Species Associations in a Species-Rich Subtropical Forest Were Not Well-Explained by Stochastic Geometry of Biodiversity

The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure.     

Evolution of the secondary structure of the rRNA internal transcribed spacer 2 (ITS2) in hard ticks (Ixodidae, Arthropoda)

ITS2 sequences are used extensively in molecular taxonomy and population genetics of arthropods and other animals yet little is known about the molecular evolution of ITS2. We studied the secondary structure of ITS2 in species from each of the six main lineages of hard ticks (family Ixodidae). The ITS2 of these ticks varied in length from 679 bp in Ixodes scapularis to 1547 bp in Aponomma concolor. Nucleotide content varied also: the ITS2 of ticks from the Prostriata lineage (Ixodes spp.) had 46-49% GC whereas ITS2 sequences of ticks from the Metastriata lineage (all other hard ticks) had 61-62% GC. Despite variation in nucleotide sequence, the secondary structure of the ITS2 of all of these ticks apparently has five domains. Stems 1, 3, 4 and 5 of this secondary structure were obvious in all of the species studied. However, stem 2 was not always obvious despite the fact that it is flanked by highly conserved sequence motifs in the adjacent stems, stems 1 and 3. The ITS2 of hard ticks has apparently evolved mostly by increases and decreases in length of the nucleotide sequences, which caused increases, and decreases in the length of stems of the secondary structure. This is most obvious when stems of the secondary structures of the Prostriata (Ixodes spp.) are compared to those of the Metastriata (all other hard ticks). Increases in the size of the ITS2 may have been caused by replication slippage which generated large repeats, like those seen in Haemaphysalis humerosa and species from the Rhipicepalinae lineage, and the small repeats found in species from the other lineages of ticks.     

林盘的形态特征和植物种类构成与分布

林盘是成都平原广泛分布的一种复合生态系统,属于极具地方特色的文化和生态资源,并作为传统的乡村聚落单元,提供重要的生态服务价值。识别林盘植物的种类和分布特征,有利于深刻揭示林盘生态服务的形成和变化机制,为林盘保护及改造提供科学建议。采用小型无人机航拍与实地调查相结合的方法,分析不同区域、类型林盘植物组成与分布特征,结果表明:(1)林盘的形态较规则,规模不大(平均面积为6678.87 m~2),植被覆盖度43.5%—76.9%,植物、房屋以及其他组成要素相互融合。(2)林盘内维管束植物合计106科254属310种,其中本地种236种,占总数76.13%,国内引进种35种,占总数11.29%,世界引进种39种,占总数的12.58%。(3)植物属的区系分布以北温带成分(22.31%)和泛热带成分(16.12%)为主,热带亚热带分布和温带分布比例较为接近。(4)从分布特征来看,远郊区林盘的植物种类最多(P0.05),其次是近郊区,而中郊区相对较少;物种多样性与林盘的规模呈显著(P0.05)正相关关系,但是与植被覆盖水平无明显关系;土木结构房屋占比高,植物种类较多,且中、高等比例和低比例的差异显著(P0.05)。     

Factors linked to interannual variation in the metazoan parasite communities of black skipjack,Euthynnus lineatus (Pisces: Scombridae)

Marine parasite communities can exhibit temporal and spatial changes in response to seasonal and local variations in several biotic and abiotic environmental factors. Limited attention has been given to the influence of abiotic factors, so their effects on parasite community structure remain unclear. A total of 496 specimens of Euthynnus lineatus were collected over a 7‐year period (2012–2018) from Acapulco Bay, Mexico. Their parasite communities were analyzed to determine if they experience interannual variations due to local biotic and abiotic factors. Thirty‐three metazoan parasite species were recovered and identified: four species of Monogenea (adults); 16 of Digenea (one larvae and 15 adults); two of Acanthocephala (adults); two of Cestoda (larvae); three of Nematoda (two larvae and one adult); and six of Crustacea (three Copepoda, and three Isopoda). Species richness was greatest among the digeneans, which represented 48% of the total species recovered, followed by the crustaceans (19% of total species). Species richness at the component community level (14–24 species) was similar to reported richness in other small tuna species. The component communities and infracommunities of E. lineatus exhibited a similar pattern: high species richness and diversity, and numerical dominance by a single species, mainly by one of the didymozoids Allopseudocolocyntotrema claviforme or Pseudocolocyntotrema yaito. Parasite community structure and species composition varied among sampling years. Variations were possibly caused by a combination of abiotic and biotic factors which generated notable changes in the infection levels of several component species during the study period. These communities may therefore be unpredictable in terms of structure and species composition, as has been suggested for other communities of marine parasites.     

