Interaction between the melanocortin-1 receptor and P genes contributes to inter-individual variation in skin pigmentation phenotypes in a Tibetan population

The melanocortin-1 receptor (MC1R) and P gene product are two important components of the human pigmentary system that have been shown to be associated with red hair/fair skin and cause type II oculocutaneous albinism, respectively. However, their contribution to inter-individual variation at the population level is not well defined. To this end, we genotyped 3 single nucleotide polymorphisms (SNPs) in the MC1R gene (Arg67Gln, Gln163Arg, Val92Met) and 2 SNPs in the P gene (IVS 13-15 and Gly780Gly) in 184 randomly ascertained Tibetan subjects, whose skin color was measured as a quantitative trait by reflective spectroscopy. Single locus analyses failed to demonstrate an association between any of the 5 SNPs and skin pigmentation. However, when an epistatic model was applied to the data, a significant gene-gene interaction was identified between Val92Met in MCIR and IVS13-15 in the P gene (F=2.43; P=0.0105). We also discuss the possible mechanisms of how gene interactions arise in signal transduction pathways.     

A variation of pigmentation in the glabrous skin of dogs

The usual pigmentation pattern in mammalian skin consists of fixed melanocytes in the basal layer of the epidermis, supplying keratinocytes with melanosomes. We observed that the glabrous skin (rhinaria and footpads) of dogs deviates from this pattern. In dogs, melanocytes are found in both the dermis and epidermis. The epidermal melanocytes are situated in the intercellular spaces of the basal and spinous layers. They are characterized by a quantity of cytoplasm containing a centriole, also developing melanosomes, and in some cases annulate lamellae. There is a high frequency of closely apposed melanocytes in the epidermis. Melanosomes in different stages of formation are also abundant. The morphology of the glabrous skin of dogs suggests transport of melanocytes from the dermis into the epidermis and formation of melanosomes in the epidermis. A distributed and intense pigment formation may be necessary to achieve the black noses of many dog breeds and wild canids, as well as dark footpads despite heavy abrasion and rapid skin renewal.     

Phenotypic, genetic, and environmental causes of variation in yellow skin pigmentation and serum carotenoids in Eurasian kestrel nestlings

In the context of sexual selection and parent-offspring communication, carotenoid-based coloration operates as a dynamic condition-dependent signal, as pigments stored in the skin and in the bill can be reallocated to other tissues in accordance with physiological needs. We studied the proximate factors affecting the carotenoid-dependent coloration of the Eurasian kestrel (Falco tinnunculus). Kestrel nestlings show carotenoid-based coloration at the integument level. Adult males and females share similar characteristics, but to a different extent. By cross-fostering nestlings, we evaluated the importance of the “nest of rearing” and the “nest of origin” to determine variation in skin color and blood carotenoids. The nest of rearing accounted for most of the observed variance in skin color, as well as serum carotenoids, while the nest of origin was not causal to the variability of carotenoids in young kestrels. The study indirectly shows that carotenoid-based color expressed by young kestrels is not affected by pre-laying conditions. Furthermore, we found that carotenoid coloration and blood carotenoid concentration were correlated at phenotypic and environmental levels, while the hereditary component of the carotenoid traits was too low to estimate their correlation at the genetic level.     

The relative contribution of environmental and genetic factors to phenotypic variation in familial Mediterranean fever (FMF)

Introduction

Familial Mediterranean fever (FMF) is an autosomal recessive disease, caused by mutations in the FMF gene MEFV (MEditerranean FeVer). It has a large phenotypic diversity even in patients with similar genotypes. Despite evidence that environmental factors (EFs) and genetic factors, including MEFV mutations (such as M694V, E148Q) and background modifier genes (MGs), affect the clinical manifestations of FMF, the relative contribution of each remains unknown.

Methods

To investigate the relative contribution of environmental and genetic factors to the phenotype of FMF, we compared the intra-pair clinical concordance of 10 mono and 7 dizygotic twins with FMF. The part played by EFs was determined by the phenotypic discordance of the monozygous twins, and the MGs effect was determined by deducing the environmental effect, computed for MZ twins, from the phenotypic discordance of the dizygous twins.

