The Analysis of Association Between Traits When Differences Between Trait States Matter

Because of their elementary significance in almost all fields of science, measures of association between two variables or traits are abundant and multiform. One aspect of association that is of considerable interest, especially in population genetics and ecology, seems to be widely ignored. This aspect concerns association between complex traits that show variable and arbitrarily defined state differences. Among such traits are genetic characters controlled by many and potentially polyploid loci, species characteristics, and environmental variables, all of which may be mutually and asymmetrically associated. A concept of directed association of one trait with another is developed here that relies solely on difference measures between the states of a trait. Associations are considered at three levels: between individual states of two variables, between an individual state of one variable and the totality of the other variable, and between two variables. Relations to known concepts of association are identified. In particular, measures at the latter two levels turn out to be interpretable as measures of differentiation. Examples are given for areas of application (search for functional relationships, distribution of variation over populations, genomic associations, spatiogenetic structure).     

The association between parasite infection and growth rates in Arctic charr: do fast growing fish have more parasites?

Trophically transmitted parasites are known to impair fish growth in experimental studies, but this is not well documented in natural populations. For Arctic charr [Salvelinus alpinus (L.)], individual growth is positively correlated with food consumption. However, increased food consumption will increase the exposure to trophically transmitted parasites. Using a correlative approach, we explore the association between parasite abundance and the individual growth of Arctic charr from five lakes within the same watercourse. The studied parasite species differ in their life cycles and cost to the host. We predicted a positive association between parasite abundance and fish growth for parasites of low pathogenicity reflecting high consumption rates, and a negative association at higher parasite abundances for more costly parasites. We found no direct negative associations between parasite abundance and fish growth. The relationship between parasite abundance and growth was linearly positive for the low costly Crepidostomum sp. and concave for the more costly Eubothrium salvelini. In natural fish populations, the negative effects of parasites on fish growth might be outweighed by the energy assimilated from feeding on the intermediate host. However, experimental studies with varying food consumption regimes are needed to determine the mechanisms underlying our observations.

     

Allometry of human fertility and energy use

The flux of energy and materials constrains all organisms, and allometric relationships between rates of energy consumption and other biological rates are manifest at many levels of biological organization. Although human ecology is unusual in many respects, human populations also face energetic constraints. Here we present a model relating fertility rates to per capita energy consumption rates in contemporary human nations. Fertility declines as energy consumption increases with a scaling exponent of ?1/3 as predicted by allometric theory. The decline may be explained by parental trade‐offs between the number of children and the energetic investment in each child. We hypothesize that the ?1/3 exponent results from the scaling properties of the networked infrastructure that delivers energy to consumers. This allometric analysis of human fertility offers a framework for understanding the demographic transition to smaller family sizes, with implications for human population growth, resource use and sustainability.     

Diel dualism in the energy consumption of the European catfish Silurus glanis

Twenty individuals of the largest European freshwater predator, the European catfish Silurus glanis, were tagged with electromyogram (EMG) physiological telemetry sensors. The fish were observed during diel cycles during the spring and summer in the Elbe and Berounka Rivers, Czech Republic. The purpose of this study was to determine whether diel dualism in the activity of S. glanis occurs naturally or is induced by the laboratory environment and by the conditions occurring in aquaculture. The results obtained from the riverine environment tended to show dualism in the use of the light and dark phases of the day because 35% of the individuals varied from a site‐specific common diel activity pattern. The EMG values increased in accordance with the mass (M) of the fish. To eliminate the influence of M on individual energy consumption, the EMG records were analysed in terms of the EMG:M ratios. High individual variability was found in these ratios. The diel activity pattern of the individuals with relatively high energy consumption differed from the common diel activity pattern. In contrast, the fish that adopted the common diel activity pattern displayed relatively low energy consumption. The results of this study indicated that dualism and energy consumption are related. The EMG values also varied with the values of the environmental variables. Increasing temperature was associated with high EMG values, whereas the EMG values decreased with increasing flow.     

