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.

Aim  The Mediterranean region is often regarded as a crossroads where species of various origins meet. However, the biogeographical relationships between this region and contiguous Saharan, Macaronesian and Irano‐Turanian regions have not been investigated in detail. The aim of this study was to characterize the phylogeography of the circum‐Mediterranean species Myrtus communis and to investigate the origin of isolated central Saharan populations of Myrtus nivellei.Location  The distribution ranges of M. communis from Macaronesia to the Irano‐Turanian region (173 sampled populations) and of M. nivellei in the mountains (Hoggar, Tassili n’Ajjer, Immidir, Tibesti) of the central Sahara (23 populations).Methods  Nuclear ribosomal DNA (nrDNA) sequences of Myrtaceae were used to root the phylogeny of Myrtus, and to date its crown node, according to a detailed review of the palaeobotanical records used for multiple fossil calibration. Chloroplast DNA (cpDNA) sequences were analysed through the determination of genetic diversity indices and by statistical phylogeography.Results  Both cpDNA and nrDNA markers indicated east–west genetic differentiation within M. communis. During the late Miocene, a key vicariance event affected the previous circum‐Mediterranean distribution of Myrtus, leading to the isolation of eastern populations. During the late Miocene or early Pliocene, two clades diverged: one is now scattered in the Mediterranean Basin and adjacent regions, whereas the other evolved in the western Mediterranean region. The differentiation of lineages during the Plio‐Pleistocene occurred mainly in the western part of the Mediterranean Basin, which has been at the origin of migrations towards Macaronesian islands and Saharan mountains. This is one of the first plant phylogeographical studies to report migrations from the Mediterranean to the Sahara.Main conclusions  The genus Myrtus has persisted in the Mediterranean region since at least the Neogene and its biogeography reflects the cumulation of the species’ responses to successive palaeoenvironmental changes. The current distribution of the genus Myrtus in the Mediterranean Basin and in isolated areas, such as the Macaronesian islands and Saharan mountains, can be explained by the striking ability of this plant not only to persist locally in various refugia, but also to migrate.

Aim Palaeoecological records indicate that Pleistocene glaciations affected the African rain forest, probably causing its fragmentation, which could explain phylogeographical breaks documented in many tree species. This refuge hypothesis was further tested through species distribution models, hindcasting persistence during the Last Glacial Maximum. However, previous studies failed to estimate with sufficient precision the divergence time between phylogeographical entities to confirm their Pleistocene origin. Developing genomic tools on a representative tree of mature rain forests, we test if parapatric genetic clusters documented in widespread tree species can be interpreted as the legacy of past population fragmentation during the last glacial period(s). Location Tropical Africa, Guineo‐Congolian forests. Taxon Greenwayodendron (Annonaceae). Methods To further test the Pleistocene refuge hypothesis by molecular dating, we sequenced the plastome of 145 individuals of the shade‐tolerant rain forest tree Greenwayodendron suaveolens and congeneric species, and genotyped the same samples using nuclear microsatellites to identify genetic clusters. Results Five plastid phylogroups of G. suaveolens occur in parapatry throughout Central Africa, following a spatial pattern generally congruent with genetic clusters. Four of them diverged 3.5–4.5 Ma, whereas the fifth one, located in the Cameroon volcanic line (CVL), diverged 8.3 Ma, in the range of divergence times between Greenwayodendron species, highlighting the key role of the CVL in hosting ancient lineages. Within phylogroups, most nodes were dated from 0.9 to 3.2 Myr and a correlation between haplotype divergence and spatial distance was still perceptible, indicating a slow population dynamic. Main conclusions The phylogeographical structures of Central African trees probably established during the Pliocene or early Pleistocene, and while they might have been reinforced during subsequent glacial–interglacial cycles, interglacial phases did not lead to genetic homogenization. Therefore, interpreting phylogeographical patterns of African trees must account for a much deeper past than previously assumed, and cannot be limited to the last glacial period.

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