The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae)

Shrimp of the family Atyidae are important members of nearly all tropical (and most temperate) fresh and brackish water ecosystems in the world. To date, a complete mitochondrial genome from this important crustacean group has not been reported. Here, we present the complete mitochondrial DNA sequence of the Hawaiian atyid Halocaridina rubra [Holthuis, L.B., 1963. On red coloured shrimps (Decapoda, Caridea) from tropical land-locked saltwater pools. Zool. Meded.16, 261-279.] (Crustacea: Decapoda: Atyidae). The genome is a circular molecule of 16,065 bp and encodes the 37 mitochondrial genes (13 protein-coding, 22 tRNAs, and two rRNAs) typically found in the metazoa. Gene order and orientation in the H. rubra mitochondrial genome is syntenic with most malacostracans that have been examined to date. Of special note is the absence of the dihydrouridine (DHU) arm stem from tRNA(Tyr) and the use of CCG as an initiation codon for cytochrome oxidase subunit I (COI); these represent the first reported examples of such phenomena in the Malacostraca. Phylogenetic analyses utilizing complete mitochondrial sequences from other malacostracans place H. rubra as sister to Macrobrachium rosenbergii, which also belongs to the Infraorder Caridea. However, the placement of this infraorder, as well as the Infraorder Dendrobrachiata, in the phylogeny of the Decapoda varied depending on outgroup selection. Data from additional mitochondrial genomes, such as basal decapods like the Stenopodidea, should contribute to a better overall understanding of decapod phylogenetics.     

Fine-scale population genetic structure of a wildlife disease vector: the southern house mosquito on the island of Hawaii

The southern house mosquito, Culex quinquefasciatus, is a widespread tropical and subtropical disease vector. In the Hawaiian Islands, where it was introduced accidentally almost two centuries ago, it is considered the primary vector of avian malaria and pox. Avian malaria in particular has contributed to the extinction and endangerment of Hawaii's native avifauna, and has altered the altitudinal distribution of native bird populations. We examined the population genetic structure of Cx. quinquefasciatus on the island of Hawaii at a smaller spatial scale than has previously been attempted, with particular emphasis on the effects of elevation on population genetic structure. We found significant genetic differentiation among populations and patterns of isolation by distance within the island. Elevation per se did not have a limiting effect on gene flow; however, there was significantly lower genetic diversity among populations at mid elevations compared to those at low elevations. A recent sample taken from just above the predicted upper altitudinal distribution of Cx. quinquefasciatus on the island of Hawaii was confirmed as being a temporary summer population and appeared to consist of individuals from more than one source population. Our results indicate effects of elevation gradients on genetic structure that are consistent with known effects of elevation on population dynamics of this disease vector.     

Influence of volcanic activity on the population genetic structure of Hawaiian Tetragnatha spiders: fragmentation, rapid population growth and the potential for accelerated evolution

Volcanic activity on the island of Hawaii results in a cyclical pattern of habitat destruction and fragmentation by lava, followed by habitat regeneration on newly formed substrates. While this pattern has been hypothesized to promote the diversification of Hawaiian lineages, there have been few attempts to link geological processes to measurable changes in population structure. We investigated the genetic structure of three species of Hawaiian spiders in forests fragmented by a 150-year-old lava flow on Mauna Loa Volcano, island of Hawaii: Tetragnatha quasimodo (forest and lava flow generalist), T. anuenue and T. brevignatha (forest specialists). To estimate fragmentation effects on population subdivision in each species, we examined variation in mitochondrial and nuclear genomes (DNA sequences and allozymes, respectively). Population subdivision was higher for forest specialists than for the generalist in fragments separated by lava. Patterns of mtDNA sequence evolution also revealed that forest specialists have undergone rapid expansion, while the generalist has experienced more gradual population growth. Results confirm that patterns of neutral genetic variation reflect patterns of volcanic activity in some Tetragnatha species. Our study further suggests that population subdivision and expansion can occur across small spatial and temporal scales, which may facilitate the rapid spread of new character states, leading to speciation as hypothesized by H. L. Carson 30 years ago.     

Patterns of genetic variation in Pacific island land snails: the distribution of cytochrome b lineages among Society Island Partula

The radiation of Partula land snails has produced a large array of distinct morphological, ecological and behavioural types occupying many tropical volcanic islands in the Pacific Ocean. Within the Society Islands of French Polynesia, the mode of evolution is thought to have involved a single colonization event on each island, with later speciation occurring largely in situ. The present study examines genetic variation in the mitochondrial cytochrome b gene among taxa within the Society Island archipelago. Levels of intraspecific variation are found to be high, but variation among species is sometimes small. Mitochondrial variants do not always cluster according to island and some species are found to be polyphyletic in the cytochrome b tree, despite other morphological and molecular evidence that strongly supports their monophyly. A possible explanation for the polyphyly of species is that different variants are derived from ancestral mitochondrial polymorphisms that have been retained despite speciation events. Although it is possible that there has been some gene flow among islands, the distribution of mitochondrial lineages across islands strongly indicates that their origins predate the colonization of the islands in the study, and that they are very unlikely to have evolved entirely in situ.     

