Field sampling bias, museum collections and completeness of the fossil record

Museum specimens, particularly old collections, typically lack comprehensive field data and determination of substrate, sampling biases, etc., is problematic. Diversity at the generic level of all identifiable latest Cretaceous (Campanian–Maastrichtian) echinoderm remains in major museum collections from the Mons (southern Belgium) and Danish (Jylland (Jutland) and Sjælland (Zealand)) basins were compared to those of the Liège-Limburg Basin. The last-named has been studied in detail, including microscopical analysis of ossicles picked from bulk samples. Echinoids of the Mons Basin show similarities to those of the Liège-Limburg Basin, but crinoids, asteroids and ophiuroids remain poorly known from the former. Echinoderms of the Danish Basin resemble those of similar chalk lithofacies in the Liège-Limburg Basin, despite significant geographical separation. These disparities can be explained, at least in part, by collector bias in sampling methodology, although differences in substrate presumably also had an influence.     

Non-lethal sampling for stable isotope analysis of pike Esox lucius: how mucus,scale and fin tissue compare to muscle

Stable isotope analysis (SIA) was used to examine the isotopic relationships between dorsal muscle and fin, scale and epidermal mucus in pike Esox lucius. δ¹³C and δ¹⁵N varied predictably within each tissue pairing, with conversion factors calculated for the surrogate tissues, enabling their application to the non-lethal sampling of E. lucius for SIA.     

Predicting and correcting bias caused by measurement error in line transect sampling using multiplicative error models

Line transect sampling is one of the most widely used methods for animal abundance assessment. Standard estimation methods assume certain detection on the transect, no animal movement, and no measurement errors. Failure of the assumptions can cause substantial bias. In this work, the effect of error measurement on line transect estimators is investigated. Based on considerations of the process generating the errors, a multiplicative error model is presented and a simple way of correcting estimates based on knowledge of the error distribution is proposed. Using beta models for the error distribution, the effect of errors and of the proposed correction is assessed by simulation. Adequate confidence intervals for the corrected estimates are obtained using a bootstrap variance estimate for the correction and the delta method. As noted by Chen (1998, Biometrics 54, 899-908), even unbiased estimators of the distances might lead to biased density estimators, depending on the actual error distribution. In contrast with the findings of Chen, who used an additive model, unbiased estimation of distances, given a multiplicative model, lead to overestimation of density. Some error distributions result in observed distance distributions that make efficient estimation impossible, by removing the shoulder present in the original detection function. This indicates the need to improve field methods to reduce measurement error. An application of the new methods to a real data set is presented.     

Allele polymorphism and haplotype diversity of HLA-A, -B and -DRB1 loci in sequence-based typing for Chinese Uyghur ethnic group

HLA haplotype analysis has important application value in human population genetics, anthropological research and HLA matching transplantation. Based on HLA-A, -B, -C, -DRB1 and -DQB1 genotyping data from 663 families including 663 leukemia patients and 991 related donors, the allele frequency (AF) and haplotype frequency (HF) of two-, three- and five-locus haplotype distribution patterns in the Chinese Han population were determined by family segregation. A total of 38 alleles at A locus, 75 alleles at B locus, 35 alleles at C locus, 53 alleles at DRB1 locus and 22 alleles at DQB1 locus were discovered in this population. The frequencies of these alleles were basically consistent with those of previous reports except for some tiny differences. The study found 11 A-C, 15 C-B, 4 B-DRB1 and 11 DRB1-DQB1 two-locus haplotypes with a frequency over 2%. The number of A-C-B and A-B-DRB1 three-locus haplotype with a frequency over 1% were 11 and 3 respectively. The most common HLA-A-C-B-DRB1-DQB1 haplotype (HF>1%) were A*3001-C*0602-B*1302-DR*0701-DQ*0202 (4.30%), A*0207-C*0102-B*4601-DR*0901-DQ*0303 (3.07%), A*3303-C*0302-B*5801-DR*0301-DQ*0201 (1.49%) and A*1101-C*0102-B*4601-DR*0901-DQ*0303 (1.01%). The results are helpful for finding matching donors for hematopoietic stem cell transplant patients and also contribute to transplant immunology, HLA-related diseases, research of human genetics and other fields.     

