Quantifying Inter- and Intra-Population Niche Variability Using Hierarchical Bayesian Stable Isotope Mixing Models

Variability in resource use defines the width of a trophic niche occupied by a population. Intra-population variability in resource use may occur across hierarchical levels of population structure from individuals to subpopulations. Understanding how levels of population organization contribute to population niche width is critical to ecology and evolution. Here we describe a hierarchical stable isotope mixing model that can simultaneously estimate both the prey composition of a consumer diet and the diet variability among individuals and across levels of population organization. By explicitly estimating variance components for multiple scales, the model can deconstruct the niche width of a consumer population into relevant levels of population structure. We apply this new approach to stable isotope data from a population of gray wolves from coastal British Columbia, and show support for extensive intra-population niche variability among individuals, social groups, and geographically isolated subpopulations. The analytic method we describe improves mixing models by accounting for diet variability, and improves isotope niche width analysis by quantitatively assessing the contribution of levels of organization to the niche width of a population.     

Detection of DNA in Ancient Skeletal Remains Using DNA Flow Cytometry

Cortical bone samples were removed from individual burials from Tomb Dk31 in the Dakhleh Oasis, Egypt. The tissue was disaggregated, stained with the DNA specific fluorescent dye DAPI and analyzed using the flow cytom-eter. DNA flow cytometry measures the cellular DNA content and this is correlated with modal chromosome content. When DNA is present in skeletal remains further investigations such as extracting, amplifying and sequencing may then be carried out. The method offers a relatively rapid and inexpensive means of pinpointing samples of skeletal DNA that can be further analyzed.     

Detection of DNA in Ancient Skeletal Remains Using DNA Flow Cytometry

Cortical bone samples were removed from individual burials from Tomb Dk31 in the Dakhleh Oasis, Egypt. The tissue was disaggregated, stained with the DNA specific fluorescent dye DAPI and analyzed using the flow cytom-eter. DNA flow cytometry measures the cellular DNA content and this is correlated with modal chromosome content. When DNA is present in skeletal remains further investigations such as extracting, amplifying and sequencing may then be carried out. The method offers a relatively rapid and inexpensive means of pinpointing samples of skeletal DNA that can be further analyzed.     

Monitoring DNA Contamination in Handled vs. Directly Excavated Ancient Human Skeletal Remains

Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14^th century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as “virgin samples” (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called “lab samples”(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from “lab samples” are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the “virgin samples” set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between “lab” and “virgin” samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history.     

Stable Isotope Ratios and Forensic Analysis of Microorganisms

In the aftermath of the anthrax letters of 2001, researchers have been exploring various analytical signatures for the purpose of characterizing the production environment of microorganisms. One such signature is stable isotope ratios, which in heterotrophs, are a function of nutrient and water sources. Here we discuss the use of stable isotope ratios in microbial forensics, using as a database the carbon, nitrogen, oxygen, and hydrogen stable isotope ratios of 247 separate cultures of Bacillus subtilis 6051 spores produced on a total of 32 different culture media. In the context of using stable isotope ratios as a signature for sample matching, we present an analysis of variations between individual samples, between cultures produced in tandem, and between cultures produced in the same medium but at different times. Additionally, we correlate the stable isotope ratios of carbon, nitrogen, oxygen, and hydrogen for growth medium nutrients or water with those of spores and show examples of how these relationships can be used to exclude nutrient or water samples as possible growth substrates for specific cultures.     

Stable Isotope Analysis in Primatology: A Critical Review

Stable isotope analysis has become an important tool in ecology over the last 25 years. A wealth of ecological information is stored in animal tissues in the relative abundances of the stable isotopes of several elements, particularly carbon and nitrogen, because these isotopes navigate through ecological processes in predictable ways. Stable carbon and nitrogen isotopes have been measured in most primate taxonomic groups and have yielded information about dietary content, dietary variability, and habitat use. Stable isotopes have recently proven useful for addressing more fine‐grained questions about niche dynamics and anthropogenic effects on feeding ecology. Here, we discuss stable carbon and nitrogen isotope systematics and critically review the published stable carbon and nitrogen isotope data for modern primates with a focus on the problems and prospects for future stable isotope applications in primatology. Am. J. Primatol. 74:969‐989, 2012. © 2012 Wiley Periodicals, Inc.     

