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

Genetics and analysis of quantitative traits

MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.

http://ieeexplore.ieee.org/iel2/4524/12820/00592460.pdf

Image Processing

What is ecological speciation

Developmental Plasticity and Evolution. In: Mary Jane West-Eberhard, Editor, Oxford University Press (2003) Pp. xi+794. Price $50.00 paper.

A focus on novel, confirmatory, and statistically significant results leads to substantial bias in the scientific literature. One type of bias, known as “p-hacking,” occurs when researchers collect or select data or statistical analyses until nonsignificant results become significant. Here, we use text-mining to demonstrate that p-hacking is widespread throughout science. We then illustrate how one can test for p-hacking when performing a meta-analysis and show that, while p-hacking is probably common, its effect seems to be weak relative to the real effect sizes being measured. This result suggests that p-hacking probably does not drastically alter scientific consensuses drawn from meta-analyses.

/pdf/the-extent-and-consequences-of-p-hacking-in-science-hxdoh51lek.pdf

The Extent and Consequences of P-Hacking in Science

The fitness consequences of mate choice are a source of ongoing debate in evolutionary biology. Recent theory predicts that indirect benefits of female choice due to offspring inheriting superior genes are likely to be negated when there are direct costs associated with choice, including any costs of mating with attractive males. To estimate the fitness consequences of mating with males of varying attractiveness, we housed female house crickets, Acheta domesticus, with either attractive or unattractive males and measured a variety of direct and indirect fitness components. These fitness components were combined to give relative estimates of the number of grandchildren produced and the intrinsic rate of increase (relative net fitness). We found that females mated to attractive males incur a substantial survival cost. However, these costs are cancelled out and may be outweighed by the benefits of having offspring with elevated fitness. This benefit is due predominantly, but not exclusively, to the effect of an increase in sons' attractiveness. Our results suggest that the direct costs that females experience when mating with attractive males can be outweighed by indirect benefits. They also reveal the value of estimating the net fitness consequences of a mating strategy by including measures of offspring quality in estimates of fitness.

/pdf/the-indirect-benefits-of-mating-with-attractive-males-299qx8kib1.pdf

The indirect benefits of mating with attractive males outweigh the direct costs

It is widely recognized that maternal phenotype can have important effects on offspring, but paternal phenotype is generally assumed to have no influence in animals lacking paternal care. Nonetheless, selection may favour the transfer of environmentally acquired condition to offspring from both parents. Using a split-brood, cross-generational laboratory design, we manipulated a key environmental determinant of condition ‐ larval diet quality ‐ of parents and their offspring in the fly Telostylinus angusticollis, in which there is no evidence of paternal provisioning. Parental diet did not affect offspring survival, but high-condition mothers produced larger eggs, and their offspring developed more rapidly when on a poor larval diet. Maternal condition had no effect on adult body size of offspring. By contrast, large, high-condition fathers produced larger offspring, and follow-up assays showed that this paternal effect can be sufficient to increase mating success of male offspring and fecundity of female offspring. Our findings suggest that both mothers and fathers transfer their condition to offspring, but with effects on different offspring traits. Moreover, our results suggest that paternal effects can be important even in species lacking conventional forms of paternal care. In such species, the transfer of paternal condition to offspring could contribute to indirect selection on female mate preferences.

/pdf/maternal-and-paternal-condition-effects-on-offspring-4njkh9tih4.pdf

Maternal and paternal condition effects on offspring phenotype in Telostylinus angusticollis (Diptera: Neriidae).

Observer bias and other “experimenter effects” occur when researchers’ expectations influence study outcome. These biases are strongest when researchers expect a particular result, are measuring subjective variables, and have an incentive to produce data that confirm predictions. To minimize bias, it is good practice to work “blind,” meaning that experimenters are unaware of the identity or treatment group of their subjects while conducting research. Here, using text mining and a literature review, we find evidence that blind protocols are uncommon in the life sciences and that nonblind studies tend to report higher effect sizes and more significant p-values. We discuss methods to minimize bias and urge researchers, editors, and peer reviewers to keep blind protocols in mind.

/pdf/evidence-of-experimental-bias-in-the-life-sciences-why-we-4ue6i6z8xf.pdf

Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording.

During sexual imprinting, offspring learn parental phenotypes and then select mates who are similar to their parents. Imprinting has been thought to contribute to the process of speciation in only a few rare cases; this is despite imprinting's potential to generate assortative mating and solve the problem of recombination in ecological speciation. If offspring imprint on parental traits under divergent selection, these traits will then be involved in both adaptation and mate preference. Such ‘magic traits’ easily generate sexual isolation and facilitate speciation. In this study, we show that imprinting occurs in two ecologically divergent stickleback species (benthics and limnetics: Gasterosteus spp.). Cross-fostered females preferred mates of their foster father's species. Furthermore, imprinting is essential for sexual isolation between species; isolation was reduced when females were raised without fathers. Daughters imprinted on father odour and colour during a critical period early in development. These traits have diverged between the species owing to differences in ecology. Therefore, we provide the first evidence that imprinting links ecological adaptation to sexual isolation between species. Our results suggest that imprinting may facilitate the evolution of sexual isolation during ecological speciation, may be especially important in cases of rapid diversification, and thus play an integral role in the generation of biodiversity.

Megan L. Head

Papers

The Extent and Consequences of P-Hacking in Science

The indirect benefits of mating with attractive males outweigh the direct costs

Maternal and paternal condition effects on offspring phenotype in Telostylinus angusticollis (Diptera: Neriidae).

Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording.

Sexual imprinting on ecologically divergent traits leads to sexual isolation in sticklebacks