Phylogeny, taxonomy and biogeography of Ceiba Mill. (Malvaceae: Bombacoideae)

The Neotropics is the most species-rich area in the world and the mechanisms that generated and maintain its biodiversity are still debated. This thesis contributes to the debate by investigating the evolutionary and biogeographic history of the genus Ceiba. Ceiba comprises 18 mostly neotropical species endemic to two major biomes, seasonally dry tropical forests (SDTFs) and rain forests, and therefore represents an ideal case to shed light on patterns of neotropical plant evolution and diversification. Species of Ceiba, with their swollen, spiny trunks and large, beautiful flowers are one of the most characteristic elements of neotropical SDTF, one of the most threatened biomes in the tropics. Despite this, Ceiba has an historically complex taxonomy with some issues of species delimitation unresolved, especially within a species complex (Ceiba insignis agg.). Initial phylogenetic analyses of DNA sequence data from the nuclear ribosomal internal transcribed spacers (ITS) for 24 accessions representing 14 species of Ceiba recovered the genus as monophyletic and showed geographical and ecological structure in three main clades: (i) a humid forest lineage of three accessions of C. pentandra sister to the remaining species; (ii) a highly supported clade composed of C. schottii and C. aesculifolia from Central American and Mexican SDTF plus two accessions of C. samauma from inter Andean valleys from Peru; and (iii) a highly supported South American SDTF clade including 10 species showing little sequence variation. Within this South American clade, no species represented by multiple accessions were resolved as monophyletic. To investigate unresolved species relationships further, next-generation hybrid capture was used to sequence 377 loci for 103 accessions representing all 18 Ceiba species. This data set was assembled using different approaches (de novo and reference mapping) and with different software and settings to assess their impact in downstream phylogenetic analysis. The 377 loci were concatenated and analysed under the maximum likelihood framework treated as a single partition. The well resolved and sampled NGS phylogenies showed a similar pattern of geographical and ecological structure as inferred using ITS. The genus Neobuchia was recovered within the SDTF Central American and Mexican clade, and should therefore be incorporated within Ceiba. In the South American SDTF clade, there were multiple examples where a monophyletic group recognised as a taxonomic species was nested within another, paraphyletic taxonomic species, which suggests recent, ancestor-descendent species relationships. Within this clade, individual gene trees showed high conflict. Coalescent-based species delimitation analysis and morphological data revealed no clear species boundaries between C. pubiflora and C. glaziovii, and these species should be synonymised. A subset of 111 loci was used to generate a dated phylogeny based on penalised likelihood analysis using the fossil flower of Eriotheca prima from the middle to late Eocene as a primary calibration. The stem node age of Ceiba was estimated as 45 Ma. The rain forest species C. pentandra and C. samauma, and the campos rupestres species C. jasminodora, were resolved with long stem lineages and shallow crown groups. Whilst some SDTF species were very old (e.g., C. trischistandra) and monophyletic, many South American SDTF species were resolved with short stem lineages and relatively deep crown groups, possibly suggesting low rates of extinction in the large Caatinga SDTF region. In addition, several South American SDTF species were not resolved as monophyletic. Such results of younger, non-monophyletic SDTF species and older, monophyletic rain forest species contrast with recent predictions that rain forest species may, on average, have more recent origins than SDTF species and will more often be non-monophyletic. Ceiba has different and distinctive phylogenetic patterns that contradict recent theoretical predictions. It demonstrates that studies of other clades sampled densely with multiple accessions of each species using a multi-locus approach are needed if we are to understand the nature of species and their boundaries, and the diversification process in neotropical trees

Target capture sequencing for phylogenomic and population studies in the Southeast Asian genus Palaquium (Sapotaceae)

ACKNOWLEDGEMENTS We thank the management of the National Parks Board and Singapore Botanic Gardens for providing continuous support, facilities and fieldwork approval in Singapore’s nature reserves. We appreciate the digital research team at the University of Aberdeen and the research/scientific computing teams at The James Hutton Institute and NIAB for providing technical support while using the computational resources on the respective HPC clusters, “Maxwell” and the “UK Crop Diversity Bioformatics HPC” (BBSRC grant BB/S019669/1), which have contributed to the results within this paper. We thank numerous staff at the Singapore Botanic Gardens, particularly Khoo-Woon Mui Hwang and Neo Wei Ling for strong technical support in the molecular lab, Matti Niissalo for generous sharing of lab protocols and bioinformatics tips, Choo Le Min for patient help with lab troubleshooting, Chong Kwek Yan and Chan Pin Jia for forest survey expertise, and Louise Neo for thoughtful field and R advice. Our sincere thanks are due to Herbarium staff at the Royal Botanic Garden Edinburgh, including Lesley Scott, for efficient assistance in sending silica-dried samples to the Singapore Botanic Gardens. We also thank Camille Christe at the Conservatoire et Jardin botaniques de la Ville de Genève for kind advice related to the taxon-specific baits’ setup and purchase FUNDING We are grateful to the Lady Yuen Peng McNeice Charitable Foundation for financial support of this study.Peer reviewedPublisher PD

Phylogeny and biogeography of Ceiba Mill. (Malvaceae, Bombacoideae)

