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.

New Guinea has the world's richest island flora.

New Guinea is the world's largest tropical island and has fascinated naturalists for centuries1,2. Home to some of the best-preserved ecosystems on the planet3 and to intact ecological gradients-from mangroves to tropical alpine grasslands-that are unmatched in the Asia-Pacific region4,5, it is a globally recognized centre of biological and cultural diversity6,7. So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea. Here we present the first, to our knowledge, expert-verified checklist of the vascular plants of mainland New Guinea and surrounding islands. Our publicly available checklist includes 13,634 species (68% endemic), 1,742 genera and 264 families-suggesting that New Guinea is the most floristically diverse island in the world. Expert knowledge is essential for building checklists in the digital era: reliance on online taxonomic resources alone would have inflated species counts by 22%. Species discovery shows no sign of levelling off, and we discuss steps to accelerate botanical research in the 'Last Unknown'8.

Population modelling and genetics of a critically endangered Madagascan palm Tahina spectabilis.

Madagascar is home to 208 indigenous palm species, almost all of them endemic and >80% of which are endangered. We undertook complete population census and sampling for genetic analysis of a relatively recently discovered giant fan palm, the Critically Endangered Tahina spectablis in 2008 and 2016. Our 2016 study included newly discovered populations and added to our genetic study. We incorporated these new populations into species distribution niche model (SDM) and projected these onto maps of the region. We developed population matrix models based on observed demographic data to model population change and predict the species vulnerability to extinction by undertaking population viability analysis (PVA). We investigated the potential conservation value of reintroduced planted populations within the species potential suitable habitat. We found that the population studied in 2008 had grown in size due to seedling regeneration but had declined in the number of reproductively mature plants, and we were able to estimate that the species reproduces and dies after approximately 70 years. Our models suggest that if the habitat where it resides continues to be protected the species is unlikely to go extinct due to inherent population decline and that it will likely experience significant population growth after approximately 80 years due to the reproductive and life cycle attributes of the species. The newly discovered populations contain more genetic diversity than the first discovered southern population which is genetically depauperate. The species appears to demonstrate a pattern of dispersal leading to isolated founder plants which may eventually lead to population development depending on local establishment opportunities. The conservation efforts currently put in place including the reintroduction of plants within the species potential suitable habitat if maintained are thought likely to enable the species to sustain itself but it remains vulnerable to anthropogenic impacts.

PalmTraits 1.0, a species-level functional trait database of palms worldwide.

Plant traits are critical to plant form and function -including growth, survival and reproduction- and therefore shape fundamental aspects of population and ecosystem dynamics as well as ecosystem services. Here, we present a global species-level compilation of key functional traits for palms (Arecaceae), a plant family with keystone importance in tropical and subtropical ecosystems. We derived measurements of essential functional traits for all (>2500) palm species from key sources such as monographs, books, other scientific publications, as well as herbarium collections. This includes traits related to growth form, stems, armature, leaves and fruits. Although many species are still lacking trait information, the standardized and global coverage of the data set will be important for supporting future studies in tropical ecology, rainforest evolution, paleoecology, biogeography, macroecology, macroevolution, global change biology and conservation. Potential uses are comparative eco-evolutionary studies, ecological research on community dynamics, plant-animal interactions and ecosystem functioning, studies on plant-based ecosystem services, as well as conservation science concerned with the loss and restoration of functional diversity in a changing world.

Exploring the floristic diversity of tropical Africa.

BACKGROUND: Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa. RESULTS: The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic. CONCLUSIONS: The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.

RAINBIO: a mega-database of tropical African vascular plants distributions.

The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

Global-change vulnerability of a key plant resource, the African palms.

Palms are keystone species in tropical ecosystems and provide essential ecosystem services to rural people worldwide. However, many palm species are threatened by habitat loss and over-exploitation. Furthermore, palms are sensitive to climate and thus vulnerable to future climate changes. Here, we provide a first quantitative assessment of the future risks to the African palm flora, finding that African palm species on average may experience a decline in climatic suitability in >70% of their current ranges by 2080. This suitability loss may, however, be almost halved if migration to nearby climatically suitable sites succeeds. Worryingly, 42% of the areas with 80-100% of species losing climate suitability are also characterized by high human population density (HPD). By 2080, >90% of all African palm species' ranges will likely occur at HPDs leading to increased risks of habitat loss and overexploitation. Additionally, up to 87% of all species are predicted to lose climatic suitability within current protected areas (PAs) by 2080. In summary, a major plant component of tropical ecosystems and provider of ecosystem services to rural populations will face strongly increased pressures from climate change and human populations in the near future.

Comprehensive Red List assessment reveals exceptionally high extinction risk to Madagascar palms.

The establishment of baseline IUCN Red List assessments for plants is a crucial step in conservation planning. Nowhere is this more important than in biodiversity hotspots that are subject to significant anthropogenic pressures, such as Madagascar. Here, all Madagascar palm species are assessed using the IUCN Red List categories and criteria, version 3.1. Our results indicate that 83% of the 192 endemic species are threatened, nearly four times the proportion estimated for plants globally and exceeding estimates for all other comprehensively evaluated plant groups in Madagascar. Compared with a previous assessment in 1995, the number of Endangered and Critically Endangered species has substantially increased, due to the discovery of 28 new species since 1995, most of which are highly threatened. The conservation status of most species included in both the 1995 and the current assessments has not changed. Where change occurred, more species have moved to lower threat categories than to higher categories, because of improved knowledge of species and their distributions, rather than a decrease in extinction risk. However, some cases of genuine deterioration in conservation status were also identified. Palms in Madagascar are primarily threatened by habitat loss due to agriculture and biological resource use through direct exploitation or collateral damage. The recent extension of Madagascar's protected area network is highly beneficial for palms, substantially increasing the number of threatened species populations included within reserves. Notably, three of the eight most important protected areas for palms are newly designated. However, 28 threatened and data deficient species are not protected by the expanded network, including some Critically Endangered species. Moreover, many species occurring in protected areas are still threatened, indicating that threatening processes persist even in reserves. Definitive implementation of the new protected areas combined with local community engagement are essential for the survival of Madagascar's palms.

