Multiple loci variable number tandem repeat (VNTR) analysis (MLVA) of Mycobacterium leprae isolates amplified from European archaeological human remains with lepromatous leprosy

Molecular typing methods based on polymorphisms in single nucleotides and short tandem repeat motifs have been developed as epidemiological typing tools for Mycobacterium leprae. We have used a variable number tandem repeat method based on three variable loci to identify strain variation in archaeological cases of lepromatous leprosy. The panel of polymorphic loci used revealed unique profiles in five cases of leprosy, including those with identical SNP type and subtype. These were also different from profiles of three previously studied lepromatous skeletons. Whilst examination with SNP typing provides evidence for disease origins, dissemination and phylogeny, tandem repeat typing may be useful for studying cases from within a defined area or community where SNP types may be identical due to geographical constraints. We envisage the technique may be useful in studying contemporaneous burials such as those associated with leprosaria and will prove invaluable in authentication of ancient DNA analyses.     

离子注入诱变莲花突变体分子机理的初步研究

低能离子注入技术作为生物物理诱变的一种新型技术, 在园艺植物育种方面具有很大的应用潜力, 但其诱变的分子机理目前知之甚少。文章对Fe+ 离子注入诱变的白洋淀红莲(Nelumbium speciosum Willd)突变体及其对照的基因组进行RAPD研究, 并将突变体和对照在辐射敏感位点的条带进行克隆测序及DNA序列分析。在已优化好的RAPD体系下扩增, 从110条随机引物中筛选出了10条可以稳定扩增出显著特异条带的引物, 引物多态性为9.09%。将这10条引物扩增出的辐射敏感位点的条带进行克隆测序, 并进行序列比对。结果显示: 突变体的总碱基突变频率为0.87%, 6个突变体的碱基突变频率存在着差异; 碱基突变类型包括碱基的颠换、转换、缺失、插入, 在检测到的159个碱基突变中, 单碱基置换的频率(61.01%)高于碱基插入或者缺失的频率(38.99%), 在碱基置换中, 转换的频率(44.65%)是颠换频率(16.35%)的2.7倍, 其中C/T之间的转换所占比例最大, A→G和A→T也具有较高的替换频率; 构成DNA的4种碱基均可以被离子束辐照诱变发生变异, 除了没有C→G的置换外, 每一种碱基都可以被其他的几种碱基所置换, 但是胸腺嘧啶(T)具有较高的辐射敏感性。通过对碱基突变位点周边序列的分析发现, 嘌呤突变位点的周围嘌呤碱居多, 嘧啶突变位点的周围嘧啶碱居多。研究结果为揭示低能离子注入诱变作用分子机理提供了依据。     

Evaluating Neanderthal Genetics and Phylogeny

The retrieval of Neanderthal (Homo neanderthalsensis) mitochondrial DNA is thought to be among the most significant ancient DNA contributions to date, allowing conflicting hypotheses on modern human (Homo sapiens) evolution to be tested directly. Recently, however, both the authenticity of the Neanderthal sequences and their phylogenetic position outside contemporary human diversity have been questioned. Using Bayesian inference and the largest dataset to date, we find strong support for a monophyletic Neanderthal clade outside the diversity of contemporary humans, in agreement with the expectations of the Out-of-Africa replacement model of modern human origin. From average pairwise sequence differences, we obtain support for claims that the first published Neanderthal sequence may include errors due to postmortem damage in the template molecules for PCR. In contrast, we find that recent results implying that the Neanderthal sequences are products of PCR artifacts are not well supported, suffering from inadequate experimental design and a presumably high percentage (>68%) of chimeric sequences due to “jumping PCR” events. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Martin Kreitman]     

First evidence of east–west migration across the North Pacific in a marine bird

Many marine birds undertake long migrations between breeding and wintering areas, including some species that undertake long‐distance east–west or west–east movements across many degrees of longitude. To date, however, no east–west migrations have been described across the North Pacific. Geolocators were deployed on Ancient Murrelets Synthliboramphus antiquus breeding in Haida Gwaii, British Columbia, in 2013 and four were retrieved the following year. Longitude positions showed that all four moved rapidly westwards after breeding, three of them reaching waters between Japan and China by November and this location was also supported by ringing data. Return migration was rapid, beginning in February and reaching Haida Gwaii in March, providing the first evidence for bird migration spanning the entire width of the North Pacific. This is the longest migration recorded in any of the Alcidae.     