山茶科3种中国特有濒危植物的遗传多样性研究

猪血木(Euryodendron excelsum)、圆籽荷(Apterosperma oblata)和杜鹃红山茶(Camellia changii)均为我国特有的山茶科珍稀濒危植物。本研究应用随机扩增多态性DNA(RAPD)检测方法,比较了这3个物种的遗传多样性。利用20－24个随机引物从猪血木、圆籽荷和杜鹃红山茶居群中分别获得206－305条RAPD谱带,多态位点百分率(PPL)分别为51.80％、80.26％和38.83％;居群间遗传分化指数G_ST分别为0.3566、0.1713、0.1242。结果显示：自然分布较广的圆籽荷的遗传多样性高于另外两种自然分布区狭窄的种类。3个物种的遗传变异均主要存在于居群内,但猪血木居群间的遗传分化明显高于圆籽荷和杜鹃红山茶,这可能与其生境的严重片断化有关。根据3个物种不同的遗传结构特点,建议加强现有自然居群的就地 保护,促进居群自然更新;收集不同分布点的种源,尽快建立广东山茶科珍稀濒危植物的保育中心,深入开展人工快繁研究,扩大这些种群的数量。     

Spatial genetic structure and clonal diversity of island populations of lady's slipper (Cypripedium calceolus) from the Biebrza National Park (northeast Poland)

Three populations of the rare and endangered plant species Cypripedium calceolus were included in a study of genetic diversity and spatial genetic structure in the Biebrza National Park, northeast Poland. Analysis of 11 allozyme loci indicate that the populations of this species contained high genetic variability (P = 45.5%, A= 1.73). On the other hand, the genetic differentiation (FST = 0.014, P < 0.05) among C. calceolus populations was very low when compared to other species with similar life history characteristics. The observed high rate of gene flow (Nm = 18) may suggest that the populations studied derived from each other in the recent past. Five polymorphic allozyme markers identified 109 multilocus genotypes in three populations and the majority of them (67%) were population-specific. One of the populations studied, characterized by particularly extensive vegetative reproduction, showed the lowest clonal diversity (G/N = 0.15) and heterozygosity (HO = 0.111) values and the highest FIS(0.380), when compared to other two populations (G/N = 0.26-0.27, HO= 0.166-178, FIS = 0.024-0.055). This may indicate that clonal reproduction has an important influence on the genetic structure of C. calceolus populations. The longevity of genets, the out-crossing breeding system and the presence of recruitment from seeds are factors maintaining genetic diversity in C. calceolus.     

气候和土地利用与空间结构在影响大熊猫同域分布大中型哺乳动物物种丰富度中的相对作用

气候因子和土地利用因子是影响生物多样性分布格局的两个主要驱动因素.然而,当前关于气候因子和土地利用因子对生物多样性影响的研究主要集中在物种层面上,在群落水平上对生物多样性的影响依然知之甚少.本研究以大熊猫同域分布大中型哺乳动物为研究对象,结合物种丰富度数据、气候数据、土地利用数据以及经纬度数据,构建基于不同变量组合的多...     

The complete amino acid sequence of bovine skeletal muscle acylphosphatase

The primary structure of bovine skeletal muscle acylphosphatase was determined by performing the sequence analyses of the complete series of tryptic peptides. The amino acid composition of the entire series of peptic peptides was used to reconstruct the sequence by the overlapping method. The proposed structure is further confirmed by analogy with known amino acid sequences of acylphosphatase from skeletal muscle of other vertebrate species. The length of the polypeptide chain is 98 residues, identical to the length of the enzymes from other known mammalian species, but different from that found in turkey. The enzyme is NH2-acetylated and a comparison with the analogous molecular forms from other vertebrate species indicates that there are several long polypeptide stretches strictly conserved (93-97% identical position among mammals, and about 80% between calf and turkey enzymes).     

Analysis of phylogenetic relationship among five mulberry (Morus) species using molecular markers.

