A taxonomic review of the coastal genus Iotarphia Cameron (Coleoptera: Staphylinidae: Aleocharinae) with a description of new species based on morphological and molecular characters

A taxonomic review of the marine littoral genus Iotarphia Cameron is presented. Three species are recognized, one of which is described as a new species (I. magna Song & Ahn, sp. n.) based on morphological and molecular characters. Genetic divergence of COI using uncorrected p-distance among Iotarphia species ranged from 10% to 11.6%, while intraspecific divergence ranged from 0% to 1.3%. All three species were strongly supported as a single lineage on both neighbor-joining and parsimony trees. The genus Iotarphia and I. australis Cameron are redescribed with illustrations of diagnostic characters. The female of I. rufobrunnea is characterized for the first time. A key and comparison table for similarities and differences among the species are presented.

Currhaeus, a new genus of net-winged beetles and phylogenetic analysis of Eurrhacini (Coleoptera: Lycidae: Lycinae)

A new genus of Neotropical Lycidae, Currhaeus gen. nov., is herein proposed as the second Eurrhacini genus lacking parameres in male genitalia. Seven new species are described: Currhaeus striatus sp. nov., C. nigroapicalis sp. nov., C. championi sp. nov., C. tabascensis sp. nov., C. ruschii sp. nov., C. polegattoi sp. nov., and C. paranaensis sp. nov. Illustrations of diagnostic characters and a key to species identification are presented. Parsimony and maximum likelihood analyses of morphological data demonstrated that Currhaeus gen. nov. belongs in the crown Eurrhacini. Implied weighting parsimony trees recovered Currhaeus as sister to Eurrhacus Waterhouse.

Continental island effect in Sichuan Basin based on the genetic structure of sparrow

Islands are ideal settings for the study of evolution, ecology and genetic diversity. The tree sparrow (Passer montanus), which is distributed both inside and outside the Sichuan Basin and is relatively easy to capture, was used as our study species to test whether any genetic differences exist between within and outside of the Sichuan Basin. We analyzed mitochondrial and nuclear gene sequence variations to illustrate the continental island effect within the Sichuan Basin. Overall, fragments from four mtDNA and one nuclear sequence (Cytb + COI + 12S rRNA + Dloop + Myo) were amplified, with the concatenated alignment comprising 3234 bp. The results of Bayesian and maximum parsimony trees indicated two major branches, one of which is composed mainly of populations within the Sichuan Basin, while the other comprised populations distributed in the surrounding mountains. The population in Sichuan Basin was more basal than that in the surrounding mountains. The genetic distance between inner and outer populations was 0.095 and genetic differentiation index (FST) between inner and outer populations was 0.342. This study shows that the overall distribution pattern of tree sparrow populations in the Sichuan Basin and its surrounding mountains is probably the result of a vicariance event due to spatial isolation.

Identification and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Ephedra Herbs Containing Ephedrine

Ephedrae Herba and Ephedrae Radix et Rhizoma (Mahuang) have been used as Chinese herbal medicines. Ephedra plants mainly live in deserts and have good governance of desertification. Despite their important medicinal and environmental protection value, dietary supplements containing ephedrine from Ephedra species may threaten the health of people. Morphological resemblance amongst species causes difficulty in identifying the original species of Ephedra herbs. Chloroplast (CP) genome shows good prospects in identification and phylogenetic analysis. This study introduced the structures of the CP genomes of three Ephedra species and analysed their phylogenetic relationships. Three complete CP genomes of Ephedra showed four-part annular structures, namely, two single-copy regions and two inverted repeat regions. The entire CP genomes of three Ephedra species in terms of size were 109,550 bp (E. sinica), 109,667 bp (E. intermedia), and 109,558 bp (E. equisetina). Each CP genome of the three Ephedra species encoded 118 genes, including 73 protein-coding genes, 37 tRNA genes and 8 ribosomal RNA genes. Eleven high-variation regions were screened through mVISTA to be potential specific DNA barcodes for identifying Ephedra species. Maximum likelihood and maximum parsimony trees showed that CP genomes could be used to identify Ephedra species. The Ephedra species had a close phylogenetic relationship with Gnetum species and Welwitschia mirabilis. This research provided valuable information for the identification and phylogenetic analysis of gymnosperms and drug safety of Ephedra.

Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

Reconstructing evolutionary histories requires accurate phylogenetic trees. Recent simulation studies suggest that probabilistic phylogenetic analyses of morphological data are more accurate than traditional parsimony techniques. Here, we use empirical data to compare Bayesian and parsimony phylogenies in terms of their congruence with the distribution of age ranges of the component taxa. Analysis of 167 independent morphological data matrices of fossil tetrapods finds that Bayesian trees exhibit significantly lower stratigraphic congruence than the equivalent parsimony trees. As such, taking stratigraphic data as an independent benchmark indicates that parsimony analyses are more accurate for phylogenetic reconstruction of morphological data. The discrepancy between simulated and empirical studies may result from historic data peaking practices or some complexities of empirical data as yet unaccounted for.

Influence of different modes of morphological character correlation on phylogenetic tree inference

Phylogenetic analysis algorithms require the assumption of character independence - a condition generally acknowledged to be violated by morphological data. Correlation between characters can originate from intra-organismal features, shared phylogenetic history or forced by particular character-state coding schemes. Although the two first sources can be investigated by biologists a posteriori and the third one can be avoided a priori with good practices, phylogenetic software do not distinguish between any of them.In this study, we propose a new metric of raw character difference as a proxy for character correlation. Using thorough simulations, we test the effect of increasing or decreasing character differences on tree topology. Overall, we found an expected positive effect of reducing character correlations on recovering the correct topology. However, this effect is less important for matrices with a small number of taxa (25 in our simulations) where reducing character correlation is not more effective than randomly drawing characters. Furthermore, in bigger matrices (350 characters), there is a strong effect of the inference method with Bayesian trees being consistently less affected by character correlation than maximum parsimony trees.These results suggest that ignoring the problem of character correlation or independence can often impact topology in phylogenetic analysis. However, encouragingly, they also suggest that, unless correlation is actively maximised or minimised, probabilistic methods can easily accommodate for a random correlation between characters.

Análisis cladístico de la familia Agavaceae

A morphological based cladistical analysis was undertaken, using 20 taxa from or associated to the family Agavaceae. To assess homologous and independent characters, the morphology of each taxa was analyzed under the next criteria: a. plants have modular construction; b. plant morphology evolves through ontogenetic changes; c. morphological characters evolve through sequential modifications. Hypotheses on character evolution were proposed and tested with comparative and cladistical methods. The morphological characters were optimized with the Wagner parsimony method using PAUP 3.1.1 , considering the genera Chlorogalum and Camassia (Hyacinthaceae), and Chlorophytum and Eremocrinum (Anthericaceae) as multiple outgroups. Two equal most parsimony trees were obtained, 163 steps long with a Consistency Index of 0.509. From the strict consensus tree, genera of Funkiaceae (Hesperocallis, Hosta) resulted as sister taxa of Agavaceae. Chlorophytum and Camassia, considered in molecular biology studies as closely related to Agavaceae, resulted further down. Within the Agavaceae sensu stricto, the previously recognized groups Yuccoideae and Agavoideae as subfamilies, appeared well delimited. The first group is associated with the South American genus Excremis (Funkiaceae) The morphological data from Excremis is not enough as to consider it within Agavaceae. At the base oftheAgaveae ciad e, Hesperaloii resulted as the sister taxon of the group, followed by the sister taxa Beschorneria and Furcraea. Finally, the group considered by authors as the tribe Agaveae formed a monophyletic clade with Agave at the base associated to Manfreda and relatives, and the sister group Polianthes and Pseudobravoa as the most derived taxa.

Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.

Molecular genetic typing reveals further insights into the diversity of animal-associated Staphylococcus aureus

Staphylococcus aureus is an important pathogen of man, but is also able to colonize and cause disease in a wide variety of mammals and birds. An extended multilocus sequencing approach, involving multilocus sequence typing (MLST), sas typing, spa typing and agr typing, was used to examine the molecular diversity of 118 S. aureus isolates recovered from a range of host species and to compare these data with the known diversity of human-derived isolates. MLST revealed that the commonest animal-associated MLST types were ST133, ST5, ST71, ST97, ST126 and ST151. ST133 appears to be an ungulate-animal-specific genotype, as no evidence of ST133 associating with humans has yet been found in the literature. Novel and unique sas alleles were identified in the animal-associated strains that may represent animal-associated sas alleles. However, sas typing exhibited a lower typeability than MLST for the animal strains (91.3 %). Phylogenetic analyses using neighbour-joining and maximum-parsimony trees localized ruminant-associated MLST lineages to both previously identified S. aureus subspecies aureus subgroups, thus explaining the finding of all four agr types within the ruminant-associated strains. S. aureus isolates recovered from chickens and rabbits were genotypically more similar to known human genotypes than the ruminant-associated lineages.