William John Baker

Royal Botanic Gardens, Kew · Science

Biological collections are at the front line of biodiversity research, informing taxonomy, evolution, conservation and sustainable livelihoods. In April 2014, we organised a meeting at the Linnean Society (UK) discussing the impact of next-generation sequencing (NGS) methods on collections-based research. Here, we explore the main themes of this me...

The systematic biology of the palm family (Arecaceae) is probably better known than that of any other tropical plant family of comparable size. As a result, the palms are now regarded as a model group for tropical rain forest research. Ten years ago, the first phylogenetic classification of palms was established as a foundation for the second editi...

Summary' I. 'Introduction' II. 'A brief history of hypotheses' III. 'Age of TRF biome and lineages' IV. 'Frequency of immigration from other biomes' V. 'Speciation and extinction' VI. 'Ecological limits' VII. 'Key methodological challenges' VIII. 'Perspectives' IX. 'Conclusions' 'Acknowledgements' References Tropical rainforest (TRF) is the most sp...

Premise: Magnoliids are a strongly supported clade of angiosperms. Previous phy-logenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families. Methods: For the...

Grasses (Poaceae) comprise c . 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome‐scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new re...

Imbalance in species richness among related clades is a pervasive, yet incompletely understood feature of biodiversity. Comparison of species-poor and species-rich clades that have evolved within the same region can shed light on the mechanisms underlying this phenomenon. The long-isolated island of Madagascar is an ideal place for doing this. Mada...

Premise Cleomaceae is an important model clade for studies of evolutionary processes including genome evolution, floral form diversification, and photosynthetic pathway evolution. Diversification and divergence patterns in Cleomaceae remain tangled as research has been restricted by its worldwide distribution, limited genetic sampling and species c...

The daisy tribe Anthemideae Cass. is one of the largest and most diverse tribes within Asteraceae. We analyzed a data set including 61 out of 111 Anthemideae genera, and all but four of the 19 currently recognized subtribes (Inulantherinae, Lapidophorinae, Lonadinae, and Vogtiinae) using a targeted high-throughput sequencing approach, the first foc...

Connaraceae is a pantropical family of about 200 species containing lianas and small trees with remarkably diverse floral polymorphisms, including distyly, tristyly, homostyly, and dioecy. To date, relationships within the family have not been investigated using a targeted molecular phylogenetic treatment, severely limiting systematic understanding...

The generation and analysis of genome-scale data—genomics—is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for its widescale use in evolutionary and conservation biology. Here, we introduce and describe a national-scale collaboration conceived to...

Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in...

Grasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a ne...

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. >4 cm—megafruits),...

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 foundation...

Abstract Background and Aims The geographical origin and evolutionary mechanisms underpinning the rich and distinctive New Caledonian flora remain poorly understood. This is attributable to the complex geological past of the island and to the scarcity of well-resolved species-level phylogenies. Here, we infer phylogenetic relationships and divergen...

A distinctive rattan from Borneo that can be distinguished from all other species of palm, even using its vegetative morphology alone, has remained undescribed for over 90 years due to the lack of reproductive material. We describe the species formally as new to science here.

New Guinea is the world’s largest tropical island and a globally significant biodiversity hotspot. Palms dominate the rainforests of New Guinea, from exquisite, forest floor palmlets to graceful canopy giants, and are vital for local people who depend on them for survival. Palms of New Guinea is the first comprehensive account of these immensely i...

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up‐to‐date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high‐throughput and Sanger sequencing data, covering all five s...

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...

Premise Magnoliidae are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families. Methods Here we p...

Poales are one of the most species‐rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test six hypotheses regarding the evolution and assembly of Poales in open and closed habitats throughout the world, and examine whether diversification patterns demonstrate p...

A diverse range of high-throughput sequencing data, such as target capture, RNA-Seq, genome skimming, and high-depth whole genome sequencing, are amenable to phylogenomic analyses but the integration of such mixed data types into a single phylogenomic dataset requires a number of bioinformatic tools and significant computational resources. Here, we...

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the u...

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the u...

What grows where? Knowledge about where to find particular species in nature must have been key to the survival of humans throughout our evolution. Over time, and as people colonised new land masses and habitats, interactions with the local biota led to a wealth of combined traditional and scientific wisdom about the distributions of species and th...

Poales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test the hypotheses that Poales species are assembled into distinct phyloregions, with centres of high phylogenetic diversity and endemism clustered in tropical regions, and t...

A genus and species of palm from the Truong Son Range in Vietnam, Truongsonia lecongkietii, is described as new to science. Phylogenomic analysis strongly supports the placement of the new taxon in subfamily Arecoideae as sister to the African endemic tribe Podococceae, which comprises a single genus Podococcus. A new tribe Truongsonieae is also de...