Species identification in mulberry (Morus) continues to be a point of great debate among scientists despite the number of criteria such as floral characters, wood, and leaf anatomical and biochemical characters used to identify the species within this genus. However, no consensus system of classification has emerged. Hence, an investigation was undertaken with inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers to find out the possibility of using these DNA markers to confirm the identity of genotypes in a particular species. Fifteen ISSR and 15 RAPD primers generated 86% and 78% polymorphism, respectively, among 19 mulberry genotypes. The polymorphism among the species varied from 50% to 57% in ISSR markers and 31% to 53% in RAPD markers. Similarity coefficients were higher among the genotypes of M. latifolia, M. bombycis and M. alba. Cluster analyses separated genotypes of M. laevigata and M. indica from those of the other species. Population structure analysis of these species further showed high genetic differentiation coefficients (GST), high heterozygosity between two species (DST), and total heterozygosity among populations (Ht) coupled with considerably low gene flow (Nm) when M. laevigata was paired with other species. Based on these parameters and the result of cluster analysis it is concluded that M. laevigata can be considered as a separate species of mulberry, whereas the other four species may be grouped together and treated as subspecies.     

五龙鹅MHC ClassⅠ基因克隆及同源建模研究

主要组织相容性复合体(MHC)与动物机体对外源性抗原的免疫应答之间存在关联。从GenBank/DDBJ/EMBL基因库中读取鸡、其他鸟类、爬行类和哺乳类的MHC ClassⅠ基因进行序列分析设计引物, 使用LA-PCR法从五龙鹅的基因组中克隆了MHC ClassⅠ基因序列(DNA序列和mRNA序列GenBank登录号分别为: AM114925和AM114924), 并分析其基因组结构。运用生物信息学技术对测序结果进行分析显示: 基因组DNA由8个外显子和7个内含子组成, 与鸡基因序列同源率为60.8%~64.1%, 与人的同源率为42.9%。分子进化树进一步揭示了五龙鹅与鸡、其他鸟类、爬行类、哺乳类以及人类的进化关系, 同源建模分析发现该基因由氨基末端结构域和羧基末端结构域构成。     

INTRAGENOMIC NUCLEOTIDE POLYMORPHISM AMONG SMALL SUBUNIT (18S) RDNA PARALOGS IN THE DIATOM GENUS SKELETONEMA (BACILLARIOPHYTA)1

Morphological features of the siliceous cell wall traditionally have been used to diagnose and classify species of diatoms, though an increasing number of studies distinguish new species, in part, by phylogenetic analysis of rDNA sequences. Intragenomic sequence variation is common among the hundreds to thousands of rDNA cistrons present within a genome, and this variation has strong potential to obscure species boundaries based on rDNA sequences. We screened six Skeletonema culture strains for intragenomic nucleotide polymorphisms in the small subunit (SSU) rDNA gene and found that all strains had polymorphic sites, with proportions ranging from 0.57% to 1.81%. In all cases, transitions accounted for more than 70% of nucleotide differences at polymorphic sites. Polymorphic sites were split nearly evenly in the SSU rRNA molecule between the base‐paired regions of helices (52%) and the unpaired regions of loops and bulges (48%). Phylogenetic analysis showed that SSU rDNA genotypes were monophyletic for two of the six culture strains examined. Genotypes from the other four culture strains either showed little or no phylogenetic structure compared with genotypes of other conspecific culture strains or had phylogenetic structure that was incongruent with existing species boundaries. Moderate to strong support for monophyly was recovered for four of the seven species included in the analysis. Phylogenetic results combined with the low sequence divergence of SSU rDNA genotypes within species suggest that concerted evolution has not proceeded to completion in these species and/or that the rate at which variation is being generated exceeds the rate at which concerted evolution is expunging variation.     

Numbers and exchangeability with water of oxygen-17 atoms coupled to molybdenum (V) in different reduced forms of xanthine oxidase

The effect of using [17O]water (24-50% enriched) as solvent on the Mo(V) electron paramagnetic resonance spectra of different reduced forms of xanthine oxidase has been investigated. All the Mo(V) signals are affected. Procedures are described, based on the use of difference spectral techniques, that facilitate interpretation of such spectra. The number of coupled oxygen atoms may be determined by estimation of the fraction of the spectrum that remains unchanged by the isotope at a known enrichment. For a species having two coupled oxygen atoms, the use of two different isotope enrichments permits elimination from the difference spectra of the contribution of the two singly substituted species. From the application of these methods, it is concluded that not only the strength of the hyperfine coupling of oxygen ligands of molybdenum but also their number and their exchangeability with the solvent vary from one reduced form of the enzyme to another. The inhibited species from active xanthine oxidase has been studied in the most detail. It has two weakly coupled oxygen atoms [A(17O)av = 0.1-0.2 mT] that do not exchange with the solvent. A cyclic structure is proposed for this species in which two oxygen ligands of molybdenum are bonded to the carbon of the formaldehyde or other alcohol or aldehyde molecule that reacted in producing the signal. Structures of the other signal-giving species from active xanthine oxidase (Very Rapid and Rapid types 1 and 2) are discussed, as is corresponding information on species from the desulfo enzyme and from sulfite oxidase.     