Differences in endemic insect assemblages among vegetation types on a small island of the oceanic Ogasawara Islands

Natural vegetation is often replaced by invasive alien plants on isolated oceanic islands. To determine how invasive alien plants affect insect diversity, we compared flying insects captured using Malaise traps among different vegetation types on a small island (Nishijima; 0.49 km²) in the oceanic Ogasawara (Bonin) Islands in the north‐western Pacific. The numbers of individuals and species, and the species composition of pollinators (bees), predators (wasps) and wood borers (cerambycid, mordellid and elaterid beetles) were compared among three vegetation types: Casuarina equisetifolia (an invasive alien tree) forest, natural forest and natural grassland (forest edge), during two seasons (June and October–November 2005). In traps, 80.0, 66.7, 87.5, 85.7 and 100.0% of bee, wasp, cerambycid, mordellid and elaterid beetle species, respectively, were endemic to the Ogasawara Islands. Grassland had the highest wasp and bee species richness, whereas natural forest had the highest species richness of wood‐boring beetles. The C. equisetifolia forest had the poorest species richness for most insect groups (except mordellid beetles). More individuals of most insect groups (except bees) were captured in June than in October–November. More individual bees and wasps were captured in grassland than in forests, whereas more individual mordellid and elaterid beetles were captured in forests than in grassland. The number of cerambycid individuals did not differ among vegetation types. Redundancy analysis suggested that most insect species preferred natural forest or grassland to alien forest. Therefore, further invasion of natural grassland and forest by the alien tree C. equisetifolia may negatively affect the endemic insect fauna of Nishijima.     

Heterozygosity-fitness correlations in a bottlenecked island species: a case study on the Seychelles warbler

We used capture-mark-recapture models to investigate the effects of both individual and parental heterozygosity, measured at microsatellite loci on the survival of Seychelles warblers (Acrocephalus sechellensis), an endemic island species which went through a severe population bottleneck in the middle of the last century. We found that an individual's survival was not correlated with multilocus heterozygosity, or with heterozygosity at any specific locus. However, maternal, but not paternal, multilocus heterozygosity was positively associated with offspring survival, but only in years with low survival probabilities. A nestling cross-fostering experiment showed that this was a direct maternal effect as there was an effect of the genetic mother's, but not of the social mother's, heterozygosity. Heterozygosity-fitness correlations at microsatellite markers were generally assumed to reflect genome-wide effects. Although this might be true in partially inbred populations, such correlations may also arise as a result of local effects with specific markers being closely linked to genes which determine fitness. However, heterozygosity at the individual microsatellite loci was not correlated and therefore does not seem to reflect genome-wide heterozygosity. This suggests that even in a small bottlenecked population, heterozygosity-fitness correlations may not be caused by genome-wide effects. Support for the local effects hypothesis was also equivocal; although three specific loci were associated with offspring survival, including all single-locus heterozygosities as independent predictors for the variation in survival was not supported by the data. Furthermore, in contrast to the local effects hypothesis, the loci which contributed most to the heterozygosity-survival relationship were not more polymorphic than the other loci. This study highlights the difficulties in distinguishing between the two hypotheses.     

Unravelling causal components of the Ordovician Radiation: the Builth Inlier (central Wales) as a case study

Hypotheses about the causes of biodiversification during the Ordovician have been focused in three main areas: tectonic activity and nutrient supply, palaeogeography, and ecological escalation. There is as yet no consensus on mechanisms, and it is unclear whether it is better to study the patterns at local or regional scales. By applying ecological knowledge to the available palaeontological information, it can be shown that neither tectonic nor palaeogeographic effects could account for the permanence of the diversity rise, in the absence of elements of ecological escalation. However, it may be possible to identify trigger mechanisms resulting in enhanced speciation or reduced extinction. Areas of local diversity increase should be distinguished from speciation centres. An ongoing study of the Middle Ordovician Builth-Llandrindod Inlier of central Wales, conducted over 10 years, has identified elements of all three of the above categories of causal mechanisms affecting local diversity. This implies that the patterns of causal relationship and diversification are complex even at very local scales, and at this stage we should not anticipate a clear correlation of global diversity with any single factor. More data are needed from small-scale but intensive studies before we can generalize about the causal mechanisms of the Ordovician Radiation.     

