A Primer to Molecular Phylogenetic Analysis in Plants

Reconstructing a tree of life by inferring evolutionary history is an important focus of evolutionary biology. Phylogenetic reconstructions also provide useful information for a range of scientific disciplines such as botany, zoology, phylogeography, archaeology and biological anthropology. Until the development of protein and DNA sequencing techniques in the 1960s and 1970s, phylogenetic reconstructions were based on fossil records and comparative morphological/physiological analyses. Since then, progress in molecular phylogenetics has compensated for some of the shortcomings of phenotype-based comparisons. Comparisons at the molecular level increase the accuracy of phylogenetic inference because there is no environmental influence on DNA/peptide sequences and evaluation of sequence similarity is not subjective. While the number of morphological/physiological characters that are sufficiently conserved for phylogenetic inference is limited, molecular data provide a large number of datapoints and enable comparisons from diverse taxa. Over the last 20 years, developments in molecular phylogenetics have greatly contributed to our understanding of plant evolutionary relationships. Regions in the plant nuclear and organellar genomes that are optimal for phylogenetic inference have been determined and recent advances in DNA sequencing techniques have enabled comparisons at the whole genome level. Sequences from the nuclear and organellar genomes of thousands of plant species are readily available in public databases, enabling researchers without access to molecular biology tools to investigate phylogenetic relationships by sequence comparisons using the appropriate nucleotide substitution models and tree building algorithms. In the present review, the statistical models and algorithms used to reconstruct phylogenetic trees are introduced and advances in the exploration and utilization of plant genomes for molecular phylogenetic analyses are discussed.     

Bayesian Insight into a Robust Test for Linear Contrast Based on Asymmetric Censored Samples

A robust test for linear contrast using modified maximum likelihood estimators based on symmetrically censored samples proposed by Tiku (1973, 1982a) is studied in this paper from the Bayesian point of view. The effects of asymmetric censoring on this testing procedure is investigated and a good approximation to its posterior distribution in this case is worked out. We also present an example which illustrates the method of obtaining the highest posterior density interval for the linear combination of the unknown location parameters.     

Migration and spawning energetics of the anadromous sea lamprey,Petromyzon marinus

Synopsis Energy expended in migration and reproduction was determined from measurements of caloric concentration and body and gonodal weight for nontrophic sea lampreys collected from different sites along the St. John River, New Brunswick. The estimated cost of locomotion in swimming the 140 km which separates the estuary from the spawning redds was 300 and 260 kcal for males and females respectively. Acutal distance which lampreys swam as well as mean swimming speed were estimated from a linear regression equation relating energy expenditure for locomotion and body weight. Energy expenditure for breeding was considerably greater than that catabolized throughout the upstream migration.     

Finessing atlas data for species distribution models

Aim The spatial resolution of species atlases and therefore resulting model predictions are often too coarse for local applications. Collecting distribution data at a finer resolution for large numbers of species requires a comprehensive sampling effort, making it impractical and expensive. This study outlines the incorporation of existing knowledge into a conventional approach to predict the distribution of Bonelli’s eagle (Aquila fasciata) at a resolution 100 times finer than available atlas data. Location Malaga province, Andalusia, southern Spain. Methods A Bayesian expert system was proposed to utilize the knowledge from distribution models to yield the probability of a species being recorded at a finer resolution (1 × 1 km) than the original atlas data (10 × 10 km). The recorded probability was then used as a weight vector to generate a sampling scheme from the species atlas to enhance the accuracy of the modelling procedure. The maximum entropy for species distribution modelling (MaxEnt) was used as the species distribution model. A comparison was made between the results of the MaxEnt using the enhanced and, the random sampling scheme, based on four groups of environmental variables: topographic, climatic, biological and anthropogenic. Results The models with the sampling scheme enhanced by an expert system had a higher discriminative capacity than the baseline models. The downscaled (i.e. finer scale) species distribution maps using a hybrid MaxEnt/expert system approach were more specific to the nest locations and were more contrasted than those of the baseline model. Main conclusions The proposed method is a feasible substitute for comprehensive field work. The approach developed in this study is applicable for predicting the distribution of Bonelli’s eagle at a local scale from a national‐level occurrence data set; however, the usefulness of this approach may be limited to well‐known species.     

Ambient UV-B radiation reduces PSII performance and net photosynthesis in high Arctic Salix arctica

Ambient ultraviolet-B (UV-B) radiation potentially impacts the photosynthetic performance of high Arctic plants. We conducted an UV-B exclusion experiment in a dwarf shrub heath in NE Greenland (74°N), with open control, filter control, UV-B filtering and UV-AB filtering, all in combination with leaf angle control. Two sites with natural leaf positions had ground angles of 0° (‘level site’) and 45° (‘sloping site’), while at a third site the leaves were fixed in an angle of 45° to homogenize the irradiance dose (‘fixed leaf angle site’). The photosynthetic performance of the leaves was characterized by simultaneous gas exchange and chlorophyll fluorescence measurements and the PSII performance through the growing season was investigated with fluorescence measurements. Leaf harvest towards the end of the growing season was done to determine the specific leaf area and the content of carbon, nitrogen and UV-B absorbing compounds. Compared to a 60% reduced UV-B irradiance, the ambient solar UV-B reduced net photosynthesis in Salix arctica leaves fixed in the 45° position which exposed leaves to maximum natural irradiance. Also a reduced Calvin Cycle capacity was found, i.e. the maximum rate of electron transport (J_max) and the maximum carboxylation rate of Rubisco (V_cmax), and the PSII performance showed a decreased quantum yield and increased energy dissipation. A parallel response pattern and reduced PSII performance at all three sites indicate that these responses take place in all leaves across position in the vegetation. These findings add to the evidence that the ambient solar UV-B currently is a significant stress factor for plants in high Arctic Greenland.     