荷花花蕾cDNA文库构建及质量评价

为理解荷花Nelumbo nucifera花器官转录组表达情况,分别选取不同花型的代表品种‘洪湖红莲’Nelumbo nucifera ‘Honghu Honglian’(单瓣)、‘唐招提寺莲’N. nucifera ‘Tangzhaotisi Lian’(重瓣)和‘千瓣莲’N. nucifera ‘Qianban Lian’(千瓣及全重瓣)的花蕾为材料分离mRNA,利用SMART技术合成双链cDNA,经限制性内切酶SfiI酶切后回收去掉接头和500 bp以下片段的cDNA。将cDNA与pUC19载体连接,构建荷花花蕾cDNA文库。经检测,该文库容量为1.12 × 106 pfu·mL-1,插入片段大小集中在500～2000 bp,重组率为95%。该文库的成功构建为荷花花蕾期转录组数据的开发及其花器官发育相关基因的功能研究奠定了分子基础。     

Ancient Lake Ohrid: biodiversity and evolution

Worldwide ancient lakes have been a major focal point of geological, biological, and ecological research, and key concepts in, for example, evolutionary biology are partly based on ancient lake studies. Ancient lakes can be found on most continents and climate zones with most actual or putative ancient lakes in Europe being restricted to the Balkan Region. The arguably most outstanding of them is the oligotrophic and karstic Lake Ohrid, a steep-sided graben of rift formation origin situated in the central Balkans. Here, an attempt is made to summarize current knowledge of the geological, limnological, and faunal history of Lake Ohrid. Additionally, existing data on biodiversity and endemism in Lake Ohrid are updated and evaluated, and patterns and processes of speciation are reviewed in the context of the Ohrid watershed, including its sister lake, Lake Prespa. Whereas the geological history of the Ohrid Graben is relatively well studied, there is little knowledge about the limnological and biotic history of the actual lake (e.g., the age of the extant lake or from where the lake first received its water, along with its first biota). Most workers agree on a time frame of origin for Lake Ohrid of 2–5 million years ago (Mya). However, until now, the exact limnological origin and the origin of faunal or floral elements of Lake Ohrid remain uncertain. Two largely contrasting opinions either favour the theory of de novo formation of Lake Ohrid in a dry polje with a spring or river hydrography or a palaeogeographical connection of Lake Ohrid to brackish waters on the Balkan Peninsula. Whereas neither theory can be rejected at this point, the data summarized in the current review support the de novo hypothesis. An assessment of the fauna and flora of Lake Ohrid confirms that the lake harbours an incredible endemic biodiversity. Despite the fact that some biotic groups are poorly studied or not studied at all, approximately 1,200 native species are known from the lake, including 586 animals, and at least 212 species are endemic, including 182 animals. The adjusted rate of endemicity is estimated at 36% for all taxa and 34% for Animalia. In terms of endemic biodiversity, Lake Ohrid is with these 212 known endemic species and a surface area of 358 km² probably the most diverse lake in the world, taking surface area into account. Preliminary phylogeographical analyses of endemic Lake Ohrid taxa indicate that the vast majority of respective sister taxa occurs in the Balkans and that therefore the most recent common ancestors of Ohrid- and non-Ohrid species likely resided in the region when Lake Ohrid came into existence. These data also indicate that there is relatively little faunal exchange and overlap between Lake Ohrid and its sister lake, Lake Prespa, despite the fact that the latter lake is a major water supplier for Lake Ohrid. Studies on selected species flocks and scatters, mostly in molluscs, point towards the assumption that only few lineages originally colonized Lake Ohrid from the Balkans and that the majority of endemic species seen today probably started to evolve within the lake during the early Pleistocene. Within the Ohrid watershed, endemism occurs at different spatial and taxonomic scales, ranging from species endemic to certain parts of Lake Ohrid to species endemic to the whole watershed and from subspecies to genus level and possibly beyond. Modes of speciation in the Ohrid watershed are largely affected by its degree of isolation. Observational evidence points towards both allopatric (peripatric) and parapatric speciation. Though sympatric speciation within a habitat is conceivable, so far there are no known examples. Today, the lake suffers from increasing anthropogenic pressure and a “creeping biodiversity crisis”. Some endemic species presumably have already gone extinct, and there are also indications of invasive species penetrating Lake Ohrid. The comparatively small size of Lake Ohrid and the extremely small range of many endemic species, together with increasing human pressure make its fauna particularly vulnerable. It is thus hoped that this review will encourage future research on the ecology and evolutionary biology of the lake’s taxa, the knowledge of which would ultimately help protecting this unique European biodiversity hot spot. Guest editors: T. Wilke, R. V?in?l? & F. Riedel Patterns and Processes of Speciation in Ancient Lakes: Proceedings of the Fourth Symposium on Speciation in Ancient Lakes, Berlin, Germany, September 4–8, 2006     

