Righteous modeling: the competence of classical population genetics

In a recent article, ??Wayward Modeling: Population Genetics and Natural Selection,?? Bruce Glymour claims that population genetics is burdened by serious predictive and explanatory inadequacies and that the theory itself is to blame. Because Glymour overlooks a variety of formal modeling techniques in population genetics, his arguments do not quite undermine a major scientific theory. However, his arguments are extremely valuable as they provide definitive proof that those who would deploy classical population genetics over natural systems must do so with careful attention to interactions between individual population members and environmental causes. Glymour??s arguments have deep implications for causation in classical population genetics.     

Age determination in the Red fox (Vulpes vulpes)–an evaluation of technique efficiency as applied to a sample of suburban foxes

A review of age determination techniques that have been applied to the family Canidae is presented. It is shown that the pattern of growth and development of the various species is very similar, the rate of development being greater in the smaller, shorter-lived species, and vice versa.
The occurrence of annuli in the hard tissues of London foxes is demonstrated; these annuli can be used reliably for age determination, despite suggestions that temperate zone animals from weakly continental climates have indistinct annuli. The objective ages determined by cementum annuli are then used to investigate the value of less time-consuming age determination techniques, particularly in the separation of the young-of-the-year from adults. The results obtained from different studies vary, and these differences are discussed. It is suggested that the speed of development varies slightly in different Red fox populations, and so caution must be exercised before data from one population areapplied to another population.     

Detection of B chromosomes in interphase hemolymph nuclei from living specimens of the grasshopper Eyprepocnemis plorans

The two most important evolutionary properties of B chromosomes are their transmission rate (which suggests their selfishness when significantly higher than 0.5) and their net effects on carrier fitness (usually negative for parasitic Bs). The study of transmission rate unavoidably requires the analysis of many controlled crosses in order to accurately measure population average transmission rate. Therefore, getting a marker closely associated to B presence is of crucial importance to alleviate the load of performing many useless crosses between lacking B individuals. After investigating several cytogenetic techniques on several tissues that may be sampled without drastically damaging live specimens of the grasshopper Eyprepocnemis plorans, we report here the excellent results provided by the CMA3 fluorescence and C-banding techniques applied to hemocyte nuclei. These cells may be easily obtained from both males and females and provide information on B presence even during the interphase stage. The two cytogenetic techniques take advantage of the heterochromatic nature of the B chromosomes, so that Bs made predominantly of ribosomal DNA are revealed by CMA3 as bright bodies in the interphase hemocytes, and Bs mostly made of satellite DNA are visualized by C-banding as intensely stained bodies in these cells.     

Estimating quantitative genetic parameters using sibships reconstructed from marker data

Previous techniques for estimating quantitative genetic parameters, such as heritability in populations where exact relationships are unknown but are instead inferred from marker genotypes, have used data from individuals on a pairwise level only. At this level, families are weighted according to the number of pairs within which each family appears, hence by size rather than information content, and information from multiple relationships is lost. Estimates of parameters are therefore not the most efficient achievable. Here, Markov chain Monte Carlo techniques have been used to partition the population into complete sibships, including, if known, prior knowledge of the distribution of family sizes. These pedigrees have then been used with restricted maximum likelihood under an animal model to estimate quantitative genetic parameters. Simulations to compare the properties of parameter estimates with those of existing techniques indicate that the use of sibship reconstruction is superior to earlier methods, having lower mean square errors and showing nonsignificant downward bias. In addition, sibship reconstruction allows the estimation of population allele frequencies that account for the relationships within the sample, so prior knowledge of allele frequencies need not be assumed. Extensions to these techniques allow reconstruction of half sibships when some or all of the maternal genotypes are known.     

The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change

Species are the unit of analysis in many global change and conservation biology studies; however, species are not uniform entities but are composed of different, sometimes locally adapted, populations differing in plasticity. We examined how intraspecific variation in thermal niches and phenotypic plasticity will affect species distributions in a warming climate. We first developed a conceptual model linking plasticity and niche breadth, providing five alternative intraspecific scenarios that are consistent with existing literature. Secondly, we used ecological niche‐modeling techniques to quantify the impact of each intraspecific scenario on the distribution of a virtual species across a geographically realistic setting. Finally, we performed an analogous modeling exercise using real data on the climatic niches of different tree provenances. We show that when population differentiation is accounted for and dispersal is restricted, forecasts of species range shifts under climate change are even more pessimistic than those using the conventional assumption of homogeneously high plasticity across a species' range. Suitable population‐level data are not available for most species so identifying general patterns of population differentiation could fill this gap. However, the literature review revealed contrasting patterns among species, urging greater levels of integration among empirical, modeling and theoretical research on intraspecific phenotypic variation.     

