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Journal ArticleDOI

Evolutionary informatics: unifying knowledge about the diversity of life

TLDR
The field of evolutionary informatics has matured into a robust discipline that is developing the conceptual, infrastructure and community frameworks for meeting this grand challenge of creating a linked system of all evolutionary data, information and knowledge organized around Darwin's ever-growing Tree of Life.
Abstract
The accelerating growth of data and knowledge in evolutionary biology is indisputable. Despite this rapid progress, information remains scattered, poorly documented and in formats that impede discovery and integration. A grand challenge is the creation of a linked system of all evolutionary data, information and knowledge organized around Darwin's ever-growing Tree of Life. Such a system, accommodating topological disagreement where necessary, would consolidate taxon names, phenotypic and geographical distributional data across clades, and serve as an integrated community resource. The field of evolutionary informatics, reviewed here for the first time, has matured into a robust discipline that is developing the conceptual, infrastructure and community frameworks for meeting this grand challenge.

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Citations
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Journal Article

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

TL;DR: FastTree as mentioned in this paper uses sequence profiles of internal nodes in the tree to implement neighbor-joining and uses heuristics to quickly identify candidate joins, then uses nearest-neighbor interchanges to reduce the length of the tree.
Journal ArticleDOI

Can We Name Earth's Species Before They Go Extinct?

TL;DR: It is argued that the number of species on Earth today is 5 ± 3 million, of which 1.5 million are named, and practical actions are proposed to improve taxonomic productivity and associated understanding and conservation of biodiversity.
Journal ArticleDOI

Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

Conrad L. Schoch, +101 more
- 30 Jun 2014 - 
TL;DR: A set of standards and protocols are proposed to improve the data quality of new sequences, and it is suggested how type and other reference sequences can be used to improve identification of Fungi.
Journal ArticleDOI

rfishbase: exploring, manipulating and visualizing FishBase data from R.

TL;DR: A direct, scriptable interface to FishBase data enables better discovery and integration essential for large-scale comparative analyses, and can be integrated into phylogenetics packages such as ape and geiger.
Journal ArticleDOI

A framework for using niche models to estimate impacts of climate change on species distributions

TL;DR: This work states that for the vast majority of species, correlative approaches are the most feasible avenue for building niche models and follows critical principles for selecting predictor variables and occurrence data, demonstrating effective performance in prediction across space, and extrapolating into nonanalog conditions.
References
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Journal ArticleDOI

Gene Ontology: tool for the unification of biology

TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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FastTree 2--approximately maximum-likelihood trees for large alignments.

TL;DR: Improvements to FastTree are described that improve its accuracy without sacrificing scalability, and FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments.
Book

On the Origin of Species by Means of Natural Selection, or, The Preservation of Favoured Races in the Struggle for Life

TL;DR: The "Penguin Classics" edition of "On the Origin of Species" as discussed by the authors contains an introduction and notes by William Bynum, and features a cover designed by Damien Hirst.
Journal ArticleDOI

A Rapid Bootstrap Algorithm for the RAxML Web Servers

TL;DR: This work developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms and can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses.
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