西双版纳片段化石灰岩森林附生兰科植物多样性研究

西双版纳石灰岩地区拥有丰富的兰科植物资源,但近年来随着橡胶树的大面积种植,使得该地区很多石灰岩森林呈片段化。为了解片段化石灰岩森林中附生兰科植物多样性状况以及片段化对附生兰科植物的影响,该研究选取了生境片段化的青岩寨和曼纳览,以及连续生境的绿石林和巴卡新寨等4个样地的29个样方进行多样性调查和对比研究。结果表明:4个石灰岩森林样共记录到附生兰科植物34属76种1 528株(丛)。通过对坡向、坡度、海拔、地形、郁闭度和森林类型等6个环境因子与附生兰科植物丰富度进行CCA分析,发现石灰岩地区附生兰科植物的分布主要受海拔和森林类型2个因素的影响,在海拔较高的青岩寨和巴卡新寨附生兰科植物物种丰富度高于低海拔的绿石林和曼纳览,而片段化对附生兰科植物的物种多样性和多度均无显著影响,这可能与片段化的历史较短有关。虽然目前来看生境片段化对石灰岩地区的附生兰科植物多样性无显著影响,但生境脆弱的石灰岩森林植被的保护对于兰科植物多样性保护则更具重要性。     

Patterns of endemism in the limestone flora of South African lowland fynbos

Taxonomie and biological aspects of endemism and Red Data Book status were studied amongst the limestone endemics of the lowland fynbos in the Cape Floristic Region, South Africa. Of the 110 limestone endemics, 1.8% are widely distributed in the Cape Floristic Region and 56.4% are regional endemics. Relative to flora of non-limestone lowland fynbos (n=538 species), the families which were overrepresented in terms of limestone endemics included the Ericaceae, Fabaceae, Polygalaceae, Rutaceae and Sterculiaceae. The Restionaceae was the only underrepresented family. The local limestone endemics were not significantly different from regional endemics in terms of their biological attributes. An analysis of the frequency of the biological traits associated with the limestone-endemic flora established a biological profile for a limestone endemic: a dwarf-to-low shrub with soil-stored seeds which are ant or wind dispersed. In terms of the species richness of limestone endemics, the De Hoop Nature Reserve was the hotspot within the region. Relative to the total species richness, the Hagelkraal and Stilbaai areas contained higher-than-predicted numbers of rare species. These areas require urgent attention if the unique floral diversity associated with limestone substrata within the Bredasdorp-Riversdale centre of endemism is to be conserved.     

Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards

Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here, we showcase an organismal system for a data‐rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5‐gene data set, we estimated phylogeny and used multilocus genetic networks, analysis of population structure and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g. morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists and conservationists.     

DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)

To assess species‐level diversity in the didelphid marsupial genus Marmosops, we obtained sequence data from the mitochondrial cytochrome b (CYTB) gene from > 200 specimens, including exemplars of every currently recognized species together with multiple specimens of all geographically widespread forms. Analyses of these data using the general mixed Yule coalescent (GMYC) model suggest that the genus could be twice as speciose as currently recognized, but putative species identified by the GMYC criterion require careful evaluation using other data. To assess phylogenetic relationships within Marmosops, we additionally sequenced a large fragment of the breast cancer activating 1 (BRCA1) gene from one specimen each of the putative species identified by the GMYC analyses of CYTB. Maximum likelihood and Bayesian analyses of a concatenated gene (CYTB + BRCA1) matrix revealed a basal dichotomy between two ancient, morphologically diagnosable clades with apparently distinct distributions and adaptive phenotypes. We describe those clades as subgenera and assign 12 nominal taxa to Sciophanes subgen. nov. (with type species Marmosops parvidens) and 27 nominal taxa to the nominotypical subgenus (with type species Marmosops incanus).     

DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China

Identification of rodents is very difficult mainly due to high similarities in morphology and controversial taxonomy. In this study, mitochondrial cytochrome oxidase subunit I (COI) was used as DNA barcode to identify the Murinae and Arvicolinae species distributed in China and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31 species, 11 genera) from Murinae and 130 sequences (23 species, 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree‐based method, online BLAST and BLOG were employed to analyse the data sets. There was no obvious barcode gap. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius and E. hintoni and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.     

Diversity of desmids in three Thai peat swamps

Three peat swamps situated in the southern part of Thailand were investigated for their desmid flora in relation to a number of physical and chemical habitat parameters. Altogether, 99 species were encountered belonging to 22 genera. 30 species are new records for the Thai desmid flora. Laempagarung peat swamp showed the highest diversity (45 species), followed by Maikhao peat swamp (32 species) and Jud peat swamp (25 species). Despite its relatively low species richness, Jud swamp appeared to house a number of rare taxa, e.g., Micrasterias subdenticulata var. ornata, M. suboblonga var. tecta and M. tetraptera var. siamensis which can be considered Indo-Malaysian endemics. Differences in composition of the desmid flora between the three peat swamps are discussed in relation to environmental conditions. Presented at the International Symposium Biology and Taxonomy of Green Algae V, Smolenice, June 26–29, 2007, Slovakia.     

