Félix Forest

Preserving the evolutionary potential of floras in biodiversity hotspots

One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots. However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change. Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa. PD therefore identifies sets of taxa that maximize the accumulation of ‘feature diversity’. Recent studies, however, concluded that taxon richness is a good surrogate for PD. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot—the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use, we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.

Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.

Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches

Supertree and supermatrix methods have great potential in the quest to build the tree of life and yet they remain controversial, with most workers opting for one approach or the other, but rarely both. Here, we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid restriction fragment length polymorphism data, and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. To construct supertrees, we used variants of matrix representation with parsimony (MRP) analysis based on input trees generated directly from subsamples of the supermatrix. All supertrees were highly resolved. Standard MRP with bootstrap-weighted matrix elements performed most effectively in this case, generating trees with the greatest congruence with the supermatrix tree and fewest clades unsupported by any input tree. Nonindependence due to input trees based on combinations of data partitions was an acceptable trade-off for improvements in supertree performance. Irreversible MRP and the use of strictly independent input trees only provided no obvious benefits. Contrary to previous claims, we found that unsupported clades are not infrequent under some MRP implementations, with up to 13% of clades lacking support from any input tree in some irreversible MRP supertrees. To build a formal synthesis, we assessed the cross-corroboration between supermatrix trees and the variant supertrees using semistrict consensus, enumerating shared clades and compatible clades. The semistrict consensus of the supermatrix tree and the most congruent supertree contained 160 clades (of a maximum of 204), 137 of which were present in both trees. The relationships recovered by these trees strongly support the current phylogenetic classification of palms. We evaluate 2 composite supertree support measures (rQS and V) and conclude that it is more informative to report numbers of input trees that support or conflict with a given supertree clade. This study demonstrates that supertree and supermatrix methods can provide effective, explicit, and complimentary mechanisms for synthesizing disjointed phylogenetic evidence while emphasizing the need for further refinement of supertree methods.

Phylogenetic Relationships in the Caesalpinioideae (Leguminosae) as Inferred from Chloroplast trnL Intron Sequences

Abstract The basal subfamily Caesalpinioideae of the Leguminosae generally is subdivided into four or five tribes, but their monophyly remains questionable. Recent cladistic analyses based on morphological characters and chloroplast rbcL sequences suggest conflicting hypotheses of relationships among tribes and subtribal groupings and of the identification of the basal Caesalpinioideae. Our phylogenetic analysis of the chloroplast trnL intron for 223 Caesalpinioideae, representing 112 genera, plus four Papilionoideae, 12 Mimosoideae and three outgroup taxa, provides some well-supported hypotheses of relationships for the subfamily. Our analysis concurs with the rbcL studies in suggesting that a monophyletic Cercideae is sister to the remainder of the Leguminosae. Among the other tribes of Caesalpinioideae, only the broadly circumscribed Detarieae (including Amherstieae or Macrolobieae) is also supported as monophyletic. The Detarieae s.l. occurs as sister to all Leguminosae, excluding Cercideae. Cassieae subtribes Dialiinae and Labicheinae together are sister to the remaining Leguminosae, which includes a monophyletic Papilionoideae, a paraphyletic Mimosoideae, and several monophyletic groups that correspond to previously defined generic groups or subtribes in the Caesalpinioideae. The trnL intron analysis suggests that basal legumes are extremely diverse in their floral morphology, and that presence of simple, actinomorphic flowers may be a derived feature in a number of lineages in the family. Communicating Editor: Matt Lavin

Origin and diversification of the Greater Cape flora: Ancient species repository, hot-bed of recent radiation, or both?

Like island-endemic taxa, whose origins are expected to postdate the appearance of the islands on which they occur, biome-endemic taxa should be younger than the biomes to which they are endemic. Accordingly, the ages of biome-endemic lineages may offer insights into biome history. In this study, we used the ages of multiple lineages to explore the origin and diversification of two southern African biomes whose remarkable floristic richness and endemism has identified them as global biodiversity hotspots (succulent karoo and fynbos). We used parsimony optimization to identify succulent karoo- and fynbos-endemic lineages across 17 groups of plants, for which dated phylogenies had been inferred using a relaxed Bayesian (BEAST) approach. All succulent karoo-endemic lineages were less than 17.5 My old, the majority being younger than 10 My. This is largely consistent with suggestions that this biome is the product of recent radiation, probably triggered by climatic deterioration since the late Miocene. In contrast, fynbos-endemic lineages showed a broader age distribution, with some lineages originating in the Oligocene, but most being more recent. Also, in groups having both succulent karoo- and fynbos-endemic lineages, there was a tendency for the latter to be older. These patterns reflect the greater antiquity of fynbos, but also indicate considerable recent speciation, probably through a combination of climatically-induced refugium fragmentation and adaptive radiation.