Global diversity of ostracods (Ostracoda,Crustacea) in freshwater

There are close to 2,000 subjective species and about 200 genera of Recent non-marine Ostracoda. Together, Cyprididae (1,000 spp.) and Candonidae (c. 550 spp.) represent more than 75% of the extant specific diversity; the remaining 11 families comprise the other 25% of the species. The Palaearctic region has the highest absolute non-marine ostracod diversity, followed by the Afrotropical. The Australian region has the highest relative endemicity. About 90% of the species and 60% of the genera occur in one zoogeographical region only. This means that all the biological mechanisms which lead up to efficient dispersal and which are present in at least part of the non-marine Ostracoda (e.g. brooding, drought-resistant eggs, parthenogenesis) have not induced common cosmopolitan distributions in ostracods. Several habitats are hotspots for ostracod diversity and endemicity. For example, it appears that the ancient lakes hold up to 25% of the total ostracod diversity. Other speciation-prone habitats are groundwater, temporary pools and Australian salt lakes; in the latter two instances, cladogenesis has often been paralleled by gigantism. The present ostracod diversity results from 9 to 12 separate invasions of the non-marine habitat, starting about 400 Myr ago. Genetic diversity can be very different in different species, mostly, but not always, related to reproductive mode. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

莲品种资源的SRAP遗传多样性分析

利用分子标记SRAP技术对国内广泛栽培以及新近育成的39个莲品种进行了DNA多态性分析。选取5对引物扩增基因组DNA,共获得101条带,其中88条为多态性条带,每对引物平均提供20个标记信息。由UPMGA方法得到的聚类分析结果表明了39个品种间的遗传关系,结果表明:花莲、籽莲和藕莲三大类群有明显的界限,花莲和籽莲的遗传距离较近,藕莲与它们的遗传距离较远。分子方差分析结果表明:莲品种间和品种内均存在遗传变异,藕莲品种内的遗传变异略低于品种间的遗传变异,而诱变籽莲、诱变花莲和常规籽莲品种内遗传变异均大于品种间的遗传变异,尤其是诱变籽莲、诱变花莲品种内遗传变异占总变异的分量分别超过了70%和60%,这种品种内的遗传变异,一方面对于莲的高产稳产具有重要的意义,另一方面也说明了从这些国内广泛栽培的品种以及新近育成的莲品种中可以直接进一步选育出更优良的新品种。     

The ontogeny of two species of Darwinuloidea (Ostracoda, Crustacea)

The ontogeny of two species of the ostracod superfamily Darwinuloidea, Darwinula stevensoni (Brady and Robertson, 1870) and Vestalenula sp., is documented. The development of the appendages of the two species is very similar, with the exception of the antennule, which shows some variation. The general appearance of appendages during ontogeny of the two species is very similar to that of species of other podocopid superfamilies, such as the Cytheroidea, Terrestricytheroidea, Bairdioidea and Cypridoidea, and different from that of the Platycopida. Using the development of the antenna and the appearance of antennal features, a revised model of darwinulid antennal terminology is presented that homologizes these features with those of the Cypridoidea.