Phytophthora palmivora from Sulawesi and Java Islands,Indonesia, reveals high genotypic diversity and lack of population structure

Phytophthora palmivora is the causal agent of cocoa black pod disease, one of the primary diseases of cocoa in Indonesia. A better understanding of P. palmivora population genetics is needed to aid the development of relevant disease management strategies. This study is the first population genetic study of P. palmivora in Indonesia using microsatellite markers based on the alleles genotyping method. The microsatellite markers were used to determine the genotype of 44 P. palmivora isolates from Sulawesi (24) and Java (20) islands. The total number of observed multilocus genotypes (MLG) from both populations was 34. The genotypic diversity of P. palmivora from Sulawesi (2.90; 16.0; 0.938) and Java (2.76; 14.3; 0.930) islands was high as seen from Shannon's diversity index (H), Stoddart and Taylor's Index (G), and Simpson's Index (λ) respectively. Evenness and Nei's unbiased gene diversity exhibited similarly high levels from both populations. The linkage disequilibrium test indicated that sexual recombination occurred in the Java population (P = 0.312). Analysis of molecular variance (AMOVA) and Bayesian clustering revealed five genetic clusters, and isolates from both islands were evenly distributed across the five gene clusters. All genetic diversity was from within individuals. P. palmivora from Sulawesi and Java showed a high genotypic diversity but a lack of genetic differentiation among populations (Fst = 0.006). Both populations formed one highly diverse group. Minimum spanning network analysis showed no particular grouping of MLGs, and shared MLGs from both populations indicated long-distance migration of P. palmivora facilitated by human activities.     

Sampling strategies for the assessment of tree species diversity

Abstract. This paper aims at proposing efficient vegetation sampling strategies. It describes how the estimation of species richness and diversity of moist evergreen forest is affected by (1) sampling design (simple random sampling, random cluster sampling, systematic cluster sampling, stratified cluster sampling); (2) choice of species richness estimators (number of observed species vs. non-parametric estimators) and (3) choice of diversity index (Simpson vs. Shannon). Two sites are studied: a 28-ha area situated in the Western Ghats of India and a 25-ha area located at Pasoh in Peninsular Malaysia. The results show that: (1) whatever the sampling strategy, estimates of species richness depend on sample size in these very diverse forest ecosystems which contain many rare species; (2) Simpson's diversity index reaches a stable value at low sample sizes while Shannon's index is affected more by the addition of rare species with increasing sample size; (3) cluster sampling strategies provide a good compromise between cost and statistical efficiency; (4) 300 - 400 sample trees grouped in small clusters (10–50 individuals) are enough to obtain unbiased and precise estimates of Simpson's index; (5) the local topography of the Western Ghats has a major influence on forest composition, the steep slopes being richer and more diverse than the ridges and gentle slopes; (6) stratified cluster sampling is thus an interesting alternative to systematic cluster sampling.     

Community structure of macrobenthos in homestead ponds of Noakhali coast,Bangladesh

The integrity of the homestead pond supply depends on how various macrobenthic communities make their living more diversified and contribute to complex food webs. In addition, the macrobenthic community are significantly used as indicator organisms to detect the pollution impacts in aquatic ecosystems. In this study, we show the data about the diversity and community structure of macrobenthos and their relationship with environmental variables in homestead ponds of Noakhali coast from January 2019 to August 2019. The current study yielded 17 species belonging to seven taxonomic groups with a mean density of 3630 ind./m². The Nematode community, comprising 48.86% of the total taxonomic groups with Prionchulus sp. as the dominant macrobenthic species represented more than 31% of the total macrobenthic taxa, and showed a significant negative correlation with the value of salinity, DO, pH. The environmental variables and diversity indices were detected significant variations (P < 0.05) among stations by the Kruskal-Wallis ANOVA, whereas Shannon-Wiener Diversity Index (H´) assessed moderate pollution, Evenness index (J) assessed uniform distributions of macrobenthic community, and environmental variables showed acceptable condition for the productivity of ponds. Cluster analysis (CA) and Non-metric multidimensional scaling (nMDS) demonstrate demarcations in the community structure of macrobenthos between samples. Within macrobenthic communities, Canonical Correspondence Analysis (CCA) provided insights and interpretations of the relationships between species and environmental gradients. Macrobenthic community reached the most abundance at a lower temperature, transparency and a higher DO, pH and salinity.     