Results

The mean ± SD of intra-pair concordance was higher in the MZ than in DZ twin group (88.1 ± 13.2 vs. 70.7 ± 14.1 respectively, P value < 0.05). Based on the concordance in clinical manifestations in MZ and DZ twins, the environmental effect on the phenotype of FMF is estimated as 11.9% ± 6.6% and the MGs effect as 17.4% ± 15.5% in average.

Conclusions

In FMF the phenotype is affected by MEFV mutations, MGs and EFs in an estimated ratio of about 6:1.5:1 respectively.     

Using GIS and remote sensing to explore the influence of physical environmental factors and historical land use on bushland structure

Bushland is a vegetation type with a dense cover of woody plants of low stature and a grass understory. We explored the influence of environmental factors (precipitation, topography, geology, hydrology and waterhole density) and historical land use in the Tsavo ecosystem bushland. We mapped vegetation patterns in the region using remote sensing, GIS and field data and tested relationships with physical factors. We used regression analysis to explore the interaction of physical factors and human influence by including a protected and a nonprotected area, representing contrasting historical land use policies, as factors in the regression model. Bushland vegetation had the largest proportion in the region as a whole, but its proportion was notably greater in the nonprotected area. Precipitation, elevation, geology and historical land use were significant predictors of vegetation patterns in the regression models. Higher precipitation and elevation make woody plants superior competitors over grasses, resulting in predominance of bushland in such areas. Geologically, marine deposits result in shallow calcareous soils that favour grasses over trees, hence, absence of bushland. Wildlife management policies such as providing water for wildlife, protective boundaries and controlling wildfires influence distribution of wildlife and result in conditions that prevent regeneration and recruitment of trees.     

The potential contribution of satellite remote sensing to the understanding of arid lands processes

This paper discusses the need for monitoring the state and evolution of arid and semi-arid environments, and compares the specific contributions of in situ and satellite-based techniques. The role of physicallybased models in the quantitative interpretation of the measurement is stressed, and a strategy is proposed for the systematic exploitation of space technologies.     

Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana)

Skin pigmentation and coat pigmentation are two of the best‐studied examples of traits under natural selection given their quantifiable fitness interactions with the environment (e.g., camouflage) and signalling with other organisms (e.g., warning coloration). Previous morphological studies have found that skin pigmentation variation in the Virginia opossum (Didelphis virginiana) is associated with variation in precipitation and temperatures across its distribution range following Gloger's rule (lighter pigmentation in temperate environments). To investigate the molecular mechanism associated with skin pigmentation variation, we used RNA‐Seq and quantified gene expression of wild opossums from tropical and temperate populations. Using differential expression analysis and a co‐expression network approach, we found that expression variation in genes with melanocytic and immune functions is significantly associated with the degree of skin pigmentation variation and may be underlying this phenotypic difference. We also found evidence suggesting that the Wnt/β‐catenin signalling pathway might be regulating the depigmentation observed in temperate populations. Based on our study results, we present several alternative hypotheses that may explain Gloger's rule pattern of skin pigmentation variation in opossum, including changes in pathogen diversity supporting a pathogen‐resistant hypothesis, thermal stress associated with temperate environments, and pleiotropic and epistatic interactions between melanocytic and immune genes.     

Diet explains interpopulation variation of plasma carotenoids and skin pigmentation in nestling white storks

Carotenoids have a dietary origin in birds, but mechanisms by which they are absorbed in the gut, transported in the blood, metabolized at various sites, and deposited in the integument remain poorly understood. Variation in both plasma carotenoid levels and external color may reflect different access to dietary carotenoids or individual physiological differences in the uptake and deposition of carotenoids. We compared total plasma carotenoid concentration in nestling white storks (Ciconia ciconia) from 11 Spanish colonies in two consecutive years. The main food item in one of the colonies was the red swamp crayfish (Procambarus clarkii), a recently introduced species. Storks in the remaining colonies ate a variety of foods but no crayfish. Total plasma carotenoid levels in the colony where crayfish were consumed were about five times higher than in any other colony. These differences were maintained after controlling for the significant interyear variability, as well as for sex, age, and body mass of birds. Skin pigmentation also differed, being intensely orange in storks that consumed crayfish but white (unpigmented) in the remaining individuals. With thin-layer chromatography (TLC) and electronic absorption spectroscopy, astaxanthin was confirmed as the major carotenoid in crayfish as well as in the plasma, skin, and body fat of crayfish-eating storks, whereas lutein was the main carotenoid in plasma samples from the other colonies. These results indicate that a newly available carotenoid in the environment, astaxanthin, can be absorbed in large quantities from the gut and be transported in the blood before deposition in different tissues.     

