Complete nuclear ribosomal DNA sequence analyses of the black-footed abalone Haliotis iris

The black-footed abalone Haliotis iris is an economically important shellfish species in New Zealand. We successfully amplified, sequenced and analysed the complete nuclear ribosomal DNA (nrDNA) of H. iris. The length of the nrDNA was determined to be around 9.6?kb and included, in order, small subunit ribosomal RNA (nrSSU, 1858bp), internal transcribed spacer (ITS, 749?bp), large subunit ribosomal RNA (nrLSU, 3412bp) and an intergenic spacer (IGS, 3560–3662?bp). The nrLSU genes were identical in two individuals, whereas the nrSSU and ITS regions existed at three and four base differences, respectively. The IGS was more variable than the other nrDNA regions. A phylogenetic tree was constructed based on the ITS sequence datasets, which revealed that Haliotidae has two major subclades, mainly distributed in the North Pacific, Europe and Australia. The complete nrDNA sequence will be useful for the classification, phylogeny and breeding of this shellfish.     

Limited phylogeographic structure for five bathyal ophiuroids at continental scales

There have been comparatively few large-scale studies on spatial genetic structure of bathyal seafloor fauna, despite the importance of these data to the successful management of the world's oceans. We use a comparative analysis of mitochondrial DNA from five bathyal (200–3500 m) species of brittle-stars (Ophiuroidea) to assess phylogeographic structure along an extensive (8000 km) longitudinal gradient at temperate latitudes (28–56°S) from south-west Australia (113°E) to seamounts east of New Zealand (175°W). We found no evidence of a genetic discontinuity between Australia and New Zealand, either across the temperate Tasman Sea or across the Southern Ocean between the South Tasman Rise and the Macquarie Ridge. However, there were latitudinal phylogeographical breaks between tropical, temperate and polar regions; longitudinal breaks across the eastern Indian Ocean; and a bathymetric break at approximately 1700 m. Although there was limited regional structure in the frequency of haplotype distributions within the major clades, and no clade appeared to be strictly panmictic, the regional structure in general was not concordant with a simple isolation-by-distance model. Demographic structure varied with three clades having a simplified haplotype network, low effective population sizes and no evidence of significant population expansion, and two clades having a high diversity of haplotypes, relatively high effective population sizes and signs of recent population expansion. These results are discussed with respect to putative dispersal strategies. We hypothesise that the ‘brooding’ species produce both brooded young and pelagic larvae, allowing for both the maintenance of local populations and long-distance dispersal.     

Biotic drivers of river and floodplain geomorphology – New molecular methods for assessing present‐day and past biota

Geomorphology has increasingly considered the role of biotic factors as controls upon geomorphic processes across a wide range of spatial and temporal scales. Where timescales are long (centennial and longer), it has been possible to quantify relationships between geomorphic processes and vegetation using, for example, the pollen record. However, where the biotic agents are fauna, longer term reconstruction of the impacts of biological activity upon geomorphic processes is more challenging. Here, we review the prospect of using environmental DNA as a molecular proxy to decipher the presence and nature of faunal influences on geomorphic processes in both present and ancient deposits. When used appropriately, this method has the potential to improve our understanding of biotic drivers of geomorphic processes, notably fauna, over long timescales and so to reconstruct how such drivers might explain the landscape as we see it today. Copyright © 2017 John Wiley & Sons, Ltd.     

洱海沉积物中有机质和DNA的分布特征

测定了洱海沉积物中有机碳、氮,提取了沉积物中的DNA。有机碳氮呈现相同的变化趋势降解主要发生在表层10cm;7cm前后氧化-还原条件变化,微生物电子受体改变,所以有机质的降解方式不同,出现不同的特征。利用分子生物学和地球化学相结合的方法,能更全面的认识和理解早期成岩过程。     

