分子生态学重要概念——遗传距离及其测度的理论研究概况

综述了遗传距离的概念、背景,有关遗传距离的几种基本的突变模型以及和遗传距离有关的参量和几种常用统计量,指出在处理蛋白质数据、分子数据以及序列数据时,如何选择相应的统计量和可用的软件包,同时还着重指明了各种模型的假设前提,为处理实际的蛋白质或分子数据时选择合适的模型,和对数据的最终解释提供一些帮助。     

Limitations and problems in deriving risk estimates for low-level radiation exposure.

Some of the problems in determining the cancer risk of low-level radiation from studies of exposed groups are reviewed and applied to the study of Hanford workers by Mancuso, Stewart, and Kneale. Problems considered are statistical limitations, variation of cancer rates with geography and race, the "healthy worker effect," calendar year and age variation of cancer mortality, choosing from long lists, use of proportional mortality rates, cigarette smoking-cancer correlations, use of averages to represent data distributions, ignoring other data, and correlations between radiation exposure and other factors that may cause cancer. The current status of studies of the Hanford workers is reviewed.     

Intraspecies variation in BMR does not affect estimates of early hominin total daily energy expenditure

We conducted a meta-analysis of 45 studies reporting basal metabolic rate (BMR) data for Homo sapiens and Pan troglodytes to determine the effects of sex, age, and latitude (a proxy for climate, in humans only). BMR was normalized for body size using fat-free mass in humans and body mass in chimpanzees. We found no effect of sex in either species and no age effect in chimpanzees. In humans, juveniles differed significantly from adults (ANCOVA: P < 0.001), and senescent adults differed significantly from adults younger than 50 years (P < 0.001). Europeans differed significantly from tropical populations (P < 0.001). On the basis of these observations, we derived new equations describing the relationship between BMR and body size, and used them to predict total daily energy expenditure (TEE) in four early hominin species. Our predictions concur with previous TEE estimates (i.e. Leonard and Robertson: Am J Phys Anthropol 102 (1997) 265-281), and support the conclusion that TEE increased greatly with H. erectus. Our results show that intraspecific variation in BMR does not affect TEE estimates for interspecific comparisons. Comparisons of more closely related groups such as humans and Neandertals, however, may benefit from consideration of this variation.     

Comparison of Zinc Reduction with Platinum Reduction for Analysis of Deuterium‐Enriched Water Samples for the Doubly Labeled Water Technique

Objective: Isotope ratio mass spectrometry of hydrogen and oxygen is frequently used to determine total energy expenditure (TEE) using doubly labeled water. Conventionally, hydrogen isotope ratio is determined in hydrogen gas generated from water samples using zinc reduction. We compare this with a new automated platinum method to determine the ratios of hydrogen isotopes in deuterium‐enriched water samples. Research Methods and Procedures: The platinum method of sample preparation was compared with the zinc method in three ways: analytical variation in deuterium enrichment (within sample; n = 51), analytical variation in TEE estimates (within sample set; n = 10), and level of agreement of TEE estimates between both methods (n = 14). Results: For the zinc method, the standard deviation for multiple sets of triplicate ²H₂O sample analysis was ±4.36‰ and ±2.07‰ for platinum. The correlation between TEE estimates when sample sets were analyzed in duplicate was r = 0.89 for zinc and r = 0.83 for platinum. The intercept and slope of the regression line were significantly different from the line of identity for duplicate TEE estimates by zinc but were not different from the line of identity for platinum. After correction for the intra‐assay variation of each method, the correlation between zinc and platinum for TEE was 0.77, and the intercept, but not the slope, of the regression was significantly different from the line of identity. The mean difference between the zinc method and the platinum method was 56 kcal/day, and the 95% confidence interval was ?438 to 550 kcal/day. Discussion: These data suggest that the platinum method is at least as reliable as the zinc method as a sample preparation technique for isotope ratio mass spectrometry of deuterium‐enriched water samples. The platinum method is also less costly and less labor‐intensive than the zinc method.     

