When structure leads to sex: Untangling signals in population genetic data sets

A robust signal of population structure often provides the first glimpse into the evolutionary history of a species and its populations. In this issue of Molecular Ecology, new work from Louis Bernatchez's group (Benestan et al., 2017 ) starts with an investigation of apparent structure in two marine species and concludes with an identification of sex‐linked genes, and in the process provides a model for robust analysis. Structure is the genetic signal left by natural selection as well as by neutral processes like migration and gene flow. Neutral areas of the genome can reveal the geographical relationships and related gene flow between populations over time and space, while selection can resist the natural genomic turnover created by recombination and generate adaptive structure between populations that can be detected. However, artefacts in a data set can easily hide the true signal of structure; mutation, whether it is a true appearance of a recent, minor allele, or more commonly, an error in SNP calling or molecular library construction, can easily conceal patterns of population structure (e.g., geographical structure in mackerel, Rodriguez‐Ezpeleta et al. ( 2016 )). A demographic structure that results from the most “forceful” evolutionary processes can overwhelm another signal generated by other, unrelated phenotypes. For example, the structure among diverged freshwater and marine threespine stickleback populations results from such strong selection and linkage disequilibrium across the genome that it impairs the ability to disentangle the genetic basis of particular evolved morphological traits (e.g., opercle development, Alligood ( 2017 )). Finally, there might be conflicting inferences for what underlies structure patterns. Structure may be created by differential patterns of meiotic recombination, and genetic maps are a reliable means for identifying genomic regions that resist recombination. But, without additional information (Anderson et al., 2012 ), it can be difficult to distinguish the recombination‐suppressing effect of a segregating genomic inversion (Small et al., 2016 ) from that of sex‐linked selection.     

基于GIS与多目标区位配置模型的沈阳市公园选址

结合地理信息系统(GIS)与多目标区位配置模型(LA),综合考虑4个相对独立的目标因子(人口密度等级、空气污染等级、城市热岛效应等级、土地利用格局)对沈阳市三环内城市公园进行优化选址,并将优化结果与公园现状空间分布进行比较,以评价城市公园空间布局的合理性.结果表明： 与其他因子相比,空气污染因子对研究区城市绿地的选址具有重要影响.与单目标因子相比,多目标综合加权分析的结果能够合理地为城市绿地提供优化的空间选址.GIS与LA相结合的方法为城市绿地的空间优化提供了新思路.     

高中生与大学生飞行学员基本认知能力的比较研究

目的：比较高中生与大学生在空军招飞基本认知能力测验成绩上是否存在差异。方法：用完全随机设计的方法,采用新编飞行员基本认知能力测验,包括无意义图形记忆、注意力持久、局部整体图形转换、图形识别、距离判断力、三维空间认知能力测验,对720名高中生与大学生进行测评,比较两者间的异同。结果：无意义图形记忆、注意力持久,局部整体图形转换,图形识别,距离判断力测验,大学生的成绩要优于高中生的成绩,差异有统计学意义（P（0．05）;大学生与高中生的三维空间认知能力测验成绩在统计学上没有显著差异（P〉O．05）。结论：大学生的记忆力、注意力的持久性和转换性、观察力等基本认知能力水平高于高中生,在三维空间认知能力方面二者的水平是相当的,建议在今后的招飞工作中可扩大对大学生的招生规模。     

Development of SCAR markers linked to a gene controlling absence of tannins in faba bean

