Evolution of Protein Molecules

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

/pdf/whole-genome-analyses-resolve-early-branches-in-the-tree-of-2wufsv5juy.pdf

Whole-genome analyses resolve early branches in the tree of life of modern birds

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

/pdf/phylotranscriptomic-analysis-of-the-origin-and-early-4cs38v80rr.pdf

Phylotranscriptomic analysis of the origin and early diversification of land plants

New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly sequenced genomes, detecting 157 erroneous labels, correcting 46 and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online.

/pdf/phylophlan-is-a-new-method-for-improved-phylogenetic-and-2irukwsujp.pdf

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http: //guidance.tau.ac.il.

/pdf/guidance2-accurate-detection-of-unreliable-alignment-regions-44f2okfkcg.pdf

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATe estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATe algorithm that improves upon SATe (which we now call SATe-I) in terms of speed and of phylogenetic and alignment accuracy. SATe-II uses a different divide-and-conquer strategy than SATe-I and so produces smaller more closely related subsets than SATe-I; as a result, SATe-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATe-I. Generally, SATe is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATe-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATe-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATe's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor model is uninformative in the worst possible sense. For all inputs, all trees optimize the likelihood score. Second, we show that a greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree can produce very poor alignments and trees. Therefore, the excellent performance of SATe-II and SATe-I is not because ML is used as an optimization criterion for choosing the best tree/alignment pair but rather due to the particular divide-and-conquer realignment techniques employed.

/pdf/sate-ii-very-fast-and-accurate-simultaneous-estimation-of-233hpywai5.pdf

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

Motivation: While phylogenetic analyses of datasets containing 1000–5000 sequences are challenging for existing methods, the estimation of substantially larger phylogenies poses a problem of much greater complexity and scale.

Methods: We present DACTAL, a method for phylogeny estimation that produces trees from unaligned sequence datasets without ever needing to estimate an alignment on the entire dataset. DACTAL combines iteration with a novel divide-and-conquer approach, so that each iteration begins with a tree produced in the prior iteration, decomposes the taxon set into overlapping subsets, estimates trees on each subset, and then combines the smaller trees into a tree on the full taxon set using a new supertree method. We prove that DACTAL is guaranteed to produce the true tree under certain conditions. We compare DACTAL to SATe and maximum likelihood trees on estimated alignments using simulated and real datasets with 1000–27 643 taxa.

Results: Our studies show that on average DACTAL yields more accurate trees than the two-phase methods we studied on very large datasets that are difficult to align, and has approximately the same accuracy on the easier datasets. The comparison to SATe shows that both have the same accuracy, but that DACTAL achieves this accuracy in a fraction of the time. Furthermore, DACTAL can analyze larger datasets than SATe, including a dataset with almost 28 000 sequences.

Availability: DACTAL source code and results of dataset analyses are available at www.cs.utexas.edu/users/phylo/software/dactal.

Contact: ude.saxetu.sc@ydnat

/pdf/dactal-divide-and-conquer-trees-almost-without-alignments-yokwquadwl.pdf

DACTAL: divide-and-conquer trees (almost) without alignments

Summary: PhamDB is a web application which creates databases of bacteriophage genes, grouped by gene similarity. It is backwards compatible with the existing Phamerator desktop software while providing an improved database creation workflow. Key features include a graphical user interface, validation of uploaded GenBank files, and abilities to import phages from existing databases, modify existing databases and queue multiple jobs. Availability and implementation: Source code and installation instructions for Linux, Windows and Mac OSX are freely available at https://github.com/jglamine/phage. PhamDB is also distributed as a docker image which can be managed via Kitematic. This docker image contains the application and all third party software dependencies as a pre-configured system, and is freely available via the installation instructions provided. Contact: snelesen@calvin.edu

/pdf/phamdb-a-web-based-application-for-building-phamerator-31fvmmjhes.pdf

PhamDB: a web-based application for building Phamerator databases

TSGL: A tool for visualizing multithreaded behavior

Multicore processors are now the standard CPU architecture, and parallel and distributed computing (PDC) is in the CS2013 core curriculum [9]. It is now the task of CS educators to begin creating pedagogical materials that will help their students understand PDC concepts. In this paper, we present TSGL (the thread-safe graphics library), a C++11 library that safely supports multithreaded graphics. We also present several multithreaded visualizations that illustrate how TSGL can be used to visualize the Parallel Loop design pattern, and present evidence that TSGL can improve student mastery of this parallel abstraction.

Serita M. Nelesen

Papers

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

DACTAL: divide-and-conquer trees (almost) without alignments

PhamDB: a web-based application for building Phamerator databases

TSGL: A tool for visualizing multithreaded behavior

Seeing Is Believing: Helping Students Visualize Multithreaded Behavior