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Article ; Online: Development and characterization of nuclear microsatellite markers for the African walnut Coula edulis Baill (Coulaceae).

Kamdem, Narcisse Guy / Sergeant, Saskia / Vercruysse, Camille / Deblauwe, Vincent / Sonké, Bonaventure / Hardy, Olivier J

Molecular biology reports

2024 Volume 51, Issue 1, Page(s) 438

Abstract: Premise of the study: Coula edulis Baill (Coulaceae) is a common tree species in the Guineo-Congolian forests producing an edible fruit known as African walnut, which is an important food and income resource for rural populations. However, the species ... ...

Abstract	Premise of the study: Coula edulis Baill (Coulaceae) is a common tree species in the Guineo-Congolian forests producing an edible fruit known as African walnut, which is an important food and income resource for rural populations. However, the species suffers from a deficit of natural regeneration. We developed here nuclear microsatellite markers for C. edulis to be able to study the genetic structure of its natural populations and gene flow. Methods and results: A genomic library was obtained using the Illumina platform, and 21 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed eight to 22 alleles per locus (average: 14.2), with a mean expected heterozygosity ranging from 0.33 to 0.72 in five populations from Central and West Africa. Conclusions: The high polymorphism of the nuclear microsatellite markers developed makes them useful to investigate gene flow and the organization of genetic diversity in C. edulis, and to assess whether particular genetic resources require conservation efforts.
MeSH term(s)	Humans ; Juglans/genetics ; Polymorphism, Genetic ; Microsatellite Repeats/genetics ; Seeds ; Fruit/genetics
Language	English
Publishing date	2024-03-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-024-09373-0
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Article: Guidelines for genetic monitoring of translocated plant populations

Van Rossum, Fabienne / Hardy, Olivier J.

Conservation biology. 2022 Feb., v. 36, no. 1

2022

Abstract: Plant translocation is a useful tool for implementing assisted gene flow in recovery plans of critically endangered plant species. Although it helps to restore genetically viable populations, it is not devoid of genetic risks, such as poor adaptation of ... ...

Abstract	Plant translocation is a useful tool for implementing assisted gene flow in recovery plans of critically endangered plant species. Although it helps to restore genetically viable populations, it is not devoid of genetic risks, such as poor adaptation of transplants and outbreeding depression in the hybrid progeny, which may have negative consequences in terms of demographic growth and plant fitness. Hence, a follow‐up genetic monitoring should evaluate whether the translocated populations are genetically viable and self‐sustaining in the short and long term. The causes of failure to adjust management responses also need to be identified. Molecular markers and fitness‐related quantitative traits can be used to determine whether a plant translocation enhanced genetic diversity, increased fitness, and improved the probability of long‐term survival. We devised guidelines and illustrated them with studies from the literature to help practitioners determine the appropriate genetic survey methods so that management practices can better integrate evolutionary processes. These guidelines include methods for sampling and for assessing changes in genetic diversity and differentiation, contemporary gene flow, mode of local recruitment, admixture level, the effects of genetic rescue, inbreeding or outbreeding depression and local adaptation on plant fitness, and long‐term genetic changes.
Keywords	endangered species ; gene flow ; genetic rescue ; genetic variation ; progeny ; surveys
Language	English
Dates of publication	2022-02
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	58735-7
ISSN	1523-1739 ; 0888-8892
ISSN (online)	1523-1739
ISSN	0888-8892
DOI	10.1111/cobi.13670
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Article ; Online: Development and characterization of microsatellite markers in the African timber tree species Cylicodiscus gabunensis (Fabaceae)

Bhasin, Oriana B. / Sergeant, Saskia / Hardy, Olivier J.

Mol Biol Rep. 2022 Nov., v. 49, no. 11 p.11209-11214

2022

Abstract: BACKGROUND: Cylicodiscus gabunensis (Fabaceae) or ‘Okan’ is a Central African multipurpose timber species that is used for heavy construction and traditional medicine. Despite being currently heavily exploited, the species shows a low population density ... ...