Combined application of remote sensing and in situ measurements in monitoring environmental processes

Combined use of remote sensing in the visible, infrared and microwave spectral regions, direct in situ measurements and model numerical experiments makes it possible to study inland water bodies as elements of water body-catchment-atmosphere-systems with good spatial and temporal resolution. In this paper examples are presented of the remote sensing methods developed for detection of hydrodynamics of large water bodies (e.g. frontal and upwelling zones, internal waves, warm and cold surface layers), monitoring of chlorophyll concentration, suspended minerals and dissolved organic matter (DOM) in lakes, mapping of shallow water zones, wetlands and landscape structures, monitoring of ecological condition and changes of drainage basins, and studying the state of the atmosphere over lakes and catchment areas.     

Susceptibility to Phytophthora ramorum in a key infectious host: landscape variation in host genotype, host phenotype, and environmental factors

Sudden oak death is an emerging forest disease caused by the invasive pathogen Phytophthora ramorum. Genetic and environmental factors affecting susceptibility to P. ramorum in the key inoculum-producing host tree Umbellularia californica (bay laurel) were examined across a heterogeneous landscape in California, USA. Laboratory susceptibility trials were conducted on detached leaves and assessed field disease levels for 97 host trees from 12 225-m(2) plots. Genotype and phenotype characteristics were assessed for each tree. Effects of plot-level environmental conditions (understory microclimate, amount of solar radiation and topographic moisture potential) on disease expression were also evaluated. Susceptibility varied significantly among U. californica trees, with a fivefold difference in leaf lesion size. Lesion size was positively related to leaf area, but not to other phenotypic traits or to field disease level. Genetic diversity was structured at three spatial scales, but primarily among individuals within plots. Lesion size was significantly related to amplified fragment length polymorphism (AFLP) markers, but local environment explained most variation in field disease level. Thus, substantial genetic variation in susceptibility to P. ramorum occurs in its principal foliar host U. californica, but local environment mediates expression of susceptibility in nature.     

山茱萸种子形态变异及与环境因子的相关性

山茱萸广泛分布于中国长江沿岸各省地区.由于土壤和气候的影响,分布区间山茱萸种子的形态变异较大.本文对4个省7个山茱萸群体的种子形态指标(种长、种宽、种子体积和种形系数)变异、种子形态指标间及与环境因子的相关性、种子形态地理变异趋势和群体聚类进行了探讨.研究表明:不同群体种子形态均存在显著差异;种子宽度与体积呈显著正相关,且二者与纬度呈显著负相关;种子宽度和种子体积的地理变异趋势明显;基于种子形态指标的聚类分析可将7个群体分为2个聚类群,北方群包括陕西佛坪、陕西汉中和河南栾川,南方群包括安徽宁国、安徽黄山、江苏镇江和安徽旌德.研究结果可为不同区域筛选优良山茱萸种源提供参考.     

土壤水分时空变异及其与环境因子的关系

土壤水分的时空变异是指在一定的景观内,不同时间、地点和土层的土壤水分特征存在明显的差异性和多样性。土壤水分时空变异是由多重尺度上的土地利用（植被）、气象（降雨）、地形、土壤、人为活动等诸因子综合作用的结果,但就其某一具体地区而言存在着重点尺度和主控因子,土壤水分时空变异的重点尺度与主控因子的时空关系因时间、空间和尺度而异。本文综述了土壤水分（尤其是黄土高原地区）的时空变异与其环境因子时空关系的研究进展,并提出了广眨开展多重时空尺度上土壤水分的时空变异与其诸因素的时空关系,研究土壤水分时空变异性的尺度转换规律,确定重点尺度及其相应的主控因子。     

