Alexandra Ley

Improving AFLP analysis of large‐scale patterns of genetic variation – a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow

AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad‐sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species.

Species delimitation in the Central African herbs Haumania (Marantaceae) using georeferenced nuclear and chloroplastic DNA sequences.

Species delimitation is a fundamental biological concept which is frequently discussed and altered to integrate new insights. These revealed that speciation is not a one step phenomenon but an ongoing process and morphological characters alone are not sufficient anymore to properly describe the results of this process. Here we want to assess the degree of speciation in two closely related lianescent taxa from the tropical African genus Haumania which display distinct vegetative traits despite a high similarity in reproductive traits and a partial overlap in distribution area which might facilitate gene flow. To this end, we combined phylogenetic and phylogeographic analyses using nuclear (nr) and chloroplast (cp) DNA sequences in comparison to morphological species descriptions. The nuclear dataset unambiguously supports the morphological species concept in Haumania. However, the main chloroplastic haplotypes are shared between species and, although a geographic analysis of cpDNA diversity confirms that individuals from the same taxon are more related than individuals from distinct taxa, cp-haplotypes display correlated geographic distributions between species. Hybridization is the most plausible reason for this pattern. A scenario involving speciation in geographic isolation followed by range expansion is outlined. The study highlights the gain of information on the speciation process in Haumania by adding georeferenced molecular data to the morphological characteristics. It also shows that nr and cp sequence data might provide different but complementary information, questioning the reliability of the unique use of chloroplast data for species recognition by DNA barcoding.

Exploring the floristic diversity of tropical Africa

BackgroundUnderstanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO – one of the largest mega-databases of tropical African vascular plant species distributions ever compiled – to address questions about plant and growth form diversity across tropical Africa.ResultsThe filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5–7% of the estimated world’s tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic.ConclusionsThe botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa’s unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011–2020.

RAINBIO: a mega-database of tropical African vascular plants distributions

Abstract The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

Evolution in African Marantaceae - Evidence from Phylogenetic, Ecological and Morphological Studies

Abstract The Marantaceae (∼530 spp.) are one of the most species rich families within the order Zingiberales which incites the search for evolutionary factors favoring speciation. A positive influence on their divergence is ascribed to their unique explosive pollination mechanism which has been proposed to be a key innovation. To test this hypothesis phylogenies of the two major African clades (Sarcophrynium and the Marantochloa clade) were established based on data from nuclear (ITS, 5S) and chloroplast (trnL/trnL-F) DNA for an almost complete taxon sample. The phylogeny was used to parsimoniously reconstruct morphological and ecological traits and geographic distribution patterns. The resulting molecular relationships of the genera are congruent with the existing family phylogeny. As in previous studies the species Ataenidia conferta is nested within Marantochloa so that a new circumscription of Marantochloa is proposed leading to the new name Marantochloa conferta . Hybridization events, adaptation to different pollinators, and Pleistocene climatic fluctuations are hypothesized evolutionary factors fostering speciation in the African clades. The explosive pollination mechanism might have played an important role in optimizing the mating system but did certainly not force speciation directly through mechanisms of reproductive isolation.

Contrasting patterns of gene flow between sister plant species in the understorey of African moist forests – the case of sympatric and parapatric Marantaceae species

Gene flow within and between species is a fundamental process shaping the evolutionary history of taxa. However, the extent of hybridization and reinforcement is little documented in the tropics. Here we explore the pattern of gene flow between three sister species from the herbaceous genus Marantochloa (Marantaceae), sympatrically distributed in the understorey of the African rainforest, using data from the chloroplast and nuclear genomes (DNA sequences and AFLP). We found highly contrasting patterns: while there was no evidence of gene flow between M. congensis and M. monophylla, species identity between M. monophylla and M. incertifolia was maintained despite considerable gene flow. We hypothesize that M. incertifolia originated from an ancient hybridization event between M. congensis and M. monophylla, considering the current absence of hybridization between the two assumed parent species, the rare presence of shared haplotypes between all three species and the high percentage of haplotypes shared by M. incertifolia with each of the two parent species. This example is contrasted with two parapatrically distributed species from the same family in the genus Haumania forming a hybrid zone restricted to the area of overlap. This work illustrates the diversity of speciation/introgression patterns that can potentially occur in the flora of tropical Africa.

Biodiversity and conservation genetics research in Central Africa: new approaches and avenues for international collaboration

A five-day international workshop was recently convened at the Université des Sciences et Techniques de Masuku in Gabon to enhance international collaboration among Central African, US and European scientists, conservation professionals and policy makers. The overall aims of the workshop were to: (1) discuss emerging priorities in biodiversity and conservation genetics research across Central Africa, and (2) create new networking opportunities among workshop participants. Here we provide a brief overview of the meeting, outline the major recommendations that emerged from it, and provide information on new networking opportunities through the meeting web site.

