Estimates Of Evolutionary Relationships Research Articles

Updating splits, lumps, and shuffles: Reconciling GenBank names with standardized avian taxonomies

Abstract Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequences from around the globe. Yet, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have required widespread scientific name changes. Taxonomic instability, colloquially “splits, lumps, and shuffles,” presents logistical challenges to large-scale biodiversity research because (1) the same species or sets of populations may be listed under different names in different data sources, or (2) the same name may apply to different sets of populations representing different taxonomic concepts. Consequently, distributional and trait data are often difficult to link directly to primary DNA sequence data without extensive and time-consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize avian taxon names in use in NCBI GenBank, a primary source of genetic data, to a widely used and regularly updated avian taxonomy: eBird/Clements. Of 14,341 avian species/subspecies names in GenBank, 11,031 directly matched an eBird/Clements; these link to more than 6 million nucleotide sequences. For the remaining unmatched avian names in GenBank, we used Avibase’s system of taxonomic concepts, taxonomic descriptions in Cornell’s Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names linked to more than 600,000 nucleotide sequences, ~9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under 2 or more GenBank names. Our taxonomic reconciliation is a first step towards rigorous and open-source curation of avian GenBank sequences and is available at GitHub, where it can be updated to correspond to future annual eBird/Clements taxonomic updates.

Evolution of drug resistance in HIV protease

BackgroundDrug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of therapy. These techniques can also be used to identify protease mutants for experimental studies of resistance and thereby assist in the development of next-generation therapies. Few studies, however, have assessed the evolution of resistance from genotype–phenotype data.ResultsThe machine learning produced highly accurate and robust classification of resistance to HIV protease inhibitors. Genotype data were mapped to the enzyme structure and encoded using Delaunay triangulation. Estimates of evolutionary relationships, based on this encoding, and using Minimum Spanning Trees, showed clusters of mutations that closely resemble the wild type. These clusters appear to evolve uniquely to more resistant phenotypes.ConclusionsUsing the triangulation metric and spanning trees results in paths that are consistent with evolutionary theory. The majority of the paths show bifurcation, namely they switch once from non-resistant to resistant or from resistant to non-resistant. Paths that lose resistance almost uniformly have far lower levels of resistance than those which either gain resistance or are stable. This strongly suggests that selection for stability in the face of a rapid rate of mutation is as important as selection for resistance in retroviral systems.

Six additional mitochondrial genomes for North American nightsnakes (Dipsadidae: Hypsiglena) and a novel gene feature for advanced snakes

The North American nightsnakes in the genus Hypsiglena is composed of nine named and at least two unnamed species. Here, we provide the first mt-genome of H. affinis, an additional mt-genome for H. sp. nov. 1, and four additional mt-genomes from the widespread H. jani. These mtDNA genomes were sequenced using both Illumina and Ion Torrent sequencing technologies. The resulting genomes contained the expected 13 protein coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions typical of colubroid snakes. Two of the H. jani samples had partial tRNAIle genes upstream of CR2 which has not been previously documented in colubroid snakes. A maximum likelihood gene-tree based on these data combined with previously published sequence data recovers a well-supported phylogeny and is in concordance with previous estimates of evolutionary relationships in this group.

The dawn of open access to phylogenetic data.

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation – extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Importantly, our survey spans recent policy initiatives and infrastructural changes; our analyses indicate that the positive impact of these community initiatives has been both dramatic and immediate. Although the results of our study indicate that the situation is dire, our findings also reveal tremendous recent progress in the sharing and preservation of phylogenetic data.

The compatibility of stratigraphic and comparative constraints on estimates of ancestor‐descendant relations

Palaeontologists have routinely used the temporal order of rock strata in which fossils are found (stratigraphy), in conjunction with comparative data, to help to estimate which species (or other evolutionary units) were the ancestors of others. The use of stratigraphy has been challenged in recent decades on the grounds that it does not accurately represent the time spans during which the species represented by fossils were extant. It is not the purpose of this paper to engage in this debate, but instead to present methods for exploring whether or not and to what extent comparative data and stratigraphy might logically contradict each other. If stratigraphy did reliably indicate the absolute or relative past time spans during which each of the species under study were extant, then some formally possible estimates of evolutionary relationships would become historically impossible, and some well known concepts concerning the compatibility of comparative data would no longer apply. Here we present new ways of assessing the compatibility of stratigraphy with comparative data, and illustrate these methods by re‐analysis of some previously published work.

Phylogenetic Relationships in Fagales Based on DNA Sequences from Three Genomes

Nucleotide sequences of six regions from three plant genomes—trnL‐F, matK, rbcL, atpB (plastid), matR (mtDNA), and 18S rDNA (nuclear)—were used to analyze inter‐ and infrafamilial relationships of Fagales. All 31 extant genera representing eight families of the order were sampled. Congruence among data sets was assessed using the partition homogeneity test, and five different combined data sets were analyzed using maximum parsimony and the Bayesian approach. At the familial level, the same phylogenetic relationships were inferred from five different analyses of these data. Nothofagus, followed by Fagaceae, are subsequent sisters to the rest of the order. Fagaceae are then sister to the core “higher” hamamelids, which consist of two main subclades, one being Myricaceae (Rhoipteleaceae (Juglandaceae)) and the other Casuarinaceae (Ticodendraceae (Betulaceae)). The combined data sets provide the best‐supported estimate of evolutionary relationships within Fagales. Our results suggest that the combination of d...

An Estimate of Phylogenetic Relationships within the Genus Crusea (Rubiaceae) Using Character Compatibility Analysis

The seventeen taxa (thirteen species and four varieties) in the genus Crusea, as recognized by W. R. Anderson, are described with fifty-eight qualitative characters. A priori estimates of the directions of evolutionary trends among the character states of each character are made. The patterns of agreement and disagreement among these fifty-eight cladistic characters were revealed using Character Compatibility analysis. A large collection of mutually compatible characters was chosen to form the basis foran estimate of phylogenetic r-elationships. This estimate was then further refined within the major phyletic lines suggested, by fur-ther studying the patterns of agreement among characters within these lines to enlarge the collection of mutually compatible characters with compatible secondary characters. Finally, characters of special interest such as annual vs. perennial, and flower color are discussed in the context of this estimate of phylogenetic relationships. The estimation of evolutionary relationships has long been a part of comparative biology. Recently, the interest of plant systematists in meeting this challenge has increased. Takhtajan (1969), Boulter et al. (1972), and Sporne (1975) provide three recent examples of estimates of evolutionary relationships for the angiosperms as a whole. Examples at the level of genus or family (except as suggested by the recognition of sections, subfamilies etc.) are not yet common. This is perhaps explained in part by our realization that such estimates usually contain a large component of uncertainty. Indeed, Hughes (1976) argues that estimates based on neobotanical data are nearly worthless. In contrast, we feel that the best estimate of a specialist may be better than no estimate at all, especially when the data, principles, and procedures with which this estimate was achieved are clearly presented. Several principles and procedures for estimating evolutionary relationships have been presented and discussed in the recent literature. Some of these are explained by Estabrook (this volume) and reviewed by Funk and Stuessy (this number). Here we wish to provide an example of the application of compatibility analysis to the estimation of evolutionary relationships among the taxa of the genus Crusea. A technical explanation of the procedures is given by Estabrook (et al. 1975, 1976a, b), an application in zoology is presented by Estabrook et al. (1977), and other related discussions are made by McMorris (1975, 1977) and Estabrook and McMorris (1977). l University Her-barium and Botany, University of Michigan, Ann Arbor, MI 48109.