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 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 Animating and exploring phylogenies with fibre plots

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2790
Author(s):  
William D. Pearse
Keyword(s):  
Short Review ◽  
Tree Of Life ◽  
Powerful Method ◽  
The World ◽  
Phylogenetic Hypotheses ◽  
Made In

Despite the progress that has been made in the visualisation of information since Haeckel's time, phylogenetic visualisation has moved forward remarkably little. In this brief essay, I give a short review of what I consider to be some recent major advances, and outline a new kind of phylogenetic visualisation. This new graphic, the fibre plot, uses the metaphor of sections through a tree to describe change in a phylogeny. As an animation, I suggest it is a powerful method to help interpret large phylogenetic hypotheses, although snapshots of it can also be displayed. As we enter the Anthropocene, I argue there has never been a greater need to know humanity's true place in the world, as depicted in the tree of life.

Ammonites phylogenetic analysis: state of the art and new prospects

2004 ◽  
Vol 175 (5) ◽  
pp. 507-512 ◽  
Author(s):  
Isabelle Rouget ◽  
Pascal Neigeet ◽  
Jean-Louis Dommergues
Keyword(s):  
Phylogenetic Reconstruction ◽  
Cladistic Analysis ◽  
Relative Weight ◽  
Morphological Characters ◽  
Quality Of Data ◽  
Phylogenetic Studies ◽  
Evolutionary Concepts ◽  
Phylogenetic Hypotheses ◽  
Definition Of ◽  
Iterative Evolution

Abstract Two main types of data are available to resolve phylogenies using fossils data: (1) stratigraphic ordering of taxa, and (2) morphological characters. In most phylogenetic studies dealing with ammonites, authors have given priority to the stratigraphic distribution of taxa. This practice is classically justified by the fact that the ammonite fossil record is frequently outstandingly good. In practice, the level of integration of stratigraphic and morphologic information in a single analysis depends on the confidence that authors have in the quality of data. Besides, many evolutionary concepts, which could differ over time and between authors (e.g. anagenesis, cladogenesis, iterative evolution), are added to these data to help infer phylogenetic relationships. As a result, phylogenetic hypotheses are based on eclectic methods which depend on the relative weight given to stratigraphic and morphologic information as well as on evolutionary concepts used. The validity of relationships proposed by previous authors is not dealt with in this paper. Instead, our goal is to draw attention to problems that these eclectic methods may cause, that is to say: (1) ammonites systematics is poorly formalised and (2) phylogenetic hypotheses as they are classically constructed are not rigorously testable. During the last 10 years, cladistic analysis has been applied to ammonites but is still unpopular among ammonitologists. However, studies have consistently shown that cladistics is not as unsuited a tool for ammonites phylogenetic reconstruction as is widely believed. Moreover, classical works open new questions about ammonite phylogeny and in particular, help to reappraise our view on the definition of morphological characters and their phylogenetic significance.

scholarly journals Phylogenetically informed spatial planning is required to conserve the mammalian tree of life

2017 ◽  
Vol 284 (1865) ◽  
pp. 20170627 ◽  
Author(s):  
Dan F. Rosauer ◽  
Laura J. Pollock ◽  
Simon Linke ◽  
Walter Jetz
Keyword(s):  
Conservation Planning ◽  
Phylogenetic Diversity ◽  
Informed Choice ◽  
Tree Of Life ◽  
Phylogenetic Information ◽  
Mammal Conservation ◽  
The Face ◽  
New Generation ◽  
The Impact ◽  
Effective Conservation

In the face of the current extinction crisis and severely limited conservation resources, safeguarding the tree of life is increasingly recognized as a high priority. We conducted a first systematic global assessment of the conservation of phylogenetic diversity (PD) that uses realistic area targets and highlights the key areas for conservation of the mammalian tree of life. Our approach offers a substantially more effective conservation solution than one focused on species. In many locations, priorities for PD differ substantially from those of a species-based approach that ignores evolutionary relationships. This discrepancy increases rapidly as the amount of land available for conservation declines, as does the relative benefit for mammal conservation (for the same area protected). This benefit is equivalent to an additional 5900 Myr of distinct mammalian evolution captured simply through a better informed choice of priority areas. Our study uses area targets for PD to generate more realistic conservation scenarios, and tests the impact of phylogenetic uncertainty when selecting areas to represent diversity across a phylogeny. It demonstrates the opportunity of using rapidly growing phylogenetic information in conservation planning and the readiness for a new generation of conservation planning applications that explicitly consider the heritage of the tree of life's biodiversity.

scholarly journals A synthetic phylogeny of freshwater crayfish: insights for conservation

2015 ◽  
Vol 370 (1662) ◽  
pp. 20140009 ◽  
Author(s):  
Christopher L. Owen ◽  
Heather Bracken-Grissom ◽  
David Stern ◽  
Keith A. Crandall
Keyword(s):  
Conservation Status ◽  
Iucn Red List ◽  
Tree Of Life ◽  
Rate Variation ◽  
Freshwater Crayfish ◽  
Life Project ◽  
Phylogenetic Studies ◽  
Taxonomic Framework ◽  
Status Data ◽  
Synthesis Approach

Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project ( opentreeoflife.org ) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts.

scholarly journals The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): assessing the potential causes and consequences

2021 ◽  
Author(s):  
Jadranka Rota ◽  
Victoria Gwendoline Twort ◽  
Andrea Chiocchio ◽  
Carlos Pena ◽  
Christopher W. Wheat ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Phylogenetics ◽  
Phylogenetic Signal ◽  
Tree Of Life ◽  
Amino Acid Sequences ◽  
Model Organisms ◽  
Compositional Bias ◽  
Sequencing Technologies ◽  
Phylogenetic Hypotheses ◽  
Phylogenomic Analyses

The field of molecular phylogenetics is being revolutionised with next-generation sequencing technologies making it possible to sequence large numbers of genomes for non-model organisms ushering us into the era of phylogenomics. The current challenge is no longer how to get enough data, but rather how to analyse the data and how to assess the support for the inferred phylogeny. We focus on one of the largest animal groups on the planet - butterflies and moths (order Lepidoptera). We clearly demonstrate that there are unresolved issues in the inferred phylogenetic relationships of the major lineages, despite several recent phylogenomic studies of the group. We assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein-coding genes and the alignment length over 290 000 base pairs, including 200 taxa representing 81% of lepidopteran superfamilies, we compare phylogenetic hypotheses inferred from amino acid and nucleotide alignments. The resulting two phylogenies are discordant, especially with respect to the placement of the superfamily Gelechioidea, which is likely due to compositional bias of both the nucleotide and amino acid sequences. With a series of analyses, we dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much of the lepidopteran tree of life. Overall, the results from the nucleotide alignment are more robust to the various perturbations of the data that we carried out. However, the lack of support for much of the backbone within Ditrysia makes the current butterfly and moth tree of life still unresolved. We conclude that taxon sampling remains an issue even in phylogenomic analyses, and recommend that poorly sampled highly diverse groups, such as Gelechioidea in Lepidoptera, should receive extra attention in the future.

scholarly journals An updated checklist of the lichens of St. Eustatius, Netherlands Antilles

MycoKeys ◽  
2018 ◽  
Vol 33 ◽  
pp. 69-84 ◽  
Author(s):  
Andre Aptroot ◽  
Michael Stech
Keyword(s):  
Molecular Identification ◽  
Dna Sequences ◽  
Species Level ◽  
Lichen Species ◽  
Vegetation Types ◽  
Netherlands Antilles ◽  
Phylogenetic Studies ◽  
Biodiversity Inventory ◽  
Unidentified Species ◽  
Chemical Characters

In the course of a multi-taxon biodiversity inventory for the island of St. Eustatius, lichens were collected from 11 plots representing different vegetation types. From these collections, 126 lichen species are reported, 54 of which are new reports for St. Eustatius. Most species could be identified to species level based on morphological and chemical characters. In a few cases, mtSSU DNA sequences were generated for a preliminary molecular identification and future phylogenetic studies. In total, 263 identified lichen species are currently known from St. Eustatius, as well as some additional genera with yet unidentified species and lichenicolous fungi.

scholarly journals Nurturing a sustainable Open Tree of Life

2018 ◽  
Vol 2 ◽  
pp. e25727
Author(s):  
Emily Jane McTavish ◽  
Mark Holder ◽  
Karen Cranston
Keyword(s):  
Community Engagement ◽  
Evolutionary History ◽  
Tree Of Life ◽  
Collaborative Effort ◽  
Biodiversity Data ◽  
Phylogenetic Information ◽  
Life Project ◽  
Analysis Tools ◽  
Ready Access

The Open Tree of Life project is a collaborative effort to synthesize, share and update a comprehensive tree of life Fig. 1. We have completed a draft synthesis of a tree summarizing digitally available taxonomic and phylogenetic knowledge for all 2.6 million named species, available at tree.opentreeoflife.org Hinchliff et al. 2015. . . This tree provides ready access to phylogenetic information which can link together biodiversity data on the basis of what we know about relevant evolutionary history. Both the unified reference taxonomy Rees and Cranston 2017 and the published phylogenetic statements underlying the tree McTavish et al. 2015 are available and accessible online. Taxa in the phylogenies are mapped to the the reference taxonomy, which aligns Open Tree taxon identifiers to those from NCBI and GBIF, among several other taxonomy resources. The synthesis tree is revised as new data become available, and captures conflict and consensus across different published phylogenetic estimates. This undertaking requires both development of novel infrastructure and analysis tools, as well as community engagement with the Open Tree of Life project. I will discuss the challenges in and the progress towards achieving these goals.

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 A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

2021 ◽  
Author(s):  
Graeme T Lloyd ◽  
Graham J Slater
Keyword(s):  
Phylogenetic Trees ◽  
Species Level ◽  
Total Group ◽  
Phylogenetic Studies ◽  
Large Numbers ◽  
Extant Species ◽  
Molecular Phylogenies ◽  
Phylogenetic Hypotheses ◽  
Fossil Data ◽  
Rapid Radiations

Abstract Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.

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