Search

The effects of selection on an organism’s genome are hard to detect on small spatial scales, as gene flow can erase signatures of local adaptation. Most genome scans to detect signatures of environmental selection are performed on large spatial scales, however divergent selection on the local scale (e.g. between contrasting soil conditions) has also been demonstrated, in particular for herbaceous plants. Here we hypothesize that in topographically complex landscapes, microenvironment variability is strong enough to leave a selective footprint in genomes of long-lived organisms. To test this, we investigated paired south- versus north-facingPinus pinasterstands in a Mediterranean mountain area. While north-facing (mesic) stands experience less radiation, south facing (xeric) stands represent especially harsh conditions, particularly during the dry summer season. Outlier detection revealed five putatively adaptive loci out of 4,034, two of which encoded non-synonymous substitutions. Additionally, one locus showed consistent allele frequency differences in all three stand pairs indicating divergent selection despite high gene flow on the local scale. Functional annotation of these candidate genes revealed biological functions related to abiotic stress response in other species. Our study highlights how divergent selection shapes the functional genetic variation within populations of long-lived forest trees on local spatial scales.

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators. ispartof: CONSERVATION GENETICS vol:24 issue:2 pages:181-191 ispartof: location:Netherlands status: published

Mutation, the source of genetic diversity, is the raw material of evolution; however, the mutation process remains understudied, especially in plants. Using both a simulation and reanalysis framework, we set out to explore and demonstrate the improved performance of variant callers developed for cancer research compared to single nucleotide polymorphism (SNP) callers in detecting de novo somatic mutations.In anin silicoexperiment, we generated Illumina-like sequence reads spiked with simulated mutations at different allelic fractions to compare the performance of seven commonly-used variant callers to recall them. More empirically, we then reanalyzed two of the largest datasets available for plants, both developed for identifying within-individual variation in long-lived pedunculate oaks.Based on thein silicoexperiment, variant callers developed for cancer research outperform SNP callers regarding plant mutation recall and precision, especially at low allele frequency. Such variants at low allelic fractions are typically expected for within-individual de novo plant mutations, which initially appear in single cells. Reanalysis of published oak data with Strelka2, the best-performing caller based on our simulations, identified up to 3.4x more candidate somatic mutations than reported in the original studies.Our results advocate the use of cancer research callers to boost de novo mutation research in plants, and to reconcile empirical reports with theoretical expectations.This version of the article has been peer-reviewed and recommended byPeer Community in Genomicshttps://doi.org/10.24072/pci.genomics.100024

Genetic diversity within species and populations is necessary for long-term survival and thus constitutes a key component of preserving biodiversity, but until now, it has rarely been integrated into conservation policies. Ancient and historical genetic data [ancient/historical DNA (a/hDNA)], such as those from specimens stored in natural history collections, can add a temporal dimension to conservation genetic inferences by providing baseline levels of diversity that contemporary data can be compared with and help guide conservation actions. To increase the use and impact of a/hDNA research in preserving biodiversity, genetic indicators must be explicitly included in conservation policies, the benefits and limitations of using a/hDNA need to be clearly communicated to all conservation actors, and relationships between academics, museums, conservation practitioners, and policy makers must be strengthened.

Tropical forest dynamics are driven by growth and survival strategies of tree species in relation to treefall gaps; however, the ecological and evolutionary roles of intraspecific variation in the response to forest gaps remain unexplored. Here, we associated genomic data of three related tree species of the genus Symphonia in a French Guiana forest with (1) each individual tree's growth potential, and (2) with its light and competition environment estimated based on 33 years of forest monitoring in plots covering 120 ha. We show that individual trees within species have genetically determined growth strategies that are adapted to the local light and competition environments, which are shaped by the time since the last treefall. Within species, fast-growing genotypes are more frequent in light-enriched environments and slow-growing genotypes in more shaded environments. Forest gap dynamics is thus a strong selection driver that shapes adaptive strategies and maintains genetic variation within tropical tree species.

