入侵种的DNA条形码鉴定

生物安全研究的范畴涉及任何由生物威胁所造成的风险。随着害虫优先考虑级别的不断变化,以及国家和部门间相互协作的不断加强,对DNA分子鉴定技术的标准化提出了更迫切的要求,而DNA条形码的出现为此类问题的解决提供了很好的机遇。我们以前人对毒蛾和果蝇的研究为例,比较了DNA条形码技术与PCR-RFLP等传统方法的鉴定效果,在此基础上提出了建立一个可对不同入侵种进行快速和准确鉴定的条形码技术平台的构想。     

山东泰山两栖爬行动物物种多样性

泰山地区有两栖爬行动物18种,其中两栖动物1目3科3属6种,爬行动物2月4科7属12种。     

Short rDNA Barcodes for Species Identification in Foraminifera

ABSTRACT. Ribosomal DNA (rDNA) sequences have been shown to be very useful for identification of microbial eukaryotes. Usually, complete or long partial sequences of the rDNA genes are analysed. However, the development of new massive sequencing technologies producing a large amount of relatively short sequences raises the question about the minimum length of rDNA fragments necessary for species distinction in environmental sampling. To answer this question, we compared six variable regions of the small subunit (SSU) rDNA of foraminifera, known to have rapidly evolving ribosomal genes. For each region, we analysed (1) the sequence divergence between and within foraminiferal morphospecies, (2) the intraspecific polymorphism, and (3) the ability of each region to recognize the phylotypes inferred from analysis of a longer fragment. Our results show that although the variable regions differ considerably between taxonomic groups, most of them perform very well as species identifiers. Taking into account different analyses, the expansion segment of Helix 37 appears to be the best candidate for barcoding foraminifera. We propose that this relatively short region, averaging 50–60 nt in length, could be an ideal barcode for identification of foraminifera in environmental samples using massive sequencing approach.     

Environmental Correlates for Species Richness among Amphibians and Reptiles in a Climate Transition Area

Correlations between environmental factors and the distribution of amphibian and reptile species richness were investigated in a climate transition area, Peneda-Gerês National Park (PNPG), in North-Western Portugal. Using presence-data at a local-scale (1 × 1 km), Ecological-Niche Factor Analysis (ENFA) identified a mixture of climatic (precipitation and number of days with fog), topographical (altitude and relief) and habitat factors (number of watercourses and water surfaces, the type of the largest water surface and tree diversity cover), as accurate predictors of species occurrence. Three factors were common for both taxonomic groups, and consistently presented a positive relation with species occurrence: precipitation, number of water surfaces, and tree diversity cover; suggesting a strong coincidence in the environmental correlates that influence amphibian and reptile species richness. Distribution patterns of observed and predicted species richness were compared using a Geographical Information System. Overall, three high species richness areas were predicted in common for both taxonomic groups and two additional areas for amphibians only. These areas matched with the observed species richness but suggested larger areas of high species richness. The location of the PNPG in a biogeographic crossroad, between Euro-Siberian and Mediterranean provinces, emphasised species richness of amphibians and reptiles and suggests a high priority conservation status for this protected area. Most of Central-Northern Portugal is located in a climatic transition area; therefore, increased species richness should be expected for other areas. Local scale studies for other protected areas should be planned as a framework for the development of multi-scale conservation planning by Portuguese authorities.     

河北衡水湖两栖爬行动物的多样性及保护

衡水湖保护区有两栖爬行动物22种,其中,两栖动物2目4科4属7种,爬行动物2目5科10属15种。对两栖爬行动物资源的保护进行了探讨。     

江西武功山两栖爬行动物资源调查及评价

2001年7月中旬～8月上旬,对江西武功山国家森林公园进行了20多天的野生动植物资源野外考察.公园内现已记录两栖类2目7科25种和爬行类3目9科37种,本次调查增加安福县爬行动物新记录7种：多疣壁虎、中国石龙子、黑背白环蛇、铅色水蛇、灰鼠蛇、乌梢蛇、银环蛇;增加武功山爬行动物新记录23种.动物地理区划属东洋界华中区东部丘陵平原亚区,动物区系组成以东洋界华中区与华南区共有种为主.两栖类东洋界种类占92.00%;生态类型以流水型9种和陆栖-静水型7种占优势.数量优势种为黑斑蛙、中华蟾蜍、黑斑肥螈、泽蛙、棘胸蛙、花臭蛙、华南湍蛙、三港树蟾、镇海林蛙和饰纹姬蛙.爬行类东洋界种类占75.68%,广布种占24.32%.数量优势种有石龙子、蓝尾石龙子、铜蜓蜥、赤链华游蛇、王锦蛇、虎斑颈槽蛇、赤链蛇、红点锦蛇、乌梢蛇、灰鼠蛇、尖吻蝮、竹叶青蛇等.公园内野生动物及其生境受人类干扰破坏大,当地群众保护意识有待增强,就此提出了保护对策.     

