Despite long-standing interest in the origin and maintenance of species diversity, little is known about historical drivers of species assemblage structure at large spatiotemporal scales. Here, we use global species distribution data, a dated genus-level phylogeny, and paleo-reconstructions of biomes and climate to examine Cenozoic imprints on the phylogenetic structure of regional species assemblages of palms (Arecaceae), a species-rich plant family characteristic of tropical ecosystems. We find a strong imprint on phylogenetic clustering due to geographic isolation and in situ diversification, especially in the Neotropics and on islands with spectacular palm radiations (e.g., Madagascar, Hawaii, and Cuba). Phylogenetic overdispersion on mainlands and islands corresponds to biotic interchange areas. Differences in the degree of phylogenetic clustering among biogeographic realms are related to differential losses of tropical rainforests during the Cenozoic, but not to the cumulative area of tropical rainforest over geological time. A largely random phylogenetic assemblage structure in Africa coincides with severe losses of rainforest area, especially after the Miocene. More recent events also appear to be influential: phylogenetic clustering increases with increasing intensity of Quaternary glacial-interglacial climatic oscillations in South America and, to a lesser extent, Africa, indicating that specific clades perform better in climatically unstable regions. Our results suggest that continental isolation (in combination with limited long-distance dispersal) and changing climate and habitat loss throughout the Cenozoic have had strong impacts on the phylogenetic structure of regional species assemblages in the tropics.biodiversity | biogeography | climate change | evolution | extinction D espite long-standing interest, the mechanisms behind the origin and maintenance of high tropical biodiversity remain elusive (1, 2). Much recent macroecological research has focused on explaining large-scale species richness gradients by contemporary climate (3-5), but the importance of evolutionary diversification and past environments has also been highlighted (2,(6)(7)(8). Over the past decades it has become increasingly clear that local community structure depends on both local processes and large-scale factors that influence regional species diversity (9, 10). Regional species assemblages are jointly shaped by within-region diversification and dispersal between regions, the former being constrained by time for speciation (7, 11) and by climatic or other factors influencing net diversification rates (12, 13), and the latter by the formation and disappearance of dispersal barriers (14, 15), time for dispersal (16), and phylogenetic niche conservatism (17). Understanding the historical assembly and present-day structure of regional species assemblages thus requires integration of ecological, paleogeographic, and phylogenetic information (10).Increasing availability of phylogenies has ignited interest in the phylogenetic str...

Determinants of palm distributions, composition and richness vary with spatial scale. For species distributions, climate appears to be important at landscape and broader scales, soil, topography and vegetation at landscape and local scales, hydrology at local scales, and dispersal at all scales. For community composition, soil appears important at regional and finer scales, hydrology, topography and vegetation at landscape and local scales, and dispersal again at all scales. For species richness, climate and dispersal appear to be important at continental to global scales, soil at landscape and broader scales, and topography at landscape and finer scales. Some scale-predictor combinations have not been studied or deserve further attention, e.g. climate on regional to finer scales, and hydrology and topography on landscape and broader scales. The importance of biotic interactions - apart from general vegetation structure effects - for the geographic ecology of palms is generally underexplored. Future studies should target scale-predictor combinations and geographic domains not studied yet. To avoid biased inference, one should ideally include at least all predictors previously found important at the spatial scale of investigation.

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The extent to which species' ecological and phylogenetic relatedness shape their co-occurrence patterns at large spatial scales remains poorly understood. By quantifying phylogenetic assemblage structure within geographic ranges of >8000 bird species, we show that global co-occurrence patterns are linked - after accounting for regional effects - to key ecological traits reflecting diet, mobility, body size and climatic preference. We found that co-occurrences of carnivorous, migratory and cold-climate species are phylogenetically clustered, whereas nectarivores, herbivores, frugivores and invertebrate eaters tend to be more phylogenetically overdispersed. Preference for open or forested habitats appeared to be independent from the level of phylogenetic clustering. Our results advocate for an extension of the tropical niche conservatism hypothesis to incorporate ecological and life-history traits beyond the climatic niche. They further offer a novel species-oriented perspective on how biogeographic and evolutionary legacies interact with ecological traits to shape global patterns of species coexistence in birds.

