So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.

/pdf/generalized-linear-mixed-models-a-practical-guide-for-3gh61pkir0.pdf

Generalized linear mixed models: a practical guide for ecology and evolution

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

Beginning with Emlen (1966) and MacArthur and Pianka (1966) and extending through the last ten years, several authors have sought to predict the foraging behavior of animals by means of mathematical models. These models are very similar,in that they all assume that the fitness of a foraging animal is a function of the efficiency of foraging measured in terms of some "currency" (Schoener, 1971) -usually energy- and that natural selection has resulted in animals that forage so as to maximize this fitness. As a result of these similarities, the models have become known as "optimal foraging models"; and the theory that embodies them, "optimal foraging theory." The situations to which optimal foraging theory has been applied, with the exception of a few recent studies, can be divided into the following four categories: (1) choice by an animal of which food types to eat (i.e., optimal diet); (2) choice of which patch type to feed in (i.e., optimal patch choice); (3) optimal allocation of time to different patches; and (4) optimal patterns and speed of movements. In this review we discuss each of these categories separately, dealing with both the theoretical developments and the data that permit tests of the predictions. The review is selective in the sense that we emphasize studies that either develop testable predictions or that attempt to test predictions in a precise quantitative manner. We also discuss what we see to be some of the future developments in the area of optimal foraging theory and how this theory can be related to other areas of biology. Our general conclusion is that the simple models so far formulated are supported are supported reasonably well by available data and that we are optimistic about the value both now and in the future of optimal foraging theory. We argue, however, that these simple models will requre much modification, espicially to deal with situations that either cannot easily be put into one or another of the above four categories or entail currencies more complicated that just energy.

Citation classic - optimal foraging - a selective review of theory and tests

A DNA test to sex most birds.

Long-lived species are expected to reduce their current reproductive effort in adverse conditions in order not to jeopardize their future reproduction. Parasitic Jaegers (Stercorarius parasiticus) breeding in Shetland, United Kingdom, have declined substantially in numbers over the last 15 years, although the causes of this decline remain unclear. By carrying out a supplementary feeding experiment during the chick-rearing period, we tested the hypothesis that food availability has contributed to this decline. Data were collected on adult territory attendance, chick growth rates, and breeding success during the experimental season, and adult return rates, body condition, and laying dates during the following season. Differences in carbon and nitrogen isotope ratios in the natural and supplementary food, analyzed in the chicks' feathers, showed that chicks received one-fifth of their protein requirements from the supplementary food, but this amount varied between broods. Compared with controls, supplemented pairs showed higher attendance on the territory, improved breeding success, and higher return rate. This emphasizes that adult return rate is more sensitive to food availability than has been assumed previously. Control birds may have maintained too high a current reproductive effort at the expense of future reproduction, perhaps due to the unpredictability of their main food source, sandeels, which seemed abundant early in the season but scarce during chick rearing. This study suggests that the consequences of poor food availability are shared between offspring and parents in this species.

Food availability affects adult survival as well as breeding success of parasitic jaegers

Increasing temperatures associated with climate change may generate phenological mismatches that disrupt previously synchronous trophic interactions. Most work on mismatch has focused on temporal trends, whereas spatial variation in the degree of trophic synchrony has largely been neglected, even though the degree to which mismatch varies in space has implications for meso-scale population dynamics and evolution. Here we quantify latitudinal trends in phenological mismatch, using phenological data on an oak–caterpillar–bird system from across the UK. Increasing latitude delays phenology of all species, but more so for oak, resulting in a shorter interval between leaf emergence and peak caterpillar biomass at northern locations. Asynchrony found between peak caterpillar biomass and peak nestling demand of blue tits, great tits and pied flycatchers increases in earlier (warm) springs. There is no evidence of spatial variation in the timing of peak nestling demand relative to peak caterpillar biomass for any species. Phenological mismatch alone is thus unlikely to explain spatial variation in population trends. Given projections of continued spring warming, we predict that temperate forest birds will become increasingly mismatched with peak caterpillar timing. Latitudinal invariance in the direction of mismatch may act as a double-edged sword that presents no opportunities for spatial buffering from the effects of mismatch on population size, but generates spatially consistent directional selection on timing, which could facilitate rapid evolutionary change.

/pdf/tritrophic-phenological-match-mismatch-in-space-and-time-4fkoeevmlr.pdf

Tritrophic phenological match-mismatch in space and time.

Although most bird species are socially monogamous, they show a large variation in both divorce rate and the proportion of extra-pair paternity (EPP). Recently, adaptive explanations of avian monogamy have considered divorce and EPP as related behavioural strategies by which individuals paired with low quality mates can improve their breeding status within ecological and time constraints. It has been suggested that, at both the intra- and inter-specific levels, divorce rate should be associated with the frequency of EPP. Divorce and EPP could coexist as alternative strategies whose relative frequencies would depend on ecological conditions, resulting in a negative association between the two phenomena. Or, they can be seen as synergistic tactics co-varying with variation in mate quality between populations or species and are thus positively associated. Here, applying two different comparative methods: the comparison of independent linear contrast and the pairwise comparison of closely related taxa, we show that high rates of divorce are positively associated with high rates of extra-pair paternity in socially monogamous species of birds, even when controlling for survival rate as a potentially confounding variable. This constitutes the first comparative evidence for a relation between divorce and adultery in animals. We discuss this result in relation to recent hypotheses on the adaptiveness of divorce and extra-pair copulations in birds and natural variation in mate quality among populations or species. The pattern found is most consistent with the hypothesis that birds may divorce to gain a better breeding position, but alternatives cannot be fully ruled out.

Comparative evidence for a positive association between divorce and extra-pair paternity in birds

The zebra finch

Oxidative stress (OS) as a proximate mechanism for life-history trade-offs is widespread in the literature. One such resource allocation trade-off involves growth rate, and theory suggests that OS might act as both a constraint on and a cost of growth, yet studies investigating this have produced conflicting results. Here, we use meta-analysis to investigate whether increased OS levels impact on growth (OS as a constraint on growth) and whether greater growth rates can increase OS (OS as a cost of growth). The role of OS as a constraint on growth was supported by the meta-analysis. Greater OS, in terms of either increased damage or reduced levels of antioxidants, was associated with reduced growth although the effect depended on the experimental manipulation used. Our results also support an oxidative cost of growth, at least in terms of increased oxidative damage, although faster growth was not associated with a change in antioxidant levels. These findings that OS can act as a constraint on growth support theoretical links between OS and animal life histories and provide evidence for a growth-self-maintenance trade-off. Furthermore, the apparent oxidative costs of growth imply individuals cannot alter this trade-off when faced with enhanced growth. We offer a starting platform for future research and recommend the use of oxidative damage biomarkers in nonlethal tissue to investigate the growth-OS relationship further.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.2080

Ruedi G. Nager

Papers

Food availability affects adult survival as well as breeding success of parasitic jaegers

Tritrophic phenological match-mismatch in space and time.

Comparative evidence for a positive association between divorce and extra-pair paternity in birds

The zebra finch

Meta-analysis indicates that oxidative stress is both a constraint on and a cost of growth.