Hybridization and Asymmetric Introgression after Secondary Contact in Two Tropical African Climber Species, Haumania danckelmaniana and Haumania liebrechtsiana (Marantaceae)

Premise of research. Interspecific hybridization is frequently observed between closely related plant species with overlapping distribution ranges, especially in zones of secondary contact after isolation in different refugia. Although well studied in temperate regions, interspecific hybridization is little documented in tropical regions, where it may be frequent in areas with high species diversity. To bridge this gap, we investigate hybridization in two closely related climber species from the genus Haumania (Haumania danckelmaniana and Haumania liebrechtsiana) originating from Gabon/Cameroon and the Democratic Republic of Congo, respectively, and co-occurring in Northern Gabon. The aim of this study was to genetically quantify and qualify the degree of hybridization between these species in their area of distributional overlap by including for the first time morphological intermediates. Methodology. We investigated 265 individuals from nine sites (seven sites containing both species) by genotyping seven microsatellites and sequencing one chloroplastic region (trnC-petN1r). Bayesian clustering analysis and simulated genotypes allowed the assignment of sampled genotypes to one or the other species or their intermediates (first-generation hybrid or backcrosses). Pivotal results. We found 13% and 41% of intermediates on the basis of morphological versus genetic data, respectively, indicating only a partial congruence. There was an equal amount of backcrosses to both parental species (15%). However, a comparison at the local scale of microsatellites and cpDNA sequence data revealed a unidirectional introgression from H. liebrechtsiana into H. danckelmaniana. At the scale of the nine sites, genetic differentiation was much lower among H. liebrechtsiana than among H. danckelmaniana populations. Conclusions. These results are in line with the previously proposed phylogeographic scenario for the genus Haumania and the theoretical expectation of chloroplast capture when an expanding species (here H. liebrechtsiana) invades the range of a local species (here H. danckelmaniana). Because the forest flora of Central Africa has undergone repeated cycles of fragmentation and expansion following past climate changes, we expect that similar scenarios of hybridization after secondary contact may be common.

Polymorphic Microsatellite Loci for Haumania danckelmaniana and Transferability to H. liebrechtsiana (Marantaceae)

Premise of the study: Microsatellite markers were developed for the species Haumania danckelmaniana (Marantaceae) from central tropical Africa. Methods and Results: Microsatellite isolation was performed simultaneously on three different species of Marantaceae through a procedure that combines multiplex microsatellite enrichment and next-generation sequencing. From 80 primers selected for initial screening, 20 markers positively amplified in H. danckelmaniana. of which 10 presented unambiguous amplification products within the expected size range and eight were polymorphic with four to nine alleles per locus. Positive transferability with the related species H. liebrechtsiana was observed for the same 10 markers. Conclusions: The polymorphic microsatellite markers are suitable for studies in genetic diversity and structure, mating system, and gene flow in H. danckelmaniana and the closely related species H. liebrechtsiana.

Flowers on the Tree of Life: Ontogenetic and phylogenetic diversification in Marantaceae

The Marantaceae Petersen (31 genera; ~530 ssp.: Andersson, 1998) are a pantropically (80% America; 11% Asia; 9% Africa: Kennedy, 2000) distributed family of perennial herbs and lianas found in the understory of tropical lowland rainforests. They are characterized by a unique pollination mechanism combining secondary pollen presentation with an explosive style movement (Kunze, 1984; Clasen-Bockhoff, 1991; Clasen-Bockhoff and Heller, 2008a). The specific pollen transfer mechanism is found in conjunction with a high synorganization of morphologically modified floral elements and has been postulated to be a key innovation responsible for the radiation of the Marantaceae (Kennedy, 2000). Flowers in Marantaceae are trimerous, with inconspicuous sepals and petals and extremely modified elements in the two androeceal whorls (Fig 10.1). In the outer whorl one or two petaloid ‘outer staminodes’ act as the showy organs of the flowers. The three elements of the inner whorl are functionally differentiated into: (1) a single (monothecate) anther, (2) a ‘fleshy (callose) staminode’ and (3) a ‘hooded (cucullate) staminode’ (Kunze, 1984; Clasen-Bockhoff, 1991). These organs closely interact with the style resulting in secondary pollen presentation, set-up of tension and finally the explosive pollination mechanism (e.g. Gris, 1859; Delpino, 1869; Schumann, 1902; Yeo, 1993; Clasen-Bockhoff and Heller, 2008a, b; Ley, 2008; Pischtschan and Clasen-Bockhoff, 2008; Fig 10.2). As the style movement demands a high degree of synorganization of floral parts and synchronization with the pollinator and as the movement is irreversible, providing the flowers with a single opportunity for pollination, one should expect rather uniform structures across the whole family, as slight morphological deviations might result in a loss of operability. However, the high degree of floral diversity in the Marantaceae contradicts this expectation (Kunze, 1984; Kennedy, 2000; Clasen-Bockhoff and Heller, 2008a; Ley, 2008). It instead raises the questions: how far are elements of a functional unit allowed to vary without jeopardizing the reproductive success, and has the variation of the flowers influenced speciation in the family?