ALFRED: An allele frequency database for anthropology

The deluge of data from the human genome project (HGP) presents new opportunities for molecular anthropologists to study human variation through the promise of vast numbers of new polymorphisms (e.g., single nucleotide polymorphisms or SNPs). Collecting the resulting data into a single, easily accessible resource will be important to facilitate this research. We created a prototype Web-accessible database named ALFRED (ALelle FREquency Database, http://alfred.med.yale.edu/alfred/) to store and make publicly available allele frequency data on diverse polymorphic sites for many populations. In constructing this database, we considered many different concerns relating to the types of information needed for anthropology, population genetics, molecular genetics, and statistics, as well as issues of data integrity and ease of access to data. We also developed links to other Web-based databases as well as procedures for others to make links to the data in ALFRED. Here we present an overview of the issues considered and provisional solutions, as well as an example of data already available. It is our hope that this database will be useful for research and teaching in a wide range of fields, and that colleagues from various fields will contribute to making ALFRED an important resource for many studies as yet unforeseen.     

Seasonal and sex variation in physical activity levels among agro-pastoralists in Nepal

Considerable attention has been devoted to variation in levels of energy expenditure between and within populations; these are commonly evaluated following international guidelines for grading light, moderate, and heavy physical activity levels (PAL). This study presents activity profiles by season and sex for subsistence agro-pastoralists in Nepal, comparing data for a sample of 20 men observed four times across the year with previously published data on women. Total energy expenditure (TEE) was estimated from direct minute-by-minute observation (totaling 1,679 h for men, 3,601 h for women) and measures of the energy cost of single tasks (117 for men, 168 for women). PAL were calculated and graded as multiples of predicted basal metabolic rate (BMR). Despite an explicitly egalitarian organization of labor, men achieved higher PAL than women (P < .0001), although according to international gradings, both men and women assume moderately heavy PAL in the winter and very heavy PAL in the monsoon. PAL were 1.88 and 2.22 × BMR for men in respective seasons (P < .005; TEE, 11.8 MJ/d and 13.9 MJ/d) and 1.77 and 2.0 × BMR for women (TEE, 9.1 MJ/d and 10.5 MJ/d). High TEE values result from time-consuming work in subsistence tasks, most of which are of moderate energy cost. Results show that the international guideline (FAO/WHO/UNU [1985]) for grading levels of energy expenditure, which adopts discrepant sex-specific values to define thresholds for moderate or heavy PAL, can mask significant gender variation. Male/female ratios of PAL values are suggested instead for population-level comparisons. © 1996 Wiley-Liss, Inc.     

Circannual Variation in the Incidence of Uterine Cervix Cancer

The impact of uterine cervix cancer (UCC) can be greatly reduced by regular vaginal examination and other preventive measures. With this aim, UCC screening programs had been developed and applied for several years in Mexico and elsewhere. One point still to be considered in such preventive programs is the possible circannual pattern in the morbidity or mortality of UCC. With the aim of identifying a possible circannual pattern of variation in the incidence of UCC, we analyzed the monthly totals of positive detected cases of UCC in the state of Nuevo León (Mexico) between 1978 and 1987. For eliminating bias due to the seasonal variation in the number of preventive check-ups, data were first expressed in percentage of tests done in the same month. The least-squares fit of a 1 -year cosine curve to the data reveals a statistically significant circannual pattern (p = 0.013), with a maximum of relative incidence detected in February. Results indicate UCC incidence higher than the yearly average during the winter, with secondary peaks in August and November. This pattern of variation is similar if one considers separately for analysis the relative incidence of type III, IV, or V UCC (relating to cases suggesting, highly suggesting, or concluding a malignant alteration, respectively). For evaluating the cost-effectiveness of the UCC screening campaign providing these data, the monthly totals of screening check-ups done over the same period were also analyzed. Results reveal a statistically significant circannual rhythm (p > 0.001), with a maximum detected in June. This timing seems to be related to the incidence of most common diseases in Mexico, such as giardiasis and salmonellosis, but not to the UCC morbidity rates. Health educational and screening campaigns for prevention of UCC and other major conditions should be timed during the year according to morbidity and mortality statistics, for which a circannual pattern of variation is documented herein.     

