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 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.

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 OpenTree: A Python package for Accessing and Analyzing data from the Open Tree of Life

2020 ◽  
Author(s):  
Emily Jane McTavish ◽  
Luna L Sanchez Reyes ◽  
Mark T. Holder
Keyword(s):  
Phylogenetic Trees ◽  
Tree Of Life ◽  
University Of California ◽  
Life Project ◽  
Application Programming ◽  
Service Application ◽  
The University ◽  
User Friendly ◽  
Programming Interfaces ◽  
Python Package

The Open Tree of Life project constructs a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the python package 'opentree', which provides a user friendly python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.

scholarly journals Synthesis of phylogeny and taxonomy into a comprehensive tree of life

2014 ◽  
Author(s):  
Cody Hinchliff ◽  
Stephen A Smith ◽  
James F Allman ◽  
J Gordon Burleigh ◽  
Ruchi Chaudhary ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Biological Diversity ◽  
Phylogenetic Reconstruction ◽  
Tree Of Life ◽  
Grand Challenge ◽  
Community Resources ◽  
Starting Point ◽  
Community Contribution ◽  
Fundamental Research ◽  
Digital Objects

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips -- the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: 1) a novel comprehensive global reference taxonomy; and 2) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. While data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

scholarly journals Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea

2021 ◽  
Author(s):  
Carolina A Martinez-Gutierrez ◽  
Frank O Aylward
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Tree Of Life ◽  
Marker Genes ◽  
Sequence Composition ◽  
Tree Construction ◽  
Taxonomic Groups ◽  
The Impact

Abstract Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, and many inter-phylum and inter-domain evolutionary relationships remain unclear. Here, we benchmark different marker genes often used in constructing multidomain phylogenetic trees of bacteria and archaea and present a set of marker genes that perform best for multidomain trees constructed from concatenated alignments. We use recently-developed Tree Certainty metrics to assess the confidence of our results and to obviate the complications of traditional bootstrap-based metrics. Given the vastly disparate number of genomes available for different phyla of bacteria and archaea, we also assessed the impact of taxon sampling on multidomain tree construction. Our results demonstrate that biases between the representation of different taxonomic groups can dramatically impact the topology of resulting trees. Inspection of our highest-quality tree supports the division of most bacteria into Terrabacteria and Gracilicutes, with Thermatogota and Synergistota branching earlier from these superphyla. This tree also supports the inclusion of the Patescibacteria within the Terrabacteria as a sister group to the Chloroflexota instead of as a basal-branching lineage. For the Archaea, our tree supports three monophyletic lineages (DPANN, Euryarchaeota, and TACK/Asgard), although we note the basal placement of the DPANN may still represent an artifact caused by biased sequence composition. Our findings provide a robust and standardized framework for multidomain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.

scholarly journals DNA Analyses Have Revolutionized Studies on the Taxonomy and Evolution in Birds

2021 ◽  
Author(s):  
Michael Wink
Keyword(s):  
Dna Sequences ◽  
Biochemical Markers ◽  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Tree Of Life ◽  
Marker Genes ◽  
Species Complexes ◽  
Systematic Relationships ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Whereas Linné aimed to classify all species of our planet by a unique binomial Latin name, later generations of taxonomists and systematicists intended to place the taxa in a natural system according to their phylogeny. This also happened in ornithology and still scientists are on the way to find the ultimate “Avian Tree of Life”. Formerly, systematic relationships were studied by comparing morphological characters. Since adaptive character evolution occurred frequently, convergences could lead to misleading conclusions. An alternative to morphological characters are biochemical markers, especially nucleotide sequences of marker genes or of complete genomes. They are less prone to convergent evolution. The use of DNA sequences of marker genes for bird systematics started around 1990. The introduction of Next Generation Sequencing (NGS) facilitated the sequence analysis of large parts of bird genomes and to reconstruct the Avian Tree of Life. The genetic analyses allowed the reconstruction of phylogenetic trees and the detection of monophyletic clades, which should be the base for a phylogenetic classification. In consequence, several orders, families and genera of birds had to be rearranged. In addition, a number of species was split into several new species because DNA data could point out hidden lineages in cryptic species or in species complexes.

