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

Thank you very much for downloading modern applied statistics with s. As you may know, people have search hundreds times for their favorite readings like this modern applied statistics with s, but end up in harmful downloads. Rather than reading a good book with a cup of coffee in the afternoon, instead they cope with some harmful virus inside their laptop. modern applied statistics with s is available in our digital library an online access to it is set as public so you can download it instantly. Our digital library saves in multiple countries, allowing you to get the most less latency time to download any of our books like this one. Kindly say, the modern applied statistics with s is universally compatible with any devices to read.

Modern Applied Statistics With S

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...

https://bioone.org/journals/Bulletin-of-the-American-Museum-of-Natural-History/volume-2006/issue-297/0003-0090(2006)297[0001:TATOL]2.0.CO;2/THE-AMPHIBIAN-TREE-OF-LIFE/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2.pdf

The amphibian tree of life

Nutritional conditions during key periods of development, when the architecture and modus operandi of the body become established, are of profound importance in determining the subsequent life-history trajectory of an organism. If developing individuals experience a period of nutritional deficit, they can subsequently show accelerated growth should conditions improve, apparently compensating for the initial setback. However, recent research suggests that, although compensatory growth can bring quick benefits, it is also associated with a surprising variety of costs that are often not evident until much later in adult life. Clearly, the nature of these costs, the timescale over which they are incurred and the mechanisms underlying them will play a crucial role in determining compensatory strategies. Nonetheless, such effects remain poorly understood and largely neglected by ecologists and evolutionary biologists.

Compensation for a bad start: grow now, pay later?

It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites Since 1975, 12% of local populations have gone extinct We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20% Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change

http://max2.ese.u-psud.fr/epc/conservation/PDFs/HIPE/Sinervo2010.pdf

Erosion of lizard diversity by climate change and altered thermal niches.

Techniques of offspring size manipulation, "allometric engineering," were used in combination with studies of natural selection to elucidate the causal relation between egg size and offspring survival of lizards The results experimentally validate premises underlying theories of optimal egg size: fecundity selection favoring the production of large clutches of small eggs was balanced by survival selection favoring large offspring However, large hatchlings did not always have the highest survival, contrary to most theoretical expectations Optimizing selection on offspring size per se was the most common pattern Moreover, matches between average and optimal egg size were qualitative, not quantitative, perhaps reflecting known functional constraints on the production of large eggs

https://science.sciencemag.org/content/sci/258/5090/1927.full.pdf

Allometric engineering: a causal analysis of natural selection on offspring size.

Mating preferences are common in natural populations, and their divergence among populations is considered an important source of reproductive isolation during speciation. Although mechanisms for the divergence of mating preferences have received substantial theoretical treatment, complementary experimental tests are lacking. We conducted a laboratory evolution experiment, using the fruit fly Drosophila serrata, to explore the role of divergent selection between environments in the evolution of female mating preferences. Replicate populations of D. serrata were derived from a common ancestor and propagated in one of three resource environments: two novel environments and the ancestral laboratory environment. Adaptation to both novel environments involved changes in cuticular hydrocarbons, traits that predict mating success in these populations. Furthermore, female mating preferences for these cuticular hydrocarbons also diverged among populations. A component of this divergence occurred among treatment environments, accounting for at least 17.4% of the among-population divergence in linear mating preferences and 17.2% of the among-population divergence in nonlinear mating preferences. The divergence of mating preferences in correlation with environment is consistent with the classic by-product model of speciation in which premating isolation evolves as a side effect of divergent selection adapting populations to their different environments.