Identification,Discrimination, and Discovery of Species of Marine Planktonic Ostracods Using DNA Barcodes

The Ostracoda (Crustacea; Class Ostracoda) is a diverse, frequently abundant, and ecologically important component of the marine zooplankton assemblage. There are more than 200 described species of marine planktonic ostracods, many of which (especially conspecific species) can be identified only by microscopic examination and dissection of fragile morphological characters. Given the complexity of species identification and increasing lack of expert taxonomists, DNA barcodes (short DNA sequences for species discrimination and identification) are particularly useful and necessary. Results are reported from analysis of 210 specimens of 78 species of marine planktonic ostracods, including two novel species, and 51 species for which barcodes have not been previously published. Specimens were collected during 2006 to 2008 from the Atlantic, Indian, and Southern Oceans, Greenland Sea and Gulf of Alaska. Samples were collected from surface to 5,000 m using various collection devices. DNA sequence variation was analyzed for a 598 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene. Kimura-2-Parameter (K2P) genetic distances within described species (mean = 0.010 ± 0.017 SD) were significantly smaller than between species (0.260 + 0.080), excluding eight taxa hypothesized to comprise cryptic species due to morphological variation (especially different size forms) and/or collection from different geographic regions. These taxa showed similar K2P distance values within (0.014 + 0.026) and between (0.221 ± 0.068) species. All K2P distances > 0.1 resulted from comparisons between identified or cryptic species, with no overlap between intra- and interspecific genetic distances. A Neighbor Joining tree resolved nearly all described species analyzed, with multiple sequences forming monophyletic clusters with high bootstrap values (typically 99%). Based on taxonomically and geographically extensive sampling and analysis (albeit with small sample sizes), the COI barcode region was shown to be a valuable character for discrimination, recognition, identification, and discovery of species of marine planktonic ostracods.     

广西猫儿山国家级自然保护区的两栖爬行动物

2004年5月～2005年12月,对猫儿山国家级自然保护区的两栖爬行动物进行了初步调查,新观察和采集到两栖动物10种、爬行动物17种.至此,猫儿山共有两栖动物35种、爬行动物38种.     

The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions

During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.     

Assessing DNA Barcoding as a Tool for Species Identification and Data Quality Control

In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating deep intraspecific and shallow interspecific divergences to discover possible taxonomic problems and other sources of error. We use the mitochondrial DNA gene encoding cytochrome b (Cytb) from turtles to test the utility of barcoding for pinpointing potential errors. This gene is widely used in phylogenetic studies of the speciose group. Intraspecific variation is usually less than 2.0% and in most cases it is less than 1.0%. In comparison, most species differ by more than 10.0% in our dataset. Overlapping intra- and interspecific percentages of variation mainly involve problematic identifications of species and outdated taxonomies. Further, we detect identical problems in Cytb from Insectivora and Chiroptera. Upon applying this strategy to 47,524 mammalian CoxI sequences, we resolve a suite of potentially problematic sequences. Our study reveals that erroneous sequences are not rare in GenBank and that the DNA barcoding can serve to confirm sequencing accuracy and discover problems such as misidentified species, inaccurate taxonomies, contamination, and potential errors in sequencing.     

Circadian Rhythms in Amphibians and Reptiles: Ecological Implications

Circadian rhythms of amphibians and reptiles in the field and under semi-natural conditions and the underlying mechanisms, including the ways of entrainment to environmental cues and the oscillators driving the rhythms, have been reviewed. Studies on the behavioral rhythms in the field are meager in both amphibians and reptiles. In anuran amphibians, Xenopus adults showed more robust nocturnal locomotor activity than did tadpoles. This indicates the ecological significance of the differences in activity pattern shown by amphibians at different life stages, because differences between adults and young in the same environment may serve to isolate partially the young from the adults' cannibalism. In reptiles, free-running rhythms are more robust and continue for a longer time compared to amphibians. In both amphibians and reptiles, multi-photoreceptors are involved in photo-entrainment of circadian rhythms. The eyes, pineal complex and deep brain comprise a multi-oscillator system as well as a multi-photoreceptor system.     

湖南小溪国家级自然保护区两栖爬行动物多样性与区系特征

本底资源是保护区建设与发展的基础,也是生物多样性深入研究与保护重要的参考资料。湖南小溪国家级自然保护区是我国中南地区具有代表性的原始次生林区,生物资源相对丰富。自2014年以来,对区内的两栖爬行动物资源、多样性及区系进行了较为系统的调查与研究。结果表明:区内现有两栖爬行动物2目16科40属63种,其中两栖动物1目7科15属33种,爬行动物1目9科25属30种;无声囊泛树蛙Polypedates mutus和老山树蛙Rhacophorus laoshan是湖南省两栖动物新记录;核心区的物种多样性指数和均匀度指数均高于缓冲区和实验区;动物区系成分缺乏古北界种类,以东洋界种类为主(48种,占76.2%),广布种有15种(23.8%);平均动物区系相似性比较发现,其与湖南省内其他6个保护区(森林公园)属于周缘关系。鉴于保护区两栖爬行动物资源的丰富性、典型性与代表性,应加强研究和保护。     

两栖类和爬行类体温调节的神经生物学研究进展

两栖类和爬行类属于变温脊椎动物,它们对外界环境温度的变化非常敏感,借助自身体温调节以适应或抵抗这种变化.本文简要介绍了它们的体温调节中枢、参与体温调节的神经递质和激素及其体温调节的研究方法和神经生物学机制.     

