The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses. An update to the ‘tree of life’ has revealed a dominance of bacterial diversity in many ecosystems and extensive evolution in some branches of the tree. It also highlights how few organisms we have been able to cultivate for further investigation.

/pdf/a-new-view-of-the-tree-of-life-wba2fdxtwo.pdf

A new view of the tree of life

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

/pdf/draft-genome-sequence-of-chickpea-cicer-arietinum-provides-a-4mz3tdzdg6.pdf

Draft genome sequence of chickpea ( Cicer arietinum ) provides a resource for trait improvement

To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria.

http://science.sciencemag.org/content/sci/339/6120/662.full.pdf

The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals

The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group. An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135-130 million yr ago (Ma); Pentapetalae is 126-121 Ma; and Rosidae (123-115 Ma) preceded Asteridae (119-110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma. This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13264

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.

/pdf/recovery-of-genomes-from-metagenomes-via-a-dereplication-p46rhshwuu.pdf

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.

Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).

/pdf/creating-the-cipres-science-gateway-for-inference-of-large-nmwbumhj3p.pdf

Creating the CIPRES Science Gateway for inference of large phylogenetic trees

The CIPRES Science Gateway (CSG) provides researchers and educators with browser-based access to community codes for inference of phylogenetic relationships from DNA and protein sequence data. The CSG allows users to deploy jobs on the high-performance computers of the TeraGrid without requiring detailed knowledge of their complexities. Use of the CSG has grown rapidly; through March 2011 it had more than 2,200 users and enabled more than 180 peer-reviewed publications. The rapid growth in resource consumption was accommodated by deploying codes on Trestles, a new TeraGrid computer. Tools and policies were developed to insure efficient and effective resource use. This paper describes progress in managing the growth of this public cyberinfrastructure resource and reviews the domain science that it has enabled.

The CIPRES science gateway: a community resource for phylogenetic analyses

The CIPRES Science Gateway is a community web application that provides public access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. These resources are made available at no charge to users by the NSF Extreme Science and Engineering Discovery Environment (XSEDE) project. Here we describe the CIPRES RESTful application programmer interface (CRA), a web service that provides programmatic access to all resources and services currently offered by the CIPRES Science Gateway. Software developers can use the CRA to extend their web or desktop applications to include the ability to run MrBayes, BEAST, RAxML, MAFFT, and other computationally intensive algorithms on XSEDE. The CRA also makes it possible for individuals with modest scripting skills to access the same tools from the command line using curl, or through any scripting language. This report describes the CRA and its use in three web applications (Influenza Research Database – www.fludb.org, Virus Pathogen Resource – www.viprbrc.org, and MorphoBank – www.morphobank.org). The CRA is freely accessible to registered users at https://cipresrest.sdsc.edu/cipresrest/v1; supporting documentation and registration tools are available at https://www.phylo.org/restusers.

/pdf/a-restful-api-for-access-to-phylogenetic-tools-via-the-5bjclodndh.pdf

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway

The CIPRES Science Gateway (CSG) provides browser-based access to computationally demanding phylogenetic codes run on large HPC resources. Since its release in December 2009, there has been a sustained, near-linear growth in the rate of CSG use, both in terms of number of users submitting jobs each month and number of jobs submitted. The average amount of computational time used per month by CSG increased more than 5-fold since its initial release. As of April 2012, more than 4,000 unique users have run parallel tree inference jobs on TeraGrid/XSEDE resources using the CSG. The steady growth in resource use suggests that the CSG is meeting an important need for computational resources in the Systematics/Evolutionary Biology community.To ensure that XSEDE resources accessed through the CSG are used effectively, policies for resource consumption were developed, and an advanced set of management tools was implemented. Studies of usage trends show that these new management tools helped in distributing XSEDE resources across a large user population that has low-to-moderate computational needs.In the first quarter of 2012, 30% of all active XSEDE users accessed computational resources through the CSG, while the analyses conducted by these users accounted for 0.7% of all allocable XSEDE computational resources. User survey results showed that the easy access to XSEDE/TeraGrid resources through the CSG had a critical and measurable scientific impact: at least 300 scholarly publications spanning all major groups within the Tree of Life have been enabled by the CSG since 2009. The same users reported that 82% of these publications would not have been possible without access to computational resources available through the CSG. The results indicate that the CSG is a critical and cost-effective enabler of science for phylogenetic researchers with limited resources.

/pdf/the-cipres-science-gateway-enabling-high-impact-science-for-2yidk2egzn.pdf

The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources

A colorimeter is provided that senses the presence of a contaminant opaque to light of a specific color which is carried in a fluid flowstream. As the flowstream passes through the colorimeter, a photocell on one side of the flowstream is illuminated only by light of the specific color which originates on the opposite side of the flowstream, the photocell sensing a change in intensity of transmitted light caused by presence of the contaminant.

Terri Schwartz

Papers

Creating the CIPRES Science Gateway for inference of large phylogenetic trees

The CIPRES science gateway: a community resource for phylogenetic analyses

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway

The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources

Colorimeter for detecting blood leaks in an artificial kidney machine