Caloric requirements of human populations: A model

Currently available models used for predicting human caloric requirements do not reflect the great variability in activity patterns observed among populations, and are insensitive to important anthropometric, demographic, and environmental variables. They are thus inadequate for application to many populations and problems of anthropological interest. We present a model for determining caloric requirements which more accurately accommodates the effects of variation in activity and in anthropometries on individual needs, and which predicts population requirements based on individual needs and demographic parameters. The model is tested on four populations (the Andean community of Nuñoa, Peru, the Dobe !Kung of Botswana, and two New Guinean villages) and is found to provide consistently better estimates of caloric requirements than are generated by the Food and Agriculture/World Health Organization's model. This model should be useful to anthropologists and human ecologists concerned with problems involving human energy consumption, such as the efficiency of subsistence strategies, optimum family composition, or certain consequences of increased labor migration or technological change.This research was supported by a grant from the Research Foundation of the State University of New York. Funds for computer time and materials were provided by the State University of New York at Binghamton and The Pennsylvania State University.     

Swedish population substructure revealed by genome-wide single nucleotide polymorphism data

The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (F_ST = 0.0005 between provinces) was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.     

Prevalence of and Factors Associated with Human Cysticercosis in 60 Villages in Three Provinces of Burkina Faso

Background

Taenia solium, a zoonotic infection transmitted between humans and pigs, is considered an emerging infection in Sub-Saharan Africa, yet individual and community-level factors associated with the human infection with the larval stages (cysticercosis) are not well understood. This study aims to estimate the magnitude of association of individual-level and village-level factors with current human cysticercosis in 60 villages located in three Provinces of Burkina Faso.

Methodology/Principal Findings

Baseline cross-sectional data collected between February 2011 and January 2012 from a large community randomized-control trial were used. A total of 3609 individuals provided serum samples to assess current infection with cysticercosis. The association between individual and village-level factors and the prevalence of current infection with cysticercosis was estimated using Bayesian hierarchical logistic models. Diffuse priors were used for all regression coefficients. The prevalence of current cysticercosis varied across provinces and villages ranging from 0% to 11.5%. The results obtained suggest that increased age, being male and consuming pork as well as a larger proportion of roaming pigs and percentage of sand in the soil measured at the village level were associated with higher prevalences of infection. Furthermore, consuming pork at another village market had the highest increased prevalence odds of current infection. Having access to a latrine, living in a household with higher wealth quintiles and a higher soil pH measured at the village level decreased the prevalence odds of cysticercosis.

Conclusions/Significance

This is the first large-scale study to examine the association between variables measured at the individual-, household-, and village-level and the prevalence odds of cysticercosis in humans. Factors linked to people, pigs, and the environment were of importance, which further supports the need for a One Health approach to control cysticercosis infection.     

Mitochondrial DNA Content Contributes to Climate Adaptation Using Chinese Populations as a Model

Maintaining a balance between ATP synthesis and heat generation is crucial for adapting to changes in climate. Variation in the mitochondrial DNA (mtDNA), which encodes 13 subunits of the respiratory chain complexes, may contribute to climate adaptation by regulating thermogenesis and the use of bioenergy. However, studies looking for a relationship between mtDNA haplogroups and climate have obtained mixed results, leaving unresolved the role of mtDNA in climate adaptation. Since mtDNA content can regulate human bioenergy processes and is known to influence many physiological traits and diseases, it is possible that mtDNA content contributes to climate adaptation in human populations. Here, we analyze the distribution of mtDNA content among 27 Chinese ethnic populations residing across China and find a significant association between mtDNA content and climate, with northern populations having significantly higher mtDNA content than southern populations. Functional studies have shown that high mtDNA content correlates with an increase in the expression of energy metabolism enzymes, which may accelerate thermogenesis. This suggests that the significantly higher mtDNA content observed in northern populations may confer a selective advantage in adapting to colder northern climates     

Spatial, environmental and human influences on the distribution of otter (Lutra lutra) in the Spanish provinces

