Apoidea of the collections of Lyon, Aix-en-Provence, Marseille and Toulon Museums of Natural History (France).

Background: Many insect species have shown dramatic declines over the last decades, as a result of man-related environmental changes. Many species which were formerly widespread are now rare. To document this trend with evidence, old records of collected specimens are vital. New information: We provide here the data on 9752 bee (Hymenoptera: Apoidea) specimens hosted in several museums of south-east France: Musée des Confluences in Lyon, Muséum d'Histoire Naturelle de Marseille, Muséum d'Aix-en-Provence and the Muséum Départemental du Var in Toulon. Most of the specimens (9256) come from France and include data on 552 named species. For most of these specimens, the geographical location, including geographical coordinates, is based on the locality (town or village) where they were collected. The specimens were captured from the beginning of the nineteenth century to 2018. The identifications of 1377 specimens, mainly belonging to the genus Bombus, are considered reliable, as these were performed or been checked since 2009. All the other reported identifications are the original ones given by the original collectors.

Plastome phylogeography in two African rain forest legume trees reveals that Dahomey Gap populations originate from the Cameroon volcanic line.

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 recent colonization history of the most widespread Podocarpus tree species in Afromontane forests.

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.

Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies.

Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.

Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse clade of African legumes.

Detarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the lack of fully resolved phylogenetic relationships. Here, we used four representative transcriptomes to develop an exome capture (target enrichment) bait for the entire subfamily and applied it to the Anthonotha clade using a complete data set (61 specimens) representing all extant floral diversity. Our phylogenetic analyses recovered congruent topologies using ML and Bayesian methods. Anthonotha was recovered as monophyletic contrary to the remaining three genera (Englerodendron, Isomacrolobium and Pseudomacrolobium), which form a monophyletic group sister to Anthonotha. We inferred a total of 35 transitions for the seven floral traits (pertaining to flower symmetry, petals, stamens and staminodes) that we analyzed, suggesting that at least 30% of the species in this group display transitions from the ancestral condition reconstructed for the Anthonotha clade. The main transitions were towards a reduction in the number of organs (petals, stamens and staminodes). Despite the high number of transitions, our analyses indicate that the seven characters are evolving independently in these lineages. Petal morphology is the most labile floral trait with a total of seven independent transitions in number and seven independent transitions to modification in petal types. The diverse petal morphology along the dorsoventral axis of symmetry within the flower is not associated with differences at the micromorphology of petal surface, suggesting that in this group all petals within the flower might possess the same petal identity at the molecular level. Our results provide a solid evolutionary framework for further detailed analyses of the molecular basis of petal identity.

Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology.

Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction. All species except G. demeusei and G. copallifera appear monophyletic. Dispersal from Africa to America across the Atlantic Ocean is the most plausible hypothesis to explain the occurrence of Neotropical Guibourtia species, which diverged ca. 11.8 Ma from their closest African relatives. The diversification of the three main clades of African Guibourtia is concomitant to Miocene global climate changes, highlighting pre-Quaternary speciation events. These clades differ by their reproductive characters, which validates the three subgenera previously described: Pseudocopaiva, Guibourtia and Gorskia. Within most monophyletic species, plastid lineages start diverging from each other during the Pliocene or early Pleistocene, suggesting that these species already arose during this period. The multiple transitions between rain forests and dry forests/savannahs inferred here through the plastid phylogeny in each Guibourtia subgenus address thus new questions about the role of phylogenetic relationships in shaping ecological niche and morphological similarity among taxa.

Characterization of microsatellite markers in the African tropical tree species Guibourtia ehie (Fabaceae, Detarioideae).

PREMISE OF THE STUDY: Microsatellite primers (simple sequence repeats [SSRs]) were developed in Guibourtia ehie (Fabaceae, Detarioideae) to study population genetic structure and the history of African vegetation. METHODS AND RESULTS: We isolated 18 polymorphic SSRs from a nonenriched genomic library. This set of primer pairs was tested on four populations, and the results showed two to 16 alleles per locus with mean observed and expected heterozygosities of 0.27 ± 0.05 and 0.57 ± 0.05, respectively. Cross-amplification tests in 13 congeneric species were successful for the four taxa belonging to the subgenus Gorskia. CONCLUSIONS: This set of microsatellite markers will be useful to investigate the phylogeography and population genetics of G. ehie, a key representative of African semideciduous moist forests.

Characterization of microsatellite markers in two exploited African trees, Entandrophragma candollei and E. utile (Meliaceae).

PREMISE OF THE STUDY: Multiplexes of nuclear microsatellite primers were developed to investigate population genetic structure and diversity in two exploited African rainforest trees: Entandrophragma candollei and E. utile (Meliaceae). METHODS AND RESULTS: Microsatellite isolation was performed simultaneously on two nonenriched genomic libraries after next-generation sequencing. We developed 16 and 22 polymorphic markers for E. candollei and E. utile in three and four multiplexes, respectively. The number of alleles ranged from two to 17 for E. candollei and from three to 19 for E. utile. Mean expected and observed heterozygosity ranged between 0.75 ± 0.13 and 0.55 ± 0.23 for E. candollei and between 0.73 ± 0.10 and 0.49 ± 0.2 for E. utile. CONCLUSIONS: These sets of nuclear microsatellite markers constitute useful tools for exploring gene flow patterns in these two Entandrophragma species.

Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae).

Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported clade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20Ma while extant tetraploid species started diverging c. 7.0 or 9.4Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics.

