ecology: A review of the ecological effects of
roads. Journal of Transport Geography, 15, 396-406.
CORANDER, J., SIRÉN, J. & ARJAS, E. 2008. Spatial modelling of genetic population structure.
Computational Statistics, 23, 111-129.
COTTENIE, K. 2005. Integrating environmental and spatial processes in ecological community
dynamics. Ecology Letters, 8, 1175-1182.
31
COULON, A., COSSON, J. F., ANGIBAULT, J. M. A., CARGNELUTTI, B., GALAN, M., MORELLET,
N., PETIT, E., AULAGNIER, S. & HEWISON, A. J. M. 2004. Landscape connectivity
influences gene flow in a roe deer population inhabiting a fragmented landscape: an
individual-based approach. Molecular Ecology, 13, 2841-2850.
COULON, A., GUILLOT, G., COSSON, J. F., ANGIBAULT, J. M. A., AULAGNIER, S., CARGNELUTTI,
B., GALAN, M. & HEWISON, A. J. M. 2006. Genetic structure is influenced by
landscape features: empirical evidence from a roe deer population. Molecular
Ecology, 15, 1669-1679.
DIEHR, G. & HOFLIN, D. R. 1974. Approximating the Distribution of the Sample R2 in Best
Subset Regressions. Technometrics, 16, 317-320.
DRAY, S. & DUFOUR, A. 2007. The ade4 package: implementing the duality diagram for
ecologists. Journal of Statistical Software, 22, 1-20.
DRAY, S., LEGENDRE, P. & PERES-NETO, P. R. 2006. Spatial modelling: a comprehensive
framework for principal coordinate analysis of neighbour matrices (PCNM). Ecological
Modelling, 196, 483-493.
DRIVER, H. E. & KROEBER, A. L. 1932. Quantitative expression of cultural relationships.
University of California Publications in American Archaeology and Ethnology, 31, 211-256.
FRANTZ, A. C., BERTOUILLE, S., ELOY, M., LICOPPE, A., CHAUMONT, F. & FLAMAND, M.
2012a. Data from: 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). Dryad Data Repository.
FRANTZ, A. C., BERTOUILLE, S., ELOY, M. C., LICOPPE, A., CHAUMONT, F. & FLAMAND, M. C.
2012b. 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).
Molecular Ecology, 21, 3445-3457.
FRANTZ, A. C., POPE, L. C., ETHERINGTON, T. R., WILSON, G. J. & BURKE, T. 2010. Using
isolation-by-distance-based approaches to assess the barrier effect of linear
landscape elements on badger (Meles meles) dispersal. Molecular Ecology, 19, 1663-1674.
GHILAGABER, G. 2004. Another Look at Chow's Test for the Equality of Two Heteroscedastic
Regression Models. Quality and Quantity, 38, 81-93.
GOWER, J. C. 1966. Some distance properties of latent root and vector methods used in
multivariate analysis. Biometrika, 53, 325-338.
32
GUILLOT, G., ESTOUP, A., MORTIER, F. & COSSON, J. F. 2005. A Spatial Statistical Model for
Landscape Genetics. Genetics, 170, 1261-1280.
HEPENSTRICK, D., THIEL, D., HOLDEREGGER, R. & GUGERLI, F. 2012. Genetic discontinuities in
roe deer (Capreolus capreolus) coincide with fenced transportation infrastructure.
Basic and Applied Ecology, 13, 631-638.
HOLDEREGGER, R. & WAGNER, H. H. 2008. Landscape genetics. BioScience, 58, 199-207.
JOMBART, T. 2008. adegenet: a R package for the multivariate analysis of genetic markers.
Bioinformatics, 24, 1403-1405.
KUEHN, R., HINDENLANG, K. E., HOLZGANG, O., SENN, J., STOECKLE, B. & SPERISEN, C. 2007.
Genetic effect of transportation infrastructure on roe deer populations (Capreolus
capreolus). Journal of Heredity, 98, 13-22.
KUTNER, M. H., NACHTSHEIM, C. J., NETER, J. & LI, W. 2005. Applied linear statistical models,
McGraw-Hill.
LEGENDRE, P. & ANDERSON, M. J. 1999. Distance-based redundancy analysis: testing
multispecies responses in multifactorial ecological experiments. Ecological
Monographs, 69, 1-24.
LEGENDRE, P., BORCARD, D., BLANCHET, F. G. & DRAY, S. 2013. PCNM: MEM spatial
eigenfunction and principal coordinate analyses. R package version 2.1-2/r109.
http://R-Forge.R-project.org/projects/sedar/.