In a previous survey of otters (Lutra lutra L. 1758) in Spain, different causes were invoked to explain the frequency of the species in each province. To find common causes of the distribution of the otter in Spain, we recorded a number of spatial, environmental and human variables in each Spanish province. We then performed a stepwise linear multiple regression of the proportion of positive sites of otter in the Spanish provinces separately on each of the three groups of variables. Geographic longitude, January air humidity, soil permeability and highway density were the variables selected. A linear regression of the proportion of otter presence on these variables explained 62.4% of the variance. We then used the selected variables in a partial regression analysis to specify which proportions of the variation are explained exclusively by spatial, environmental and human factors, and which proportions are attributable to interactions between these components. Pure environmental effects accounted for only 5.5% of the variation, while pure spatial and pure human effects explained 18% and 9.7%, respectively. Shared variation among the components totalled 29.2%, of which 10.9% was explained by the interaction between environmental and spatial factors. Human factors explained globally less variance than spatial and environmental ones, but the pure human influence was higher than the pure environmental one. We concluded that most of the variation in the proportion of occurrences of otter in Spanish provinces is spatially structured, and that environmental factors have more influence on otter presence than human ones; however, the human influence on otter distribution is less structured in space, and thus can be more disruptive. This effect of large infrastructures on wild populations must be taken into account when planning large‐scale conservation policies.     

Correcting for measurement error in individual ancestry estimates in structured association tests

We present theoretical explanations and show through simulation that the individual admixture proportion estimates obtained by using ancestry informative markers should be seen as an error-contaminated measurement of the underlying individual ancestry proportion. These estimates can be used in structured association tests as a control variable to limit type I error inflation or reduce loss of power due to population stratification observed in studies of admixed populations. However, the inclusion of such error-containing variables as covariates in regression models can bias parameter estimates and reduce ability to control for the confounding effect of admixture in genetic association tests. Measurement error correction methods offer a way to overcome this problem but require an a priori estimate of the measurement error variance. We show how an upper bound of this variance can be obtained, present four measurement error correction methods that are applicable to this problem, and conduct a simulation study to compare their utility in the case where the admixed population results from the intermating between two ancestral populations. Our results show that the quadratic measurement error correction (QMEC) method performs better than the other methods and maintains the type I error to its nominal level.     

Many colorectal cancers are “flat” clonal expansions

Population geneticists can reconstruct the ancestries of macroscopic populations from polymorphisms in present day individuals. For example, the migration “out of Africa” is recorded in human genome variation in different parts of the world. Here we apply this approach to human colorectal cancer cell populations and polymorphic passenger methylation patterns. By sampling molecular variation from different parts of the same cancer, it should be possible to infer how individual tumors grow because recent clonal expansions should be less diverse than older expansions. Average diversity was different between cancers implying that some cancers are older clonal expansions than others. For individual cancers, methylation pattern diversity was relatively uniform throughout the tumor (right versus left side, superficial versus invasive), which is more consistent with a single, uniform or “flat” clonal expansion than with stepwise sequential progression. Many colorectal cancers appear to invade and expand early, but subsequently stall. Epiallele diversity within individual small cancer gland fragments was high and more consistent with frequent rather than extremely rare cancer stem cells (CSCs). These studies suggest that many human colorectal cancers are relatively old uniform clonal expansions, that cancer cell populations contain frequent long-lived CSC lineages, and that some passenger methylation patterns record somatic cell ancestry.     

中国省域环境可持续性时空格局及其影响因素

人类活动已成为人类世背景下全球环境变化的主要驱动力,因此将其合理调控在地球环境边界之内是实现可持续发展的前提条件。作为全球尺度的环境边界,行星边界秉持"地球系统观",为统筹不同区域的环境可持续性评估提供了新视角。以行星边界为切入点,评估中国省域主要人类活动的环境可持续性状况,揭示其时空格局演变及社会经济影响因素。结果表明：（1）中国省域碳、氮、磷排放的不可持续性北部整体高于南部,分异程度随时间逐步拉大,不可持续省份数量的占比均已超出2/3;省域水、土地利用的可持续性南部整体高于北部,保持相对稳定,可持续省份数量的占比均已超出3/4。（2）中国省域环境可持续性大体受人口、经济、技术等因素的综合影响,且各类环境要素的可持续性之间存在一定的协同效应。其中,各类环境可持续性均受人口规模的正向驱动,同时氮、磷、水和土地的可持续性均受农业活动的负向驱动。（3）碳排放可持续性主要受能源消费强度的负向驱动,而磷排放可持续性同时受人口城镇化率的负向驱动,水可持续性受二产占比的负向驱动。基于行星边界的环境可持续性研究,可为区域合理界定和有效承担全球环境可持续性责任提供科学参考。     