Species composition of benthic fish fauna in the Sea of Marmara,Turkey

In order to determine the present benthic fish fauna in the Sea of Marmara, sampling was conducted at a total of 10 stations for 2 weeks in August 2009, using a commercial twin beam trawling vessel with 18 and 36 mm stretched mesh sizes at the cod-end. In addition, some physicochemical parameters that play important roles, such as temperature, salinity, dissolved oxygen, and pH, were measured for each station. As a result, 31 fish species from 23 families were found at a total of 10 stations in depths of 30–1000 m. At each station, the Shannon–Weaver diversity index, Simpson dominance index, species richness index, and evenness index were estimated. This study reports on species composition of the demersal fish catches in the Sea of Marmara for a preliminary assessment of the status of these fish communities.     

Signals from the benthos: Development and evaluation of a benthic index for the nearshore Gulf of Maine

We developed a benthic index for the nearshore Gulf of Maine to provide researchers and environmental managers a way to make spatial and year-to-year comparisons of benthic condition. The data set used included 248 stations sampled for physical, chemical, and biological variables by the National Coastal Assessment in 2000–2003. We used logistic regression with 49 candidate measures of benthic species diversity, pollution sensitivity-tolerance, and community composition to discriminate sites with high and low benthic environmental quality (BEQ). BEQ was based on the concentrations of metal and organic contaminants in the sediments, total organic carbon, sediment toxicity, and dissolved oxygen level of the bottom water. An analysis of similarity test showed that the community composition of low BEQ stations was significantly different (p < 0.001) from high BEQ stations. Ten of the 49 benthic metrics showed a strong ability to discriminate stations. We developed several candidate benthic indices and tested them with independent data from Massachusetts Bay and Casco Bay to help select and validate the best index. A model using the Shannon-Wiener diversity measure, Rosenberg's species pollution tolerance measure, and the percent capitellid polychaetes (or percent Capitella spp.) strongly discriminated stations, with an area under the receiver operating characteristic (ROC) curve of 0.82 and a classification accuracy of 80%. Signal detection theory (ROC curves and positive–negative predictive value curves) was used to evaluate the index and to predict how well an index developed for one geographic area might work in another area with a different prevalence of the degraded condition. We show how these techniques can also guide decisions by environmental managers about choosing thresholds and weighing costs and benefits of particular actions.     

Tree species composition and diversity in natural temperate forests of the North-Western Himalayas

The present study was undertaken in the natural temperate Himalayan forests of Himachal Pradesh, India, to assess the tree species composition and diversity. For this purpose, six major forest types (FT) viz., FT1- Upper Himalayan Pinus roxburghii forest, FT2- Quercus leucotrichophora forest, FT3- Low-level P. wallichiana forest, FT4- Moist C. deodara forest, FT5- Western Mixed Coniferous Forest, FT6- Pinus gerardiana forest were selected. Detailed sampling was carried out in these forest types, and the sample plots in each forest type were laid out using the stratified random approach. Tree stem density varied from 191.11 N ha^?1 (FT6) to 441.11 N ha^?1 (FT2), whereas the tree total basal cover varied from 20.01 m² ha^?1 (FT6) to 47.59 m² ha^?1 (FT5). The diversity indices reflected that a total of 21 tree species (16 genera, 11 families) were identified, with tree species richness ranging from 3 (FT6) to 9 (FT1 & FT5). The forest type FT5 recorded the maximum Shannon index of diversity (2.36), Simpson Index of diversity (0.75), Margalef's Index of richness (1.37), pielou equitability (0.74), menheink index of species richness (0.49), whereas the highest Shannon Index of diversity (0.73) and species heterogeneity (0.85) in FT6 forest type. Furthermore, dominance-diversity (d-d) curves drawn that all the six forest types showed geometric curves reveals that one or two tree species are dominant in a particular forest type. Simultaneously, the research area's species diversity, tree stem density, and tree total basal cover were equivalent to those seen in other sections of Western Himalayas.     