基于线粒体COI和16S rRNA基因的中国沿海相手蟹系统发育研究

相手蟹科的诸多种类因其形态极其相似成为方蟹总科分类中疑问较多的一个类群。通过对中国沿海相手蟹线粒体COI和16S rRNA基因序列进行分子系统发育分析,结果表明14种相手蟹COI和16S rRNA基因序列之间差异分别为5.7%～14.5%和1.5%～12.1%,均达到了种间差异水平。构建的系统发育树显示,14种相手蟹分别为独立有效物种,但分属于拟相手蟹属和近相手蟹属的4种拟相手蟹和3种近相手蟹,没有分别形成2个独立的支系,而是混合聚成一大支系。而属于螳臂相手蟹属的无齿螳臂相手蟹则首先与属于中相手蟹属的中华中相手蟹聚成一支,再与红螯螳臂相手蟹聚为一大支,表现出与形态分类的不一致。错综复杂的分子系统关系预示着相手蟹类为多系起源,也表明它们之间的种间关系乃至于属间关系尚有诸多问题有待进一步厘定。     

高效非损伤性扇贝DN A提取方法的建立及效果评价

本研究建立了一种高效、经济的非损伤性扇贝DNA提取方法,在不影响扇贝个体生存状态的前提下,采用擦拭法和室温裂解相结合的方式在20 min内即可获得个体基因组DNA。以虾夷扇贝(Patinopecten yessoensis)、栉孔扇贝(Chlamys farreri)和海湾扇贝(Argopecten irradians)为实验对象,研究了不同擦拭材料(棉签、滤纸)和不同擦拭部位(外套膜、鳃丝、内脏团)的核酸提取效果,评估了本方法在贝类基因分型领域应用的可行性。研究表明,用棉签、滤纸2种材料擦拭扇贝的鳃丝、内脏团或外套膜组织均能获得主带清晰完整的基因组DNA,且不影响扇贝的存活状态。在3种扇贝中采用棉签擦拭法的DNA得率均高于滤纸法,以这2种方式获得的DNA为模板进行SSR和SNP标记分析,能获得均一稳定的扩增条带,SSR标记分型结果准确可靠。本研究建立了简便、快速进行扇贝基因型分析的非损伤性DNA提取方法,为贝类全基因组选育和珍稀贝类资源的种质保护开发提供了新的技术手段。     

Phylogenetic analysis of Pectinidae(Bivalvia) based on the ribosomal DNA internal transcribed spacer region

The ribosomal DNA internal transcribed spacer (ITS) region is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, the molecular phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) was performed using the nucleotide sequences of the nuclear ITS region in nine species of this family. The sequences were obtained from the scallop species Argopecten irradians, Mizuhopecten yessoensis, Amusium pleuronectes and Mimachlamys nobilis, and compared with the published sequences of Aequipecten opercularis, Chlamys farreri, C. distorta, M. varia, Pecten maximus, and an outgroup species Perna viridis. The molecular phylogenetic tree was constructed by the neighbor-joining and maximum parsimony methods. Phylogenetic analysis based on ITS1, ITS2, or their combination always yielded trees of similar topology. The results support the morphological classifications of bivalve and are nearly consistent with classification of two subfamilies (Chlamydinae and Pectininae) formulated by Waller. However, A. irradians, together with A. opercularis made up of genera Amusium, evidences that they may belong to the subfamily Pectinidae. The data are incompatible with the conclusion of Waller who placed them in Chlamydinae by morphological characteristics. These results provide new insights into the evolutionary relationships among scallop species and contribute to the improvement of existing classification systems.     

中国鲎基因组微卫星富集文库的构建及分析

本研究旨在从DNA分子水平上研究中国鲎(Tachypleus tridentatus)种群遗传多样性及种群结构等相关信息,以期为保护其野生群体种质资源提供科学依据。本研究通过生物素—磁珠富集法筛选微卫星标记,构建中国鲎基因组微卫星文库。基因组DNA经Fast Digest Tru1I酶切后,选取400 bp~1000 bp片段,用生物素标记的(GT)15、(CT)15混合探针与其杂交,杂交复合物与链霉亲和素磁珠结合,捕获含有重复序列的微卫星片段,纯化后连接PMD19-T载体克隆,构建基因组微卫星文库。从334个阳性克隆中随机选取196个片段大于400 bp的阳性克隆进行测序,共获得127个微卫星序列,其中完美型占69.3%、非完美型占11.0%、复合型占19.7%。除探针使用的GT和CT的重复序列外,还筛选到多碱基GCT、TGG、AAAC、ACAA、GATTT、TTTTA的重复序列。根据微卫星序列设计选择合成40对引物,结果显示其中3对具有较高多态性,可作为进一步评价中国鲎野生种质资源等遗传信息的有效遗传标记。