scholarly journals A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

2021 ◽  
Author(s):  
William J. Baker ◽  
Paul Bailey ◽  
Vanessa Barber ◽  
Abigail Barker ◽  
Sidonie Bellot ◽  
...  
Keyword(s):  
Natural History ◽  
Flowering Plants ◽  
Tree Of Life ◽  
Flowering Plant ◽  
Target Sequence ◽  
Sequence Capture ◽  
Natural History Collections ◽  
Public Data ◽  
Data Release ◽  
Life On Earth

AbstractThe 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. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents 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 dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a “first pass” angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards 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 standardised 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.

scholarly journals Visualizing natural history collection data provides insight into collection development and bias

2018 ◽  
Vol 6 ◽  
Author(s):  
Vaughn Shirey
Keyword(s):  
Natural History ◽  
Large Body ◽  
Aggregated Data ◽  
Natural History Collections ◽  
Natural History Collection ◽  
Drexel University ◽  
Collection Data ◽  
Spatial Domains ◽  
Life On Earth ◽  
Insight Into

Natural history collections contain estimated billions of records representing a large body of knowledge about the diversity and distribution of life on Earth. Assessments of various forms of bias within the aggregated data associated with specimens in these collections have been conducted across temporal, taxonomic, and spatial domains. Considering that these biases are the sum of biases across all contributing collections to aggregate datasets, the assessment of bias at the collection level is warranted. Interactive visualization provides a powerful tool for the assessment of these biases and insight into the historical development of natural history collections, providing context for where sources of bias may originate and developing historical narratives to clarify our understanding of our own knowledge about life on Earth. Here, I present a case study on using Sankey diagrams to illustrate the development of the entomology type collection at the Academy of Natural Sciences of Drexel University in Philadelphia, Pennsylvania with the hope that extensions of these practices among individual natural history collections are modified and adopted.

Joseph Sidebotham: vicissitudes of a Victorian collector

2015 ◽  
Vol 42 (2) ◽  
pp. 197-210 ◽  
Author(s):  
Laurence M. Cook
Keyword(s):  
Natural History ◽  
Species Limits ◽  
Clear Cut ◽  
Natural History Collections ◽  
As Species ◽  
Scientific World

Joseph Sidebotham (1824–1885) was a Manchester cotton baron whose natural history collections are now in the Manchester Museum. In addition to collecting he suggested a method for identifying and classifying Lepidoptera and investigated variation within species as well as species limits. With three close collaborators, he is credited with discovering many species new to Britain in both Lepidoptera and Coleoptera. A suspicion of fraud attaches to these claims. The evidence is not clear-cut in the Lepidoptera, but a possible reason is suggested why Sidebotham, as an amateur in the increasingly professional scientific world, might have engaged in deceit.

The Banksian natural history collections of the Endeavour voyage and their relevance to modern taxonomy

1981 ◽  
Vol 1981 (1) ◽  
pp. 61-70
Author(s):  
H. B. Carter ◽  
Judith A. Diment ◽  
C. J. Humphries ◽  
Alwyne Wheeler
Keyword(s):  
Natural History ◽  
Natural History Collections

Correspondence between Adolphe Brongniart and Robert Schomburgk: trading natural history collections for honours

2002 ◽  
Vol 29 (3) ◽  
pp. 333-336
Author(s):  
PIOTR DASZKIEWICZ ◽  
MICHEL JEGU
Keyword(s):  
Nineteenth Century ◽  
Natural History ◽  
Dominican Republic ◽  
Southeast Asia ◽  
Herbarium Specimens ◽  
British Guiana ◽  
Natural History Collections ◽  
History Of ◽  
Source Of Information ◽  
German Naturalist

ABSTRACT: This paper discusses some correspondence between Robert Schomburgk (1804–1865) and Adolphe Brongniart (1801–1876). Four letters survive, containing information about the history of Schomburgk's collection of fishes and plants from British Guiana, and his herbarium specimens from Dominican Republic and southeast Asia. A study of these letters has enabled us to confirm that Schomburgk supplied the collection of fishes from Guiana now in the Laboratoire d'Ichtyologie, Muséum National d'Histoire Naturelle, Paris. The letters of the German naturalist are an interesting source of information concerning the practice of sale and exchange of natural history collections in the nineteenth century in return for honours.

Assessing Environmental Acidity in Storerooms of Natural History Collections

2021 ◽  
Vol 64 (1) ◽  
pp. 155-182
Author(s):  
Marta Pérez‐Azcárate ◽  
Berta Caballero‐López ◽  
Francesc Uribe ◽  
Neus Ibáñez ◽  
Glòria Masó ◽  
...  
Keyword(s):  
Natural History ◽  
Natural History Collections

scholarly journals Flowering plant embryos: How did we end up here?

2021 ◽  
Author(s):  
Stefan A. Rensing ◽  
Dolf Weijers
Keyword(s):  
Current Knowledge ◽  
General Structure ◽  
Three Dimensional ◽  
Flowering Plants ◽  
Flowering Plant ◽  
Adult Plant ◽  
Ancestral State ◽  
Evolutionary Trajectory ◽  
Current State ◽  
Plant Embryo

AbstractThe seeds of flowering plants are sexually produced propagules that ensure dispersal and resilience of the next generation. Seeds harbor embryos, three dimensional structures that are often miniatures of the adult plant in terms of general structure and primordial organs. In addition, embryos contain the meristems that give rise to post-embryonically generated structures. However common, flowering plant embryos are an evolutionary derived state. Flowering plants are part of a much larger group of embryo-bearing plants, aptly termed Embryophyta. A key question is what evolutionary trajectory led to the emergence of flowering plant embryos. In this opinion, we deconstruct the flowering plant embryo and describe the current state of knowledge of embryos in other plant lineages. While we are far yet from understanding the ancestral state of plant embryogenesis, we argue what current knowledge may suggest and how the knowledge gaps may be closed.

scholarly journals Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci

2021 ◽  
Author(s):  
Lauren A. Eserman ◽  
Shawn K. Thomas ◽  
Emily E. D. Coffey ◽  
James H. Leebens‐Mack
Keyword(s):  
Single Copy ◽  
Target Sequence ◽  
Sequence Capture

scholarly journals Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

2021 ◽  
Author(s):  
Anne E. Thomas ◽  
Javier Igea ◽  
Heidi M. Meudt ◽  
Dirk C. Albach ◽  
William G. Lee ◽  
...  
Keyword(s):  
New Zealand ◽  
Target Sequence ◽  
Rapid Radiation ◽  
Sequence Capture ◽  
Phylogenetic Resolution
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