Metabolic targeted therapy of cancer: current tracer technologies and future drug design strategies in the old metabolic network

Targeted drugs tailored against genes and signaling proteins have formed the new era termed Targeted Therapies. Although the field is relatively young, since only about 5 years ago clinical trials started showing promise, there have are already been significant setbacks due to drug resistance caused by point mutations, alterations in gene expression or complete loss of target proteins with disease progression. Although new drugs are continuously designed and tried, it seems inevitable that genetic and signal protein targets pose too broad flexibility and variability, often changing target characteristics and thus escape treatments turning “magic bullets” into rather “wondering bullets”. This is especially true in cancer, where old and new targeted therapies continue to fail and the most recent ones do not offer much improvement on clinical outcome parameters. Metabolic targeted therapies are aimed at control points of the metabolic network by targeting particular enzymes of major macromolecule synthesis pathways in cancer. This review summarizes the potential benefits of targeted therapies in the metabolic network as applied with genetic and proteomic approaches. The metabolic target approach is most efficient if and when pathway flux information is available for drug target development using the stable isotope based dynamic metabolic profile (SIDMAP) of tumor cells, in vitro or in vivo.This revised version was published online in June 2005. The previous version did not contain colour images.     

Determination of water quality,and trace metals in endemic Sarotherodon linellii,Pungu maclareni and Clarias maclareni,in crater Lake Barombi Mbo,Cameroon

Considering water pollution as a potential threat to some endemic cichlids of Lake Barombi Mbo, Cameroon, an investigation was done in 2011 to determine trace metals in its water, linking their uptake in gills and liver of fish to water chemistry. ICP-MS and ICP-OES analyses of trace metals based on total concentration of unfiltered lake water samples showed the presence of trace metals. All fish species accumulated Al, Mn and Sr in the highest concentrations in their gills, with Cu, Cd, Co, Cr, Pb and U highest in the liver. Pungu maclareni accumulated Al, Cr, Co, Sr and Pb in the highest concentrations. The highest mean gill Al concentration of 140 µg g^?1 dry weight was measured in P. maclareni gills, this being one of the critically endangered cichlids of the lake. Stable isotope analyses of carbon δ¹³C and nitrogen δ¹⁵N showed that P. maclareni had the highest mean δ¹³C (?30.2‰) and highest concentrations of Cr, Co, Pb and U in liver, probably linking the carbon source to the accumulation of metals. Though trace metal levels in the lake water were low, their presence in fish tissues suggest they are bioavailable, bioaccumulate and may pose a threat to the aquatic biota, and therefore should be monitored.     

Positive feedback and alternative stable states in inbreeding, cooperation, sex roles and other evolutionary processes

A large proportion of studies in systems science focus on processes involving a mixture of positive and negative feedbacks, which are also common themes in evolutionary ecology. Examples of negative feedback are density dependence (population regulation) and frequency-dependent selection (polymorphisms). Positive feedback, in turn, plays a role in Fisherian 'runaway' sexual selection, the evolution of cooperation, selfing and inbreeding tolerance under purging of deleterious alleles, and the evolution of sex differences in parental care. All these examples feature self-reinforcing processes where the increase in the value of a trait selects for further increases, sometimes via a coevolutionary feedback loop with another trait. Positive feedback often leads to alternative stable states (evolutionary endpoints), making the interpretation of evolutionary predictions challenging. Here, we discuss conceptual issues such as the relationship between self-reinforcing selection and disruptive selection. We also present an extension of a previous model on parental care, focusing on the relationship between the operational sex ratio and sexual selection, and the influence of this relationship on the evolution of biparental or uniparental care.     