Beyond Phylogeny Reconstruction—Tree-Based Analyses in Paleontology: Foreword

Paleobiology ◽  
2001 ◽  
Vol 27 (2) ◽  
pp. 187-187
Author(s):  
Lisa Park ◽  
Andrew. B. Smith
Keyword(s):  
Statistical Inference ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Phylogeny Reconstruction ◽  
Exact Methods ◽  
The Past ◽  
Tree Construction ◽  
Starting Point ◽  
Wide Range ◽  
Phylogenetic Hypotheses

The reconstruction of phylogenies using cladistic methods is a powerful and well-established tool for evolutionary biologists and paleobiologists. Indeed, the construction of rigorous phylogenetic hypotheses has become widely accepted as an essential first step in the analysis of historical patterns for both extant and extinct organisms. In the past few years, there has arisen a healthy and constructive debate as to the exact methods that will lead to the most accurate tree (for example whether statistical inference or stratigraphic information has any part to play in phylogenetic reconstruction). Although important, this debate has tended to focus on the problems of tree construction and divert attention away from the applications of tree-based research. The construction of a phylogeny is, after all, only a first step, and phylogenetic trees provide the starting point from which to address a wide range of interesting biological and geological topics.

scholarly journals Synthesis of phylogeny and taxonomy into a comprehensive tree of life

2015 ◽  
Vol 112 (41) ◽  
pp. 12764-12769 ◽  
Author(s):  
Cody E. Hinchliff ◽  
Stephen A. Smith ◽  
James F. Allman ◽  
J. Gordon Burleigh ◽  
Ruchi Chaudhary ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Biological Diversity ◽  
Phylogenetic Reconstruction ◽  
Tree Of Life ◽  
Grand Challenge ◽  
Community Resources ◽  
Starting Point ◽  
Community Contribution ◽  
Fundamental Research ◽  
Digital Objects

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

2014 ◽  
Vol 80 ◽  
pp. 54-65 ◽  
Author(s):  
Xiaoyan Zheng ◽  
Danying Cai ◽  
Daniel Potter ◽  
Joseph Postman ◽  
Jing Liu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees

A reassessment of apheloriine millipede phylogeny: additional taxa, Bayesian inference, and direct optimization (Polydesmida: Xystodesmidae)

Zootaxa ◽  
2007 ◽  
Vol 1610 (1) ◽  
pp. 27-39 ◽  
Author(s):  
PAUL E. MAREK ◽  
JASON E. BOND
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Bayes Factor ◽  
Appalachian Mountains ◽  
Deciduous Forests ◽  
Eastern United States ◽  
Undescribed Species ◽  
Direct Optimization ◽  
Species List ◽  
Phylogenetic Hypotheses

Millipedes in the tribe Apheloriini occur throughout the eastern United States, predominately in the deciduous forests of the Appalachian Mountains. Herein we present a reassessment of apheloriine millipede phylogeny using mitochondrial DNA sequences and an additional 29 exemplar taxa (including 15 undescribed species and all of the species in the genus Brachoria, except one). In this study, first we check the results of the previous phylogeny of the tribe (Marek and Bond, 2006) with different alignment and phylogenetic techniques (direct optimization and maximum likelihood), and second reconstruct a new phylogeny evaluating it in the same way with Bayesian, maximum likelihood, and direct optimization. Using this updated and expanded phylogeny, we tested historical classifications with Bayes factor and Shimodaira-Hasegawa hypothesis testing, consistently finding very strong evidence against their implied phylogenetic hypotheses. Lastly, using the new phylogeny as a foundation, we make taxonomic modifications and provide an updated species list of Apheloriini (106 species/17 genera).

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