Exploring possible human influences on the evolution of Darwin's finches

Humans are an increasingly common influence on the evolution of natural populations. Potential arenas of influence include altered evolutionary trajectories within populations and modifications of the process of divergence among populations. We consider this second arena in the medium ground finch (Geospiza fortis) on Santa Cruz Island, Galápagos, Ecuador. Our study compared the G. fortis population at a relatively undisturbed site, El Garrapatero, to the population at a severely disturbed site, Academy Bay, which is immediately adjacent to the town of Puerto Ayora. The El Garrapatero population currently shows beak size bimodality that is tied to assortative mating and disruptive selection, whereas the Academy Bay population was historically bimodal but has lost this property in conjunction with a dramatic increase in local human population density. We here evaluate potential ecological-adaptive drivers of the differences in modality by quantifying relationships between morphology (beak and head dimensions), functional performance (bite force), and environmental characteristics (diet). Our main finding is that associations among these variables are generally weaker at Academy Bay than at El Garrapatero, possibly because novel foods are used at the former site irrespective of individual morphology and performance. These results are consistent with the hypothesis that the rugged adaptive landscapes promoting and maintaining diversification in nature can be smoothed by human activities, thus hindering ongoing adaptive radiation.     

东北三省“水-能源-碳”系统仿真模拟——基于系统动力学模型

水资源和能源消费量及碳排放制约区域发展水平,也影响区域生态环境质量,区域多要素资源耦合作用与协同管理成为近年来的研究热点。水资源、能源和碳排放三个系统通过不同的流程相互连接,探究"水-能源-碳"系统耦合关系,是区域探索绿色协调发展的重要基础。以东北三省为研究对象,采用系统动力学研究方法,从自然、社会、经济三个维度来探索水-能源-碳三者的关联模式。以2001-2019年东北三省的水资源、能源、碳排放现状为基础数据,梳理三个子系统的耦合关系,并对未来二十年其发展变化仿真模拟。结果表明：（1）水资源、能源、碳排放在未来二十年均呈现增长的趋势,水资源增长趋势最快,在仿真情景5下,与2020年相比2040年水资源、能源消费量和碳排放量分别增长230.4%、210.7%和36.9%;（2）决策变量对"水-能源-碳"系统的影响程度依次是清洁节能>产业调控>国内生产总值（GDP）增长率,随着GDP增长率升高,水资源和能源消耗量、碳排放量升增加,随着产业转型升级,居民意识提高及清洁能源增加,水资源和能源消耗量、碳排放量减少。在综合调控情景下,未来水资源消耗量高于基础情景,能源消耗量和碳排放量则得到了良好的控制;（3）2020-2040年,水资源、能源消费量和碳排放量呈现强相关性,纽带关系呈协同优化方向改善,供需缺口减小,有效的缓解了环境压力;（4）情景3的能源结构调整和居民意识的提高可有效降低碳排放量,情景4产业结构的调整对水资源和能源的影响较为明显。情景5权衡经济发展与节能节水以减少碳排放,严格按照"双碳"目标,将水资源、能源向较高质量发展的可持续发展方向推进,更具参考性。研究结果有利于东北三省"水-能源-碳"系统可持续发展,促进经济发展水平。     

Molecular and morphometric variation in chromosomally differentiated populations of the grasshopper Sinipta dalmani (Orthopthera: Acrididae)

