Genome analyses substantiate male mutation bias in many species

In many species the mutation rate is higher in males than in females, a phenomenon denoted as male mutation bias. This is often observed in animals where males produce many more sperm than females produce eggs, and is thought to result from differences in the number of replication-associated mutations accumulated in each sex. Thus, studies of male mutation bias have the capacity to reveal information about the replication-dependent or replication-independent nature of different mutations. The availability of whole genome sequences for many species, as well as for multiple individuals within a species, has opened the door to studying factors, both sequence-specific and those acting on the genome globally, that affect differences in mutation rates between males and females. Here, we assess the advantages that genomic sequences provide for studies of male mutation bias and general mutation mechanisms, discuss major challenges left unresolved, and speculate about the direction of future studies.     

Molecular considerations in the evolution of bacterial genes

Summary Synonymous and nonsynonymous substitution rates at the loci encoding glyceraldehyde-3-phosphate dehydrogenase (gap) and outer membrane protein 3A (ompA) were examined in 12 species of enteric bacteria. By examining homologous sequences in species of varying degrees of relatedness and of known phylogenetic relationships, we analyzed the patterns of synonymous and nonsynonymous substitutions within and among these genes. Although both loci accumulate synonymous substitutions at reduced rates due to codon usage bias, portions of thegap andompA reading frames show significant deviation in synonymous substitution rates not attributable to local codon bias. A paucity of synonymous substitutions in portions of theompA gene may reflect selection for a novel mRNA secondary structure. In addition, these studies allow comparisons of homologous protein-coding sequences (gap) in plants, animals, and bacteria, revealing differences in evolutionary constraints on this glycolytic enzyme in these lineages.     

Reduction of maternal care: a new benefit of multiple mating?

Cost/benefit analyses have been used to understand the evolutionof mating by females with multiple males, as in extrapair copulations(EPCs), which are now known to occur commonly in socially monogamousand polygynous birds. Indirect (genetic) benefits have beeninvoked to explain such mating patterns in some cases, butdirect benefits have received less attention. We report a studyof direct benefits in the communally rearing Mexican jay (Aphelocoma ultramarina). The social mate of the mother (putative father)is the most reliable feeder of the young in his nest, regardlessof cuckoldry. Feedings provided by social fathers are not reducedin relation to their paternity loss. In contrast, mothers havingnestlings sired by a second male tend to have lower feedingrates than those without such young. Secondary fathers provideda significantly higher level of feeding to the brood of theirfemale than did (1) random nonbreeders of all ages and bothsexes, (2) random male nonbreeders of all ages, and (3) older(2+ years), male nonbreeders. Surprisingly, however, broodswith two fathers did not receive a higher level of total feeding,despite our observation that two-father broods had two more helpers, on average, compared to broods without extra fathers.Regardless of age or breeding status, males were more frequentfeeders than females. This study provides the first evidencethat one of the major costs of reproduction, maternal careof nestlings, is reduced for females that have young sired by secondary males.     

Measuring Attentional Biases for Threat in Children and Adults

Investigators have long been interested in the human propensity for the rapid detection of threatening stimuli. However, until recently, research in this domain has focused almost exclusively on adult participants, completely ignoring the topic of threat detection over the course of development. One of the biggest reasons for the lack of developmental work in this area is likely the absence of a reliable paradigm that can measure perceptual biases for threat in children. To address this issue, we recently designed a modified visual search paradigm similar to the standard adult paradigm that is appropriate for studying threat detection in preschool-aged participants. Here we describe this new procedure. In the general paradigm, we present participants with matrices of color photographs, and ask them to find and touch a target on the screen. Latency to touch the target is recorded. Using a touch-screen monitor makes the procedure simple and easy, allowing us to collect data in participants ranging from 3 years of age to adults. Thus far, the paradigm has consistently shown that both adults and children detect threatening stimuli (e.g., snakes, spiders, angry/fearful faces) more quickly than neutral stimuli (e.g., flowers, mushrooms, happy/neutral faces). Altogether, this procedure provides an important new tool for researchers interested in studying the development of attentional biases for threat.     

Non-uniqueness of factors constraint on the codon usage in Bombyx mori

Background

The analysis of codon usage is a good way to understand the genetic and evolutionary characteristics of an organism. However, there are only a few reports related with the codon usage of the domesticated silkworm, Bombyx mori (B. mori). Hence, the codon usage of B. mori was analyzed here to reveal the constraint factors and it could be helpful to improve the bioreactor based on B. mori.