Genetic diversity and genetic structure of populations of Ranunculus japonicus Thunb. (Ranunculaceae)

Abstract In order to clarify the genetic diversity and population structure of Ranunculus japonicus , allozymic analysis was conducted on 60 populations in southwestern Japan. Considerable genetic variati ons were detected among the populations of R. japonicus . The genetic diversities within species ( H _es = 0.215) and within populations ( H _ep = 0.172) were slightly higher than those of other perennial herbs with widespread distribution and outcrossing plants. Significantly higher values of fixation index were detected in some populations, which might have arisen from restricted mating partners. The majority of genetic variation (approx. 80%) resided within a population and a moderate level of genetic differentiation ( G _ST = 0.203) was observed among populations. The F _ST value (0.203) suggests the existence of a substantial population structure in this species. The highly significant correlation between geographic distance and F _ST values indicates that isolation by distance has played an important role in the construction of the genetic structure of this species.     

家蚕内网虫属微孢虫核糖体小亚单位RNA(SSUrRNA)核心序列的克隆和序列分析

Endoreticulatus bombycis is a new pathogenic microspordia isolated from the silkworm larvae.With polymerase chain reaction(PCR) method,we amplified a fragment of the core sequence of the small subunit ribosomal RNA( SSUr-RNA) of Endoreticulatus bombycis.The SSUrRNA fragment was inserted into pMD18-T Vector and then cloned.It had a length of 1230 nucleotides and a percentage GC content of 51.3%.The accession number in Genbank is gill 181769|AY009115.The secondary structure model of the SSUrRNA of Endoreticulatus bombycis was constructed both on the bases of the sequence alignment and RNAFOLD program of the PC-GENE package.The secondary structure model revealed that Endoreticulatus bombycis lacked many cukaryotic hclices.such as heli10,helix 11.helix 18,helix 43 and helix 46,but it has V4 region and has more of prokaryotic character.Analyzed by Blast,Endoreticulatus bombycis.Endoreticulatus schubergi and pleistophora sp.(Sd-Nu-IW8201) have a high similarity,over 98%,Phylogeny tree of Endoreticulatus and Pleistophora species showed that Endoreticulatus and Pleistophora sp.(Sd0Nu-IW8201) was in a group and the other Pleistophora species were in another group[Acta Zoologica Sinica 49(3):414-420,2001].     

Crystalline ricin D, a toxic anti-tumor lectin from seeds of Ricinus communis

A toxic lectin, ricin D, present in the seeds of Ricinus communis has been purified and crystallized in a form suitable for high resolution crystallographic structure studies. This protein is different from a previously found form of ricin (also present in the same seeds), the only ricin for which a preliminary x-ray investigation has been reported so far. Ricin D crystallizes from an aqueous solution in an orthorhombic unit cell of symmetry P2(1)2(1)2(1) and a = 79.0, b = 114.7, and c = 72.8 A. The asymmetric unit contains one molecule with an average molecular weight of 62,400. The crystal is fairly stable to x-radiation and has a water content of approximately 54% by volume. It appears to comprise two closely related species of proteins, the major species corresponding to recin D and the other presumably corresponding to a deamidation product of ricin D. The two species have nearly identical molecular size and amino acid compositions, but different charges.     

Fish abundance and trophic structure from the commercial catch in Lake Patzcuaro, Mexico

The composition, abundance and trophic structure of the fish community in Lake Patzcuaro is analyzed, using data from eight samples taken from the commercial fishery acquired between August 1990 and April 1991. A total of 65 767 individuals, caught with gillnets selective to all fish and size, were analyzed. Eleven species (8 native and 3 exotic) were recorded during the study. Zooplanktivorous were the most representative species, amounting to 91% of the total number. Also, they were the most characteristic species (36.4%) when feeding habits were considered, followed by carnivore and omnivore (27.3% each), and herbivore (9.1%). Three species groups and three time-associated groups were detected by means of classification methods. Lake Patzcuaro's ichthyofauna is to be considered as a transitional community that has not reached equilibrium, particularly after the introduction of exotic species and local extinction of native species. However, Lake Patzcuaro has the greatest fishery production of all tropical lakes in the Central Plain of Mexico and it is mainly sustained by native species. The differential use of feeding resources by the fish species and the diversity in their habits must be taken into account to design strategies to maintain the fish structure (avoiding new introduction of exotic species) and the fish production in Lake Patzcuaro.     

