The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
Systematic Biology (Impact Factor: 14.39). 07/2008; 57(3):335-46. DOI: 10.1080/10635150802158688
Source: PubMed


As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (, which offers a view of GenBank tailored for molecular phylogenetics. The first release of the Browser is computed from 2.6 million sequences representing the taxonomically enriched subset of GenBank sequences for eukaryotes (excluding most genome survey sequences, ESTs, and other high-throughput data). In addition to summarizing sequence diversity and species diversity across nodes in the NCBI taxonomy, it reports 87,000 potentially phylogenetically informative clusters of homologous sequences, which can be viewed or downloaded, along with provisional alignments and coarse phylogenetic trees. At each node in the NCBI hierarchy, the user can display a "data availability matrix" of all available sequences for entries in a subtaxa-by-clusters matrix. This matrix provides a guidepost for subsequent assembly of multigene data sets or supertrees. The database allows for comparison of results from previous GenBank releases, highlighting recent additions of either sequences or taxa to GenBank and letting investigators track progress on data availability worldwide. Although the reported alignments and trees are extremely approximate, the database reports several statistics correlated with alignment quality to help users choose from alternative data sources.

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    • "We mined GenBank for all available bat mitochondrial and nuclear sequences, utilizing scripts that automated sequence identification, cleaning, and alignment, and generally followed the supermatrix approaches of Hinchcliff and Roalson (2013) and Zanne et al. (2014). We first used the PhyLoTa Browser (Sanderson et al. 2008) to identify all loci sequenced for at least 20 unique bat species within GenBank release 194. We then downloaded the entire national center for biotechnology information (NCBI) SQLite3 database of Chiroptera nucleotide data using the program PHLAWD (Smith et al. 2009). "
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    ABSTRACT: Species richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference, we assemble a time-calibrated, species-level phylogeny using a supermatrix of mitochondrial and nuclear sequence data. We analyze the phylogeny using a Bayesian method for modeling complex evolutionary dynamics. Surprisingly, we find that variation in family richness can largely be explained without invoking heterogeneous diversification dynamics. We document only a single well-supported shift in diversification dynamics across bats, occurring at the base of the subfamily Stenodermatinae. Bat diversity is phylogenetically imbalanced, but - contrary to previous hypotheses - this pattern is unexplained by any simple patterns of diversification rate heterogeneity. This discordance may indicate that diversification dynamics are more complex than can be captured using the statistical tools available for modeling data at this scale. We infer that bats as a whole are almost entirely united into one macroevolutionary cohort, with decelerating speciation through time. There is also a significant relationship between clade age and richness, suggesting that global bat diversity may still be expanding. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Evolution 05/2015; 69(6). DOI:10.1111/evo.12681 · 4.61 Impact Factor
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    • "Our dataset was assembled using the PhyLoTA browser release 1.5 (Sanderson et al., 2008). A total of five mitochondrial (cytochrome b – cytb, cytochrome oxidase I – coxI, NADH dehydrogenase subunit 2 – nd2, and ribosomal 12S and 16S) and four nuclear (myoglobin exons 2 and 3 – myo, ornithine decarboxylase exons 6 through 8 – odc, and the recombination-activating protein genes 1 and 2 – rag1, rag2) genes were selected. "
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    ABSTRACT: In this study, we present a detailed family-level phylogenetic hypothesis for the largest avian order (Aves: Passeriformes) and an unmatched multi-calibrated, relaxed clock inference for the diversification of crown passerines. Extended taxon sampling allowed the recovery of many challenging clades and elucidated their position in the tree. Acanthisittia appear to have diverged from all other passerines at the early Paleogene, which is considerably later than previously suggested. Thus, Passeriformes may be younger and represent an even more intense adaptive radiation compared to the remaining avian orders. Based on our divergence time estimates, a novel hypothesis for the diversification of modern Suboscines is proposed. According to this hypothesis, the first split between New and Old World lineages would be related to the severing of the Africa-South America biotic connection during the mid-late Eocene, implying an African origin for modern Eurylaimides. The monophyletic status of groups not recovered by any subsequent study since their circumscription, viz. Sylvioidea including Paridae, Remizidae, Hyliotidae, and Stenostiridae; and Muscicapoidea including the waxwing assemblage (Bombycilloidea) were notable topological findings. We also propose possible ecological interactions that may have shaped the distinct Oscine distribution patterns in the New World. The insectivorous endemic Oscines of the Americas, Vireonidae (Corvoidea), Mimidae, and Troglodytidae (Muscicapoidea), probably interfered with autochthonous Suboscines through direct competition. Thus, the Early Miocene arrival of these lineages before any other Oscines may have occupied the few available niches left by Tyrannides, constraining the diversification of insectivorous Oscines that arrived in the Americas later. The predominantly frugivorous-nectarivorous members of Passeroidea, which account for most of the diversity of New World-endemic Oscines, may not have been subjected to competition with Tyrannides. In fact, the vast availability of frugivory niches combined with weak competition with the autochthonous passerine fauna may have been crucial for passeroids to thrive in the New World. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 03/2015; DOI:10.1016/j.ympev.2015.03.018 · 3.92 Impact Factor
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    • "We used the PhyLoTa browser version 1.5 (Sanderson et al. 2008), based on GenBank release 194 (15 February 2013) to determine which among the nuclear and mitochondrial genes commonly used in vertebrate phylogenetics included the highest number of sphyraenid species. Sequences for 16, 13 and nine species were available in GenBank (as of March 2014) for the mitochondrial markers cox1, Cytb, and 16s, respectively, with no other gene being available for more than four species. "
    Italian Journal of Zoology 01/2015; 82(1):133-142. · 0.79 Impact Factor
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