Results

A total of 1,097 annotated mRNA sequences from B. mori were analyzed, revealing there is only a weak codon bias. It also shows that the gene expression level is related to the GC content, and the amino acids with higher general average hydropathicity (GRAVY) and aromaticity (Aromo). And the genes on the primary axis are strongly positively correlated with the GC content, and GC3s. Meanwhile, the effective number of codons (ENc) is strongly correlated with codon adaptation index (CAI), gene length, and Aromo values. However, the ENc values are correlated with the second axis, which indicates that the codon usage in B. mori is affected by not only mutation pressure and natural selection, but also nucleotide composition and the gene expression level. It is also associated with Aromo values, and gene length. Additionally, B. mori has a greater relative discrepancy in codon preferences with Drosophila melanogaster (D. melanogaster) or Saccharomyces cerevisiae (S. cerevisiae) than with Arabidopsis thaliana (A. thaliana), Escherichia coli (E. coli), or Caenorhabditis elegans (C. elegans).

Conclusions

The codon usage bias in B. mori is relatively weak, and many influence factors are found here, such as nucleotide composition, mutation pressure, natural selection, and expression level. Additionally, it is also associated with Aromo values, and gene length. Among them, natural selection might play a major role. Moreover, the “optimal codons” of B. mori are all encoded by G and C, which provides useful information for enhancing the gene expression in B. mori through codon optimization.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1596-z) contains supplementary material, which is available to authorized users.     

On comparison of mixture models for closed population capture-recapture studies

Summary .  A mixture model is a natural choice to deal with individual heterogeneity in capture–recapture studies. Pledger (2000, Biometrics 56, 434–442; 2005, Biometrics 61, 868–876) advertised the use of the two-point mixture model. Dorazio and Royle (2003, Biometrics 59, 351–364; 2005, Biometrics 61, 874–876) suggested that the beta-binomial model has advantages. The controversy is related to the nonidentifiability of the population size ( Link, 2003 , Biometrics 59, 1123–1130) and certain boundary problems. The total bias is decomposed into an intrinsic bias, an approximation bias, and an estimation bias. We propose to assess the approximation bias, the estimation bias, and the variance, with the intrinsic bias excluded when comparing different estimators. The boundary problems in both models and their impacts are investigated. Real epidemiological and ecological examples are analyzed.     

Analysis of mitochondrial protein‐coding genes of Antheraea assamensis: Muga silkworm of Assam

To understand the synonymous codon usage pattern in mitochondrial genome of Antheraea assamensis, we analyzed the 13 mitochondrial protein‐coding genes of this species using a bioinformatic approach as no work was reported yet. The nucleotide composition analysis suggested that the percentages of A, T, G,and C were 33.73, 46.39, 9.7 and 10.17, respectively and the overall GC content was 19.86, that is, lower than 50% and the genes were AT rich. The mean effective number of codons of mitochondrial protein‐coding genes was 36.30 and it indicated low codon usage bias (CUB). Relative synonymous codon usage analysis suggested overrepresented and underrepresented codons in each gene and the pattern of codon usage was different among genes. Neutrality plot analysis revealed a narrow range of distribution for GC content at the third codon position and some points were diagonally distributed, suggesting both mutation pressure and natural selection influenced the CUB.     

Ab initio investigations on the geometric and electronic structures of a diblock molecular diode under the influence of an external bias

Theoretical investigations on the diblock molecular diode, thiophene–thiazole compound, have been carried out at the Hartree–Fock (HF) level by considering the interaction under the external bias. They demonstrate that the electronic structures of this kind of diode molecule are essentially different from those based on the Aviram and Ratner model, in which donor and acceptor π-conjugated segments are separated by an insulating σ-bonded segment, in terms of the energy levels of the frontier molecular orbitals as well as their spatial distributions. The introduction of the external bias modifies both the geometric and electronic structures. In particular, the spatial distributions of the frontier molecular orbitals are also shifted under the external bias. Moreover, all these features show a strong dependence on the polarity of the applied bias due to the build in intrinsic molecular asymmetric structures, which could be used to intuitively interpret the asymmetrical current–voltage behaviours of molecules.     

What are we measuring? Novices agree amongst themselves (but not always with experts) in their assessment of dog behaviour

Humans differ in how they perceive, assess, and measure animal behaviour. This is problematic because strong observer bias can reduce statistical power, accuracy of scientific inference, and in the worst cases, lead to spurious results. Unfortunately, reports and studies of measurement reliability in animal behaviour studies are rare. Here, we investigated two aspects of measurement reliability in working dogs: inter‐observer agreement and criterion validity (comparing novice ratings with those given by experts). Here, we extend for the first time a powerful framework used in human psychological studies to investigate three potential aspects of (dis)agreement in nonhuman animal behaviour research: (a) that some behaviours are easier to observe than others; (b) that some subjects are easier to observe than others; and (c) that observers with different levels of experience with the subject animal give the same or different ratings. We found that novice observers with the same level of experience agreed upon measures of a wide range of behaviours. We found no evidence that age of the dogs affected agreement between these same novice observers. However, when observers with different levels of experience (i.e., novices vs. a working dog expert) assessed the same dogs, agreement appeared to be strongly affected by the measurement instrument used to assess behaviour. Given that animal behaviour research often utilizes different observers with different levels of experience, our results suggest that further tests of how different observers may measure behaviour in different ways are needed across a wider variety of organisms and measurement instruments.