福建漳江口红树林鹭科鸟类巢址选择

2011年4～5月、2012年4～5月,采用样线调查和样方调查相结合的方法对福建漳江口红树林国家级自然保护区内鹭科鸟类巢址与影响其选择的因子进行研究.t-检验结果显示,红树基径、盖度、距地面平均高度、植株密度及秋茄比5个参数在巢区样方(n=23)与对照样方(n=37)之间存在显著差异(P＜0.05),桐花比、距道路距离、距村庄距离与距池塘距离4个参数存在极其显著差异(P＜0.01).主成分分析表明,植被结构和干扰条件是影响鹭科鸟类巢址选择的主要因子,植被结构不仅能够影响鹭科鸟类群落结构,还受到鹭科鸟类集群繁殖影响.     

草鹭染色体的研究

在鸟类中,由于染色体标本制作比较困难,加之含有大量的微小染色体,要得到质优量多的中期分裂相很不容易,以致影响了对鸟类染色体的分带研究。因此,至今有关的报道尚少。本文报告了鹳形目(Ciconiiformes)鹭科(Ardeidae)鹭属草鹭(Ardea purpurea)的核型及G带、C带和Ag-NORs的研究结果。     

鹳形目12种鸟类核c-mos 基因和线粒体12S rRNA基因序列分析及其系统发生研究

鹳形目鸟类的传统分类一直存在分歧,而近期的分子系统学研究大多只用单个基因,其结论的可信度需要进一步验证.本文通过核c-mos基因和线粒体12S rRNA基因序列分别和合并分析,采用分子系统学方法探讨了鹳形目6科12种鸟类的系统发生关系.文中测出鹳形目鸟类6种核c-mos基因的片断序列,结合来自Genebank的其他种类的c-mos和12S rRNA基因序列,分别经Clustal W软件对位排列后,以原鸡为外类群用最大似然法、邻接法和最大简约法建立系统树.系统树分析表明, 鹳形目6科之间的系统发生关系总结为：（鹭科,（（鹮科,美洲鹫科）,（鹳科,（鲸头鹳科,锤头鹳科））））.鹭科7个属之间的系统发生关系总结为：（麻（开鸟）属（夜鹭属（池鹭属（苍鹭属（中白鹭属（白鹭属,大白鹭属））））））.分别基于两个单基因的系统树有一定差异,而基于合并数据的系统树支持率和分辨率都高于基于单基因的系统树,表明使用在遗传上相对独立的分子数据合并建立系统树有较高的可信度和分辨率,是一种更好的研究方法.     

草鹭染色体的研究

在鸟类中,由于染色休标本制作比较困难, 加之含有大量的微小染色体,要得到质优量多 的中期分裂相很不容易,以致影响了对鸟类染 色体的分带研究。因此,至今有关的报道尚少。 本文报告了鹤形目（Ciconiiformes)鹭科 (Ardeidae) 鹭属草鹭(Ardea purpurea） 的 核型及G带、C带和Ag-NORs的研究结果。     

基于12S rRNA基因的鹳形目系统发生关系

采用分子系统学的方法探讨鹳形目5个科之间的系统发生关系.文中测出鹳形目鸟类7种mtDNA 12SrRNA基因全序列,并结合来自Genbank的鹳形目另外7个物种及原鸡的同源区序列,经Clustal W软件对位排列后共1 009位点,包含405个变异位点,其中多态性位点381个,260个简约信息位点.基于上述序列数据,以原鸡为外群,使用距离邻接法、最大简约法、最大似然法及贝叶斯法分别重建了鹳形目5科14种的系统发生树.重建的系统发生树显示,内群中的14个种聚合为4支:鹮科构成第一支,聚在系统树的基部;锤头鹳科与鲸头鹳科聚为一支;鹭科和鹳科各自聚成一支.在比较不同建树方法的结果并进行合意树分析后认为:在鹳形目的系统发生中,鹮科可能是最早分化出的一支;锤头鹳科与鲸头鹳科之间的亲缘关系最近,它们祖先与鹭科、鹳科之间的分歧在时间上可能非常接近.鹳形目5个科之间的系统关系可以表示为:(鹮科,(鹭科,鹳科,(锤头鹳科,鲸头鹳科))).     

云南鸟类种的新记录——海南鸦

2006年10月28日凌晨3点,笔者在位于云南省新平县哀牢山的金山丫口鸟类环志站进行夜间鸟类环志工作时,用灯光诱捕到一只鹭科鸟类,经鉴定为海南鸦（Gorsachius magnificus）,为云南省鸟类物种新记录。     

云南鸟类种的新记录——海南(开鸟)

2006年10月28日凌晨3点,笔者在位于云南省新平县哀牢山的金山丫口鸟类环志站进行夜间鸟类环志工作时,用灯光诱捕到一只鹭科鸟类,经鉴定为海南(开鸟) (Gorsachius magnificus),为云南省鸟类物种新记录.     