基于物种运动路径识别的动物通道选址——以武深高速为例

动物通道是缓解高速公路对其周边野生动物生境隔离的有效措施,通道的位置是影响其使用效率的关键因素,然而现有研究对通道的选址却甚少涉及。以武深高速为例,推荐一种基于物种运动路径识别的通道选址方法,选取影响动物生境选择的环境因子构建评价体系,借助GIS手段对公路周边野生动物生境适宜性进行分析,在此基础上借鉴水文分析原理快速准确地刻画出物种在生境中的潜在活动路径,从而确定了5处高速公路上建设动物通道的理想位置。结果表明,该方法能定量地反映出生境的质量格局对于物种运动的影响,准确定位出物种运动受到阻碍的关键区域,在景观层次上,提出的通道位置能有效地缓解栖息地破碎化造成的生态压力;研究不但能弥补目前研究的不足,同时亦为道路网设计、城市生态规划等相关领域研究提供科学参考。     

海岛型城市生态安全格局研究——以平潭岛为例

在快速城市化带来的城市生态安全严重威胁着城市可持续发展的这一时代背景下,构建城市生态安全格局是实现区域和城市生态安全的基本保障和重要途径。结合平潭综合实验区总体规划,从城市生态安全角度出发,在对平潭岛生态环境本底条件的调研基础上,选取与平潭岛的城市生态安全关系密切的6个关键生态因子进行深入分析,并通过层次分析法和GIS空间叠置法综合多要素分析了平潭岛的生态敏感性,最终有针对性地提出了面向新一轮大规模城市开发热潮的平潭岛城市生态安全格局。研究成果可为平潭岛的城市开发建设提供决策支持,对维护平潭岛城市生态安全、促进平潭岛可持续发展具有重要的理论和现实意义,同时也对其它海岛型城市的生态安全格局研究具有一定的借鉴意义。     

Genetic differentiation among populations of an oceanic island: The case of Metrosideros boninensis, an endangered endemic tree species in the Bonin Islands

Conservation of endemic species on oceanic islands is an essential issue for biodiversity conservation. Metrosideros boninensis (Myrtaceae) is an endangered tree species endemic to the Bonin Islands of the western North Pacific Ocean. This species is considered to be extremely rare with less than 400 adult individuals, a number that has fluctuated between the 1880s and 1980s through human influence. We analyzed the genetic diversity and genetic structure of this species using amplified fragment length polymorphism markers and microsatellite markers. Genetic diversity of M. boninensis was extremely low compared to related taxa and similar endemic species from small islands. This low genetic diversity might be attributed to a stepwise colonization process with repeated founder bottlenecks in the dispersal pathway to the Bonin Islands. Populations of M. boninensis showed significant genetic differentiation and isolation by distance over a small geographical scale, despite the fact that this species should have extensive gene dispersal ability. This genetic differentiation might be caused by limited gene flow via pollen and seed among populations and genetic drift amid a small number of remnant individuals. Taken together, these findings suggest that the genetic diversity and connectivity of tree populations on islands are more vulnerable to habitat fragmentation than previously thought. We offer some recommendations for management to ameliorate habitat fragmentation and biological invasion.     

Hybridization of reef fishes at the Indo-Pacific biogeographic barrier: a case study

Hybridization is recognized as an important source of genetic variation. In some reef fishes, including the Acanthuridae, hybridization has been detected due to intermediate colouration. This study used a molecular genetic approach to investigate hybridization in two Acanthurid species: Acanthurus leucosternon and Acanthurus nigricans, which have Indian and Pacific Ocean distributions respectively and are sympatric in the eastern Indian Ocean. In this area a putatitve hybrid, Acanthurus cf. leucosternon has been recognized based on intermediate colouration and restriction to the sympatric region of otherwise allopatric putative parental species. This study aimed to test this hypothesis using genetic tools. The three species were sampled from Cocos (Keeling) and Christmas Islands, the biogeographic boundary where many Indian and Pacific Ocean biota meet. Representatives from allopatric populations of both parental species and outgroups were also sampled. Mitochondrial COI and intron 1 of the nuclear ribosomal protein S7 were sequenced from 13 and 30 specimens respectively. Although sample sizes in this study are relatively small and more genetic data, including an extended phylogeographic sampling, is required to further evaluate these findings, the COI results support hybrid origins of Acanthurus cf. leucosternon, but S7 data are inconclusive due to the possibility of incomplete lineage sorting. The fourfold more abundant Acanthurus nigricans is most often the maternal parent. Inter-fertile hybrids apparently backcross with rare Acanthurus leucosternon males, transferring Acanthurus nigricans mitochondria to this species. These results suggest that Acanthurus leucosternon may eventually be lost from these islands, due to their relative rarity and introgressive hybridization.     