海河流域拒马河鱼类群落结构特征及其与环境因子的关系

为了解拒马河鱼类时空分布及影响因子,基于2019—2021在拒马河的6次季节性鱼类调查,分析了拒马河鱼类群落结构及其与环境因子的关系。结果显示:共采集37种鱼类,隶属5目11科,鲤形目最多,占总种数的64.86%。相对重要指数(Index of relative importance,IRI>)显示,IRI>≥500的优势种鱼类有10种,以鲫Carassius auratus Linnaeus、麦穗鱼Pseudorasbora parva Temminck & Schlegel、黑鳍鳈Sarcochilichthys nigripinnis Günther和宽鳍鱲Zacco platypus Temminck&Schlegel为主。单因素方差分析(ANOVA)表明,春、夏、秋季鱼类群落的个体数(N)、物种数(S)、Shannon-Wiener多样性指数(H’)和Margalef丰富度指数(D_Ma)存在显著差异,Pielou均匀度指数(J’)无显著差异。SNK多重比较检验(Student-Newman-Keuls)显示个体数、种类数以20...     

Impact of habitat diversity on the sampling effort required for the assessment of river fish communities and IBI

The spatial variation in the fish communities of four small Belgian rivers with variable habitat diversity was investigated by electric fishing to define the minimum sampling distance required for optimal fish stock assessment and determination of the Index of Biotic Integrity. This study shows that the standardised sampling distance of 100 m was not always sufficient to collect most species present. The required minimum sampling distance seems to be correlated with habitat diversity. In homogeneous streams, a mean sample distance of 282, 452 and 572 m is necessary to capture 80, 90 and 95% of all species present, respectively. In heterogeneous streams, these sample distances decrease to 217, 380 and 503 m. Hence, at least 300 m should be sampled to catch most species present with a single-pass sampling method. However, our results show that a 100 m sampling distance as presently used in the Flemish monitoring programs is sufficient to accurately describe the ecological quality since differences in IBI evaluation between adjacent stretches could at least for some rivers be explained by differences in habitat heterogeneity.     

Quantifying the responses of biological indices to rare macroinvertebrate taxa exclusion: Does excluding more rare taxa cause more error?

Including or excluding rare taxa in bioassessment is a controversial topic, which essentially affects the reliability and accuracy of the result. In the present paper, we hypothesize that biological indices such as Shannon–Wiener index, Simpson's index, Margalef index, evenness, BMWP (biological monitoring working party), and ASPT (Average Score Per Taxon) respond differently to rare taxa exclusion. To test this hypothesis, a benthic macroinvertebrate data set based on recent fifteen‐year studies in China was built for suppositional plot analyses. A field research was conducted in the Nansi Lake to perform related analyses. The results of suppositional plot simulations showed that Simpson's index placed more weight on common taxa than any other studied indices, followed by Shannon–Wiener index which remained a high value with the exclusion of rare taxa. The results indicated that there was not much of effect on Simpson's index and Shannon–Wiener index when rare taxa were excluded. Rare taxa played an important role in Margalef index and BMWP than in other indices. Evenness showed an increase trend, while ASPT varied inconsistently with the exclusion of rare taxa. Results of the field study also indicated that rare taxa had few impacts on the Shannon–Wiener index. By examining the relationships between the rare taxa and biological indices in our study, it is suggested that including the rare taxa when using BMWP and excluding them in the proposed way (e.g., fixed‐count subsampling) to calculate Shannon–Wiener index and Simpson's index could raise the efficiency and reduce the biases in the bioassessment of freshwater ecosystems.     

澜沧江糯扎渡季雨林厚皮树+家麻树群落的研究

根据5个20m×25m样地的调查资料,对分布于澜沧江糯扎渡河岸山地,以厚皮树、家麻树为优势种的季雨林群落进行了分析研究,结果显示:(1)该群落乔木层以落叶成分厚皮树和家麻树为优势种,层间以常绿的大型木质藤本云南翅子藤为特征;(2)在群落2500m2样地内,共计维管束植物72种,隶属于38科65属;其中有乔木25种,草本植物25种,灌木10种和层间藤本植物12种;(3)综合5个样地后计算所得群落乔木层树种丰富度为25种,Shannon-Wiener指数为2.9010,Pielou均匀度指数为0.9012,Simpson指数为0.9346,在群落中,随着乔木径级的增大,个体数和种数逐渐减小;(4)该群落主要以高位芽植物为主,并以中高位芽植物为优势,占所统计总种数的35.8%;(5)该群落中落叶种类占总种数的62.5%,中叶占47.2%,小叶占41.7%,单叶占69.4%,纸质叶占61.1%,全缘叶占56.9%;(6)该群落的物种数/样地面积关系曲线显示在取样面积1000m2时开始趋于平缓,意味着该取样面积可以考虑作为群落最小取样面积。     

