Society of Systematic Biologists

Morphological characters are essential for establishing phylogenetic relationships, delimiting higher-level taxa, and testing phylogenetic relationships inferred from molecular sequence data. In cases where relationships between large clades remain unresolved, it becomes imperative to establish which character systems are sound predictors of phylogenetic signal. In the case of Laniatores, the largest suborder of Opiliones, some superfamilial relationships remain unresolved or unsupported, and traditionally employed phenotypic characters are typically of utility only at the family level. Here we investigated a promising set of morphological characters that can be discretized and scored in all Opiliones: cuticular structures of the distal podomeres (metatarsi and tarsi). We intensively sampled members of all known families of Laniatores, and define here three new, discrete appendicular characters toward refinement of Laniatores superfamilial systematics: metatarsal paired slits (MPS; occurring in all Laniatores except Sandokanidae), proximal tarsomeric gland (PTG; in Icaleptidae, Fissiphalliidae, and Zalmoxidae), and tarsal aggregate pores (TAP; found in Gonyleptoidea, Epedanoidea, and Pyramidopidae). We conducted statistical tests on each character to characterize the strength of phylogenetic signal and assess character independence, based on alternative tree topologies of Laniatores. All three characters had high retention indices and bore significantly strong phylogenetic signal. Excepting one pairwise comparison, morphological characters did not evolve in a correlated manner, indicating that appendicular morphology does not constitute a single character system. Our results demonstrate the predictive power and utility of appendicular characters in Opiliones phylogeny, and proffer a promising source of diagnostic synapomorphies for delimiting superfamilies.

This is the first genus-level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiini and Micronetini), and Erigoninae, and a representative of the family Pimoidae, the sister-group to Linyphiidae. No fewer than 147 of the morphological characters used in this study are new and defined for this study, and come mainly from male and female genitalia. Parsimony analysis with equal weights resulted in three most parsimonious trees of length 871. The monophyly of the subfamily Mynogleninae and the genera Novafroneta, Parafroneta, Laminafroneta, Afroneta, Promynoglenes, Metamynoglenes, and Haplinis are supported, whereas Pseudafroneta is paraphyletic. The remaining seven mynoglenine genera are either monotypic or represented by only one taxon. Diagnoses are given for all genera included in the analysis. The evolution of morphological traits is discussed and we summarize the diversity and distribution patterns of the 124 known species of mynoglenines. The preferred topology suggests a single origin of mynoglenines in New Zealand with two dispersal events to Africa, and does not support Gondwana origin.

A phylogenetic analysis of Hormaphidinae is presented based on a total-evidence approach. Four genes (two mitochondrial, COI and CytB, and two nuclear, EF-1α and LWO) are combined with 65 morphological and seven biological characters. Sixty-three hormaphidine species representing three tribes and 36 genera as well as nine outgroups are included. Parsimony and model-based approaches are used, and several support values and implied weighting schemes are explored to assess clade stability. The monophyly of Hormaphidinae and Nipponaphidini is supported, but Cerataphidini and Hormaphidini are not recovered as monophyletic. Based on the parsimony hypothesis from the total-evidence analysis, the phylogenetic relationships within Hormaphidinae are discussed. Cerataphidini is re-delimited to exclude Doraphis and Tsugaphis, and Hormaphidini is redefined to include Doraphis. Ceratocallis Qiao & Zhang is established as a junior synonym of Ceratoglyphina van der Goot, syn. nov. Lithoaphis quercisucta Qiao, Guo & Zhang is transferred to the genus Neohormaphis Noordam as Neohormaphis quercisucta (Qiao, Guo & Zhang) comb. nov. Galls have evolved independently within three tribes of Hormaphidinae. In Cerataphidini, pseudogalls are ancestral, both single-cavity and multiple-cavity galls have evolved once, and galls appear to have evolved towards greater complexity. Galling on secondary hosts has evolved twice in hormaphidines.

Phylogenetic analyses that incorporate the most character information also provide the most explanatory power. Here I demonstrate the value of such an approach through a direct optimization sensitivity analysis of apid bee phylogeny. Whereas prior studies have relied solely on one class of data or the other, this analysis combines previously published molecular, morphological, and behavioural characters into a single supermatrix. The final dataset includes 191 ingroup and 30 outgroup taxa, and includes data from seven unaligned gene sequences (18S, 28S, wingless, EF1-α, polII, Nak, LW rhodopsin), 209 adult and larval morphological characters, and two behavioural characters. Nine different sets of transformation cost parameters are evaluated, along with their relative degrees of character incongruence. The preferred parameter set returns a strict consensus tree somewhat similar to, but more resolved than, a previous parsimony tree based on molecules alone. I also describe the effects of including EF1-α and LW rhodopsin intron sequences on the outcome of the direct optimization analysis. By accounting for more evidence, this study provides the most comprehensive treatment yet of apid phylogenetic relationships.

