Phylogenetic composition and structure of tree communities shed light on historical processes influencing tropical rainforest diversity

The Neotropics, Afrotropics and Madagascar have different histories which have influenced their respective patterns of diversity. Based on current knowledge of these histories, we developed the following predictions about the phylogenetic structure and composition of rainforest tree communities: (Hypothesis 1) isolation of Gondwanan biotas generated differences in phylogenetic composition among biogeographical regions; (H2) major Cenozoic extinction events led to lack of phylogenetic structure in Afrotropical and Malagasy communities; (H3) greater angiosperm diversification in the Neotropics led to greater phylogenetic clustering there than elsewhere; (H4) phylogenetic overdispersion is expected near the Andes due to the co‐occurrence of magnoliids tracking conserved habitat preferences and recently diversified eudicot lineages. Using abundance data of tropical rainforest tree species from 94 communities in the Neotropics, Afrotropics and Madagascar, we computed net relatedness index (NRI) to assess local phylogenetic structure, i.e. phylogenetic clustering vs. overdispersion relative to regional species pools, and principal coordinates of phylogenetic structure (PCPS) to assess variation in phylogenetic composition across communities. We observed significant differences in phylogenetic composition among biogeographical regions (agreement with H1). Overall phylogenetic structure did not differ among biogeographical regions, but results indicated variation from Andes to Amazon. We found widespread phylogenetic randomness in most Afrotropical and all Malagasy communities (agreement with H2). Most of central Amazonian communities were phylogenetically random, although some communities presented phylogenetic clustering (partial agreement with H3). We observed phylogenetic overdispersion near the Andes (agreement with H4). We were able to identify how differences in lineage composition are related to local phylogenetic co‐occurrences across biogeographical regions that have been undergoing different climatic and orographic histories during the past 100 Myr. We observed imprints of the history following Gondwana breakup on phylobetadiversity and local phylogenetic structure of rainforest tree communities in the Neotropics, Afrotropics and Madagascar

Isoprenoid emission in hygrophyte and xerophyte European woody flora: ecological and evolutionary implications

Aim The relationship between isoprenoid emission and hygrophily was investigated in woody plants of the Italian flora, which is representative of European diversity. Methods Volatile isoprenoids (isoprene and monoterpenes) were measured, or data collected from the literature, for 154 species native or endemic to the Mediterranean. The Ellenberg indicator value for moisture (EIVM) was used to describe plant hygrophily. Phylogenetic analysis was carried out at a broader taxonomic scale on 128 species, and then refined on strong isoprene emitters (Salix and Populus species) based on isoprene synthase gene sequences (IspS). Results Isoprene emitters were significantly more common and isoprene emission was higher in hygrophilous EIVM classes, whereas monoterpene emitters were more widespread and monoterpene emission was higher in xeric classes. However, when controlling for phylogeny, isoprene emission was not associated with EIVM, possibly due to the large presence of Salicaceae among hygrophilous isoprene emitters. Moreover, the distribution of isoprene emitters among EIVM classes was not related to IspS-based phylogenesis in Populus and Salix, suggesting that the gene has not undergone evolution linked to ecological pressure. In contrast, the monoterpene emission pattern is independent of phylogeny, suggesting that the evolution of monoterpenes is associated with transitions to more xeric habitats. Main conclusions Our results reveal an interesting ecological pattern linking isoprenoids and water availability. We suggest that isoprene is a trait that: (1) evolved in plants adapted to high water availability; (2) is replaced by more effective protection mechanisms, e.g. more stable isoprenoids, in plants adapting to more xeric environments; and (3) being strongly constrained by phylogeny, persists in Salicaceae adapted to more xeric environments

Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms

Seed dispersal affects gene flow and hence genetic differentiation of plant populations. During the Late Quaternary, most fruit-eating and seed-dispersing megafauna went extinct, but whether these animals have left signatures in the population genetics of their food plants, particularly those with large, ‘megafaunal’ fruits (i.e. &gt;4 cm—megafruits), remains unclear. Here, we assessed the population history, genetic differentiation and recent migration among populations of four animal-dispersed palm (Arecaceae) species with large (Borassus madagascariensis), medium-sized (Hyphaene coriacea, Bismarckia nobilis) and small (Chrysalidocarpus madagascariensis) fruits on Madagascar. We integrated double-digest restriction-site-associated DNA sequencing (ddRAD) of 167 individuals from 25 populations with (past) distribution ranges for extinct (e.g., giant lemurs and elephant birds) and extant seed-dispersing animals, landscape and human impact data, and applied linear mixed-effects models to explore the drivers of genetic variation in Malagasy palms. Palm populations that shared more megafrugivore species in the past had lower genetic differentiation than populations that shared fewer megafrugivore species. This suggests that megafrugivore-mediated seed dispersal in the past may have led to frequent gene flow among populations. In comparison, extant frugivore diversity only decreased genetic differentiation in the small-fruited palm. Furthermore, genetic differentiation of all palm species decreased with landscape connectivity (i.e. environmental suitability, forest cover and river density) and human impact (i.e. road density), while migration rates of the small-fruit palm increased with road density. Synthesis. Our results suggest that the legacy of megafrugivores regularly achieving long dispersal distances is still reflected in the population genetics of palms that were formerly dispersed by such animals. Furthermore, low genetic differentiation was possibly maintained after the megafauna extinctions through alternative dispersal (e.g. human- or river-mediated), long generation times and long lifespans of these megafruit palms. Our study illustrates how species interactions that happened &gt;1000 years ago can leave imprints in their population genetics.</p

Taxonomy based on science is necessary for global conservation

Peer reviewe

Global diversification of a tropical plant growth form: environmental correlates and historical contingencies in climbing palms

Tropical rain forests (TRF) are the most diverse terrestrial biome on Earth, but the diversification dynamics of their constituent growth forms remain largely unexplored. Climbing plants contribute significantly to species diversity and ecosystem processes in TRF. We investigate the broad-scale patterns and drivers of species richness as well as the diversification history of climbing and non-climbing palms (Arecaceae). We quantify to what extent macroecological diversity patterns are related to contemporary climate, forest canopy height and paleoclimatic changes. We test whether diversification rates are higher for climbing than non-climbing palms and estimate the origin of the climbing habit. Climbers account for 22% of global palm species diversity mostly concentrated in Southeast Asia. Global variation in climbing palm species richness can be partly explained by past and present-day climate and rain forest canopy height, but regional differences in residual species richness after accounting for current and past differences in environment suggest a strong role of historical contingencies in climbing palm diversification. Climbing palms show a higher net diversification rate than non-climbers. Diversification analysis of palms detected a diversification rate increase along the branches leading to the most species-rich clade of climbers. Ancestral character reconstructions revealed that the climbing habit originated between early Eocene and Miocene. These results imply that changes from non-climbing to climbing habit may have played an important role in palm diversification, resulting in the origin of one fifth of all palm species. We suggest that, in addition to current climate and paleoclimatic changes after the late Neogene, present-day diversity of climbing palms can be explained by morpho-anatomical innovations, the biogeographic history of Southeast Asia, and/or ecological opportunities due to the diversification of high-stature dipterocarps in Asian TRFs

The Darwinian shortfall in plants : phylogenetic knowledge is driven by range size

The Darwinian shortfall, i.e. the lack of knowledge of phylogenetic relationships, significantly impedes our understanding of evolutionary drivers of global patterns of biodiversity. Spatial bias in the Darwinian shortfall, where phylogenetic knowledge in some regions is more complete than others, could undermine eco- and biogeographic inferences. Yet, spatial biases in phylogenetic knowledge for major groups – such as plants – remain poorly understood. Using data for 337 023 species (99.7%) of seed plants (Spermatophyta), we produced a global map of phylogenetic knowledge based on regional data and tested several potential drivers of the observed spatial variation. Regional phylogenetic knowledge was defined as the proportion of the regional seed plant flora represented in GenBank's nucleotide database with phylogenetically relevant data. We used simultaneous autoregressive models to explain variation in phylogenetic knowledge based on three biodiversity variables (species richness, range size and endemism) and six socioeconomic variables representing funding and accessibility. We compared observed patterns and relationships to established patterns of the Wallacean shortfall (the lack of knowledge of species distributions). We found that the Darwinian shortfall is strongly and significantly related to the macroecological distribution of species' range sizes. Small-ranged species were significantly less likely to have phylogenetic data, leading to a concentration of the Darwinian shortfall in species-rich, tropical countries where range sizes are small on average. Socioeconomic factors were less important, with significant but quantitatively small effects of accessibility and funding. In conclusion, reducing the Darwinian shortfall and smoothen its spatial bias will require increased efforts to sequence the world's small-ranged (endemic) species

Using and navigating the plant tree of life

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143797/1/ajb21071.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143797/2/ajb21071_am.pd