The Length of a Generation

After comparing a number of definitions of the length of a generation, two new ones are proposed. One is the mean age of mothers having new born children in the current population, the other is the period of decay of departures from the stable age distribution. Numerical examples are given.     

Measurement of Lifespan in Drosophila melanogaster

Aging is a phenomenon that results in steady physiological deterioration in nearly all organisms in which it has been examined, leading to reduced physical performance and increased risk of disease. Individual aging is manifest at the population level as an increase in age-dependent mortality, which is often measured in the laboratory by observing lifespan in large cohorts of age-matched individuals. Experiments that seek to quantify the extent to which genetic or environmental manipulations impact lifespan in simple model organisms have been remarkably successful for understanding the aspects of aging that are conserved across taxa and for inspiring new strategies for extending lifespan and preventing age-associated disease in mammals.The vinegar fly, Drosophila melanogaster, is an attractive model organism for studying the mechanisms of aging due to its relatively short lifespan, convenient husbandry, and facile genetics. However, demographic measures of aging, including age-specific survival and mortality, are extraordinarily susceptible to even minor variations in experimental design and environment, and the maintenance of strict laboratory practices for the duration of aging experiments is required. These considerations, together with the need to practice careful control of genetic background, are essential for generating robust measurements. Indeed, there are many notable controversies surrounding inference from longevity experiments in yeast, worms, flies and mice that have been traced to environmental or genetic artifacts^1-4. In this protocol, we describe a set of procedures that have been optimized over many years of measuring longevity in Drosophila using laboratory vials. We also describe the use of the dLife software, which was developed by our laboratory and is available for download (http://sitemaker.umich.edu/pletcherlab/software). dLife accelerates throughput and promotes good practices by incorporating optimal experimental design, simplifying fly handling and data collection, and standardizing data analysis. We will also discuss the many potential pitfalls in the design, collection, and interpretation of lifespan data, and we provide steps to avoid these dangers.     

Population genomics of transposable elements in Drosophila melanogaster

Transposable elements (TEs) are the primary contributors to the genome bulk in many organisms and are major players in genome evolution. A clear and thorough understanding of the population dynamics of TEs is therefore essential for full comprehension of the eukaryotic genome evolution and function. Although TEs in Drosophila melanogaster have received much attention, population dynamics of most TE families in this species remains entirely unexplored. It is not clear whether the same population processes can account for the population behaviors of all TEs in Drosophila or whether, as has been suggested previously, different orders behave according to very different rules. In this work, we analyzed population frequencies for a large number of individual TEs (755 TEs) in five North American and one sub-Saharan African D. melanogaster populations (75 strains in total). These TEs have been annotated in the reference D. melanogaster euchromatic genome and have been sampled from all three major orders (non-LTR, LTR, and TIR) and from all families with more than 20 TE copies (55 families in total). We find strong evidence that TEs in Drosophila across all orders and families are subject to purifying selection at the level of ectopic recombination. We showed that strength of this selection varies predictably with recombination rate, length of individual TEs, and copy number and length of other TEs in the same family. Importantly, these rules do not appear to vary across orders. Finally, we built a statistical model that considered only individual TE-level (such as the TE length) and family-level properties (such as the copy number) and were able to explain more than 40% of the variation in TE frequencies in D. melanogaster.     

Pseudoautosomal Region 1 Length Polymorphism in the Human Population

The human sex chromosomes differ in sequence, except for the pseudoautosomal regions (PAR) at the terminus of the short and the long arms, denoted as PAR1 and PAR2. The boundary between PAR1 and the unique X and Y sequences was established during the divergence of the great apes. During a copy number variation screen, we noted a paternally inherited chromosome X duplication in 15 independent families. Subsequent genomic analysis demonstrated that an insertional translocation of X chromosomal sequence into theMa Y chromosome generates an extended PAR. The insertion is generated by non-allelic homologous recombination between a 548 bp LTR6B repeat within the Y chromosome PAR1 and a second LTR6B repeat located 105 kb from the PAR boundary on the X chromosome. The identification of the reciprocal deletion on the X chromosome in one family and the occurrence of the variant in different chromosome Y haplogroups demonstrate this is a recurrent genomic rearrangement in the human population. This finding represents a novel mechanism shaping sex chromosomal evolution.     

A Method For Measuring the Generation Time and Length of Dna Synthesizing Phase of Clonogenic Cells In A Heterogenous Population

Information on the cell cycle of progenitor cells in haemopoietic tissue is useful for understanding population control under physiological and abnormal conditions. Unfortunately, methods that have been developed for measuring cell cycle parameters are applicable only to cells of homogenous populations and not to morphologically non-recognizable progenitor cells such as colony forming units (CFU) that are present at low frequency in a heterogenous population. to circumvent this difficulty, a method was developed to measure CFU cell cycle parameters based on specific killing of cells in S phase by [³H]thymidine ([³H]TdR). This was done by estimating the number of CFU killed following exposure of the cell suspension to [³H]TdR for various time periods. Since cycling CFU are continuously entering S phase, a linear curve relating the percentage CFU-kill to the length of exposure of the cells to [³H]TdR in culture can be obtained. the slope of the curve (percentage kill/hr) indicates the rate that CFU enter the S phase and travel through the cell cycle. the inverse of this value will then represent a time period for CFU to move through a complete cell cycle (generation time). the length of S phase can then be obtained by multiplying generation time by the fraction of cells in S phase at time zero. This method has been used to measure generation time and length of S phase of three kinds of haemopoietic progenitor cells: mouse granulocyte-macrophage CFU, human T lymphocyte CFU and CFU from regenerating mouse spleens. This method should be applicable to any normal or neoplastic clonogenic cell populations and the latter could be either of haematological or of solid tumour origin.     