蜜蜂遗传多态性的影响因素及主要研究方法

蜜蜂遗传多态性与蜜蜂种质资源保存、优良品种繁育和科学引种等问题密切相关,具有重要的研究价值。文章综述蜜蜂遗传多态性的影响因素和研究方法,影响因素包括自然因素和人为因素,自然因素主要有环境因子和种群竞争等,人为因素主要有品种引进和农药毒害作用等;研究方法包括形态学检测和DNA分析检测等。通过比较各研究方法的优缺点,认为宜采用多种方法相结合的手段进行全方位、多角度地综合评价蜜蜂的遗传多态性。     

Modelling life history strategies with capture–recapture data: Evolutionary demography of the water skink Eulamprus tympanum

Matrix population models, elasticity analysis and loop analysis can potentially provide powerful techniques for the analysis of life histories. Data from a capture–recapture study on a population of southern highland water skinks (Eulamprus tympanum) were used to construct a matrix population model. Errors in elasticities were calculated by using the parametric bootstrap technique. Elasticity and loop analyses were then conducted to identify the life history stages most important to fitness. The same techniques were used to investigate the relative importance of fast versus slow growth, and rapid versus delayed reproduction. Mature water skinks were long‐lived, but there was high immature mortality. The most sensitive life history stage was the subadult stage. It is suggested that life history evolution in E. tympanum may be strongly affected by predation, particularly by birds. Because our population declined over the study, slow growth and delayed reproduction were the optimal life history strategies over this period. Although the techniques of evolutionary demography provide a powerful approach for the analysis of life histories, there are formidable logistical obstacles in gathering enough high‐quality data for robust estimates of the critical parameters.     

Validation of gum-line recession as a reliable technique to age tigers

Like other members of the Panthera genus, tigers are threatened throughout their range. Given their conservation status research focused on their population dynamics in the wild is needed, including population growth, lifespan, and breeding success, which requires reliable estimates of age. Current techniques to estimate age in tigers are either not reliable and/or difficult to apply in the field. Gum-line recession accurately estimates age for mountain lions, but has never been tested for tigers. The goal of this study was to determine whether gum-line recession of the upper canine teeth is a reliable indicator of age in tigers and if so, to define the equation that enables age estimation. We measured gum-line recession in 12 individuals of known ages and performed linear regression analysis to investigate the validity of this technique for tigers. We found a strong relationship between gum-line recession and age, where the model provided reliable age estimates for animals within 1-year age classes in 10 out of 12 tigers measured, providing increased accuracy over current methods.     

Freeze substitution of fungi for cytological analysis

The preparatory techniques of freeze substitution for electron microscopy are given in detail. Included is a simple, reliable method for the selection of individual freeze-substituted cells from flat embedments via light microscopy for subsequent electron microscope analysis. These mthods are intended for studying cells in monolayer cultures, tissues, suspensions of cells, or cell fractions and are widely applicable for cell biologists in any field. An historical background and review of the relevant literature is included so that the reader will be fully prepared to use of modify the techniques and to troubleshoot results as required. All materials that are needed are thoroughly discussed so that any laboratory can adopt freeze substitution as a routine procedure.     

Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history

Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species' geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.     

甘肃鼢鼠不同地理种群的形态变异分析

甘肃鼢鼠(Myospalax cansus)隶属于啮齿目(Rodentia)、鼹形鼠科(Spalacidae)、鼢鼠亚科(Myospalacinae)、鼢鼠属(Myospalax)(Norris et al.,2004),主要分布于我国西北地区的黄土高原,为陕西、甘肃、宁夏及青海东部地区农田和草原的主要害鼠之一,对林业幼苗也有一定的损伤,同时亦是水土保持的主要破坏因素之一(江廷安等,1996).作为地下掘土类食草动物,由于地下积水和空气不流通,甘肃鼢鼠经受着食物匮乏等的环境压力,很可能促使甘肃鼢鼠身体结构向有利于适应洞道系统的方向变化,导致种群分化.     

Why are some genetic diseases common?

Various processes (selection, mutation, migration and genetic dirft) are known to determine the frequency of genetic disease in human populations, but so far it has proved almost impossible to decide to what extent each is responsible for the presence of a particular genetic disease. The techniques of gene and haplotype analysis offer new hope in addressing this issue, and we review relevant studies of three haemoglobinopathies: sickle cell anaemia, and and thalassaemia. We show how for each disease it is possible to recognize a pattern of regionally specific mutations, found in association with one or a few haplotypes, that is best explained as the result of selection; other patterns are due to population migration and genetic drift. However, we caution that such conclusions can be drawn in special circumstances only. In the case of the haemoglobinopathies it is possible because a selective agent (malaria) was already suspected, and the investigations could be carried out in relatively genetically homogenous populations whose migratory histories are known. Moreover, some data reviewed here suggest that gene conversion and the haplotype composition of a population may affect the frequency of a mutation, making interpretation of gene frequencies difficult on the basis of standard population genetics theory. Hence attempts to use the same approaches with other genetic diseases are likely to be frustrated by a lack of suitably untrammelled populations and by difficulties accounting for poorly understood genetic processes. We conclude that although this combination of molecular and population genetics is successful when applied to the study of haemoglobinopathies, it may not be so easy to apply it to the study of other genetic diseases.     