The turnover of phylogenetic clades across space is a fundamental biodiversity pattern that may depend on long-term evolutionary processes, and that has downstream effects on other aspects of diversity including species richness and community structure. Limited niche evolution and limited dispersal are two major processes causing spatial restriction, and thus turnover, of clades. We studied the determinants of clade turnover within the World's richest floristic kingdom, the Neotropics, using the palm family (Arecaceae) as a model. We show that continental-scale clade turnover is driven by a combination of limited niche evolution — with respect to temperature and soil tolerances — and limited dispersal. These findings are consistent with strong dispersal barriers within the Neotropics, and the observation that some palm lineages are most diverse in certain biomes or climates. The importance of such deep-time effects suggest that palms might be slow to adapt or disperse in response to anthropogenic climate change.

Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.

To advance our understanding of the processes that govern the assembly of palm communities and the local coexistence of numerous palm species, we here synthesize available information in the literature on species diversity and growth-form composition in palm communities across the Americas. American palm communities surveyed had 4-48 (median 16) species in study plots covering 0.09-7.2 ha. Climate, soils, hydrology, and topography are the main factors determining palm community species richness. Tropical lowland terra firme rain forests are the most species-rich whereas forests that are inundated or grow on sandy soils or in areas with seasonal climate have much fewer species. Palm communities in the central-western Amazon and in Central America are significantly richer than the average region and those in the Caribbean significantly poorer in species. As for branching, the 789 species of tropical American palms belong to Corner's model (solitary, 268 species, 33%), Tomlinsons model (cespitose, 521 species, 66%) and Schoute's model (dichotomous branching, three species, <1%). We assigned the species to eight different growth forms: (i) Large tall-stemmed Palms (102 spp), (ii) Large-leaved medium-short-stemmed Palms (31 spp), (iii) Medium-sized Palms (95 spp), (iv) Medium/Small Palms with Stout Stem (42 spp), (v) Small Palms (423 spp), (vi) Large acaulescent Palms (28 spp), (vii) Small acaulescent Palms (56 spp), and (viii) Climbing Palms (12 spp). The eight growth forms are differently represented in the palm communities, and the categories Small Palms and Large tall-stemmed Palms dominate the communities both in terms of species richness and in number of individuals.

Aim  It is a central issue in ecology and biogeography to understand what governs community assembly and the maintenance of biodiversity in tropical rain forest ecosystems. A key question is the relative importance of environmental species sorting (niche assembly) and dispersal limitation (dispersal assembly), which we investigate using a large dataset from diverse palm communities. Location  Lowland rain forest, western Amazon River Basin, Peru. Methods  We inventoried palm communities, registering all palm individuals and recording environmental conditions in 149 transects of 5 m × 500 m. We used ordination, Mantel tests and indicator species analysis (ISA) to assess compositional patterns, species responses to geographical location and environmental factors. Mantel tests were used to assess the relative importance of geographical distance (as a proxy for dispersal limitation) and environmental differences as possible drivers of dissimilarity in palm species composition. We repeated the Mantel tests for subsets of species that differ in traits of likely importance for habitat specialization and dispersal (height and range size). Results  We found a strong relationship between compositional dissimilarity and environmental distance and a weaker but also significant relationship between compositional dissimilarity and geographical distance. Consistent with expectations, relationships with environmental and geographical distance were stronger for understorey species than for canopy species. Geographical distance had a higher correlation with compositional dissimilarity for small‐ranged species compared with large‐ranged species, whereas the opposite was true for environmental distance. The main environmental correlates were inundation and soil nutrient levels. Main conclusions  The assembly of palm communities in the western Amazon appears to be driven primarily by species sorting according to hydrology and soil, but with dispersal limitation also playing an important role. The importance of environmental characteristics and geographical distance varies depending on plant height and geographical range size in agreement with functional predictions, increasing our confidence in the inferred assembly mechanisms.