A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9

Made available in DSpace on 2021-06-25T15:04:36Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-05 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Investissement d'Avenir grants of the ANR Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) LabEx COTE mobility grant Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) SISBIO SERFOR IDEFLOR-Bio/PA SEMARH/GO IEF/MG Both genetic drift and divergent selection are predicted to be drivers of population differentiation across patchy habitats, but the extent to which these forces act on natural populations to shape traits is strongly affected by species' ecological features. In this study, we infer the genomic structure of Pitcairnia lanuginosa, a widespread herbaceous perennial plant with a patchy distribution. We sampled populations in the Brazilian Cerrado and the Central Andean Yungas and discovered and genotyped SNP markers using double-digest restriction-site associated DNA sequencing. In addition, we analyzed ecophysiological traits obtained from a common garden experiment and compared patterns of phenotypic and genetic divergence (P-ST-F-ST comparisons) in a subset of populations from the Cerrado. Our results from molecular analyses pointed to extremely low genetic diversity and a remarkable population differentiation, supporting a major role of genetic drift. Approximately 0.3% of genotyped SNPs were flagged as differentiation outliers by at least two distinct methods, and Bayesian generalized linear mixed models revealed a signature of isolation by environment in addition to isolation by distance for high-differentiation outlier SNPs among the Cerrado populations. P-ST-F-ST comparisons suggested divergent selection on two ecophysiological traits linked to drought tolerance. We showed that these traits vary among populations, although without any particular macro-spatial pattern, suggesting local adaptation to differences in micro-habitats. Our study shows that selection might be a relevant force, particularly for traits involved in drought stress, even for populations experiencing strong drift, which improves our knowledge on eco-evolutionary processes acting on non-continuously distributed species. Univ Estadual Paulista, Dept Ecol, Inst Biociencias, Rio Claro, SP, Brazil Univ Bordeaux, INRAE, Biogeco, Cestas, France Univ Nacl Mayor San Marcos, Dept Ecol, Museo Hist Nat, Lima, Peru Univ Estadual Campinas, Inst Biol, Dept Biol Vegetal, Campinas, SP, Brazil Univ Estadual Paulista, Dept Ecol, Inst Biociencias, Rio Claro, SP, Brazil FAPESP: 2014/15588-6 Investissement d'Avenir grants of the ANR: CEBA:ANR-10-LABX-2501 CAPES: 001 FAPESP: 2014/08087-0 FAPESP: 2016/04396-4 FAPESP: 2016/20273-0 CNPq: 300819/2016-1 SISBIO: 44062-1 SERFOR: 2017-2016 IDEFLOR-Bio/PA: 001/15 SEMARH/GO: 187/2014 IEF/MG: 081/2014

Made available in DSpace on 2020-12-10T19:44:43Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-08-16 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Investissement d'Avenir grants of the ANR Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Pro Reitoria de Pesquisa e Extensao/UNESP Background and Aims Isolated populations constitute an ideal laboratory to study the consequences of intra-specific divergence, because intrinsic incompatibilities are more likely to accumulate under reduced gene flow. Here, we use a widespread bromeliad with a patchy distribution, Pitcairnia lanuginosa, as a model to infer processes driving Neotropical diversification and, thus, to improve our understanding of the origin and evolutionary dynamics of biodiversity in this highly speciose region. Methods We assessed the timing of lineage divergence, genetic structural patterns and historical demography of P. lanuginosa, based on microsatellites, and plastid and nuclear sequence data sets using coalescent analyses and an Approximate Bayesian Computation framework. Additionally, we used species distribution models (SDMs) to independently estimate potential changes in habitat suitability. Key Results Despite morphological uniformity, plastid and nuclear DNA data revealed two distinct P. lanuginosa lineages that probably diverged through dispersal from the Cerrado to the Central Andean Yungas, following the final uplift of the Andes, and passed through long-term isolation with no evidence of migration. Microsatellite data indicate low genetic diversity and high levels of inbreeding within populations, and restricted gene flow among populations, which are likely to be a consequence of bottlenecks (or founder events), and high selfing rates promoting population persistence in isolation. SDMs showed a slight expansion of the suitable range for P. lanuginosa lineages during the Last Glacial Maximum, although molecular data revealed a signature of older divergence. Pleistocene climatic oscillations thus seem to have played only a minor role in the diversification of P. lanuginosa, which probably persisted through adverse conditions in riparian forests. Conclusions Our results imply drift as a major force shaping the evolution of P. lanuginosa, and suggest that dispersal events have a prominent role in connecting Neotropical open and forest biomes. Univ Estadual Paulista, Dept Ecol, Inst Biociencias, BR-13506900 Sao Paulo, SP, Brazil Univ Nacl Mayor San Marcos, Dept Ecol, Museo Hist Nat, Lima 15072, Peru Univ Bordeaux, INRA, Biogeco, F-33610 Cestas, France Univ Estadual Campinas, Dept Biol Vegetal, Inst Biol, BR-13083862 Campinas, SP, Brazil Univ Estadual Paulista, Dept Ecol, Inst Biociencias, BR-13506900 Sao Paulo, SP, Brazil FAPESP: 2014/15588-6 Investissement d'Avenir grants of the ANR: CEBA:ANR-10-LABX-25-01 CAPES: 001 FAPESP: 2014/08087-0 FAPESP: 2016/04396-4 CNPq: 300819/2016-1

