Baker and DeSalle
Abstract. A phylogenetic hypothesis of relationships among 33 species of stalk-eyed flies was generated from a molecular data set comprised of three mitochondrial and three nuclear gene regions. A combined analysis of all the data equally weighted produced a single most parsimonious cladogram with relatively strong support at the majority of nodes. The phylogenetic utility of different classes of molecular data was also examined. In particular, using a number of different measures of utility in both a combined and separate analysis framework, we focus on the distinction between mitochondrial and nuclear genes, and faster-evolving characters and slower-evolving characters. For the first comparison, by nearly any measure of utility, the nuclear genes are substantially more informative for resolving diopsid relationships than are the mitochondrial genes. The nuclear genes exhibit less homoplasy, are less incongruent both with one another and with the combined data, and contribute more support to the combined analysis topology than the mitochondrial genes. Results from the second comparison, however, provide little evidence of a clear difference in utility. Despite indications of rapid divergence and saturation, faster-evolving characters in both the nuclear and mitochondrial data sets still provide substantial phylogenetic signal. In general, inclusion of the more rapidly evolving data consistently improves the congruence among partitions. [Diopsidae; nuclear genes; saturation; incongruence; partitioned Bremer support]
Buckley et al.
Abstract. We have investigated the effects of different among-site rate variation models on the estimation of substitution model parameters, branch lengths, topology and bootstrap proportions under minimum evolution (ME) and maximum likelihood (ML). Specifically we examined equal rates, invariable sites, gamma-distributed rates and site-specific rates (SSR) models using mitochondrial DNA sequence data from three protein coding genes and one tRNA gene from species of the New Zealand cicada genus Maoricicada. Estimates of topology were found to be relatively insensitive to the substitution model employed; however, estimates of bootstrap support, branch lengths and R-matrices (underlying relative substitution rate matrix) were observed to be strongly influenced by the assumptions of the substitution model. We did identify one situation where ME and ML tree building became inaccurate when implemented with an inappropriate among-site rate variation model. Despite the fact the SSR models often have a better fit to the data than invariable sites and gamma rates models, SSR models have some serious weaknesses. First, SSR rate parameters are not comparable across data sets, unlike the proportion of invariable sites or the alpha shape parameter of the gamma distribution. Second, the extreme among-site rate variation within codon positions is problematic for SSR models, which explicitly assume rate homogeneity within each rate class. Third, the SSR models appear to give severe underestimates of R-matrices and branch lengths relative to invariable sites and gamma rates models in this example. We recommend performing phylogenetic analyses under a range of substitution models in order to test the effects of model assumptions not only on estimates of topology but also on estimates of branch length and nodal support. [Maximum likelihood; nucleotide substitution models; among-site rate variation; likelihood ratio test; insect mitochondrial DNA; bootstrapping; Maoricicada]
Caterino et al.
Abstract. Although it is widely agreed that data from multiple sources are necessary to confidently resolve phylogenetic relationships, procedures for accommodating and incorporating heterogeneity in such data remain underdeveloped. We explored the use of partitioned, model-based analyses of heterogeneous molecular data in the context of a phylogenetic study of swallowtail butterflies (Lepidoptera: Papilionidae). Despite substantial basic and applied study, phylogenetic relationships among the major lineages of this prominent group remain contentious. We sequenced 3.3 kb of mitochondrial (COI/COII 2.3 kb) and nuclear (EF-1a 1.0 kb) DNA for 22 swallowtails, including representatives of Baroniinae, Parnassiinae, and Papilioninae, and several moth and butterfly outgroups. Parsimony encountered considerable difficulty in resolving the deepest splits among these taxa. We therefore chose two outgroups whose relationships to each other and to Papilionidae were undisputed and undertook detailed likelihood analyses of alternative topologies. Following previous studies that have demonstrated substantial heterogeneity in the evolutionary dynamics among process partitions of these genes, we estimated evolutionary parameters separately for gene-based and codon-based partitions. These values were then used as the basis for examining the likelihoods of possible resolutions and rootings under several partitioned and unpartitioned likelihood models. Partitioned models gave significantly better fits to the data than did unpartitioned models, and supported different topologies. However, the most likely topology varied from model to model. The most likely ingroup topology under the best-fitting, six partition GTR + G model favors a paraphyletic Parnassiinae. However, when examining the likelihoods of alternative rootings of this tree relative to rootings of the classical hypothesis two rootings of the latter emerge as most likely. Of these two, the most likely rooting is within the Papilioninae, although a rooting between Baronia and the remaining Papilionidae is only nonsignificantly less likely. [process partitions, data partitioning, likelihood, heterogeneity]
Joy and Conn
Abstract. Ecological adaptation within islands may have figured prominently in the insular radiation of black flies (subgenus Inseliellum) in the Society Islands, French Polynesia. To aid in understanding the sequence of ecological shifts in this group, we have constructed a phylogeny using morphology, the cytochrome oxidase I (COI) gene, and the small ribosomal subunit (12S) gene. The strong influence of COI on the combined analysis tree was evident from its contribution to the partitioned Bremer support (62%). The net effect of including 12S was to reduce overall tree support. Different character sets resolved different portions of the combined analysis tree, with COI resolving recent lineages, 12S resolving basal relationships and morphology supporting the monophyly of taxa possessing reduced larval feeding fans (oviceps group). The PartitionHomogeneity and Kashino-Hasegawa tests indicated significant incongruence between morphological and mitochondrial data. The Templeton test revealed that morphology and the combined (COI+12S) mitochondrial data were incongruent. This conflict stems primarily from disagreement over the monophyly of taxa with highly reduced larval feeding fans. Either 1) convergence in a subset of morphological characters, 2) low phylogenetic signal among mitochondrial sequences, or 3) lineage sorting causing the mitochondrial data to track an incorrect evolutionary history, may be responsible. [Black flies; combined-data analysis; insular radiation; molecular systematics; Simuliidae]
Quicke et al.
