Distribution patterns in butterflies and birds of the Czech Republic: separating effects of habitat and geographical position

Aim To evaluate the relative role of environmental factors and geographical position (latitude and longitude) in determining species distribution and composition of local assemblages of butterflies and birds. Location Czech Republic, central Europe. Methods Canonical correspondence analysis that ordinates species and samples (grid cells in distribution atlases) such that interspecific and intersample differences attributable to environmental factors are maximized. The technique allowed us to test the significance of individual factors, including the geographical ones, by controlling the other factors and accounting for spatial autocorrelation. Results Altitude and climate (temperature and precipitation) accounted for most variance in the interspecific differences in distribution of both butterflies and birds. The distribution of birds was also strongly affected by the area of water bodies, and less strongly, but still significantly, by the area of meadows and mountain open habitats. Habitat types important for the differences in butterfly distribution were deciduous forests, meadows, swamps and mountain open habitats. Some less common habitat types were important only because of the presence of rare species. Latitude and longitude invariably accounted for a large proportion of total variance, and their effect was highly significant even after controlling for the effect of all other environmental factors. Main conclusions Although environmental factors, especially those related to elevation and climate, represent the main determinants of species distribution and composition of local assemblages, the geographical position is very important on this scale of resolution. Understanding distribution patterns, thus, must include not only an understanding of species ecological requirements, but also an understanding of geographical context, which affects structure and dynamics of species’ geographical ranges.     

First confirmed record of the Corsac Fox,Vulpes corsac,from Iran and considerations on its status (Mammalia: Canidae)

The occurrence of the Corsac Fox, Vulpes corsac, is replete with ambiguity and uncertainty in the literature. We present the first confirmed record of the species from Iran. In the course of a survey, we found two Corsac Fox furs in Tehran Market in 2013 and separately recorded one adult and a group of three young in semi-arid steppes in central Turkmen Sahra, Golestan Province, in June 2014. Great Gerbil (Rhomobomys opimus), Libyan Jird (Meriones libycus), and Long-eared Hedgehog (Hemiechinus auritus) are among prey items. The Corsac Fox has a limited range in Iran and is threatened by habitat fragmentation and road kill.     

Quantitative metrics of overlaps in Grinnellian niches: advances and possible drawbacks

Aim Studies of environmental niche shift/niche conservatism that are based on species distribution modelling require a quantification of niche purity and potential overlap. Although various metrics have been proposed for this task, no comparisons of their performance are available yet that express the linearity of range shifts and error‐proneness. Herein, we assess the performance of six niche overlap metrics using three sister pairs of plethodontid salamanders as well as artificial species to test for linearity of overlap curves, impacts of varying potential distribution sizes and study area sizes. Location North America, artificial environments. Methods Species distribution models for the salamanders were performed with Maxent , and artificial species were created in the R environment. Potential distributions of species with varying range sizes and extents of the study area were compared using the Bray–Curtis distance BC, Schoener's D, two different modifications of the Hellinger distance I_mod, I_cor, Pianka's O and Horn's R. Niche overlaps in ecological space were compared using linear discriminant analyses based on principal components. Results Simulations of niche overlaps revealed strong variations in the performance of the niche overlap metrics. In artificial species, BC and D performed best, followed by O, R and I_cor, but the modified Hellinger distance I_mod showed a nonlinear slope and a truncated range. Furthermore, the simulations suggest that, in proportionally small potential distributions on large grids, an inclusion of a high proportion of grid cells with low occurrence probabilities representing background noise may bias assessments of niche overlaps. Main conclusions Both the salamander examples and simulations suggest that Schoener's D and the Bray–Curtis distance BC are best suited to compute niche overlaps from potential distributions derived from species distribution models. However, like all analysed metrics, both D and BC are seriously affected by the inclusion of high numbers of grid cells where the species are probably absent, i.e. with low occurrence probabilities. Therefore, pre‐processing to eliminate background noise in the potential distribution grids is highly recommended.     