ispartof: CONSERVATION GENETICS vol:22 issue:4 pages:533-536 status: published

International audience; Forest inventories in Amazonia include around 5000 described tree species belonging to more than 800 genera. Numerous species-rich genera share genetic variation among species because of recent speciation and/or recurrent hybridisation, forming species complexes. Despite the key role that tree species complexes play in understanding Neotropical diversification, and their need to exploit a diversity of niches, little is known about the mechanisms that allow local coexistence of tree species complexes and their species in sympatry. In this study, we explored the fine-scale distribution of five tree species complexes and 22 species within these complexes. Combining forest inventories, botanical determination, and LiDAR-derived topographic data over 120 ha of permanent plots in French Guiana, we used a Bayesian modelling framework to test the role of fine-scale topographic wetness and tree neighbourhood on the occurrence of species complexes and the relative distribution of species within complexes. Species complexes of Neotropical trees were widely spread across the topographic wetness gradient at the local scale. Species within complexes showed pervasive niche differentiation along with topographic wetness and competition gradients. Similar patterns of species-specific habitat preferences were observed within several species complexes: species more tolerant to competition for resources grow in drier and less fertile plateaus and slopes. If supported by partial reproductive isolation of species and adaptive introgression at the species complex level, our results suggest that both species-specific habitat specialisation within species complexes and the broad ecological distribution of species complexes might explain the success of these species complexes at the regional scale.

ispartof: BIOLOGICAL CONSERVATION vol:253 status: published

The most remarkable feature of our planet is the diversity of its life forms, ranging from viruses and nanobacteria to blue whales and giant sequoias to satanic leaf‐tailed geckos and leafy seadragons (look them up!). Life is found in essentially all environments on earth, and the number of species living on our planet is many times greater than we could have imagined a century ago. A well‐regarded estimate pegs the number of eukaryotic species on earth at 8.7 million (±1.3 million), of which fewer than 15% are currently described (Mora et al., 2011). The diversity of prokaryotes is less clear (and highly controversial), but an analysis of 1.6 billion 16S ribosomal RNA sequences estimated that 0.8–1.6 million prokaryotic operational taxonomic units exist globally (Louca et al., 2019). While we do not know how many species are currently extant, or have existed in the past, we do know that this biodiversity is valuable, providing food, fibre and medicine, furnishing ecosystem services such as water and air purification, nutrient cycling, pollination and carbon uptake, and contributing to technological innovations ranging from biotechnology to robotics to material science. Moreover, biodiversity underlies the cultural identity of human populations and is important to human health and well‐being. Geographically, species richness increases from the Polar Regions to the tropics in terrestrial and surface marine ecosystems. Thus, some countries, especially those in tropical and subtropical regions, are endowed with much greater biodiversity than others. Unfortunately, benefits arising from the access and utilization of this biodiversity have been unequally shared, with (paradoxically) biodiversity‐poor countries often accruing the lion's share of economic gains. There can be imbalances within countries as well, wherein some segments of the population obtain greater economic benefits from biodiversity and associated traditional knowledge than indigenous peoples. The “Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization,” which came into force in 2014, is an international agreement designed to ensure that the benefits arising from biodiversity are shared equitably (https://www.cbd.int/abs/). However, few scientific journals require compliance with the Nagoya Protocol or the reporting of benefits from biodiversity research. In this editorial, we (the editors of Molecular Ecology and Molecular Ecology Resources) express support for the Nagoya Protocol and the principle of benefit sharing. We believe that scientific journals publishing research on biodiversity can play an important role in implementing the Nagoya Protocol and in reporting on benefits generated from such research. Below, we provide background on the Nagoya Protocol, discuss the kinds of benefits that may arise from biodiversity research, describe the rationale for reporting on these benefits and introduce changes to the journals’ Data Accessibility Statements to incorporate the requirements and goals of the Nagoya Protocol.

