Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling

Mountains are among the most biodiverse places on Earth, and plant lineages that inhabit them have some of the highest speciation rates ever recorded. Plant diversity within the alpine zone - the elevation above which trees cannot grow-contributes significantly to overall diversity within mountain systems, but the origins of alpine plant diversity are poorly understood. Here, we quantify the processes that generate alpine plant diversity and their changing dynamics through time in Saxifraga (Saxifragaceae), an angiosperm genus that occurs predominantly in mountain systems. We present a time-calibrated molecular phylogenetic tree for the genus that is inferred from 329 low-copy nuclear loci and incorporates 73% (407) of known species. We show that upslope biome shifts into the alpine zone are considerably more prevalent than dispersal of alpine specialists between regions, and that the rate of upslope biome shifts increased markedly in the last 5 Myr, a timeframe concordant with a cooling and fluctuating climate that is likely to have increased the extent of the alpine zone. Furthermore, alpine zone specialists have lower speciation rates than generalists that occur inside and outside the alpine zone, and major speciation rate increases within Saxifraga significantly pre-date increased rates of upslope biome shifts. Specialisation to the alpine zone is not therefore associated with speciation rate increases. Taken together, this study presents a quantified and broad scale perspective of processes underpinning alpine plant diversity.

Global hotspots of plant phylogenetic diversity

Regions harbouring high unique phylogenetic diversity (PD) are priority targets for conservation. Here, we analyse the global distribution of plant PD, which remains poorly understood despite plants being the foundation of most terrestrial habitats and key to human livelihoods. Capitalising on a recently completed, comprehensive global checklist of vascular plants, we identify hotspots of unique plant PD and test three hypotheses: (1) PD is more evenly distributed than species diversity; (2) areas of highest PD (often called 'hotspots') do not maximise cumulative PD; and (3) many biomes are needed to maximise cumulative PD. Our results support all three hypotheses: more than twice as many regions are required to cover 50% of global plant PD compared to 50% of species; regions that maximise cumulative PD substantially differ from the regions with outstanding individual PD; and while (sub-)tropical moist forest regions dominate across PD hotspots, other forest types and open biomes are also essential. Safeguarding PD in the Anthropocene (including the protection of some comparatively species-poor areas) is a global, increasingly recognised responsibility. Having highlighted countries with outstanding unique plant PD, further analyses are now required to fully understand the global distribution of plant PD and associated conservation imperatives across spatial scales.

A global assessment of the Raunkiaeran shortfall in plants: geographic biases in our knowledge of plant traits

This article is part of the Special Collection ‘Global plant diversity and distribution’. See https://www.newphytologist.org/global-plant-diversity for more details.

Climate change and land use threaten global hotspots of phylogenetic endemism for trees

Across the globe, tree species are under high anthropogenic pressure. Risks of extinction are notably more severe for species with restricted ranges and distinct evolutionary histories. Here, we use a global dataset covering 41,835 species (65.1% of known tree species) to assess the spatial pattern of tree species' phylogenetic endemism, its macroecological drivers, and how future pressures may affect the conservation status of the identified hotspots. We found that low-to-mid latitudes host most endemism hotspots, with current climate being the strongest driver, and climatic stability across thousands to millions of years back in time as a major co-determinant. These hotspots are mostly located outside of protected areas and face relatively high land-use change and future climate change pressure. Our study highlights the risk from climate change for tree diversity and the necessity to strengthen conservation and restoration actions in global hotspots of phylogenetic endemism for trees to avoid major future losses of tree diversity.

Occurrence-based diversity estimation reveals macroecological and conservation knowledge gaps for global woody plants

Incomplete sampling of species' geographic distributions has challenged biogeographers for many years to precisely quantify global-scale biodiversity patterns. After correcting for the spatial inequality of sample completeness, we generated a global species diversity map for woody angiosperms (82,974 species, 13,959,780 occurrence records). The standardized diversity estimated more pronounced latitudinal and longitudinal diversity gradients than the raw data and improved the spatial prediction of diversity based on environmental factors. We identified areas with potentially high species richness and rarity that are poorly explored, unprotected, and threatened by increasing human pressure: They are distributed mostly at low latitudes across central South America, Central Africa, subtropical China, and Indomalayan islands. These priority areas for botanical exploration can help to efficiently fill spatial knowledge gaps for better describing the status of biodiversity and improve the effectiveness of the protected area network for global woody plant conservation.