Morphology,diet, and stable carbon isotopes: On the diet of Theropithecus and some limits of uniformitarianism in paleoecology

Geladas were long supposed to be the only living primates feeding almost entirely on graminoids and accordingly display dramatic dental and manual adaptive traits. A recent study of Theropithecus gelada, the first in a relatively undisturbed habitat, revealed a more diverse diet, also incorporating large quantities of forbs. The peculiar adaptive traits of T. gelada are also observed in extinct Theropithecus as early as 3.7 Ma. Stable carbon isotopic data of extinct Theropithecus from eastern Africa indicate that specimens older than 3 Ma consumed a significant proportion of C₃ plants (on average ca. 40% of total food intake) whereas specimens younger than 2 Ma consumed more C₄ plants (on average ca. 80%). Recent paleobotanical evidence suggests that C₃ herbaceous plants were still present in non‐negligible proportions in Plio‐Pleistocene lowland tropical ecosystems. Together, the shared morphological adaptive traits of extant and extinct Theropithecus and the varied diets of extant T. gelada suggest that the paleodiets of Theropithecus may have been dominated by herbaceous plants, comprising both C₃ forbs and graminoids and C₄ graminoids. The changes in stable carbon isotopes could correspond to a replacement of C₃ plants by C₄ plants within the herbaceous strata rather than a shift from C₃ woody vegetation to C₄ graminoids. This synthesis highlights the need for a more exhaustive knowledge of the ecology of extant species to achieve meaningful paleodietary and paleoenvironmental reconstructions. A strong selectivity for food resources that are rare in the landscapes (as in T. gelada) should also be considered when interpreting stable carbon isotopes of extinct African mammals (and notably hominids).     

准噶尔盆地东南缘多枝柽柳、白刺和红砂水分来源的异同

荒漠生态系统中, 水是植物生长最主要的限制因子。为了比较同一生境下不同荒漠植物的水分来源特征, 选取了同一生境下的多枝柽柳(Tamarix ramosissima)、白刺(Nitraria sibirica)和红砂(Reaumuria soongorica), 测定了这3种植物茎水和各潜在水源(降水、土壤水和地下水)的氢、氧稳定同位素比率(δD和δ¹⁸O)值, 并利用IsoSource软件计算了3种植物对潜在水源的利用比例。结果表明: 红砂和白刺的茎水δD和δ¹⁸O值及其水分来源有明显的季节波动特征。其中, 红砂为浅根系植物, 春季(3-5月)以表层土壤水为主要水源, 夏秋季节(6-10月)表层土壤含水量显著降低, 其主要的水分来源逐渐偏向于较深层的土壤水; 白刺的根系分布范围介于红砂和多枝柽柳之间, 在春季能够较多地利用表层土壤水, 而到了夏秋季节, 所利用的水分更多地来源于深层土壤水或地下水; 多枝柽柳为深根系植物, 其90%以上的水分来源于深层土壤水和地下水, 而且茎水δD和δ¹⁸O值及其水分来源没有季节波动特征。3种植物水分来源特征的差异与其水分利用策略密切相关, 同时, 也说明荒漠灌木可以通过自身调节向着最优(最有利)表现型发展, 从而最大限度地获取水分。     

Diet and trophic niche of Antarctic silverfish Pleuragramma antarcticum in the Ross Sea,Antarctica

The diet of Antarctic silverfish Pleuragramma antarcticum was evaluated by examining stomach contents of specimens collected in the Ross Sea (71°–77° S; 165°–180° E) in January to March 2008. Pleuragramma antarcticum (50–236 mm standard length, L_S) and prey items were analysed for stable‐isotopic composition of carbon and nitrogen. According to index of relative importance (I_RI), which incorporates frequency of occurrence, mass and number of prey items, the most important prey items were copepods (81%I_RI over all specimens), predominantly Metridia gerlachei and Paraeuchaeta sp., with krill and fishes having low I_RI (2·2 and 5·6%I_RI overall). According to mass of prey (M) in stomachs, however, fishes (P. antarcticum and myctophids) and krill dominated overall diet (48 and 22%M, respectively), with copepods being a relatively minor constituent of overall diet by mass (9·9%M). Piscivory by P. antarcticum occurred mainly in the extreme south‐west of the region and near the continental slope. Krill identified to species level in P. antarcticum stomachs were predominantly Euphausia superba (14·1%M) with some Euphausia crystallophorias (4·8%M). Both DistLM modelling (PRIMER‐permanova+) on stomach contents (by I_RI) and stepwise generalized linear modelling on stable isotopes showed that L_S and location were significant predictors of P. antarcticum diet. Postlarval P. antarcticum (50–89 mm L_S) consumed exclusively copepods. Juvenile P. antarcticum (90–151 mm L_S) consumed predominantly krill and copepods by mass (46 and 30%M, respectively). Small adult P. antarcticum (152–178 mm L_S) consumed krill, fishes and copepods (37, 36 and 15%M, respectively). Large adult P. antarcticum (179–236 mm L_S) consumed predominantly fishes and krill (55 and 17%M, respectively), especially in the north (near the Ross Sea slope) and in the SW Ross Sea. Amphipods were occasionally important prey items for P. antarcticum (western Ross Sea, 39%M). General concordance between stomach contents and trophic level of P. antarcticum and prey based on δ¹⁵N was demonstrated. Pleuragramma antarcticum trophic level was estimated as 3·7 (postlarval fish) and 4·1 (fish aged 3+ years).     