Molecular phylogeny reveals high diversity and endemism in the limestone karst-restricted land snail genus Sophina Benson, 1859 from Myanmar (Eupulmonata: Helicarionidae), with description of four new species

Sophina is a poorly known and neglected genus due to the inaccessibility of the Salween Basin, Southern Myanmar. Taxonomic status, distribution, and phylogeny are being revised based on an integrative analysis of genitalia, radula, and molecular data. Morphological variation in shells and genitalia, together with a phylogenetic tree from concatenated data of mitochondrial and nuclear genes, revealed the existence of ten species/subspecies. Penial morphology and genetic divergence were generally consistent and useful in delimiting species, while shell characters showed little overall taxonomic utility in some species. Taxonomic placement of the previous subspecies “bensoni” shows clear distinction in both genitalia and molecular evidence, and is currently recognized as a distinct species. The nominal species “S. schistostelis” and “S. calias” possess similar genitalia and shell morphology, and molecular evidence suggested that they are sister taxa representing geographically isolated populations. Four new species are additionally described herein as S. furfuracea n. sp., S. pisinna n. sp., S. salweenica n. sp., and S. tonywhitteni n. sp. based on both morphology and molecular evidence. Phylogenetic analyses supported monophyly of Sophina, and further a split into two principal clades. These two clades showed little difference in genitalia, but more clear differences in the umbilical area and allopatric distribution in upper and lower reaches of the Gyaing River. High genetic divergence was revealed and this coincided with remarkable degree of endemism and localization with a pattern of one outcrop for one lineage. These data highlight the importance of the Salween Basin's karst ecosystems as an evolutionary and endemic biodiversity hotspot, and indicate that a focus on conservation and management in this area is urgently required.     

A new integrative framework for large‐scale assessments of biodiversity and community dynamics,using littoral gastropods and crabs of British Columbia,Canada

Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here, we present and apply an integrative approach that links high‐throughput, multicharacter taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community‐level data set. We collected 1195 gastropods and crabs in British Columbia. First, the General mixed Yule‐coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species‐hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co‐occurrence patterns for nonrandomness using community‐wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species‐hypotheses in community‐level data sets. Nonrandom species co‐occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of carnivorous gastropods and crabs appeared influenced by random processes. Species‐pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co‐occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.     

Diversity, endemism and evolution in the Coral Triangle

In a recent paper by D. R. Bellwood and C. P. Meyer ('Searching for heat in a marine biodiversity hotspot', Journal of Biogeography , 2009, 36 , 569–576), the authors had two evident objectives: (1) to disprove the theory that the geographical origins of reef organisms could be determined by locating concentrations of endemic species, and (2) to emphasize that the high diversity of the Coral Triangle was due to an accumulation of species from outside that area. With regard to the first point, no such theory had previously been proposed to my knowledge. Second, the accumulation theory was promoted without consideration of the facts supporting the centre of origin hypothesis, except to dismiss it by saying that it had its origin in pre-continental drift ideas. This short response outlines the properties and evidence for the operation of centres of origin in this region.     

Detecting cryptic species in sympatry and allopatry: analysis of hidden diversity in Polyommatus (Agrodiaetus) butterflies (Lepidoptera: Lycaenidae)

Modern multilocus molecular techniques are a powerful tool in the detection and analysis of cryptic taxa. However, its shortcoming is that with allopatric populations it reveals phylogenetic lineages, not biological species. The increasing power of coalescent multilocus analysis leads to the situation in which nearly every geographically isolated or semi‐isolated population can be identified as a lineage and therefore raised to species rank. It leads to artificial taxonomic inflation and as a consequence creates an unnecessary burden on the conservation of biodiversity. To solve this problem, we suggest combining modern lineage delimitation techniques with the biological species concept. We discuss several explicit principles on how genetic markers can be used to detect cryptic entities that have properties of biological species (i.e. of actually or potentially reproductively isolated taxa). Using these principles we rearranged the taxonomy of the butterfly species close to Polyommatus (Agrodiaetus) ripartii. The subgenus Agrodiaetus is a model system in evolutionary research, but its taxonomy is poorly elaborated because, as a rule, most of its species are morphologically poorly differentiated. The taxon P. (A.) valiabadi has been supposed to be one of the few exceptions from this rule due to its accurately distinguishable wing pattern. We discovered that in fact traditionally recognized P. valiabadi is a triplet of cryptic species, strongly differentiated by their karyotypes and mitochondrial haplotypes.     