Abstract. In this paper we describe a new heuristic strategy designed to find optimal (parsimonious) trees for data sets with large numbers of taxa and characters. This new strategy uses an iterative searching process of branch swapping with equally weighted characters followed by swapping with reweighted characters. This process increases the efficiency of the search because, after each round of swapping with reweighted characters, the subsequent swapping with equal weights will start from a different group (island) of trees that are only slightly, if at all, less optimal. In contrast, conventional heuristic searching with constant equal weighting can become trapped on islands of sub-optimal trees. We test the new strategy against a conventional, and a modified conventional strategy and show that in a given time the new strategy finds trees that are significantly more parsimonious. We also compare our new strategy to a recently, and independently developed strategy known as the Parsimony Ratchet [Large phylogenies, search time, heuristic algorithms, Parsimony Ratchet]
Salter and Pearl
Abstract. The maximum likelihood (ML) method of phylogenetic tree construction is not as widely used as other tree construction methods (e.g., parsimony, neighbor-joining) because of the prohibitive amount of time required to find the ML tree when the number of sequences under consideration is large. To overcome this difficulty, we propose a stochastic search strategy for estimation of the ML tree that is based on a simulated annealing algorithm. The algorithm works by moving through tree space by way of a "local rearrangement" strategy so that topologies that improve the likelihood are always accepted, whereas those that decrease the likelihood are accepted with a probablility that is related to the proportionate decrease in likelihood. Besides greatly reducing the time required to estimate the ML tree, the stochastic search strategy is less likely to become trapped in local optima than are existing algorithms for ML tree estimation. We demonstrate the success of the modified simulated annealing algorithm by comparing it with two existing algorithms (Swoffords PAUP* and Felsensteins DNAMLK) for several theoretical and real data examples. [Maximum likelihood; simulated annealing; stochastic probing; stochastic search.]
Abstract. We studied the molecular phylogeny of the carabid subgenus Ohomopterus (genus Carabus) using two mtDNA regions (16SrRNA and ND5) and three nuclear DNA regions (wingless, phosphoenolpyruvate carboxykinase, and an anonymous locus). We revisited the previously reported incongruence between the distribution of mtDNA markers and morphologically defined species (Su et al., 1996, J. Mol. Evol., 43:662-671) which they attributed to "type switching", a concerted change in many morphological characters that results in the repeated evolution of a particular morphological type. Our mtDNA gene tree obtained from 44 individuals representing all 15 currently recognized species of Ohomopterus revealed that haplotypes isolated from individuals of a single "species" were frequently separated into distant clades, confirming the previous report. The three nuclear markers generally conformed better with the morphologically defined species. The phylogenetic signal in mtDNA and nuclear DNA data differed strongly and these two partitions were significantly incongruent with each other according to Farris et al.s (1994) ILD test, although the three nuclear partitions were not homogeneous either. Our results did not support the type switching hypothesis which was proposed to fit the morphological data to the mitochondrial gene tree: incongruence of the mtDNA tree with other nuclear markers indicates that the mtDNA-based tree does not reflect species history any better than the morphological data. Incongruence of gene trees in Ohomopterus may have been promoted by the complex processes of geographic isolation and hybridization in the Japanese Archipelago that led to occasional gene flow and recombination between separated entities. It is intriguing that reticulate patterns occurred in this group, as species of Ohomopterus exhibit extremely divergent genitalic structures that represent a highly efficient reproductive isolation mechanism. [Carabid beetles; Carabus; molecular phylogeny; mitochondrial DNA; nuclear DNA; Ohomopterus; phylogenetic incongruence.]