scholarly journals Assembling an illustrated family-level tree of life for exploration in mobile devices

2021 ◽  
Author(s):  
Andres A. Del Risco ◽  
Diego A. Chacon ◽  
Lucia Angel ◽  
David A. Garcia
Keyword(s):  
Dna Sequences ◽  
Morphological Diversity ◽  
Mobile App ◽  
Tree Of Life ◽  
Phylogenetic Studies ◽  
Large Trees ◽  
Family Level ◽  
Phylogenetic Hypotheses ◽  
Life On Earth ◽  
Diversity Of Life

Since the concept of the tree of life was introduced by Darwin about a century and a half ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive tree of life for its exploration has been a difficult task to achieve due to two main obstacles: i) information is scattered into a plethora of individual sources and ii) practical visualization tools for exceptionally large trees are lacking. To overcome both challenges, we aimed to synthetize a family-level tree of life by compiling over 1400 published phylogenetic studies, ensuring that the source trees represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the synthetic tree by employing over 550 secondary-calibration points, using publicly available sequences for more than 5000 taxa, and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app (Tree of Life) for smartphones in order to facilitate the visualization and interactive exploration of the resulting tree. Interactive features include an easy exploration by zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, a timescale to determine extinction and divergence dates, and quick links to Wikipedia. Small illustrations of organisms are displayed at the tips of the branches, to better visualize the morphological diversity of life on earth. Our assembled Tree of Life currently includes over 7000 taxonomic families (about half of the total family-level diversity) and its content will be gradually expanded through regular updates to cover all life on earth at family-level.

scholarly journals Towards a barnacle tree of life: integrating diverse phylogenetic efforts into a comprehensive hypothesis of thecostracan evolution

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7387 ◽  
Author(s):  
Christine Ewers-Saucedo ◽  
Christopher L. Owen ◽  
Marcos Pérez-Losada ◽  
Jens T. Høeg ◽  
Henrik Glenner ◽  
...  
Keyword(s):  
Tree Of Life ◽  
Phylogenetic Information ◽  
Barnacle Species ◽  
Phylogenetic Studies ◽  
Coastal Species ◽  
New Synthesis ◽  
Unidentified Species ◽  
Cryptic Taxa ◽  
Phylogenetic Hypotheses ◽  
Tree Approach

Barnacles and their allies (Thecostraca) are a biologically diverse, monophyletic crustacean group, which includes both intensely studied taxa, such as the acorn and stalked barnacles, as well as cryptic taxa, for example, Facetotecta. Recent efforts have clarified phylogenetic relationships in many different parts of the barnacle tree, but the outcomes of these phylogenetic studies have not yet been combined into a single hypothesis for all barnacles. In the present study, we applied a new “synthesis” tree approach to estimate the first working Barnacle Tree of Life. Using this approach, we integrated phylogenetic hypotheses from 27 studies, which did not necessarily include the same taxa or used the same characters, with hierarchical taxonomic information for all recognized species. This first synthesis tree contains 2,070 barnacle species and subspecies, including 239 barnacle species with phylogenetic information and 198 undescribed or unidentified species. The tree had 442 bifurcating nodes, indicating that 79.3% of all nodes are still unresolved. We found that the acorn and stalked barnacles, the Thoracica, and the parasitic Rhizocephala have the largest amount of published phylogenetic information. About half of the thecostracan families for which phylogenetic information was available were polyphyletic. We queried publicly available geographic occurrence databases for the group, gaining a sense of geographic gaps and hotspots in our phylogenetic knowledge. Phylogenetic information is especially lacking for deep sea and Arctic taxa, but even coastal species are not fully incorporated into phylogenetic studies.

scholarly journals Physcraper: a python package for continual update of evolutionary estimates using the Open Tree of Life

2020 ◽  
Author(s):  
Luna L. Sanchez Reyes ◽  
Martha Kandziora ◽  
Emily Jane McTavish
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Reconstruction ◽  
Open Science ◽  
Tree Of Life ◽  
List Type ◽  
Matrix Assembly ◽  
Life Project ◽  
Character Matrix ◽  
Molecular Dataset ◽  
Phylogenetic Hypotheses

AbstractPhylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and nonspecialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study.Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases.Physcraper can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies).The Physcraper workflow demonstrates the benefits of doing open science for phylogenetics, encour-aging researchers to strive for better sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and use are available at https://physcraper.readthedocs.

The Tree of Life Web Project*

Zootaxa ◽  
2007 ◽  
Vol 1668 (1) ◽  
pp. 19-40 ◽  
Author(s):  
DAVID R. MADDISON ◽  
KATJA-SABINE SCHULZ ◽  
WAYNE P. MADDISON
Keyword(s):  
Current Knowledge ◽  
Tree Of Life ◽  
Scientific Content ◽  
Driven System ◽  
Open Access Database ◽  
History Of ◽  
Current Content ◽  
Life On Earth ◽  
Diversity Of Life ◽  
Analytical Tools