Molecular data reveal cryptic lineages within the northeastern Atlantic and Mediterranean small mussel drills of the Ocinebrina edwardsii complex (Mollusca: Gastropoda: Muricidae)

We used a molecular phylogenetic approach to investigate species delimitations and diversification in the mussel drills of the Ocinebrina edwardsii complex by means of a combination of nuclear (internal transcribed spacer 2, ITS2) and mitochondrial [cytochrome oxidase subunit I (COI) and 16S] sequences. Our sample included 243 specimens ascribed to seven currently accepted species from 51 sites. Five of the samples were from either the type locality of a nominal species or a close nearby locality (O. edwardsii from Corsica, O. carmelae and O. piantonii from the Kerkennah Islands, O. hispidula from the Gulf of Gabès and O. leukos from the Canary Islands), one from the inferred original locality (O. ingloria from Venice Lagoon), and specimens assigned in the recent literature to O. nicolai. We used a combination of distance‐ and tree‐based species delimitation methods to identify Molecular Operational Taxonomic Units (MOTUs) to compare with the a priori species identifications. The consensus tree obtained by BEAST on the COI alignment allows the recognition of several distinct clades supported by the three species delimitation methods employed. The eight‐MOTUs scenario, shared by the Automatic Barcode Gap Discovery (ABGD) and Generalized Mixed Yule‐Coalescent (GMYC) methods, comprises the following major clades: clade A contains the south Tunisian species Ocinebrina piantonii Cecalupo, Buzzurro & Mariani from which the sympatric taxon O. carmelae Cecalupo, Buzzurro & Mariani (new synonym) cannot be separated; clades B and C bring together all populations from the Aegean Sea and some from the Ionian Sea, respectively; clade D groups, on the one hand, the south Tunisian samples morphologically assigned to O. hispidula Pallary and, on the other, Atlantic and Alboran Sea samples (including the Canarian taxon O. leukos Houart); clade E includes a sample from the type locality of O. edwardsii and several samples from the Tyrrhenian Sea; clades F and G correspond to a few samples from the Venice Lagoon and the Tyrrhenian Sea, respectively; clade H groups the bulk of samples from the Adriatic Sea, including samples from the Venice Lagoon morphologically identified as Ocinebrina ingloria (Crosse), and some from the Ionian Sea. No final conclusions could be reached to reconcile the currently recognized morphological taxa with the clades suggested by the COI data. The geographical structure proposed by the mitochondrial markers is similar to that found in other marine invertebrates and partially corresponds to the species defined by shell characters. We propose here a framework for the revision of the Ocinebrina edwardsii species complex, suggesting a geographical pattern for the diversification of this group in the studied area. © 2013 The Linnean Society of London     

甘肃河西走廓不同生境中鼠类群落结构初步研究

本文对河西走廓不同生境中鼠类群落的物种组成和多样性进行了初步研究,在6种生境中进行了定量调查和采集,共获13种标本,隶于6（亚）科9属,其中古北界种类占优势。多样性分析结果表明：6种生境的物种丰富度指数RMargaler在.6139-1.9689之间。Shannon-Wiener指数（H')为1.0695-1.5607,Pielou旨数（J')和Simpson指数（D）分别为0.7242-0.9735和0．2768－0．4683,不同生境的丰富种数量（N1)变化趋势与H'相似,而非常丰富种数量（N2）的变化趋势为：半莫荒灌丛生境＞山地草原生境＞戈壁荒漠生境＞农田生境＞森林生境＞山地半荒漠灌丛生境。降水对不同生境类型中鼠类群落物种组成和多样性起直接的限制作用,同时海拔和人类干扰也是影响的因素。     

Species diversity and population dynamics of rodents in a farm‐fallow field mosaic system in Central Tanzania

A Capture‐Mark‐Recapture study was undertaken in Central Tanzania to compare variations in community structure and population dynamics of rodents in two types of habitats. The study was conducted in fallow field mosaic habitat dominated by perennial and annual grasses (grid BEA) and a more heterogeneous habitat (grid BEB) which was previously woodland cleared of most trees with vegetation dominated by shrubs, bushes, scattered trees and perennial grass. The relative abundance of rodents in BEA was: Mastomys natalensis (73.5%) > Aethomys chrysophilus (8.9%) > Gerbilliscus vicina (7.3%) > Arvicanthis neumanni (6.1%) > Acomys spinosissimus (4.1%) and for grid BEB: M. natalensis (67.6%) > G. vicina (11.2%) > A. neumanni (10.3%) > A. chrysophilus (7.6%) > A. spinosissimus (2.9%). Graphiurus sp., Mus minutoides, Saccostomus mearnsi, Lemniscomys striatus and L. griselda were rare and only occasionally trapped in BEB. Spatial variations in population density were non‐significant except for A. chrysophilus. Significant temporal variations within grids were observed, with synchrony of population peaks for some species. The rare species boosted species richness of grid BEB rather artificially, without significantly contributing to higher species diversity. Temporal variations in Simpson’s Diversity indices between grids were non‐significant except for three out of twenty‐one trapping sessions.     

