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

Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia 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. We...

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Published inAmerican journal of botany Vol. 107; no. 3; pp. 498 - 509
Main Authors Donkpegan, Armel S. L., Piñeiro, Rosalía, Heuertz, Myriam, Duminil, Jérôme, Daïnou, Kasso, Doucet, Jean‐Louis, Hardy, Olivier J.
Format Journal Article Web Resource
LanguageEnglish
Published United States Botanical Society of America, Inc 01.03.2020
Botanical Society of America
Subjects
Afzelia
Afzelia africana
Afzelia quanzensis
Bayes Theorem
Bayesian analysis
Biologie végétale (sciences végétales, sylviculture, mycologie...)
Climate change
Clustering
Demographic expansion
Environmental Sciences
Evolutionary genetics
Fabaceae
Fabaceae - Detarioideae
Fragmentation
Genetic diversity
Genetic Variation
Genetics & genetic processes
Genetics, Population
Genotypes
Genotyping
Geographical distribution
Génétique & processus génétiques
Humans
Indicator species
Isolation by distance
Kinship
Life sciences
Markers
Metagenomics
Microsatellite Repeats
Microsatellites
Nucleotides
Oscillations
Phylogeography
Phytobiology (plant sciences, forestry, mycology...)
Pleistocene
Quaternary
Rainforests
Resolution
Savannah trees
Savannahs
Sciences du vivant
Single-nucleotide polymorphism
SNPs
Spatial genetic structure
Species
Species diversity
SSRs
Trees
Fabaceae - Detarioideae
savannah trees
demographic expansion
isolation by distance
spatial genetic structure
SSRs
kinship
SNPs
Afzelia
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Abstract Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia 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. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. Methods We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping‐by‐sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high‐quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. Results Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large‐scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. Conclusions These results suggest that 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 the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
AbstractList Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia 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. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes.Methods We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals.Results Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation.Conclusions These results suggest that 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 the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia 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. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. These results suggest that 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 the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia 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. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. Methods We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping‐by‐sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high‐quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. Results Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large‐scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. Conclusions These results suggest that 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 the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia 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. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. Methods We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites ( SSR s) and genotyping‐by‐sequencing ( GBS ) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high‐quality single nucleotide polymorphisms ( SNP s) were identified in 30 A. africana individuals. Results Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana , 0.0075 for SSR in A. quanzensis ). The patterns were consistent with isolation by distance expectations in the absence of large‐scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana , illustrating the higher resolving power of GBS . However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. Conclusions These results suggest that 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 the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
PREMISEFew studies have addressed the evolutionary history of tree species from African savannahs. Afzelia 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. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. METHODSWe characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. RESULTSBoth species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. CONCLUSIONSThese results suggest that 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 the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
PREMISE: Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia 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. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. METHODS: We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. RESULTS: Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. CONCLUSIONS: These results suggest that 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 the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
Author Donkpegan, Armel S. L.
Daïnou, Kasso
Heuertz, Myriam
Piñeiro, Rosalía
Doucet, Jean‐Louis
Duminil, Jérôme
Hardy, Olivier J.
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  orcidid: 0000-0003-2052-1527
  surname: Hardy
  fullname: Hardy, Olivier J.
  organization: Université Libre de Bruxelles
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Copyright Botanical Society of America, Inc. Mar 2020
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Issue 3
Keywords Fabaceae - Detarioideae
savannah trees
demographic expansion
isolation by distance
spatial genetic structure
SSRs
kinship
SNPs
Afzelia
Language English
License 2020 Botanical Society of America.
Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0
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OpenAccessLink http://orbi.ulg.ac.be/handle/2268/246204
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Snippet Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species,...
Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including...
Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species,...
Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species,...
PREMISEFew studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species,...
PREMISE: Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species,...
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SubjectTerms Afzelia
Afzelia africana
Afzelia quanzensis
Bayes Theorem
Bayesian analysis
Biologie végétale (sciences végétales, sylviculture, mycologie...)
Climate change
Clustering
Demographic expansion
Environmental Sciences
Evolutionary genetics
Fabaceae
Fabaceae - Detarioideae
Fragmentation
Genetic diversity
Genetic Variation
Genetics & genetic processes
Genetics, Population
Genotypes
Genotyping
Geographical distribution
Génétique & processus génétiques
Humans
Indicator species
Isolation by distance
Kinship
Life sciences
Markers
Metagenomics
Microsatellite Repeats
Microsatellites
Nucleotides
Oscillations
Phylogeography
Phytobiology (plant sciences, forestry, mycology...)
Pleistocene
Quaternary
Rainforests
Resolution
Savannah trees
Savannahs
Sciences du vivant
Single-nucleotide polymorphism
SNPs
Spatial genetic structure
Species
Species diversity
SSRs
Trees
Title Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis reveals no significant past fragmentation of their distribution ranges
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fajb2.1449
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https://search.proquest.com/docview/2381847050
https://hal.inrae.fr/hal-03300540
http://orbi.ulg.ac.be/handle/2268/246204
Volume 107
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