滇金丝猴分布区森林面积变化的时空特征及其影响因素

森林生态系统是滇金丝猴(Rhinopithecus bieti)的主要生境,森林面积变化会直接影响滇金丝猴的生存。本研究基于全球森林变化(Global Forest Change)数据,采用Theil-Sen趋势分析和Mann-Kendall检验、热点分析与地理探测器模型等方法,探讨了滇金丝猴分布区2001—2019年森林面积变化的时空特征及其影响因素。结果表明:(1)近20年间,滇金丝猴分布区森林面积变化总量为3.81×10~4 hm~2,约占研究区森林面积的2.44%,逐年森林面积变化呈现较大的年际波动,其中5个保护地森林面积变化总量达5456 hm~2,约占研究区森林面积变化总量的14.3%,老君山风景区和云岭保护区森林面积变化的比例较高;(2)滇金丝猴分布区森林面积变化趋于缓和,其中森林面积减少呈现显著增加的区域面积为1.03×10~5 hm~2,占整个研究区面积的2.9%;森林面积减少呈现显著减少的区域面积为3.05×10~5 hm~2,占整个研究区面积的7.9%;同时森林面积变化的热点区域面积呈不断下降的趋势;(3)滇金丝猴分布区森林面积变化呈现向低海拔、高坡度转移的趋势;...     

Comparative study of SP[6-11] and its analogs using simulated annealing

In this study we compared the steric structures of the bioactive part of substance P (SP[6-11]) and its analogs (NY3460 and pHOPA-SP5). The molecular dynamics-simulated annealing method was used to explore the conformational space, and the structural differences and similarities of these molecules were identified. For the three peptides, the conformational distributions were represented in Ramachandran density plots. The occurring secondary structural elements of the investigated molecules were identified, namely alpha-Helix, type III beta-Turn, gamma-Turn, and inverse gamma-Turn. For SP[6-11] and its two analogs, different intramolecular interactions (H-bonds between the main-chain atoms, aromatic-aromatic interactions, and amino-aromatic interactions) that can stabilize the various conformations of the three peptides were investigated. Detailed examination of these intramolecular interactions revealed that H-bonds between the main-chain atoms are relevant in the determination and stabilization of the conformer structures of the peptides, while the aromatic-aromatic interactions do not play an important stabilizing role. Furthermore, in the conformers of NY3460 and pHOPA-SP5, different types of amino-aromatic interactions were identified that contribute to the formation of the various structures of these peptides. For all three molecules, the orientations of the side chains were investigated and the rotamer populations were determined.     

Testing concordance in species boundaries using acoustic,morphological, and molecular data in the field cricket genus Itaropsis (Orthoptera: Grylloidea,Gryllidae: Gryllinae)

In most taxa, species boundaries are inferred based on differences in morphology or DNA sequences revealed by taxonomic or phylogenetic analyses. In crickets, acoustic mating signals or calling songs have species‐specific structures and provide a third data set to infer species boundaries. We examined the concordance in species boundaries obtained using acoustic, morphological, and molecular data sets in the field cricket genus Itaropsis. This genus is currently described by only one valid species, Itaropsis tenella, with a broad distribution in western peninsular India and Sri Lanka. Calling songs of males sampled from four sites in peninsular India exhibited significant differences in a number of call features, suggesting the existence of multiple species. Cluster analysis of the acoustic data, molecular phylogenetic analyses, and phylogenetic analyses combining all data sets suggested the existence of three clades. Whatever the differences in calling signals, no full congruence was obtained between all the data sets, even though the resultant lineages were largely concordant with the acoustic clusters. The genus Itaropsis could thus be represented by three morphologically cryptic incipient species in peninsular India; their distributions are congruent with usual patterns of endemism in the Western Ghats, India. Song evolution is analysed through the divergence in syllable period, syllable and call duration, and dominant frequency. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 285–303.     