Aberrant Water Homeostasis Detected by Stable Isotope Analysis

While isotopes are frequently used as tracers in investigations of disease physiology (i.e., ¹⁴C labeled glucose), few studies have examined the impact that disease, and disease-related alterations in metabolism, may have on stable isotope ratios at natural abundance levels. The isotopic composition of body water is heavily influenced by water metabolism and dietary patterns and may provide a platform for disease detection. By utilizing a model of streptozotocin (STZ)-induced diabetes as an index case of aberrant water homeostasis, we demonstrate that untreated diabetes mellitus results in distinct combinations, or signatures, of the hydrogen (δ²H) and oxygen (δ¹⁸O) isotope ratios in body water. Additionally, we show that the δ²H and δ¹⁸O values of body water are correlated with increased water flux, suggesting altered blood osmolality, due to hyperglycemia, as the mechanism behind this correlation. Further, we present a mathematical model describing the impact of water flux on the isotopic composition of body water and compare model predicted values with actual values. These data highlight the importance of factors such as water flux and energy expenditure on predictive models of body water and additionally provide a framework for using naturally occurring stable isotope ratios to monitor diseases that impact water homeostasis.     

An Analysis of the Alleged Skeletal Remains of Carin G?ring

In 1991, treasure hunters found skeletal remains in an area close to the destroyed country residence of former Nazi leader Hermann Göring in northeastern Berlin. The remains, which were believed to belong to Carin Göring, who was buried at the site, were examined to determine whether it was possible to make a positive identification. The anthropological analysis showed that the remains come from an adult woman. The DNA analysis of several bone elements showed female sex, and a reference sample from Carin''s son revealed mtDNA sequences identical to the remains. The profile has one nucleotide difference from the Cambridge reference sequence (rCRS), the common variant 263G. A database search resulted in a frequency of this mtDNA sequence of about 10% out of more than 7,000 European haplotypes. The mtDNA sequence found in the ulna, the cranium and the reference sample is, thus, very common among Europeans. Therefore, nuclear DNA analysis was attempted. The remains as well as a sample from Carin''s son were successfully analysed for the three nuclear markers TH01, D7S820 and D8S1179. The nuclear DNA analysis of the two samples revealed one shared allele for each of the three markers, supporting a mother and son relationship. This genetic information together with anthropological and historical files provides an additional piece of circumstantial evidence in our efforts to identify the remains of Carin Göring.     

Factor Analysis as a Technique for Exploring Patterned Variability in Archaeological Remains

Abstract

The utility of factor analysis for exploring underlying patterns of variation in a data-set was assessed by means of a factor analytic arrangement of provenience units from the Medicine Crow Site (39BF2), South Dakota, based on similarities in the formal qualities of the ceramic vessels contamed within each provenience. Results indicate that two patterns, interpreted as relating to temporal and spatial variation at Medicine Crow, may be Isolated.     