Enfleurage, lipid recycling and the origin of perfume collection in orchid bees

Enfleurage, the extraction of elusive floral scents with the help of a lipophilic carrier (grease), is widely used in the perfume industry. Male neotropical orchid bees (Euglossini), which accumulate exogenous fragrances as pheromone analogues, use a similar technique. To collect fragrances, the bees apply large amounts of straight-chain lipids to odoriferous surfaces from their cephalic labial glands, which dissolve the volatiles, and the mixture is then transferred to voluminous hind-leg pockets. Here, we show that males do in fact operate a lipid conveyor belt to accumulate and concentrate their perfume. From the hind-leg pockets of caged male Euglossa viridissima, deuterated derivatives of carrier lipids were consecutively sequestered, shuttled back to the labial glands and reused on consecutive bouts of fragrance collection. Such lipid cycling is instrumental in creating complex perfume bouquets. Furthermore, we found that labial glands of male orchid bees are strikingly similar to those of scent-marking male bumblebees in terms of size, form and structure. This, and a prominent overlap in secretory products, led us to propose that perfume collection evolved from scent-marking in ancestral corbiculate bees.     

Mobility,mortality, and the middle ages: Identification of migrant individuals in a 14th century black death cemetery population

Mobility and migration patterns of groups and individuals have long been a topic of interest to archaeologists, used for broad explanatory models of cultural change as well as illustrations of historical particularism. The 14th century AD was a tumultuous period of history in Britain, with severely erratic weather patterns, the Great Famine of 1315–1322, the Scottish Wars of Independence, and the Hundred Years' War providing additional migration pressures to the ordinary economic issues drawing individuals to their capital under more stable conditions. East Smithfield Black Death Cemetery (Royal Mint) had a documented use period of only 2 years (AD 1348–1350), providing a precise historical context (～50 years) for data. Adults (n = 30) from the East Smithfield site were sampled for strontium and oxygen stable isotope analyses of tooth enamel. Five individuals were demonstrated to be statistical outliers through the combined strontium and oxygen isotope data. Potential origins for migrants ranged from London's surrounding hinterlands to distant portions of northern and western Britain. Historic food sourcing practices for London were found to be an important factor for consideration in a broader than expected ⁸⁷Sr/⁸⁶Sr range reflected in a comparison of enamel samples from three London datasets. The pooled dataset demonstrated a high level of consistency between site data, divergent from the geologically predicted range. We argue that this supports the premise that isotope data in human populations must be approached as a complex interaction between behavior and environment and thus should be interpreted cautiously with the aid of alternate lines of evidence. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.     