Development and characterization of microsatellite markers in the African deciduous tree Terminalia superba (Combretaceae).

PREMISE OF THE STUDY: Microsatellites were designed and characterized in the African timber forest tree Terminalia superba (Combretaceae). Due to their high variability, these markers are suitable to investigate gene flow patterns and the structure of genetic diversity. METHODS AND RESULTS: From a genomic library obtained by next-generation sequencing, seven monomorphic and 14 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed two to 27 alleles (mean 11.4; expected heterozygosity range 0.283-0.940, mean 0.736) in one population from southeastern Cameroon. Genotypes were typical of an outbreeding diploid species, although null alleles explain a significant heterozygote deficit in three loci. Cross-amplification in three congeneric species (T. ivorensis, T. avicennioides, and T. mantaly) failed, suggesting that T. superba is rather divergent. CONCLUSIONS: This set of newly developed microsatellite markers will be useful for assessing the genetic diversity, population structure, and demographic history of T. superba in tropical African forests.

Surviving in mountain climate refugia: new insights from the genetic diversity and structure of the relict shrub Myrtus nivellei (Myrtaceae) in the Sahara Desert.

The identification of past glacial refugia has become a key topic for conservation under environmental change, since they contribute importantly to shaping current patterns of biodiversity. However, little attention has been paid so far to interglacial refugia despite their key role for the survival of relict species currently occurring in climate refugia. Here, we focus on the genetic consequences of range contraction on the relict populations of the evergreen shrub Myrtus nivellei, endemic in the Saharan mountains since at least the end of the last Green Sahara period, around 5.5 ka B.P. Multilocus genotypes (nuclear microsatellites and AFLP) were obtained from 215 individuals collected from 23 wadis (temporary rivers) in the three main mountain ranges in southern Algeria (the Hoggar, Tassili n'Ajjer and Tassili n'Immidir ranges). Identical genotypes were found in several plants growing far apart within the same wadis, a pattern taken as evidence of clonality. Multivariate analyses and Bayesian clustering revealed that genetic diversity was mainly structured among the mountain ranges, while low isolation by distance was observed within each mountain range. The range contraction induced by the last episode of aridification has likely increased the genetic isolation of the populations of M. nivellei, without greatly affecting the genetic diversity of the species as a whole. The pattern of genetic diversity observed here suggests that high connectivity may have prevailed during humid periods, which is consistent with recent paleoenvironmental reconstructions.

Phylogeography sheds light on the central-marginal hypothesis in a Mediterranean narrow endemic plant.

BACKGROUND AND AIMS: Understanding the factors that shape variation in genetic diversity across the geographic ranges of species is an important challenge in the effort to conserve evolutionary processes sustaining biodiversity. The historical influences leading to a central-marginal organization of genetic diversity have been explored for species whose range is known to have expanded from refugia after glacial events. However, this question has rarely been addressed for Mediterranean endemic plants of azonal habitats such as rocky slopes or screes. In this context, this comprehensive study examined molecular and field data from Arenaria provincialis (Caryophyllaceae), a narrow endemic plant of south-eastern France. METHODS: Across the whole geographic range, an investigation was made of whether high levels of abundance and genetic diversity (estimated from amplified fragment length polymorphism markers) are centrally distributed, to evaluate the relevance of the central-marginal hypothesis. Phylogeographic patterns inferred from chloroplast DNA (cpDNA) were used, applying Bayesian methods to test the influence of past biogeographic events. Multivariate analysis combining phylogeographic and ecological data was used to reveal the historical and ecological distinctiveness of populations. KEY RESULTS: Despite the narrow distribution of A. provincialis, a high level of nucleotide variation is found within cpDNA loci, supporting its persistence throughout the Pleistocene period. The area characterized by the highest genetic diversity is centrally located. Structured phylogeography and Bayesian factor analysis supported the hypothesis that the central area of the distribution was the source of both westward and eastward migrations, probably during arid periods of the Pleistocene, and more recently was a crossroads of backward migrations. By contrast, the two areas located today at the range limits are younger, have reduced genetic diversity and are marginal in the ecological gradients. CONCLUSIONS: This study highlights a case of strong population distinctiveness within a narrow range. Phylogeography sheds light on the historical role of the areas centrally situated in the distribution. The current range size and abundance patterns are not sufficient to predict the organization of genetic diversity.

[Pollen analysis from two littoral marshes (Bourdim and Garaat El-Ouez) in the El-Kala wet complex (North-East Algeria). Lateglacial and Holocene history of Algerian vegetation]. / Nouvelles contributions à l'histoire tardiglaciaire et holocène de la végétation en Algérie: analyses polliniques de deux profils sédimentaires du complexe humide d'El-Kala.

The study of two pollen sequences from El-Kala marshes allowed the reconstruction of the regional vegetation history supported by eight radiocarbon dates. Pollen assemblages from Bourdim site were dominated by local input of Alnus and Salix, while regional vegetation was characterized by scattered Quercus suber forests with a well-developed Erica arborea matorral. While the vegetation dynamics recorded at Bourdim is recent (Late Holocene), the majority of the pollen diagram from Garaat El-Ouez is contemporaneous to the Late Pleniglacial and is characterized by open woodlands with Pinus, Poaceae and several heliophilous herbs. The significant values of Cedrus pollen identified in this period indicate that the region of El-Kala most probably played the role of a refugium for this tree.