Stable Isotope Probing Analysis of Interactions between Ammonia Oxidizers

The response of natural microbial communities to environmental change can be assessed by determining DNA- or RNA-targeted changes in relative abundance of 16S rRNA gene sequences by using fingerprinting techniques such as denaturing gradient gel electrophoresis (DNA-DGGE and RNA-DGGE, respectively) or by stable isotope probing (SIP) of 16S rRNA genes following incubation with a ¹³C-labeled substrate (DNA-SIP-DGGE). The sensitivities of these three approaches were compared during batch growth of communities containing two or three Nitrosospira pure or enriched cultures with different tolerances to a high ammonia concentration. Cultures were supplied with low, intermediate, or high initial ammonia concentrations and with ¹³C-labeled carbon dioxide. DNA-SIP-DGGE provided the most direct evidence for growth and was the most sensitive, with changes in DGGE profiles evident before changes in DNA- and RNA-DGGE profiles and before detectable increases in nitrite and nitrate production. RNA-DGGE provided intermediate sensitivity. In addition, the three molecular methods were used to follow growth of individual strains within communities. In general, changes in relative activities of individual strains within communities could be predicted from monoculture growth characteristics. Ammonia-tolerant Nitrosospira cluster 3b strains dominated mixed communities at all ammonia concentrations, and ammonia-sensitive strains were outcompeted at an intermediate ammonia concentration. However, coexistence of ammonia-tolerant and ammonia-sensitive strains occurred at the lowest ammonia concentration, and, under some conditions, strains inhibited at high ammonia in monoculture were active at high ammonia in mixed cultures, where they coexisted with ammonia-tolerant strains. The results therefore demonstrate the sensitivity of SIP for detection of activity of organisms with relatively low yield and low activity and its ability to follow changes in the structure of interacting microbial communities.Molecular characterization of natural microbial communities has demonstrated the existence of novel high-level taxonomic groups with no cultured representatives and with significant diversity within phylogenetic and functional groups already established through analysis of organisms in laboratory culture. Autotrophic ammonia-oxidizing bacteria (AOB) exemplify the latter situation. Their low growth rates and the limited number of readily measured phenotypic characteristics available for identification of these organisms necessitate the use of molecular techniques for characterization of their diversity in natural environments. Phylogenetic analysis of 16S rRNA gene sequences places the majority of cultivated autotrophic bacterial ammonia oxidizers in a monophyletic group within the Betaproteobacteria (8, 26). Amplification and phylogenetic analysis of 16S rRNA gene sequences from enrichment cultures of ammonia oxidizers and sequences of environmental clones (31) suggest the existence of novel groups with no cultivated representative and considerable diversity within those represented by pure cultures.Increased awareness of microbial diversity has raised questions regarding links between species diversity and functional diversity, functional redundancy, and the influence of environmental conditions on the activities of representatives of different phylotypes. For ammonia-oxidizing bacteria, relationships exist between broad phylogenetic groups and the environments from which laboratory isolates were obtained, which are linked, in some cases, to differences in physiological characteristics (11). There is also evidence of links between the relative abundance of different ammonia oxidizer groups and environmental conditions (1, 13, 14, 18, 21, 23, 34), suggesting selection for organisms with particular physiological characteristics. In one study (36), a combination of molecular and physiological studies has demonstrated links between species diversity, functional diversity, and soil nitrification kinetics. However, for ammonia oxidizers and other groups, there is little direct evidence about which strains within diverse communities are active under particular conditions or the extent of competition for substrates.Stable isotope probing (SIP) (24, 27) of nucleic acids provides direct evidence of which members of mixed communities are active. This involves addition of substrates labeled with a stable isotope (most commonly ¹³C), extraction of nucleic acids, separation of ¹²C- and ¹³C-labeled nucleic acids by density gradient centrifugation, and subsequent molecular analysis. Sequences amplified from ¹³C-labeled DNA or RNA are derived from organisms actively assimilating the substrate. This approach has been used to identify organisms that utilize methane or methanol (4, 19), organic compounds (15, 20), or CO₂ (6, 9) in microcosms and those that assimilate plant root exudates in the field (28). SIP therefore links phylogeny to ecosystem function and has identified established and novel groups by utilizing labeled compounds in complex soil communities. The technique also enables in situ physiological studies and investigation of interactions between organisms in mixed cultures belonging to the same functional group. For autotrophic betaproteobacterial ammonia oxidizers, amplification of 16S rRNA genes from ¹³C-labeled DNA during incubation with [¹³C]CO₂ has the potential for discriminating which strains are active under specific conditions. Assessment of the discriminatory ability of this approach in complex natural environments requires studies under controlled and well-characterized conditions. The first aim of this study was, therefore, to assess the ability of SIP to discriminate activities of different members of simple mixed communities in comparison with direct measurement of product concentration and DNA- and RNA-denaturing gradient gel electrophoresis (DGGE). The second was to determine whether the activities of members of mixed communities of ammonia-oxidizing bacteria, in particular, their ability to grow at high ammonia concentrations, could be predicted from their physiological characteristics in monoculture. Of particular interest was whether strains with low ammonia tolerance are competitive at low ammonia concentrations. Mixed cultures were assembled from pure culture representatives of Nitrosospira clusters 0, 3a, and 3b (26, 36), which are frequently found in soil environments, and from enrichment cultures containing representatives of these clusters with heterotrophic contaminants. Other criteria for choice of community members were similarities in specific growth rate and cultivation conditions to enable meaningful competition experiments.     