Distribution of plant species in Israel in relation to spatial variation in rainfall

Abstract. Relations between the distribution of herbaceous and woody species from the flora of Israel and the variation (25–900 mm) in mean annual rainfall are described using a grid-based approach integrating multivariate techniques (cluster analysis and DCA-ordination) and GIS. The analysis was based on an extensive data base of vascular plant records in 10 km × 10 km grid cells representing the climatic zones of Israel. Cluster analysis revealed three geographically distinct clusters of grid cells which could be arranged along the main rainfall gradient in the study area. The main subdivision is between cells from the Mediterranean region and cells from the more arid region. The second subdivision separated cells from the arid region into two distinct groups which differed significantly in rainfall. Clustering of herbaceous and woody species was similar, but boundaries separating adjacent clusters based on woody species were consistently linked to more rainy areas. Cell scores on the first DCA-axis were significantly correlated with mean annual rainfall, but this relationship was not linear. Log-transformation of the rainfall data resulted in a higher correlation between the DCA-scores and rainfall, indicating that variation in rainfall had a stronger effect on species composition in relatively dry than in more mesic regions. Slopes of linear regression models relating cell scores on the first DCA-axis to mean annual rainfall, as well as the corresponding R²-values, were highest in the desert, intermediate in the dry Mediterranean, and lowest in the mesic Mediterranean territory. These results indicate that both the per-unit effect of rainfall on plant species composition and its relative importance as a determinant of compositional variation decreased from relatively dry to more mesic regions. The length of the first axis, as well as the slopes of regression models relating cell scores on the first DCA-axis to mean annual rainfall were consistently higher in the case of woody species which are characterized by a higher rate of compositional variation. Due to lack of comparable data, it is difficult to evaluate whether our results can be generalized to other regions. However, an analysis of data obtained from different parts of the world points to a considerable variability in the degree to which rainfall affects patterns of floristic variation. Our findings that compositional responses to rainfall may vary between different groups of species and may depend on the part of the rainfall range which is being considered may partially explain this inconsistency.     

Physical activity in aging: comparison among young, aged, and nonagenarian individuals.

Physical activity (PA) is known to decline with age; however, there is a paucity of data on activity in persons who are in their nineties and beyond. We used objective and reliable methods to measure PA in nonagenarians (>or=90 yr; n=98) and hypothesized that activity would be similar to that of aged (60-74 yr; n=58) subjects but less than in young (20-34 yr; n=53) volunteers. Total energy expenditure (TEE) was measured by doubly labeled water over 14 days and resting metabolic rate (RMR) by indirect calorimetry. Measures of PA included activity energy expenditure adjusted for body composition, TEE adjusted for RMR, physical activity level (PAL), and activity over 14 days by accelerometry expressed as average daily durations of light and moderate activity. RMR and TEE were lower with increasing age group (P<0.01); however, RMR was not different between aged and nonagenarian subjects after adjusting for fat-free mass, fat mass, and sex. Nonagenarians had a lower PAL and were more sedentary than the aged and young groups (P<0.01); however, the nonagenarians who were more active on a daily basis walked further during a timed test, indicating higher physical functionality. For all measures of activity, no differences were found between young and aged volunteers. PA was markedly lower in nonagenarians compared with young and aged adults. Interestingly, PA was similar between young volunteers and those who were in their 60s and 70s, likely due to the sedentary nature of our society, particularly in young adults.     

Measuring Free‐Living Energy Expenditure and Physical Activity with Triaxial Accelerometry