海南新村湾海草床主要鱼类及大型无脊椎动物的食源

利用稳定碳同位素技术,分析了海南岛新村湾海草床中主要鱼类及大型无脊椎动物的食物来源。结果显示,有机碳源δ¹³C值的变化范围为-16.9‰--6.8‰,以海草叶片及其碎屑最高(-7.8‰ ±0.2‰),悬浮颗粒有机质(POM)最低(-16.9±0.2)‰,而附生藻类(-12.0±0.9)‰和沉积物有机质(SOM)(-13.2±0.2)‰居中。消费者δ¹³C值的变化范围为-15.4‰--6.4‰,表明其食物来源较广。IsoSource 混合模型计算结果表明,本海草床棘皮动物、多毛类、甲壳类和大部分的鱼类以海草为主要有机碳源,双壳类主要同化附生藻类和SOM的混合有机碳源,少数鱼类以POM为主要碳源。以上结果表明,海草是海草床中主要鱼类及大型无脊椎动物的重要食物来源。     

Population structure,life cycle,and trophic niche of the glacial relict amphipod,Gammaracanthus lacustris,in a large boreal lake

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白云岩风化剖面的粒度分布、元素迁移及碳同位素特征——以黔北新蒲剖面为例

研究了影响喀斯特地区土壤有机碳(SOC)更替的因素及其与元素地球化学行为的关系。选取黔北新蒲地区的两个白云岩风化剖面,以粒度分布、有机碳δ~(13)C和元素质量迁移系数为基础,对该区域红色风化壳中有机碳及δ~(13)C值随深度变化的趋势和元素的地球化学特征进行了探讨。结果显示,该区土壤分级后粉粒(5—50μm)含量占50%—80%,粘粒次之,砂粒最少;δ~(13)CSOC值介于-26.4‰―-23.6‰,且分级后的土样和原样中δ~(13)C值随着剖面深度的增加均减小,各粒级间差异不明显;草地覆被的剖面中铁、钾、钡、钒和锌表现出一定的富集,钠和钴在风化原岩处有一个富集端点,锰在岩粉处富集,镁、钙则完全迁出土体。而耕地剖面中,钒和锌呈现一定程度富集,铁、钾在岩土界面富集,钴在风化原岩富集,而钡在表层微弱富集。     

Below-threshold mortality: implications for studies in evolution,ecology and demography

Evolutionary biologists, ecologists and experimental gerontologists have increasingly used estimates of age-specific mortality as a critical component in studies of a range of important biological processes. However, the analysis of age-specific mortality rates is plagued by specific statistical challenges caused by sampling error. Here we discuss the nature of this ‘demographic sampling error’, and the way in which it can bias our estimates of (1) rates of ageing, (2) age at onset of senescence, (3) costs of reproduction and (4) demographic tests of evolutionary models of ageing. We conducted simulations which suggest that using standard statistical techniques, we would need sample sizes on the order of tens of thousands in most experiments to effectively remove any bias due to sampling error. We argue that biologists should use much larger sample sizes than have previously been used. However, we also present simple maximum likelihood models that effectively remove biases due to demographic sampling error even at relatively small sample sizes.     

若尔盖草甸退化对土壤碳、氮和碳稳定同位素的影响

为了解不同退化阶段高寒草甸土壤碳、氮和碳稳定同位素的差异,对若尔盖湿地内沼泽草甸、草原化草甸、退化草甸3个阶段土壤的碳、氮和碳稳定同位素进行了分析.结果表明:若尔盖湿地草甸土壤δ¹³C 值介于-26.21‰～-24.72‰之间,土壤δ¹³C 值随土层加深而增大.土壤δ¹³C 值与有机碳含量对数值呈线性负相关.表层土壤(0～10 cm)δ¹³C值大小顺序为草原化草甸>退化草甸>沼泽草甸,β值大小顺序为草原化草甸>沼泽草甸>退化草甸.沼泽草甸、草原化草甸、退化草甸0～30 cm 土壤碳含量分别为105.32、42.11和31.12 g·kg^-1,氮含量分别为8.74、3.41和2.81 g·kg^-1,C/N分别为11.26、11.23和10.89.随着草甸的退化,土壤碳、氮呈降低趋势,退化草甸C/N值低于沼泽草甸和草原化草甸.随着土层深度加深,碳、氮含量呈现降低趋势.草甸退化导致的土壤δ¹³C 值差异主要发生在表层0～10 cm.3个退化阶段中,退化草甸土壤的β值和C/N最低,表明退化草甸土壤矿化作用较强.     