宁夏六盘山国家级自然保护区两栖爬行动物资源调查

宁夏六盘山保护区自成立以来,对其两栖爬行动物资源调查的相关报道较少。为掌握两栖爬行动物本底资源现状,评价保护区生物多样性,2011年7月~2013年7月共7次对保护区两栖爬行动物资源进行了实地调查。结合文献记载,保护区两栖爬行动物共14种,隶属于2目7科9属,占宁夏28种两栖爬行动物的50.0%;其中两栖类共5种,隶属于1目3科4属,占宁夏7种两栖动物的71.4%,爬行类共9种,隶属于4科5属,占宁夏21种爬行动物的43.8%。保护区两爬动物以古北界物种和广布种为主,分别为8种和5种,东洋界物种仅1种。在此基础上与其相邻的保护区做了动物区系相似性(AFR)比较,结果显示,随着纬度的增高,各保护区两栖爬行动物存在规律性的替代现象。     

Identification of single copy nuclear DNA markers for North American pit vipers

We describe 18 single copy nuclear DNA loci (10 loci cloned from a Sistrurus catenatus catenatus genomic library and eight intron-based loci amplified using conserved primers) that detect sequence variation in species from all genera (Sistrurus, Agkistrodon and Crotalus) of North American pit viper snakes. These loci (mean size in bp ± SE: 433 ± 51) show large numbers of phylogenetically informative sites across species (mean + SE: 10.2 ± 1.5), but limited variation within subspecies suggesting that they will be most useful for multilocus species-level phylogenetic analyses in these snakes.     

广西底定自然保护区两栖爬行动物物种多样性调查

广西底定自然保护区地处南亚热带湿润气候区,两栖爬行动物物种多样性相当丰富。经实地调查及文献资料查阅,现已知两栖动物22种、爬行动物23种。两栖动物反映华中华南区系特征,优势科为角蟾科和蛙科,均有6种;爬行动物反映华南区系特征,优势科为游蛇科,有11种。就该保护区内两栖爬行动物多样性的保护与管理进行了简要探讨。     

Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes

Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel’s λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities.     

More Than Just Records: Analysing Natural History Collections for Biodiversity Planning

Natural History Collections (NHCs) play a central role as sources of data for biodiversity and conservation. Yet, few NHCs have examined whether the data they contain is adequately representative of local biodiversity. I examined over 15,000 databased records of Hymenoptera from 1435 locations across New Zealand collected over the past 90 years. These records are assessed in terms of their geographical, temporal, and environmental coverage across New Zealand. Results showed that the spatial coverage of records was significantly biased, with the top four areas contributing over 51% of all records. Temporal biases were also evident, with a large proportion (40%) of records collected within a short time period. The lack of repeat visits to specific locations indicated that the current set of NHC records would be of limited use for long-term ecological research. Consequently, analyses and interpretation of historical data, for example, shifts in community composition, would be limited. However, in general, NHC records provided good coverage of the diversity of New Zealand habitats and climatic environments, although fewer NHC records were represented at cooler temperatures (<5°C) and the highest rainfalls (>5000 mm/yr). Analyses of NHCs can be greatly enhanced by using simple techniques that examine collection records in terms of environmental and geographical space. NHCs that initiate a systematic sampling strategy will provide higher quality data for biodiversity research than ad hoc or point samples, as is currently the norm. Although NHCs provide a rich source of information they could be far better utilised in a range of large-scale ecological and conservation studies.     

Species diversity in North American temperate forests

Summary Samples from temperate forest communities across the North American continent were analysed for correlations of plant species diversity with environment and community structure.Alpha diversity relationships are complicated by different vegetation patterns and community history. The differences in community diversity patterns may be due to the independent evolution of communities in different regions.Results of analyses were: 1) on a continental scale plant species diversity is related to mean annual temperature, but not precipitation; 2) diversity is substantially greater in continental climates than in maritime regions; 3) diversity-community structure relationships are generally weak, except 4) there is an inverse relationship between diversity and abundance of conifer tree species. Attempts to relate diversity to environmental parameters with multiple regression techniques met with only moderate success.I thank R. H. Whittaker, R. K. Peet and H. G. Gauch, Jr., for their help and comments. I am especially grateful to R. H. Whittaker for making his data available to me. Computation was supported in part by N.S.F. grant No. GB-30679. I was supported by a Nat. Inst. of Health Traineeship during part of this study.