Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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

This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls.

genepop'007: a complete re-implementation of the genepop software for Windows and Linux

We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w1118; iso-2; iso-3 strain and the reference y1; cn1 bw1 sp1 strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in...

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

Ecological changes in the phenology and distribution of plants and animals are occurring in all well-studied marine, freshwater, and terrestrial groups These observed changes are heavily biased in the directions predicted from global warming and have been linked to local or regional climate change through correlations between climate and biological variation, field and laboratory experiments, and physiological research Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change Tropical coral reefs and amphibians have been most negatively affected Predator-prey and plant-insect interactions have been disrupted when interacting species have responded differently to warming Evolutionary adaptations to warmer conditions have occurred in the interiors of species’ ranges, and resource use and dispersal have evolved rapidly at expanding range margins Observed genetic shifts modulate local effects of climate change, but there is little evidence that they will mitigate negative effects at the species level

https://www.fws.gov/southwest/es/documents/R2ES/LitCited/LPC_2012/Parmesan_2006.pdf

Ecological and Evolutionary Responses to Recent Climate Change

Hybrid zones are, roughly speaking, narrow regions in which genetically distinct populations meet, mate, and produce hybrids. They are often only a few hundred meters wide and yet may be several hundred kilometers long. They are found in a wide variety of organisms: Tables 1 and 2 list about 150 reasonably clear examples, in which there is a spatial transition between two hybridizing forms. Such a widespread and striking phenomenon requires explanation; more importantly, it offers us several ways of understanding the nature and origin of species. First, hybrid zones pose interesting questions for the taxonomist, for they contrast two views of the species: as a set of populations delimited by genetic barriers to gene exchange; and as a set of populations maintained in a particular stable equilibrium by selection. Second, the wide range of genotypes found in a hybrid zone can be used to analyze the genetic differences and selective forces that separate the taxa involved. This may allow some inferences about the way these differences evolved and, by extrapolation, about the way fully isolated species diverge from each other. Finally, models of parapatric speciation, and of Wright's "shifting balance," involve the formation, move­ ment, and modification of hybrid zones. Hybrid zones must be understood before the plausibility of these models can be judged. After clarifying our terminology, we will summarize the relevant theory and then see how this can be used to make inferences from field data. A notable increase in the number of detailed genetic studies of hybrid zones occurred over

Analysis of Hybrid Zones

Hybridization may influence evolution in a variety of ways. If hybrids are less fit, the geographical range of ecologically divergent populations may be limited, and prezygotic reproductive isolation may be reinforced. If some hybrid genotypes are fitter than one or both parents, at least in some environments, then hybridization could make a positive contribution. Single alleles that are at an advantage in the alternative environment and genetic background will introgress readily, although such introgression may be hard to detect. ‘Hybrid speciation’, in which fit combinations of alleles are established, is more problematic; its likelihood depends on how divergent populations meet, and on the structure of epistasis. These issues are illustrated using Fisher’s model of stabilizing selection on multiple traits, under which reproductive isolation evolves as a side-effect of adaptation in allopatry. This confirms a priori arguments that while recombinant hybrids are less fit on average, some gene combinations may be fitter than the parents, even in the parental environment. Fisher’s model does predict heterosis in diploid F1s, asymmetric incompatibility in reciprocal backcrosses, and (when dominance is included) Haldane’s Rule. However, heterosis arises only when traits are additive, whereas the latter two patterns require dominance. Moreover, because adaptation is via substitutions of small effect, Fisher’s model does not generate the strong effects of single chromosome regions often observed in species crosses.

The role of hybridization in evolution

Three methods for estimating the average level of gene flow in natural population are discussed and compared. The three methods are FST , rare alleles, and maximum likelihood. All three methods yield estimates of the combination of parameters (the number of migrants [Nm] in a demic model or the neighborhood size [4πDσ2 ] in a continuum model) that determines the relative importance of gene flow and genetic drift. We review the theory underlying these methods and derive new analytic results for the expectation of FST in stepping-stone and continuum models when small sets of samples are taken. We also compare the effectiveness of the different methods using a variety of simulated data. We found that the FST and rare-alleles methods yield comparable estimates under a wide variety of conditions when the population being sampled is demographically stable. They are roughly equally sensitive to selection and to variation in population structure, and they approach their equilibrium values at approximately the same rate. We found that two different maximum-likelihood methods tend to yield biased estimates when relatively small numbers of locations are sampled but more accurate estimates when larger numbers are sampled. Our conclusion is that, although FST and rare-alleles methods are expected to be equally effective in analyzing ideal data, practical problems in estimating the frequencies of rare alleles in electrophoretic studies suggest that FST is likely to be more useful under realistic conditions.

A comparison of three indirect methods for estimating average levels of gene flow.

Gene flow from the center of a species' range can stymie adaptation at the periphery and prevent the range from expanding outward. We study this process using simple models that track both demography and the evolution of a quantitative trait in a population that is continuously distributed in space. Stabilizing selection acts on the trait and favors an optimum phenotype that changes linearly across the habitat. One of three outcomes is possible: the species will become extinct, expand to fill all of the available habitat, or be confined to a limited range in which it is sufficiently adapted to allow population growth. When the environment changes rapidly in space, increased migration inhibits local adaptation and so decreases the species' total population size. Gene flow can cause enough maladaptation that the peripheral half of a species' range acts as a demographic sink. The trait's genetic variance has little effect on species persistence or the size of the range when gene flow is sufficiently...

/pdf/evolution-of-a-species-range-nhpxx4ohg1.pdf

Evolution of a Species' Range

Many species are divided into a mosaic of genetically distinct populations, separated by narrow zones of hybridization. Studies of hybrid zones allow us to quantify the genetic differences responsible for speciation, to measure the diffusion of genes between diverging taxa, and to understand the spread of alternative adaptations.

Nicholas H. Barton

Papers

Analysis of Hybrid Zones

The role of hybridization in evolution

A comparison of three indirect methods for estimating average levels of gene flow.

Evolution of a Species' Range

Adaptation, speciation and hybrid zones.