朱鹮线粒体DNA的分子系统发育

朱Huan是一种濒危鸟类。过度开发和栖息地的破坏导致了朱Huan日本种群的绝灭,而在中国目前也仅存一野生种群。本文利用NJ法和最大简约法分析了鹳形目鸟类977bp的线粒体DNA细胞色素b基因的部分序列,以期从DNA水平上阐明朱Huan的系统地位。结果表明,朱Huan与彩Huan和非洲琶鹭组成一姐妹群;NJ法分析得出的结果与DNA杂交分析结果一致,即((Huan科,鹭科),鹳科);而最大简约法分析的结果则与形态学结果一致,即((鹭科,鹳科),Huan科)。同时,这两种系统树上较低的置信度,认为部分是由于可用细胞色素b基因序列的有限所致。     

鸟类鸣声在鸟类系统学研究中的作用初探

报道了近年来建立了鸟类鸣声基础上的鸟类系统学研究新方法,新思路及其意义。鸟声不仅是鸟类很重要的行为表现,而且可应用于鸟类系统学研究,尤其对于物种界限的确立,亲缘种,姊妹种的区别以及推测新种形成的种系发生及其亲缘关系等方面有一定的意义。     

广西大苗山“打鸟坳”趋光性鸟类调查

2000年9月、2001年5月和10月2、002年5月和10月、2003年10月、2005年9月,通过实地调查和访问当地群众的方法,对广西大苗山“打鸟坳”的趋光性鸟类进行了调查,在大苗山发现了规模较大的“打鸟坳”共5个,并记录趋光性鸟类58种,隶属于10目14科。其中留鸟16种,夏候鸟15种,冬候鸟17种,旅鸟10种。趋光性鸟类主要以鹭科(Ardeidae)、三趾鹑科(Turnicidae)、秧鸡科(Rallidae)等涉禽为主。鹭科鸟类数量较多的有白鹭(Egretta garzetta)和池鹭(Ardeola bacchus);三趾鹑科数量最多的为黄脚三趾鹑(Turnix tanki);秧鸡科以白胸苦恶鸟(Amaurornis phoenicurus)最多。文中还对“打鸟坳”的形成以及部分留鸟被捕获的现象进行了讨论,并对大苗山“打鸟坳”鸟类的保护提出了建议。     

基于逻辑斯蒂回归模型的鹭科水鸟栖息地适宜性评价

近年来湿地生态系统遭到不同程度破坏,湿地水鸟及其生存空间日益受到威胁。以香港米埔-后海湾湿地为例,收集2003年1月份与鹭科水鸟密切相关的15个自变量和鹭科水鸟实测数据作为因变量构建逻辑斯蒂回归模型,通过筛选获取9个变量因子,分别为土地利用,NDVI,坡度,降雨,TM4纹理,TM3纹理,道路密度,道路距离,人居密度。经Nagelkerke R2检验模型精度达到0.743,拟合度较高。利用模型结果快速聚类,对栖息地进行适宜性分级,分级结果与同期鹭科水鸟实测数据做拟合,精度达到77.4%。最后采集2009年1月份各变量因子数据对回归方程进行时间尺度检验,与同期实测鹭科水鸟数据拟合精度同样达到75.8%,模型具有较好的通用性。     

Relative patterns and rates of evolution in heron nuclear and mitochondrial DNA

Mitochondrial cytochrome b sequence data from 15 species of herons (Aves: Ardeidae), representing 13 genera, were compared with DNA hybridization data of single-copy nuclear DNA (scnDNA) from the same species in a taxonomic congruence assessment of heron phylogeny. The two data sets produced a partially resolved, completely congruent estimate of phylogeny with the following basic structure: (Tigrisoma, Cochlearius, (((Zebrilus, (Ixobrychus, Botaurus)), (((Ardea, Casmerodius), Bubulcus), ((Egretta thula, Egretta caerulea, Egretta tricolor), Syrigma), Butorides, Nycticorax, Nyctanassa)))). Because congruence indicated similar phylogenetic information in the two data sets, we used the relatively unsaturated DNA hybridization distances as surrogates of time to examine graphically the patterns and rates of change in cytochrome b distances. Cytochrome b distances were computed either from whole sequences or from partitioned sequences consisting of transitions, transversions, specific codon site positions, or specific protein-coding regions. These graphical comparisons indicated that unpartitioned cytochrome b has evolved at 5-10 times the rate of scnDNA. Third-position transversions appeared to offer the most useful sequence partition for phylogenetic analysis because of their relatively fast rate of substitution (two times that of scnDNA) and negligible saturation. We also examined lineage-based rates of evolution by comparing branch length patterns between the nuclear and cytochrome b trees. The degree of correlation in corresponding branch lengths between cytochrome b and DNA hybridization trees depended on DNA sequence partitioning. When cytochrome b sequences were not partitioned, branch lengths in the cytochrome b and DNA hybridization trees were not correlated. However, when cytochrome b sequences were reduced to third-position transversions (i.e., unsaturated, relatively fast changing data), branch lengths were correlated. This finding suggests that lineage-based rates of DNA evolution in nuclear and mitochondrial genomes are influenced by common causes.     