东太湖鱼类群落结构特征及其与环境因子的关系

基于2019年4月、7月和10月的调查数据,用多元分析方法研究了围网拆除后东太湖鱼类群落结构的变化,及其与主要环境因子的关系。共调查到鱼类4目10科31属39种,其中鲤形目鱼类占69.23%。按不同生态类型东太湖鱼类主要为定居性鱼类、中上层鱼类以及肉食性和杂食性鱼类。优势种为鲫（Carassius auratus）、大鳍鱊（Acheilognathus macropterus）和（Hemiculter leucisculus）等。鱼类的种类数、渔获量、丰富度指数和多样性指数在监测月份间均差异显著（P＜0.05）,均为4月 > 7月 > 10月。鱼类个体呈现小型化,鱼类物种多样性处在一般水平。等级聚类分析（Cluster）结果表明,除10月份的1号点和3号点外,各样方间的相似度在46.75%以上。单因子相似性分析（ANOSIM）和相似性百分比分析（SIMPER）也表明,4月和10月的鱼类群落物种组成差异显著,平均相异性为59.41%。丰度/生物量曲线（ABC）分析表明,东太湖鱼类群落结构处于中度干扰状态。冗余分析（RDA）表明,总磷对主要鱼类变化的解释量为21.0%,是重要的解释因子（蒙特卡罗检验P＝0.036）。而总磷、pH、溶解氧等是目前影响东太湖鱼类群落的主要环境因子。     

Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories

Biodiversity, a multidimensional property of natural systems, is difficult to quantify partly because of the multitude of indices proposed for this purpose. Indices aim to describe general properties of communities that allow us to compare different regions, taxa, and trophic levels. Therefore, they are of fundamental importance for environmental monitoring and conservation, although there is no consensus about which indices are more appropriate and informative. We tested several common diversity indices in a range of simple to complex statistical analyses in order to determine whether some were better suited for certain analyses than others. We used data collected around the focal plant Plantago lanceolata on 60 temperate grassland plots embedded in an agricultural landscape to explore relationships between the common diversity indices of species richness (S), Shannon's diversity (H'), Simpson's diversity (D₁), Simpson's dominance (D₂), Simpson's evenness (E), and Berger–Parker dominance (BP). We calculated each of these indices for herbaceous plants, arbuscular mycorrhizal fungi, aboveground arthropods, belowground insect larvae, and P. lanceolata molecular and chemical diversity. Including these trait‐based measures of diversity allowed us to test whether or not they behaved similarly to the better studied species diversity. We used path analysis to determine whether compound indices detected more relationships between diversities of different organisms and traits than more basic indices. In the path models, more paths were significant when using H', even though all models except that with E were equally reliable. This demonstrates that while common diversity indices may appear interchangeable in simple analyses, when considering complex interactions, the choice of index can profoundly alter the interpretation of results. Data mining in order to identify the index producing the most significant results should be avoided, but simultaneously considering analyses using multiple indices can provide greater insight into the interactions in a system.     

云南蒙自坝区湖泊越冬水鸟组成和变化趋势初报

第264号国际重点鸟区位于云南蒙自坝区,但缺乏系统的鸟类数据。2006-2014 年,每年1月下旬至2月上旬,在蒙自坝区的三个湖泊长桥海、大屯海和三角海（简称“三湖”）进行水鸟调查,累计记录到水鸟12科33属63种。其中有国家I级保护动物1种（黑鹳Ciconia nigra）,国家II级保护动物2种（白琵鹭Platalea leucorodia,彩鹮Plegadis falcinellus）,极危（CR）鸟类1种（青头潜鸭Aythya baeri）,近危（NT）鸟类4种。在长桥海记录的水鸟种类和数量最多,但Shannon-Wiener多样性指数较低,优势度指数较高。在三角海记录到的鸟类种类较多,Shannon-Wiener多样性指数较高而优势度指数较低。在大屯海记录到的鸟种和数量都很少。分别对三湖越冬水鸟种数、数量和雁形目、骨顶鸡和鹳形目水鸟数量变化趋势进行了Man-Kendall检验,发现调查期间,三湖越冬水鸟种数和数量无显著变化,骨顶鸡数量无显著变化趋势,雁形目水鸟略有下降趋势,而鹳形目水鸟有显著下降趋势。鉴于三角海记录到的国家一、二级保护动物和鹳形目水鸟数量,建议扩大第264号国际重点鸟区范围,将其纳入。     