Diversity of rodents and shrews along an elevational gradient in Bwindi Impenetrable National Park, south-western Uganda

Small mammal species diversity in the major vegetation zones of Bwindi Impenetrable National Park is discussed in relation to altitude. Species richness of the small mammals was found to decrease with an increase in altitude. The main factors accounting for the observed diversity are the wide altitudinal variation and a complex array of vegetation types. Sixty‐seven species of rodents and shrews were found to exist in the Park; 47 of which were rodents and 20 shrews. Of these, 26 species are new to the Bwindi Park list. Three species have probably not been described before. The study found 10 species of small mammals to be Albertine Rift endemics. Three genera are recorded in Uganda for the first time: Rwenzorisorex, Suncus and Paracrocidura. Five species are new records for East Africa. These are Crocidura stenocephala, Lophuromys rahmi, L. medicaudatus, Paracrocidura maxima and Hylomyscus aeta. Because of the high endemism of plants, butterflies, birds and now of small mammal species, Bwindi forest is a unique biodiversity hotspot and is among the highest conservation priorities in the Albertine Rift.     

Mitochondrial phylogeographic structure of the white-browed piculet (Sasia ochracea): cryptic genetic differentiation and endemism in Indochina

Aim Our understanding of the geographic patterns of gene flow between populations of birds in the Indo‐Malayan faunal region is surprisingly poor compared with that in other parts of the world. A thorough knowledge of general patterns of phylogeographic structure is, however, of utmost importance for conservation purposes. Species with poor dispersal capabilities could serve as indicators of endemism and genetic isolation in the Indochinese subregion. From their morphology (tiny size, short tail, short and rounded wings), piculets of the genus Sasia are inferred to have poor dispersal capabilities, and thus form a suitable focal species. This study analysed the pattern of genetic variation within the White‐browed Piculet (Sasia ochracea). Location Southeast Asia, north of the Isthmus of Kra. Methods We sampled 43 individuals throughout the breeding range of S. ochracea. DNA was extracted both from fresh tissues (n = 15) and from toe pads from ancient museum skins (n = 28). We amplified a 801‐bp fragment of the mitochondrial ND2 gene to reconstruct the phylogeographic history of the White‐browed Piculet. The sequence data were analysed using Bayesian inference, statistical parsimony, and population genetics methods (analysis of molecular variance, mismatch distributions). We estimated the amount of ongoing gene flow between populations using the coalescent‐based method implemented in Mdiv . Results The analysis of molecular variance indicated that the current taxonomy does not adequately reflect the amount of genetic variation within S. ochracea, as the great majority of genetic variation was nested within the nominal subspecies, which is distributed from Nepal to southern Vietnam. Bayesian inference analyses and haplotype networks suggested the occurrence of five main lineages that are strongly correlated with geography. Our coalescent‐based analyses indicated a very limited amount of ongoing gene flow between these five lineages. Our dating analyses suggested that the genetic structuring probably occurred during the last 400,000 years. Main conclusions Our analyses revealed that S. ochracea is composed of at least five lineages: south Vietnam (South Annam and ‘Cochinchina’), India and Nepal, Myanmar and India, the remainder of Indochina, and probably southern Myanmar (Tenasserim). We strongly recommend that studies aiming to understand the phylogeographic structure within Indo‐Malayan species sample these areas.     

Three genetic lineages of the Japanese skink Plestiodon japonicus (Scincidae, Squamata) and the genetic composition of their contact zones

Geographic differentiation of the Japanese skink ( Plestiodon japonicus ) throughout the entire Japanese main islands was surveyed using two DNA markers, mitochondrial DNA (mtDNA) and an internal transcribed spacer of nuclear ribosomal genes (ITS-1). Both of the markers concordantly demonstrated geographically discontinuous differentiation between three genetic lineages: the northeastern, central and western lineages. Little to no gene flow occurs between the western and central lineages despite their parapatric distribution suggesting an existence of reproductive isolation despite no known morphological and ecological dissimilarities. On the other hand, the geographic ranges of the northeastern and central lineages are partially separated by a wide area occupied by genetically intermediate type having northeastern mtDNA and central ITS-1. The current data imply that the intermediate type was established by past secondary hybridization between the northeastern and central lineages. Although current gene flow status between the northeastern and central lineages should be elaborated by further data, at least the divergence between the central and western lineages should be maintained by reproductive isolation and therefore taxonomic revision of the species is desired.