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Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis (Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges

View ORCID ProfileArmel S.L. Donkpegan, Rosalía Piñeiro, View ORCID ProfileMyriam Heuertz, Jérôme Duminil, Kasso Daïnou, Jean-Louis Doucet, View ORCID ProfileOlivier J. Hardy
doi: https://doi.org/10.1101/730911
Armel S.L. Donkpegan
University of Liège, Gembloux Agro-Bio Tech, Management of Forest Resources, Tropical Forestry, TERRA, 2 Passage des Déportés, B-5030 Gembloux, BelgiumEvolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, BelgiumUMR 1332 BFP, INRA, Université de Bordeaux, F-33140, Villenave d’Ornon, France
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  • For correspondence: armel.donkpegan@gmail.com
Rosalía Piñeiro
University of Exeter, Geography, College of Life and Environmental Sciences, Stocker road, EX44QD, Exeter, UKEvolutionary Genomics, Centre for Geogenetics - Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
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Myriam Heuertz
Biogeco, INRA, Univ. Bordeaux, 69 route d’Arcachon, F-33610 Cestas, France
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Jérôme Duminil
Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, BelgiumDIADE, IRD, Univ Montpellier, 911 Avenue Agropolis, BP 64501, 34394 Montpellier, FranceBioversity International, Forest Genetic Resources and Restoration Programme, Sub-Regional Office for Central Africa, P.O. Box 2008 Messa, Yaoundé, Cameroon
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Kasso Daïnou
University of Liège, Gembloux Agro-Bio Tech, Management of Forest Resources, Tropical Forestry, TERRA, 2 Passage des Déportés, B-5030 Gembloux, BelgiumEvolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, BelgiumUniversité d’Agriculture de Kétou, BP: 43, Kétou, Benin
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Jean-Louis Doucet
University of Liège, Gembloux Agro-Bio Tech, Management of Forest Resources, Tropical Forestry, TERRA, 2 Passage des Déportés, B-5030 Gembloux, Belgium
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Olivier J. Hardy
Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium
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  • ORCID record for Olivier J. Hardy
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ABSTRACT

Few studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region). Afzelia (Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana and 12 A. quanzensis individuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= −0.005 and −0.007 and bLd (SNP)= −0.008 and −0.006 for A. africana and A. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, populations have remained connected throughout the large, continuous Savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during past climate changes, in contrast to patterns commonly found in African rainforest trees.

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Posted August 09, 2019.
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Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis (Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges
Armel S.L. Donkpegan, Rosalía Piñeiro, Myriam Heuertz, Jérôme Duminil, Kasso Daïnou, Jean-Louis Doucet, Olivier J. Hardy
bioRxiv 730911; doi: https://doi.org/10.1101/730911
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Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis (Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges
Armel S.L. Donkpegan, Rosalía Piñeiro, Myriam Heuertz, Jérôme Duminil, Kasso Daïnou, Jean-Louis Doucet, Olivier J. Hardy
bioRxiv 730911; doi: https://doi.org/10.1101/730911

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