Objective: To investigate the ability of a newly developed triaxial accelerometer to predict total energy expenditure (EE) (TEE) and activity‐related EE (AEE) in free‐living conditions. Research Methods and Procedures: Subjects were 29 healthy subjects between the ages of 18 and 40. The Triaxial Accelerometer for Movement Registration (Tracmor) was worn for 15 consecutive days. Tracmor output was defined as activity counts per day (ACD) for the sum of all three axes or each axis separately (ACD‐X, ACD‐Y, ACD‐Z). TEE was measured with the doubly labeled water technique. Sleeping metabolic rate (SMR) was measured during an overnight stay in a respiration chamber. The physical activity level was calculated as TEE × SMR^?1, and AEE was calculated as [(0.9 × TEE) ? SMR]. Body composition was calculated from body weight, body volume, and total body water using Siri's three‐compartment model. Results: Age, height, body mass, and ACD explained 83% of the variation in TEE [standard error of estimate (SEE) = 1.00 MJ/d] and 81% of the variation in AEE (SEE = 0.70 MJ/d). The partial correlations for ACD were 0.73 (p < 0.001) and 0.79 (p < 0.001) with TEE and AEE, respectively. When data on SMR or body composition were used with ACD, the explained variation in TEE was 90% (SEE = 0.74 and 0.77 MJ/d, respectively). The increase in the explained variation using three axes instead of one axis (vertical) was 5% (p < 0.05). Discussion: The correlations between Tracmor output and EE measures are the highest reported so far. To measure daily life activities, the use of triaxial accelerometry seems beneficial to uniaxial.     

Relationship between male head size and mating opportunity in the harem-defence, polygynous tree weta

The most distinguishing feature of the tree weta genus Hemideina (Orthoptera: Anostostomatidae) is their cephalic weaponry, which is thought to be the result of sexual selection on males to aggressively defend groups of reproductive females. Mountain stone weta H. maori is a tree weta that shelters in cavities under flat rocks on rocky outcrops in the alpine region of the South Island. The main objectives of this study were to determine whether males with larger heads have access to greater numbers of females, and whether head size has an effect on male survival and longevity. Males with larger heads associated with larger groups of females than males with smaller heads. Male head size only accounted for 11% of the variation in mating opportunity when all rocks with females were considered, but explained 36% of the variation when only a few specific rocks that had large numbers of females were taken into account. The lower recapture rates of males in general and of smallheaded males in particular, further suggested that small males intermittently retreat to small cracks or cavities within tor columns, where there are unlikely to be large female groups. Thus, larger males had access to more females than smaller males. Moreover, larger males had no detectable disadvantage in terms of daily survival and longevity. This study provides strong evidence that larger male tree weta do associate with larger harems in the wild, however, questions relating to male weaponry size and mating success will become clearer only through paternity testing of weta under natural conditions.     

The role of group size and environmental factors on survival in a cooperatively breeding tropical passerine

1. Variation in survival, a major determinant of fitness, may be caused by individual or environmental characteristics. Furthermore, interactions between individuals may influence survival through the negative feedback effects of density dependence. Compared to species in temperate regions, we have little knowledge about population processes and variation in fitness in tropical bird species. 2. To investigate whether variation in survival could be explained by population size or climatic variables we used capture-recapture models in conjunction with a long-term data set from an island population of the territorial, cooperatively breeding Seychelles warbler (Acrocephalus sechellensis). The lack of migration out of the study population means that our results are not confounded by dispersal. 3. Annual survival was high, both for adults (84%) and juveniles (61%), and did not differ between the sexes. Although there was significant variation in survival between years, this variation could not be explained by overall population size or weather variables. 4. For territorial species, resource competition will work mainly on a local scale. The size of a territory and number of individuals living in it will therefore be a more appropriate measure of density than overall population density. Consequently, both an index of territory quality per individual (food availability) and local density, measured as group size, were included as individual covariates in our analyses. 5. Local density had a negative effect on survival; birds living in larger groups had lower survival probabilities than those living in small groups. Food availability did not affect survival. 6. Our study shows that, in a territorial species, although density-dependent effects might not be detectable at the population level they can be detected at the individual territory level - the scale at which individuals compete. These results will help to provide a better understanding of the small-scale processes involved in the dynamics of a population in general, but in particular in tropical species living in relatively stable environments.     

