William John Baker

William John Baker
Royal Botanic Gardens, Kew · Kew Science

BA, MSc, PhD

About

252
Publications
188,588
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
8,708
Citations
Introduction
My research explores the diversity and evolution of plants, especially the palm family. I also lead Kew’s Plant and Fungal Trees of Life (PAFTOL) programme, which aims to gather and analyse genomic data for every genus of plant and fungus.
Additional affiliations
November 2014 - present
Royal Botanic Gardens, Kew
Position
  • Research Assistant
Description
  • Full job title: Senior Research Leader, Integrated Monography and Assistant Head of Comparative Plant and Fungal Biology
December 2012 - November 2014
Royal Botanic Gardens, Kew
Position
  • Research Assistant
April 2005 - November 2014
Royal Botanic Gardens, Kew
Position
  • Head of Palm Research
Education
September 1994 - December 1997
University of Reading
Field of study
  • Plant systematics
September 1993 - September 1994
University of Reading
Field of study
  • Pure and Applied Plant and Fungal Taxonomy
September 1990 - June 1993
University of Oxford
Field of study
  • Plant Sciences

Publications

Publications (252)
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
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...
Article
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.
Article
Full-text available
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...
Article
Full-text available
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,...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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 resources and absence of b...
Article
Full-text available
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...
Article
Full-text available
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.
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
PREMISE: Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from th...
Chapter
The date palm (Phoenix dactylifera L.)Date palm (Phoenix dactylifera) is an iconic crop of hot and arid regions of North AfricaNorth Africa, the Middle East and up to northwestern India. It is a member of the genus PhoenixPhoenix that constitutes a monophyletic group within the Coryphoideae subfamily, in the palm family. The genus Phoenix is compos...
Article
Full-text available
Premise: The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family's complex infra-familial classification. With the advent of molecular systematics, revisions of the various pro...
Article
We present a densely sampled phylogenomic study of the mulberry tribe (Moreae, Moraceae), an economically important clade with a global distribution, revealing multiple losses of inflexed stamens, a character traditionally used to circumscribe Moreae. Inflexed stamens facilitate ballistic pollen release and are associated with wind pollination, and...
Article
Full-text available
Premise: Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically desig...
Article
Full-text available
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...
Article
Full-text available
Premise: Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furtherm...
Article
Full-text available
PREMISE: Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specifi...
Article
Full-text available
Premise: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 ta...
Article
Full-text available
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 under...
Article
Full-text available
Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology because of their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including m...
Preprint
Full-text available
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 under...
Article
Unprecedented changes in the Earth’s biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs — comprehensive systematic treatments of a family or genus — have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk tha...
Article
Full-text available
Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectie...
Article
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,...
Article
Morphological characterizations of genera in Cyperaceae tribe Abildgaardieae have been highly problematic and the subject of much debate. Earlier molecular phylogenetic studies based on Sanger sequencing and a limited sampling have indicated that several generic circumscriptions are not monophyletic. Here, we provide the first phylogenetic hypothes...
Book
Full-text available
The Useful Plants and Fungi of Colombia project is a 2.5-year initiative led by Royal Botanic Gardens, Kew in collaboration with the Alexander von Humboldt Biological Resources Research Institute. Its aim is to develop pathways to enhance nature’s contribution to people in Colombia by increasing, consolidating and making accessible the knowledge of...
Technical Report
Full-text available
Madagascar fait partie des territoires les plus importants dans le monde en termes de diversité spécifique pour les palmiers ou la famille des Arecaceae. Sur les quelques 2800 espèces reconnues dans le monde, l'ile possède à elle seule 208 espèces natives dont plus de 98% en sont endémiques. Certains taxons sont uniques du point de vue biologique c...
Technical Report
Full-text available
Madagascar is one of the most important areas in the world in terms of species diversity for palms, the family Arecaceae. Out of the approximately 2500 species recognized in the world, the island alone has 208 indigenous species, of which more than 98% are endemic, found naturally nowhere else. Some taxa are unique from a biological point of view b...
Preprint
Full-text available
The date palm ( Phoenix dactylifera ) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild re...
Article
Urera Gaudich, s.l. is a pantropical genus comprising c. 35 species of trees, shrubs, and vines. It has a long history of taxonomic uncertainty, and is repeatedly recovered as polyphyletic within a poorly resolved complex of genera in the Urticeae tribe of the nettle family (Urticaceae). To provide generic delimitations concordant with evolutionary...
Preprint
Full-text available
Premise of the study Evolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to...
Preprint
Full-text available
Universal target enrichment kits maximise utility across wide evolutionary breadth while minimising the number of baits required to create a cost-efficient kit. Locus assembly requires a target reference, but the taxonomic breadth of the kit means that target references files can be phylogenetically sparse. The Angiosperms353 kit has been successfu...
Article
Full-text available
In this article we explain what DNA barcoding means and its utility for palm research and conservation.
Article
Full-text available
Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and...
Article
Full-text available
New Guinea is the world’s largest tropical island and has fascinated naturalists for centuries. Home to some of the best-preserved ecosystems on the planet and to intact ecological gradients—from mangroves to tropical alpine grasslands—that are unmatched in the Asia-Pacific region, it is a globally recognized centre of biological and cultural diver...
Preprint
Full-text available
Now published in the book The date palm genome, Vol. 1 (Springer): https://link.springer.com/chapter/10.1007/978-3-030-73746-7_2 The date palm (Phoenix dactylifera L.) is the iconic crop of hot and arid regions of North Africa, the Middle East and up to northwestern India. It is a member of the genus Phoenix, that constitutes a monophyletic group...
Article
Full-text available
Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) an...
Article
Full-text available
With over 300 species, Borneo has the richest palm flora of any Malesian island. Here, we describe an expedition to Lanjak Entimau Wildlife Sanctuary, a remote region of Sarawak in the heart of Borneo and provide a checklist of the 46 palm species that we found there.
Article
Full-text available
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...
Preprint
Full-text available
We present a densely-sampled phylogenomic study of the mulberry tribe (Moreae, Moraceae), an economically important clade with a global distribution, revealing multiple losses of inflexed stamens, a character traditionally used to circumscribe Moreae. Inflexed stamens facilitate ballistic pollen release and are associated with wind pollination, and...
Technical Report
Full-text available
Medemia argun is an endemic palm species occurring in the Nubian Desert of Egypt and Sudan (Republic of Sudan). Its fruit was first discovered as an archaeological relic of the ancient tombs of Egypt. The living palm was discovered in 1837 and subsequently was sporadically observed throughout the 19th and 20th centuries. By the end of the 1980s sig...
Preprint
Extinction has increased as human activities impact ecosystems. Conservation assessments for the IUCN red list are a fundamental tool in aiding the prevention of further extinction, yet, relatively few species have been thoroughly assessed. To increase the efficiency of assessments, novel approaches are needed to highlight threatened species that a...
Article
Full-text available
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 populatio...