The teaching of ecology in Spain

The design of an interactive computer program in microbial genetics is described. The program is divided into three stages: background information, questions, and the simulation. The results of simulated conjugation experiments with Escherichia coli allow eight chromosomal genes to be sequenced. These genes can be mapped relative to eight different sites of F plasmid insertion and transfer orientation. The simulation requires the student to choose appropriate donor and recipient strains of the bacterium, and to specify the constituents of selective media on which the progeny of each cross are grown. The simulation mimics the experimental errors which can affect the results and hence their interpretation. The value of this simulation is that it permits the student to work at his own pace and to develop an understanding of techniques for studying microbial genetics.     

On extending the usefulness of projectors in teaching biology

This paper reports the design of an interactive computer program in microbial genetics. The computer program is divided into three stages, background information, simulation, and data treatment. The results obtained from the simulation allow four genes to be sequenced along the bacterial chromosome. The simulation mimics experimental errors, the production of exconjugants and backmutants. The data can be analysed using options contained in the program. The simulation is of particular educational value because it allows the student to work at his own pace and to develop his ability to analyse data in relation to a complex conceptual model.     

Sequence-level population simulations over large genomic regions

Simulation is an invaluable tool for investigating the effects of various population genetics modeling assumptions on resulting patterns of genetic diversity, and for assessing the performance of statistical techniques, for example those designed to detect and measure the genomic effects of selection. It is also used to investigate the effectiveness of various design options for genetic association studies. Backward-in-time simulation methods are computationally efficient and have become widely used since their introduction in the 1980s. The forward-in-time approach has substantial advantages in terms of accuracy and modeling flexibility, but at greater computational cost. We have developed flexible and efficient simulation software and a rescaling technique to aid computational efficiency that together allow the simulation of sequence-level data over large genomic regions in entire diploid populations under various scenarios for demography, mutation, selection, and recombination, the latter including hotspots and gene conversion. Our forward evolution of genomic regions (FREGENE) software is freely available from www.ebi.ac.uk/projects/BARGEN together with an ancillary program to generate phenotype labels, either binary or quantitative. In this article we discuss limitations of coalescent-based simulation, introduce the rescaling technique that makes large-scale forward-in-time simulation feasible, and demonstrate the utility of various features of FREGENE, many not previously available.     

WinPop 2.5: software for representing population genetics phenomena

The curriculum for genetics courses is shifting from a classical to a more molecular genetics focus, increasing the importance of subjects such as population genetics. Population genetics is a computational and statistical field that requires a good understanding of the nature of stochastic events. It is a difficult field for biology students with a limited mathematical background and there is a need for visualisation tools to facilitate understanding by the use of practical examples. WinPop provides students and researchers with a visual tool to allow the simulation and representation of population genetics phenomena. WinPop is a user-friendly software meant for use in population genetics courses and basic research. WinPop 2.5 contains six different modules that represent and simulate population genetics models. Genotype and allele frequencies are calculated under the different models: panmixia, genetic drift, assortative matings, selection, gene flow and mutation. The program's interface presents information in Cartesian graphics and isosceles triangular coordinate systems, allowing the user to save graphical and textual data output from the simulations. WinPop is developed in Visual Basic 6.0 and uses Windows 95 and higher. WinPop 2.5 can be downloaded from http://www.genedrift.org/winpop.php.     

图位克隆技术新型遗传学实验教学项目的设计与实践

染色体重组与连锁互换是遗传学教学的重点和难点。为使学生更好地理解此方面知识, 我们课题组前期利用图位克隆(map-based cloning)技术, 克隆了1个调控水稻(Oryza sativa)类病变表型的基因SPL5, 并基于此设计了一个新的综合型遗传学实验, 即利用DNA分子标记对基因进行定位。实验中学生利用水稻spl5突变体与野生型杂交获得的F₂代定位群体和多态性分子标记, 对spl5突变进行染色体连锁分析、初步定位和遗传作图。该教学实验不仅可有效促进学生对遗传学三大定律的理解, 而且对其开阔视野、提高解决问题和团队协作的能力也有促进作用。     

Principles and Perspectives for Educational Biology

Computer-aided learning (CAL) techniques are now used at many levels of biological education. Many of these CAL programs are written by teachers because suitable material is unavailable. However, the amount of time required for the design and coding of a reliable CAL program can deter many teachers. Any CAL program can be split into two components: the ‘non-educational’ part, for example, program control structures, input–output routines; and the educational material. The ‘non-educational’ component can be organized into a program shell which can then be used with a wide range of biological topics. A program shell, for use on the BBC microcomputer, is described with an example of an application. The example is ‘LINKAGE’, a genetics teaching program.     