A new phylogenetic hypothesis for the Neotropical butterfly genus Hamadryas, based on the combination of a morphological matrix, one mitochondrial (COI) and four nuclear markers (CAD, RpS5, EF1a, and Wingless), is presented. Results from analyses of the molecular evidence are compared with a previously published morphological phylogeny. Molecular data and the analysis of the complete dataset support the monophyly of Hamadryas and most sister groups suggested by morphological data alone. The addition of DNA sequences to the morphological matrix helped define species groups for which no morphological synapomorphies were found. Partitioned Bremer support indicates that COI, CAD, and morphology were consistently in agreement with the combined evidence tree. In contrast, signal from the nuclear markers Rps5, EF1a, and Wingless showed indifference at most levels of the tree, and minor conflict at nodes solving the relationships between species groups. Though resolved, the combined evidence tree shows low resample values, particularly among species groups whose relationships were characterized by short internodes. A reassessment about the pattern of character change for sound production is presented and discussed.

Complete genome sequences from a genus of Gammaproteobacteria, Shewanella, are used to generate a genome-wide exploration of the gene-tree species-tree dichotomy. A number of datasets were constructed and analyses were attempted. Single genes were chosen from 243 regions of collinear gene homology (128 of these 243 chosen genes are from the core Shewanella genome and 162 of 243 have the complete taxon sampling) from a previous study (Dikow, 2011) and subjected to phylogenetic analysis both individually and concatenated. In addition, three of the 243 sets of collinear genes from the core Shewanella genome were also chosen (comprising 15, 17, and 23 genes each) to be analysed in detail, this time to maximize the expectation of gene concordance. Analysis of these 55 genes in maximum parsimony (MP) and maximum likelihood (ML) produced 164 unique topologies (out of 166 resulting topologies). No genes from within collinear regions were congruent with one another, and none of these 164 topologies matches the result from concatenation. This result is particularly striking given that we chose collinear sets of genes. Analyses in MP and ML of 243 genes distributed across the genome produced 567 unique topologies (out of 571 resulting topologies for those 162 genes with complete taxon sampling). These results are discussed in light of recent works focused on incongruence. The gene as a phylogenetic unit is also discussed. It is our conclusion that molecular systematics has been reliant on the gene as a unit without a critical eye on the distinction between gene homology and character homology.

We present phylogenomic analyses of the most comprehensive molecular character set compiled for Annelida and its constituent taxa, including over 347 000 aligned nucleotide sites for 39 taxa. The nucleotide data set was recovered using a pre-existing amino acid data set of almost 48 000 aligned sites as a backbone for tBLASTn searches against NCBI. In addition, orthology determinations of the loci in the original amino acid data set were scrutinized using an All vs All Reciprocal Best Hit approach, employing BLASTp, and examining for statistical interdependency among the loci. This approach revealed considerable sequence redundancy among the loci in the original data set and a new data set was compiled, with the redundancy removed. The newly compiled nucleotide data set, the original amino acid data set, and the new reduced amino acid data set were subjected to parsimony analyses and two forms of bootstrap resampling. The last-named data set also was analysed using a maximum-likelihood approach. There were two main objectives to these analyses: (i) to examine the general topology, including support, resulting from the analyses of the new data sets and (ii) to assess the consistency of the branching patterns across optimality criteria by comparison with previous probabilistic approaches. The phylogenetic hypotheses resulting from analyses of the three data sets are largely unsupported, reflecting the continued difficulty of finding numerous, reliable, and suitable loci for a group as ancient as Annelida. Resulting parsimonious hypotheses disagree, in some respects, with the previous probabilistic approaches; Sedentaria and, in most cases, Errantia are not supported as monophyletic groups but Pleistoannelida is recovered as a (unsupported) monophyletic group in one of the three parsimony analyses as well as the likelihood analysis. In addition, we performed missing data titration studies to estimate the impact of missing data on overall support and support for specific clades.