Population structure, life histories and abundance of copepods in Tjeukemeer, the Netherlands

SUMMARY. The copepod zooplankton of Tjeukemeer was sampled at weekly intervals for 3 years (1969–1971), and ten species were recorded. Five species contributed more than 99% of all individuals collected. Acanthocyclops robustus is the most abundant species (66%), followed by Mesocyclops leuckarti (13%), Cyclops vicinus (11%), Eurytemora affinis (9%) and Diacyclops bicuspidatus (1%).
The ecology of the A. robustus population in Tjeukemeer differs from other A. robustus populations in that it dominates the open water zone. This is an additional argument for a taxonomic revision of the A. vernalis-robustus complex.
Seasonal periodicity in abundance of each species was very similar in 3 successive years.
All cyclopoid species went into diapause, A. robustus and M. leuckarti during winter, D. bicuspidatus and C. v. vicinus during summer. Most species diapause in a particular copepodite stage.
The seasonal variation in the population structure, the fecundity and the sex ratio are described. Both population structure and sex ratio were influenced by diapause and size-dependent mortality. The fecundity was more influenced by the water temperature and the age structure of the female population than by food situation or size of the females.     

湖南省阳明山山顶苔藓矮林物种组成与多样性的十年动态

于2005年在湖南省阳明山国家级自然保护区的阳明山山顶苔藓矮林聚集区建立了3块样地,从物种数量特征、物种重要值、径级结构、高度结构和物种多样性等方面分析了2005-2016年苔藓矮林物种组成和多样性的变化.结果表明: 从2005年到2016年,样地内乔木层植物基径(DGH)≥1.0 cm的个体数量减少了30.9%,其中减少率最大的物种为荚蒾,达到98.6%,减少率最小的物种是云锦杜鹃,为1.8%.样地内的物种数有所上升,但均匀度下降.除云锦杜鹃重要值增加外,其余各物种的重要值在10年后均大幅下降,云锦杜鹃为山顶苔藓矮林的优势种.矮林内物种的径级分布以1 cm 等级排列,整个矮林的物种表现为小径木(1 cm≤DGH＜6 cm)个体数量多,而中径木(6 cm≤DGH＜15 cm)和大径木(15 cm≤DGH)个体数量少的特点.云锦杜鹃的径级结构呈倒“J”型,群落高度增高,表现出稳定和发展良好的趋势;而其他物种更新不良,径级结构不规律.整体上,样地Patrick和Menhinick物种丰富度指数和Simpson指数上升,Shannon指数和Pielou指数下降.     

The crystal structure of the superoxide dismutase from Helicobacter pylori reveals a structured C-terminal extension

Superoxide dismutases (SODs) are key enzymes for fighting oxidative stress. Helicobacter pylori produces a single SOD (HpSOD) which contains iron. The structure of this antioxidant protein has been determined at 2.4 A resolution. It is a dimer of two identical subunits with one iron ion per monomer. The protein shares 53% sequence identity with the corresponding enzyme from Escherichia coli. The model is compared with those of other dimeric Fe-containing SODs. HpSOD shows significant differences in relation to other SODs, the most important being an extended C-terminal tail. This structure provides a model for closely related sequences from species such as Campylobacter, where no structures are currently known. The structure of extended carboxyl termini is discussed in light of putative functions it may serve.     

裸子植物5S rRNA基因序列变异及二级结构特征

在高等植物中,5SrRNA基因一级结构是高度保守的,二级结构也相当一致。通过比较18种裸子植物5SrRNA基因序列和二级结构变异,发现55％的核苷酸位点是可变的,这种变异有68％发生在干区（双链区）,其中一些变异,如双链的互补性核苷酸替代,GU配对等能够维系5SrRNA二级结构的稳定性。环区相对保守,这与5SrRNA三级结构折叠或在转录翻译过程中蛋白质、RNA的结合相关。另外,首次报道了松属环E区核苷酸的变异性,这可能与其他区域的变异一样,是假基因造成的结果。5SrRNA基因信息可反映大分类群的系统进化关系,但由于基因长度短,信息量小,其在近缘种系统分类的应用受到限制。