Estimating phylogenetic inertia in Tithonia (Asteraceae): a comparative approach

Abstract.— Phylogenetic inertia is a difficult issue in evolutionary biology because we have yet to reach a consensus about how to measure it. In this study a comparative approach is used to evaluate phylogenetic inertia in 14 demographic and morphological characters in 10 species and one subspecies of the genus Tithonia (Asteraceae). Three different methods, autocorrelational analysis, phylogenetic correlograms, and ancestor-state reconstruction, were used to evaluate phylogenetic inertia in these traits. Results were highly dependent on the method applied. Autoregression and phylogenetic eigenvector regression (PVR) methods found more inertia in morphological traits. In contrast, phylogenetic correlograms and ancestor-state reconstruction suggest that morphological characters exhibit less phylogenetic inertia than demographic ones. The differences between results are discussed and methods are compared in an effort to understand phylogenetic inertia more thoroughly.     

Evidence for a phylogenetic position of button quails (Turnicidae: Aves) among the Gruiformes

The phylogenetic position of the Turnicidae (Aves) was unresolved. Historically, they were classified as members of the Struthioniformes, Galliformes, Charadriiformes, Columbiformes or the Gruiformes. In these classifications they had taxonomic rank of order 'Turniciformes' or family 'Turnicidae'. However, most of these studies followed phenetic methodology and used morphological similarity of taxa and plesiomorphic characters to classify Turnix . Recent phylogenetic studies on the basis of morphological character analyses or phenetic comparisons based on DNA-DNA hybridization experiments failed to clarify the phylogenetic realtionship of Turnix and suggested a position as 'incerte sedis', either among the Gruiformes or as the parvclass 'Turnicac'as a sistergroup to the 'Neoaves'.
We studied skeletal and myological material of Turnix to resolve its phylogenetic position. Further, we considered all characters that were previously discussed in literature to classify Turnix and tested them for their potential use in phylogenetic analysis. We added several yet unemployed morphological characters of phylogenetic significance to the analysis. The Struthioniformes, 'Galloanseres', and Columbiformes are each characterized by a clear set of autapomorpies. Only one autapomorphy in known for the Gruiformes but this character is of satisfying consistency and can be found in all families of the Gruiformes (Gruidae, Psophiidae, Aramidae. Rallidae) and Turnix. Turnix and the Rallidae share four complex morphological characters implying a close phylogenetic relationship. The data presented in this paper support the hypothesis that Turnix is a member of the Gruiformes with close relationships to the Rallidae. No evidence was found that would support a parvclass 'Turnicae'as sistergroup to the 'Neoaves'.     

Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

Background  

Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility.     

Phylogeography of a facultatively migratory dragonfly, Libellula quadrimaculata (Odonata: Anisoptera)

The biogeography of a widely distributed dragonfly (Libellula quadrimaculata) was examined via a phylogenetic analysis of 416 bp of the mitochondrial cytochrome oxidase I subunit (COI). Phylogenetic analyses under parsimony and minimum evolution produced trees with similar topologies, and revealed strong support for three clades corresponding to populations in Asia, Europe and North America. However, resolution was poor within clades, and genetic distances between populations within continents was quite low (1–2%). Several populations of this species are known to engage in periodic mass migrations, and it is possible that introgression from gene flow due to the mobility of this species has obscured phylogenetic patterns within continents. I was unable to test for phylogenetic patterns coincident with historical glacial refugia given the lack of phylogenetic patterns within continents. However, given that some sequence divergence was observed between populations within continents, it is possible that phylogenetic patterns exist, and subsequent studies should make use of larger data sets, and molecular data from faster evolving genes. Despite the propensity for periodic, short distance migrations in L. quadrimaculata, gene flow appears to be limited and does not influence the phylogenetic relationships of populations between continents.     

