单倍型及其在菌物学研究中的应用

单倍型分析在人和动、植物的许多学科领域都取得了丰硕的研究成果。本文主要介绍了单倍型的概念、研究方法,以及常用的可视化网络分析软件的操作步骤,同时综述和讨论了单倍型在菌物学一些领域,如种群的遗传多样性、生物地理来源及迁徙、复合种群中隐存种的界定及其与系统发育关系、生物入侵及新兴病原的单倍型分析侦测等的研究进展,以期为菌物学向更深层次发展提供新的视角和途径。     

Allopatric divergence and regional range expansion of Juniperus sabina in China

In this study, we aimed to study the phylogeographic pattern of Juniperus sabina, a shrub species commonly occurring in the northern, northwestern and western China. We sequenced three chloroplast DNA fragments (trnL-trnF, trnS-trnG, and trriD-trriT) for 137 individuals from 16 populations of this species. Five chloroplast DNA chlorotypes (A, B, C, D, and E) were identified and they showed no overlapping distribution. The population subdivision is very high (GST = 0.926, NST= 0.980), suggesting a distinct phylogeographic structure (NST > GST, P < 0.05). Phylogenetic analyses of the five chlorotypes were clustered into three clades, consistent with their respective distributions in three separate regions: northern Xinjiang, western Xinjiang, and northern-northwestern China. However, within each region, the interpopulation differentiation is extremely low. These results as well as statistical tests suggested distinct allopatric differentiations between regional populations and independent glacial refugia for postglacial recolonization. The deserts that developed during the late Quaternary might have acted as effective barriers to promote genetic differentiation among these regions. However, the low diversity dominated by the single chlorotype within each fragmented region suggested that all current populations were derived from a common regional range expansion.     

Phylogeography of the invasive weed Hypochaeris radicata (Asteraceae): from Moroccan origin to worldwide introduced populations

In an attempt to delineate the area of origin and migratory expansion of the highly successful invasive weedy species Hypochaeris radicata, we analysed amplified fragment length polymorphisms from samples taken from 44 populations. Population sampling focused on the central and western Mediterranean area, but also included sites from Northern Spain, Western and Central Europe, Southeast Asia and South America. The six primer combinations applied to 213 individuals generated a total of 517 fragments of which 513 (99.2%) were polymorphic. The neighbour-joining tree presented five clusters and these divisions were supported by the results of Bayesian analyses: plants in the Moroccan, Betic Sierras (Southern Spain), and central Mediterranean clusters are all heterocarpic. The north and central Spanish, southwestern Sierra Morena, and Central European, Asian and South American cluster contain both heterocarpic (southwestern Sierra Morena) and homocarpic populations (all other populations). The Doñana cluster includes two homocarpic populations. Analyses of fragment parameters indicate that the oldest populations of H. radicata are located in Morocco and that the species expanded from this area in the Late Quaternary via at least three migratory routes, the earliest of which seems to have been to the southwestern Iberian Peninsula, with subsequent colonizations to the central Mediterranean area and the Betic Sierras. Homocarpic populations originated in the southwestern Iberian Peninsula and subsequently spread across north and central Spain, Central Europe and worldwide, where they became a highly successful weed.     

Population differentiation and phylogeographic pattern of a relict species, Conandron ramondioides (Gesneriaceae), revealed from sequence polymorphism and haplotypes of the CYCLOIDEA gene

Historical events are expected to affect population genetic differentiation and DNA molecular evolution,but the impact of these effects remains a matter of debate.Here,for Conandron ramondioides (Gesne...     

中国湛江市和哈尔滨市褐家鼠种群遗传结构及其年度变化特征

为探索褐家鼠Rattus norvegicus地理种群的遗传结构及其年度变化特点,本研究以广东省湛江市的褐家鼠指名亚种和黑龙江省哈尔滨市的褐家鼠东北亚种为主要研究对象,结合我国及世界其他褐家鼠种群的D-loop序列分析这2个褐家鼠地理种群间D-loop序列的遗传分化情况及系统进化关系,重点分析2008—2015年褐家鼠湛江种群和哈尔滨种群D-loop单倍型的年度频率变化特点。结果表明,褐家鼠湛江种群和哈尔滨种群共有32种不同的单倍型,其中有11种单倍型是2个种群共有的,有4种单倍型仅在湛江种群中出现,有17种单倍型仅在哈尔滨种群中出现。褐家鼠湛江种群D-loop区的核苷酸多态性为0.005,有27个变异位点,单倍型多态性为0.695,褐家鼠哈尔滨种群D-loop区的核苷酸多态性比湛江种群略高,为0.008,有35个变异位点,单倍型多态性为 0.793。褐家鼠湛江种群和哈尔滨种群没有经历过暴发性的扩增。褐家鼠湛江、哈尔滨和湖北3个地理种群的D-loop序列之间发生了明显的遗传分化,其中湛江种群和哈尔滨种群之间的分化程度最高,遗传分化系数F_st为0.245。褐家鼠湛江种群和哈尔滨种群的单倍型数目和主单倍型频率都发生明显波动,推测主要原因可能是由于灭鼠剂的大量使用或其他灭鼠活动导致种群出现瓶颈或更替的现象。     

