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

Large datasets are increasingly common and are often difficult to interpret. Principal component analysis (PCA) is a technique for reducing the dimensionality of such datasets, increasing interpretability but at the same time minimizing information loss. It does so by creating new uncorrelated variables that successively maximize variance. Finding such new variables, the principal components, reduces to solving an eigenvalue/eigenvector problem, and the new variables are defined by the dataset at hand, not a priori , hence making PCA an adaptive data analysis technique. It is adaptive in another sense too, since variants of the technique have been developed that are tailored to various different data types and structures. This article will begin by introducing the basic ideas of PCA, discussing what it can and cannot do. It will then describe some variants of PCA and their application.

https://royalsocietypublishing.org/doi/pdf/10.1098/rsta.2015.0202

Principal component analysis: a review and recent developments

Statistics and Data Analysis in Geology

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

/pdf/the-amphioxus-genome-and-the-evolution-of-the-chordate-2hi9ggv8nx.pdf

The amphioxus genome and the evolution of the chordate karyotype

Many organisms are currently polyploid, or have a polyploid ancestry and now have secondarily 'diploidized' genomes. This finding is surprising because retained whole-genome duplications (WGDs) are exceedingly rare, suggesting that polyploidy is usually an evolutionary dead end. We argue that ancient genome doublings could probably have survived only under very specific conditions, but that, whenever established, they might have had a pronounced impact on species diversification, and led to an increase in biological complexity and the origin of evolutionary novelties.

/pdf/the-evolutionary-significance-of-ancient-genome-duplications-1vfes15hej.pdf

The evolutionary significance of ancient genome duplications

Vertebrate evolution has been punctuated by three episodes of widespread gene or genome duplication, which have been linked with the origin of vertebrates, gnathostomes and teleosts, respectively. These three events coincide with bursts of character acquisition and increases in phenotypic complexity, and many researchers have suggested a causal relationship between the two. However, this pattern is derived from data for living taxa only; we argue here that, when fossils are taken into account, bursts of character acquisition disappear and gen(om)e duplication in vertebrate phylogeny can no longer be correlated with the origin of body plans. If patterns of character acquisition or morphological gaps between higher taxa are a reflection of phenotypic complexity, then more inclusive data sets incorporating fossil taxa provide no support for hypotheses linking gen(om)e duplications and the evolution of complexity in vertebrates.

/pdf/genome-duplication-extinction-and-vertebrate-evolution-1q4cc7u0ic.pdf

Genome duplication, extinction and vertebrate evolution

All aspects of conodont paleontology rely on the identification and description of homologous anatomical units or elements. But the current schemes of anatomical notation and terms for orientation were formulated at a time when little was known of conodont anatomy or skeletal architecture, resulting in some confusion and difficulties in their application. With improving knowledge of cono- donts, these problems are becoming increasingly acute. In an attempt to address current problems, we introduce new terms for orientation in conodonts and their elements, and a modified scheme of anatomical notation. The principal axes of the conodont body are identified as rostrocaudal, dorsoventral, and mediolateral, with opposite lateral sides designated dextral and sinistral. Anatomical notation is defined according to topological relationships between elements with reference to the principal axes of the body and takes the form of letters with numeric subscripts (e.g., P 1 ,P 2 ,S 0-S4). The ozarkodinid apparatus serves as a standard, but the Pn-Sn scheme can be applied rigorously to all taxa that are known from natural assemblages or where an hypothesis of topological homology can be inferred from secondary morphological criteria. homology as an hypothesis of similarity that is based on topo- logical relations and which contains potential phylogenetic in- formation (see Rieppel, 1994 for discussion). Topology refers to the numbers of, and the relative spatial relationships between, recognizable anatomical units. Similarity, in this context, does not mean morphological similarity of the units under consider- ation. We should also point out that homology is hierarchical, operating at different levels including genes, development, and structure. It is also contextual as illustrated by the classic ex- ample of batwings and birdwings; these structures are homolo- gous as tetrapod forelimbs but not as wings. In this paper we deal only with homology of whole elements within the conodont apparatus (not homology of the apparatus, nor homology of parts of elements).

