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

Whether inbreeding affects the demography and persistence of natural populations has been questioned. However, new pedigree data from field populations and molecular and analytical tools for tracing patterns of relationship and inbreeding have now enhanced our ability to detect inbreeding depression within and among wild populations. This work reveals that levels of inbreeding depression vary across taxa, populations and environments, but are usually substantial enough to affect both individual and population performance. Data from bird and mammal populations suggest that inbreeding depression often significantly affects birth weight, survival, reproduction and resistance to disease, predation and environmental stress. Plant studies, based mostly on comparing populations that differ in size or levels of genetic variation, also reveal significant inbreeding effects on seed set, germination, survival and resistance to stress. Data from butterflies, birds and plants demonstrate that populations with reduced genetic diversity often experience reduced growth and increased extinction rates. Crosses between such populations often result in heterosis. Such a genetic rescue effect might reflect the masking of fixed deleterious mutations. Thus, it might be necessary to retain gene flow among increasingly fragmented habitat patches to sustain populations that are sensitive to inbreeding.

Inbreeding effects in wild populations.

Biological invasions cause ecological and economic impacts across the globe. However, it is unclear whether there are strong patterns in terms of their major effects, how the vulnerability of different ecosystems varies and which ecosystem services are at greatest risk. We present a global meta-analysis of 199 articles reporting 1041 field studies that in total describe the impacts of 135 alien plant taxa on resident species, communities and ecosystems. Across studies, alien plants had a significant effect in 11 of 24 different types of impact assessed. The magnitude and direction of the impact varied both within and between different types of impact. On average, abundance and diversity of the resident species decreased in invaded sites, whereas primary production and several ecosystem processes were enhanced. While alien N-fixing species had greater impacts on N-cycling variables, they did not consistently affect other impact types. The magnitude of the impacts was not significantly different between island and mainland ecosystems. Overall, alien species impacts are heterogeneous and not unidirectional even within particular impact types. Our analysis also reveals that by the time changes in nutrient cycling are detected, major impacts on plant species and communities are likely to have already occurred.

Ecological impacts of invasive alien plants: a meta-analysis of their effects on species, communities and ecosystems

/pdf/molecular-evolutionary-genetics-analysis-1uvpbl4lte.pdf

Molecular Evolutionary Genetics Analysis

Genetic diversity is one of the three forms of biodiversity recognized by the World Conservation Union (IUCN) as deserving conservation. The need to conserve genetic diversity within populations is based on two arguments: the necessity of genetic diversity for evolution to occur, and the expected relation- ship between heterozygosity and population fitness. Because loss of genetic diversity is related to inbreed- ing, and inbreeding reduces reproductive fitness, a correlation is expected between heterozygosity and pop- ulation fitness. Long-term effective population size, which determines rates of inbreeding, should also be correlated with fitness. However, other theoretical considerations and empirical observations suggest that the correlation between fitness and heterozygosity may be weak or nonexistent. We used all the data sets we could locate (34) to perform a meta-analysis and resolve the issue. Data sets were included in the study, provided that fitness, or a component of fitness, was measured for three or more populations along with heterozygosity, heritability, and/or population size. The mean weighted correlation between measures of genetic diversity, at the population level, and population fitness was 0.4323. The correlation was highly sig- nificant and explained 19% of the variation in fitness. Our study strengthens concerns that the loss of het- erozygosity has a deleterious effect on population fitness and supports the IUCN designation of genetic di- versity as worthy of conservation.

Correlation between Fitness and Genetic Diversity

The developmental stability of an organism is reflected in its ability to produce an ‘ideal’ form under a particular set of conditions (Zakharov, 1992). The lower its stability, the greater the likelihood it will depart from this ‘ideal’ form. Ideal forms are rarely known a priori. However, bilateral structures in bilaterally symmetrical organisms offer a precise ideal, perfect symmetry, against which departures may be compared (Palmer & Strobeck, 1986). Thus they provide a very convenient method for assessing deviations from the norm, and studying the factors that might influence such deviations.

Fluctuating asymmetry analyses: a primer

Because of its simplicity, the binary-switch nature of left-right asymmetry permits meaningful comparisons among many different organisms. Phylogenetic analyses of asymmetry variation, inheritance, and molecular mechanisms reveal unexpected insights into how development evolves. First, directional asymmetry, an evolutionary novelty, arose from nonheritable origins almost as often as from mutations, implying that genetic assimilation ("phenotype precedes genotype") is a common mode of evolution. Second, the molecular pathway directing hearts leftward-the nodal cascade-varies considerably among vertebrates (homology of form does not require homology of development) and was possibly co-opted from a preexisting asymmetrical chordate organ system. Finally, declining frequencies of spontaneous asymmetry reversal throughout vertebrate evolution suggest that heart development has become more canalized.

https://science.sciencemag.org/content/sci/306/5697/828.full.pdf

Symmetry breaking and the evolution of development.