Orchids constitute one of the most spectacular radiations of flowering plants. However, their geographical origin, historical spread across the globe, and hotspots of speciation remain uncertain due to the lack of a broad phylogenomic framework. ⍰ We present a new Orchidaceae phylogeny based on high-throughput and Sanger sequencing datasets, coveri...

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most...

Background and aims: Understanding diaspore morphology and how much a species invests on dispersal appendages is key for improving our knowledge of dispersal in fragmented habitats. We investigate diaspore morphological traits in high-Andean Compositae, their main abiotic and biotic drivers and test whether they play a role in species distribution...

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...

The production of flowers and fruit below ground (geoflory and geocarpy, respectively) is a paradoxical reproductive strategy that seemingly hinders pollination and dispersal. Though rare, these phenomena occur in 33 angiosperm families. Plants that flower and fruit entirely below ground are exceptionally unusual. Pinanga subterranea (Arecaceae), a...

A new acaulescent species of Pinanga (Arecoideae: Areceae: Arecinae) is described and illustrated here. This remarkable new species is the first palm described as flowering and fruiting underground, highlighting Borneo as a hotspot for palm diversity.

Background Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical...

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target captu...

Premise: Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris. The main objective of this work was to better resolve the deep phylogenetic relationships among the main lin...

The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological and biogeographic transitions within the clade. We used target capture sequencing with the Angiosperms353 probes, taxon-sampling encompassing nearly all genera of t...

1. Seed dispersal is a key process in the generation and maintenance of genetic diversity and genetic differentiation of plant populations in tropical ecosystems. During the Last Quaternary, most seed-dispersing megafauna was lost globally, but whether this has caused dispersal limitation, loss of genetic diversity, and increased genetic differenti...

Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting...

Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevan...

Protecting nature’s contributions to people requires accelerating extinction risk assessment and better integrating evolutionary, functional and used diversity with conservation planning. Here, we report machine learning extinction risk predictions for 1,381 palm species (Arecaceae), a plant family of high socio-economic and ecological importance....

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies b...

With 178 species, palm subtribe Dypsidinae is one of the largest plant radiations on Madagascar. A well‐resolved species‐level phylogeny is required not only to unpick the drivers of this spectacular radiation, but also to define natural and useful generic limits in this taxonomically difficult group. The only recent taxonomic revision of Dypsidina...

As part of the Palms of New Guinea project we discovered a species of Licuala new to science with large white flowers, which is described here for the first time.

Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species of high economic importance, such as the crop sweet potato (Ipomoea batatas L.), the ornamental morning glories (Ipomoea L.), bindweeds (Convolvulus L.), and dodders, the parasitic vines (Cuscuta L.). Earlier phylogenetic studies,...

Genome size varies 2400‐fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat ‘communities’ are analogous to those structuring ecological communiti...

Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world’s most important engineers of terrestrial ecosystems, we...

We examined the impact of successive alignment quality‐control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target‐sequence‐capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemp...

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific commun...

Reference: Lim, J.Y., Huang, H., Farnsworth, A., Lunt, D.J., Baker, W.J., Morley, R.J., Kissling, W.D. & Hoorn, C. (2022) The Cenozoic history of palms: Global diversification, biogeography, and the decline of megathermal forests. Contact: Jun Ying Lim (junyinglim@gmail.com), Huasheng Huang (buxushuang@gmail.com)

Aim Megathermal rain forests and mangroves are much smaller in extent today than in the early Cenozoic, primarily owing to global cooling and drying trends since the Eocene–Oligocene transition (c. 34 Ma). The general reduction of these biomes is hypothesized to shape the diversity and biogeographical history of tropical plant clades. However, thi...

Genome size varies 2,400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants’ environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat ‘communities’ are analogous to those structuring ecological communit...

The palm tribe Lepidocaryeae (Arecaceae) comprises seven genera and 51 currently accepted species that are distributed in lowland tropical forests and savannas across Africa and the Americas. Subtribal relationships within Lepidocaryeae have been a persistent challenge,limiting our understanding of its systematics, morphology, and biogeography. Sev...

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...

Societal Impact Statement Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as “Digital Sequence Information” (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic...

Premise To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. Methods We combined high-throug...

In this special issue of the American Journal of Botany, together with a companion issue of Applications in Plant Sciences, we gather a set of papers that focus on a new, common phylogenomic toolkit, the Angiosperms353 probe set, and illustrate its potential for evolutionary synthesis by promoting open collaboration across our community.

Premise: The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address th...

Premise: Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with othe...

Premise: Cunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long-range disjunctions. Methods: We performed a phylogenomic study...

Aim Since Wallace's and Engler's 19th-century biogeographical schemes, biogeographers have sought to classify the world into biogeographical regions according to patterns in biotic distribution. Yet, while most of the world's plant biodiversity can be found in the tropics, basic phytogeographical relationships and boundaries within this zone remain...

PREMISE: Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several altern...

Premise: The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the e...