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Although today the forest cover is continuous in Central Africa, this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the ice ages. Our aim was to investigate whether the dry ice age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five widespread legume trees and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea) and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades--congruent across species--cannot be explained by geographic barriers, we tested other hypotheses with demographic model testing using δαδ?. The best estimates indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with nonassisted seed dispersal than for light-demanding species with longdistance wind-dispersed seeds. Different recolonization abilities after recurrent cycles of forest fragmentation seem to explain why species with long-distance dispersal show more recent genetic admixture between the two clades than species with limited seed dispersal. Despite their old history, our results depict the African rainforests as a dynamic biome where tree species have expanded relatively recently after the last glaciation. [ABSTRACT FROM AUTHOR]

Background: Comparative phylogeographic studies on rainforest species that are widespread in Central Africa often reveal genetic discontinuities within and between biogeographic regions, indicating (historical) barriers to gene flow, possibly due to repeated and/or long-lasting population fragmentation during glacial periods according to the forest refuge hypothesis. The impact of forest fragmentation seems to be modulated by the ecological amplitude and dispersal capacities of each species, resulting in different demographic histories. Moreover, while multiple studies investigated the western part of Central Africa (Lower Guinea), few have sufficiently sampled the heart of the Congo Basin (Congolia). In this study, we look for genetic discontinuities between populations of the widespread tropical tree Scorodophloeus zenkeri Harms (Fabaceae, Detarioideae) in Central Africa. Additionally, we characterize genetic diversity, selfing rate and fine-scale spatial genetic structure within populations to estimate the gene dispersal capacity of the species. Results: Clear intraspecific genetic discontinuities occur throughout the species' distribution range, with two genetic clusters in Congolia and four in Lower Guinea, and highest differentiation occurring between these bioregions. Genetic diversity is higher in Lower Guinea than Congolia. A spatial genetic structure characteristic of isolation by distance occurs within the genetic clusters. This allowed us to estimate gene dispersal distances (σg) for this outcrossing species with ballistic seed dispersal, which range between 100 and 250 m in areas where S. zenkeri occurs in high densities, and are in the low range of σg values compared to other tropical trees. Gene dispersal distances are larger in low density populations, probably due to extensive pollen dispersal capacity. Conclusions: Fragmentation of S. zenkeri populations seems to have occurred not only in Lower Guinea but also in the Congo Basin, though not necessarily according to previously postulated forest refuge areas. The lower genetic diversity in Congolia compared to Lower Guinea parallels the known gradient of species diversity, possibly reflecting a stronger impact of past climate changes on the forest cover in Congolia. Despite its bisexual flowers, S. zenkeri appears to be mostly outcrossing. The limited dispersal observed in this species implies that genetic discontinuities resulting from past forest fragmentation can persist for a long time before being erased by gene flow. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Combining genetic and morphological markers is a powerful approach for species delimitation, much needed in tropical species complexes. Greenwayodendron (Annonaceae) is a widespread genus of trees distributed from West to East African rainforests. Two species and four infra‐specific taxa are currently recognized. However, preliminary genetic studies and morphological observations suggested the occurrence of additional species, undescribed to date. We tested species delimitation within Greenwayodendron by combining morphological and population genetics data. First, a visual inspection of about a thousand specimens suggested the existence of seven morphogroups: four of them occur in Central Africa and overlap in Gabon while three others are allopatric, occurring respectively in West Africa, East Africa, and the islands of São Tomé and Príncipe. Their morphological differentiation was confirmed by analysis of 27 morphological characters coded from 233 herbarium specimens. Second, after genotyping 800 samples at eight nuclear microsatellites, Bayesian clustering analyses (STRUCTURE) identified four genetic clusters corresponding to the well‐sampled morphogroups but failed to separate the three remaining morphogroups represented by few samples. However, we show that this is an inherent limit of the STRUCTURE algorithm, whereas factorial correspondence analysis (FCA) and pairwise FST and RST measures confirmed the genetic differentiation of all morphogroups. We considered that a clear genetic differentiation occurring between sympatric populations advocates for recognizing distinct species following the biological species concept. Our analyses highlight that the current taxonomic treatment of Greenwayodendron underestimates the total number of species. We identified two new species and support separation at the rank of species of two varieties (G. suaveolens subsp. suaveolens var. gabonica, G. suaveolens subsp. suaveolens var. suaveolens) and one subspecies (G. suaveolens subsp. usambaricum). The taxonomic status of specimens collected in São Tomé and Príncipe remains inconclusive, partly due to the limited fertile material available. Our study highlights the strength of combining morphological and population genetics data for discovering new taxa. Guidelines for using genetic clustering approaches in species delimitation are provided. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The fossil record in tropical Africa suggests that dry conditions during the Ice Ages caused expansion of savannahs and contraction of the rainforest. Forest refugia have been proposed to be located in areas of Central Africa that currently harbour high rates of endemic species. However, to what extent the forestwas fragmented remains unknown. Nuclear microsatellites and plastid sequences of 732 trees of two species occurring in the same habitat-mature lowland evergreen rainforests-but with remarkably different dispersal capacities-animal versus gravity-were analysed. Geographical information system tools revealed intraspecific lineages partially congruent across the two species, suggesting common past barriers to gene flow in Central Africa. According to approximate Bayesian computation, the intraspecific genetic clusters diverged during the Pleistocene (less than 2 Ma), so that intraspecific differentiation is the appropriate scale to test the aridification effect of the Ice Ages on tree populations. Demographic tests revealed clear genetic signals of population expansion in both taxa, possibly following bottleneck events after forest fragmentation, with stronger evidence of expansion after the Penultimate rather than after the Last Glacial Maximum. The differential dispersal capacity may have modulated the particular response of each species to climate change, as revealed by the stronger evidence of expansion found in the animal-dispersed species than in the gravity-dispersed one. [ABSTRACT FROM AUTHOR]

