Inference of Gene Flow between Species under Misspecified Models

Genomic sequence data provide a rich source of information about the history of species divergence and interspecific hybridization or introgression. Despite recent advances in genomics and statistical methods, it remains challenging to infer gene flow, and as a result, one may have to estimate introgression rates and times under misspecified models. Here we use mathematical analysis and computer simulation to examine estimation bias and issues of interpretation when the model of gene flow is misspecified in analysis of genomic datasets, for example, if introgression is assigned to the wrong lineages. In the case of two species, we establish a correspondence between the migration rate in the continuous migration model and the introgression probability in the introgression model. When gene flow occurs continuously through time but in the analysis is assumed to occur at a fixed time point, common evolutionary parameters such as species divergence times are surprisingly well estimated. However, the time of introgression tends to be estimated towards the recent end of the period of continuous gene flow. When introgression events are assigned incorrectly to the parental or daughter lineages, introgression times tend to collapse onto species divergence times, with introgression probabilities underestimated. Overall, our analyses suggest that the simple introgression model is useful for extracting information concerning between-specific gene flow and divergence even when the model may be misspecified. However, for reliable inference of gene flow it is important to include multiple samples per species, in particular, from hybridizing species.     

报春花属的保育遗传学及亲缘地理学研究进展

现存物种的分布格局、遗传结构是当前因素和历史因素共同作用的结果。人类的过度开发、全球变暖等当前因素造成的生境片段化是目前许多报春花属植物濒危的一大原因。该文总结了近年来报春花属内的保育遗传学研究进展,期望以此为更好地保护报春花属植物提供一定的理论基础。应用亲缘地理学研究方法可以弥补古生物学难以研究报春花植物历史成因的不足,因此也总结该方法在报春花属内的研究进展,并初步整理不同地区间的报春花属植物的分化式样,同时期望这些研究成果能为为研究报春花属植物在应对全球气候变化的响应机制方面提供一些参考。     

Multiple differentiation centres of a non-Mediterranean butterfly species in south-eastern Europe

Aim  The analysis of the phylogeographical structures of many European species reveals the importance of Mediterranean glacial refugia for many thermophilic species, but also underlines the relevance of extra-Mediterranean glacial differentiation centres for a number of temperate species. In this context, phylogeographical analyses of species from south-eastern Europe are highly important for a comprehensive understanding of Europe as a whole.
Location  Romania and Bulgaria.
Methods  We analysed 19 allozyme loci for 615 individuals of the temperate butterfly species Erebia medusa from 28 populations.
Results  These populations had an intermediate genetic diversity, but the Bulgarian populations were significantly more diverse than the ones north of the Danube in Romania. The differentiation among populations was strong, and 52.1% of the genetic variance among populations was distributed between these two countries. The genetic differentiation was considerably stronger in Romania than in Bulgaria, but several sublineages were distinguished within each of these countries.
Main conclusions  The observed genetic structure is so strong that it is most probably the result of glacial differentiation processes in south-eastern Europe and not a post-glacial structure. The strong differentiation into the two groups north and south of the Danube suggests a separating effect by this river valley. The strong differentiation accompanied with genetic impoverishment in Romania suggests the existence of several differentiation centres: at least two small ones on the southern slopes of the southern Carpathians and one in the eastern Carpathian Basin. The considerably weaker differentiation among the Bulgarian samples and their significantly higher genetic diversity imply that gene flow occurred among different regions of Bulgaria during the last ice age.     

小菜蛾热休克蛋白基因的鉴定及其表达模式分析

热休克蛋白(heat shock protein, HSP)在昆虫应对外界胁迫刺激时起着重要作用。为了系统研究小菜蛾Plutella xylostella HSP基因家族, 根据家蚕的HSP蛋白序列, 采用本地Blast程序对小菜蛾全基因组数据库进行同源序列检索, 从小菜蛾基因组数据库中鉴定了25个HSP基因, 包括2个HSP90、 8个HSP70和15个sHSP（small heat shock protein, sHSP）基因。小菜蛾、 家蚕Bombyx mori、 黑腹果蝇Drosophila melanogaster和赤拟谷盗Tribolium castaneum的HSP系统进化分析显示, 昆虫的小分子量热休克蛋白sHSP具有很强的种属特异性, HSP70家族的保守性比sHSP强。小菜蛾HSP基因表达模式分析显示, 与敏感品系对比, 抗性品系（抗毒死蜱和抗氟虫氰品系）中HSP基因具有不同的表达模式。小菜蛾1, 2和3龄幼虫HSP基因表达模式较为接近, 而与4龄幼虫中的表达模式相差较大; 4龄幼虫和蛹中的表达模式相近; 雌成虫和雄成虫中的表达模式显著不同, 与果蝇精子形成有关的两个热休克蛋白HSP23和HSP27基因［分别为CCG003980.1 (Px23.5)和CCG005412.2 (Px27.5)］, 在小菜蛾雄成虫中的表达量显著高于雌成虫。研究结果表明小菜蛾HSP基因不仅在杀虫剂抗性、 发育分化, 甚至在生殖上均可能起着重要的作用。本研究为深入研究小菜蛾HSP与生长发育、 抗逆行为的相互关系奠定了基础。     