Sinipta dalmani is an Argentine grasshopper whose chromosome polymorphisms have been widely studied through cytogenetic, morphometric, and fitness component analyses. The present work analysed molecular and morphometric variation in seven chromosomally differentiated populations from Entre Rios and Buenos Aires provinces to analyse population structure. Molecular studies were performed studying RAPD loci and morphometric analyses were carried out measuring five morphometric traits. Genetic variability was high in all studied populations and was characterized by a decrease in H as a function of latitude and temperature. Both conventional F(ST) analysis and Bayesian approach for dominant marker showed that there were significant genetic differences among all populations, between provinces, and among populations within provinces. Entre Rios populations showed higher mean numbers of migrants per generation as well as low genetic differentiation and high gene flow with almost all populations whereas Buenos Aires populations may be considered as a result of a more recently colonization. There is considerable morphometric variation between populations and this variation correlates with latitude and temperature. Our results suggest that selection contributes to phenotypic differentiation among populations by moulding the differences in trait means whereas genetic drift is responsible for differences in the matrix of variance-covariance. The gene flow detected is insufficient to prevent phenotypic and chromosome divergences.     

The role of climate in limiting European resident bird populations

Abstract Aim To study densities of eight groups of resident forest bird populations across Europe to examine their association with abiotic (temperature, precipitation) factors. Location Europe. Methods Densities of residents (and migrant birds, which were used as a control group) were extracted from published breeding bird censuses. For each census location we obtained geographical co‐ordinates (latitude and longitude), temperature and precipitation variables describing both breeding and non‐breeding seasons. Resident densities were first examined separately in relation to co‐ordinates and principal component axes, which were extracted from temperature and precipitation variables. The relative impact of each explaining factor (co‐ordinates and principal component axis) on resident densities was checked by using residual examination and partial correlation. Results Densities of resident birds were in general negatively correlated with both latitude and longitude and temperature and precipitation factors, but latitude and temperature proved to be the strongest individual factors along which resident densities varied. The higher the latitude or the lower the temperatures, the lower were the densities of most resident birds. Partial correlation analysis suggested that of those two factors, latitude was the dominant one. Both the density of resident and migrant birds decreased towards the north, but the decrease of residents was steeper, and in the north they comprised only a small fraction of breeding bird numbers, whereas further south they commonly comprise half of the breeding bird numbers. Main conclusions The best explanatory factor for resident densities was latitude. For this reason, it was difficult to separate the relative effect of each individual factor, because latitude partly describes all the original variables (temperature and precipitation). The results suggested that precipitation was of less importance and that the interplay between latitude and ambient temperatures was not the sole factor behind the strong effect of latitude. We suggest that the coupled effect of harshening climate and decreasing amount of available energy with increasing latitude is limiting the population sizes of resident birds. We also propose that the effect of those factors is most apparent in northern Fennoscandia, where resident densities are suggested to be lower than would be expected on the basis of summer time carrying capacity.     

Clinal variation in Chinese height and weight: Evidence from the descendants of emigrants to Taiwan

Surveys reveal that Chinese from the southernmost provinces are, on average, consistently shorter and lighter than their peers in provinces to the north, though explanations for this variation differ. The present study helps to distinguish between genetic and developmental explanations by comparing differences in regional and provincial heights and weights of 3184 children born in Taiwan between 1975 and 1980 whose families had emigrated from different regions of China at varying times in the past, but who all lived in a relatively affluent district in Taipei at the time of measurement. Linear regression analyses adjusted heights for measurement age and relevant (and available) socioeconomic and demographic variables. Results of these analyses suggested that clinal genetic variation is an important contributor to regional differences in China. Whether entering primary school or departing middle school, children of northern Chinese ancestry living in Taipei were significantly taller (males, 25-30 mm, p0.014; females, 18 mm; p0.008) and heavier (males, 2.5-3.8 kg; p0.081; females, 0.9-3.4 kg, p0.046) than those of southern ancestry, with those from central provinces intermediate in most comparisons. Additionally, provincial backgrounds of Taipei middle school girls with family origins in 12 provinces across China and in Taiwan were significantly associated with height (n=905; p=0.003) and weight (n=900; p=0.001). The pattern of change in mean values across provinces of origin suggests that as developmental circumstances become more equal for residents of various provinces in China, already documented declines in mean height differences, particularly in some central and southern provinces, will shrink further.     