图位克隆技术新型遗传学实验教学项目的设计与实践

染色体重组与连锁互换是遗传学教学的重点和难点。为使学生更好地理解此方面知识, 我们课题组前期利用图位克隆(map-based cloning)技术, 克隆了1个调控水稻(Oryza sativa)类病变表型的基因SPL5, 并基于此设计了一个新的综合型遗传学实验, 即利用DNA分子标记对基因进行定位。实验中学生利用水稻spl5突变体与野生型杂交获得的F₂代定位群体和多态性分子标记, 对spl5突变进行染色体连锁分析、初步定位和遗传作图。该教学实验不仅可有效促进学生对遗传学三大定律的理解, 而且对其开阔视野、提高解决问题和团队协作的能力也有促进作用。     

Host genotype controls ecological change in the leaf fungal microbiome

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

Leaf fungal microbiomes can strongly influence host plant success. Monitoring the leaf fungal microbiome of switchgrass over time shows microbial ecological succession, and reveals the host plant genes that influence community-wide changes.     

Use of computer simulations in microbial and molecular genetics

The development of five computer programs in microbial and molecular genetics is described. Four of these are simulations of genetic and physical mapping experiments, designed to give students experience in generating and analysing meaningful data, and to help in the consolidation of the concepts underlying the simulation. They should be used after the experiment proper has been performed, rather than as a substitute for it. The fifth is an interactive learning program on the genetic coding mechanism.     

The use of scenario-based-learning interactive software to create custom virtual laboratory scenarios for teaching genetics

Mutagenesis screens and analysis of mutant phenotypes are one of the most powerful approaches for the study of genetics. Yet genetics students often have difficulty understanding the experimental procedures and breeding crosses required in mutagenesis screens and linking mutant phenotypes to molecular defects. Performing these experiments themselves often aids students in understanding the methodology. However, there are limitations to performing genetics experiments in a student laboratory. For example, the generation time of laboratory model organisms is considerable, and a laboratory exercise that involves many rounds of breeding or analysis of many mutants is not often feasible. Additionally, the cost of running a laboratory practical, along with safety considerations for particular reagents or protocols, often dictates the experiments that students can perform. To provide an alternative to a traditional laboratory module, we have used Scenario-Based-Learning Interactive (SBLi) software to develop a virtual laboratory to support a second year undergraduate course entitled "Genetic Analysis." This resource allows students to proceed through the steps of a genetics experiment, without the time, cost, or safety constraints of a traditional laboratory exercise.     

Human minisatellite markers: D1S80 locus in population studies

Minisatellite loci are a part of the human genome, playing an important role in various genomic and population studies. The review describes characteristics of this group of hypervariable tandem repeats and models that explain the reasons for their high diversity. The use of this kind of markers in population genetics studies is demonstrated by an example of the D1S80 minisatellite locus. Particular emphasis was placed on the D1S80 diversity in different populations of Eastern Europe. The capabilities of D1S80 for population analyses that allow the resolution of both main human groups and small differences to be resolved in population structures.     

孟德尔豌豆基因克隆的研究进展及其在遗传学教学中的应用

150多年前, 孟德尔进行了豌豆7对相对性状的杂交试验, 发现了遗传学的两个基本规律。1900年, 孟德尔定律被重新发现以后, 人们从生理生化、细胞和分子水平等不同层次上对豌豆的这7个性状进行了深入研究。近年, 随着分子生物学技术的发展, 已有种子形状(R)、茎的长度(Le)、子叶颜色(I)和花的颜色(A)等4个性状的基因被克隆; 未成熟豆荚的颜色(Gp)、花的着生位置(Fa)和豆荚形状(V)的基因已被定位在各自的连锁群上。4个孟德尔基因的鉴定和克隆加深了人们对基因概念的理解：如基因功能的多样性、在分子水平上基因变异原因的多样性、显性和隐性的分子实质等。在遗传学教学中, 把孟德尔基因克隆和研究的最新进展介绍给学生, 在分子水平上诠释经典遗传规律, 有助于提高学生的学习兴趣, 帮助学生全面把握从形式遗传学到分子遗传学的内容和遗传学的发展方向。     

Rethinking Hardy-Weinberg and genetic drift in undergraduate biology

Population genetics is often taught in introductory biology classes, starting with the Hardy-Weinberg principle (HWP) and genetic drift. Here I argue that teaching these two topics first aligns neither with current expert knowledge, nor with good pedagogy. Student difficulties with mathematics in general, and probability in particular, make population genetics difficult to teach and learn. I recommend an alternative, historically inspired ordering of population genetics topics, based on progressively increasing mathematical difficulty. This progression can facilitate just-in-time math instruction. This alternative ordering includes, but does not privilege, the HWP and genetic drift. Stochastic events whose consequences are felt within a single generation, and the deterministic accumulation of the effects of selection across multiple generations, are both taught before tackling the stochastic accumulation of the effects of accidents of sampling.     

Invasion genetics of the Mediterranean fruit fly: variation in multiple nuclear introns

Biological invasions generally start from low initial population sizes, leading to reduced genetic variation in nuclear and especially mitochondrial DNA. Consequently, genetic approaches for the study of invasion history and population structure are difficult. An extreme example is the Mediterranean fruit fly, Ceratitis capitata (Medfly), for which successive invasions during this century have resulted in a loss of 60% of ancestral genetic variation in isozymes and 75% of variation in mitochondrial DNA. Using Medflies as an example, we present a new approach to invasion genetics that measures DNA sequence variation within introns from multiple nuclear loci. These loci are so variable that even relatively recently founded Medfly populations within California and Hawaii retain ample genetic diversity. Invading populations have only lost 35% of the ancestral genetic variation. Intron variation will allow high-resolution genetic characterization of invading populations in both natural and managed systems, although non-equilibrium methods of analysis may be necessary if the genetic diversity represents sorting ancestral polymorphism.     