鸟类组织稳定同位素分析样品的预处理方法

稳定同位素分析样品在进行同位素质谱分析之前需要适当的处理,然而如何处理尚未形成统一的标准。本文结合鸟类组织稳定同位素分析样品的测试流程,介绍了鸟类学研究领域稳定同位素技术应用中涉及的分析样品解冻清洗、干燥、分离纯化、研磨和储存等前处理方法,并对不同组织常用的处理方法及分析样品测定中有待解决的问题展开了讨论。旨在抛砖引玉,为利用稳定同位素技术开展鸟类学方面的研究提供科学参考和技术支持。     

Eating between the Lines: Mississippian Migration and Stable Carbon Isotope Variation in Fort Ancient Populations

ABSTRACT   Appreciating variation along the edges of traditional archaeological Culture Historical boundaries requires close consideration of social contexts associated with culture contact. We focus on dietary variation as a function of these concerns through a case study of Fort Ancient populations who, on average, consumed lower quantities of maize than their Mississippian neighbors as determined by stable carbon isotope ratios of bone collagen. However, this dichotomy is not as rigid as initially thought, with some Fort Ancient burials producing stable carbon isotope ratios similar to Mississippian cases. Detailed investigation of internal variation of carbon isotopes for human burials at the SunWatch site provides evidence that contact included small-scale Mississippian migrations to Fort Ancient sites. The main conclusion is that variation in diet and archaeological context can be a useful approach for examining prehistoric migration.     

Compound-Specific Stable Isotope Analysis: Implications in Hexachlorocyclohexane in-vitro and Field Assessment

Assessment of biotic and abiotic degradation reactions by studying the variation in stable isotopic compositions of organic contaminants in contaminated soil and aquifers is being increasingly considered during the last two decades with development of Compound specific stable isotope analysis (CSIA) technique. CSIA has been recognized as a potential tool for evaluating both qualitative and quantitative degradation with measurement of shifts in isotope ratios of contaminants and their degradation products as its basis. Amongst a wide variety of environmental pollutants including monoaromatics, chlorinated ethenes and benzenes etc., it is only recently that its efficacy is being tested for assessing biodegradation of a noxious pollutant namely hexachlorocyclohexane (HCH), by pure microbial cultures as well as directly at the field site. Anticipating the increase in demand of this technique for monitoring the microbial degradation along with natural attenuation, this review highlights the basic problems associated with HCH contamination emphasizing the applicability of emerging CSIA technique to absolve the major bottlenecks in assessment of HCH. To this end, the review also provides a brief overview of this technique with summarizing the recent revelations put forward by both in vitro and in situ studies by CSIA in monitoring HCH biodegradation.     

