Phylogenetic analysis of Themira (Sepsidae: Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study

Abstract

In this study we use sensitivity analysis sensu Wheeler (1995) for a matrix entirely composed of DNA sequences. We propose that not only congruence but also phylogenetic structure, as measured by character resampling, should be used to choose among competing weighting regimes. An extensive analysis of a five-gene data set for Themira (Sepsidae: Diptera) reveals that even with different ways of partitioning the data, measures of topological congruence, character incongruence, and phylogenetic structure favor similar weighting regimes involving the down-weighting of transitions. We furthermore use sensitivity analysis for obtaining empirical evidence that allows us to select weights for third positions, deciding between treating indels as fifth character states or missing values, and choosing between manual and computational alignments. For our data, sensitivity analysis favors manual alignment over a Clustal-generated numerical alignment, the treatment of indels as fifth character states over considering them missing values, and equal weights for all positions in protein-encoding genes over the down-weighting of third positions. Among the topological congruence measures compared, symmetric tree distance performed best. Partitioned Bremer Support analysis reveals that COI contributes the largest amount of support for our phylogenetic tree for Themira.Ó The Willi Hennig Society 2005.Reconstructing phylogenetic relationships based on DNA sequence data is sometimes naı¨vely considered more objective than reconstructing trees based on morphological characters. This belief is rooted in the objectivity of raw nucleotide sequence data, but overlooks that there are many different analysis strategies, weighting schemes, and ⁄ or evolutionary models that can be used to derive trees from sequences (Wheeler, 1995;Wheeler and Hayashi, 1998). It is thus not surprising that much of the recent literature in systematic biology treats the advantages and disadvantages of different analysis philosophies (e.g., Maximum Likelihood, Bayesian Likelihood, Neighbor Joining, Parsimony) and discusses the best techniques for choosing appropriate evolutionary models and ⁄ or weighting schemes. In maximum likelihood and Bayesian likelihood estimation, different methods for model choice have been established (e.g., Aris-Brosou, 2003;Posada and Crandall, 1998). In parsimony, some proponents strongly favor equal weighting under all circumstances (e.g., Kluge and Wolf, 1993), while others prefer to choose analysis conditions for their data sets based on a variety of more or less explicit criteria.In parsimony, one of the most popular methods for choosing among weighting regimes (Giribet, 2003) is Wheeler's (1995) sensitivity analysis, which uses the congruence between different data partitions for this selection. Traditionally, such sensitivity analyses have

Sensitivity analysis, molecular systematics and natural history evolution of Scathophagidae (Diptera: Cyclorrhapha: Calyptratae)

“…However, in the current analysis we go beyond Laamanen et al. (2005) and other studies comparing alignment algorithms (Terry and Whiting, 2005) in that we compare three different alignment strategies: ClustalX (default parameters), Direct Optimization (POY), and “manual” alignment.…”

Stability, sensitivity, science and heurism

“…The purpose of this paper is to clarify our different points of view regarding: (1) the meaning of test in science, (2) the relationship of this method of sensitivity analysis to the other methods of data exploration discussed by Giribet (2003a), (3) stability as a scientific goal of phylogenetic inference and (4) the validity of this approach to sensitivity analysis as advancing objective knowledge claims. Because some authors appear unaware of the criticisms of this method of sensitivity analysis (e.g., Laamanen et al., 2005; Worsaae, 2005), as background we begin with a summary of our views on the evaluation of methods of data exploration.…”

Across the Baltic: a new record for an enigmatic black scavenger fly, Zuskamira inexpectata (Pont, 1987) (Sepsidae) in Finland

“…The species is morphologically distinct from other sepsids, based on the following male characters: (1) 4 th sternite heavily spinose, (2) syn-sternite 7+8 absent, (3) epandrium enlarged, and (4) hypandrium firmly attached to syntergite 7+8 at one point (Pont 1987). Subsequent phylogenetic research (Zhao et al 2013, Su et al 2008, Laamanen et al 2005, Pont and Meier 2002) showed that this morphological distinctness is associated with a similarly distinct phylogenetic position on the phylogenetic tree of Sepsidae: Zuskamira inexpectata is not nested within any other sepsid genus, and behaves like a "wildcard" taxon whose actual placement on the sepsid phylogeny remains unclear because different topologies are supported by the same data depending on how the data are analyzed (Zhao et al 2013). …”