模拟风雨对麦长管蚜自然种群发展的干扰作用

麦长管蚜Macrosiphum avenae（Fabricius）是我国小麦生产上的重大害虫,给小麦生产造成严重的威胁。本研究采用人工模拟风雨气象因子的方法,研究了吹风和喷水对麦长管蚜种群数量的干扰作用,解析了麦长管蚜在种群不同发展阶段受模拟风雨干扰后种群变化的特征,明确了麦长管蚜受模拟风雨作用影响其种群生长的关键时期。结果表明,在小麦田进行模拟风雨试验,处理强度越大,防治效果越好;有目标的对靶喷施处理的防治效果明显高于非目标喷施处理;确定人工喷水或吹风处理的最佳时期为小麦灌浆初期,即在该阶段进行一次喷水处理,可以获得最佳的防治效果和保产作用。     

利用CASA模型模拟西南喀斯特植被净第一性生产力

基于SPOT NDVI遥感数据并结合数字高程模型、气象数据和植被参数,利用实测植被生产力计算和修正最大光能利用率,通过改进CASA过程模型,本文估算了中国西南喀斯特地区1999—2003年的植被净第一性生产力（NPP）。结果表明：1）改进后的CASA模型模拟的植被NPP与实测值相关性显著,可较好用于西南喀斯特植被的NPP估算;2）西南8省市区1999—2000年喀斯特和非喀斯特植被的NPP有轻度增加,但空间变化不显著,2001年低值区范围增加,2002年NPP高值区的范围明显扩大,随后在2003年又降低,但仍高于2001年;3）5年间西南喀斯特地区年NPP的变化范围是381.7—439.9 gC m-2 yr-1,平均值为402.34 gC m-2 yr-1,逐年NPP波动中呈现总体增长趋势,平均增加值为9.93 gC m-2 yr-1,5年总增加量为11TgC,但非喀斯特地区的年NPP平均值和增加值都大于喀斯特地区;4）5年间喀斯特地区的热带森林、亚热带森林、灌丛和草地的逐年NPP均小于非喀斯特地区,温带森林和农业植被则相反;这6种典型植被年NPP均呈增加趋势,热带森林的增加值最大,草地最小,非喀斯特地区植被NPP的增长趋势相似,但每种植被的年NPP增加值均大于喀斯特地区。西南喀斯特地区植被NPP的时空变化与气温、降水和太阳辐射的变化有关,而喀斯特植被NPP低于非喀斯特地区,则主要由喀斯特地区水分匮缺、土壤贫瘠等恶劣条件而抑制植物生长造成的。     

Behavioral thermoregulation, temperature tolerance and oxygen consumption in the Mexican bullseye puffer fish, Sphoeroides annulatus Jenyns (1842), acclimated to different temperatures

An inverse and unusual relationship was found between preferred temperature and acclimation temperature in the bullseye puffer, Sphoeroides annulatus. The final preferendum temperature (PT) was 26.8 °C. The critical thermal maxima (CTMax) were 37.7, 38.8, 40.0, 40.8 and 41.3 °C where the temperatures of acclimation were 19, 22, 25, 28 and 31 °C±1 °C, respectively, and the endpoint of CTMax was loss of the righting response. The acclimation response ratio presented an interval of 0.22-0.38; these values are in agreement with results for other subtropical and tropical fishes. The temperature significantly affected the oxygen consumption of bullseye puffer juveniles. The oxygen consumption rate (OCR) increased significantly with an increment in the temperature from 19 to 31 °C. The range of the temperature coefficient Q₁₀ in bullseye puffer individuals was lowest between 25 and 28 °C, at 1.37. The optimal temperature for growth was 26 °C. The results of this study will be useful for optimizing the culture of bullseye puffer juveniles in controlled conditions.     

Attraction of pepper weevil to volatiles from damaged pepper plants

Pioneer herbivorous insects may find their host plants through a combination of visual and constitutive host‐plant volatile cues, but once a site has been colonized, feeding damage changes the quantity and quality of plant volatiles released, potentially altering the behavior of conspecifics who detect them. Previous work on the pepper weevil, Anthonomus eugenii Cano (Coleoptera: Curculionidae), demonstrated that this insect can detect and orient to constitutive host plant volatiles released from pepper [Capsicum annuum L. (Solanaceae)]. Here we investigated the response of the weevil to whole plants and headspace collections of plants damaged by conspecifics. Mated weevils preferred damaged flowering as well as damaged fruiting plants over undamaged plants in a Y‐tube olfactometer. They also preferred volatiles from flowering and fruiting plants with actively feeding weevils over plants with old feeding damage. Both sexes preferred volatiles from fruiting plants with actively feeding weevils over flowering plants with actively feeding weevils. Females preferred plants with 48 h of prior feeding damage over plants subjected to weevil feeding for only 1 h, whereas males showed no preference. When attraction to male‐ and female‐inflicted feeding damage was compared in the Y‐tube, males and females showed no significant preference. Wind tunnel plant assays and four‐choice olfactometer assays using headspace volatiles confirmed the attraction of weevils to active feeding damage on fruiting plants. In a final four‐choice olfactometer assay using headspace collections, we tested the attraction of mated males and virgin and mated females to male and female feeding damage. In these headspace volatile assays, mated females again showed no preference for male feeding; however, virgin females and males preferred the headspace volatiles of plants fed on by males, which contained the male aggregation pheromone in addition to plant volatiles. The potential for using plant volatile lures to improve pepper weevil monitoring and management is discussed.