Changes in plant species diversity along a chronosequence of vegetation restoration in the humid evergreen broad-leaved forest in the Rainy Zone of West China

Plant species diversity has been recognized as one of the vital attributes for assessing vegetation restoration. Changes in the diversity may be related to different stages of succession. In this study, 54 sites of humid, evergreen, broad-leaved forest were selected in the Rainy Zone of West China. A chronosequence of the sites was used to study the successive patterns of the diversity in the forest that had undergone natural regeneration for 5 to 350 years and to test the hypothesis that the diversity is maximized in mid-succession. Data were collected simultaneously at different stages of succession, and four α-diversity indices (species richness, Margalef index, Shannon-Wiener index, Pielou Evenness index) and two β-diversity indices (Whittaker index, Sørensen’s index) were calculated for each stratum in each plot. A total of 394 vascular plant species were recorded. From the β-diversity indices, the forest succession may be divided into the early-successional stage (before 50 years), mid-successional stage (from 50 to 300 years), and late-successional stage (after 300 years). In this community, the species diversity and richness were found to be the greatest at the mid-successional stage, followed by the late- and early-successional stages. The results of regression analysis indicated that the richness and Margalef index peaked around the 175th and 165th year, respectively. Shannon-Wiener index values also appeared to follow an approximately humped pattern of succession and were maximal around the 100th year. However, the species evenness did not show any significant relationship with successional age. Our results demonstrate (1) forest restoration is a long-term process and the formation of climax forest requires at least 300 years and (2) the forest has a strong capacity for restoration. Our results also suggest Lindera limprichitii and Machilus pingii as ideal tree species for afforestation because of their wide niche.     

Changes in the taxonomic diversity of the reef fish community of San José Island, Gulf of California, Mexico

Although San José Island is considered one of the most important islands in the lower Gulf of California due to its commercial fishing activities, few studies have evaluated their fish taxonomic diversity. The aim of this study was to determine the variation in the taxonomic diversity of the conspicuous fish community in eight locations around San José Island from March 2001 to February 2002. We assessed the changes in the diversity of rocky reef fish based on the taxonomic distances between species, using Fisher’s alpha diversity index, average taxonomic distinctiveness (AvTD Δ+), and taxonomic distinctiveness (Δ*). Visual censuses were conducted in 48 transects consisting of 100?×?5?m quadrants (500?m² sampling area) at an average depth of 5?m, from 09:00 to 16:00. A total of 26,608 fishes belonging to 112 species and 76 genera were found. The index of relative abundance was used to determine the most important species, which were in order of abundance: Abudefduf troschelii, Thalassoma lucasanum, Stegastes rectifraenum, Mulloidichthys dentatus, Chromis atrilobata, Lutjanus argentiventris, and Scarus ghobban. According to Fisher’s alpha diversity index, the highest diversity of species was found in July and the lowest in February. The indices of Δ+ and Δ* indicated significant temporal and spatial differences.     

Amphibian abundance and diversity in Meru National Park, Kenya

The diversity and abundance of amphibians were investigated in Meru National Park, Kenya, using transect sampling, drift‐fence and pitfall trapping and opportunistic collecting. A total of 430 individuals under seven genera (Amietophrynus, Hemisus, Hyperolius, Phrynobatrachus, Phrynomantis, Ptychadena, Xenopus) comprising eleven species were sampled in three different habitats (apart from this, two additional species are known from Meru National Park): Acacia‐wooded grassland; Combretum‐wooded grassland; Acacia–Commiphora bushland. The sex ratio for almost all species was balanced (chi‐square, χ²; P > 0.5) and was not affected by habitat type (ANOVA: F = 8.3026, P = 0.6914). Shannon–Weaver Index (2.227) and Simpson's Index (8.244) were relatively high, and most of the eleven species sampled appeared to have a relatively even distribution (Shannon's Evenness Index, E = 0.927). However, Hemisus marmoratus and Phrynomantis bifasciatus were exclusively recorded in Acacia‐wooded grassland and in low abundances. There was a positive linear relationship of body weight against snout–vent length for two randomly selected anurans (Hyperolius glandicolor, Phrynobatrachus natalensis) among all three vegetation communities.     