MicroRNA expression profiling of single whole embryonic stem cells

MicroRNAs (miRNAs) are a class of 17-25 nt non-coding RNAs that have been shown to have critical functions in a wide variety of biological processes during development. Recently developed miRNA microarray techniques have helped to accelerate research on miRNAs. However, in some instances there is only a limited amount of material available for analysis, which requires more sensitive techniques that can preferably work on single cells. Here we demonstrate that it is possible to analyse miRNA in single cells by using a real-time PCR-based 220-plex miRNA expression profiling method. Development of this technique will greatly facilitate miRNA-related research on cells, such as the founder population of primordial germ cells where rapid and dynamic changes occur in a few cells, and for analysing heterogeneous population of cells. In these and similar cases, our method of single cell analysis is critical for elucidating the diverse roles of miRNAs.     

蛋白质组研究中的分析技术

蛋白质组分析技术已在生物科学各领域被广泛应用,蛋白质组的研究已成为目前国际上的前沿和研究热点。概述了蛋白质组研究中的常用分析技术,包括样品制备、双向凝胶电泳、凝胶图像分析、质谱鉴定及数据库检索等。直观地列出了蛋白质组研究的技术体系流程图。各种分析技术的连用和分析过程的自动化将是蛋白质组研究技术的发展方向。     

Abdominal aortic surgery: anesthetic implications.

The objectives of the review are to highlight the clinical characteristics of the patient population; to assess multivariate risk factor analysis and the invasive/non-invasive techniques available for risk factor identification and management in this high-risk surgical population; to assess the major hemodynamic, metabolic, and regional blood flow changes associated with aortic cross-clamping/unclamping procedures and techniques for their modification or attenuation; and to assess the influence of perioperative anesthetic techniques and management on patient outcome.     

Multiple group principal component analysis and population differentiation

This paper explores the requirements and advantages of multiple group principal component analysis (MGPCA) when it is used to investigate population differentiation. A distinction is drawn between equality of orientation of the within-group axes and equality of variance along these axes. Several examples of the use of MGPCA are discussed and it is shown that MGPCA per se does not require equality of variance along the axes although it may be a requirement of some of the techniques subsequently used to analyse the component scores. MGPCA is simple and direct, being based on the mathematically well defined eigenvector analysis of a symmetric positive definite (pooled within-group covariance) matrix and it can be thought of as a step in the computation of canonical variate analysis (CVA). It can be used with CVA (which is the most popular method of biometrically assessing population affinities) to assess the contribution of within-group components to among-group discrimination. It is also one of a range of appropriate techniques that can be used to define (and delete if required) within-group growth effects and is particularly suitable when CVA is being used to assess the population affinities. When used in this way it has the advantage of being more influenced by the groups with the greatest growth range.     

The genetic demography of a chimpanzee colony

Chimpanzees used for biomedical research must be bred in captivity because of restrictions on importation. Because they are large and expensive animals, population sizes at breeding facilities are limited. This implies that inbreeding at some level is inevitable and that genetic management techniques should be employed to minimize matings between related individuals. The purpose of this paper is to consider the genetic history of the chimpanzee colony at the Southwest Foundation for Biomedical Research (SFBR) and to suggest ways in which genetic variability may be affected by management schemes. A total of 339 chimpanzees resided at SFBR between January, 1980, and January, 1990. Although only one mating between related individuals has occurred so far, the average level of kinship in the colony and between potential breeders is increasing. Population structure techniques were employed to assess the mating patterns which have occurred and to explore the degree of change in the characteristics of potential mates. A “gene dropping” simulation method was used to predict expected levels of heterozygosity and strategies for maintaining variability by increasing the breeding portion of the population were evaluated using a simulation approach. © 1995 Wiley-Liss, Inc.     

Comparison of Parameters from Rhythmometric Models with Multiple Components on Hybrid Data

Population multiple components is a statistical tool useful for the analysis of time-dependent hybrid data. With a small number of parameters, it is possible to model and to predict the periodic behavior of a population. In this article, we propose two methods to compare among populations rhythmometric parameters obtained by multiple component analysis. The first is a parametric method based in the usual statistical techniques for comparison of mean vectors in multivariate normal populations. The method, through MANOVA analysis, allows comparison of the MESOR and amplitude-acrophase pair of each component among two or more populations. The second is a nonparametric method, based in bootstrap techniques, to compare parameters from two populations. This test allows one to compare the MESOR, the amplitude, and the acrophase of each fitted component, as well as the global amplitude, orthophase, and bathyphase estimated when all fitted components are harmonics of a fundamental period. The idea is to calculate a confidence interval for the difference of the parameters of interest. If this interval does not contain zero, it can be concluded that the parameters from the two models are different with high probability. An estimation of p-value for the corresponding test can also be calculated. Both methods are illustrated with an example, based on clinical data. The nonparametric test can also be applied to paired data, a special situation of great interest in practice. By the use of similar bootstrap techniques, we illustrate how to construct confidence intervals for any rhythmometric parameter estimated from population multiple components models, including the orthophase, bathyphase, and global amplitude. These tests for comparison of parameters among populations are a needed tool when modeling the nonsinusoidal rhythmic behavior of hybrid data by population multiple component analysis.