Taxonomic status and relationships of bracken ferns (Pteridium: Dennstaedtiaceae) of Laurasian affinity in Central and North America

Detailed quantitative comparisons confirm and extend the discrimination of four major morphotypes amongst brackens of Laurasian affinity in Central and North America. These are recognized here at subspecies level as: Pteridium aquilinum sspp. feei , pubescens , latiusculum , and pseudocaudatum . Measurements of spore size indicate that sporophytes of P. aquilinum ssp. feei are diploid (2 n  = 104), as are sspp. pubescens , latiusculum , and pseudocaudatum . Phenetic cluster analysis based on DNA fingerprinting by arbitrarily primed polymerase chain reaction groups these four subspecies as genomically more similar to each other than to any taxa from other geographical regions. The chloroplast haplotype of ssp. feei is the same as that of sspp. latiusculum , pseudocaudatum , and pubescens with respect to the absence of both of the short direct repeats in the rps 4– trn S region (haplotype A), whereas the European ssp. aquilinum (haplotype B) has one of these repeats, and the Southern Hemisphere brackens P. arachnoideum and P. esculentum (haplotype C) have the other.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 1–17.     

三峡水库175 m试验性蓄水期库区及其上游江段鱼类群落结构时空分布格局

根据2010—2012年在三峡水库及其上游江段5个江段的商业性渔获物调查结果,对该区域鱼类群落结构的时空分布格局进行了分析。调查中共收集到鱼类87种,隶属于8目18科63属。沿坝前江段溯河而上至库尾以上流水江段,鱼类种类数逐渐增加。采用聚类分析(CA)和非度量多维标度(NMDS)方法对三峡水库175 m试验性蓄水期间各江段的鱼类种类组成进行分析,发现这5个调查江段的鱼类种类组成可以分为两个类群:类群Ⅰ包括秭归、巫山、云阳3个库区的江段,其鱼类种类组成在各年间的差异程度较大;而类群Ⅱ包括库尾的涪陵江段以及上游的江津江段,其鱼类种类组成在各年间差异程度较小。采用CA和NMDS方法对鱼类群落结构时空分布格局的分析结果表明,5个调查江段的鱼类群落结构在各年间可以分为不同类群;云阳与涪陵江段的鱼类群落结构的相似性逐年增加,而与秭归、巫山江段的相似性逐年减少;涪陵江段与江津江段的鱼类群落结构相似性也呈逐年减少趋势。总体而言,175m试验性蓄水对库中和库尾江段的鱼类群落结构的影响较大,但对库首以及库尾以上流水江段的影响均较小。     

The Bornean Lithocarpus B1. section Synaedrys (Lindl.) Barnett (Fagaceae): its circumscription and description of a new species

The Bomean species of Lithocarpus B1. section Synaedrys edl.) Barnett (Fagaceae) are discussed in terms of their unifying characteristics, and keys to the species are provided. A novel morphological feature present in the genus, where the seed in the mature fruit is enclosed by a lignified and thickened receptacle, is illustrated. A new species, L palungensis Cannon & Manos, is described. It can be distinguished from L. pulcher (King) Markgr. by its submontane distribution, prominent reflexed cupular spines, present at all stages, and broadly oblong leaves with scattered open fasciculate trichomes on the abaxial surface. Foliar trichome types present within the section are also described. Distinctiveness of fruit wall and receptacle shape, as described by two-dimensional elliptic Fourier transformation, is demonstrated by principal components analysis.     