▪ Abstract Selective reporting—e.g., the preferential publication of results that are statistically significant, or consistent with theory or expectation—presents a challenge to meta-analysis and seriously undermines the quest for generalizations. Funnel graphs (scatterplots of effect size vs. sample size) help reveal the extent of selective reporting. They also allow the strength of biological effects to be judged easily, and they reaffirm the value of graphical presentations of data over statistical summaries. Funnel graphs of published results, including: (a) sex-ratio variation in birds, (b) field estimates of heritabilities, and (c) relations between fluctuating asymmetry and individual attractiveness or fitness, suggest selective reporting is widespread and raise doubts about the true magnitude of these phenomena. Quasireplication—the “replication” of previous studies using different species or systems—has almost completely supplanted replicative research in ecology and evolution. Without incentives...

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QUASIREPLICATION AND THE CONTRACT OF ERROR: Lessons from Sex Ratios, Heritabilities and Fluctuating Asymmetry

Marine gastropod molluscs exhibit a wide range of shell forms, many of which are believed to provide some defense against predation. Vermeij (1974) has suggested that narrow or occluded apertures, low spires, thickened shells and strong sculpture act in various ways to deter the attacks of shell-breaking or shell-entering predators. In addition, Vermeij (1976, 1977a) has presented evidence suggesting that inter-oceanic differences in crab predation intensity may have been responsible for the evolution of less vulnerable shells among Indo-West Pacific gastropods when compared with Eastern Pacific and Tropical Atlantic ones. Similarly, one might expect regional differences in the intensity of a particular mode of predation to lead to geographic variation in the frequencies and degree of development of a mode-specific morphological defense. Crabs and fishes are almost certainly the most important shell-breaking predators on lower intertidal and subtidal gastropods. Their modes of feeding, however, are rather different. Crabs are able to manipulate shells more precisely and can apply their chelae to a shell in a variety of ways. They should be less deterred by strong external sculpture than by thickened shells, reduced spires, or reinforced or occluded apertures, except when shells are small relative to chelae. On the other hand, fishes that crush gastropods must use their jaws and hence can only apply stress to very restricted portions of a shell in a restricted manner. They should be more effectively deterred by certain types of strong external sculpture than by thickened lips or restrictive apertures. More specifically, stout spines or nodes appear to reduce susceptibility to being crushed by fish. Such sculpture may act in at least four ways (Fig. 1): 1) it increases the effective diameter of the shell, thus decreasing the mechanical advantage of the predator's crushing apparatus; 2) it distributes the stress over a larger area of the shell; 3) it localizes the stress at the thickest parts of the shell; and 4) it focuses the applied force to a very restricted area of the crushing surface, increasing the chance of damage to the predator. The structural similarity of strong axial ribbing suggests it should perform in a similar manner. Shell thickness and to some degree overall shell shape may also affect susceptibility to crushing. In this paper I directly test the importance of stout spines as a potential defense against crushing by fish. Observations on the type of damage inflicted by crushing fishes serve as the basis for some speculation about how other morphologies might also reduce vulnerability. Finally I consider the geographic distribution of stout spinose sculpture and how it relates to the distribution of shell-destroying fishes. Experimental studies that examine the importance of gastropod shells as a defense against predation have almost exclusively employed crabs as predators (Ebling et al., 1964; Kitching et al., 1966; Kitching and Lockwood, 1974; Vermeij, 1976; Zipser and Vermeij, 1978; but see Ivlev's 1961 study of freshwater carp, roach and perch on Limnaea ovata of different shell thicknesses, p. 102). The present study represents the first experimental examination of the types of shell morphologies that offer an effective defense against shell-crushing fishes and rays. Although I have only

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1979.tb04722.x

Fish predation and the evolution of gastropod shell sculpture: experimental and geographic evidence.

Those familiar with human nature and the publication process acknowledge that biases due to selective reporting of results are likely widespread in all fields of academic inquiry that depend on tools of statistical inference (e.g., see Begg and Berlin 1988; Iyengar and Greenhouse 1988; and the extensive discussion following each). However, although qualitative and quantitative methods exist for assessing the prevalence of selective reporting, and selective reporting has been studied in the medical and social sciences (Begg 1994, and references therein), the issue has received little attention in recent meta-analyses of ecological and evolutionary patterns. Clearly, “if publication bias is present, and if it operates in the same direction for all studies (as is likely), then [meta-analysis] is likely not only to produce biased summary estimates but also to produce estimates which are apparently precise and accurate leading to conclusions which may not only be wrong but appear convincing” (Begg and Berlin 1988, p. 437). To biologists unacquainted with the formal study of publication patterns, the terms “selective reporting” (statistical significance of an outcome influences its likelihood of being reported or published) and “publication bias” (the inflation of average effect size due to selective reporting) may imply a conscious intent to deceive, but this

/pdf/detecting-publication-bias-in-meta-analyses-a-case-study-of-3dnwuhiq72.pdf

A. Richard Palmer

Papers

Fluctuating asymmetry analyses: a primer

Symmetry breaking and the evolution of development.

QUASIREPLICATION AND THE CONTRACT OF ERROR: Lessons from Sex Ratios, Heritabilities and Fluctuating Asymmetry

Fish predation and the evolution of gastropod shell sculpture: experimental and geographic evidence.

Detecting publication bias in meta-analyses: A case study of fluctuating asymmetry and sexual selection