Aim The aim of this study was to understand the origin of the forest flora currently found in the Dahomey Gap ( DG), a 200-km-wide forest-savanna mosaic separating the West African and Central African rain forest blocks. More specifically, using a widespread rain forest tree species, Distemonanthus benthamianus (Fabaceae), we will test the hypothesis that the DG populations are remnants of a population dating back from the African Humid Period of the Holocene, when West African and Central African rain forests were supposedly connected. Location Tropical forests of Upper Guinea (West Africa) and Lower Guinea (Atlantic Central Africa) and the forest-savanna mosaic of the DG extending from eastern Ghana to Benin. Methods Four hundred and twenty-nine D. benthamianus samples from West to Central Africa were genotyped with 11 nuclear microsatellite markers. After detecting geographically coherent gene pools, their genetic diversity and differentiation were estimated and their demographic histories were inferred using coalescent simulations and approximate Bayesian computation ( ABC) tests. Results Five parapatric gene pools were identified: three in Lower Guinea, one in Upper Guinea and one in the DG. ABC tests indicate that the DG gene pool probably originates from the admixture of adjacent Upper and Lower Guinean gene pools, with a higher contribution from Upper Guinea, at a timeframe consistent with the early Holocene (around 13-7 ka). The lower genetic diversity documented in the DG could result from a founder effect and/or from a demographic decline consistent with the Holocene climatic pejoration documented around 3 ka. Main conclusions This phylogeographical study inferring the history of the DG populations of D. benthamianus is consistent with palaeovegetation data that suggest that the forest flora of the DG might be essentially relicts of the early Holocene period when the Guineo-Congolian forest reached its maximum geographical distribution. [ABSTRACT FROM AUTHOR]

Phylogeographic studies in the high mountains of Africa are hampered by the limited material available, resulting in insufficient knowledge of taxonomic variation within and among closely related species. Here, we address genetic and morphological variation in three grass species, of which one ( Deschampsia angusta) has been reported as narrowly endemic and vulnerable whereas Deschampsia cespitosa and Koeleria capensis are widely distributed also outside the afro-alpine region. We used amplified fragment length polymorphisms (AFLPs) to assess genetic structuring and diversity in material collected during recent field expeditions and included additional herbarium material in morphometric analyses. The plants identified as the endemic D. angusta were genetically very similar to those identified as D. cespitosa from the same mountain (Mt Ruwenzori), forming a single coherent genetic group in STRUCTURE analysis. The plants identified as D. angusta seem to represent extremes of continuous gradients of morphological variation within a single, variable species, D. cespitosa. We found that the afro-alpine material of Deschampsia consists of three genetically very distinct groups corresponding to the three mountains investigated, suggesting persistence in isolated afro-alpine refugia during one or more glacial cycles. In contrast, we found no clear genetic structure in K. capensis. This species harbored very little genetic diversity in all six mountain areas examined, and little genetic rarity except in the Ethiopian Simen Mts. This pattern may be explained by recent colonization of the afro-alpine region from a single source population or possibly by extensive recent gene flow combined with bottlenecks. We found, however, some differentiation between different K. capensis populations from Mt Kilimanjaro, corresponding to two described varieties. This study demonstrates the need for further taxonomic exploration of the enigmatic flora of the isolated afro-alpine 'sky islands' and highlights that different species may have conspicuously different phylogeographic histories. [ABSTRACT FROM AUTHOR]