大车前与平车前营养器官的比较解剖学研究

利用光学显微镜和石蜡切片技术对生长在盐碱地的大车前和平车前的营养器官进行了比较解剖学研究。结果表明二者的解剖结构存在差异:平车前根的木栓层较大车前的狭窄,栓内层细胞层数较少;平车前叶表皮的细胞角质膜较薄,孔下室较小,构成维管束鞘的薄壁细胞较大车前小,束鞘细胞两层。二者都具有适应盐渍环境的结构特征:营养器官中通气组织发达;根结构中薄壁组织和木栓发达;叶表皮角质层发达。     

聚苹果酸生产菌出芽短梗霉CCTCC M2012223的全基因组测序及序列分析

【目的】解析出芽短梗霉CCTCC M2012223的基因组序列信息,分析其代谢产物聚苹果酸、黑色素、普鲁兰多糖合成相关基因,为深入研究遗传多样性和代谢工程改造提供序列背景信息。【方法】使用Illumina Hi Seq高通量测序平台对出芽短梗霉CCTCC M2012223菌株进行全基因组测序,并对测序数据进行序列拼接,基因预测与功能注释,COG/GO聚类分析,比较基因组学分析等。下载其他5株出芽短梗霉基因组序列,比较分析6株菌的种内同源基因、全基因组进化以及代谢产物合成相关基因。【结果】出芽短梗霉CCTCC M2012223基因组序列全长30756831 bp,GC含量47.49%,编码9452个基因。比较基因组分析表明出芽短梗霉CCTCC M2012223的基因组组装长度最长,6株菌的同源基因数达到7092个,普鲁兰多糖和聚苹果酸合成相关基因的蛋白序列有很高的保守性。出芽短梗霉CCTCC M2012223和Aureobasidium pullulans var.melanogenum亲缘关系最近,而这2株菌的黑色素合成相关基因的蛋白序列有一些插入和突变。【结论】本研究解析了出芽短梗霉CCTCC M2012223的基因组序列信息,获得黑色素、普鲁兰多糖和聚苹果酸合成相关基因,为后续的代谢机制解析和改造提供相关依据。     

Molecular Views of Human Origins

Over the last half century, comparative genomics has increasingly contributed to the definition, resolution and interpretation of human evolution. Early comparisons demonstrated that African apes and humans were more closely related and diverged later than commonly thought. However, it was difficult to determine the branching between humans, chimpanzees and gorillas. By the 1990s, sufficient biomolecular data had accumulated to demonstrate that chimpanzees and humans shared a common ancestor after the divergence of the gorilla. Current reconstructions place the divergence of humans and chimpanzees at 6–8 million years. Comparative genomics from complete genome sequencing to chromosome painting provide a scenario for the origin of the human genome. Starting form the ancestral mammalian karyotype, we can determine the major steps over the last 90 million years leading to the formation of each human chromosome. Despite considerable technical problems, studies of ancient DNA now provide a direct genetic witness of human evolution and add a temporal dimension to reconstructions of our evolutionary history and phylogeny. Ancient DNA has shown that Neanderthals probably did not interbreed with anatomically modern humans and did not make a significant contribution to the gene pool of our species. Ancient DNA has also contributed to the studies of the colonization of the Americas and the Pacific Island, and the domestication of plants and animals. Understanding the genetic basis of the physical and behavioral traits that distinguish humans from other primates presents one of the great future challenges of science.     

The Influences of Environment, Mating Habitat, and Predation on Evolution of Pinniped Lactation Strategies

Seals have adapted their social systems and lactation strategies to marine environments that include open and ice-covered oceans, high and low productivity, extremes in seasonality, and ocean- and terrestrial-type predators. Different explanations for the variation in pinniped lactation systems have been proposed but tests of alternative hypotheses have not sufficiently accounted for phylogeny and body size. After controlling for this variation, I predicted that environment, mating habitat, and predation would yield a fuller explanation. Lactation traits, duration, pup growth rate, and fat content were significantly influenced by both body size and phylogeny, which together explained 20–69% of the variation. After controlling for this variation, initial results did not support the environment hypothesis, as no differences in lactation traits were found between species living in polar (≥60°N) versus equatorial (<60°N) environments. In contrast, seals that nurse in areas of Arctic sea ice contending with ice-hunting predators, such as polar bears, had relatively short lactation compared to species living in the Antarctic and more equatorial regions. Also, the availability of predator-free islands for terrestrial mating and parturition was related to a harem mating system, increased sexual size dimorphism (SSD), and slow juvenile growth rates, less fat in milk, and longer lactation. Using structural equation modeling, latitude and size of harems provided independent explanations for all three lactation traits. Thus, use of islands in ice-free waters, predation in Arctic ice-covered waters, and more milk fat in high-latitude seals together provided adequate explanations for the evolution of lactation diversity among pinnipeds.