基于景观连接度的森林景观恢复研究——以巩义市为例

景观连接度是研究景观促进或阻碍生物体或某种生态过程在斑块间运动的程度。基于景观连接度原理,借用景观连接度指数,在地理信息系统支持下,探讨了巩义市丘陵和低山地区森林景观在不同景观距离阈值下连接度的变化,确定了分析森林景观连接度的合适距离阈值。在此基础上分析了要恢复为森林景观的农业斑块的重要值的大小,确定了对要恢复为森林景观的每一农业景观斑块对新形成的森林景观的连接度贡献大小,并结合区域地形特征,明确了森林恢复之初的重要斑块的选取及恢复的先后次序。结果显示,在不同的距离阈值下,低山地区森林景观的整体连通性指数值(IIC)都大于丘陵地区森林景观的IIC值;森林景观的适宜距离阈值,在丘陵地区可选择750 m,在低山地区可选择500 m,或者更小尺度;通过农业景观斑块重要值(dIIC)确定的对森林景观连接度作用起"非常高"和"高"的斑块的数量非常少,但对森林景观连接度的贡献作用却比较大。提出的基于景观连接来分析在森林恢复时重要斑块的选取的方法,具有一定的可操作性与实用性,对区域生态恢复和生态建设具有重要意义。     

土地利用变化对鸟类栖息地连通性的影响——以鄂州市为例

土地利用变化是造成栖息地破碎、缺失与退化的重要原因。生态网络能保护重要栖息地,促进栖息地之间的物质与能量流动,对区域土地利用规划和生物多样性保护具有重要意义。以鄂州市为研究区,基于CLUE-S模型预测现状延续、生态保护和城市扩张3种土地利用情景,将生境质量作为遴选生境斑块的依据之一,以鸟类最大迁徙距离为阈值构建生态网络,从连通概率指数PC和斑块重要性指数dPC两方面,探讨土地利用变化对鸟类栖息地连通性的影响。结果表明：(1)不同情景的地类数量和空间结构均有差异,与生态保护相比,城市扩张情景的建设用地增加11603.52 hm~2,林地、耕地和水体减少5041.8 hm~2、2540.16 hm~2、3385.8 hm~2,新城区、山地风景区与水体周边是主要变化区域;(2)现状延续和城市扩张情景的生境斑块降至235块和216块,网络出现破碎化,生态保护情景增至367块,网络结构完整但空间位置改变;(3)2004—2024年PC表现为先上升后下降再上升的趋势,生态保护的PC高于现状延续和城市扩张,且利于保护短距离迁徙鸟类;(4)生态保护情景边缘型和关键小型斑块得到保护,第一等级斑块增加,城...     

On the comparison of population-level estimates of haplotype and nucleotide diversity: a case study using the gene cox1 in animals

Estimates of genetic diversity represent a valuable resource for biodiversity assessments and are increasingly used to guide conservation and management programs. The most commonly reported estimates of DNA sequence diversity in animal populations are haplotype diversity (h) and nucleotide diversity (π) for the mitochondrial gene cytochrome c oxidase subunit I (cox1). However, several issues relevant to the comparison of h and π within and between studies remain to be assessed. We used population-level cox1 data from peer-reviewed publications to quantify the extent to which data sets can be re-assembled, to provide a standardized summary of h and π estimates, to explore the relationship between these metrics and to assess their sensitivity to under-sampling. Only 19 out of 42 selected publications had archived data that could be unambiguously re-assembled; this comprised 127 population-level data sets (n ≥ 15) from 23 animal species. Estimates of h and π were calculated using a 456-base region of cox1 that was common to all the data sets (median h=0.70130, median π=0.00356). Non-linear regression methods and Bayesian information criterion analysis revealed that the most parsimonious model describing the relationship between the estimates of h and π was π=0.0081 h(2). Deviations from this model can be used to detect outliers due to biological processes or methodological issues. Subsampling analyses indicated that samples of n>5 were sufficient to discriminate extremes of high from low population-level cox1 diversity, but samples of n ≥ 25 are recommended for greater accuracy.     

