Cuticular hydrocarbon profiles as a taxonomic tool: advantages,limitations and technical aspects

Cuticular hydrocarbons (CHCs) are expressed on an insect's cuticle and are one of the major factors allowing insects to identify members of their own species, colony and gender. As a result of their species‐specificity, CHCs are increasingly used to delimit species in addition to more conventional methods, such as morphology or genetic markers, and so play an important role in chemotaxonomy. Species vary in the type of CHCs that they produce, as well as in the relative quantities of shared compounds. This review summarizes not only how taxonomists may differentiate between species based on CHC profiles, but also the incentive for using CHC composition as taxonomic tool. Benefits regarding the identification of cryptic species and early signs of reproductive isolation are then discussed, giving examples from studies of taxonomy, behaviour and biosynthesis. For taxonomic characters to reliably indicate species boundaries, their limitations need to be known. Potential problems caused by environmental effects, intra‐species variation in profiles and other technical issues are highlighted, and suggestions are made regarding their avoidance. It remains a challenge to determine the variation beyond which two species can be called independent; a problem shared by most methods of delimitation. Recently, there has been a shift towards using a combination of different taxonomic tools, both molecular and non‐molecular, to test observed species differences.     

Spatial and temporal patterns of genetic variation in the widespread antitropical deep‐sea coral Paragorgia arborea

Numerous deep‐sea species have apparent widespread and discontinuous distributions. Many of these are important foundation species, structuring hard‐bottom benthic ecosystems. Theoretically, differences in the genetic composition of their populations vary geographically and with depth. Previous studies have examined the genetic diversity of some of these taxa in a regional context, suggesting that genetic differentiation does not occur at scales of discrete features such as seamounts or canyons, but at larger scales (e.g. ocean basins). However, to date, few studies have evaluated such diversity throughout the known distribution of a putative deep‐sea species. We utilized sequences from seven mitochondrial gene regions and nuclear genetic variants of the deep‐sea coral Paragorgia arborea in a phylogeographic context to examine the global patterns of genetic variation and their possible correlation with the spatial variables of geographic position and depth. We also examined the compatibility of this morphospecies with the genealogical‐phylospecies concept by examining specimens collected worldwide. We show that the morphospecies P. arborea can be defined as a genealogical‐phylospecies, in contrast to the hypothesis that P. arborea represents a cryptic species complex. Genetic variation is correlated with geographic location at the basin‐scale level, but not with depth. Additionally, we present a phylogeographic hypothesis in which P. arborea originates from the North Pacific, followed by colonization of the Southern Hemisphere prior to migration to the North Atlantic. This hypothesis is consistent with the latest ocean circulation model for the Miocene.     

A new species of Onychopterochelius Blüthgen (Hymenoptera: Vespidae: Eumeninae) from Turkey

Onychopterocheilus sarikamisensis sp. n. is described and illustrated from eastern Turkey. The species is related to O. hellenicus (Morawitz, 1885) but differs by the shape of the clypeus and antennae, and by the pale colouration of the maculations.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:A3E75353-EC16-458F-908FAB9240E8016B     

Three new species of penicillium

Three new species of microfungi belonging to the genus Penicillium Link ex Fries are described and illustrated. All but one have been isolated from the atmosphere of las Palmas, capital city of the island of Gran Canaria (Canary Islands, Spain). They clearly differ from all species of the genus described so far and are, therefore, described and proposed as new species: Penicillium hispanicum sp. nov., Penicillium grancanariae sp. nov., and Penicillium palmensis sp. nov.     

A new species of <Emphasis Type="Italic">Sebastes</Emphasis> (Scorpaeniformes: Scorpaenidae) from the Pacific coast of southern Japan

A new rockfish, Sebastes kiyomatsui, is described on the basis of 13 specimens from the Pacific coast of southern Japan. The new species resembles S. scythropus in having two sharp preorbital and robust preocular, supraocular, and postocular spines, but differs from the latter in having a black blotch on the opercle not extending to the subopercle, indistinct crimson marks on the body, blackish region of the oral cavity reaching to the prevomer and palatine, blackish tongue, a small ridge on the upper edge of the lachrymal, somewhat larger orbit, somewhat lower caudal peduncle, and seven lower unbranched pectoral fin rays. Sebastes kiyomatsui is a deep water (ca. 250m) inhabitant.     

