Rhh: an R extension for estimating multilocus heterozygosity and heterozygosity-heterozygosity correlation

Individual multilocus heterozygosity estimates based on a limited number of loci are expected to correlate only weakly with the inbreeding level of an individual. Before using multilocus heterozygosity estimates in studies of inbreeding, their ability to capture information on inbreeding in the given setting should be tested. A convenient method for this is to compute the heterozygosity-heterozygosity correlation, i.e. the mean correlation between multilocus heterozygosity estimates calculated from random samples of loci, which should be positive if multilocus heterozygosity carries a signature of inbreeding. Rhh is an extension package for the statistical software r that estimates this correlation and calculates three measures of individual multilocus heterozygosity: homozygosity by loci, internal relatedness and standardized heterozygosity. The extension package is available through the CRAN (http://cran.r-project.org) and has a homepage at http://www.helsinki.fi/biosci/egru/research/software.     

云南文山黄牛和迪庆黄牛遗传多样性的蛋白电泳研究

采用水平淀粉胶蛋白电泳技术分析了云南文山黄牛和迪庆黄牛的３３种血液蛋白及同工酶,共计３７个遗传座位,其中６个座位检测到多态性。文山黄牛的多态座位百分比Ｐ＝０．１３８９,平均杂合度Ｈ＝０．０６１０,迪庆黄牛Ｐ＝０．１６６７,Ｈ＝０．０６９１。通过Ｎｅｉ氏遗传距离计算,运用ＰＨＹＬＩＰ３．５Ｃ软件包中的“ＵＰＧＭＡ”,“ＣＯＮＴＭＬ”和“ＮＥＩＧＨＢＯＲ”法,结合前人报道的数据对１０个黄牛品种进行聚类分析。结果得出：文山黄牛可能主要起源于瘤牛（Ｂｏｓｉｎｄｉｃｕｓ）,迪庆黄牛可能主要起源于普通黄牛（Ｂｏｓｔａｕｒｕｓ）。我们的结果提示,云南黄牛可能是由当地人驯化的野生牛群与外来的驯化牛群相结合并适应当地气候和环境逐渐形成的,因而在蛋白水平上具有较为丰富的多样性。     

Direct fitness benefits explain mate preference,but not choice,for similarity in heterozygosity levels

Under sexual selection, mate preferences can evolve for traits advertising fitness benefits. Observed mating patterns (mate choice) are often assumed to represent preference, even though they result from the interaction between preference, sampling strategy and environmental factors. Correlating fitness with mate choice instead of preference will therefore lead to confounded conclusions about the role of preference in sexual selection. Here we show that direct fitness benefits underlie mate preferences for genetic characteristics in a unique experiment on wild great tits. In repeated mate preference tests, both sexes preferred mates that had similar heterozygosity levels to themselves, and not those with which they would optimise offspring heterozygosity. In a subsequent field experiment where we cross fostered offspring, foster parents with more similar heterozygosity levels had higher reproductive success, despite the absence of assortative mating patterns. These results support the idea that selection for preference persists despite constraints on mate choice.     

‘Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160 ± 3 μmol L^?1 d^?1. The DCM degrader attained 5.25 × 10⁷ ± 1.0 × 10⁷ cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4 ± 0.8 μm long and 0.4 ± 0.1 μm wide. Based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, ‘Candidatus Dichloromethanomonas elyunquensis’.     

Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs

The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1 kb regions of 13 genic (within gene or <1 kb away from gene) and 13 nongenic (>10 kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between‐lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within‐lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad‐scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine‐scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions.     

Strikingly high levels of heterozygosity despite 20 years of inbreeding in a clonal honey bee

Inbreeding (the mating between closely related individuals) often has detrimental effects that are associated with loss of heterozygosity at overdominant loci, and the expression of deleterious recessive alleles. However, determining which loci are detrimental when homozygous, and the extent of their phenotypic effects, remains poorly understood. Here, we utilize a unique inbred population of clonal (thelytokous) honey bees, Apis mellifera capensis, to determine which loci reduce individual fitness when homozygous. This asexual population arose from a single worker ancestor approximately 20 years ago and has persisted for at least 100 generations. Thelytokous parthenogenesis results in a 1/3 of loss of heterozygosity with each generation. Yet, this population retains heterozygosity throughout its genome due to selection against homozygotes. Deep sequencing of one bee from each of the three known sub‐lineages of the population revealed that 3,766 of 10,884 genes (34%) have retained heterozygosity across all sub‐lineages, suggesting that these genes have heterozygote advantage. The maintenance of heterozygosity in the same genes and genomic regions in all three sub‐lineages suggests that nearly every chromosome carries genes that show sufficient heterozygote advantage to be selectively detrimental when homozygous.     

Correlated pedigree and molecular estimates of inbreeding and their ability to detect inbreeding depression in the Icelandic sheepdog, a recently bottlenecked population of domestic dogs

We examine the relationship of the inbreeding coefficient (f) and molecular estimates of inbreeding (IR, sMLH) in the Icelandic sheepdog. The breed experienced a severe genetic bottleneck and near extinction in the last century. Molecular estimates and the inbreeding coefficient are significantly correlated despite the moderate number of markers and individuals used in this study. This is most likely an effect of the extreme relatedness and relatively high variance in individual inbreeding coefficients in the population. There is a significant relationship between inbreeding (f) and the occurrence of hip dysplasia. However, the molecular measures did not detect hip dysplasia as an inbreeding effect.     

Human health risks of metals and metalloids in muscle tissue of Synodontis zambezensis Peters, 1852 from Flag Boshielo Dam,South Africa

Muscle tissue from 63 Synodontis zambezensis collected bimonthly in 2013 at Flag Boshielo Dam were analysed for metals and metalloids in a desktop human health risk assessment. The Hazard Quotient, based on a weekly meal of 67 g of fish muscle, exceeded the maximum acceptable level of one for lead, cobalt, cadmium, mercury, arsenic and selenium. The concentrations of these elements were higher in 2013 than those recorded in 2009 and 2012 in other fish species from Flag Boshielo Dam and these may pose a long-term health risk if consumed regularly by impoverished rural communities reliant on fish as a source of protein.     

Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis

Experiments that longitudinally collect RNA sequencing (RNA-seq) data can provide transformative insights in biology research by revealing the dynamic patterns of genes. Such experiments create a great demand for new analytic approaches to identify differentially expressed (DE) genes based on large-scale time-course count data. Existing methods, however, are suboptimal with respect to power and may lack theoretical justification. Furthermore, most existing tests are designed to distinguish among conditions based on overall differential patterns across time, though in practice, a variety of composite hypotheses are of more scientific interest. Finally, some current methods may fail to control the false discovery rate. In this paper, we propose a new model and testing procedure to address the above issues simultaneously. Specifically, conditional on a latent Gaussian mixture with evolving means, we model the data by negative binomial distributions. Motivated by Storey (2007) and Hwang and Liu (2010), we introduce a general testing framework based on the proposed model and show that the proposed test enjoys the optimality property of maximum average power. The test allows not only identification of traditional DE genes but also testing of a variety of composite hypotheses of biological interest. We establish the identifiability of the proposed model, implement the proposed method via efficient algorithms, and demonstrate its good performance via simulation studies. The procedure reveals interesting biological insights, when applied to data from an experiment that examines the effect of varying light environments on the fundamental physiology of the marine diatom Phaeodactylum tricornutum.