Simulation modelling in landscape genetics: on the need to go further

With the emergence of landscape genetics, the basic assumptions and predictions of classical population genetic theories are being re‐evaluated to account for more complex spatial and temporal dynamics. Within the last decade, there has been an exponential increase in such landscape genetic studies ( Holderegger & Wagner 2006 ; Storfer et al. 2010 ), and both methodology and underlying concepts of the field are under rapid and constant development. A number of major innovations and a high level of originality are required to fully merge existing population genetic theory with landscape ecology and to develop novel statistical approaches for measuring and predicting genetic patterns. The importance of simulation studies for this specific research has been emphasized in a number of recent articles (e.g., Balkenhol et al. 2009a ; Epperson et al. 2010 ). Indeed, many of the major questions in landscape genetics require the development and application of sophisticated simulation tools to explore gene flow, genetic drift, mutation and natural selection in landscapes with a wide range of spatial and temporal complexities. In this issue, Jaquiéry et al. (2011) provide an excellent example of such a simulation study for landscape genetics. Using a metapopulation simulation design and a novel ‘scale of phenomena’ approach, Jaquiéry et al. (2011) demonstrate the utility and limitations of genetic distances for inferring landscape effects on effective dispersal.     

Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source–sink metapopulation structure,founder events and population bottlenecks

Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation–drift equilibrium. Dominant downstream migration over both short‐ and long‐time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source–sink metapopulation, with the tributary furthest downstream representing a ‘super sink’, receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.     

EXPERFARM: a new package in BASIC for teaching genetics

We have developed two interactive computer programs (togetherreferred to as EXPERFARM), which enable simulation of a greatvariety of genetic situations. This package is designed forteaching basic genetics as well as quantitative and populationgenetics. The main advantages of EXPERFARM are its great versatility,as different situations can be simulated by simply changingthe inputs, and the small amount of training necessary for theusers. Received on August 15, 1985; accepted on February 3, 1986     

MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory

Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion.     

Complete characterization of killer Ig-like receptor (KIR) haplotypes in Mauritian cynomolgus macaques: novel insights into nonhuman primate KIR gene content and organization

Killer Ig-like receptors (KIRs) are implicated in protection from multiple pathogens including HIV, human papillomavirus, and malaria. Nonhuman primates such as rhesus and cynomolgus macaques are important models for the study of human pathogens; however, KIR genetics in nonhuman primates are poorly defined. Understanding KIR allelic diversity and genomic organization are essential prerequisites to evaluate NK cell responses in macaques. In this study, we present a complete characterization of KIRs in Mauritian cynomolgus macaques, a geographically isolated population. In this study we demonstrate that only eight KIR haplotypes are present in the entire population and characterize the gene content of each. Using the simplified genetics of this population, we construct a model for macaque KIR genomic organization, defining four putative KIR3DL loci, one KIR3DH, two KIR2DL, and one KIR1D. We further demonstrate that loci defined in Mauritian cynomolgus macaques can be applied to rhesus macaques. The findings from this study fundamentally advance our understanding of KIR genetics in nonhuman primates and establish a foundation from which to study KIR signaling in disease pathogenesis.     

Interactive effects of productivity and predation on zooplankton diversity

Recent studies suggest the necessity of understanding the interactive effects of predation and productivity on species coexistence and prey diversity. Models predict that coexistence of prey species with different competitive abilities can be achieved if inferior resource competitors are less susceptible to predation and if productivity and/or predation pressure are at intermediate levels. Hence, predator effects on prey diversity are predicted to be highly context dependent: enhancing diversity from low to intermediate levels of productivity or predation and reducing diversity of prey at high levels of productivity or predation. While several studies have examined the interactive effects of herbivory and productivity on primary producer diversity, experimental studies of such effects in predator‐prey systems are rare. We tested these predictions using an aquatic field mesocosm experiment in which initial density of the zooplankton predator Notonecta undulata and productivity were manipulated to test their interactive effects on diversity of seven zooplankton, cladoceran species that were common in surrounding ponds. Two productivity levels were imposed via phosphorus enrichment at levels comparable to low and intermediate levels found within neighboring natural ponds. We used open systems to allow for natural dispersal and behaviorally‐mediated numerical responses by the flight‐capable predator. Effects of predators on zooplankton diversity depended on productivity level. At low and high productivity, prey species richness declined while at high productivity it showed a unimodal relationship with increasing the predator density. Effects of treatments were weaker when using Pielou's evenness index or the inverse Simpson index as measures of prey diversity. Our findings are generally consistent with model predictions in which predators can facilitate prey coexistence and diversity at intermediate levels of productivity and predation intensity. Our work also shows that the functional form of the relationship between prey diversity and predation intensity can be complex and highly dependent on environmental context.