Statistics for Spatial Data.

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

▪ Abstract About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.

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Genetic Analyses from Ancient DNA

Attempts to relate estimates of regional FST to gene flow and drift via Wright's (1931) equation FST ≈ 1/ (4Nm + 1) are often inappropriate because most natural sets of populations probably are not at equilibrium (McCauley 1993), as assumed by the island model upon which the equation is based, or ineffective because the influences of gene flow and drift are confounded in the product Nm. Evaluations of the association between genetic (FST ) and geographic distances separating all pairwise populations combinations in a region allows one to test for regional equilibrium, to evaluate the relative influences of gene flow and drift on population structure both within and between regions, and to visualize the behavior of the association across all degrees of geographic separation. Tests of the model using microsatellite data from 51 populations of eastern collared lizards (Crotaphytus collaris collaris) collected from four distinct geographical regions gave results highly consistent with predicted patterns of association based on regional differences in various historical and ecological factors that affect the amount of drift and gene flow. The model provides a prerequisite for and an alternative to regional FST analyses, which often simply assume regional equilibrium, thus potentially leading to erroneous and misleading inferences regarding regional population structure.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1999.tb04571.x

Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability

The analysis of food webs and their dynamics facilitates understanding of the mechanistic processes behind community ecology and ecosystem functions. Having accurate techniques for determining dietary ranges and components is critical for this endeavour. While visual analyses and early molecular approaches are highly labour intensive and often lack resolution, recent DNA-based approaches potentially provide more accurate methods for dietary studies. A suite of approaches have been used based on the identification of consumed species by characterization of DNA present in gut or faecal samples. In one approach, a standardized DNA region (DNA barcode) is PCR amplified, amplicons are sequenced and then compared to a reference database for identification. Initially, this involved sequencing clones from PCR products, and studies were limited in scale because of the costs and effort required. The recent development of next generation sequencing (NGS) has made this approach much more powerful, by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). Continual improvement of NGS technologies, on-going decreases in costs and current massive expansion of reference databases make this approach promising. Here we review the power and pitfalls of NGS diet methods. We present the critical factors to take into account when choosing or designing a suitable barcode. Then, we consider both technical and analytical aspects of NGS diet studies. Finally, we discuss the validation of data accuracy including the viability of producing quantitative data.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2011.05403.x

Who is eating what: diet assessment using next generation sequencing.

Pollen Records of Late Quaternary North American Sediments

Publisher Summary This chapter discusses the role of palynology in archaeology. A primary objective of archaeological investigation is to reconstruct and explain as fully as possible mechanisms and directions of prehistoric culture change. To accomplish this task, the archaeologist must look beyond the recovery and identification of cultural materials, such as lithic debris, points, grinding stones, perishables, and pottery. Through the careful analysis of other sources of information—such as plant macrofossils, namely, seeds, leaves, bark, flowers, and wood; animal remains, namely, bones, hair, tooth, and shells; soil chemistry, charcoal identification, and pollen—the archaeologist is able to speak more confidently about many aspects of past cultures. Once these analyses are completed, the archaeologist also is afforded an opportunity to test hypotheses about the paleoenvironment, diet, subsistence, disease, and the level of prehistoric technology and trade. One of these formerly peripheral areas of archaeological study being investigated with increased regularity is the recovery and analysis of fossil pollen. Although most archaeologists are aware of the basics of palynology, many of them are still not aware of the wide range of data that palynology can provide; they are neither familiar with new sampling techniques that yield these data nor aware of the importance of asking for the advice of a palynologist prior to conducting actual field investigations.

The Role of Palynology in Archaeology

DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2–4 different animal species and 4–8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

/pdf/a-molecular-analysis-of-dietary-diversity-for-three-archaic-2qq5oz2gmx.pdf

A molecular analysis of dietary diversity for three archaic Native Americans

Paleoenvironmental records spanning more than 30,000 years are used to reconstruct an overview of vegetational changes occurring in Texas during the late-Quaternary. Primary emphasis is devoted to reconstructions based on published and unpublished palynologi­ cal data. Those records are supplemented, where appropriate, by supporting information gained from geological, archaeological, paleontological. and non-palynological botanical sources. Briefly, the combined record indicates that elements of the northern and southeastern United States flora, including Picea glauca, invaded regions of east and central Texas during the late-Quaternary period and remained part of the regional vegetation until late-glacial times. Although vast regions of west Texas were probably covered by conifer forests during the full-glacial period, those forests were not as widespread as some earlier reports have indicated. The area of south Texas revealed that a mosaic vegetational pattern proba­ bly was well established throughout the post-glacial period and perhaps even longer. And, it appears that regions of north Texas contained grassland savannas during the post-glacial and part of the late-glacial period.

Vaughn M. Bryant

Papers

Pollen Records of Late Quaternary North American Sediments

The Role of Palynology in Archaeology

A molecular analysis of dietary diversity for three archaic Native Americans

A late-quaternary paleoenvironmental record of texas: an overview of the pollen evidence

Forensic palynology: why do it and how it works.