Global beta-diversity of angiosperm trees is shaped by Quaternary climate change

As Earth's climate has varied strongly through geological time, studying the impacts of past climate change on biodiversity helps to understand the risks from future climate change. However, it remains unclear how paleoclimate shapes spatial variation in biodiversity. Here, we assessed the influence of Quaternary climate change on spatial dissimilarity in taxonomic, phylogenetic, and functional composition among neighboring 200-kilometer cells (beta-diversity) for angiosperm trees worldwide. We found that larger glacial-interglacial temperature change was strongly associated with lower spatial turnover (species replacements) and higher nestedness (richness changes) components of beta-diversity across all three biodiversity facets. Moreover, phylogenetic and functional turnover was lower and nestedness higher than random expectations based on taxonomic beta-diversity in regions that experienced large temperature change, reflecting phylogenetically and functionally selective processes in species replacement, extinction, and colonization during glacial-interglacial oscillations. Our results suggest that future human-driven climate change could cause local homogenization and reduction in taxonomic, phylogenetic, and functional diversity of angiosperm trees worldwide.

High exposure of global tree diversity to human pressure

Safeguarding Earth's tree diversity is a conservation priority due to the importance of trees for biodiversity and ecosystem functions and services such as carbon sequestration. Here, we improve the foundation for effective conservation of global tree diversity by analyzing a recently developed database of tree species covering 46,752 species. We quantify range protection and anthropogenic pressures for each species and develop conservation priorities across taxonomic, phylogenetic, and functional diversity dimensions. We also assess the effectiveness of several influential proposed conservation prioritization frameworks to protect the top 17% and top 50% of tree priority areas. We find that an average of 50.2% of a tree species' range occurs in 110-km grid cells without any protected areas (PAs), with 6,377 small-range tree species fully unprotected, and that 83% of tree species experience nonnegligible human pressure across their range on average. Protecting high-priority areas for the top 17% and 50% priority thresholds would increase the average protected proportion of each tree species' range to 65.5% and 82.6%, respectively, leaving many fewer species (2,151 and 2,010) completely unprotected. The priority areas identified for trees match well to the Global 200 Ecoregions framework, revealing that priority areas for trees would in large part also optimize protection for terrestrial biodiversity overall. Based on range estimates for >46,000 tree species, our findings show that a large proportion of tree species receive limited protection by current PAs and are under substantial human pressure. Improved protection of biodiversity overall would also strongly benefit global tree diversity.

OUP accepted manuscript

Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from the erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analyzing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with the species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation. [Divergence time estimation; gene trees; species tree; topological incongruence.]

The demographic history of Madagascan micro-endemics: have rare species always been rare?

Extinction has increased as human activities impact ecosystems, yet relatively few species have conservation assessments. Novel approaches are needed to highlight threatened species that are currently data-deficient. Many Madagascan plant species have extremely narrow ranges, but this may not have always been the case-it is unclear how the island's diverse flora evolved. To assess this, we generated restriction-site associated DNA sequence data for 10 Madagascan plant species, estimated effective population size (Ne) for each species and compared this to census (Nc) sizes. In each case, Ne was an order of magnitude larger than Nc-signifying rapid, recent population decline. We then estimated species' demographic history, tracking changes in Ne over time. We show that it is possible to predict extinction risk, particularly in the most threatened species. Furthermore, simulations showed that our approach has the power to detect population decline during the Anthropocene. Our analyses reveal that Madagascar's micro-endemics were not always rare, having experienced a rapid decline in their recent history. This casts further uncertainty over the processes that generated Madagascar's exceptional biodiversity. Our approach targets data-deficient species in need of conservation assessment, particularly in regions where human modification of the environment has been rapid.

Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document}) and 2333 genera (17\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document}). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]

A robust phylogenomic framework for the calamoid palms

Well-supported phylogenies are a prerequisite for the study of the evolution and diversity of life on earth. The subfamily Calamoideae accounts for more than one fifth of the palm family (Arecaceae), occurs in tropical rainforests across the world, and supports a billion-dollar industry in rattan products. It contains ca. 550 species in 17 genera, 10 subtribes and three tribes, but their phylogenetic relationships remain insufficiently understood. Here, we sequenced almost one thousand nuclear genomic regions for 75 systematically selected Calamoideae, representing the taxonomic diversity within all calamoid genera. Our phylogenomic analyses resolved a maximally supported phylogenetic backbone for the Calamoideae, including several higher-level relationships not previously inferred. In-depth analysis revealed low gene tree conflict for the backbone but complex deep evolutionary histories within several subtribes. Overall, our phylogenomic framework sheds new light on the evolution of palms and provides a robust foundation for future comparative studies, such as taxonomy, systematics, biogeography, and macroevolutionary research.

On the origin of giant seeds: the macroevolution of the double coconut (Lodoicea maldivica) and its relatives (Borasseae, Arecaceae)

Seed size shapes plant evolution and ecosystems, and may be driven by plant size and architecture, dispersers, habitat and insularity. How these factors influence the evolution of giant seeds is unclear, as are the rate of evolution and the biogeographical consequences of giant seeds. We generated DNA and seed size data for the palm tribe Borasseae (Arecaceae) and its relatives, which show a wide diversity in seed size and include the double coconut (Lodoicea maldivica), the largest seed in the world. We inferred their phylogeny, dispersal history and rates of change in seed size, and evaluated the possible influence of plant size, inflorescence branching, habitat and insularity on these changes. Large seeds were involved in 10 oceanic dispersals. Following theoretical predictions, we found that: taller plants with fewer-branched inflorescences produced larger seeds; seed size tended to evolve faster on islands (except Madagascar); and seeds of shade-loving Borasseae tended to be larger. Plant size and inflorescence branching may constrain seed size in Borasseae and their relatives. The possible roles of insularity, habitat and dispersers are difficult to disentangle. Evolutionary contingencies better explain the gigantism of the double coconut than unusually high rates of seed size increase.

Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes identified by the One Thousand Plant Transcriptomes Initiative to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm group. To maximize the phylogenetic potential of the probes, while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, 5-15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order groups of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order groups, including the entire angiosperm clade itself.

A roadmap for global synthesis of the plant tree of life

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.

Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome

I. II. III. IV. V. VI. VII. VIII. IX. References SUMMARY: Tropical rainforest (TRF) is the most species-rich terrestrial biome on Earth, harbouring just under half of the world's plant species in c. 7% of the land surface. Phylogenetic trees provide important insights into mechanisms underpinning TRF hyperdiversity that are complementary to those obtained from the fossil record. Phylogenetic studies of TRF plant diversity have mainly focused on whether this biome is an evolutionary 'cradle' or 'museum', emphasizing speciation and extinction rates. However, other explanations, such as biome age, immigration and ecological limits, must also be considered. We present a conceptual framework for addressing the drivers of TRF diversity, and review plant studies that have tested them with phylogenetic data. Although surprisingly few in number, these studies point to old age of TRF, low extinction and high speciation rates as credible drivers of TRF hyperdiversity. There is less evidence for immigration and ecological limits, but these cannot be dismissed owing to the limited number of studies. Rapid methodological developments in DNA sequencing, macroevolutionary analysis and the integration of phylogenetics with other disciplines may improve our grasp of TRF hyperdiversity in the future. However, such advances are critically dependent on fundamental systematic research, yielding numerous, additional, well-sampled phylogenies of TRF lineages.