Faba beans are inexpensive, nutrient-dense sources of plant protein, but anti-nutritional factors such as condensed tannins reduce the biological value of their protein. Two recessive genes, zt-1 and zt-2, control the absence of tannins in faba bean seeds and also determine a white flower character on the plant. However, crosses between them produce coloured F₁ plants with tannins that contaminate the crop. Therefore, it is important to identify the gene present in all tannin-free cultivars and gene bank accessions to enable breeders to choose appropriate genitors for their crosses. The aim of this study was the identification of markers linked to zt-1, one of the genes governing free tannin content in faba bean. A segregating F₂ population derived from the cross between the coloured flower and high tannin content genotype Vf6 and a zt-1 line was developed and characterized phenotypically. Bulked Segregant Analysis (BSA) was used to identify Random Amplified Polymorphic DNA (RAPD) markers linked to the zt-1 gene. Four RAPD loci (OPC5₅₅₁, OPG15₆₀₀, OPG11₁₁₇₁ and OPAF20₇₇₆) showed polymorphism between the contrasting bulks. The markers were sequenced to develop specific Sequence Characterised Amplified Regions (SCARs). Amplification of SCC5₅₅₁ produced a single product which was only observed in the white flowered and zero tannin content genotypes, whereas SCAR SCG11₁₁₇₁only produced a band in F₂ plants with coloured flower and high tannin content. SCARs SCC5₅₅₁ and SCG11₁₁₇₁ were tested for their applicability for routine screening in 37 faba bean genotypes differing in flower colour and tannin content. SCC5₅₅₁, allowed the prediction of the zt-1 genotypes with a 95% of accuracy, underscoring the potential of this SCAR marker as a cost-effective tool for MAS in large faba bean breeding populations.     

Size and Partner Choice in Dysdercus maurus Distant (Hemiptera: Pyrrhocoridae)

This study investigates whether females of Dysdercus maurus (Hemiptera) are considering male’s sizes in order to make their reproductive partner choice. Morphometric and biomass measurements were obtained from single males and copulating pairs. Positive correlations were identified for both sizes and weights between males and females in copula. The average ratios established between the couples sizes/weight were around 1.66. Female choice may operate in such a way that each female has her own optimal male size for mating, resulting from a trade-off between the negative influence of large partner size in female fecundity and the advantages of large male size for offspring fitness. Thus, the best choice for a D. maurus female may be a male of average size in relation with her own size.     

The evolution of premating isolation: local adaptation and natural and sexual selection against hybrids

Although reinforcement is ostensibly driven by selection against hybrids, there are often other components in empirical cases and theoretical models of reinforcement that may contribute to premating isolation. One of these components is local adaptation of a trait used in mate choice. I use several different comparisons to assess the roles that local adaptation and selection against hybrids may play in reinforcement models. Both numerical simulations of exact recursion equations and analytical weak selection approximations are employed. I find that selection against hybrids may play a small role in driving preference evolution in a reinforcement model where the mating cue is separate from loci causing hybrid incompatibilities. When females have preferences directly for purebreds of their own population, however, selection against hybrids can play a large role in premating isolation evolution. I present some situations in which this type of selection is likely to exist. This work also illustrates shortfalls of using a weak selection approach to address questions about reinforcement.     

Predicting disulfide connectivity patterns

Disulfide bonds play an important role in stabilizing protein structure and regulating protein function. Therefore, the ability to infer disulfide connectivity from protein sequences will be valuable in structural modeling and functional analysis. However, to predict disulfide connectivity directly from sequences presents a challenge to computational biologists due to the nonlocal nature of disulfide bonds, i.e., the close spatial proximity of the cysteine pair that forms the disulfide bond does not necessarily imply the short sequence separation of the cysteine residues. Recently, Chen and Hwang (Proteins 2005;61:507-512) treated this problem as a multiple class classification by defining each distinct disulfide pattern as a class. They used multiple support vector machines based on a variety of sequence features to predict the disulfide patterns. Their results compare favorably with those in the literature for a benchmark dataset sharing less than 30% sequence identity. However, since the number of disulfide patterns grows rapidly when the number of disulfide bonds increases, their method performs unsatisfactorily for the cases of large number of disulfide bonds. In this work, we propose a novel method to represent disulfide connectivity in terms of cysteine pairs, instead of disulfide patterns. Since the number of bonding states of the cysteine pairs is independent of that of disulfide bonds, the problem of class explosion is avoided. The bonding states of the cysteine pairs are predicted using the support vector machines together with the genetic algorithm optimization for feature selection. The complete disulfide patterns are then determined from the connectivity matrices that are constructed from the predicted bonding states of the cysteine pairs. Our approach outperforms the current approaches in the literature.     

