Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

/pdf/arlequin-version-3-0-an-integrated-software-package-for-4cs6nd3y2p.pdf

Arlequin (version 3.0): An integrated software package for population genetics data analysis

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

When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.

https://www.genetics.org/content/genetics/144/4/2001.full.pdf

Description and Power Analysis of Two Tests for Detecting Recent Population Bottlenecks from Allele Frequency Data

Animal mitochondrial DNA is a small, extrachromosomal genome, typically ~16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems—‘mitochondrial genomics’— serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.

Animal mitochondrial genomes

In animals, mitochondrial DNA (mtDNA) inheritance is predominantly maternal. In a few cases incidental transmission of paternal mtDNA was observed and estimated to account for only 10(-4)-10(-3) of an individual's mtDNA content. In contrast, biparental inheritance is common in mussels of the genus Mytilus. Here we present direct evidence that sex and mtDNA inheritance are coupled in Mytilus. Females inherit mtDNA only from their mother, but they transmit it to both daughters and sons. Males inherit mtDNA from both parents, but they transmit to sons only the mtDNA they inherited from their father. In pair matings, this mtDNA inheritance pattern is associated with a strong sex-ratio bias. These findings establish a newly discovered type of cytoplasmic DNA transmission. We also present evidence that the phenomenon breaks down in interspecific hybrids.

/pdf/an-unusual-type-of-mitochondrial-dna-inheritance-in-the-blue-2f8xoso53i.pdf

An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus.

Possible explanations of heterozygote deficiency in bivalve molluscs

Exchange of homologous sequences between mitochondrial DNA (mtDNA) molecules is thought to be absent in animals, primarily because of a failure to observe clear cases of recombinant haplotypes in natural populations. However, whether mtDNA recombination occurs is a different issue from whether it produces new haplotypes. A requirement for the latter is heteroplasmy – the presence of more than one type of mtDNA in an individual, which is rare in animals. In male mussels, in which heteroplasmy is the rule, recombination is common, arguing against an innate impediment to mtDNA recombination in animals. In addition, recent biochemical studies suggest that recombination is an indispensable part of the mtDNA replication and repair machinery and that most animal genomes have the necessary enzymes for mtDNA recombination. When strict maternal mtDNA transmission is compromised, recombinant haplotypes can be generated and eventually become fixed. Although the pervasiveness of mtDNA recombination in animals is unknown, its presence could have important consequences for phylogenetic studies of closely related taxa (e.g. leading to incorrect phylogenetic inferences and incorrect rejection of the molecular clock) and human mtDNA-associated diseases.

http://www.lifesci.susx.ac.uk/CSE/members/mladoukakis/pdfs/rokas.TREE03.pdf

Animal mitochondrial DNA recombination revisited

Mitochondrial dna inheritance

It is a well established phenomenon that homozygosity induced either by inbreeding or by especially designed experiments (such as, e.g., the technique of Sved and Ayala [1970] for comparing overall performance of chromosomal heterozygotes) generally results in low fitness. Because in all such cases a large part of the genome is made homozygous, the reduction in fitness can be equally well attributed to either reduced heterozygosity at heterotic loci, or to homozygosity for detrimental recessive genes. The problem of distinguishing between the two explanations is one of major importance in population genetics and is thoroughly discussed by Lewontin (1974). Another approach to studying the effect of heterozygosity is to correlate heterozygosity with a quantifiable character in individuals drawn randomly from a population. This approach does not rely on inbreeding, and although some inbreeding may occur in the population, if reduced homozygote performance is observed, it may well be attributed to other factors. Chromosomal inversions and electrophoretic variants provide suitable means for such an approach, the latter having the additional advantage of allowing one to study the effect of homozygosity or heterozygosity at a rather small segment of the genome. It appears, however, that most researchers have preferred to search for balancing selection in natural populations by comparing the observed levels of heterozygosity in the populations with that expected under the assumption of no selection (e.g., Marshall and Allard, 1970; Richmond and Powell, 1970; Allard et al., 1972). Only rarely has the individual's state in regard to homozygosity or heterozygosity been compared with its score for a quantitative character. Most of these studies have shown that heterozygotes perform differently than homozygotes (Koehn et al., 1973; Chaisson et al., 1976; Schaal and Levin, 1976; Stalker, 1976; Mitton, 1978). In a previous paper (Singh and Zouros, 1978) we reported the main findings from a study of a cohort of oysters. The cohort consisted of individuals of same age, drawn as spat (settling larvae) from a natural population, and grown under uniform conditions. We observed that the number of heterozygous individuals in the population was much lower than predicted from Hardy-Weinberg equilibrium. We also observed that there was a correlation between an individual's weight and the number of loci at which the individual was heterozygous. The first observation is common for populations of marine molluscs (for references see Singh and Zouros, 1978, and Skibinski et al., 1978). The second observation is less common in the literature and has an obvious bearing on the question of adaptive significance of enzyme heterozygosity. Here we report the findings of a second study. Our main objective was to see whether the patterns observed in the first study are reproducible. We have employed more loci and analyzed a much larger sample. This allowed us to firmly establish the correlation between heterozygosity and growth rate. It also provided us with a sizeable body of informati6n on which to evaluate certain hypotheses about the nature of the correlation, and ' Present address: Department of Zoology, University of Western Ontario, London, Ontario, Canada N6A 5B7.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1980.tb04024.x

Eleftherios Zouros

Papers

An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus.

Possible explanations of heterozygote deficiency in bivalve molluscs

Animal mitochondrial DNA recombination revisited

Mitochondrial dna inheritance

Growth rate in oysters: an overdominant phenotype and its possible explanations