LEGENDRE, P. & GAUTHIER, O. 2014. Statistical methods for temporal and space–time
analysis of community composition data(). Proceedings of the Royal Society B:
Biological Sciences, 281, 20132728.
LEGENDRE, P. & LEGENDRE, L. 2012. Numerical ecology, Amsterdam, Elsevier.
LYNEBORG, L. & DEN HOED, G. 1972. Wilde zoogdieren in Europa, Amsterdam, Moussault's
uitgeverij NV.
MANEL, S., GUGERLI, F., THUILLER, W., ALVAREZ, N., LEGENDRE, P., HOLDEREGGER, R.,
GIELLY, L., TABERLET, P. & CONSORTIUM, I. 2012. Broad-scale adaptive genetic
variation in alpine plants is driven by temperature and precipitation. Molecular
Ecology, 21, 3729-3738.
MANEL, S. & HOLDEREGGER, R. 2013. Ten years of landscape genetics. Trends in Ecology &
Evolution, 28, 614-621.
33
MANEL, S., SCHWARTZ, M. K., LUIKART, G. & TABERLET, P. 2003. Landscape genetics:
combining landscape ecology and population genetics. Trends in Ecology and
Evolution, 18, 189-197.
MATA, C., HERVÁS, I., HERRANZ, J., SUÁREZ, F. & MALO, J. E. 2008. Are motorway wildlife
passages worth building? Vertebrate use of road-crossing structures on a Spanish
motorway. Journal of Environmental Management, 88, 407-415.
MORAN, P. A. P. 1950. Notes on Continuous Stochastic Phenomena. Biometrika, 37, 17-23.
MORELLE, K., PODGÓRSKI, T., PRÉVOT, C., KEULING, O., LEHAIRE, F. & LEJEUNE, P. 2015.
Towards understanding wild boar Sus scrofa movement: a synthetic movement
ecology approach. Mammal Review, 45, 15-29.
OKSANEN, J., BLANCHET, F. G., KINDT, R., LEGENDRE, P., MINCHIN, P. R., O'HARA, R. B.,
SIMPSON, G. L., SOLYMOS, P., STEVENS, M. H. H. & WAGNER, H. H. 2014. vegan:
Community Ecology Package. R package version 2.2-1/r2913. http://R-Forge.Rproject.org/projects/vegan/.
ORSINI, L., VANOVERBEKE, J., SWILLEN, I., MERGEAY, J. & DE MEESTER, L. 2013. Drivers of
population genetic differentiation in the wild: isolation by dispersal limitation,
isolation by adaptation and isolation by colonization. Molecular Ecology, 22, 5983-5999.
PEARSON, K. 1901. On lines and planes of closest fit to systems of points in space.
Philosophical Magazine, 2, 559-572.
PRÉVOT, C. & LICOPPE, A. 2013. Comparing red deer (Cervus elaphus L.) and wild boar (Sus
scrofa L.) dispersal patterns in southern Belgium. European Journal of Wildlife
Research, 59, 795-803.
PRÉVOT, C. & MORELLE, K. 2012. Potentiel de dispersion du sanglier et historique de la
colonisation de la plaine agricole en Wallonie. Demain la chasse: comment reprendre
l'initiative? Wépion, Belgique: Forêt Wallonne asbl.
PRITCHARD, J. K., STEPHENS, M. & DONNELLY, P. 2000. Inference of population structure
using multilocus genotype data. Genetics, 155, 945-959.
R CORE TEAM 2014. R: A language and environment for statistical computing. R Foundation
for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
VAN DEN WOLLENBERG, A. 1977. Redundancy analysis an alternative for canonical
correlation analysis. Psychometrika, 42, 207-219.
34
VAN DER ZEE, F. F., WIERTZ, J., TER BRAAK, C. J. F. & VAN APELDOORN, C. 1992. Landscape
change as a possible cause of the badger Meles meles L. decline in The Netherlands.
Biological Conservation, 61, 17-22.
VANGESTEL, C., MERGEAY, J., DAWSON, D. A., CALLENS, T., VANDOMME, V. & LENS, L. 2012.
Genetic diversity and population structure in contemporary house sparrow
populations alons an urbanization gradient. Heredity, 109, 163-172.
VERKEM, S., DE MAESENEER, J., VANDENDRIESSCHE, B., VERBEYLEN, G. & YSKOUT, S. 2003.
Zoogdieren in Vlaanderen: Ecologie en verspreiding van 1987 tot 2002, Mechelen &
Gent, Natuurpunt Studie & JNM-Zoogdierenwerkgroep.
WRIGHT, S. 1943. Isolation by Distance. Genetics, 28, 114-138.
ZHAO, J. H. 2007. gap: Genetic Analysis Package. Journal of Statistical Software, 23, 1-18.
