New methods for species and sex determination in three sympatric Mustelids, Mustela itatsi, Mustela sibirica and Martes melampus

We developed novel species and sex determination methods for three Japanese mustelid species. We used DDX3Y to determine sex and generated a primer set to amplify both DDX3X and DDX3Y DNA in Mustela itatsi, M. sibirica and Martes melampus. To determine species and sex simultaneously, we generated fluorescence-labelled primers that give different fragment lengths at D-loop, DDX3X and DDX3Y of these three species using a DNA sequencer.     

G-band homology and C-band variation in the Japanese mustelids,Mustela erminea nippon andM. sibirica itatsi

The diploid number(2n)and fundamental number (FN) were 44 and 64 inMustela erminea nippon and 38 and 64 inM. sibirica itatsi. In spite of such a marked dissimilarity in their chromosome constitution, most of the chromosomes of these two species showed high G-band homology. On the other hand, interspecific variations in the amount of C-heterochromatin were observed in several pairs of chromosomes which were regarded, based on their G-banding patterns, to have arisen from a common origin. Some of the chromosome pairs associated with the C-heterochromatin variations showed significant differences in length or arm ratio, whereas others did not. These findings strongly indicate that the G-banding patterns might have been well conserved, at least in the euchromatic regions, through the speciation process; in contrast, C-heterochromatin showed quantitative variations, some of which could be regarded to have been formed by duplication. Thus, the karyological relationships between the Japanese ermine and the Japanese weasel could be explained by Robertsonian fusion and quantitative alteration of C-heterochromatin.     

Assembly and comparison of two closely related Brassica napus genomes

As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor‐bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor‐bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome.     

On co-existence,foraging strategy and the biogeography of weasels and stoats (Mustela nivalis and M. erminea) in Britain

Summary Mustela nivalis and M. erminea, two sympatric species of weasels of superficially similar appearance and habits, have different breeding and foraging strategies associated with the difference in their body size. M. nivalis is more efficient in exploiting small rodent prey, and can breed rapidly to take immediate advantage of rodent peaks, but is vulnerable to local extinction during rodent declines. M. erminea has more generalized food habits, and is the larger and probably the dominant species, but is limited by delayed implantation to producing only one litter a year. M. nivalis is therefore superior in exploitation competition, and erminea in interference competition. We offer the hypothesis that the co-existence of the two species is permitted by a balance of these competitive advantages determined, at a given time or place, by the heterogeneity of the environment and the distribution of the prey fauna. We use this hypothesis to explain cases where co-existence has either broken down or is not recorded (the results of simultaneous introductions to New Zealand and Terschelling Island, and of myxomatosis in Britain, and the distribution of nivalis and Erminea on the offshore islands of Britain). We argue that the diversity and size distribution of the prey fauna of an island (which are both related to its area and isolation) are important in deciding the species and size of mustelids surviving there; for example, we suggest that nivalis was present in Ireland in immediate post-glacial times but became extinct with the lemmings.     

Food habits of British stoats (Mustela ermined) and weasels (Mustela nivalis)

Information on the food habits of stoats and weasels was obtained chiefly from gut analyses of carcasses sent from various parts of Britain. Lagomorphs, small rodents and birds form the bulk of the food taken by these predators. The three food classes appear to be equally important to stoats, whereas weasels obtain nearly half of their food from small rodents. Microtus was the most important small rodent in the diet of both stoats and weasels. Game birds were taken more by stoats than weasels; the chief bird prey of the latter was passerines.     

Possible coding for recognition of sexes,individuals and species in anal gland volatiles of Mustela eversmanni and M. sibirica

With a combination of solvent extraction and gas chromatography-mass spectrometry, we found eight new compounds in the two sympatric Mustela species, M. eversmanni and M. sibirica. These compounds had not been detected by headspace sampling with solvent desorption. Two of the newly detected compounds are nitrogen-containing compounds, indole and o-aminoacetophenone and the remaining are sulfur-containing volatiles. By comparing same and opposite sexes between the two Mustela species, we found that qualitative differences in the anal gland secretion are most likely to be used to code for information about species, corresponding to the idea of digital coding. In the Siberian weasel (M. sibirica), both presence or absence of sex-specific compounds (Z-2-ethyl-3-methylthietane only in females) and relative abundance of some compounds between males and females could be used to code for information about sex, corresponding to the idea of digital and analog coding, respectively. In the steppe polecat (M. eversmanni), only quantitative differences provided the possibility for inter-sexual communication. Thus coding for information about sex appeared to be digital. Coding for individual information could also be either digital or analog or both through the presence or absence of certain compounds and/or the difference in the relative abundances of certain compounds among individuals. Comparing with other Mustela spp., we failed to find a congruence between the chemical composition of anal gland secretions and the phylogenetic relationship among the species in this genus.     