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics. Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.\ud\ud Previous article in issue

M.H. receives funding from an “Investissement d’Avenir” grant managed by Agence Nationale de la Recherche [Centre d’etude de la biodiversite amazonienne (CEBA), ref. ANR-10-LABX-25-01].

17 Pág., A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic; that is, they have a genetic architecture determined by numerous loci, each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyse this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response) in a clonal common-garden network planted in contrasted environments (over 20,500 trees). Most of the analysed traits showed evidence of local adaptation based on Qst -Fst comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0%-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change., This study was funded by the Spanish Ministry of Economy and Competitiveness through projects RTA2010-00120-C02- 02 (CLONAPIN), CGL2011-30182- C02- 01 (AdapCon) and AGL2012-40151- C03- 02 (FENOPIN). The study was also supported by the “Initiative d’Excellence (IdEx) de l’Université de Bordeaux - Chaires d'installation 2015” (EcoGenPin) and the European Union's Horizon 2020 research and innovation programme under grant agreement No 773383 (B4EST)

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., SCOPUS: ar.j, info:eu-repo/semantics/published

Backgrounds and AimsDimorphandra wilsonii Rizzini, a critically endangered and protected tree, has a restricted distribution in the ecotone between the Cerrado and the Atlantic Forest in south-eastern Brazil. In this area, it co-occurs with D. mollis Benth., a common tree from the Cerrado, and D. exaltata Schott., a rare tree from the Atlantic Forest. Previous studies of D. wilsonii indicated heterozygosity excess at the individual level. Field observation of some intermediate phenotypes between D. wilsonii and both congeners suggests hybridization of D. wilsonii with D. mollis and/or D. exaltata. Here, we tested the hypothesis that D. wilsonii may have originated from hybridization between D. exaltata and D. mollis. We also performed cytogenetic analysis to examine if the heterozygosity excess could be explained by polyploidy in D. wilsonii.MethodsWe evaluated the genetic diversity and population structure of D. wilsonii using 11 nuclear simple sequence repeats (SSRs) genotyped in 152 individuals sampled across the taxon’s range. We performed comparative genetic analyses using overlapping SSR markers between D. wilsonii and previously published SSR data in D. mollis and D. exaltata to subsequently perform a series of allelic comparisons, multivariate and Bayesian analysis.Key ResultsOur results suggest that D. wilsonii individuals are most likely to correspond to F1 hybrids between D. exaltata and D. mollis. Cytogenetic analysis indicated that D. wilsonii is diploid with the same chromosome number as D. mollis (2n = 2x = 28).ConclusionsOur study raises questions about the taxonomic status and the evolutionary future of D. wilsonii. We suggest that the conservation and management strategy for D. wilsonii should be revised and that it should take into account both parental Dimorphandra species in the ecotone, with special emphasis on the threatened D. exaltata. Finally, this study highlights the value of genetic information for the design of conservation strategies.