DNA条形码技术在海洋贝类鉴定中的实践: 以大亚湾生态监控区为例

为提高物种鉴定的准确性, 本研究采用DNA条形码技术对大亚湾生态监控区冬季采集的贝类样品进行了种类鉴定。结果表明, 26个形态种中, 有15个可以通过线粒体COI和16S rRNA基因的系统发育分析鉴定到种的水平。部分形态上难以鉴定的种类, 如线缝摺塔螺(Ptychobela suturalis)和区系螺(Funa sp.)可以通过条形码实现有效鉴定。锯齿巴非蛤(Paphia gallus)、西格织纹螺(Nassarius siquijorensis)、爪哇拟塔螺(Turricula javana)等种类存在相当大的种内遗传距离, 有存在隐存种的可能性。尽管基于线粒体COI和16S rRNA基因的种内遗传距离和属内种间的遗传距离发生重合, 无明显的条形码间隙, 但通过系统树的方法仍能有效鉴定物种。可见, DNA条形码技术能有效提高海洋贝类物种鉴定的准确性并发现隐存种。     

Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar

Game species are often manipulated by human beings, whose activities can deeply affect their genetic make-up and population structure. We focused on a geographically isolated wild boar population (Sardinia, Italy), which is classified, together with the Corsican population, as a separate subspecies (Sus scrofa meridionalis). Two hundred and ten wild boars collected across Sardinia were analysed with a set of 10 microsatellites and compared with 296 reference genotypes from continental wild populations and to a sample of domestic pigs. The Sardinian population showed remarkable diversity and a high proportion of private alleles, and strongly deviated from the equilibrium. A Bayesian cluster analysis of only the Sardinian sample revealed a partition into five subpopulations. However, two different Bayesian approaches to the assignment of individuals, accounting for different possible source populations, produced consistent results and proved the admixed nature of the Sardinian population. Indeed, introgressive hybridization with boars from multiple sources (Italian peninsula, central Europe, domestic stocks) was detected, although poor evidence of crossbreeding with free-ranging domestic pigs was unexpectedly found. After excluding individuals who carried exotic genes, the population re-entered Hardy-Weinberg proportions and a clear population structure with three subpopulations emerged. Therefore, the inclusion of introgressed animals in the Bayesian analysis implied an overestimation of the number of clusters. Nonetheless, two of them were consistent between analyses and corresponded to highly pure stocks, located, respectively, in north-west and south-west Sardinia. This work shows the critical importance of including adequate reference samples when studying the genetic structure of managed wild populations.     

Cospeciation of figs and fig-wasps: a case study of endemic species pairs in the Ogasawara Islands

The interactions between figs (Ficus, Moraceae) and fig-wasps (Agaonidae, Chalcidoidea, Hymenoptera) are special plant-pollinator relationships that are highly species-specific, in that each fig species is pollinated by a single fig-wasp species that can breed only in that particular fig species. This study examined the degree of pre-mating isolation and genetic differentiation for three fig/fig-wasp pairs endemic to the Ogasawara Islands. Simple Y-tube tests revealed that fig-wasps from Ficus nishimurae and Higashidaira type chose their own host figs significantly more often, while fig-wasps from F. boninsimae did not. Based on RAPD markers, the genetic differentiation among the fig species was low, but F. boninsimae formed a cluster within the F. nishimurae cluster. The Higashidaira type has been derived from a subpopulation of F. nishimurae. Five mitochondrial DNA haplotypes were found in the fig-wasps and each haplotype correlated well with the fig species on their island of origin. These results led to a three-step hypothesis on the cospeciation process: (1) spatial separation of fig/fig-wasp populations arises; (2) gene flow is restricted and character differentiation of fig-wasps occurs; (3) there is further restriction of gene flow and genetic and character differentiation of figs.     

Effects of habitat fragmentation on genetic diversity and gene flow among the Homidia socia (Collembola: Entomobryidae) populations in the Thousand Island Lake

In the present study, partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene of 22 island populations of the springtail Homidia socia in the Thousand Island Lake were sequenced. Across all sequences, 37 haplotypes were identified for the 510‐bp mitochondrial (mt) DNA COI gene. Haplotype 2 was the most common, and was distributed in the most of the 22 island populations. Haplotype diversity ranged from 0.065 to 0.733, and the total genetic diversity was 0.56216. The genetic characteristics of the 22 island populations were analyzed using the fixation index and gene flow, with values of 0.00043–0.94900 and 0.02703–703.72540, respectively. Comparison between (island area and isolations) with population genetic diversity revealed that there were no significant correlations between them, except for a significant correlation between the number of haplotypes and island area. Mantel tests showed that there was no significant correlation between geographic distance and genetic distance among various groups. All the results indicated that there were no obvious relationships between island characteristics and the genetic diversity of the springtails. We consider that the low dispersal capacity of springtails and the island patches surrounded by water in the Thousand Island Lake are the major factors affecting the genetic diversity of H. socia.