Field Of Molecular Systematics Research Articles

Phylogenetic relationships of Burmeistera (Campanulaceae: Lobelioideae): Combining whole plastome with targeted loci data in a recent radiation

The field of molecular systematics has benefited greatly with the advent of high-throughput sequencing (HTS), making large genomic datasets commonplace. However, a large number of targeted Sanger sequences produced by many studies over the last two decades are publicly available and should not be overlooked. In this study, we elucidate the phylogenetic relationships of the plant genus Burmeistera (Campanulaceae: Lobelioideae), while investigating how to best combine targeted Sanger loci with HTS data. We sequence, annotate, and analyze complete to nearly complete plastomes for a subset of the genus. We then combine these data with a much larger taxonomic dataset for which only Sanger sequences are available, making this the most comprehensively sampled study in the genus to date. We show that using a phylogeny inferred from the species with plastome data as a topological constraint for the larger dataset increases the resolution of our data and produces a more robust evolutionary hypothesis for the group. We then use the resulting phylogeny to study the evolution of morphological traits thought to be important in Burmeistera, and assess their usefulness in the current taxonomic classification of the genus. The main morphological character used to delimit subgeneric sections, the presence or absence of hairs on the apex of the two ventral anthers, shows a complex evolutionary history with many changes in the tree, suggesting that this character should not be used for taxonomic classification. Although it is too soon to propose a new subgeneric classification for Burmeistera, our results highlight some morphological traits shared by whole clades that could potentially be used in future taxonomic work.

Improved Harmonic Mean Estimator for Phylogenetic Model Evidence

Bayesian phylogenetic methods are generating noticeable enthusiasm in the field of molecular systematics. Many phylogenetic models are often at stake, and different approaches are used to compare them within a Bayesian framework. The Bayes factor, defined as the ratio of the marginal likelihoods of two competing models, plays a key role in Bayesian model selection. We focus on an alternative estimator of the marginal likelihood whose computation is still a challenging problem. Several computational solutions have been proposed, none of which can be considered outperforming the others simultaneously in terms of simplicity of implementation, computational burden and precision of the estimates. Practitioners and researchers, often led by available software, have privileged so far the simplicity of the harmonic mean (HM) estimator. However, it is known that the resulting estimates of the Bayesian evidence in favor of one model are biased and often inaccurate, up to having an infinite variance so that the reliability of the corresponding conclusions is doubtful. We consider possible improvements of the generalized harmonic mean (GHM) idea that recycle Markov Chain Monte Carlo (MCMC) simulations from the posterior, share the computational simplicity of the original HM estimator, but, unlike it, overcome the infinite variance issue. We show reliability and comparative performance of the improved harmonic mean estimators comparing them to approximation techniques relying on improved variants of the thermodynamic integration.

Application of molecular methods to classification and identification of bacteria of the genus Bifidobacterium

The molecular methods currently used in the classification and identification of bifidobacteria are reviewed. The sequencing of the 16S rRNA gene and some other genes considered to be phylogenetic markers is a universal and effective approach for taxonomic characterization of members of the genus Bifidobacterium and to reliable identification of new isolates. Various techniques of obtaining DNA fingerprints (PFGE, RAPD, rep-PCR) are widely used for solving particular problems in identifying bifidobacteria. Bacteria of the genus Bifidobacterium are important organisms in biotechnology and medicine. The research in the field of molecular systematics of bifidobacteria provides a basis not only for the solution of taxonomic problems, but also for monitoring of individual species in the environment and for more detailed study of the genetics and ecology of this group of microorganisms.

Phylogenetic relationships among Nearctic shrews of the genus Sorex (Insectivora, Soricidae) inferred from combined cytochrome b and inter-SINE fingerprint data using Bayesian analysis

The field of molecular systematics has relied heavily on mitochondrial DNA (mtDNA) analysis since its inception. Despite the obvious utility of mtDNA, such data inevitably only presents a limited (i.e., single genome) perspective on species evolution. A combination of mitochondrial and nuclear markers is essential for reconstructing more robust phylogenetic trees. To evaluate the utility of one category of nuclear marker (short interspersed elements or SINEs) for resolving phylogenetic relationships, we constructed an inter-SINE fingerprint for nine putative species of the genus Sorex. In addition, we analyzed 1011 nucleotides of the cytochrome b gene. Traditional neighbor-joining and maximum parsimony analyses were applied to the individual cytochrome b and inter-SINE fingerprint data sets, along with Bayesian analysis to the combined data sets. We found inter-SINE fingerprinting to be an effective species level marker; however, we were unable to reconstruct deeper branching patterns within the Sorex genus using these data. The combined data analyzed under a Bayesian analysis showed higher levels of structuring within the Otisorex subgenus, most notably recognizing a monophyletic group consisting of sister-taxa S. palustris and S. monticolus, S. cinereus and S. haydeni, and S. hoyi. An additional noteworthy result was the detection of an historic mitochondrial introgression event between S. monticolus and S. palustris. When combining disparate data sets, we emphasize researcher diligence as certain types of data and processes may overly influence the analysis. However, there is considerable phylogenetic potential stemming from inter-SINE fingerprinting.