/pdf/orientation-and-anatomical-notation-in-conodonts-1xsro7wqz5.pdf

Orientation and anatomical notation in conodonts

Exceptional preservation of soft-bodied Cambrian chordates provides our only direct information on the origin of vertebrates. Fossil chordates from this interval offer crucial insights into how the distinctive body plan of vertebrates evolved, but reading this pre-biomineralization fossil record is fraught with difficulties, leading to controversial and contradictory interpretations. The cause of these difficulties is taphonomic: we lack data on when and how important characters change as they decompose, resulting in a lack of constraint on anatomical interpretation and a failure to distinguish phylogenetic absence of characters from loss through decay. Here we show, from experimental decay of amphioxus and ammocoetes, that loss of chordate characters during decay is non-random: the more phylogenetically informative are the most labile, whereas plesiomorphic characters are decay resistant. The taphonomic loss of synapomorphies and relatively higher preservation potential of chordate plesiomorphies will thus result in bias towards wrongly placing fossils on the chordate stem. Application of these data to Cathaymyrus (Cambrian period of China) and Metaspriggina (Cambrian period of Canada) highlights the difficulties: these fossils cannot be placed reliably in the chordate or vertebrate stem because they could represent the decayed remains of any non-biomineralized, total-group chordate. Preliminary data suggest that this decay filter also affects other groups of organisms and that 'stem-ward slippage' may be a widespread but currently unrecognized bias in our understanding of the early evolution of a number of phyla.

Non-random decay of chordate characters causes bias in fossil interpretation

The origin and radiation of mammals are key events in the history of life, with fossils placing the origin at 220 million years ago, in the Late Triassic period1. The earliest mammals, representing the first 50 million years of their evolution and including the most basal taxa, are widely considered to be generalized insectivores1, 2. This implies that the first phase of the mammalian radiation—associated with the appearance in the fossil record of important innovations such as heterodont dentition, diphyodonty and the dentary–squamosal jaw joint1, 3—was decoupled from ecomorphological diversification2, 4. Finds of exceptionally complete specimens of later Mesozoic mammals have revealed greater ecomorphological diversity than previously suspected, including adaptations for swimming, burrowing, digging and even gliding2, 5, 6, but such well-preserved fossils of earlier mammals do not exist1, and robust analysis of their ecomorphological diversity has previously been lacking. Here we present the results of an integrated analysis, using synchrotron X-ray tomography and analyses of biomechanics, finite element models and tooth microwear textures. We find significant differences in function and dietary ecology between two of the earliest mammaliaform taxa, Morganucodon and Kuehneotherium—taxa that are central to the debate on mammalian evolution. Morganucodon possessed comparatively more forceful and robust jaws and consumed ‘harder’ prey, comparable to extant small-bodied mammals that eat considerable amounts of coleopterans. Kuehneotherium ingested a diet comparable to extant mixed feeders and specialists on ‘soft’ prey such as lepidopterans. Our results reveal previously hidden trophic specialization at the base of the mammalian radiation; hence even the earliest mammaliaforms were beginning to diversify—morphologically, functionally and ecologically. In contrast to the prevailing view2, 4, this pattern suggests that lineage splitting during the earliest stages of mammalian evolution was associated with ecomorphological specialization and niche partitioning.

https://lra.le.ac.uk/bitstream/2381/29192/2/Final_merged_main.pdf

Dietary specializations and diversity in feeding ecology of the earliest stem mammals

FEEDING mechanisms may hold the key to understanding the selective pressures that led to the evolution of vertebrates1–3. But in the absence of direct evidence, hypotheses of feeding mechanisms in the most primitive extinct vertebrates are somewhat speculative, and scenarios that seek to explain vertebrate origins remain controversial. The recognition that the affinities of conodonts lie among the most primitive vertebrates4–6 shifts the balance in this debate. I illustrate here microscopic wear patterns on conodont elements that provide the first unequivocal evidence that they functioned as teeth. These microwear patterns were produced as food was crushed and sheared between opposed conodont elements brought into bilateral occlusion. The presence of teeth and evidence of macrophagy in such primitive and early vertebrates support hypotheses that the first vertebrates were predators.

Mark A. Purnell

Papers

Genome duplication, extinction and vertebrate evolution

Orientation and anatomical notation in conodonts

Non-random decay of chordate characters causes bias in fossil interpretation

Dietary specializations and diversity in feeding ecology of the earliest stem mammals

Microwear on conodont elements and macrophagy in the first vertebrates