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring

This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.     

The mitochondrial genome of the Cinnamon Bittern, Ixobrychus cinnamomeus (Pelecaniformes: Ardeidae): sequence, structure and phylogenetic analysis

Ixobrychus cinnamomeus is a member of the large wading bird family, known as Ardeidae. In the present study, we determined the complete mitochondrial genome of I. cinnamomeus for use in future phylogenetic analysis. This circular mitochondrial genome is 17,180 bp in length and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one putative control region. Three conserved domains and a minisatellite of 17 nucleotides with 22 tandem repeats were detected at the end of the control region. Phylogenetic relationships were reconstructed using the nucleotide and corresponding amino acid datasets of 12 concatenated protein-coding genes from the mitochondrial genome. Using maximum likelihood, maximum parsimony and Bayesian inference methods, the monophyly of Ciconiidae, Ardeidae and Threskiornithidae were confirmed; however, the monophyly of traditional Ciconiiformes and Pelecaniformes failed to be recovered. Although further studies are recommended to clarify relationships among and within the orders of Ciconiiformes, Pelecaniformes, Suliformes and Phaethontiformes, our results provide preliminary exploratory results that can be useful in the current understanding of avian phylogenetics.     

Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species

Biodiversity studies require species level analyses for the accurate assessment of community structures. However, while specialized taxonomic knowledge is only rarely available for routine identifications, DNA taxonomy and DNA barcoding could provide the taxonomic basis for ecological inferences. In this study, we assessed the community structure of sediment dwelling, morphologically cryptic Chironomus larvae in the Rhine-valley plain/Germany, comparing larval type classification, cytotaxonomy, DNA taxonomy and barcoding. While larval type classification performed poorly, cytotaxonomy and DNA-based methods yielded comparable results: detrended correspondence analysis and permutation analyses indicated that the assemblages are not randomly but competitively structured. However, DNA taxonomy identified an additional species that could not be resolved by the traditional method. We argue that DNA-based identification methods such as DNA barcoding can be a valuable tool to increase accuracy, objectivity and comparability of the taxonomic assessment in biodiversity and community ecology studies.     

Review: Taxonomy of Nitella (Charales, Charophyceae) based on comparative morphology of oospores and multiple DNA marker phylogeny using cultured material

The genus Nitella is the largest group in the Charales and has the highest diversity of vegetative and oospore morphologies. In his worldwide monograph on the Charales, R. D. Wood characterized the sections and species of Nitella mainly on the basis of vegetative morphology and treated oospore wall morphology as diagnostic at the infraspecific level. Therefore, many species of Nitella exhibiting distinct external morphology of the oospore wall (EMOW) were reduced to infraspecific rank and only 53 of 204 species previously described were recognized within Nitella . However, recent morphological and molecular phylogenetic studies have demonstrated the phylogenetic validity of using EMOW for diagnosing some species of Nitella . More recently, a scanning electron microscopy (SEM) study of internal morphology of the oospore wall (IMOW) and multiple DNA marker analyses using both nuclear and chloroplast gene sequences were conducted to improve our understanding of the taxonomy of Nitella at the species level, on the basis of cultured material of a large number of species. Multiple DNA marker analyses resolved detailed and robust phylogenetic relationships within the genus and demonstrated the taxonomic and phylogenetic significance of IMOW. In addition, they supported the taxonomic decisions based on differences in oospore morphology, suggesting that an integrated approach, involving both SEM studies of the EMOW and IMOW and multiple DNA marker analyses, is appropriate to address problems at lower taxonomic levels within the genus, as well as to construct a natural taxonomic system for the genus. In this paper, recent morphological and molecular phylogenetic studies are reviewed and recent improvements in taxonomy of Nitella are summarized. Moreover, the evolution of morphological features and phylogenetic relationships within Nitella are discussed, focusing especially on oospore morphology.     

DNA barcodes as a tool in biodiversity research: testing pre-existing taxonomic hypotheses in Delphic Apollo butterflies (Lepidoptera,Papilionidae)

Numerous studies have demonstrated that DNA barcoding is an effective tool for detecting DNA clusters, which can be viewed as operational taxonomic units (OTUs), useful for biodiversity research. Frequently, the OTUs in these studies remained unnamed, not connected with pre-existing taxonomic hypotheses, and thus did not really contribute to feasible estimation of species number and adjustment of species boundaries. For the majority of organisms, taxonomy is very complicated with numerous, often contradictory interpretations of the same characters, which may result in several competing checklists using different specific and subspecific names to describe the same sets of populations. The highly species-rich genus Parnassius (Lepidoptera: Papilionidae) is but one example, such as several mutually exclusive taxonomic systems have been suggested to describe the phenotypic diversity found among its populations. Here we provide an explicit flow chart describing how the DNA barcodes can be combined with the existing knowledge of morphology-based taxonomy and geography (sympatry versus allopatry) of the studied populations in order to support, reject or modify the pre-existing taxonomic hypotheses. We then apply this flow chart to reorganize the taxa within the Parnassius delphius species group, solving long-standing taxonomic problems.