Morphology in the contemporary landscape of systematics: learning from the trilobite

Fossils, Phylogeny, and Form: An Analytical Approach. Edited by Jonathan M. Adrain, Gregory D. Edgecombe, and Bruce S. Lieberman. Kluwer Academic/Plenum Press, New York. 2001. 402 pages. Cloth $130.00. ### Morphological Characters and Contemporary Systematics Circumscribing morphological characters in contemporary systematics research, and doing this with efficiency on a large scale, is a topic of paramount importance to practicing systematists. The enormous infusion of data from the relatively young field of molecular systematics has transformed the entire landscape of systematics research because thousands of molecular sequence characters can be generated quickly, efficiently, and with little ambiguity. This facilitates the rapid growth of enormous molecular sequence data matrices. Although most morphological systematists employ modern methods of phylogenetic analysis, the mechanics of collecting morphological data (which present a variety of complex problems) have not been transformed to keep pace with the developments in molecular systematics. Morphological data remain difficult to collect, hard to convert to discrete characters, and poorly archived. There remains, for example, no morphological equivalent of GenBank, the public-access molecular sequence database that systematists use to deposit and retrieve raw data. Without equivalent infrastructural support, many morphological systematists find themselves recollecting data that have been published only as text descriptions and often publishing their own work without thoroughly documenting their characters through labeled illustrations. Morphological systematics thereby advances relatively slowly. That morphological data (and by this I mean any phenotypic character) should be included in phylogenetic analysis is not in serious dispute. The need to include such data is subsumed by arguments that more data are better than fewer data (Kluge 1989; Nixon and Carpenter 1996) when reconstructing phylogeny, and each year combined analyses of fossils, extant taxa, and molecular and phenotypic data appear. However, until morphological matrices can come to include the hundreds or thousands of characters necessary to describe an organism's phenotype, collected …

In Memoriam: Charles Gald Sibley, 1917-1998

Charles Gald Sibley was born in Fresno, California, on 7 August 1917; he died at age 80 in Santa Rosa, California. He was no small town boy who simply moved upstate, however. Between his early years in Fresno and his ultimate move to Santa Rosa, Charles traveled the world to conduct and report on his research, and he rose to prominence in the scientific community. He became one of the leading ornithologists during the last half of the 20th century, was one of the founders and a major player in the emerging field of molecular systematics, and contributed significantly to our knowledge of the evolutionary relationships

DNA Sequence Data in Phylogeny Reconstruction: An Overview of Techniques and Analyses

DNA Sequence Data in Phylogeny Reconstruction: An Overview of Techniques and Analyses

Continuous Track Analysis: A New Phylogenetic and Biogeographic Method

Continuous track analysis (CTA) can depict reticulate evolutionary patterns in phylogenetics and biogeography. A reticulate connection implies convergence, hybridization, or introgression in an evolutionary graph of taxa and implies dispersal in an evolutionary graph of biogeographic areas. CTA finds graphs that (1) have a minimal number of connections and (2) imply that most character states or taxa have distributions or tracks across taxa or areas (objects) that are continuous, i.e., can be traced across the connections among the objects including that state without traveling through any other objects. Continuous tracks imply either that character states in phylogenies have unique evolutionary origins or that taxa in biogeographic analyses are monophyletic. Relatively simple graphs usually cannot imply completely continuous tracks. There? fore, CTA graphs seek to minimize the number of track fragments, which are locally continuous parts of a track; tracks with more than one fragment are discontinuous. Minimizing fragments is the same as minimizing character-state transitions only if there are no reticulations. Because hy? pothetical ancestors do little to reduce the number of fragments, CTA tends to place known taxa or areas at internal nodes. A heuristic algorithm analogous to tree bisection-reconnection is used to find highly parsimonious CTA graphs. In phylogenetic analyses, CTA employs a special com? plementary binary coding convention that serendipitously solves the missing characters/missing data problem. Although the problem of ancestors inheriting states from hybrid descendants is irrelevant if reticulations merely represent convergence patterns, CTA includes an optional algo? rithm that avoids such instances by explicitly identifying ancestors and descendants. CTA was compared with standard parsimony analysis using a data set of 17 Neogene species of North American fossil hipparionine horses. CTA separates the three major clades and illustrates their convergent features with reticulations, whereas standard parsimony analysis groups the three in an unresolved polytomy. CTA also minimizes the number of hypothetical, unsampled ancestors and lineages. [Ancestors; biogeographic methods; dispersal; homology; Hipparionini; hybridiza? tion; phylogenetic methods; reticulation.] Reticulate evolution and biogeographic dispersal are two of evolutionary biology's greatest methodological puzzles. In this paper, a new means of analyzing the pat? terns created by either of these superficial? ly dissimilar processes is introduced. A unified approach is possible because both reticulating phylogenetic hypotheses and dispersal hypotheses imply more than the smallest possible number of evolutionary connections among taxa or areas. Al-, though this fact has been noted by other authors (e.g., Nelson, 1983), the method presented here is the first to base an ex? plicit parsimony criterion on the idea of minimizing the number of connections. The implications of this criterion are com? plex and require detailed discussion. Phylogenetic reticulation has inspired 1 E-mail; jack@homebrew.geo.arizona.edu. rel tively little debate since a symposium on the topic in 1981 (Platnick and Funk, 1983). Several different approaches to the problem were described (Humphries, 1983; Nelson, 1983; Wagner, 1983; Wanntorp, 1983), and the stage seemed set for a synthetic approach. However, even the ex? isting methods have attracted little atten? tio since then (but see Humphries and Funk, 1984; Funk, 1985). The only related developments are in the field of molecular systematics, where several methods are us d to recognize ambiguous nodes. How? ever, the split decomposition method of Bandelt and Dress (1992) identifies alter? native taxonomic bipartitions, not reticu? lations, and the cladogram estimation pro? cedure of Templeton et al. (1992) is nar? rowly applicable to haplotype data, makes restrictive probabilistic assumptions about the evolutionary process, and treats addi-