黄瓜RIL群体瓜长和把长的QTL定位分析

以黄瓜野生变种‘PI183967’(Cucumis sativus L.hardwickii)和新泰密刺选系‘931’为亲本,通过单粒传法获得包含160个株系的F9代重组自交系群体(RIL)。结合分子遗传图谱和不同年份(2012年春、秋季和2013年春、秋季)的表型调查数据,利用MapQTL4.0软件进行黄瓜瓜长和把长的QTL定位。结果显示:(1)共检测到8个与瓜长和把长相关的QTLs,分布在染色体3、4、5、6、7上,LOD值在2.78~10.24之间,可解释7.4%~32.7%的表型变异率,贡献率≥10.0%的QTL位点4个,占QTLs总数的1/2,在春秋两季重复检测出的QTL位点有4个。(2)检测到4个与瓜长相关的QTLs位点Fl3.1、Fl4.1、Fl5.1、Fl6.1,4个与把长相关的QTLs位点Fsl3.1、Fsl3.2、Fsl5.1、Fsl6.1。(3)Fl6.1和Fsl6.1在2012、2013年春秋季中均可检测到,位于第6号染色体的109.2cM处,标记SSR17591~C80之间;Fl6.1在4次中的贡献率在13.8%~32.7%之间,Fsl6.1在4次中贡献率为12.1%~24.1%;(4)Fl3.1和Fsl3.2位于第6号染色体标记SSR16152~SSR07706之间,其中Fl3.1在2012年秋季和2013年春秋两季中均可检测到,贡献率总共为25.1%,Fsl3.2仅在2012年秋季中检测到,解释8.8%的表型变异率。研究表明,第6号染色体上标记SSR17591~C80和第3号染色体上的SSR16152~SSR07706等2个区域聚集了控制瓜长和把长的主效QTL位点,这2个区域应作为今后研究的重点。     

定量荧光原位杂交测定端粒长度

目的:应用定量荧光原位杂交(Q-FISH)方法测定端粒长度。方法:选取4种端粒长度均一的标准细胞株采用Q-FISH的方法做出荧光亮度与端粒长度的标准曲线,从而得出实验细胞株的端粒长度,与DNA印迹法测定末端限制性片段(TRF)长度进行二者之间的相关性分析。结果:检测荧光强度的最佳线性曝光时间为400ms,相对于DNA印迹法,定量荧光原位杂交(Q-FISH)法所需标本量少,实验周期短,端粒长度结果与Southern杂交法具有很好的相关性。结论:采用定量荧光原位杂交方法测端粒长度具有重复性好、精确可靠的特点,适用于对珍贵标本的端粒改变进行分析。     

Population and behaviour genetics of Drosophila ananassae

Drosophila ananassae is a cosmopolitan and domestic species. It occupies a nuique status among the Drosophila species due to certain peculiarities in its genetic behaviour. The most unusual feature of this species is spontaneous male recombination in appreciable frequency. The present review summarises the work done on population and behaviour genetics of D. ananassae from India. Population dynamics of three cosmopolitan inversions has been studied in Indian population of D. ananassae and it is evident from the results that there is a considerable degree of genetic divergence at the level of inversion polymorphism. In general, the populations from south India show more differentiation than those from the north. These three cosmopolitan inversions, which are coextensive with the species, exhibit heterosis. Interracial hybridization does not lead to beaakdown of heterosis, which suggests that evidence for coadaptation is lacking in geographic populations of D. ananassae. Heterosis appears to be simple luxuriance rather than populational heterosis (coadaptation). Unlinked inversions occur in random associations, indicating no interchromosomal interactions. However, two inversions of the third chromosome often show strong linkage disequilibrium in laboratory populations, which is due to epistatic gene interaction and suppression of crossing-over. Genetic variations for certain allozyme polymorphism and sternoleural bristle phenotypes in Indian populations of D. ananassae have also been observed.A number of investigations have also been carried out on certain aspects of behaviour genetics of Indian D. ananassae. There is evidence for sexual isolation within D. ananassae. Significant variations in mating propensity of several isofemale strains, inversion karyotypes, the diminishing effects of certain mutations on sexual activity of males and positive response to selection for high and low mating propensity provide evidence for genetic control of sexual behaviour in D. ananassae. Males contribute more to variation and thus are more subject to intra-sexual selection than females. Evidence for rare male mating advantage has also been presented. Geographic strains of D. ananassae show variation with respect to oviposition site preference. The results of studies on pupation site preference, which is an important component of larval behaviour, suggest that larval pupation behaviour in D. ananassae is under polygenic control with a substantial amount of additive genetic variation.     