Long term oviposition preference and larval performance of Schizomyia macrocapillata (Diptera: Cecidomyiidae) on larger shoots of its host plant Bauhinia brevipes (Fabaceae)

The Plant Vigor Hypothesis (PVH) proposes that natural selection on female oviposition choice results from higher fitness of larvae on more vigorous and larger plant modules. For six consecutive years we tested the PVH predictions by investigating the effect of shoot size of Bauhinia brevipes (Fabaceae) on the oviposition preference and offspring survival of the gall-midge Schizomyia macrocapillata (Diptera: Cecidomyiidae). Additionally, we analyzed the effects of bottom-up and top-down mortality forces on the system. The hypersensitive reaction (bottom-up effect) accounted for more than 90% larval mortality of S. macrocapillata, making available few galls to be found and killed by natural enemies (top-down effect). Smaller shoots were always more abundant while longer shoots were rare. Nevertheless, the percent number of galls induced by S. macrocapillata was up to 10-fold greater on the largest shoots, corroborating the preference prediction of the PVH. Schizomyia macrocapillata should use over-exploit larger shoots to maximize the preference for, and consequently increase the performance on these shoots. Our results partially support the performance prediction of the PVH: (1) the observed survival was higher than expected on longer shoots, and (2) the ratio of survival per shoot was positively related with shoot length only in 2 years. Thus, we found a link between female preference and larval performance on large-sized shoots, at least in some years. The gall-midge attack pattern in this study might be an evolved response to maximize the female preference and increased larval performance on longer shoots of the host plant.     

镜鲤体长性状的QTL定位分析

以镜鲤良种后代为祖父母本所培育的杂交F2群体的68个个体为材料,利用553个分子标记(217个SSR和336个SNP标记)对其进行基因型检测,运用JoinMap4.0软件包对遗传连锁图谱进行构建。利用MapQTL5.0区间作图法(Interval mapping)进行QTL检测,通过置换实验(1 000次重复)确定连锁群显著性水平阈值。在对体长的区间定位中共检测到12个与体长性状相关的QTLs区间,分布在BL-1-1(SNP0137-SNP1481)、BL-4-1(SNP0092-HLJ797)、BL-5-1(SNP1268-HLJ423)、BL-7-1(HLJ870-SNP0702)、BL-12-1(SNP0922-HLJ639)、BL-16-1(HLJE351-SNP0674)、BL-25-1(SNP0394-SNP0862)、BL-35-1(HLJ668-SNP0832)、BL-43-1(SNP0389-SNP1425)、BL-47-1(HLJ057-HLJ1113)、BL-47-2(HLJ1439-HLJ1418)等11个连锁群上,解释表型变异范围是13.8%~64.9%,其中贡献率大于20%的主效QTLs有8个,是体长性状的主效QTLs区间。     

Inbred mouse strains and genetic stability: a review

Inbred mice were essential animal models for scientific research during the 20th century and will contribute decisive results in the current and next centuries. Far from becoming an obsolete research tool, the generation of new inbred strains is continuing and such strains are being used in many research fields. However, their genetic properties have been overlooked for decades, although recent research has revealed new insights into their genetic fragility and relative instability. Contrary to what we usually assume, inbred mice are far from being completely isogenic and both single-gene major mutations and polygenic mutational variability are continuously uploading into inbred populations as new sources of genetic polymorphisms. Note that several inbred strains from new major mutations are released every year, whereas small mutations can accumulate up to accounting for a significant percentage of the phenotypic variance (e.g. 4.5% in a recent study on C57BL/6J mice). Moreover, this genetic heterogeneity can be maintained for several generations by heterozygote selection and, if fixed instead of dropping off, genetic drift must be anticipated. The contribution of accidental genetic contamination in inbred strains must also be considered, although its incidence in current breeding stocks should be minimal, or even negligible. This review revisits several relevant topics for current inbred strains, discussing the latest cutting-edge results within the context of the genetic homogeneity and stability of laboratory mice. Inbred mice can no longer be considered as completely isogenic, but provide a remarkably homogeneous animal model with an inevitable moderate-to-low degree of genetic variability. Despite a certain degree of genetic heterogeneity becoming inescapable, inbred mice still provide very useful animal models with evident advantages when compared with outbred, that is, highly variable, populations.