CRATER LAKE COLONIZATION BY NEOTROPICAL CICHLID FISHES

Volcanic crater lakes are isolated habitats that are particularly well suited to investigating ecological and evolutionary divergence and modes of speciation. However, the mode, frequency, and timing of colonization of crater lakes have been difficult to determine. We used a statistical comparative phylogeographic approach, based on a mitochondrialDNA dataset, to infer the colonization history of two Nicaraguan crater lakes by populations of genetically and ecologically divergent cichlid lineages: Midas (Amphilophus cf. citrinellus complex) and moga (Hypsophrys nematopus). We compared estimates of diversity among populations within the two cichlid lineages and found that Midas were the most genetically diverse. From an approximate Bayesian computation analysis, we inferred that the crater lakes were each founded by both cichlid lineages in single waves of colonization: Masaya 5800 ± 300 years ago and Xiloá 5400 ± 750 years ago. We conclude that natural events are likely to have a dominant role in colonization of the crater lakes. Further, our findings suggest that the higher species richness and more rapid evolution of the Midas species complex, relative to other lineages of fishes in the same crater lakes, cannot be explained by earlier or more numerous colonization events.     

The limits of cryptic diversity in groundwater: phylogeography of the cave shrimp Troglocaris anophthalmus (Crustacea: Decapoda: Atyidae)

Recent studies have revealed high local diversity and endemism in groundwaters, and showed that species with large ranges are extremely rare. One of such species is the cave shrimp Troglocaris anophthalmus from the Dinaric Karst on the western Balkan Peninsula, apparently uniform across a range of more than 500 kilometres. As such it contradicts the paradigm that subterranean organisms form localized, long-term stable populations that cannot disperse over long distances. We tested it for possible cryptic diversity and/or unexpected evolutionary processes, analysing mitochondrial (COI, 16S rRNA) and nuclear (ITS2) genes of 232 specimens from the entire range. The results of an array of phylogeographical procedures congruently suggested that the picture of a widespread, continuously distributed and homogenous T. anophthalmus was wrong. The taxon is composed of four or possibly five monophyletic, geographically defined phylogroups that meet several species delimitation criteria, two of them showing evidence of biological reproductive isolation in sympatry. COI genetic distances between phylogroups turned out to be a poor predictor, as they were much lower than the sometimes suggested crustacean threshold value of 0.16 substitutions per site. Most results confirmed the nondispersal hypothesis of subterranean fauna, but the southern Adriatic phylogroup displayed a paradoxical pattern of recent dispersal across 300 kilometres of hydrographically fragmented karst terrain. We suggest a model of migration under extreme water-level conditions, when flooded poljes could act as stepping-stones. In the north of the range (Slovenia), the results confirmed the existence of a zone of unique biogeographical conflict, where surface fauna is concordant with the current watershed, and subterranean fauna is not.     

外生菌根真菌土生空团菌种群遗传多样性与结构研究

土生空团菌Cenococcum geophilum是生态系统中广泛分布的外生菌根真菌,具有丰富的遗传多样性和重要的生态功能.为揭示土生空团菌的种群遗传多样性和结构,本研究对采集自中国10个森林地点的桦木科Betulaceae、壳斗科Fagaceae和松科Pinaceae植物根系219份样品高通量测序的土生空团菌ITS2...     

基于形态学性状和SSR标记的辣椒种质资源遗传多样性分析(长英文摘要）

分析了146份辣椒(Capsicum spp.)种质资源的形态学性状, 同时利用简单重复序列(SSR)标记分析了其遗传多样性和群体遗传结构。形态学性状多样性分析结果表明, 质量性状和数量性状的变异系数分别为8.22%-267.58%与14.35%- 72.51%, Shannon多样性指数分别为0.04-1.91与1.58-2.02, 说明辣椒种质资源多样性丰富。利用SSR标记从22对引物中检测出102个等位基因, 平均每对引物检测出4.636个等位基因, 有效等位基因变异范围为1.191-5.311, Shannon多样性指数为0.345-2.056, 多态性信息含量(PIC)为0.153-0.795, 146份辣椒种质资源平均遗传距离为0.429。基于表型和分子标记的聚类分析分别将辣椒种质资源分为6类和7类, 但2种聚类结果相关性较弱(r=0.396 7)。群体遗传结构分析将辣椒种质遗传结构分为2组, 不同组之间界限明显。研究阐明了146份辣椒种质资源的遗传多样性和群体遗传结构, 为后续种质鉴定及新品种选育奠定了理论基础。     

植物保护遗传学

从遗传多样性、系统发育和地理系统发育角度对当前保护遗传学在植物保护中的作用进行了探讨。在植物保护过程中,要考虑多群遗传多样性的大小,在就地和迁地保护的过程要减少近交和远交衰退影响,并可利用遗传标记为提供关于种群大小、基因流动等方面的信息。系统发育和地理系统发育的研究在于了解物种进化的历史,以确定物种保护单元。同时结合两个具体生态学问题（生境片段化和外来种）对当前植物保护遗传学的研究进行了介绍,揭示了保护遗传学在植物保护上重要作用和不可取代性,为今后研究提供参考。