CARAGANA FABR. PROMOTES REVEGETATION AND SOIL REHABILITATION IN SALINE-ALKALI WASTELAND

To determine how plantations of Caragana microphylla shrubs affect saline-alkali soil amelioration and revegetation, we investigated the vegetation and sampled soils from saline-alkali wasteland (SAW), perennial Caragana forestland (PCF), Caragana forest after fire disturbance (CFF). Results showed that with the development of Caragana Fabr., highly dominant species of Poaceae family, including Elymus dahuricus, Thermopsis lanceolata, Stipa tianschanica, died out in PCF. Moreover, Papilionaceae family, including Lespedeza indica, Oxytropis psammocharis, and Astragalus scaberrimus, was established both in PCF and CFF. Phytoremediation of saline-alkali wasteland (SAW) was achieved by plantation, resulting in the reduced soil pH, sodium adsorption ratio, exchangeable sodium percentage, salinity, and Na⁺ concentration around Caragana shrubs. Greater amounts of soil organic, total nitrogen, ammonium nitrogen, available phosphorus, and available potassium were observed in PCF topsoil than in SAW topsoil. The concentration of mineralized N in PCF soil was significantly lower than that in SAW soil at all sampled depths, indicating that Caragana shrubs were just using N and therefore less measured in soils. Fire disturbance resulted in decreased soil pH and salinity, but increased organic content, total nitrogen, and ammonium nitrogen. The improved soil parameters and self-recovery of shrubs indicated that Caragana shrubs were well established after burning event.     

Ground beetle species (Carabidae,Coleoptera) activity and richness in relation to crop type,fertility management and crop protection in a farm management comparison trial

Ground beetle activity and species richness was monitored using pitfall traps in a plot trial system on a farm in northern England where the effects of organic and conventional fertility and crop protection management were separated within different crop types between 2005 and 2008. As well as analyses on species activity the beetles were split into small, medium‐sized and large groups, and into groups of herbivores and specific Collembola feeders. Crop type had significant effects on the activity of the 20 most abundant species and all groups, generally with most in beans and winter barley and least in vegetables and spring barley. Most significant reactions to crop protection and fertility management were in cereals and grass/clover. Activity of small species was highest in conventionally crop‐protected cereals but not in vegetables, with more medium‐sized and herbivorous species in organic plots, but there was little influence of crop protection management on large and Collembola feeding species. However, large species were significantly more active in organically fertilised cereals and grass/clover, but not in vegetables, and there were more Collembola feeders in conventional cereals but not in grass/clover. Small species were more abundant in conventionally fertilised grass/clover but there were more in organic cereals and vegetables. These inconsistent activity reactions to management were also observed with individual species but most preferred organically managed plots. There were few significant crop protection : fertility management interactions. Species richness was also significantly affected by crop type and where management had an influence, more species were found in organically managed plots. Constrained ordination emphasised that ground beetle activity was influenced more by crops than by management. Given the diverse nature of organic crop rotations, crop type should be considered a major influence in any environmental manipulation aimed at increasing ground beetle activity for provision of ecosystem services.     

Accurate genome relative abundance estimation for closely related species in a metagenomic sample

Background

Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.

Results

We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn’s disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn’s disease.

Conclusions

By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-242) contains supplementary material, which is available to authorized users.     

The role of landscape change and paleoclimatic events in shaping the evolutionary history of the Polioptila gnatcatchers (Passeriformes,Polioptilidae) with emphasis on species associated with open habitats

We conducted a large‐scale phylogenetic and biogeographical inference of the Poliptila gnatcatchers and investigated the evolutionary history of two closely related neotropical bird species linked to open habitats, Polioptila dumicola and Polioptila plumbea. A Bayesian inference was employed based on the NADH subunit 2 gene to reconstruct the phylogenetic relationship of the gnatcatchers, and ancestral area reconstructions were estimated using BioGeoBEARS. For the phylogeographic analysis, we analyzed two mitochondrial genes, cytochrome b and ND2, of 102 individuals from P. dumicola and P. plumbea distributed throughout the complete range of both species. To reconstruct the dates related to the splitting events, we included a subset of sequences from the nuclear gene beta‐fibrinogen intron‐7. A striking result was the recovery of the sister relationship between the lineages of P. dumicola /plumbea and the paraphyly among the subspecies of P. plumbea: the first group was formed by P. dumicola, P. p. plumbea, P. p. parvirostris, P. p. atricapilla and P. lactea, occurring mainly on the Brazilian shield; while the second group consisted of lineages from north of the Amazon, west of the Andes, and Central America, and included P. maior, P. p. cinericia, P. p. bilineata and P. p. innotata. Significant phylogeographic structure was evident within lineages attributed to P. plumbea, with high levels of differentiation in the well‐defined clades according to all phylogenetic analyses. Our biogeographic analyses support distinct evolutionary histories related to founder events and vicariance, occurring during the late Pliocene and early Pleistocene. Several dispersal episodes between North/Central America and South America led to the establishment of populations which became differentiated due to landscape changes, such as the establishment of riverine barriers, the uplift of the Andes and the formation of the Panama Isthmus.