Hybrid speciation in angiosperms: parental divergence drives ploidy

Hybridization and polyploidy are now hypothesized to have regularly stimulated speciation in angiosperms, but individual or combined involvement of these two processes seems to involve significant differences in pathways of formation, establishment and evolutionary consequences of resulting lineages. We evaluate here the classical cytological hypothesis that ploidy in hybrid speciation is governed by the extent of chromosomal rearrangements among parental species. Within a phylogenetic framework, we calculate genetic divergence indices for 50 parental species pairs and use these indices as surrogates for the overall degree of genomic divergence (that is, as proxy for assessments of dissimilarity of the parental chromosomes). The results confirm that genomic differentiation between progenitor taxa influences the likelihood of diploid (homoploid) versus polyploid hybrid speciation because genetic divergence between parents of polyploids is found to be significantly greater than in the case of homoploid hybrid species. We argue that this asymmetric relationship may be reinforced immediately after hybrid formation, during stabilization and establishment. Underlying mechanisms potentially producing this pattern are discussed.

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

BACKGROUND Molecular dating has gained ever-increasing interest since the molecular clock hypothesis was proposed in the 1960s. Molecular dating provides detailed temporal frameworks for divergence events in phylogenetic trees, allowing diverse evolutionary questions to be addressed. The key aspect of the molecular clock hypothesis, namely that differences in DNA or protein sequence between two species are proportional to the time elapsed since they diverged, was soon shown to be untenable. Other approaches were proposed to take into account rate heterogeneity among lineages, but the calibration process, by which relative times are transformed into absolute ages, has received little attention until recently. New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record. SCOPE AND CONCLUSIONS The use of the fossil record as a source of independent information in the calibration process is the main focus of this paper; other sources of calibration information are also discussed. Particularly error-prone aspects of fossil calibration are identified, such as fossil dating, the phylogenetic placement of the fossil and the incompleteness of the fossil record. Methods proposed to tackle one or more of these potential error sources are discussed (e.g. fossil cross-validation, prior distribution of calibration points and confidence intervals on the fossil record). In conclusion, the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account.

Phylogeny of the tribe Indigofereae (Leguminosae–Papilionoideae): Geographically structured more in succulent-rich and temperate settings than in grass-rich environments

This analysis goes beyond many phylogenies in exploring how phylogenetic structure imposed by morphology, ecology, and geography reveals useful evolutionary data. A comprehensive range of such diversity is evaluated within tribe Indigofereae and outgroups from sister tribes. A combined data set of 321 taxa (over one-third of the tribe) by 80 morphological characters, 833 aligned nuclear ribosomal ITS/5.8S sites, and an indel data set of 33 characters was subjected to parsimony analysis. Notable results include the Madagascan dry forest Disynstemon resolved as sister to tribe Indigofereae, and all species of the large genus Indigofera comprise just four main clades, each diagnosable by morphological synapomorphies and ecological and geographical predilections. These results suggest niche conservation (ecology) and dispersal limitation (geography) are important processes rendering signature shapes to the Indigofereae phylogeny in different biomes. Clades confined to temperate and succulent-rich biomes are more dispersal limited and have more geographical phylogenetic structure than those inhabiting tropical grass-rich vegetation. The African arid corridor, particularly the Namib center of endemism, harbors many of the oldest Indigofera lineages. A rates analysis of nucleotide substitutions confirms that the ages of the oldest crown clades are mostly younger than 16 Ma, implicating dispersal in explaining the worldwide distribution of the tribe.

Extinction risk and diversification are linked in a plant biodiversity hotspot

Plant extinction risks in the Cape, South Africa differ from those for vertebrates worldwide, with young and fast-evolving plant lineages marching towards extinction at the fastest rate, but independently of human effects.

The Use of Phylogeny to Interpret Cross-Cultural Patterns in Plant Use and Guide Medicinal Plant Discovery: An Example from Pterocarpus (Leguminosae)

Background The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce. Methodology/Principal Findings In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships. Conclusions/Significance This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into similar research areas, such as pest management or the search for bioactive plant-based compounds.