Climate-driven extinctions shape the phylogenetic structure of temperate tree floras.

When taxa go extinct, unique evolutionary history is lost. If extinction is selective, and the intrinsic vulnerabilities of taxa show phylogenetic signal, more evolutionary history may be lost than expected under random extinction. Under what conditions this occurs is insufficiently known. We show that late Cenozoic climate change induced phylogenetically selective regional extinction of northern temperate trees because of phylogenetic signal in cold tolerance, leading to significantly and substantially larger than random losses of phylogenetic diversity (PD). The surviving floras in regions that experienced stronger extinction are phylogenetically more clustered, indicating that non-random losses of PD are of increasing concern with increasing extinction severity. Using simulations, we show that a simple threshold model of survival given a physiological trait with phylogenetic signal reproduces our findings. Our results send a strong warning that we may expect future assemblages to be phylogenetically and possibly functionally depauperate if anthropogenic climate change affects taxa similarly.

Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide.

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.

The Tracking of Moist Habitats Allowed Aiphanes (Arecaceae) to Cover the Elevation Gradient of the Northern Andes.

The topographic gradients of the Tropical Andes may have triggered species divergence by different mechanisms. Topography separates species' geographical ranges and offers climatic heterogeneity, which could potentially foster local adaptation to specific climatic conditions and result in narrowly distributed endemic species. Such a pattern is found in the Andean centered palm genus Aiphanes. To test the extent to which geographic barriers and climatic heterogeneity can explain distribution patterns in Aiphanes, we sampled 34 out of 36 currently recognized species in that genus and sequenced them by Sanger sequencing and/or sequence target capture sequencing. We generated Bayesian, likelihood, and species-tree phylogenies, with which we explored climatic trait evolution from current climatic occupation. We also estimated species distribution models to test the relative roles of geographical and climatic divergence in their evolution. We found that Aiphanes originated in the Miocene in Andean environments and possibly in mid-elevation habitats. Diversification is related to the occupation of the adjacent high and low elevation habitats tracking high annual precipitation and low precipitation seasonality (moist habitats). Different species in different clades repeatedly occupy all the different temperatures offered by the elevation gradient from 0 to 3,000 m in different geographically isolated areas. A pattern of conserved adaptation to moist environments is consistent among the clades. Our results stress the evolutionary roles of niche truncation of wide thermal tolerance by physical range fragmentation, coupled with water-related niche conservatism, to colonize the topographic gradient.

Twenty-five years of progress in understanding pollination mechanisms in palms (Arecaceae).

BACKGROUND: With more than 90 published studies of pollination mechanisms, the palm family is one of the better studied tropical families of angiosperms. Understanding palm-pollinator interactions has implications for tropical silviculture, agroforestry and horticulture, as well as for our understanding of palm evolution and diversification. We review the rich literature on pollination mechanisms in palms that has appeared since the last review of palm pollination studies was published 25 years ago. SCOPE AND CONCLUSIONS: Visitors to palm inflorescences are attracted by rewards such as food, shelter and oviposition sites. The interaction between the palm and its visiting fauna represents a trade-off between the services provided by the potential pollinators and the antagonistic activities of other insect visitors. Evidence suggests that beetles constitute the most important group of pollinators in palms, followed by bees and flies. Occasional pollinators include mammals (e.g. bats and marsupials) and even crabs. Comparative studies of palm-pollinator interactions in closely related palm species document transitions in floral morphology, phenology and anatomy correlated with shifts in pollination vectors. Synecological studies show that asynchronous flowering and partitioning of pollinator guilds may be important regulators of gene flow between closely related sympatric taxa and potential drivers of speciation processes. Studies of larger plant-pollinator networks point out the importance of competition for pollinators between palms and other flowering plants and document how the insect communities in tropical forest canopies probably influence the reproductive success of palms. However, published studies have a strong geographical bias towards the South American region and a taxonomic bias towards the tribe Cocoseae. Future studies should try to correct this imbalance to provide a more representative picture of pollination mechanisms and their evolutionary implications across the entire family.

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae.

The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced 3,988 genomic regions for 85% of the species of the tribe, including 84% of the species of the largest genus, Geonoma. Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.

Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae).

Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow bands of montane forests on each side of the Andes in Ecuador and northeastern Peru. First, we tested the hypothesis of C. echinulatum being a geographic cline species crossing the Andes in the Amotape-Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross-Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio-genetic patterns. Individual-based Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron-Paute deflection. F-statistics derived from BC suggested an east-to-west dispersal history. Population-based analyses revealed strong genetic structuring at both small and large geographic scales. Interpopulation relationships and Mantel tests strongly supported the cline model with cross-Andean dispersal in the AHZ. Along the cline, gene flow measured as F(ST) was mainly limited by distance, with less but significant impact of climatic friction. Coalescent analysis revealed that cross-Andean divergence took place during the Quaternary. Significant historical isolation (R(ST) > F(ST)) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance and historical isolation on patterns of Andean diversity and distribution.

Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health.

Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species (Ambrosia spp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in 'high allergy risk' (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27-100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe.

The effect of nitrogen deposition on the species richness of acid grasslands in Denmark: a comparison with a study performed on a European scale.

The effect of atmospheric nitrogen deposition on the species richness of acid grasslands was investigated by combining data from a large Danish monitoring program with a large European data set, where a significant non-linear negative effect of nitrogen deposition had been demonstrated (Stevens et al., 2010). The nitrogen deposition range in Denmark is relatively small and when only considering the Danish data a non-significant decrease in the species richness with nitrogen deposition was observed. However, when both data sets were combined, then the conclusion of the European survey was further corroborated by the results of the Danish monitoring. Furthermore, by combining the two data sets a more comprehensive picture of the threats to the biodiversity of acid grasslands emerge; i.e., species richness in remnant patches of acid grassland in intensively cultivated agricultural landscapes is under influence not only from nitrogen deposition, but also from current and historical land use.

A dated phylogeny of the palm tribe Chamaedoreeae supports Eocene dispersal between Africa, North and South America.

The palm tribe Chamaedoreeae reaches its higher diversity in Central America, however, its distribution ranges from the north eastern part of Mexico to Bolivia with a disjunction to the Mascarene Islands in the Indian Ocean. The disjunct distribution of Chamaedoreeae is generally considered a result of Gondwana vicariance and extinction from Africa and/or Madagascar. However, latitudinal migrations and their role in shaping the distribution of this tribe in the Americas have been largely overlooked. In this study we used seven plastid and two nuclear DNA regions to investigate the phylogenetic relationships and biogeography of the Chamaedoreeae. The resulting phylogeny fully resolved the generic relationships within the tribe. The exact area of origin of the tribe remains uncertain, but dating analyses indicated an initial diversification of the Chamaedoreeae during the Early Eocene, followed by long distance dispersion to the Mascarene Islands in the late Miocene. The radiation of Hyophorbe could have taking place on islands in the Indian Ocean now submerged, but its former presence in Africa or Madagascar cannot be ruled out. At least two independent migrations between North and South America predating the rise of the Panama isthmus need to be postulated to explain the distribution of Chamaedoreeae, one during the Middle Eocene and a second during the Miocene. Whereas the traditional interpretation of distribution of Chamaedoreeae species assumes a west Gondwana origin of the group, the findings presented in this paper make it equally possible to interpret the group as a primarily boreotropical element.

Mid-Tertiary dispersal, not Gondwanan vicariance explains distribution patterns in the wax palm subfamily (Ceroxyloideae: Arecaceae).

The Ceroxyloideae is a small but heterogeneous subfamily of palms (Arecaceae, Palmae). It includes a Caribbean lineage (tribe Cyclospathae), a southern hemisphere disjunction (tribe Ceroxyleae), and an amphi-Andean element (tribe Phytelepheae), until recently considered a distinct subfamily (Phytelephantoideae) due to its highly derived morphology. A variety of hypotheses have been proposed to account for the biogeography of the subfamily, involving Gondwanan vicariance, austral interplate dispersal from South America to Australia via Antarctica, Andean orogeny, and Pleistocene refuges. We assessed the systematic classification and biogeography of the group based on a densely sampled phylogeny using >5.5kb of DNA sequences from three plastid and two nuclear genomic regions. The subfamily and each of its three tribes were resolved as monophyletic with high support. Divergence time estimates based on penalized likelihood and Bayesian dating methods indicate that Gondwanan vicariance is highly unlikely as an explanation for basic disjunctions in tribe Ceroxyleae. Alternative explanations include a mid-Tertiary trans-Atlantic/trans-African dispersal track and the "lemurian stepping stones" hypothesis. Austral interplate dispersal of Oraniopsis to Australia could have occurred, but apparently only in the mid-Eocene/early Oligocene interval after global cooling had begun. Our data do not support Pleistocene climatic changes as drivers for speciation in the Andean-centered Phytelepheae as previously proposed. Radiation in this tribe coincides largely with the major uplift of the Andes, favoring Andean orogeny over Pleistocene climatic changes as a possible speciation-promoting factor in this tribe.