Stable Isotope Trophic Shifts in White-Tailed Deer

Abstract Differences between diet and tissue isotope values known as trophic shifts (Δδ¹³C and Δδ¹⁵N) occur during digestion and assimilation of consumed food. Consideration of trophic shifts is essential when using stable isotopes for dietary reconstruction but has received little attention for cervids. Therefore, our purpose was to determine C and N trophic shifts in tissues of captive white-tailed deer (Odocoileus virginianus) fed corn and alfalfa in known amounts over a 4-month period. Antler has also received limited consideration for use in dietary reconstruction, thus, we analyzed tissue to expose variation among locations along the main beam and between antler components. We collected antler, hair, red blood cells (RBCs), and serum at the end of the feeding trial and analyzed them to determine C (δ¹³C) and N (δ¹⁵N) isotope values. Trophic shifts occurred between diet and all tissues for both isotopes with mean Δδ¹³C = 1.19 ± 2.23% and Δδ¹⁵N = 4.93 ± 0.74%. Antler trophic shifts were greater than those in all other tissues for δ¹³C, whereas antler and RBCs shared similar trophic enrichment over diet but differed from hair and serum for Δδ¹⁵N. Trophic shift values were significantly related to diet in hair and serum for δ¹³C and antler and RBCs for Δδ¹⁵N. Isotope values for antler core and periphery plus antler locations along the main beam did not vary. Antler collagen significantly varied from whole antler for δ¹³C but not δ¹⁵N. Our findings provide mean trophic shift values by tissue that can be used for dietary reconstruction in the study and management of cervids.     

稳定同位素技术在个体溯源中的应用

个体身份确认是自然灾害、空难、爆炸、火灾、交通事故等事（案）件处置中的一项重要工作。利用稳定同位素分布的地域差异性对个体进行溯源，可以为个体身份确认提供重要信息。本文简要介绍了稳定同位素技术原理，系统阐述了用于个体溯源的元素类型和不同人体组织中稳定同位素蕴含的特征信息，并对该技术在个体溯源中的应用现状、存在问题以及未来发展进行了分析和展望。     

鸟类组织中稳定同位素周转率研究现状

稳定同位素分析技术被广泛应用于鸟类生态学多个方面的研究,如鸟类迁徙、营养级关系、生活史、食性等。根据不同的研究目的和要求,选择目标周期相对应的组织进行研究。在此前提下,掌握不同组织稳定同位素的周转率就显得尤为重要。目前国内有关鸟类组织稳定同位素周转率及其差异的研究较为有限,本文对国际上研究周转率的常见假说、方法和影响周转率的因素进行综述,旨在抛砖引玉,为利用稳定同位素技术开展鸟类学方面的研究提供依据。     

Subterranean Sympatry: An Investigation into Diet Using Stable Isotope Analysis

In the Western Cape three species of mole-rat occur in sympatry, however, little is known about differences in their dietary preferences. Dietary composition of the three species; the common mole-rat (Cryptomys hottentotus hottentotus), the Cape mole-rat (Georychus capensis) and the Cape dune mole-rat (Bathyergus suillus) were examined using stable isotope analysis. Blood, fur and claw samples were collected from 70 mole-rats, in addition to several potential food items, to assess food selection of the three species under natural conditions. Overall there was a significant difference in the isotopic composition (δ¹³C and δ¹⁵N) between all three species and significant differences in their diet composition. There were also significant differences between tissues in all three species suggesting temporal variation in diet. The small size and colonial lifestyle of C. h. hottentotus allows it to feed almost 100% on bulbs, while the solitary and larger species G. capensis and B. suillus fed to a greater extent on other resources such as grasses and clover. B. suillus, the largest of the species, had the most generalized diet. However, overall all species relied most heavily upon geophytes and consumed the same species suggesting competition for resources could exist. We also showed a high level of individual variation in diet choices. This was most pronounced in B. suillus and G. capensis and less so in C. h. hottentotus. We demonstrate that stable isotope analysis can successfully be applied to examine dietary patterns in subterranean mammals and provide insights into foraging patterns and dietary variation at both the inter and intra population level.     

Termite Prey Specialization in the Pitcher Plant Nepenthes albomarginata--Evidence from Stable Isotope Analysis

Old World pitcher plants (Nepenthes spp., Nepenthaceae) trapand digest invertebrate prey to derive nutrients, primarilynitrogen (N). In the majority of lowland Nepenthes species studiedto date, ants (Hymenoptera, Formicidae) are numerically thedominant prey taxon. Nepenthes albomarginata is unusual in showingan apparent bias towards the capture of termites (Isoptera).We tested the hypothesis that N. albomarginata derives N fromtermite capture, by comparison of foliar stable N isotope abundance(