基于稳定同位素技术的海州湾海洋牧场食物网基础及营养结构的季节性变化

基于稳定同位素技术对2015年春季海州湾海洋牧场海域采集的中小型生物消费者,包括鱼类、虾类、蟹类、头足类、螺类和双壳类等与其潜在碳源样品进行分析,利用IsoSource模型计算该海域消费者碳源贡献率,并对2014年夏季生物学样品与2015年春季样品比较,分析食物网营养结构的季节性变化,根据稳定同位素测定结果绘制二维双标图,计算出6种营养结构的量化指标.结果表明: 2015年春季海州湾海洋牧场海域消费者的δ¹³C值范围为-18.9‰～-17.1‰,3种潜在碳源[浮游植物、悬浮颗粒有机物(POM)、沉积物(SOM)]的δ¹³C值范围为-18.1‰～-23.4‰,根据模型计算得出浮游植物对消费者的平均碳源贡献最大,为80.8%,其余依次为SOM和POM,分别为10.8%和8.4%.2014年夏季生物样品与2015年春季样品的δ¹³C值存在显著差异,而δ¹⁵N值无显著性差异;6种量化指标表明群落营养结构存在季节性差异, 2014年夏季的δ¹³C比值范围(CR)、总面积(TA)、平均最邻近距离(NND)和平均最邻近距离标准差(SDNND)均大于2015年春季,δ¹⁵N比值范围(NR)和平均离心距离(CD)无明显变化,夏季群落营养结构冗余度小于春季,且食源多样性水平高于春季,存在季节差异.     

基于稳定同位素和热扩散技术的张北杨树水分关系差异

利用稳定氢同位素和热扩散技术研究张北防护林杨树的水分来源和蒸腾耗水,分析确定未退化与退化杨树的水分关系差异.结果表明:在生长季节中退化杨树主要利用0～30 cm土壤水分,未退化杨树主要利用30～80 cm土壤水分,两者的水分来源不同.旱季时,未退化杨树利用深层土壤水分和地下水的比例明显高于退化杨树.雨季中,杨树对0～30 cm土壤水分的利用比例增加,退化杨树增加幅度明显高于未退化杨树,对30～180 cm土壤水分的利用比例均减少.未退化杨树的液流速率大于退化杨树,不同天气中液流速率表现出相似的变化趋势,但未退化杨树液流的启动时间比退化杨树早.相关分析表明,未退化和退化杨树液流速率与土壤温度、风速、太阳辐射、相对湿度、空气温度均呈极显著的相关关系.退化杨树液流速率与土壤温度和空气相对湿度呈极显著负相关,与其他因素呈显著正相关,而未退化杨树仅与空气相对湿度呈极显著负相关,与其他因素均呈显著正相关关系,表明退化和未退化杨树蒸腾耗水易受环境条件的影响.退化杨树液流日累计量明显小于未退化杨树,表明其蒸腾耗水量较少;退化杨树水分来源浅,蒸腾耗水的减少并不能阻止林分退化.     

山东东营和烟台潮间带海草床食物网结构特征

为了探明海草床内主要生物类群间的营养关系以及食物网结构, 作者于2018年8月分别在东营黄河口潮间带和烟台西海岸潮间带海草床采集大型底栖生物样品, 采用δ ¹³C和δ ¹⁵N稳定同位素方法, 对生物样品的碳、氮同位素组成进行了测定和分析。结果表明: 东营海草床内生物的δ ¹³C、δ ¹⁵N值范围分别为-21.99‰至-12.13‰和5.23‰-11.05‰, 烟台海草床内生物的δ ¹³C、δ ¹⁵N值范围分别为-18.11‰至-14.06‰和6.60‰-10.22‰。东营海草床主要生物的营养级范围为2.00-3.85, 烟台海草床主要生物的营养级范围为2.00-3.15。根据δ ¹⁵N值计算所得的营养级图分析可知两区域海草床内初级消费者主要为滤食性双壳类和多毛类, 次级消费者为植食性或杂食性甲壳类,肉食性鱼类和腹足类。与近海海域大型底栖生物食物网相比, 海草床内底栖生物的营养级均值普遍较低。