International audience; Tropical forests shelter the highest species diversity worldwide, although genus diversity is lower than expected. In the species-rich genera, species complexes are composed of closely-related species that share large amounts of genetic variation. Despite the key role of species complexes in diversification, evolution and functioning of ecological communities, little is known on why species complexes arise and how they are maintained in Neotropical forests. Examining how individual phenotypes vary along environmental gradients, within and among closely-related species within species complexes, can reveal processes allowing species coexistence within species complexes. We examined leaf functional trait variation with topography in a hyperdiverse tropical forest of the Guiana Shield. We collected leaf functional traits from 766 trees belonging to five species in two species complexes in permanent plots encompassing a diversity of topographic positions. We tested the role of topography on leaf functional trait variation with a hierarchical Bayesian model, controlling for individual tree diameter effect. We show that, mirroring what has been previously observed among species and communities, individual leaf traits covary from acquisitive to conservative strategy within species. Moreover, decreasing wetness from bottomlands to plateaus was associated with a shift of leaf traits from an acquisitive to a conservative strategy both across and within closely-related species. Our results suggest that intraspecific trait variability widens species' niches and converges at species' margins where niches overlap, potentially implying local neutral processes. Intraspecific trait variability favors local adaptation and divergence of closely-related species within species complexes. It is potentially maintained through interspecific sharing of genetic variation through hybridization.

Background and aims – The evolutionary history of Amazonia’s hyperabundant tropical tree species, also known as “hyperdominant” species, remains poorly investigated. We assessed whether the hyperdominant Eschweilera coriacea (DC.) S.A.Mori (Lecythidaceae) represents a single genetically cohesive species, and how its genetic constitution relates to other species from the same clade with which it occurs sympatrically in French Guiana.Methods – We sampled 152 individuals in nine forest sites in French Guiana, representing 11 species of the genus Eschweilera all belonging to the Parvifolia clade, with emphasis on E. coriacea. Samples were genotyped at four simple sequence repeat (SSR) markers. We delimited gene pools, i.e., genetically coherent putative taxa, using STRUCTURE software and principal component analysis. We compared the genetic assignment of individuals with their morphological species determination and estimated genetic diversity and differentiation for gene pools and species. We also estimated genome size using flow cytometry.Key results – SSR profiles commonly displayed up to four alleles per genotype, suggesting that the investigated Eschweilera species bear a paleopolyploid signature. Flow cytometry suggested that the studied species are diploid with haploid genome sizes of 871–1046 Mbp. We detected five gene pools and observed a good correspondence between morphological and genetic delimitation for Eschweilera sagotiana Miers and the undescribed morphospecies E. sp. 3 (which resembles E. grandiflora (Aubl.) Sandwith), and to a lesser extent for E. decolorans Sandwith and E. micrantha (O.Berg) Miers. Eschweilera coriacea was the most genetically diverse species and included individuals assigned to each gene pool.Conclusions – We found no conclusive evidence for cryptic species within E. coriacea in French Guiana. SSRs detected fewer gene pools than expected based on morphology in the Parvifolia clade but discriminated evolutionary relationships better than available plastid markers. A positive trend between demographic abundance of species and allelic richness illustrates that hyperdominants may have a high evolutionary potential. This hypothesis can be tested using more powerful genomic data in combination with tree phenotypic trait variation and characterization of niche breadth, to enhance our understanding of the causes of hyperdominance in Amazonian trees.

Paleo-environmental data show that the distribution of African rain forests was affected by Quaternary climate changes. In particular, the Dahomey Gap (DG) – a 200 km wide savanna corridor currently separating the West African and Central African rain forest blocks and containing relict rain forest fragments – was forested during the mid-Holocene and possibly during previous interglacial periods, whereas it was dominated by open vegetation (savanna) during glacial periods. Genetic signatures of past population fragmentation and demographic changes have been found in some African forest plant species using nuclear markers, but such events appear not to have been synchronous or shared across species. To better understand the colonization history of the DG by rain forest trees through seed dispersal, the plastid genomes of two widespread African forest legume trees, Anthonotha macrophylla and Distemonanthus benthamianus, were sequenced in 47 individuals for each species, providing unprecedented phylogenetic resolution of their maternal lineages (857 and 115 SNPs, respectively). Both species exhibit distinct lineages separating three regions: 1. Upper Guinea (UG, i.e. the West African forest block), 2. the area ranging from the DG to the Cameroon volcanic line (CVL), and 3. Lower Guinea (LG, the western part of the Central African forest block) where three lineages co-occur. In both species, the DG populations (including southern Nigeria west of Cross River) exhibit much lower genetic diversity than UG and LG populations, and their plastid lineages originate from the CVL, confirming the role of the CVL as an ancient forest refuge. Despite the similar phylogeographic structures displayed by A. macrophylla and D. benthamianus, molecular dating indicates very contrasting ages of lineage divergence (UG diverged from LG since c. 7 Ma and 0.7 Ma, respectively) and DG colonization (probably following the Mid Pleistocene Transition and the Last Glacial Maximum, respectively). The stability of forest refuge areas and repeated similar forest shrinking/expanding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales.

