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Scotti, I.; Montaigne, W.; Cseke, K.; Traissac, S. |
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Title |
Life after disturbance (II): the intermediate disturbance hypothesis explains genetic variation in forest gaps dominated by Virola michelii Heckel (Myristicaceae) |
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Journal Article |
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2015 |
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Annals of Forest Science |
Abbreviated Journal |
Annals of Forest Science |
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72 |
Issue |
8 |
Pages |
1035-1042 |
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Amazon; Bayesian clustering; Demogenetics; Guiana shield; Parentage analysis; Regeneration; Spatial genetic structure; Tropical rainforest |
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Key message: Genetic diversity appears to be unaffected by disturbance in a stand of the light-demanding Neotropical treeV. michelii. Although spatial genetic structure is modified in post-disturbance cohorts, mixing of seeds from different mother trees in canopy gaps appears to efficiently maintain genetic admixture. Context: The interplay between genetic and demographic processes has major consequences on population viability. Population size affects demographic trends, while genetic diversity insures viability by reducing risks of inbreeding depression and by maintaining adaptive potential. Yet, the consequences of increases in census size (as opposed to effective size) on genetic diversity of forest populations are poorly known. Aims: We have studied the structure of genetic diversity in populations of saplings of the light-responsive tree, Virola michelii (Myristicaceae, the nutmeg family), in two plots having undergone different levels of canopy-gap opening disturbance. This allowed us to test the “intermediate disturbance” hypothesis, which generally applies to species diversity, at the intra-specific scale. Methods: Levels and distribution of genetic diversity were compared between plots and between life stages. Sapling parentage was analysed to infer each adult tree’s contribution to regeneration. Results: Genetic diversity was higher, and spatial genetic structure was stronger in the post-disturbance than in the control seedling population. Parentage analysis suggested that a limited number of parents contributed to most of the regeneration, but that efficient mixing of their progeny may have enhanced the diversity of saplings occupying canopy gaps. Conclusion: A mixture of demo-genetic processes may contribute to maintain genetic diversity in spite of, or possibly due to, ecosystem disturbance in V. michelii. © 2015, INRA and Springer-Verlag France. |
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Solicaz, Guyane Technopôle, 16 bis Rue du 14 Juillet, Cayenne, French Guiana |
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Export Date: 14 December 2015 |
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EcoFoG @ webmaster @ |
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642 |
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Scotti, I.; Paglia, G.; Magni, F.; Morgante, M. |
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Title |
Population genetics of Norway spruce (Picea abies Karst.) at regional scale: sensitivity of different microsatellite motif classes in detecting differentiation |
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Journal Article |
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2006 |
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Annals of Forest Science |
Abbreviated Journal |
Ann. For. Sci. |
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63 |
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5 |
Pages |
485-491 |
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Keywords |
conifers; SSR; divergence; statistical testing; genetic distance |
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Four populations of Norway spruce (Picea abies Karst.) were screened using nine nuclear microsatellite markers (three trinucleotides and six dinucleotides) and four chloroplast markers (all mononucleotides). Marker classes were compared for their variability, mutation rate and ability to detect differentiation between stands. Dinucleotide markers proved to be the most variable group and chloroplast stretches the least variable, with differences in mutation rate between the former and the latter spanning over two orders of magnitude. Variability correlated to the number of repeats but not to the absolute length of the microsatellite region. The different marker classes were combined with two different measures of genetic distance in order to investigate the performance of markers and evolutionary models for the study of genetic variation in natural populations of Norway spruce. Weir and Cockeram's F-ST generally performed better in this clear-cut, four-population model study. Chloroplast haplotypes turned out to be the most sensitive marker system, being able to differentiate populations and to detect differences in genetic variability between sub-regions. |
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INRA, UMR ECOFOG, Kourou 97387, French Guiana, Email: ivan.scotti@kourou.cirad.fr |
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EDP SCIENCES S A |
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1286-4560 |
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ISI:000240514800005 |
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EcoFoG @ eric.marcon @ |
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177 |
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Scotti-Saintagne, C.; Bertocchi, E.; Barreneche, T.; Kremer, A.; Plomion, C. |
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Title |
Quantitative trait loci mapping for vegetative propagation in pedunculate oak |
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Journal Article |
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Year |
2005 |
Publication |
Annals of Forest Science |
Abbreviated Journal |
Ann. For. Sci. |
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62 |
