A new individual-based spatial approach for identifying genetic discontinuities in natural populations
International audience The population concept is central in evolutionary and conservation biology, but identifying the boundaries of natural populations is often challenging. Here, we present a new approach for assessing spatial genetic structure without the a priori assumptions on the locations of...
Published in: | Molecular Ecology |
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Online Access: | https://hal.science/halsde-00276499 https://doi.org/10.1111/j.1365-294X.2007.03293.x |
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ftunivsavoie:oai:HAL:halsde-00276499v1 2024-04-28T08:41:07+00:00 A new individual-based spatial approach for identifying genetic discontinuities in natural populations Manel, S. Berthoud, F. Bellemain, E. Gaudeul, M. Luikart, G. Swenson, J. E. Waits, L. P. Taberlet, P. Intrabiodiv, Consortium Laboratoire d'Ecologie Alpine (LECA) Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS) Laboratoire de physique et modélisation des milieux condensés (LPM2C) Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS) Department of Ecology and Natural Resource Management Norwegian University of Life Sciences (NMBU) Department of Fish and Wildlife Resources University of Idaho Moscow, USA 2007 https://hal.science/halsde-00276499 https://doi.org/10.1111/j.1365-294X.2007.03293.x en eng HAL CCSD Wiley info:eu-repo/semantics/altIdentifier/doi/10.1111/j.1365-294X.2007.03293.x halsde-00276499 https://hal.science/halsde-00276499 doi:10.1111/j.1365-294X.2007.03293.x ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology https://hal.science/halsde-00276499 Molecular Ecology, 2007, 16 (10), pp.2031-2043. ⟨10.1111/j.1365-294X.2007.03293.x⟩ spatial genetics assignment test genetic discontinuity moving windows multilocus genotype [SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment info:eu-repo/semantics/article Journal articles 2007 ftunivsavoie https://doi.org/10.1111/j.1365-294X.2007.03293.x 2024-04-11T00:46:23Z International audience The population concept is central in evolutionary and conservation biology, but identifying the boundaries of natural populations is often challenging. Here, we present a new approach for assessing spatial genetic structure without the a priori assumptions on the locations of populations made by adopting an individual-centred approach. Our method is based on assignment tests applied in a moving window over an extensively sampled study area. For each individual, a spatially explicit probability surface is constructed, showing the estimated probability of finding its multilocus genotype across the landscape, and identifying putative migrants. Population boundaries are localized by estimating the mean slope of these probability surfaces over all individuals to identify areas with genetic discontinuities. The significance of the genetic discontinuities is assessed by permutation tests. This new approach has the potential to reveal cryptic population structure and to improve our ability to understand gene flow dynamics across landscapes. We illustrate our approach by simulations and by analysing two empirical datasets: microsatellite data of Ursus arctos in Scandinavia, and amplified fragment length polymorphism (AFLP) data of Rhododendron ferrugineum in the Alps. Article in Journal/Newspaper Ursus arctos Université Savoie Mont Blanc: HAL Molecular Ecology 16 10 2031 2043 |
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Open Polar |
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Université Savoie Mont Blanc: HAL |
op_collection_id |
ftunivsavoie |
language |
English |
topic |
spatial genetics assignment test genetic discontinuity moving windows multilocus genotype [SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment |
spellingShingle |
spatial genetics assignment test genetic discontinuity moving windows multilocus genotype [SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment Manel, S. Berthoud, F. Bellemain, E. Gaudeul, M. Luikart, G. Swenson, J. E. Waits, L. P. Taberlet, P. Intrabiodiv, Consortium A new individual-based spatial approach for identifying genetic discontinuities in natural populations |
topic_facet |
spatial genetics assignment test genetic discontinuity moving windows multilocus genotype [SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment |
description |
International audience The population concept is central in evolutionary and conservation biology, but identifying the boundaries of natural populations is often challenging. Here, we present a new approach for assessing spatial genetic structure without the a priori assumptions on the locations of populations made by adopting an individual-centred approach. Our method is based on assignment tests applied in a moving window over an extensively sampled study area. For each individual, a spatially explicit probability surface is constructed, showing the estimated probability of finding its multilocus genotype across the landscape, and identifying putative migrants. Population boundaries are localized by estimating the mean slope of these probability surfaces over all individuals to identify areas with genetic discontinuities. The significance of the genetic discontinuities is assessed by permutation tests. This new approach has the potential to reveal cryptic population structure and to improve our ability to understand gene flow dynamics across landscapes. We illustrate our approach by simulations and by analysing two empirical datasets: microsatellite data of Ursus arctos in Scandinavia, and amplified fragment length polymorphism (AFLP) data of Rhododendron ferrugineum in the Alps. |
author2 |
Laboratoire d'Ecologie Alpine (LECA) Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS) Laboratoire de physique et modélisation des milieux condensés (LPM2C) Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS) Department of Ecology and Natural Resource Management Norwegian University of Life Sciences (NMBU) Department of Fish and Wildlife Resources University of Idaho Moscow, USA |
format |
Article in Journal/Newspaper |
author |
Manel, S. Berthoud, F. Bellemain, E. Gaudeul, M. Luikart, G. Swenson, J. E. Waits, L. P. Taberlet, P. Intrabiodiv, Consortium |
author_facet |
Manel, S. Berthoud, F. Bellemain, E. Gaudeul, M. Luikart, G. Swenson, J. E. Waits, L. P. Taberlet, P. Intrabiodiv, Consortium |
author_sort |
Manel, S. |
title |
A new individual-based spatial approach for identifying genetic discontinuities in natural populations |
title_short |
A new individual-based spatial approach for identifying genetic discontinuities in natural populations |
title_full |
A new individual-based spatial approach for identifying genetic discontinuities in natural populations |
title_fullStr |
A new individual-based spatial approach for identifying genetic discontinuities in natural populations |
title_full_unstemmed |
A new individual-based spatial approach for identifying genetic discontinuities in natural populations |
title_sort |
new individual-based spatial approach for identifying genetic discontinuities in natural populations |
publisher |
HAL CCSD |
publishDate |
2007 |
url |
https://hal.science/halsde-00276499 https://doi.org/10.1111/j.1365-294X.2007.03293.x |
genre |
Ursus arctos |
genre_facet |
Ursus arctos |
op_source |
ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology https://hal.science/halsde-00276499 Molecular Ecology, 2007, 16 (10), pp.2031-2043. ⟨10.1111/j.1365-294X.2007.03293.x⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/j.1365-294X.2007.03293.x halsde-00276499 https://hal.science/halsde-00276499 doi:10.1111/j.1365-294X.2007.03293.x |
op_doi |
https://doi.org/10.1111/j.1365-294X.2007.03293.x |
container_title |
Molecular Ecology |
container_volume |
16 |
container_issue |
10 |
container_start_page |
2031 |
op_container_end_page |
2043 |
_version_ |
1797571486573133824 |