Palaeo-precipitation is a major determinant of palm species richness patterns across Madagascar: a tropical biodiversity hotspot.

The distribution of rainforest in many regions across the Earth was strongly affected by Pleistocene ice ages. However, the extent to which these dynamics are still important for modern-day biodiversity patterns within tropical biodiversity hotspots has not been assessed. We employ a comprehensive dataset of Madagascan palms (Arecaceae) and climate reconstructions from the last glacial maximum (LGM; 21 000 years ago) to assess the relative role of modern environment and LGM climate in explaining geographical species richness patterns in this major tropical biodiversity hotspot. We found that palaeoclimate exerted a strong influence on palm species richness patterns, with richness peaking in areas with higher LGM precipitation relative to present-day even after controlling for modern environment, in particular in northeastern Madagascar, consistent with the persistence of tropical rainforest during the LGM primarily in this region. Our results provide evidence that diversity patterns in the World's most biodiverse regions may be shaped by long-term climate history as well as contemporary environment.

Multimillion-year climatic effects on palm species diversity in Africa.

Past climatic changes have caused extinction, speciation, and range dynamics, but assessing the influence of past multimillion-year climatic imprints on present-day biodiversity patterns remains challenging. We analyzed a new continental-scale data set to examine the importance of paleoclimatic effects on current gradients in African palm richness patterns. Using climate reconstructions from the late Miocene (-10 mya), the Pliocene (-3 mya), and the Last Glacial Maximum (0.021 mya), we found that African palm diversity patterns exhibit pronounced historical legacies related to long-term climate change. Notably, pre-Pleistocene paleoprecipitation variables differentially affected current diversity patterns of palms grouped by contrasting habitat requirements. Accounting for present-day environment, rain forest palms exhibit greater species richness in localities where Pliocene precipitation was relatively high, whereas open-habitat palms show higher species richness in areas of relatively low precipitation during the Miocene Epoch. Our results demonstrate that diversity-climate relationships among African palm species include multimillion-year lagged dynamics, i.e., with historical legacies persisting across much longer time periods than commonly recognized.

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.

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.

Low-copy nuclear DNA, phylogeny and the evolution of dichogamy in the betel nut palms and their relatives (Arecinae; Arecaceae).

For the betel nut palm genus Areca and the other seven genera in subtribe Arecinae (Areceae; Arecoideae; Arecaceae) we collected DNA sequences from two low-copy nuclear genes, phosphoribulokinase (PRK) and the second largest subunit of RNA polymerase II (RPB2). The data were used to evaluate monophyly of the subtribe and its component genera, explore the radiation of the group across its range, and examine evolution of protandry and protogyny, which is particularly diverse in Arecinae. The subtribe and some genera are not monophyletic. Three lineages of Arecinae are recovered: one widespread, but centered on the Sunda Shelf, another endemic to the islands east of Wallace's line and a third, comprising the Sri Lanka endemic Loxococcus, that is most closely related to genera from outside subtribe Arecinae. Strong support is obtained for broadening the circumscription of the genus Hydriastele to include Gronophyllum, Gulubia and Siphokentia. In clarifying phylogenetic relationships, we have demonstrated that a perceived bimodal distribution of the subtribe across Wallace's line does not in fact exist. Character optimizations indicate that the evolution of protogyny, an unusual condition in palms, is potentially correlated with a large radiation in the genus Pinanga and possibly also to dramatic diversification in pollen morphology and genome size. The evolution of dichogamy in the clade endemic to the east of Wallace's line is complex and reveals a pattern of numerous transformations between protandry and protogyny that is in marked contrast with other Arecinae. We suggest that this contrast is most likely a reflection of differing geological histories and pollinator spectra in each region.

Homoplasious character combinations and generic delimitation: a case study from the Indo-Pacific arecoid palms (Arecaceae: Areceae).

The complex distributions of morphological character states in the Indo-Pacific palm tribe Areceae (Arecaceae; Arecoideae) are potentially challenging for the delimitation of its genera. In the first exhaustive sampling of all 65 genera of the Areceae, we examined relationships of two of the tribe's most problematic genera, Heterospathe and Rhopaloblaste, using portions of the low-copy nuclear genes phosphoribulokinase (PRK) and RNA-polymerase II subunit B (RPB2). Both genera fell within a highly supported clade comprising all Areceae genera, but are clearly unrelated. Rhopaloblaste was strongly supported as monophyletic and is most closely related to Indian Ocean genera. Heterospathe was resolved with strong support within a clade of western Pacific genera, but with the monotypic Alsmithia nested within it. Ptychosperma micranthum, which has previously been included in both Heterospathe and Rhopaloblaste, is excluded from these and from Ptychosperma, supporting its recent placement in a new genus Dransfieldia. Morphological comparisons indicate that the crownshaft is putatively synapomorphic for the Areceae with numerous reversals within the clade and some independent origins elsewhere. The putative diagnostic characters of Heterospathe show high levels of homoplasy, and the genus can only be distinguished by a suite of characters, whereas Rhopaloblaste is more clearly defined. Our results have implications not only for the two genera in focus, but have also been influential for the new classification of the Areceae.