Éditeur(s) : HAL CCSD Wiley
Résumé :
How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rain fall and temperature changes during and/or immediately after the Last Glacial Maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the Eastern Guiana Shield over a time scale of several thousand generations, through the application of Approximate Bayesian Computation (ABC) and Maximum Likelihood (ML) methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rain forests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.
ISSN: 0962-1083

hal-01512150
https://hal.archives-ouvertes.fr/hal-01512150
https://hal.archives-ouvertes.fr/hal-01512150/document
https://hal.archives-ouvertes.fr/hal-01512150/file/Barthe_et_al-_%7B0B6A8C5E-DDFF-4C4E-822C-4E7BC22A6C9B%7D.pdf
DOI : 10.1111/mec.13949

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.
ISSN: 1932-6203

hal-01190764
https://hal.archives-ouvertes.fr/hal-01190764
PRODINRA : 214530
PUBMED : 22808236
DOI : 10.1371/journal.pone.0040699

Résumé : La distribution actuelle des espèces d’arbres des forêts tropicales humides amazoniennes est le résultat de processus dynamiques sur lesquels les perturbations passées, d’origine climatique ou anthropique, peuvent avoir jouées un rôle majeur. Des outils génétiques actuels associés à des méthodes d’analyses puissantes permettent d’inférer et de dater l’empreinte génomique des évènements démographiques subits par les populations naturelles. Le but de cette thèse est de contribuer à une vision d’ensemble de l’évolution démographique de la forêt tropicale humide du plateau des Guyanes pendant le Quaternaire. J’ai d’abord étudié les propriétés des microsatellites (répétitions simple de séquences, SSR) et les limites de leurs applications en tant que marqueurs moléculaires en phylogéographie. Plusieurs allèles SSR contenu dans diverses populations de trois genres d’arbres différents ont été séquencés et le polymorphisme, porté par chaque partie des fragments ADN contenant des SSR, a été étudié. J’ai observé que la quantité de variation génétique était aussi importante dans les régions encadrant le microsatellite que dans le SSR lui-même. Ces régions ont contribué significativement à l’information phylogénétique et ont parfois été la principale source de différenciation entre les individus et les populations. Cette expérience m’a permis de choisir la meilleure stratégie à adopter pour traiter les données de variation génétique des SSR dans des modèles démographiques. J’ai ensuite utilisé ces marqueurs SSR et des méthodes ABC pour étudier l’impact local des occupations humaines précolombiennes sur les forêts en Guyane française. Les changements démographiques subis par des populations de quatre espèces d’arbres ont été comparés entre cinq sites occupés et quatre sites non perturbés. Les perturbations naturelles et induites par l’homme ont contribué à la mise en place de la diversité observée actuellement, comme le suggère des signatures d’effet fondateur détectées sur les sites perturbés ou non. Néanmoins, la taille des populations fondatrices semble être proportionnelle à l’impact humain estimé, indiquant que les perturbations anthropique ont induit un remplacement des populations plus important que les processus écologiques naturels. Pour terminer, j’ai mené une étude de démographie comparative d’espèces d’arbres tropicaux à l’échelle régionale de la Guyane française. Cinq scénarios démographiques ont été testés pour neuf populations de huit espèces en utilisant des microsatellites nucléaires et des séquences chloroplastiques. Les changements démographiques les plus récents détectés convergent vers une signature générale d’expansion de la forêt humide depuis probablement la dernière glaciation. Cela peut suggérer, soit que la composition des forêts du plateau des Guyanes était différente, ou que le couvert forestier était moins étendu. Ce résultat constitue le premier indice de changement passé, probablement d’origine climatique, subi par les communautés forestières du plateau des Guyanes ; qui n’avait jusque-là pas pu être testé avec des méthodes standards en raison d’un manque de fossiles. En conclusion, j’ai recueilli des preuves génétiques que les perturbations, à différents échelles de temps, ont marqué la structure et la composition génétique des forêts du plateau des Guyanes. L’application de ces méthodes à d’autres régions Néotropicales pourrait contribuer, à l’avenir, à reconstruire l’histoire écologique de la forêt amazonienne de façon détaillée.
The current tree species distribution in Amazonian tropical rainforests is the outcome of dynamic processes in which past perturbations, climatic or anthropogenic, may have played a major role. Currently available genetic tools associated with powerful analytical methods allow inferring and dating the genomic imprint of demographic events undergone by natural populations. The aim of my thesis is to contribute to an overview of the demographic evolution of the tropical rainforest in the Guiana shield during the Quaternary. I have first studied the properties of microsatellites or Simple sequence repeat (SSR) and the limits in their applications as molecular markers in phylogeography. Several SSR alleles in multiple populations of three divergent tree genera have been sequenced and the sources of polymorphisms, carried by each portion of SSR-containing DNA amplicons, have been broken apart. I have observed that the amount of variation was as large in flanking regions as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations. This experiment allowed me to choose the best strategy to treat SSR variation in demographic modeling. I have subsequently used SSR markers and ABC methods to study the impact of pre-Columbian human settlements at the local level on rainforests in French Guiana. Demographic changes undergone by populations of four tree species were compared between five settled and four undisturbed sites. Both natural turnover and human-induced disturbances appeared as shaping currently observed genetic diversity, with signatures of founder effect both at disturbed and undisturbed sites. Nevertheless, the size of founding populations appeared to be proportional to the estimated human impact, suggesting that human-made disturbance caused deeper population turnover than background ecological processes. Finally, I have conducted a comparative demography study of tropical tree species at the regional level across French Guiana. Five demographic scenarios have been tested for nine populations from eight species using both nuclear microsatellites and chloroplastic sequences. The most recent demographic signals detected converge on a global signature of expansion of the rainforest since probably the last glaciation. This finding can suggest either that the composition of the Guiana shield rainforests was different, or that its global extent was smaller, during earlier epochs of the Pleistocene than today. This result is the first firm indication of changes undergone by the forest communities of the Guiana shield in the distant climatic past – something which could not be tested with standard methods due to almost complete lack of fossil evidence. In conclusion, I have gathered genetic evidence that disturbances, both in historical and geological times, have marked the structure and composition of forests in the Guiana shield.The extensive application of these methods to other regions of the Neotropics maycontribute, in the future, to the detailed reconstruction of the ecological history ofAmazonian forests.

http://www.theses.fr/2012AGUY0568/document