The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis, A. pachyloba, and A. bella. Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09–14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 – 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome.

Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled ‘Genomics and Forest Tree Genetics’ was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.

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. africanain the Sudanian region andA. quanzensisin 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 241A. africanaand 113A. quanzensisindividuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30A. africanaand 12A. quanzensisindividuals, 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)= −0.005and −0.007andbLd (SNP)= −0.008and −0.006 forA. africanaandA. 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.

International audience; A recommendation – based on reviews by Marcela Van Loo, David Macaya-Sanz and one anonymous reviewer – of the article: Stoeckel, S., Porro, B., and Arnaud-Haond, S. (2019). The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates. ArXiv:1902.09365 [q-Bio] v4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. Retrieved from http://arxiv.org/abs/1902.09365v4

A remnant population ofAnadenanthera colubrinavar.cebilin Northern Argentina showed a mixed mating system, high genetic diversity, and moderate spatial genetic structure, which was stronger in saplings than in adults. Demographic history analyses revealed an ancient population expansion. Despite high genetic diversity, high inbreeding suggests caution in the use of this stand as seed source. Context: Information on fine-scale spatial genetic structure (FSGS) and demographic history is essential to determine which mechanisms are responsible for population persistence and evolution. This is particularly important in fragmented biomes, such as the seasonally dry tropical forests. Aims: To assess the level of genetic diversity and population genetic structure in a remnant population of A. colubrina var. cebil, and to evaluate the influence of historical and contemporary environmental change on the genetic constitution of this population. Methods: Eight microsatellites were typed in 60 adults and 59 saplings. The existence of (non-spatial) genetic clusters was evaluated using STRUCTURE and PCAs. FSGS was evaluated by kinship analyses and sPCA. MCMCglmm models were used to provide insights into factors underlying FSGS. Demographic history was studied using bottleneck statistics and approximate Bayesian computation. Results: We found high levels of genetic diversity and high inbreeding. Genetic structure was stronger in saplings than in adult trees, probably due to assortative mating, and was not explained by altitude or DBH. Demographic analyses suggested an ancient population expansion. Conclusion: Patterns of inbreeding and relatedness suggest a mixed mating system. High genetic diversity and moderate genetic structure suggest long-term population viability. High inbreeding suggests caution when using this stand as a source of material for reforestation. Fil: Goncalves, Alejandra Lorena. Universidad Nacional de Misiones; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina Fil: García, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina Fil: Heuertz, Myriam. Institut National de la Recherche Agronomique; Francia. Universite de Bordeaux; Francia Fil: González Martínez, Santiago C.. Institut National de la Recherche Agronomique; Francia. Universite de Bordeaux; Francia

International audience; Reconstructing species trees from multi-loci datasets is becoming a standard practice in phylogenetics. Nevertheless, access to high-throughput sequencing may be costly, especially with studies of many samples. The potential high cost makes a priori assessments desirable in order to make informed decisions about sequencing. We generated twelve transcriptomes for ten species of the Brazil nut family (Lecythidaceae), identified a set of putatively orthologous nuclear loci and evaluated, in silico, their phylogenetic utility using genome skimming data of 24 species. We designed the markers using MarkerMiner, and developed a script, GoldFinder, to efficiently sub-select the best makers for sequencing. We captured, in silico, all designed 354 nuclear loci and performed a maximum likelihood phylogenetic analysis on the concatenated sequence matrix. We also calculated individual gene trees with maximum likelihood and used them for a coalescent-based species tree inference. Both analyses resulted in almost identical topologies. However, our nuclear-loci phylogenies were strongly incongruent with a published plastome phylogeny, suggesting that plastome data alone is not sufficient for species tree estimation. Our results suggest that using hundreds of nuclear markers (i.e. 354) will significantly improve the Lecythidaceae species tree. The framework described here will be useful, generally, for developing markers for species tree inference.