Development and assessment of simple PCR markers for SNP genotyping in barley

Simple molecular marker assays underpin routine plant breeding and research activities in many laboratories worldwide. With the rapid growth of single nucleotide polymorphism (SNP) resources for many important crop plants, the availability of routine, low-tech marker assays for genotyping SNPs is of increased importance. In this study, we demonstrate that temperature-switch PCR (TSP) supports the rapid development of robust, allele-specific PCR markers for codominant SNP genotyping on agarose gel. A total of 87 TSP markers for assessing gene diversity in barley were developed and used to investigate the efficacy for marker development, assay reliably and genotyping accuracy. The TSP markers described provide good coverage of the barley genome, are simple to use, easy to interpret and score, and are amenable to assay automation. They provide a resource of informative SNP markers for assessing genetic relationships among individuals, populations and gene pools of cultivated barley (Hordeum vulgare L.) and its wild relative H. spontaneum K. Koch. TSP markers provide opportunities to use available SNP resources for marker-assisted breeding and plant genetic research, and to generate information that can be integrated with SNP data from different sources and studies. TSP markers are expected to provide similar advantages for any animal or plant species. M. J. Hayden and T. Tabone contributed equally to this work.     

The contribution of spontaneous mutation to variation in environmental response in Arabidopsis thaliana: responses to nutrients

Abstract Although the evolutionary importance of spontaneous mutation is evident, its contribution to the evolution of ecological specificity remains unclear, because the environmental sensitivity of effects of new mutations has received little empirical attention. To address this issue, we report a greenhouse in which we grew plants from 20 mutation-accumulation (MA) lines, advanced by selfing and single-seed descent from a single common founder to generation 17, as well as plants from five lines representing the founder, in high and low nutrient conditions. We examined 11 traits throughout life history, including germination, survivorship, bolting date, flowering date, leaf number, leaf size, early and late height, mean fruit size, total seed weight, and reproductive biomass. Comparison of trait means between the two generations did not support the commonly held view that new mutations affecting fitness in these MA lines are strongly biased toward deleterious effects. We detected significant variance among MA lines for one fitness component, mean fruit size, but we did not detect a significant contribution of mutations accumulated in these MA lines to genotype by environment interaction (GEI). These results suggest that other evolutionary mechanisms play a more important role than spontaneous mutation alone in establishing the GEI found for wild collections and lab accessions of Arabidopsis thaliana in previous studies.     

Application of remote sensing to site characterisation and environmental change analysis of North African coastal lagoons

This article describes the use of satellite imagery for identifying key environmental characteristics within three North African coastal lagoons (Merja Zerga, Morocco; Ghar El Melh, Tunisia and Lake Manzala, Egypt) and for detecting the major environmental changes within these environments. A combination of Landsat MSS, Landsat TM, Landsat ETM+ and ASTER imagery was acquired for the three sites for a period covering the last three decades (1972–2004). Following geometric correction and enhancement, the interpretation of the most recent image acquired for each of the three lagoons provides important insights into their current conditions. For Merja Zerga, these include the distribution of the largest channels which drain extensive inter-tidal mudflats and the two major depositional features associated with sources of freshwater. The distribution of marginal aquatic vegetation is highlighted as is the intensive use of the surrounding landscape for agriculture. Intensive agriculture around Ghar El Melh is also indicated. The influence of the Mejerda River, which was diverted away from the lagoon over 100 years ago, is shown to persist as a residual area of deltaic deposits in shallow water that has been eroded over time. Coastal processes including the direction of the alongshore sediment transport and the influence of engineering work associated with port construction can also be recognised. Within Lake Manzala, vegetated islands divide the lake into a series of sub-basins which can be clearly distinguished. The large influence of human activities within this lake can be identified and include reclamation for agriculture and the conversion of parts of the lake bed for fish farms. The historical images available for the three lagoons provide important insights into decadal scale changes, which have been greatest at Lake Manzala. Since the early 1970s large parts of the lake, in particular in the southwest where the shoreline has migrated northwards, have been reclaimed. Major engineering works, such as the El Salam Canal and road embankments, are shown to have resulted in significant lake change. The distribution of emergent vegetation within the lake has also changed. Classification of images for this lake into open water, vegetation and land enables the quantification of these changes. Between 1973 and 2003, the lake declined in area by approximately 50%. Changes at Merja Zerga over the last three decades include reconfiguration of the marine outlet and the expansion of the internal delta at the end of the Nador Canal. The images of this site clearly demonstrate the intensification of agriculture around the lagoon. The most marked changes evident within the images of Ghar El Melh concern the sand bars that separate the lagoon from the sea. Geomorphological processes operating within the coastal zone have resulted in the straightening of the bars with central sections migrating out towards the sea. Remote sensing is established as a promising application for detecting the quantitative surface cover changes in coastal lagoons and their near landscapes. Guest editors: J. R. Thompson & R. J. Flower Hydro-ecological Monitoring and Modelling of North African Coastal Lagoons     

