Genetic and morphological analyses of tub gurnard Chelidonichthys lucerna populations in Turkish marine waters

Genetic and morphological structure of tub gurnard Chelidonichthys lucerna populations in Turkish marine waters were investigated with mtDNA sequencing of 16S rRNA and morphological characters. C. lucerna samples were collected from the Black Sea, Marmara, Aegean and northeastern Mediterranean coasts of Turkey. The lowest genetic diversity was found in the northeastern Mediterranean (Iskenderun Bay) population, while the highest was in the Marmara population with overall average value of genetic diversity within populations. A total of 14 haplotypes was found, and the highest haplotype diversity was in the Black Sea whereas the lowest was in the northeastern Mediterranean population (Iskenderun Bay). The Black Sea and Iskenderun Bay populations showed the least genetic divergence (0.001081), while the highest was between the Marmara Sea and northeastern Mediterranean (Antalya Bay) populations (0.002067). Pairwise comparisons of genetic distance revealed statistically significant differences (P < 0.05) between the Marmara and both the Aegean and northeastern Mediterranean (Antalya Bay) samples. Neighbour joining tree analyses clustered the northeastern Mediterranean populations (Antalya Bay and Iskenderun Bay) as genetically more interrelated populations, whereas the Aegean Sea population was clustered as most isolated one. Discriminant function analysis of morphological characters showed that only the Black Sea population is differentiated from the other populations.     

四川大头茶若干生态问题的研究

四川大头茶(Gordonia acumenata)是我国亚热带西南地区常绿阔叶林优势种之一,材质好,生长快而又未被人注意的一种优良树种。由于它是喜阳的常绿阔叶顶极先锋种(pioneer climax species)其幼苗耐阴,所以在针阔叶混交林中排挤了先锋树种(pioneer species)马尾松,而本身又在常绿阔叶林演替阶段,被更耐阴的顶极种(climax species)所代替,这是由于顶极种有较高的生态位重叠(niche overiap)和最大的生态位宽度(niche breadth)值。四川大头茶Pn日变化具有双峰曲线型和单峰曲线型两种模式,而年变化有明显的季节现象。光照强度和温度是决定Pn的两个主要生态因子,并具有较高的饱和净光合速率和降低暗呼吸能力使其成为喜阳速生的特性。由于速生,其生物量可达176.62t·ha-1;生产量达10.86t·ha-1。四川大头茶幼苗的蒸腾强度与大气湿度、叶温、光强、相对湿度、叶含水量等参数的变化有密切关系。干旱胁迫使光合速率明显下降,从而影响地上部分的生物生产力,但根／冠比却增加18.18%,这可能是植株对干旱胁迫的一种生态适应对策。四川大头茶各器官的营养元素分配与季节有密切关系,同时与土壤中相应的元素含量也有关。     

Non-equilibrium allele frequency spectra via spectral methods

A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see Press et al. (2007). In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright–Fisher process with migration of K populations, influx of mutations, and multiple population splitting events.     

General population growth models with Allee effects in a random environment

Allee effects on population growth are quite common in nature, usually studied through deterministic models with a specific growth rate function.In order to seek the qualitative behaviour of populations induced by such effects, one should avoid model-specific behaviours. So, we use as a basis a general deterministic model, i.e. a model with a general growth rate function, to which we add the effect on the growth rate of the random fluctuations in environmental conditions. The resulting model is the general stochastic differential equation (SDE) model that we propose here.We consider two possible cases, weak Allee effects and strong Allee effects, which lead to different qualitative behaviours of the model.We will study the model properties for both cases in terms of existence and uniqueness of the solution, extinction and stationary behaviour of the population. The two cases will be compared with each other and with the general density-dependent SDE model without Allee effects.We then consider as an example the particular case of the classic logistic model and an Allee effect version of it.     

A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array

Tibetan goats, Taihang goats, Jining grey goats, and Meigu goats are the representative indigenous goats in China, found in Qinghai-Tibet Plateau, Western pastoral area, Northern and Southern agricultural regions. Very few studies have conducted a comprehensive analysis of the genomic diversity and selection of these breeds. We genotyped 96 unrelated individuals, using goat 53 K Illumina BeadChip array, of the following goat breeds: Tibetan (TG), Taihang (THG), Jining grey (JGG), and Meigu (MGG). A total of 45 951 single nucleotide polymorphisms were filtered to estimate the genetic diversity and selection signatures. All breeds had a high proportion (over 95%) of polymorphic loci. The observed and excepted heterozygosity ranged from 0.338 (MGG) to 0.402 (JGG) and 0.339 (MGG) to 0.395 (JGG), respectively. Clustering analysis displayed a genetically distinct lineage for each breed, and their Fst were greater than 0.25, indicating that they had a higher genetic differentiation between groups. Furthermore, effective population size reduced in all four populations, indicating a loss of genetic diversity. In addition, runs of homozygosity were mainly distributed in 5–10 Mb. Lastly, we identified signature genes, which were closely related to high-altitude adaptation (ADIRF) and prolificity (CNTROB, SMC3, and PTEN). This study provides a valuable resource for future studies on genome-wide perspectives on the diversity and selection signatures of Chinese indigenous goats.     