Key message This review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology. Context A decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving genomics and bioinformatics toolbox has advanced our understanding of the structure, functioning, and evolution of forest tree genomes. Aims and methods This review highlights some of the discoveries and applications that “omics” technologies have made possible for forest trees over the past 10 years. Results In this review, we start by our current understanding of genome evolution and intricacies of gene regulation for reproduction, development, and responses to biotic and abiotic stresses. We then skim over advances in interactome analysis and epigenomics, the knowledge of the extent of genetic variation within and between species, revealing micro- and macro-evolutionary processes and species history, together with the complex architecture of quantitative traits. We finally end with applications in genetic resource conservation and breeding. Conclusion The knowledge gained through the use of these technologies has a huge potential impact for adapting forests to the main challenges they will have to face: changing demand from ecosystem services with potentially conflicting strategies in terms of conservation and use, as well as climate changes and associated threats. Genomics will undoubtedly play a major role over the next decade and beyond, not only to further understand the mechanisms underlying adaptation and evolution but also to develop and implement innovative management and policy actions to preserve the adaptability of natural forests and intensively managed plantations.

The cosmopolitan genus Fraxinus comprises about 40 species occupying several habitats in the Northern Hemisphere. With some species hybridizing and sharing genetic variants, questions remain on the species assignment of germplasm within the genus Fraxinus despite numerous species-specific assessments. A multidisciplinary approach was employed to provide a definitive insight into the genetics of an endangered Fraxinus &ldquo, manna ash&rdquo, collection, located in a rich plant biodiversity hotspot of the Madonie Mountains (Sicily). Although the collection size was small, genetic diversity, assessed by chloroplast (cpSSR) and nuclear (nSSR) microsatellites (SSR&mdash, Simple Sequence Repeats), allowed identifying three different chloroplast haplotypes, with one (H5) dominant, and several polymorphic loci, able to discriminate most of the local accessions studied. Molecular data were linked to cytofluorimetric and phenotypic evaluations and, contrary to popular belief that manna ash is Fraxinus ornus L., the germplasm currently used for manna production belongs to Fraxinus angustifolia Vahl. Interestingly, joint analysis of our genetic panel with a large European dataset of Fraxinus spp. suggested the presence of a possible glacial refuge in Sicily, confirming its importance as biodiversity source. Our results will be helpful for the design of long-term conservation programs for genetic resources, such as in situ and ex situ conservation, seed collection and tree reintroduction.

Evolutionary history of tropical tree species complexes: species delimitation and adaptive genetic variation in the Brazil nut clade (Lecythidaceae). European Conference of Tropical Ecology (GTOE2018)

Understanding characteristics, causes and consequences of biodiversity is a fundamental challenge in ecology and evolution. Biodiversity presents three nested levels, from individuals, over species, to ecosystems. Intraspecific variability affects the individual level of biodiversity. High levels of intraspecific variability, notably in ecologically important traits has been reported. Intraspecific variability is shaped by the interaction between (1) genetic variability, (2) environmental heterogeneity and (3) stochastic factors. However, we still know little about the effects of this variability on population dynamics, species interactions and ecosystem processes. Interestingly though, variability at the level of genotypes and traits has been suggested to promote local adaptation of populations and to promote species coexistence at the community level, thus suggesting a role for this variability in the origin and maintenance of biodiversity. We here present the conceptual framework of the recently started PhD thesis of S. Schmitt. The main objective of the thesis is to further explore the genotype-environment interactions in shaping the intraspecific trait variability of biodiversity. The study site for the thesis is the lowland rainforest in the research station of Paracou, French Guiana, where detailed inventory and tree growth data, as well as environmental characterization are available. We specifically wish to consider the intraspecific genomic variability as a continuum within structured populations of closely related species, and measure its role on individual tree performance through growth over time, while accounting for effects of a finely-characterized environment at the abiotic and biotic level. Eventually, we expect to help building a theory of community ecology starting with individuals, because interactions with environment is based at the individual level.