Habitat suitability modeling based on remote sensing to realize time synchronization of species and environmental variables

基于遥感实现物种和环境变量时间同步性的生境适宜性建模遥感是一种有效获取大规模现实数据的技术方法。我们旨在生境适宜性建模中基于遥感实现物种与环境变量之间的时间同步性,并提取与物种实际生长相关的变量,为物种管理提供更有效的参考。本研究以入侵中国的豚草(Ambrosia artemisiifolia)为例,开展生境适宜性建模,温度和降水变量分别依据中分辨率成像光谱仪(MODIS)提供的地表温度和气象站点数据计算;此外,本研究还包括直接影响豚草生长或繁殖的其他变量,如前一年花期的相对湿度和有效紫外辐射。选择随机森林模型开展生境适宜性建模,根据采样时间,把环境变量和样本分为4个时间段(1990–2000、2001–2005、2006–2010和2011–2016),同时对基于RS (1990–2016)和WorldClim (1960–1990)的长时间序列的变量也进行建模。结果显示,从遥感提取环境变量开展生境适宜性建模是可行的,而且比基于WorldClim变量预测结果更准确。1990–2000年和2006–2010年豚草的潜在分布面积小于2001–2005年和2011–2016年,影响豚草生长和繁殖的重要环境变量包括最干旱月降水量(bio14)、降水变异系数(bio15)、前一年花期的相对湿度和有效紫外辐射。我们的研究结果表明,实现物种与环境变量的时间同步性提高了豚草潜在分布的预测精度,在生境适宜性建模(尤其为一年生物种)中应予以考虑。本研究为管理和预防豚草入侵扩散提供了重要参考。     

The contribution of spontaneous mutation to variation in environmental responses of Arabidopsis thaliana: responses to light

It has been hypothesized that new, spontaneous mutations tend to reduce fitness more severely in more stressful environments. To address this hypothesis, we grew plants representing 20 Arabidopsis thaliana mutation-accumulation (M-A) lines, advanced to generation 17, and their progenitor, in differing light conditions. The experiment was conducted in a greenhouse, and two treatments were used: full sun and shade, in which influx of red light was reduced relative to far-red. The shade treatment was considered the more stressful because mean absolute fitness was lower in that treatment, though not significantly so. Plants from generation 17 of M-A developed significantly faster than those from generation 0 in both treatments. A significant interaction between generation and treatment revealed that, counter to the hypothesis, M-A lines tended to have higher fitness on average relative to the progenitor in the shaded conditions, whereas, in full sun, the two generations were similar in fitness. A secondary objective of this experiment was to characterize the contribution of new mutations to genotype x environment interaction. We did not, however, detect a significant interaction between M-A line and treatment. Plots of the line-specific environmental responses indicate no tendency of new mutations to contribute to fitness trade-offs, between environments. They also do not support a model of conditionally deleterious mutation, in which a mutant reduces fitness only in a particular environment. These results suggest that interactions between genotype and light environment previously documented for A. thaliana are not explicable primarily as a consequence of steady input of spontaneous mutations having environment-specific effects.     

东北地区植被物候期遥感模拟与变化规律

使用1982—2003年GIMMS-NDVI数据,借助GIS空间分析功能,提取东北地区不同植被NDVI时间序列数据,使用分段式Logistic函数模拟了东北地区不同植被物候期,分析了1982—2003年不同植被物候期的变化趋势。结果表明:针叶林、阔叶林、草丛、草甸和沼泽植被生长季开始日期提前,生长季延长,其中沼泽植被生长季开始日期提前和生长季延长的趋势明显,针叶林次之;结束日期的变化趋势表现不一,针叶林和沼泽植被生长季结束日期推迟,阔叶林、草丛和草甸植被呈现微弱提前趋势;针阔混交林、灌丛、草原和农田植被生长季开始日期推迟,生长季缩短,其中农田植被生长季开始日期推迟和生长季缩短的趋势明显,草原次之;针阔混交林、灌丛、草原和农田4种植被生长季结束日期呈现提前的变化趋势,其中灌丛结束日期的提前趋势明显。