A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes

Phylogenetic analysis is currently used worldwide for taxonomic classification and identification of microorganisms. However, despite the countless trees that have been reconstructed and published in recent decades, so far, no user-friendly compilation of recommendations to standardize the data analysis and tree reconstruction process has been published. Consequently, this standard operating procedure for phylogenetic inference (SOPPI) offers a helping hand for working through the process from sampling in the field to phylogenetic tree reconstruction and publication. It is not meant to be authoritative or comprehensive, but should help to make phylogenetic inference and diversity analysis more reliable and comparable between different laboratories. It is mainly focused on using the ribosomal RNA as a universal phylogenetic marker, but the principles and recommendations can be applied to any valid marker gene. Feedback and suggestions from the scientific community are welcome in order to improve these guidelines further. Any updates will be made available on the SILVA webpage at http://www.arb-silva.de/projects/soppi.     

Position specificity in Chitonomyces (Ascomycota, Laboulbeniomycetes) on Laccophilus (Coleoptera, Dytiscidae): a molecular approach resolves a century-old debate

The occurrence of Laboulbeniomycete species consistently on a precise portion of beetle integument was investigated in 13 species of Chitonomyces ectoparasitic on the aquatic diving beetle Laccophilus maculosus (Coleoptera, Dytiscidae). The phenomenon was called "position specificity" by Roland Thaxter in 1896, yet the mechanism has remained unknown. By using molecular analysis of the nucSSU rRNA gene and the 5.8S and partial ITS1 rRNA regions, 13 species of Chitonomyces reported to exhibit position specificity on Laccophilus maculosus were placed neatly into pairs of morphotypes, resulting in synonomies and recognition of six phylogenetic species (one species is a triplet). Each phylogenetic species was located at corresponding positions on male and female beetles that make contact during mating. In addition, ecological data and video footage of the mating behaviors of Laccophilus confirmed that sexual transmission is the mechanism behind this enigmatic phenomenon.     

The complete mitochondrial genome of Chrysolophus pictus (Galliformes: Phasianidae) and a phylogenetic analysis with related species

The 16,678 bp mitochondrial genome of the Chrysolophus pictus has been sequenced in this paper. To determine the phylogentic position of C. pictus with related species within Phasianidae, the phylogenetic tree was reconstructed with the concatenated nucleotide dataset of the 12 heavy-strand-encoded protein genes. The phylogenetic analysis was carried out using maximum parsimony (MP) and Bayesian inference (BI) methods. MP and BI phylogenetic trees here showed similar topology and consistently suggested that C. pictus shared a close relationship with Phasianus versicolor. The results also showed that the Meleagris gallopavo possessed a basal phylogenetic position within Phasianidae, which may imply that it should be classified into the Phasianidae.     

Are Polyphaga (Coleoptera) really a basal neopteran lineage – a reply to Kazantsev

In a study on the mandible and mandibular articulation of larvae of the lycid genus Platerodrilus Kazantsev proposes a phylogenetic scheme with Polyphaga as a basal group of Neoptera and Lycidae as a basal group within Polyphaga. Here we point out different problems with his interpretation. The taxon sampling was not sufficient. The characters of endopterygote larvae cannot be compared to characters of adults in a phylogenetic context. The neotenic characters of female and adult male Lycidae are not sufficiently taken into account. A phylogenetic hypothesis should be based on multiple character systems and all available data must be considered. Kazantsev based his conclusions on a single isolated character complex. His hypothesis is in deep conflict with a phylogeny based on the molecular data, which clearly show that Lycidae are nested within Elateroidea. The molecular and morphological evidence also implies that females are aberrant neotenic forms and by no means ‘primitive’. Kazantsev's hypothesis is problematic because the presented data are insufficient and the character evaluation is not based on a numerical analysis.     

Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex

Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with respect to several other genera and ultimately provided minimal phylogenetic resolution within and between North American and European groups. Character support from each gene suggested inconsistency between the phylogenetic signal of the CAD gene and that of the other four genes. However, removal of CAD from subsequent phylogenetic analyses did not substantially change the initial phylogenetic results or return Carmenta and Synanthedon as reciprocally monophyletic, suggesting that it was not impacting the overall phylogenetic signal. The lack of resolution using genes that are typically informative at the species level for other lepidopterans suggests a surprisingly rapid radiation of species in Carmenta/Synanthedon. This group also exhibits a wide range of mimicry strategies and hostplant usage, which could be fertile ground for future study.