Differences in Diet Between Six Neighbouring Groups of Vervet Monkeys

The comparative approach provides a powerful tool to study evolutionary questions on both intra‐ and interspecific variation. It has been applied to a great variety of taxa, including primates. Primate studies differ from those on most other taxa in two ways: first, data from most study sites contain information about only one group. Second, primatologists have used the comparative approach also to identify local traditions, that is, behaviours that spread through social learning. Here, we evaluate the appropriateness of such data by comparing the diet composition of six neighbouring groups of vervet monkeys, Cercopithecus aethiops. We used scan samples to collect diet data, and abundance measures and phenology to assess the availability of the 14 most important tree species utilised during the study. We calculated indices of diet overlap, which were highly variable and could be remarkably low. Furthermore, we found significant differences between group diets with respect to the relative utilisation of 13 of the 14 tree species. For all 13 species, we found positive correlations between local abundance and appearance in the diet, consistent with the importance of local ecology for diet composition. Nevertheless, more detailed comparisons of pairs of groups often revealed significant mismatches between the relative importance of a tree species and its local abundance. In conclusion, local variation merits increased attention by primatologists. While our results are compatible with the possibility that traditions exist on a local (group) rather than population scale, alternative explanations have to be considered.     

From pixels to picograms: a beginners' guide to genome quantification by Feulgen image analysis densitometry.

The study of genome size variation is important from a number of practical and theoretical perspectives. For example, the long-standing "C-value enigma" relating to the more than 200,000-fold range in eukaryotic genome sizes is best studied from a broad comparative standpoint. Genome size data are also required in detailed analyses of genome structure and evolution. The choice of future genome sequencing projects will be dependent on knowledge regarding the sizes of genomes to be sequenced, and so on. To date, genome size data have been acquired primarily by Feulgen microdensitometry or flow cytometry. Each has several advantages but also important limitations. In this review, we provide a practical guide to the new technique of Feulgen image analysis densitometry. The review is designed for those interested in genome size measurements but not extensively experienced in histochemistry, densitometry, or microscopy. Therefore, relevant historical and technical background information is included. For easy reference, we provide recipes for required reagents, guidelines for cell staining, and a checklist of steps for successful image analysis. We hope that the accuracy, rapidity, and cost-effectiveness of Feulgen image analysis demonstrated here will stimulate further surveys of genome sizes in a variety of taxa.     

Energetics during reproduction: a doubly labeled water study of lactating baboons

Understanding the costs and regulation of reproduction in primates requires understanding the separate but linked effects of energy availability and total energy expenditure (TEE). We compared variation in TEE and energy intake (EI) between two periods, early lactation and after the resumption of sexual cycling, for eight females from two groups of normally reproducing colony-living baboons (Papio h. anubis). Total energy expenditure was assessed using the doubly labeled water method. TEE was correlated with maternal mass both during early lactation and after the resumption of cycling. TEE after the resumption of cycling was positively related to infant growth rates; mothers with rapidly growing infants had higher energy expenditure. TEE was however unrelated to maternal rank and only weakly associated with reproductive parameters such as delay to conception. EI in early lactation was related to infant mass and interbirth intervals, but unrelated to infant growth or reproductive parameters once cycling had resumed. Energy availability (EA; the difference between intake and expenditure) differed significantly between subordinate and dominant females during early lactation, was highly variable among individuals as a function of body composition, and is suggested to follow a nonlinear relationship as a complex function of social status, lactation stage, infant growth, and female fertility. Thus, as a consequence of reduced energy availability, subordinate females in this captive context may experience reproductive delays even though the total energy expenditure after the return of cycling was similar between high and low ranking females.     

Evolution in heterogeneous environments and the potential of maintenance of genetic variation in traits of adaptive significance

The maintenance of genetic variation in traits of adaptive significance has been a major dilemma of evolutionary biology. Considering the pattern of increased genetic variation associated with environmental clines and heterogeneous environments, selection in heterogeneous environments has been proposed to facilitate the maintenance of genetic variation. Some models examining whether genetic variation can be maintained, in heterogeneous environments are reviewed. Genetic mechanisms that constrain evolution in quantitative genetic traits indicate that genetic variation can be maintained but when is not clear. Furthermore, no comprehensive models have been developed, likely due to the genetic and environmental complexity of this issue. Therefore, I have suggested two empirical approaches to provide insight for future theoretical and empirical research. Traditional path analysis has been a very powerful approach for understanding phenotypic selection. However, it requires substantial information on the biology of the study system to construct a causal model and alternatives. Exploratory path analysis is a data driven approach that uses the statistical relationships in the data to construct a set of models. For example, it can be used for understanding phenotypic selection in different environments, where there is no prior information to develop path models in the different environments. Data from Brassica rapa grown in different nutrients indicated that selection changed in the different environments. Experimental evolutionary studies will provide direct tests as to when genetic variation is maintained.     