Abstract	BACKGROUND: Cylicodiscus gabunensis (Fabaceae) or ‘Okan’ is a Central African multipurpose timber species that is used for heavy construction and traditional medicine. Despite being currently heavily exploited, the species shows a low population density and a natural regeneration deficit in dense forest. METHODS AND RESULTS: We aimed to characterize polymorphic microsatellite markers that can be used to study patterns of genetic structure and gene flow (mating system, pollen and seed dispersal and inbreeding depression) and ultimately, help to develop sustainable forest management practices. We developed 24 polymorphic markers that can be amplified in three PCR multiplexes that were tested in 647 individuals of C. gabunensis from three populations. The number of alleles ranged from 4 to 27 and the average observed and expected heterozygosity across loci and populations were Ho = 0.585 (0.081–0.936) and He = 0.510 (0.076–0.914), respectively. CONCLUSIONS: This set of markers is a useful tool for exploring intra-specific diversity, genetic structure and gene flow of C. gabunensis.
Keywords	Cylicodiscus ; forest trees ; forests ; gene flow ; genetic structure ; heterozygosity ; microsatellite repeats ; natural regeneration ; pollen ; population density ; seed dispersal ; sustainable forestry ; traditional medicine
Language	English
Dates of publication	2022-11
Size	p. 11209-11214.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-07908-x
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Article ; Online: Development and characterization of microsatellite markers in the African timber tree species Cylicodiscus gabunensis (Fabaceae).

Bhasin, Oriana B / Sergeant, Saskia / Hardy, Olivier J

Molecular biology reports

2022 Volume 49, Issue 11, Page(s) 11209–11214

Abstract: Background: Cylicodiscus gabunensis (Fabaceae) or 'Okan' is a Central African multipurpose timber species that is used for heavy construction and traditional medicine. Despite being currently heavily exploited, the species shows a low population density ...

Abstract	Background: Cylicodiscus gabunensis (Fabaceae) or 'Okan' is a Central African multipurpose timber species that is used for heavy construction and traditional medicine. Despite being currently heavily exploited, the species shows a low population density and a natural regeneration deficit in dense forest. Methods and results: We aimed to characterize polymorphic microsatellite markers that can be used to study patterns of genetic structure and gene flow (mating system, pollen and seed dispersal and inbreeding depression) and ultimately, help to develop sustainable forest management practices. We developed 24 polymorphic markers that can be amplified in three PCR multiplexes that were tested in 647 individuals of C. gabunensis from three populations. The number of alleles ranged from 4 to 27 and the average observed and expected heterozygosity across loci and populations were Ho = 0.585 (0.081-0.936) and He = 0.510 (0.076-0.914), respectively. Conclusions: This set of markers is a useful tool for exploring intra-specific diversity, genetic structure and gene flow of C. gabunensis.
MeSH term(s)	Humans ; Male ; Trees/genetics ; Fabaceae/genetics ; Genetics, Population ; Microsatellite Repeats/genetics ; Gene Flow
Language	English
Publishing date	2022-09-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-07908-x
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Article ; Online: Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate.

Hardy, Olivier J

Molecular ecology resources

2016 Volume 16, Issue 1, Page(s) 103–117

Abstract: Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals ... ...

Abstract	Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals and (iii) a form of inbreeding resulting from the mechanism of 'double reduction'. Consequently, few data analysis computer programs are applicable to autopolyploids. To contribute bridging this gap, this article first derives theoretical expectations for the inbreeding and identity disequilibrium coefficients under polysomic inheritance in a mixed mating model. Moment estimators of these coefficients are proposed when exact genotypes or just markers phenotypes (i.e. allelic dosage unknown) are available. This led to the development of estimators of the selfing rate based on adult genotypes or phenotypes and applicable to any even-ploidy level. Their statistical performances and robustness were assessed by numerical simulations. Contrary to inbreeding-based estimators, the identity disequilibrium-based estimator using phenotypes is robust (absolute bias generally < 0.05), even in the presence of double reduction, null alleles or biparental inbreeding due to isolation by distance. A fairly good precision of the selfing rate estimates (root mean squared error < 0.1) is already achievable using a sample of 30-50 individuals phenotyped at 10 loci bearing 5-10 alleles each, conditions reachable using microsatellite markers. Diallelic markers (e.g. SNP) can also perform satisfactorily in diploids and tetraploids but more polymorphic markers are necessary for higher ploidy levels. The method is implemented in the software SPAGeDi and should contribute to reduce the lack of population genetics tools applicable to autopolyploids.
MeSH term(s)	Alleles ; Breeding ; Genetics, Population/methods ; Genotype ; Microsatellite Repeats ; Models, Genetic ; Polyploidy ; Software
Language	English
Publishing date	2016-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.12431
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Article: Genetic diversity assessment of

Van Rossum, Fabienne / Godé, Cécile / Baruca Arbeiter, Alenka / Raspé, Olivier / Simsek, Melike / Barigand, Benjamin / Hardy, Olivier J / Bandelj, Dunja

Ecology and evolution

2024 Volume 14, Issue 2, Page(s) e10953

Abstract: Helichrysum ... ...

