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。     

大别山地区两栖爬行动物区系调查

为掌握大别山地区两栖爬行动物资源现状,于2006年9月起至2013年6月通过53条样线对大别山地区进行实地考察。调查结果显示,在大别山地区共发现两栖爬行动物56种,隶属4目16科。其中两栖动物2目8科21种,爬行动物2目8科35种。大别山地区两栖、爬行动物的分布型主要为南中国型,动物区系类型则主要为华中型和华南型。黄喉拟水龟(Mauremys mutica)、黄脊游蛇(Coluber spinalis)、平鳞钝头蛇(Pareas boulengeri)、棕黑腹链蛇(Amphiesma sauteri)和福建颈斑蛇(Plagiopholis styani)为该地区的新纪录,大别山原矛头蝮(Protobothrops dabieshanensis)为近期在大别山地区发现的蛇类新种。东方蝾螈(Cynops orientalis)、中华大蟾蜍(Bufo gararizans)、泽陆蛙(Fejervarya multistriata)、黑斑侧褶蛙(Pelophylax nigromaculatus)、中国林蛙(Rana chensinensis)为两栖类的优势种,中国石龙子(Eumeces chinensis)、蝘蜓(Sphenomorphus indicus)、北草蜥(Takydromus septentrionalis)、赤链蛇(Dinodon rufozonatum)、王锦蛇(Elaphe carinata)、虎斑颈槽蛇(Rhabdophis tigrinus)和乌梢蛇(Zaocys dhumnades)为爬行类的优势种。鉴于大别山两栖爬行动物多样性的丰富度和动物区系的代表性,应加强对该地区两栖爬行动物的保护工作。     

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.     

黑龙江省两栖爬行类物种多样性分布格局的研究

2000～2006年对黑龙江省两栖爬行动物的种类及分布进行大范围的调查,并结合历史资料及现代有关成果,应用3种物种多样性指数分析方法（丰富度、均匀度和G—F指数）,对黑龙江省的两栖爬行动物物种多样性分布格局进行了探讨。结果表明,东部山地省和小兴安岭省的物种丰富度要高于其它地理省,松嫩平原省和三江平原省的物种均匀度高于其它地理省,而G指数与物种数分布规律相似,F指数和G-F指数相似,只有东部山地省物种才有一定的丰富度。     

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.     

The Middle Ear--Morphological Types in Amphibians and Reptiles

The middle ear regions of reptiles and amphibians frequentlyare grouped into morphological types on the basis of structuralresemblances. The arrays of animals resulting from such a groupinghave a fair degree of taxonomic continuity. The types in mostinstances include a "central" pattern, presumed to be primitive,and modifications that are considered to have been derived fromthe "central" type by evolutionary processes. Some understandingof phylogeny, thus, is a necessary precursor to the formationof the groups. This raises problems when, as is often the case,the groups based on ear structures are used as a basis for phylogeneticinterpretations. Among reptiles the theropsid-sauropsid caseis the best known. The principal morphological types are described and discussed.The middle ear, as a sound-transmitting apparatus and in itsassociations with the masticatory apparatus, is highly susceptibleto adaptive modifications. Some morphological types, such asthose in archosaurs and labyrinthodonts, are quite stable. Othersshow marked evolutionary diversity. The middle ear structures,hence, appear quite useful as phylogenetic indicators withinmorphological types but less so when relationships between typesare considered.     

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.     

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.     

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.     

4种两栖爬行动物血细胞的显微结构及细胞化学特征观察

光镜下两栖动物中华蟾蜍Bufo gargarizans和牛蛙Rana catesbeiana、爬行动物铜蜓蜥Sphenomorphus indicus和青海沙蜥Phrynocephalus vlangalii4种动物外周血中均可观察到红细胞、血栓细胞、淋巴细胞、单核细胞、嗜中性粒细胞和嗜碱性粒细胞,中华蟾蜍和牛蛙的外周血中还观察到嗜酸性粒细胞。细胞化学染色显示:脂类存在于中华蟾蜍和牛蛙的单核细胞和粒细胞中,2种爬行动物的血细胞中未发现脂类。4种动物的血细胞中均未检测到碱性磷酸酶,但均检测到酸性磷酸酶,在中华蟾蜍和牛蛙血细胞中含量最多。过氧化物酶存在除青海沙蜥以外的3种动物的血细胞中,以在嗜中性粒细胞中居多;4种动物的外周血细胞中均检测到酸性-α-醋酸萘酯酶。     

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。     

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.     

Using DNA Barcodes to Identify Bird Species Involved in Birdstrikes

Abstract: We determined effectiveness of using mitochondrial DNA barcodes (cytochrome c oxidase subunit 1 [CO1]) to identify bird-aircraft collision (birdstrike) cases that lacked sufficient feather evidence for morphological diagnosis. From September through December 2006, 821 samples from birdstrike events occurring in the United States were submitted for DNA analysis. We successfully amplified a CO1 DNA barcode product from 554 (67.5%) of the samples; 267 (32.5%) did not contain viable DNA and depended on morphological methods (microscopy) for Order or Family level identification. We deemed 19 cases inconclusive either because the DNA barcode recovered from the sample did not meet our 98% match criteria when compared to the Barcode of Life Database (BoLD) or because the DNA barcode matched to a set of ≥ 2 closely related species with overlapping barcodes, preventing complete species identification. Age of the sample (≤6 months) did not affect DNA viability, but initial condition of the sample and the collection method was critical to DNA identification success. The DNA barcoding approach has great potential in aiding in identification of birds (and wildlife) for airfield management practices, particularly in regions of the world that lack the vast research collections and individual expertise for morphologic identifications.     

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.