Effective Population Sizes with Multiple Paternity

While the concept of effective population size is of obvious applicability to many questions in population genetics and conservation biology, its utility has suffered due to a lack of agreement among its various formulations. Often, mathematical formulations for effective sizes apply restrictive assumptions that limit their applicability. Herein, expressions for effective sizes of populations that account for mating tactics, biases in sex ratios, and differential dispersal rates (among other parameters) are developed. Of primary interest is the influence of multiple paternity on the maintenance of genetic variation in a population. In addition to the standard inbreeding and variance effective sizes, intragroup (coancestral) and intergroup effective sizes also are developed. Expressions for effective sizes are developed for the beginning of nonrandom gene exchanges (initial effective sizes), the transition of gene correlations (instantaneous effective sizes), and the steady-state (asymptotic effective size). Results indicate that systems of mating that incorporate more than one male mate per female increase all effective sizes above those expected from polygyny and monogamy. Instantaneous and asymptotic sizes can be expressed relative to the fixation indices. The parameters presented herein can be utilized in models of effective sizes for the study of evolutionary biology and conservation genetics.     

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.     

The Effective Size of a Subdivided Population

This paper derives the long-term effective size, N(e), for a general model of population subdivision, allowing for differential deme fitness, variable emigration and immigration rates, extinction, colonization, and correlations across generations in these processes. We show that various long-term measures of N(e) are equivalent. The effective size of a metapopulation can be expressed in a variety of ways. At a demographic equilibrium, N(e) can be derived from the demography by combining information about the ultimate contribution of each deme to the future genetic make-up of the population and Wright's F(ST)'s. The effective size is given by N(e) = 1/(1 + var ( &))<(1 - f(STi))/N(i)n>, where n is the number of demes, &(i) is the eventual contribution of individuals in deme i to the whole population (scaled such that σ(i) &(i) = n), and < > denotes an average weighted by &(i)(2). This formula is applied to a catastrophic extinction model (where sites are either empty or at carrying capacity) and to a metapopulation model with explicit dynamics, where extinction is caused by demographic stochasticity and by chaos. Contrary to the expectation from the standard island model, the usual effect of population subdivision is to decrease the effective size relative to a panmictic population living on the same resource.     

The Inbreeding Effective Population Number in Dioecious Populations

The inbreeding effective population number in a dioecious population with discrete, nonoverlapping generations is investigated for both autosomal and X-linked loci. The recursion relations for the probabilities of genic identity and the effective population numbers are analyzed and compared in two cases: (i) the offspring identified by sex in the calculation of the probability of common parentage and (ii) the offspring not so identified. Case i gives the correct evolution of the probabilities of identity, but case ii has been more widely studied and applied. A general symmetric framework that reduces the number of parameters is developed and used to examine a wide variety of models of panmixia and monogamy. Cases i and ii agree in many, but not all, models.     

Measurement of Subcellular Force Generation in Neurons

Forces are important for neuronal outgrowth during the initial wiring of the nervous system and after trauma, yet subcellular force generation over the microtubule-rich region at the rear of the growth cone and along the axon has never, to our knowledge, been directly measured. Because previous studies have indicated microtubule polymerization and the microtubule-associated proteins Kinesin-1 and dynein all generate forces that push microtubules forward, a major question is whether the net forces in these regions are contractile or expansive. A challenge in addressing this is that measuring local subcellular force generation is difficult. Here we develop an analytical mathematical model that describes the relationship between unequal subcellular forces arranged in series within the neuron and the net overall tension measured externally. Using force-calibrated towing needles to measure and apply forces, in combination with docked mitochondria to monitor subcellular strain, we then directly measure force generation over the rear of the growth cone and along the axon of chick sensory neurons. We find the rear of the growth cone generates 2.0 nN of contractile force, the axon generates 0.6 nN of contractile force, and that the net overall tension generated by the neuron is 1.3 nN. This work suggests that the forward bulk flow of the cytoskeletal framework that occurs during axonal elongation and growth-cone pauses arises because strong contractile forces in the rear of the growth cone pull material forward.     

Measurement of Metabolic Rate in Drosophila using Respirometry

Metabolic disorders are a frequent problem affecting human health. Therefore, understanding the mechanisms that regulate metabolism is a crucial scientific task. Many disease causing genes in humans have a fly homologue, making Drosophila a good model to study signaling pathways involved in the development of different disorders. Additionally, the tractability of Drosophila simplifies genetic screens to aid in identifying novel therapeutic targets that may regulate metabolism. In order to perform such a screen a simple and fast method to identify changes in the metabolic state of flies is necessary. In general, carbon dioxide production is a good indicator of substrate oxidation and energy expenditure providing information about metabolic state. In this protocol we introduce a simple method to measure CO₂ output from flies. This technique can potentially aid in the identification of genetic perturbations affecting metabolic rate.