Abstract	Helichrysum arenarium
Language	English
Publishing date	2024-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.10953
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Article: How fast are viruses spreading in the wild?

Dellicour, Simon / Bastide, Paul / Rocu, Pauline / Fargette, Denis / Hardy, Olivier J / Suchard, Marc A / Guindon, Stéphane / Lemey, Philippe

bioRxiv : the preprint server for biology

2024

Abstract: Genomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatially explicit reconstructions can subsequently be used ... ...

Abstract	Genomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatially explicit reconstructions can subsequently be used to estimate dispersal metrics allowing to unveil the dispersal dynamics and evaluate the capacity to spread among hosts. Heterogeneous sampling intensity of genomic sequences can however impact the accuracy of dispersal insights gained through phylogeographic inference. In our study, we implement a simulation framework to evaluate the robustness of three dispersal metrics - a lineage dispersal velocity, a diffusion coefficient, and an isolation-by-distance signal metric - to the sampling effort. Our results reveal that both the diffusion coefficient and isolation-by-distance signal metrics appear to be robust to the number of samples considered for the phylogeographic reconstruction. We then use these two dispersal metrics to compare the dispersal pattern and capacity of various viruses spreading in animal populations. Our comparative analysis reveals a broad range of isolation-by-distance patterns and diffusion coefficients mostly reflecting the dispersal capacity of the main infected host species but also, in some cases, the likely signature of rapid and/or long-distance dispersal events driven by human-mediated movements through animal trade. Overall, our study provides key recommendations for the lineage dispersal metrics to consider in future studies and illustrates their application to compare the spread of viruses in various settings.
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.10.588821
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Article ; Online: Guidelines for genetic monitoring of translocated plant populations.

Van Rossum, Fabienne / Hardy, Olivier J

Conservation biology : the journal of the Society for Conservation Biology

2021 Volume 36, Issue 1, Page(s) e13670

Abstract	Plant translocation is a useful tool for implementing assisted gene flow in recovery plans of critically endangered plant species. Although it helps to restore genetically viable populations, it is not devoid of genetic risks, such as poor adaptation of transplants and outbreeding depression in the hybrid progeny, which may have negative consequences in terms of demographic growth and plant fitness. Hence, a follow-up genetic monitoring should evaluate whether the translocated populations are genetically viable and self-sustaining in the short and long term. The causes of failure to adjust management responses also need to be identified. Molecular markers and fitness-related quantitative traits can be used to determine whether a plant translocation enhanced genetic diversity, increased fitness, and improved the probability of long-term survival. We devised guidelines and illustrated them with studies from the literature to help practitioners determine the appropriate genetic survey methods so that management practices can better integrate evolutionary processes. These guidelines include methods for sampling and for assessing changes in genetic diversity and differentiation, contemporary gene flow, mode of local recruitment, admixture level, the effects of genetic rescue, inbreeding or outbreeding depression and local adaptation on plant fitness, and long-term genetic changes.
MeSH term(s)	Conservation of Natural Resources ; Gene Flow ; Genetic Fitness ; Genetic Variation ; Inbreeding ; Plants/genetics
Language	English
Publishing date	2021-02-16
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	58735-7
ISSN	1523-1739 ; 0888-8892
ISSN (online)	1523-1739
ISSN	0888-8892
DOI	10.1111/cobi.13670
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Article ; Online: Spatially explicit phylogeographical reconstruction sheds light on the history of the forest cover in the Congo Basin

Matvijev, Katarina / Dellicour, Simon / Kaymak, Esra / Hardy, Olivier J.

Journal of Biogeography. 2022 Dec., v. 49, no. 12 p.2256-2268

2022

Abstract: AIM: The impact of Pleistocene climatic oscillations on the biodiversity of African tropical rain forests remains poorly understood, and the Congo Basin is particularly understudied. We aim to elucidate how Pleistocene climatic oscillations shaped ... ...