An atlas of CNV maps in cattle,goat and sheep

Copy number variation(CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region(CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study(GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected(P0.00001), and these CNVRs may be more persist than the single nucleotide polymorphisms(SNPs) shared between species. We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes. This study provides the evidence that balancing selection might be more common in mammals than previously considered, and might play an important role in the daily activities of these ruminant species.     

Demographic and socioeconomic determinants of variation in food and nutrient intake in an Andean community

Understanding the sources of variation in a community's diet is vital for development work, as well as being a source of anthropological and cultural insights. Previous surveys in the South American Andes suggest that nutrient deficiencies may be widespread; however, such interpretations have remained tentative since variance in Andean populations' diet has not been thoroughly examined. In this paper we consider the variation in diet due to variation in age, sex, and socioeconomic status and variation attributed to inter- and intraindividual variation in the diet. One to six days of dietary data (mean = 3.1) were collected via 24 h recalls from 221 residents of a small, rural community in highland Ecuador. The contribution of various food groups to the diet varied with land holdings and age but not sex. For example, animal-derived foods contribute more and tubers contribute less to the diet of the households with ≥5 Ha, and sweets contribute more to the diet of children. The interindividual variation in energy and nutrient intake was low and the intraindividual variation high relative to developed countries. The consequence are twofold. First, because interindividual variability is low, group mean intake can be estimated relatively easily, facilitating group comparisons. Second, because intraindividual variation is high, individual nutrient intake cannot be easily estimated, which will decrease the ability to detect associations between nutrient intake and health measures. This knowledge of the sources of dietary variation can lead to better study and survey designs in the rural Andes and elsewhere in the developing world. Am J Phys Anthropol 105:407–417, 1998. © 1998 Wiley-Liss, Inc.     

Use of a bovine genome chip to identify new biological pathways for beef quality in cattle

The accumulation of muscle is largely influenced by the genetic background of cattle. Muscle tissue was collected from the longissimus muscle of Lilu beef cattle at 12, 18, 24 and 30?months old. Using meat quality analysis, we found that the Lilu beef cattle have good production and slaughter performance, the performance meets the criterion of beef cattle. Microarray analysis was able to identify a total of 4,219 genes that are differentially expressed (P?≤?0.01) between the two groups of cattle (12 vs 18; 18 vs 24; 24 vs 30). Bioinformatics analysis results suggested that most of the differentially expressed genes are involved in the metabolic pathways and neuroactive ligand–receptor interaction pathways. In the future study that aims to look for genes relating to growth and meat quality, we will focus on the genes that have been shown to have a significant variation between groups and are involved in the two pathways.     

The evolution of thermal performance curves in semi-aquatic newts: Thermal specialists on land and thermal generalists in water?

The position and shape of thermal performance curves (TPCs, the functions relating temperature to physiological performance) for ecologically relevant functions will directly affect the fitness of ectotherms and therefore should be under strong selection. However, thermodynamic considerations predict that relationships between the different components of the TPC will confound its evolutionary optimization. For instance, the “jack-of-all-temperatures” hypothesis predicts a trade-off between the breadth of the TPC and the maximal performance capacity; the “warmer is better” hypothesis suggests that low thermal optima will come with low absolute performances. Semi-aquatic organisms face the additional challenge of having to adjust their TPCs to two environments that are likely to differ in mean temperature and thermal variability. In this paper, we examine how parameters of the TPCs for maximal running and swimming speed have co-evolved in the semi-aquatic newt genus Triturus. We consider evolutionary relationships between the width and the height of the TPCs, the optimal temperatures and maximal performance. Phylogenetic comparative analyses reveal that in Triturus, swimming and running differ substantially in the (co-)variation of TPC parameters. Whereas evolutionary changes in the TPC for swimming primarily concern the shape of the curve (generalist versus specialist), most interspecific variation in running speed TPCs involves shifts in overall performance across temperatures.