The diet of weasels (Mustela nivalis vulgaris) from Purerua Peninsula,Bay of Islands,New Zealand

We studied the diet of weasels (Mustela nivalis vulgaris) caught on Purerua Peninsula, Bay of Islands, by examining gut contents of 16 individuals caught between 2011 and 2012. Mammals were the prey group most consumed by weasels, when measured both as frequency of occurrence and dry weight. In addition, weasels consumed introduced birds, native invertebrates and reptiles, including the endemic copper skink (Oligosoma aeneum), supporting previous studies and suggesting that weasels have greater effects on biodiversity losses than previously acknowledged.     

Mycoplasma pneumoniae and Mycoplasma genitalium: a comparison of two closely related bacterial species

The rapid progress in sequencing large quantities of DNA will provide an increasing number of complete genome sequences of closely related bacterial species as well as of pairs of isolates from the same species with different features, such as a pathogenic and an apathogenic representative. This opens the way to apply subtractive comparative analysis as a tool to select from the large pool of all bacterial genes a relatively small set of genes that can be correlated with the expression of a certain phenotype. These selected genes can then be the target for further functional analyses.     

Female mate choice and species recognition between two closely related cichlid fish of Lake Malawi,Metriaclima estherae and M. callainos

Cichlids are one of the most diverse and colourful groups of freshwater fishes in the world. Despite much investigation, the factors that promote speciation in these fishes are still uncertain. However, previous studies suggest that sexual selection on male colour is one of the main drivers of speciation among these fishes. Metriaclima estherae is a polymorphic cichlid species from Lake Malawi, and thus provides an ideal model for the investigation of the importance of colour as a species recognition cue. M. callainos is a closely related and morphologically similar species, with male colour pattern very similar to that of M. estherae. We tested female choice by giving females of the two species a choice between conspecific and heterospecific males in the presence and absence of visual (colour) and chemical cues. The results show that females of M. callainos were able to reliably recognize conspecific males, even when colour was eliminated as a cue. However, females of M. estherae did not prefer conspecific males, although they were able to discriminate between red and blue conspecific colour morphs by using chemical cues. These results suggest that species recognition cues may differ even among closely related species of cichlid fish, and that female preferences for male coloration may be weak in certain species.     

Widely different off rates of two closely related cellulose-binding domains from Trichoderma reesei.

The filamentous fungus Trichoderma reesei produces two cellobiohydrolases (CBHI and CBHII). These, like most other cellulose-degrading enzymes, have a modular structure consisting of a catalytic domain linked to a cellulose-binding domain (CBD). The isolated catalytic domains bind poorly to cellulose and have a much lower activity towards cellulose than the intact enzymes. For the CBDs, no function other than binding to cellulose has been found. We have previously described the reversibility and exchange rate for the binding of the CBD of CBHI to cellulose. In this work, we studied the binding of the CBD of CBHII and showed that it differs markedly from the behaviour of that of CBHI. The apparent binding affinities were similar, but the CBD of CBHII could not be dissociated from cellulose by buffer dilution and did not show a measurable exchange rate. However, desorption could be triggered by shifting the temperature. The CBD of CBHII bound reversibly to chitin. Two variants of the CBHII CBD were made, in which point mutations increased its similarity to the CBD of CBHI. Both variants were found to bind reversibly to cellulose.     

Nad+-dependent isocitrate dehydrogenase from Arabidopsis thaliana. Characterization of two closely related subunits

Two cDNA clones which appear to encode different subunits of NAD⁺-dependent isocitrate dehydrogenase (IDH; EC 1.1.1.41) were identified by homology searches from the Arabidopsis EST database. These cDNA clones were obtained and sequenced; both encoded full-length messages and displayed 82.7% nucleotide sequence identity over the coding region. The deduced amino acid sequences revealed preprotein lengths of 367 residues, with an amino acid identity of 86.1%. Genomic Southern blot analysis showed distinct single-copy genes for both IDH subunits. Both IDH subunits were expressed as recombinant proteins in Escherichia coli, and polyclonal antibodies were raised to each subunit. The Arabidopsis cDNA clones were expressed in Saccharomyces cerevisiae mutants which were deficient in either one or both of the yeast NAD⁺-dependent IDH subunits. The Arabidopsis cDNA clones failed to complement the yeast mutations; although both IDH-I and IDH-II were expressed at detectable levels, neither protein was imported into the mitochondria.