The Tree of Life Web Project (ToL) provides information on the Internet about our current knowledge of the evolutionary tree of life and associated information about characteristics and diversity of life on Earth. Development of this open-access, database-driven system began in 1994; its official release was in 1996. Core scientific content in the project is compiled collaboratively by more than 540 biologists, all experts in particular groups of organisms, from over 35 countries.  Additional learning materials are contributed by over 200 students, teachers, and amateur scientists, while images, movies, and sounds are contributed by both of these groups and over 200 media-only contributors. Administration of the project follows a hierarchical, community-based model, with authors for different parts of the ToL chosen by the scientists working in that particular field. The goals of the project are to document all species on Earth, as well as all significant clades; to provide basic information about the phylogeny of life; to share this information with other databases and analytical tools; and to encourage understanding and appreciation for biodiversity, evolution, and the interrelationships of Earth's wealth of species. Here we provide an outline of the goals and history of the project; the current content, administration, architecture, contributors, and audience, the challenges we have faced, and the future of the project.

scholarly journals Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luna L. Sánchez-Reyes ◽  
Martha Kandziora ◽  
Emily Jane McTavish
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Open Science ◽  
Tree Of Life ◽  
Matrix Assembly ◽  
Life Project ◽  
Character Matrix ◽  
Molecular Dataset ◽  
Phylogenetic Hypotheses

Abstract Background Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and non-specialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. Results Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. The program can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). Conclusion The Physcraper workflow showcases the benefits of doing open science for phylogenetics, encouraging researchers to strive for better scientific sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and usage are available at https://physcraper.readthedocs.io.

scholarly journals Zoological taxonomy at 250: showcasing species descriptions in the cyber era

Zootaxa ◽  
2008 ◽  
Vol 1671 (1) ◽  
pp. 1 ◽  
Author(s):  
ZHI-QIANG ZHANG
Keyword(s):  
Tree Of Life ◽  
The Internet ◽  
Publication Date ◽  
Official Publication ◽  
250Th Anniversary ◽  
Theory Of Evolution ◽  
Life On Earth ◽  
Diversity Of Life ◽  
Species Descriptions ◽  
The Way

January 1, 2008 marks the 250th anniversary of the official publication date of Systema Naturae (Linnaeus 1758)recognized by ICZN (1999). During the last two and a half centuries, Linnaeus (1758)’ system for naming, ranking andclassifying organisms has allowed us to document the pattern of life on Earth, Darwin (1850)’s theory of evolution hashelped us to understand the process how this diversity of life came about, and Hennig (1966)’s phylogeneticmethodology has enabled us reconstruct the tree of life. During the last two decades or so, the internet has dramaticallychanged the way we live and work. The rapid advances in bioinformatics have provided taxonomists unprecedentedopportunities to do their research more efficiently and make their findings more accessible. Cybertaxonomy is emergingas an exciting new branch of taxonomy (Wheeler 2007).

Phoronida

2017 ◽  
Author(s):  
Judith Fuchs
Keyword(s):  
Life Cycle ◽  
Small Group ◽  
Larval Stage ◽  
Intertidal Zone ◽  
Marine Invertebrates ◽  
Tree Of Life ◽  
General Morphology ◽  
Family Level ◽  
Planktonic Larval Stage

This chapter describes the taxonomy of Phoronida, a small group of exclusively marine invertebrates found in most of the world's oceans from the intertidal zone to about 400 metres depth. Phoronids are meroplanktonic with a planktonic larval stage usually less than 2 mm in length and a benthic adult whose length ranges from a few cm up to 50 cm. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Anellida: Holoplanktonic Polychaeta

2017 ◽  
Author(s):  
Claudia Castellani ◽  
Robert Camp
Keyword(s):  
Life Cycle ◽  
Marine Environment ◽  
Tree Of Life ◽  
General Morphology ◽  
Family Level

This chapter describes the taxonomy of Polychaeta, an almost exclusively marine group of organisms belonging to the phylum Annelida. With over 10,000 species described worldwide, they represent one of the most abundant animal taxa in the marine environment. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Crustacea: Euphausiacea

2017 ◽  
Author(s):  
Alistair J. Lindley
Keyword(s):  
Life Cycle ◽  
Tree Of Life ◽  
General Morphology ◽  
Family Level

This chapter describes the taxonomy of Euphausiacea, exclusively marine holoplanktonic crustaceans commonly known as krill. Although not highly diverse, with only two families and ~ 86 species worldwide, they are often a major component of the biomass of the plankton and micronekton of the world's oceans. This chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Crustacea: Lophogastrida and Mysida

2017 ◽  
Author(s):  
Claudia Castellani ◽  
Maiju Lehtiniemi ◽  
Kenneth Meland
Keyword(s):  
Life Cycle ◽  
Ballast Water ◽  
Water Systems ◽  
Tree Of Life ◽  
Brood Pouch ◽  
General Morphology ◽  
Family Level ◽  
Adaptive Nature

This chapter describes the taxonomy of Lophogastrida and Mysida, small shrimp-like crustaceans commonly known as ‘opossum shrimps’ because of the ventral brood pouch in the female. Because of their highly adaptive nature, they have progressively invaded new areas via new connections of water systems and through ballast water. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Crustacea: Ostracoda

2017 ◽  
Author(s):  
Martin V. Angel ◽  
Anthony W.G. John
Keyword(s):  
Life Cycle ◽  
Tree Of Life ◽  
General Morphology ◽  
Family Level ◽  
Oceanic Species

This chapter describes the taxonomy of Ostracoda, small bivalved crustaceans ranging in size from 0.2 to > 30 mm. The majority are benthic and belong to the subclass Podocopa. The chapter focuses on the holoplanktonic oceanic species. It covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

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