Issue |
4 |
Pages |
369-374 |
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Keywords |
vegetative propagation; QTL; Quercus robur |
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Vegetative propagation is one of the main methods used for the deployment of improved genetic forest tree species. The objective of this paper was to study the genetic architecture of vegetative propagation by detecting Quantitative Trait Loci (QTL) in pedunculate oak ( Quercus robur). The mapping population consisted on an F-1 family of 278 offspring. Assessment of rooting ability over three years permitted the detection of 10 QTLs explaining between 4.4 and 13.8% of phenotypic variance, of which the two strongest were stable across years. Ongoing genomics programs in trees and in Arabidopsis are starting to shed light on the nature of the underlying genes. |
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Equipe Genet, INRA, UMR 1202, BIOGECO, F-33612 Cestas, France, Email: christophe.plomion@pierroton.inra.fr |
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E D P SCIENCES |
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1286-4560 |
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ISI:000229668600010 |
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EcoFoG @ eric.marcon @ |
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255 |
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Scotti-Saintagne, C.; Bodenes, C.; Barreneche, T.; Bertocchi, E.; Plomion, C.; Kremer, A. |
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Title |
Detection of quantitative trait loci controlling bud burst and height growth in Quercus robur L |
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Journal Article |
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Year |
2004 |
Publication |
Theoretical and Applied Genetics |
Abbreviated Journal |
Theor. Appl. Genet. |
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109 |
Issue |
8 |
Pages |
1648-1659 |
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Genetic variation of bud burst and early growth components was estimated in a full-sib family of Quercus robur L. comprising 278 offspring. The full sibs were vegetatively propagated, and phenotypic assessments were made in three field tests. This two-generation pedigree was also used to construct a genetic linkage map (12 linkage groups, 128 markers) and locate quantitative trait loci (QTLs) controlling bud burst and growth components. In each field test, the date of bud burst extended over a period of 20 days from the earliest to the latest clone. Bud burst exhibited higher heritability (0.15-0.51) than growth components (0.04-0.23) and also higher correlations across field tests. Over the three tests there were 32 independent detected QTLs (Pless than or equal to5% at the chromosome level) controlling bud burst, which likely represent at least 12 unique genes or chromosomal regions controlling this trait. QTLs explained from 3% to 11% of the variance of the clonal means. The number of QTLs controlling height growth components was lower and varied between two and four. However the contribution of each QTL to the variance of the clonal mean was higher (from 4% to 19%). These results indicate that the genetic architecture of two important fitness-related traits are quite different. On the one hand, bud burst is controlled by several QTLs with rather low to moderate effects, but contributing to a high genetic (additive) variance. On the other hand, height growth depends on fewer QTLs with moderate to strong effects, resulting in lower heritabilities of the trait. |
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INRA, UMR Biodivers Genes & Ecosyst, F-33612 Cestas, France, Email: antoine.kremer@pierroton.inra.fr |
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SPRINGER |
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0040-5752 |
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ISI:000225054800012 |
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EcoFoG @ eric.marcon @ |
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260 |
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Scotti-Saintagne, C.; Bodenes, C.; Barreneche, T.; Pot, D.; Plomion, C.; Kremer, A. |
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Title |
Distribution of genomic regions differentiating oak species assessed by QTL detection |
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Journal Article |
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Year |
2004 |
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Abbreviated Journal |
Heredity |
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92 |
Issue |
1 |
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20-30 |
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QTL; leaf morphology; repeatability; genetic map; Q. robur |
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Pedunculate oak and sessile oak are two sympatric inter-fertile species that exhibit leaf morphological differences. We aimed to detect quantitative trait loci (QTLs) of these traits in order to locate genomic regions involved in species differentiation. A total of 15 leaf morphological traits were assessed in a mixed forest stand composed of Quercus petraea and Q. robur and in a full-sib pedigree of Q. robur. The progeny of the full-sib family were vegetatively propagated in two successive experiments comprising 174 and 216 sibs, and assessments were made on two leaves collected on each of the 1080 and 1530 cuttings corresponding to the two experiments. Traits that exhibited strong species differences in the mixed stand tended also to have higher repeatability values in the mapping population, thus indicating higher genetic control. A genetic map was constructed for QTL detection. Composite interval mapping with the one QTL model was used for QTL detection. From one to three QTLs were detected for 13 traits. In-depth analysis of the QTLs, controlling the five morphological traits that exhibited the highest interspecific differences in the mixed stand, indicated that they were distributed on six linkage groups, with two clusters comprising QTLs of at least two discriminant traits. These results were reinforced when error 1 for QTL detection was set at 5% at the chromosome level, as up to nine clusters could be identified. In conclusion, traits involved in interspecific differentiation of oaks are under polygenic control and widespread in clusters across the genome. |