Viability of the Endangered Little Bustard <Emphasis Type="Italic">Tetrax tetrax</Emphasis> Population of Western France

Stochastic computer simulations are used to evaluate the sensitivity of Little bustard population parameters, estimating the survival probabilities of the seven endangered Little bustard populations of central-western France for which conservation actions are currentlybeing or have been implemented. Different scenarios of parameter compensation for those nuclei to establish parameter levels assuring population viability are discussed. Adult survival, productivity per female, initial population size and carrying capacity were the most sensitive parameters in a hypothetical, isolated population. Juvenile survival also affected population survival, although its sensitivity was lower. Sex ratio did not have a linear effect on population survival, but probability of extinction increased for extreme values. Productivity per female and initial population size, varied strongly among the populations studied, determining their average time of extinction and growth rate. When a metapopulation scenario was simulated, the survival probabilities of each population and the metapopulations stayed close to 1.0 if no mortality was associated to migration. When mortality during migration was included in the simulations, the metapopulation's probability of survival significantly decreased under 90%. This approach may help managers to correctly address conservation measures and design effective strategies, which should be directed mainly to improve productivity, enhance female survival, and minimise mortality during migration (e.g. promoting insect-rich nesting substrates, avoiding female killing and nest destruction at harvesting, reducing the risk of collision with powerlines, or controlling poaching).     

两种泥鳅不同群体遗传变异的RAPD分析

应用RAPD技术,分析了采自于我国黄河、长江和珠江三大水系中游的大鳞副泥鳅和泥鳅不同群体间的遗传变异。结果表明：种内不同群体间带纹相似度在0．730－0．938之间;遗传距离为0．089－0．245;种间不同群体间的带纹相似度为0．392－0．505,遗传距离为0．620－0．800。两种泥鳞采自武汉的群体,其不同个体间的相似度较之其它群体为低,表明其群体内遗传变异程度较高。     

Investigating damselfly populations at springs in Banff National Park, Canada, with special focus on Argia vivida, Amphiagrion abbreviatum, and Ischnura cervula (Odonata: Coenagrionidae)

The objective of this study was to estimate Argia vivida (Odonata: Coenagrionidae) populations, identify breeding habitat, and investigate movement of adults within Banff National Park, Alberta, Canada, during the summer of 2003. Mark-recapture techniques and standardized dip-net surveys were used to monitor Argia vivida at various life stages. A reproductive index identified which sites Argia vivida recognized as suitable breeding habitat, and exuvia surveys confirmed breeding sites. The basic structure of emergent and surrounding vegetation was measured to investigate the importance of available ovipositing or roosting sites and the condition of the matrix habitat. Data was recorded for Amphiagrion abbreviatum and Ischnura cervula (both Odonata: Coenagrionidae) to determine if these spring-associated damselflies were successfully breeding within Banff National Park. Comparisons were made between the highly protected Middle Springs and the heavily altered Cave & Basin Springs. Additional surveys at the Vermilion Lake cool spring and Middle Springs Bog investigated their use as breeding habitat for Amphiagrion abbreviatum and Argia vivida, respectively. Results suggest the ecological value of thermal springs extends beyond their origin to outflows and downstream pools. Conservation of Argia vivida must recognize the value of unobstructed thermal outflows, and consider the condition of the forested habitat surrounding springs with regard to its potential use as nocturnal roosts and dispersal corridors. Amphiagrion abbreviatum was confirmed breeding within Banff National Park, while no sign of breeding activity was recorded for Ischnura cervula.     

狼毒种子萌发特性与种群更新机制的研究

研究了采集于植株上的和收集于土壤种子库的狼毒(Stellera chamaejasme)种子在不同温度、光照和5种预处理(即破裂种皮、去除种皮、98％H2SO4浸种5min、0．2％KNO3浸种24h、10℃低温保存1周)条件下的萌发力。结果表明,狼毒种子萌发率较低,25℃恒温、黑暗条件下萌发率为13％,较适宜的萌发温度为30℃恒温或10～30℃变温,破裂种皮和去除种皮萌发率显著提高,25℃恒温、光暗交替条件下萌发率分别为49％和47％,浓硫酸浸种5min处理萌发率可达到32％,KON3浸种和10℃低温保存两个处理对促进狼毒种子萌发效果不明显,狼毒种子萌发对光照条件不敏感,种子硬实性是导致狼毒种子萌发率较低的主要原因,取自土壤种子库内的狼毒种子萌发率高于当年采集的种子,在自然条件下,并非每年都有狼毒种子萌发长成幼苗,种群更新时机是随机的或周期性的。     

Mathematical simulation of the interactions among cyanobacteria, purple sulfur bacteria and chemotrophic sulfur bacteria in microbial mat communities

Abstract: A deterministic one-dimensional reaction diffusion model was constructed to simulate benthic stratification patterns and population dynamics of cyanobacteria, purple and colorless sulfur bacteria as found in marine microbial mats. The model involves the major biogeochemical processes of the sulfur cycle and includes growth metabolism and their kinetic parameters as described from laboratory experimentation. Hence, the metabolic production and consumption processes are coupled to population growth. The model is used to calculate benthic oxygen, sulfide and light profiles and to infer spatial relationships and interactions among the different populations. Furthermore, the model is used to explore the effect of different abiotic and biotic environmental parameters on the community structure. A strikingly clear pattern emerged of the interaction between purple and colorless sulfur bacteria: either colorless sulfur bacteria dominate or a coexistence is found of colorless and purple sulfur bacteria. The model predicts that purple sulfur bacteria only proliferate when the studied environmental parameters surpass well-defined threshold levels. However, once the appropriate conditions do occur, the purple sulfur bacteria are extremely successful as their biomass outweighs that of colorless sulfur bacteria by a factor of up to 17. The typical stratification pattern predicted closely resembles the often described bilayer communities which comprise a layer of purple sulfur bacteria below a cyanobacterial top-layer; colorless sulfur bacteria are predicted to sandwich in between both layers. The profiles of oxygen and sulfide shift on a diel basis similarly as observed in real systems.