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Ancient rapid divergence events, such as those that took place during the Mesozoic, are pervasive in evolution and represent a major challenge to phylogenetic biologists. The number of molecular phylogenetic studies in which rapid divergence has been invoked to account for poor phylogenetic resolution has steadily increased over the past few years. In this study, rapid divergence events are again hypothesized to have taken place, this time within the two major tribes of Simuliidae, Prosimuliini and Simuliini. This inference is based upon the failure of portions of 28S rDNA, EF-1alpha, DDC, PEPCK, and 12S rDNA to adequately reconstruct relationships among their constituent genera and the presence of short internal and long terminal nodes within both tribes for all character partitions of these genes. Sequence divergence, other than synonymous variation within coding genes, was low among genera and node support weak, except largely for those joining morphologically similar taxa previously recognized as closely related. Strong attraction between a long terminal node (Austrosimulium Tonnoir) and a long internal node (Simuliini), is hypothesized to be the reason for strong support for the placement of Austrosimulium as the basal-most lineage in this tribe. In spite of these problems, a preferred tree intended to be a reasonable estimate of simuliid phylogeny is tentatively presented. Based upon the considerable genomic sampling conducted in this and previous studies, it is clear that new types of genes are needed to more adequately resolve rapid divergence phenomena. The CAD and GART loci, currently under development as phylogenetic markers by the author, show greater promise for resolving simuliid relationships than do any of the genes examined herein.
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PMID:Can the current molecular arsenal adequately track rapid divergence events within Simuliidae (Diptera)? 1267 70

Chalcidoidea (approximately 22,000 described species) is the most ecologically diverse superfamily of parasitic Hymenoptera and plays a major role in the biological control of insect pests. However, phylogenetic relationships both within and between chalcidoid families have been poorly understood, particularly for the large family Pteromalidae and relatives. Forty-two taxa, broadly representing Chalcidoidea but concentrated in the 'pteromalid lineage,' were sequenced for 4620 bp of protein-coding sequence from four nuclear genes for which we present new primers. These are: CAD (1719 bp) DDC (708 bp), enolase (1149 bp), and PEPCK (1044 bp). The combined data set was analyzed using parsimony, maximum likelihood, and Bayesian methods. Statistical significance of the apparent non-monophyly of some taxonomic groups on our trees was evaluated using the approximately unbiased test of Shimodaira [Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51(3), 492-508]. In accord with previous studies, we find moderate to strong support for monophyly of Chalcidoidea, a sister-group relationship of Mymaridae to the remainder of Chalcidoidea, and a relatively basal placement of Encarsia (Aphelinidae) within the latter. The 'pteromalid lineage' of families is generally recovered as monophyletic, but the hypothesis of monophyly for Pteromalidae, which appear paraphyletic with respect to all other families sampled in that lineage, is decisively rejected (P < 10(-14)). Within Pteromalidae, monophyly was strongly supported for nearly all tribes represented by multiple exemplars, and for two subfamilies. All other multiply-represented subfamilies appeared para- or polyphyletic in our trees, although monophyly was significantly rejected only for Miscogasterinae, Ormocerinae, and Colotrechninae. The limited resolution obtained in the analyses presented here reinforces the idea that reconstruction of pteromalid phylogeny is a difficult problem, possibly due to rapid radiation of many chalcidoid taxa. Initial phylogenetic comparisons of life history traits suggest that the ancestral chalcidoid was small-bodied and parasitized insect eggs.
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PMID:Phylogeny of pteromalid parasitic wasps (Hymenoptera: Pteromalidae): initial evidence from four protein-coding nuclear genes. 1791 Oct 33

Increasing the number of characters used in phylogenetic studies is the next crucial step towards generating robust and stable phylogenetic hypotheses - i.e., strongly supported and consistent across reconstruction method. Here we describe a genomic approach to finding new protein-coding genes for systematics in nonmodel taxa, which can be PCR amplified from standard, slightly degraded genomic DNA extracts. We test this approach on Lepidoptera, searching the draft genomic sequence of the silk moth Bombyx mori, for exons > 500 bp in length, removing annotated gene families, and compared remaining exons with butterfly EST databases to identify conserved regions for primer design. These primers were tested on a set of 65 taxa primarily in the butterfly family Nymphalidae. We were able to identify and amplify six previously unused gene regions (Arginine Kinase, GAPDH, IDH, MDH, RpS2, and RpS5) and two rarely used gene regions (CAD and DDC) that when added to the three traditional gene regions (COI, EF-1alpha and wingless) gave a data set of 8114 bp. Phylogenetic robustness and stability increased with increasing numbers of genes. Smaller taxanomic subsets were also robust when using the full gene data set. The full 11-gene data set was robust and stable across reconstruction methods, recovering the major lineages and strongly supporting relationships within them. Our methods and insights should be applicable to taxonomic groups having a single genomic reference species and several EST databases from taxa that diverged less than 100 million years ago.
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PMID:Genomic outposts serve the phylogenomic pioneers: designing novel nuclear markers for genomic DNA extractions of lepidoptera. 1839 68