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INRA, UMR Biodivers Genes & Ecosyst, F-33612 Cestas, France |
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NATURE PUBLISHING GROUP |
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0018-067X |
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ISI:000187216300005 |
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EcoFoG @ eric.marcon @ |
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267 |
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Scotti-Saintagne, C.; Dick, C.W.; Caron, H.; Vendramin, G.G.; Guichoux, E.; Buonamici, A.; Duret, C.; Sire, P.; Valencia, R.; Lemes, M.R.; Gribel, R.; Scotti, I. |
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Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa, Meliaceae) |
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Journal Article |
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2013 |
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Journal of Biogeography |
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40 |
Issue |
4 |
Pages |
676-692 |
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Amazonia; Carapa; Historical biogeography; Mahogany family; Molecular markers; Neogene diversification; Phylogeography; Quaternary diversification; Species complexes |
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Aim Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species. Location Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America. Methods Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times. Results Two genetic clusters (nuguianensis and nusurinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal. Main conclusions The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex. © 2012 Blackwell Publishing Ltd. |
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Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão 915, Jardim Botânico, 22460-030, Rio de Janeiro, RJ, Brazil |
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Export Date: 26 March 2013; Source: Scopus |
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EcoFoG @ webmaster @ |
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477 |
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Scotti-Saintagne, C.; Dick, C.W.; Caron, H.; Vendramin, G.G.; Troispoux, V.; Sire, P.; Casalis, M.; Buonamici, A.; Valencia, R.; Lemes, M.R.; Gribel, R.; Scotti, I. |
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Title |
Amazon diversification and cross-Andean dispersal of the widespread Neotropical tree species Jacaranda copaia (Bignoniaceae) |
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Journal Article |
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Year |
2013 |
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Journal of Biogeography |
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40 |
Issue |
4 |
Pages |
707-719 |
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Amazonia; Bignoniaceae; Centre of diversity; Dispersal; Historical biogeography; Neotropics; Phylogeography; Pleistocene; Tropical forest; Vicariance |
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Aim: The phylogeographical history of Neotropical species can be difficult to reconstruct because of superimposed Neogene and Quaternary histories, and because of taxonomic uncertainty. We analysed range-wide genetic diversity in a widespread pioneer tree species, Jacaranda copaia (Aubl.) D. Don, to characterize phylogeographical structure, date the evolutionary relationships among lineages, and evaluate the role of dispersal and vicariance in establishing the present geographical range. Location: Guiana Shield; central, southern and western Amazon Basin; Chocó region; Central America. Methods: We analysed nine nuclear simple sequence repeat loci (nuSSR), eight chloroplast SSRs (cpSSR), and two cpDNA intergenic sequences in 341 adult trees. Genetic differentiation at nuSSRs was inferred using Bayesian clustering. Dating of chloroplast lineage divergence was obtained using a range of published mutation rates and Bayesian coalescence analyses. Population divergence dating was performed using an isolation-with-migration model for eight loci (one cp sequence and seven nuSSRs). Results: Nuclear SSR variation identified three geographically overlapping clusters (nu-1, nu-2, nu-3). Twelve cpDNA haplotypes were clustered into two haplogroups (cp-1, cp-2) with the central Amazon harbouring the highest diversity. Molecular dating analysis suggests that cpDNA haplotype diversification started around the end of the Pliocene (2.61 Ma on average), whereas population divergence was more recent and occurred during the mid-Quaternary (point estimates between 357 and 436 ka). Main conclusions: The genetic variation of J. copaia in the Neotropics was shaped mainly by Pleistocene events. Chloroplast diversity did not display the expected cis/trans Andean disjunction, indicating recent dispersal. Nuclear variation revealed that separate regions share a recent history, with a centre of diversity in the central Amazon Basin. The geographical pattern of diversity is congruent with the distribution of the two subspecies, J. copaia copaia and J. copaia spectabilis, and evidence of nuSSR admixture between the two taxa supports their classification as subspecies. © 2012 Blackwell Publishing Ltd. |
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Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão 915, Jardim Botânico, 22460-030, Rio de Janeiro, RJ, Brazil |
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Export Date: 26 March 2013; Source: Scopus |
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EcoFoG @ webmaster @ |
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476 |
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Scotti-Saintagne, C.; Mariette, S.; Porth, I.; Goicoechea, P.G.; Barreneche, T.; Bodenes, K.; Burg, K.; Kremer, A. |