Morphological adaptation to climate in modern Homo sapiens crania: the importance of basicranial breadth

The aim of this study is to investigate whether the variation in breadth of the cranial base among modern human populations that inhabit different regions of the world is linked with climatic adaptation. This work provides an examination of two hypotheses. The first hypothesis is that the correlation between basicranial breadth and ambient temperature is stronger than the correlation between temperature and other neurocranial variables, such as maximum cranial breadth, maximum neurocranial length, and the endocranial volume. The second hypothesis is that the correlation between the breadth of the cranial base and the ambient temperature is significant even when other neurocranial features used in this study (including the size of the neurocranium) are constant. For the sake of this research, the necessary neurocranial variables for fourteen human populations living in diverse environments were obtained from Howells' data (except for endocranial volume which was obtained by means of estimation). The ambient temperature (more precisely, the mean yearly temperature) of the environments inhabited by these populations was used as a major climatic factor. Data were analysed using Pearson correlation coefficients, linear regression and partial correlation analyses. The results supported the two hypotheses, thus suggesting that ambient temperature may contribute to the observed differences in the breadth of the cranial base in the studied modern humans.     

Calculating the free energy of association of transmembrane helices

A large number of experimental studies have been devoted to quantifying the interaction between transmembrane (TM) helices in detergent micelles and, more recently, in bilayers. Theoretical calculation of association free energy of TM helices would be useful for predicting the propensity of given sequences to oligomerize and for understanding the difference between association in micelles and in bilayers. In this article, the theoretical foundation for calculating the standard association free energy of TM helices is laid out and is applied to glycophorin A in both micelles and bilayers. The standard association free energy is decomposed into the effective energy, translational, rotational, and conformational entropy terms. The effective energy of association is obtained by molecular dynamics simulations in an implicit membrane model. The translational and rotational entropy of association is calculated from the probability distribution of the translational and rotational degrees of freedom obtained from the molecular dynamics simulations. The side-chain conformational entropy of association is estimated from the probability distribution obtained by rigid rotation of all side-chain dihedral angles. The calculated standard association free energy of glycophorin A in N-dodecylphosphocholine micelles is in good agreement with the experimental value. The translational entropy cost is larger, whereas the rotational entropy cost is smaller in bilayers than in micelles. The standard association free energy in 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayers is calculated to be approximately 1.3 kcal/mol more favorable than in N-dodecylphosphocholine micelles, consistent with available experimental data.     

Predicting the distribution of cryptic species: the case of the spur-thighed tortoise in Andalusia (southern Iberian Peninsula)

Some species are very difficult to observe in the wild, and some of these present an apparently incongruent distribution, as is the case of the spur-thighed tortoise Testudo graeca in the southern Iberian Peninsula. This species has a discontinuous distribution with two main reproductive areas: one in the contiguous provinces of Almeria and Murcia, and the other in Huelva province. Both populations are thought to maintain reproductive isolation. However, we present new records obtained from two areas (the provinces of Malaga and Cadiz) which are outside their previously known range. Malaga province and Cadiz province are located between the two traditional reproductive areas. The new records were based on 16 interviews with shepherds as well as information provided by three naturalists. The aim of this work was to analyze the spatial distribution of areas favourable to the spur-thighed tortoise in the southern Iberian Peninsula, using different models with the same group of variables but with a different number of records: known records, new records and a combination of them. We obtained a distribution model for the species in Andalusia consistent with all observations, which was related to climatic stability, climatic disturbances, and spatial situation. This model presented three main favourable areas: two are coincident with the two known nuclei, and the other is situated in the southern part of the region, in the contiguous provinces of Cadiz and Malaga. We conclude that it is important to consider all the observations in the distribution models because records outside the traditional reproductive areas can include other environmental characteristics appropriate for the species.