/pdf/divergent-selection-and-the-evolution-of-signal-traits-and-32cbnme7hi.pdf

Divergent Selection and the Evolution of Signal Traits and Mating Preferences

We demonstrate that egg size in side-blotched lizards is heritable (parent-offspring regressions) and thus will respond to natural selection. Because our estimate of heritability is derived from free-ranging lizards, it is useful for predicting evolutionary response to selection in wild populations. Moreover, our estimate for the heritability of egg size is not likely to be confounded by nongenetic maternal effects that might arise from egg size per se because we estimate a significant parent-offspring correlation for egg size in the face of dramatic experimental manipulation of yolk volume of the egg. Furthermore, we also demonstrate a significant correlation between egg size of the female parent and clutch size of her offspring. Because this correlation is not related to experimentally induced maternal effects, we suggest that it is indicative of a genetic correlation between egg size and clutch size. We synthesize our results from genetic analyses of the trade-off between egg size and clutch size with previously published experiments that document the mechanistic basis of this trade-off. Experimental manipulation of yolk volume has no effect on offspring reproductive traits such as egg size, clutch size, size at maturity, or oviposition date. However, egg size was related to offspring survival during adult phases of the life history. We partitioned survival of offspring during the adult phase of the life history into (1) survival of offspring from winter emergence to the production of the first clutch (i.e., the vitellogenic phase of the first clutch), and (2) survival of the offspring from the production of the first clutch to the end of the reproductive season. Offspring from the first clutch of the reproductive season in the previous year had higher survival during vitellogenesis of their first clutch if these offspring came from small eggs. We did not observe selection during these prelaying phases of adulthood for offspring from later clutches. However, we did find that later clutch offspring from large eggs had the highest survival over the first season of reproduction. The differences in selection on adult survival arising from maternal effects would reinforce previously documented selection that favors the production of small offspring early in the season and large offspring later in the season-a seasonal shift in maternal provisioning. We also report on a significant parent-offspring correlation in lay date and thus significant heritable variation in lay date. We can rule out the possibility of yolk volume as a confounding maternal effect-experimental manipulation of yolk volume has no effect on lay date of offspring. However, we cannot distinguish between genetic effects (i.e., heritable) and nongenetic maternal effects acting on lay date that arise from the maternal trait lay date per se (or other unidentified maternal traits). Nevertheless, we demonstrate how the timing of female reproduction (e.g., date of oviposition and date of hatching) affect reproductive attributes of offspring. Notably, we find that date of hatching has effects on body size at maturity and fecundity of offspring from later clutches. We did not detect comparable effects of lay date on offspring from the first clutch.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1996.tb02371.x

Interactive effects of offspring size and timing of reproduction on offspring reproduction: experimental, maternal, and quantitative genetic aspects

Life history trade-offs should be detectable as negative correlations between the relevant traits (e.g. reproductive output versus energy storage), but may be masked by variation in resource levels among individuals. One way to detect underlying trade-offs, at least in organisms that rely on stored energy for reproduction ("capital breeders"), may be to monitor an individual's energy stores before and after reproduction. We analysed energy stores and reproductive output in Eulamprus tympanum, a viviparous scincid lizard that stores energy for reproduction in its tail. One predicted trade-off (that between the size and number of offspring in a litter) is consistently observed, and is detectable with minimal information. Another predicted trade-off (that between offspring size and subsequent energy reserves) is not apparent in our data, perhaps because of constraints imposed by correlations among other traits. Finally, trade-offs between reproductive output and subsequent energy stores are evident in this species, but are only detectable with information on the extent of pre-reproductive as well as post-reproductive energy stores. For "capital breeders", non-destructive measurement of pre- and post-reproductive energy stores may greatly enhance our ability to detect significant life history trade-offs.

Detecting life history trade-offs : measuring energy stores in capital breeders reveals costs of reproduction

When animals reproduce, does energy for the brood come from stored re- serves (from food eaten months or years before), or from food eaten during the current reproductive season? Variation in the duration of energy storage prior to reproduction is an important, but little-studied, axis of life history variation. We experimentally manipulated the availability of resources to females of a long-lived viviparous lizard (Eulamprus tym- panum. Scincidae) in the first year of a two-year study to assess the relative importance of current food intake vs. stored reserves as sources of energy for breeding. Females given greater access to high temperatures (and hence, to resources) in the laboratory amassed larger caudal energy stores than did females with lesser opportunities. Energy intake during gestation slightly influenced offspring size, but the magnitude of energy stores prior to ovulation had a more dramatic effect: females with larger caudal energy stores produced much larger litters in the following year. Growth rates of females were unaffected by basking treatments or by reproduction in either year, but females that reproduced in the second year showed a large concomitant decrease in caudal energy stores compared to females that did not reproduce, indicating a large energetic cost of reproduction. Hence, reproductive output within this species can be influenced by resource availability over 12 months prior to reproduction, and simple comparisons of reproductive output with current resource avail- ability may fail to detect the ways in which phenotypically plastic life history traits are influenced by environmental features. In addition to an appropriate temporal framework, models of resource allocation should also incorporate the possible roles of physiological and morphological constraints (e.g., maternal inability, in some species, to modify post- ovulation reproductive expenditure) and trade-offs with other life history currencies (e.g., decrements in maternal survival due to high relative clutch masses). The time lag between resource acquisition and expenditure may have significant consequences for a population's demographic response to shifts in resource availability or predation pressure (via tail au- totomy). Finally, this study illustrates the way in which thermal aspects of the environment can influence life history phenotypes in ectothermic vertebrates with long-term energy stores.

Paul Doughty

Papers

Allometric engineering: a causal analysis of natural selection on offspring size.

Divergent Selection and the Evolution of Signal Traits and Mating Preferences

Interactive effects of offspring size and timing of reproduction on offspring reproduction: experimental, maternal, and quantitative genetic aspects

Detecting life history trade-offs : measuring energy stores in capital breeders reveals costs of reproduction

Reproductive energy allocation and long‐term energy stores in a viviparous lizard (eulamprus tympanum)