Aim Arctic plant phylogeography has largely focused on seed plants, and studies on other plant groups are necessary for comparison. Bryophytes have a unique life cycle and can be resistant to extreme conditions, suggesting that their phylogeographic patterns may differ from those of vascular plants. We address the history of the bryophyte genus Cinclidium in order to assess: (1) interspecific relationships, (2) whether its current broad circumarctic distribution results from recent dispersal or has been maintained by long-term local survival under severe glacial conditions, and (3) the origin of its bipolar disjunction. Location Arctic/boreal and bipolar. Methods We sequenced three plastid regions ( atpH -atpI, rpl32- trnL and clpP1.1- clpP1.2) in 129 accessions covering the entire geographical range of all four described species, and inferred phylogenetic relationships and phylogeographical patterns using maximum parsimony, statistical parsimony and Bayesian inference. Results Cinclidium subrotundum was inferred to be monophyletic, in agreement with its distinct morphology and ecology. The three remaining known species (the haploids C. latifolium and C. arcticum, and the diploid C. stygium) shared a number of closely related or identical haplotypes despite their clear morphological differentiation. In all species, identical haplotypes occurred across the entire circumpolar region, including North Atlantic islands. In the bipolar species C. stygium, the haplotype observed in South America (Tierra del Fuego) was identical to one found in Iceland. Three populations originally referred to C. latifolium harboured highly divergent haplotypes and may represent a new species. Main conclusions The extensive haplotype sharing suggests a polyploid origin of C. stygium from C. arcticum, as well as incomplete lineage sorting and/or hybridization between the two haploids C. arcticum and C. latifolium. We interpret the finding of identical haplotypes over vast areas, including isolated islands, as a result of recent dispersal causing the circumpolar distribution of all species in the Northern Hemisphere and the extreme bipolar disjunction in C. stygium. The patterns in the bryophyte genus Cinclidium resemble those previously documented in arctic-alpine and bipolar vascular plants, suggesting that similar mechanisms have shaped species distributions in bryophytes and higher plants. [ABSTRACT FROM AUTHOR]

The genetic diversity and possible geographic structure of the Madeiran endemic Armeria maderensis have been assessed with AFLP. Its scarce distribution (less than 3 km between the two most distant localities) and restricted habitat (vertical pastures on the highest elevations of Madeira), at least in part due to grazing by goats, suggest an assessment of its conservation status. Diversity estimates obtained for A. maderensis were evaluated through comparison with reference values of AFLP diversity for outcrossing plants and, in order to correct for phylogenetic constraints, with a widespread congener analyzed with the same AFLP markers. Our results reveal that low levels of genetic diversity and a weak intraspecific genetic structure underlie the restricted distribution of A. maderensis. [ABSTRACT FROM AUTHOR]

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Inferring the evolutionary history of Mediterranean plant lineages from current genetic, distributional and taxonomic patterns is complex because of a number of palaeoclimatic and geological interconnected factors together with landscape heterogeneity and human influence. Therefore, choosing spatially simplified systems as study groups is a suitable approach. An amplified fragment length polymorphism (AFLP) study using two restriction enzyme combinations ( EcoRI/ MseI and KpnI/ MseI) was carried out to estimate the structure of genetic variation throughout the range of Armeria pungens. This species has a West Iberian-Corso/Sardinian disjunct distribution on coastal sand-dune ecosystems. Bayesian,amova and genetic distance analyses of the AFLP data revealed the same distinguishable genetic groups, which do not match the main geographical disjunction. Corso-Sardinian populations were found to be genetically closer to southwest Portuguese than to those from the Gulf of Cadiz (the closest geographically). Eastwards long-distance dispersal is therefore invoked to explain this geographical disjunction. A GIS analysis based on bioclimatic envelope modelling aiming to characterize the current locations of A. pungens found strong similarities between the Portugal and Corsica-Sardinia sites and less so between these areas and the Gulf of Cadiz. This coincident pattern between AFLP and climatic data suggests that the geographical disjunction is better explained by climatic factors than by the likeliness of a stochastic dispersal event. Such a combined phylogeographical–GIS modelling approach proves to be enlightening in reconstructing the evolutionary history of plant species. [ABSTRACT FROM AUTHOR]

Scorodophloeus zenkeri is a tropical tree from mature rainforests of Central Africa, locally threatened by overexploitation. Ten nuclear microsatellite markers, amplifiable in two multiplexed reactions, were developed and characterized in one population. The levels of polymorphism observed (3-15 alleles per locus, expected heterozygosity ranging from 0.198 to 0.905) point at the promising application of the markers for conservation purposes regarding the location of past forest refugia, assessment of mating system and evaluation of genetic diversity in isolated and threatened populations. [ABSTRACT FROM AUTHOR]