Background and Aims Various studies and conservationist reports have warned about the contraction of the last subtropical Afro-Macaronesian forests. These relict vegetation zones have been restricted to a few oceanic and continental islands around the edges of Africa, due to aridification. Previous studies on relict species have generally focused on glacial effects on narrow endemics; however, little is known about the effects of aridification on the fates of previously widespread subtropical lineages. Methods Nuclear microsatellites and ecological niche modelling were used to understand observed patterns of genetic diversity in two emblematic species, widely distributed in these ecosystems: Canarina eminii (a palaeoendemic of the eastern Afromontane forests) and Canarina canariensis (a palaeoendemic of the Canarian laurel forests). The software DIYABC was used to test alternative demographic scenarios and an ensemble method was employed to model potential distributions of the selected plants from the end of the deglaciation to the present. Key Results All the populations assessed experienced a strong and recent population decline, revealing that locally widespread endemisms may also be alarmingly threatened. Conclusions The detected extinction debt, as well as the extinction spiral to which these populations are subjected, demands urgent conservation measures for the unique, biodiversity-rich ecosystems that they inhabit., This work was supported by a PhD research grant (BES-2010–037261) to M.M., including short research stays at JBCVC-CSIC (J.C.C.), University of Lausanne (N.A.) and University of Fribourg (L.P. and M.H.) funded by MINECO (grants CGL2009-1332-C03-01 (MICINN), CGL2012- 40129-C02-01 and CGL2015-67849-P) (MINECO/FEDER) to I.S.; grant CGL2012-40129-C02-02 (MINECO) and a Marie Curie Intra-European Fellowship (PIEF-GA-2012-329088) to M.H. and project grant DEMIURGO MAC/1/C20) to J.C.C.

Hybridization and patterns of adaptive genetic variation in tropical trees of the Bertholletia clade (Lecythidaceae) in French Guiana. Meeting of the German Society for Tropical Ecology (GTOE2017)

Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this paper, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridizes with P. tremula, a species that grows in highly contrasted ecological conditions. We used 73 nuclear microsatellites to test whether genomic background (species ancestry) is a relevant cause of clonal success, and to assess the evolutionary consequences of clonal dominance by a few genets. Additional Genotyping-by-Sequencing (GBS) data were produced to estimate the age of the largest clones. We found that a few ancient (over a few thousand years old) and widespread genets dominate the population, both in terms of clone size and number of sexual offspring produced. Interestingly, large clones possessed two genomic regions introgressed from P. tremula, which may have favored their spread under stressful environmental conditions. At the population level, the spread of large genets was accompanied by an overall ancient (>0.1 Myr) but soft decline of effective population size. Despite this decrease, and the high clonality and dominance of sexual reproduction by large clones, the Douro hybrid zone still displays considerable genetic diversity and low inbreeding. This suggests that, even in extreme cases as in the Douro, asexual and sexual dominance of a few large, geographically-extended individuals does not threaten population survival. This article is protected by copyright. All rights reserved.

Is homoploid hybrid speciation that rare? An empiricist’s view

Narrow endemics have historically been hypothesized to have low levels of genetic diversity. However, recent research has shown an opposite pattern in numerous plants. Antirrhinum charidemi is a narrow range endemic, critically endangered snapdragon from south-eastern Spain. The genetic diversity and its distribution are described based on eight sampling sites across its range (10 × 4 km) using plastid DNA haplotypes, amplified fragment length polymorphism (AFLP) markers, and nuclear simple sequence repeats (SSRs). Plastid diversity was high, with seven haplotypes (h = 0.58), and differentiation among populations was strong and significant (GST = 0.470). Nuclear genetic diversity was also medium to high; for SSRs, there were four to 15 alleles per locus and Ht = 0.48, and for AFLP 90% of loci were polymorphic and Ht = 0.243. The genetic structure was weak but significant (FST = 0.095 for SSRs, 0.096 for AFLP) although Bayesian analysis could not detect more than a single gene pool with any confidence. Antirrhinum charidemi therefore displays medium to high levels of genetic diversity despite its narrow distribution and endemicity. A survey of levels of genetic diversity in narrow endemic angiosperms gave congruent results and revealed a different view than the traditional hypothesis in population genetics. Indeed, narrow endemics do not necessarily harbour low levels of genetic diversity, which appears to depend strongly on multiple factors, particularly the evolutionary history of the populations.