The Neotropics is the most species-rich area in the world, and the mechanisms that generated and maintain its biodiversity are still debated. This paper contributes to the debate by investigating the evolutionary and biogeographic history of the genus Ceiba Mill. (Malvaceae, Bombacoideae). Ceiba comprises 18 mostly Neotropical species, largely endemic to two major biomes, seasonally dry tropical forests (SDTFs) and rain forests. Its species are among the most characteristic elements of Neotropical SDTF, one of the most threatened biomes in the tropics. Phylogenetic analyses of DNA sequence data (from the nuclear ribosomal internal transcribed spacers [nrITS] for 30 accessions representing 14 species of Ceiba) recovered the genus as monophyletic. The phylogeny showed geographic and ecological structure in three main clades: (i) a rain forest lineage of nine accessions of C. pentandra sister to the remaining species; (ii) a highly supported clade composed of C. schottii and C. aesculifolia from Central American and Mexican SDTF, plus two accessions of C. samauma from semi-humid, inter Andean valleys in Peru; and (iii) a highly supported South American SDTF clade including 10 species showing little sequence variation. Within this South American SDTF clade, no species represented by multiple accessions were resolved as monophyletic. We demonstrate that the patterns of species age, monophyly, and geographic structure previously reported for SDTF species within the Leguminosae family are not shared by Ceiba, suggesting that further phylogenetic studies of unrelated groups are required to understand general patterns

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples

Plant diversity patterns in neotropical dry forests and their conservation implications

This is the author accepted manuscript. The final version is available from American Association for the Advancement of Science via the DOI in this record.Seasonally dry tropical forests are distributed across Latin America and the Caribbean and are highly threatened, with less than 10% of their original extent remaining in many countries. Using 835 inventories covering 4660 species of woody plants, we show marked floristic turnover among inventories and regions, which may be higher than in other neotropical biomes, such as savanna. Such high floristic turnover indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests. Our results provide a scientific framework within which national decision-makers can contextualize the floristic significance of their dry forest at a regional and continental scale.This paper is the result of the Latin American and Caribbean Seasonally Dry Tropical Forest Floristic Network (DRYFLOR), which has been supported at the Royal Botanic Garden Edinburgh by a Leverhulme Trust International Network Grant (IN-074). This work was also supported by the U.K. Natural Environment Research Council grant NE/I028122/1; Colciencias Ph.D. scholarship 529; Synthesys Programme GBTAF-2824; the NSF (NSF 1118340 and 1118369); the Instituto Humboldt (IAvH)–Red colombiana de investigación y monitoreo en bosque seco; the Inter-American Institute for Global Change Research (IAI; Tropi-Dry, CRN2-021, funded by NSF GEO 0452325); Universidad Nacional de Rosario (UNR); and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). The data reported in this paper are available at www.dryflor.info. R.T.P. conceived the study. M.P., A.O.-F., K.B.-R., R.T.P., and J.W. designed the DRYFLOR database system. K.B.-R. and K.G.D. carried out most analyses. K.B.-R. R.T.P., and K.G.D. wrote the manuscript with substantial input from A.D.-S., R.L.-P., A.O.-F., D.P., C.Q., and R.R. All the authors contributed data, discussed further analyses, and commented on various versions of the manuscript. K.B.-R. thanks G. Galeano who introduced her to dry forest research. We thank J. L. Marcelo, I. Huamantupa, C. Reynel, S. Palacios, and A. Daza for help with fieldwork and data entry in Peru

Phylogeny and biogeography of Ceiba Mill. (Malvaceae, Bombacoideae)

The Neotropics is the most species-rich area in the world, and the mechanisms that generated and maintain its biodiversity are still debated. This paper contributes to the debate by investigating the evolutionary and biogeographic history of the genus Ceiba Mill. (Malvaceae, Bombacoideae). Ceiba comprises 18 mostly Neotropical species, largely endemic to two major biomes, seasonally dry tropical forests (SDTFs) and rain forests. Its species are among the most characteristic elements of Neotropical SDTF, one of the most threatened biomes in the tropics. Phylogenetic analyses of DNA sequence data (from the nuclear ribosomal internal transcribed spacers [nrITS] for 30 accessions representing 14 species of Ceiba) recovered the genus as monophyletic. The phylogeny showed geographic and ecological structure in three main clades: (i) a rain forest lineage of nine accessions of C. pentandra sister to the remaining species; (ii) a highly supported clade composed of C. schottii and C. aesculifolia from Central American and Mexican SDTF, plus two accessions of C. samauma from semi-humid, inter Andean valleys in Peru; and (iii) a highly supported South American SDTF clade including 10 species showing little sequence variation. Within this South American SDTF clade, no species represented by multiple accessions were resolved as monophyletic. We demonstrate that the patterns of species age, monophyly, and geographic structure previously reported for SDTF species within the Leguminosae family are not shared by Ceiba, suggesting that further phylogenetic studies of unrelated groups are required to understand general patterns

Supplementary material 6 from: Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM (2023) Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodiversity Data Journal 11: e102317. https://doi.org/10.3897/BDJ.11.e102317

Case study 6 sample, DNA and read data descriptio