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.

Fifty years ago David Lack put forward a key hypothesis in life-history theory: that avian clutch is ultimately determined by the number of young that parents can provide with food. Since then, a plethora of brood manipulations has shown that birds can rear more young than the number of eggs they lay, and prompted a search for negative effects of increased effort on future reproduction. However, recent studies have shown that the demands of laying and incubating eggs generally omitted from experiments, could affect parental fitness. Lack's hypothesis, and the tests of its validity, need to be extended to encompass the full demands of producing and rearing the brood.

Why don't birds lay more eggs?

Sex ratio theory predicts that, if prevailing ecological or social circumstances differentially influence the fitness benefits of offspring of each sex, parents should adjust their production accordingly to maximize fitness. For species in which sex is chromosomally determined, such as birds and mammals, a differential effect of maternal condition on the fitness of male and female young is one important route whereby selection is expected to favor a bias in the offspring sex ratio at birth or egg laying. However, despite its central place in sex allocation theory, this hypothesis has rarely been tested in wild populations. We manipulated maternal condition upward and downward in a sexually dimorphic wild bird and examined the effect on offspring survival and on offspring sex ratio. The survival to fledging of male, but not female, young was substantially reduced if they came from less well provisioned eggs produced by females in relatively poor condition. As female condition, and thereby her capacity to produce high quality eggs, declined, she progressively skewed the sex ratio of her eggs toward females; i.e., she produced more of the sex with the higher survival prospects. The decline in the survival of male offspring, and the sex ratio bias, was removed when maternal condition was enhanced. These results provide experimental evidence of an adaptive, facultative adjustment of sex ratio in response to changes in maternal condition in wild birds.

https://www.pnas.org/content/pnas/96/2/570.full.pdf

Experimental demonstration that offspring sex ratio varies with maternal condition

Egg quality is a phenotype of, and can profoundly influence fitness in, both mother and offspring. However, the physiological mechanisms that underlie this maternal effect are poorly understood. Carotenoids are hypothesized to enhance antioxidant activity and immune function, and are responsible for the pigmentation of egg yolk. The proximate basis and consequences of this maternal investment, however, have not previously been studied in wild birds. In this supplemental feeding study of lesser black-backed gulls, Larus fuscus, carotenoid-fed females are shown to have increased integument pigmentation, higher plasma concentrations of carotenoids and antioxidant activity, and lower plasma concentrations of immunoglobulins (Igs) in comparison with controls. In turn, carotenoid-fed females produced eggs containing high carotenoid but low Ig concentrations (i.e. passive immunity), whereas control females produced eggs containing low carotenoid but high Ig concentrations. Within-clutch patterns of these resources varied over the laying sequence in a similar manner in both carotenoid-fed and control nests. Our results suggest that carotenoids could be one resource responsible for egg quality maternal effects in birds. We discuss the possible implications of carotenoid-mediated effects on phenotype for fitness in mothers and their offspring.

/pdf/carotenoids-and-egg-quality-in-the-lesser-black-backed-gull-3v6pq5b78a.pdf

Carotenoids and egg quality in the lesser black-backed gull Larus fuscus: a supplemental feeding study of maternal effects

Understanding the selective pressures shaping the number of offspring per breeding event is a key area in the study of life-history strategies. However, in species with parental care, costs incurred in offspring production, rather than rearing, have been largely ignored in both theoretical and empirical studies until relatively recently. Furthermore, the few experimental studies that have manipulated production costs have not yet teased apart effects that operate via the parental phenotype from effects on the quality of the resulting young. To examine whether increased egg production influences parental brood rearing capacity independently of effects operating via egg quality, we experimentally increased egg production in gulls and then examined their capacity to rear a control clutch. We found that the capacity of parents to rear the control brood was substantially reduced solely as a consequence of having themselves produced one extra egg. The paradox that, in many species, parents apparently aim for fewer young per breeding event than the experimentally and theoretically demonstrated optimum, has partly arisen from the failure to take into account the constraints imposed by production costs.

/pdf/the-price-of-eggs-increased-investment-in-egg-production-5533ccifbj.pdf

The price of eggs: increased investment in egg production reduces the offspring rearing capacity of parents

Naef-Daenzer, L., Naef-Daenzer, B. and Nager, R. G. 2000. Prey selection and foraging performance of breeding Great Tits Parus major in relation to food availability. ‐ J. Avian Biol. 31: 206‐214. We studied the nestling diet and the foraging performance of Great Tits in relation to prey abundance in the field. Numerous experimental studies present data on foraging decisions in captive Great Tits. Little is, however, known about prey selection in the field in relation to the food available and the consequences this has for the food delivery rate to nestlings. Since the foraging performance of the parents is one of the main determinants of fledging weight and juvenile survival, foraging behaviour is an important part of Great Tit reproduction. During the early breeding season up to 75% of the prey biomass delivered to the nestlings were spiders, which is in contrast with other studies. Only when caterpillars reached a size of 10‐12 mg (approximately the average size of the spiders caught at that time) did the Great Tits change their preferences and 80‐90% of the delivered prey masses were caterpillars, as reported by other authors. This ‘switching’ between prey occurred within a few days. It was not related to the changes in abundance but to size of caterpillars. The rate at which caterpillars were delivered to the nestlings (in mg:nestling:h) was strongly correlated with the caterpillar biomass available (in mg:m of branches) and nestling growth rate was significantly influenced by the mass of available caterpillars. The results provide evidence why perfect timing of breeding is so important for the Great Tit, and contribute to the understanding of the causal link between food supply, growth and breeding success.

Ruedi G. Nager

Papers

Why don't birds lay more eggs?

Experimental demonstration that offspring sex ratio varies with maternal condition

Carotenoids and egg quality in the lesser black-backed gull Larus fuscus: a supplemental feeding study of maternal effects

The price of eggs: increased investment in egg production reduces the offspring rearing capacity of parents

Prey selection and foraging performance of breeding Great Tits Parus major in relation to food availability