An all-evidence species-level supertree for the palms (Arecaceae)

Several attempts have been made to generate complete species-level phylogenies for large clades, enabling comprehensive analyses of ecological or evolutionary hypotheses at the species level. No such phylogeny has, however, been generated for any major plant group yet, but here we generate such a phylogeny for the palm family (Arecaceae). We do this using a novel Bayesian approach, estimating the validity of intra-generic taxonomic groupings as topological constraints to assist in placing species without genetic or morphological data. From these we implement those that are supported by genetic or morphological data for a given genus or for related genera. The intergeneric relationships in our new phylogeny are surprisingly different from earlier phylogenies in the placement of genera within tribes, but largely identical to previous findings in the deeper branches in the phylogeny, pointing to the need for incorporating phylogenetic uncertainty in analyses based on this phylogeny. Initial analyses of the new phylogeny suggest non-constancy in diversification rates over time within genera, with an apparent increase in diversification rate over time, but no evidence for any geographic variation in the magnitude of this increase. We hope that our study will stimulate further evolutionary or ecological studies using palms as study organisms as well as discussions of the optimal way to place the many species without genetic or morphological data.

Assembly of forest communities across East Asia--insights from phylogenetic community structure and species pool scaling

Local communities are assembled from larger-scale species pools via dispersal, environmental filtering, biotic interactions, and local stochastic demographic processes. The relative importance, scaling and interplay of these assembly processes can be elucidated by comparing local communities to variously circumscribed species pools. Here we present the first study applying this approach to forest tree communities across East Asia, focusing on community phylogenetic structure and using data from a global network of tropical, subtropical and temperate forest plots. We found that Net Relatedness Index (NRI) and Nearest Taxon Index (NTI) values were generally lower with geographically broad species pools (global and Asian species pools) than with an East Asian species pool, except that global species pool produced higher NTI than the East Asian species pool. The lower NRI for the global relative to the East Asian species pool may indicate an important role of intercontinental migration during the Neogene and Quaternary and climatic conservatism in shaping the deeper phylogenetic structure of tree communities in East Asia. In contrast, higher NTI for the global relative to the East Asian species pool is consistent with recent localized diversification determining the shallow phylogenetic structure.

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.

Dispersal and niche evolution jointly shape the geographic turnover of phylogenetic clades across continents

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.

Geographical ecology of the palms (Arecaceae): determinants of diversity and distributions across spatial scales

BACKGROUND

The palm family occurs in all tropical and sub-tropical regions of the world. Palms are of high ecological and economical importance, and display complex spatial patterns of species distributions and diversity.

SCOPE

This review summarizes empirical evidence for factors that determine palm species distributions, community composition and species richness such as the abiotic environment (climate, soil chemistry, hydrology and topography), the biotic environment (vegetation structure and species interactions) and dispersal. The importance of contemporary vs. historical impacts of these factors and the scale at which they function is discussed. Finally a hierarchical scale framework is developed to guide predictor selection for future studies.

CONCLUSIONS

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.

Testing the water-energy theory on American palms (Arecaceae) using geographically weighted regression

Water and energy have emerged as the best contemporary environmental correlates of broad-scale species richness patterns. A corollary hypothesis of water-energy dynamics theory is that the influence of water decreases and the influence of energy increases with absolute latitude. We report the first use of geographically weighted regression for testing this hypothesis on a continuous species richness gradient that is entirely located within the tropics and subtropics. The dataset was divided into northern and southern hemispheric portions to test whether predictor shifts are more pronounced in the less oceanic northern hemisphere. American palms (Arecaceae, n = 547 spp.), whose species richness and distributions are known to respond strongly to water and energy, were used as a model group. The ability of water and energy to explain palm species richness was quantified locally at different spatial scales and regressed on latitude. Clear latitudinal trends in agreement with water-energy dynamics theory were found, but the results did not differ qualitatively between hemispheres. Strong inherent spatial autocorrelation in local modeling results and collinearity of water and energy variables were identified as important methodological challenges. We overcame these problems by using simultaneous autoregressive models and variation partitioning. Our results show that the ability of water and energy to explain species richness changes not only across large climatic gradients spanning tropical to temperate or arctic zones but also within megathermal climates, at least for strictly tropical taxa such as palms. This finding suggests that the predictor shifts are related to gradual latitudinal changes in ambient energy (related to solar flux input) rather than to abrupt transitions at specific latitudes, such as the occurrence of frost.