Genetic diversity of two endemic and endangered Plantago species

Plantago algarbiensis and Plantago almogravensis are two endangered and endemic species from Portugal. Due to the rarity and endangered nature of these species as well as the lack of molecular data, their genetic variation was evaluated using ISSR and RAPD markers. P. algarbiensis species showed higher genetic variability (73.9% of polymorphism) than P. almogravensis (61.2%). The two species revealed a high level of genetic diversity, with a Nei's genetic diversity of 0.1965 and 0.2309 and a Shannon's diversity index of 0.2975 and 0.3520, for P. almogravensis and P. algarbiensis, respectively. A low level of genetic differentiation was observed (Gst = 0.1873) among the species. However, the cluster and PCA analyses, based on genetic similarity, revealed two main, clearly separate clusters, which directly corresponded to the plants isolated from each species. In situ and ex situ measures should be applied in order to preserve both species but, based on these results, P. almogravensis population should be a priority for conservation.     

A botanical inventory and diversity assessment of Mt. Marsabit forest, a sub-humid montane forest in the arid lands of northern Kenya

A botanical inventory and diversity of trees, shrubs (≥5 cm diameter at breast height [dbh]), herbs, climbers and lianas was assessed in plots (154) of 20 × 5 m in Mt. Marsabit forest, northern Kenya. We recorded 52 species of trees and shrubs, twelve species of herbs and six species of climbers and lianas. They belonged to 35 families and 64 genera. Rubiaceae was the richest family with nine species followed by Euphorbiaceae (six), Oleaceae (five), Rutaceae (four), Capparaceae, Labiatae and Leguminosae (three each). The rest of the families were represented by one or two species. Rinorea convallarioides (Bak.f.) Eyles ssp. marsabitensis Grey‐Wilson (Violaceae), an endemic species, and Drypetes gerrardii Hutch. (Euphorbiaceae), were the two most important species, accounting for more than third of the combined importance value. Species diversity indices were 2.735 (Shannon–Wiener), 0.88 (Simpson's) and 0.296 (Evenness). There was a strong evidence of disturbance arising from anthropogenic and wildlife foraging activities. This inventory has affirmed Mt. Marsabit forest as a unique habitat for several endemic, rare, threatened or vulnerable plant species, which should be conserved.     

四川诺水河珍稀水生动物国家级自然保护区鱼类资源现状

四川诺水河珍稀水生动物国家级自然保护区由嘉陵江支流渠江上游的大通江及支流小通江组成, 为全面了解该保护区的鱼类资源现状, 作者于2015年11月至2017年1月对30个采样点进行了5次资源调查。结果显示, 保护区共分布鱼类57种, 隶属4目13科45属, 其中调查采集47种, 访问调查获得10种。国家二级重点保护鱼类有1种, 即岩原鲤(Procypris rabaudi), 长江上游特有鱼类有12种, 列入《中国脊椎动物红色名录》的易危鱼类3种。保护区以小型鱼类为主, 优势种为宽鳍鱲(Zacco platypus)、嘉陵颌须鮈(Gnarhopogon herzensteini)和切尾拟鲿(Pseudobagrus truncatus)。保护区鱼类多样性较高, Shannon- Wiener多样性指数、Margalef物种丰富度指数、Simpson优势度指数和Pielou均匀度指数分别为2.900、5.198、0.931、0.753。Jaccard相似性系数表明, 大通江和小通江鱼类群落相似度较高, 同一河流不同河段间的相似度整体上与河段间距离成反比; 而不同河流相似海拔高度河段间鱼类群落相似度更高。保护区鱼类资源的衰退主要由过度捕捞、栖息地破坏以及水体污染等人类活动所致。