Abstract	AIM: The impact of Pleistocene climatic oscillations on the biodiversity of African tropical rain forests remains poorly understood, and the Congo Basin is particularly understudied. We aim to elucidate how Pleistocene climatic oscillations shaped lowland tropical rain forests by investigating the intraspecific diversity and evolutionary history of a widespread tree species. LOCATION: Guineo‐Congolian rain forest, Central Africa. TAXON: Staudtia kamerunensis Warb. (Myristicaceae). METHODS: We used genome skimming combined with maximum likelihood and Bayesian inference to infer the plastid phylogeny. We estimated the time of speciation and differentiation, genetic diversity, and we employed a continuous phylogeographical approach to infer the dispersal history of its plastid lineages. RESULTS: We sequenced an average of 5,827,783 reads per sample, and the reconstructed reference plastome had a mean depth of 73.3. We identified five plastid lineages that diverged during the Early or Middle Pleistocene and are parapatric, suggesting past population fragmentation. Four lineages are endemic to Lower Guinea, and one spans the Congo Basin. We found contrasting patterns of expansion in the two regions, with a rapid and recent range expansion of the Congolian lineage in the last 200,000 years, while the spread of the Lower Guinean lineages was substantially slower. MAIN CONCLUSION: The contrasting demographic histories between eastern and western lineages, associated with contrasted levels of plant species richness and rates of endemism, suggest that forest cover was more stable in Lower Guinea during the Late Pleistocene than in Congolia, where the biodiversity might have been eroded before the forest re‐expanded in the Congo basin. This study illustrates how a continuous phylogeographical inference approach, mostly applied so far for inferring the spread of fast‐evolving pathogens over months or years, can provide new insights to reconstruct the dispersal history of tropical tree species over thousands or millions of years.
Keywords	Bayesian theory ; Myristicaceae ; Pleistocene epoch ; basins ; genetic variation ; genome ; indigenous species ; phylogeny ; phylogeography ; rain ; rain forests ; species richness ; statistical analysis ; trees ; tropical plants ; Central Africa ; Guinea
Language	English
Dates of publication	2022-12
Size	p. 2256-2268.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	188963-1
ISSN	0305-0270
ISSN	0305-0270
DOI	10.1111/jbi.14507
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Article ; Online: The recent colonization history of the most widespread Podocarpus tree species in Afromontane forests.

Migliore, Jérémy / Lézine, Anne-Marie / Hardy, Olivier J

Annals of botany

2020 Volume 126, Issue 1, Page(s) 73–83

Abstract: Background and aims: Afromontane forests host a unique biodiversity distributed in isolated high-elevation habitats within a matrix of rain forests or savannahs, yet they share a remarkable flora that raises questions about past connectivity between ... ...

Abstract	Background and aims: Afromontane forests host a unique biodiversity distributed in isolated high-elevation habitats within a matrix of rain forests or savannahs, yet they share a remarkable flora that raises questions about past connectivity between currently isolated forests. Here, we focused on the Podocarpus latifolius-P. milanjianus complex (Podocarpaceae), the most widely distributed conifers throughout sub-Saharan African highlands, to infer its demographic history from genetic data. Methods: We sequenced the whole plastid genome, mitochondrial DNA regions and nuclear ribosomal DNA of 88 samples from Cameroon to Angola in western Central Africa and from Kenya to the Cape region in eastern and southern Africa to reconstruct time-calibrated phylogenies and perform demographic inferences. Key results: We show that P. latifolius and P. milanjianus form a single species, whose lineages diverged during the Pleistocene, mostly between approx, 200 000 and 300 000 years BP, after which they underwent a wide range expansion leading to their current distributions. Confronting phylogenomic and palaeoecological data, we argue that the species originated in East Africa and reached the highlands of the Atlantic side of Africa through two probable latitudinal migration corridors: a northern one towards the Cameroon volcanic line, and a southern one towards Angola. Although the species is now rare in large parts of its range, no demographic decline was detected, probably because it occurred too recently to have left a genetic signature in our DNA sequences. Conclusions: Despite the ancient and highly fluctuating history of podocarps in Africa revealed by palaeobotanical records, the extended distribution of current P. latifolius/milanjianus lineages is shown to result from a more recent history, mostly during the mid-late Pleistocene, when Afromontane forests were once far more widespread and continuous.
MeSH term(s)	Africa ; Africa, Eastern ; Africa, Western ; Forests ; Genetic Variation ; Phylogeny ; Phylogeography ; Trees
Language	English
Publishing date	2020-02-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1461328-1
ISSN	1095-8290 ; 0305-7364
ISSN (online)	1095-8290
ISSN	0305-7364
DOI	10.1093/aob/mcaa049
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