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Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q petraea (Matt.) Liebl.] |
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Journal Article |
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2004 |
Publication |
Genetics |
Abbreviated Journal |
Genetics |
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168 |
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3 |
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1615-1626 |
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Interspecific differentiation values (G(ST)) between two closely related oak species (Quercus petraea and Q. robur) were compiled across different studies with the aim to explore the distribution of differentiation at the genome level. The study was based on a total set of 389 markers (isozymes, AFLPs, SCARs, microsatellites, and SNPs) for which allelic frequencies were estimated in pairs of populations sampled throughout the sympatric distribution of the two species. The overall distribution of GST values followed an L-shaped curve with most markers exhibiting low species differentiation (G(ST) < 0.01) and only a few loci reaching >10% levels. Twelve percent of the loci exhibited significant G(ST) deviations to neutral expectations, suggesting that selection contributed to species divergence. Coding regions expressed higher differentiation than noncoding regions. Among the 389 markers, 158 could be mapped on the 12 linkage groups of the existing Q. robur genetic map. Outlier loci with large G, values were distributed over 9 linkage groups. One cluster of three outlier loci was found within 0.51 cM; but significant autocorrelation of GST was observed at distances <2 cM. The size and distribution of genomic regions involved in species divergence are discussed in reference to hitchhiking effects and disruptive selection. |
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INRA, UMR Biodivers Genes & Ecosyst, F-33612 Cestas, France, Email: kremer@pierronton.inra.fr |
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GENETICS |
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0016-6731 |
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ISI:000225767400041 |
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EcoFoG @ eric.marcon @ |
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258 |
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Sebbenn, A.M.; Blanc-Jolivet, C.; Mader, M.; Meyer-Sand, B.R.V.; Paredes-Villanueva, K.; Honorio Coronado, E.N.; García-Dávila, C.; Tysklind, N.; Troispoux, V.; Delcamp, A.; Degen, B. |
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Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia |
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Journal Article |
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Year |
2019 |
Publication |
Conservation Genetics Resources |
Abbreviated Journal |
Conserv. Gen. Res. |
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11 |
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3 |
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341-343 |
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DNA fingerprints; Geographical origin; Jacaranda copaia; MassARRAY; MiSeq; RADSeq; Tropical timber |
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Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin. |
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BIOGECO, INRA, Univ. Bordeaux, Cestas, 33610, France |
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Springer Netherlands |
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EcoFoG @ webmaster @ |
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907 |
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Seibold, Sebastien ; Rammer, Werner ; Hothorn, Torsten ; Seidl, Rupert ; Ulyshen, Michael ; Lorz, Janina ; Cadotte, Marc ; Lindenmayer, David ; Adhikari, Yagya ; Aragón, Roxana ; Bae, Soyeon ; Baldrian, Petr ; Barimani Varandi, Hassan ; Barlow, Jos ; Bässler, Clauss ; Beauchêne, Jacques ; and all ................... |
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The contribution of insects to global forest deadwood decomposition |
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2021 |
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Nature |
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597 |
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7874 |
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77-81 |
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The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2-5 with decomposer groups-such as microorganisms and insects-contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains poorly understood7. Here we present a field experiment of wood decomposition across 55 forest sites and 6 continents. We find that the deadwood decomposition rates increase with temperature, and the strongest temperature effect is found at high precipitation levels. Precipitation affects the decomposition rates negatively at low temperatures and positively at high temperatures. As a net effect-including the direct consumption by insects and indirect effects through interactions with microorganisms-insects accelerate the decomposition in tropical forests (3.9% median mass loss per year). In temperate and boreal forests, we find weak positive and negative effects with a median mass loss of 0.9 per cent and -0.1 per cent per year, respectively. Furthermore, we apply the experimentally derived decomposition function to a global map of deadwood carbon synthesized from empirical and remote-sensing data, obtaining an estimate of 10.9 ± 3.2 petagram of carbon per year released from deadwood globally, with 93 per cent originating from tropical forests. Globally, the net effect of insects may account for 29 per cent of the carbon flux from deadwood, which suggests a functional importance of insects in the decomposition of deadwood and the carbon cycle. |
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NATURE PUBLISHING GROUP |
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EcoFoG @ webmaster @ |
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1046 |
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