我国入侵植物多样性的区域分异及其影响因素——以74个地区数据为基础

以我国74个地理单位282种外来入侵植物的分布和环境数据为基础,应用除趋势对应分析、典范对应分析和回归分析方法,探讨了我国境内入侵植物区系组成、地理分布格局及其影响因素。主要结果如下:(1)我国74个地区共有282种外来入侵种,出现频率相对较高的外来入侵种是小飞蓬(Conyza canadensis)、刺苋(Amaranthus spinosus)、一年蓬(Erigeron annuus)、空心莲子草(Alternathera philoxeroides)、土荆芥(Chenopodium ambrosioides)、圆叶牵牛(Pharbitis purpurea)、曼陀罗(Datura stramonium)、皱果苋(Amaranthus viridis)、裂叶牵牛(Pharbitis nil)、反枝苋(Amaranthus retroflexus)、三叶鬼针草(Bidens pilosa)、凤眼莲(Eichhornia crassipes)等;(2)菊科(Compositae,67,种数)、禾本科(Gramineae,32)、豆科(Leguminosae,29)、苋科(Amaranthaceae,23)、旋花科(Convolvulaceae,13)是我国境内含入侵种最丰富的5个科,共计有164种,占我国入侵植物总数的58.16%;(3)我国外来入侵植物主要源自于热带美洲、北美洲、欧洲、地中海-西亚和中亚、非洲和南亚;(4)外来入侵植物多样性在我国的区域分异明显,热带-南亚热带、中(北)亚热带和温带三大区域的入侵种组成有较大差异:马缨丹(Lantana camara)、含羞草(Mimosapudica)、胜红蓟(Ageratum conyzoides)、刺苋、小飞蓬、飞扬草(Euphorbia hirta)、五爪金龙(Ipomoea cairica)、空心莲子草、三叶鬼针草和金腰箭(Synedrella nodiflora)是热带-南亚热带区域中出现频率最高的前10种入侵植物;中亚热带和北亚热带区域出现频率最高的入侵种分别是一年蓬、小飞蓬、刺苋、土荆芥、北美独行菜(Lepidium virginicum)、美洲商陆(Phytolacca americana)、牛筋草(Eleusine indica)、紫茉莉(Mirabilis jalapa)、空心莲子草和三叶鬼针草;温带区域出现频率最高的是反枝苋、小飞蓬、圆叶牵牛、一年蓬、野西瓜苗(Hibiscus trionum)、杂配藜(Chenopodium hybridum)、苦苣菜(Sonchus oleraceus)、野燕麦(Avena fatua)、曼陀罗和皱果苋;(5)年降雨量、年均温度、年极端低温、无霜期和年均积温是影响我国外来入侵种空间分布格局的主要气象因素,年极端高温和年日照时数的影响相对较小;人口密度和交通密度对入侵种的地理分布也均有很大的影响;(6)随着年均温度、无霜期、人口密度、交通密度、年极端低温、年均降雨量和年积温的增加,外来入侵植物的种数呈线性增加,随着纬度的增加,种数则呈线性递减,种数与这8个环境因素间的关系达到极显著的水平;(7)不同地理来源的外来入侵种在我国的分布主要受纬度、年降雨量、年均无霜期、年均温度、交通密度、年极端低温和年均积温的影响。由于外来入侵种在我国分布呈现明显的区域分化,因此,应用建立具有区域特点的外来植物入侵风险评估系统。     

The introduction to Japan of the Titan barnacle,Megabalanus coccopoma (Darwin, 1854) (Cirripedia: Balanomorpha) and the role of shipping in its translocation

The Titan Acorn barnacle, Megabalanus coccopoma, a native of the tropical eastern Pacific, has become established in the western Atlantic (Brazil and the northern Gulf of Mexico to the Carolinas), northwestern Europe and the western Indian Ocean (Mauritius), and therefore its dispersal capabilities are well known. This study reports its introduction to Japan and confirms its occurrence in Australia. In an attempt to determine the source of this introduction, phylogeographic techniques, involving cytochrome c oxidase I sequences of various widely separate populations of M. rosa and M. volcano, were utilized. No significant genetic differentiation or haplotype patterns between widely separated populations of each of the three species were found. Lack of such differentiation indicates recent geographical isolation and thus negates a null hypothesis predicting that the occurrence of one of more of these species in Australia was natural.     

TWARIT: an extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences

Phylogenetic assignment of individual sequence reads to their respective taxa, referred to as 'taxonomic binning', constitutes a key step of metagenomic analysis. Existing binning methods have limitations either with respect to time or accuracy/specificity of binning. Given these limitations, development of a method that can bin vast amounts of metagenomic sequence data in a rapid, efficient and computationally inexpensive manner can profoundly influence metagenomic analysis in computational resource poor settings. We introduce TWARIT, a hybrid binning algorithm, that employs a combination of short-read alignment and composition-based signature sorting approaches to achieve rapid binning rates without compromising on binning accuracy and specificity. TWARIT is validated with simulated and real-world metagenomes and the results demonstrate significantly lower overall binning times compared to that of existing methods. Furthermore, the binning accuracy and specificity of TWARIT are observed to be comparable/superior to them. A web server implementing TWARIT algorithm is available at http://metagenomics.atc.tcs.com/Twarit/