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Developmental Genetics


Every cell in a multicellular organism contains the same identical genome - yet in a human being there are eye cells, bone cells, and brain cells - which all serve different purposes yet genetically are identical. How can this be?

There are two key differences between cells that we call differentiated.

    Cells differentiate through a complex system that involves the establishment of positional information and cell differentiation through paracrine signaling and other processes.
    The genome interacts with proteins which enable or disable certain genes. Due to the initial developmental processes, a different set of proteins is maintained in a given cell, allowing for an identical genome but with entirely different functions, and proteins.

When development begins, positional information must be established.

Once positional information is established, cells begin to change due to differences in gene transcription among the developing zygote. Some cells become intermediates - cells that would never be found in an adult organism but nonetheless act as a starting point for a number of other cells. These are known as pluripotent cells.

There are 204 different cell types in Human beings - so not every cell can be "unique". When development occurs, pluripotent cells divide and through signalling prescribe a cell fate to a set of cells, known as a developmental field. The end result is a large number of grouped cells all develop identically, into a muscle for example, while a set somewhere else will develop into something else altogether.

Population Genetics

Population Genetics is the field of genetics which studies allele distributions and genetic variation in populations. Population geneticists study the processes of mutation, migration, natural selection and genetic drift on populations, and in doing so are studying evolution as it occurs. Foundations of Population Genetics Templeton states that the three premises of population genetics are the same premises for population genetics: Templates/DNA can replicate Templates/DNA can mutate and recombine Phenotypes emerge from the interaction of templates/DNA and environment. Replication of Populations There are three major properties that a population must maintain with replication: They are composed of reproducing individuals They are distributed over space and time They host a population of genes The first property indicates that individuals of the population must reproduce to keep the population stable. This is necessary because individuals breakdown over time do to the introduction of entropy and inability for an individual to continuously remove the entropy added by the environment. Thus to maintain the population, individuals must pass down their DNA, or organizational encoding, to the next generation. Through continuous reproduction, a population can be maintained over a much longer time than the individuals that comprise it. In addition, the continuous reproduction of over time enables for the population to have properties and components of its own. The second property is that a population is distributed over a space. Populations can exists as: small isolated groups a collection of groups with a varied amount of genetic exchange a large interbreeding population that exists over a vast space In general though the population can be divided into a primary group that can be considered as interbreeding and a secondary group that mates occasionally with the primary group. It is this primary group that population geneticists generally study, as it is generally stable. They define the group as a group of interbreeding individuals that share a common system of mating. The secondary group is generally ignored, and treated as noise in the system, unless it is having a major effect on the primary group. The third property that must be maintained with reproduction is the population's gene pool. The gene pool is the collection of all the genes, organizational templates, in the population that can be used to create new individuals. By studying this gene pool, geneticists can determine the frequency of alleles, and or groups of alleles in the population and how they are changing over time. From the patterns of result that are obtained, geneticists then can start to understand what forces are acting on the population. Template Mutations Change is a requirement of evolution and one method of introducing change is through modification of the templates used sustain the population. In the case of living life, these templates are genes. Sources of Mutation: Insertions Deletions Single Nucleotide Substitutions (sometimes changing the protein sequences and sometimes not) Transpositions Duplications An allele is an alternate form of an template. In the case of biological systems, an allele is a form of a gene. Zooming further out, a version of a region of templates is called a haplotype. Biological systems would call this a sequence of nucleotides, while a in a computer system, this would be a sequence of linked objects. Modeling Evolution Initially we are going to consider populations with genetic architectures of two loci per template. Hardy-Weinberg Model The genetic architecture of the Hardy Weinberg model is one locus, two allele model (Templeton, p. 35). Hardy-Weinberg Equilibrium If a population has no forces of evolution acting upon it is in Hardy Weinberg Equilibrium. Quantitatively it says that if the allele proportions of two alleles A and a are denoted p and q then the genotype proportions will be such that the homozygote AA will be of proportion p2, the heterozygote Aa will have proportion 2pq and the homozygote aa will be of proportion q2. Testing for Hardy-Weinberg To do this test you do what is known as a Chi Square test ( χ 2 ). Where:
Population-Genetics-Formula
Population-Genetics-Formula-2
Therefore we can accept the hypothesis is in Hardy-Weinberg Equilibrium and that there are no forces of equilibrium on these alleles. Two Autosomal Loci, Two Allele Model Extending the H.W. model to two autosomal locus model with two alleles. For the purpose of this discussion, the first locus will have alleles A and a and the second locus will have B and b. From this we can get the following gamete types and their frequencies through recombination:
Gamate Frequency
AB FreqAB
Ab FreqAb
aB FreqaB
ab Freqab
Sum 1
A population producing the above four gamates can produce the following genotypes:
Population-Genetics-Formula-3
Notice that the sum of FreqAB, FreqAb, FreqaB, and Freqab is one. This follows from the earlier model where the sum of p and q equaled one.

Genetics, Ecology, and Modern Synthesis Theory

The History of Evolutionary Theory, and the Implications of Genetics Had Charles Darwin, the man who coined the mechanism of evolution as "natural selection" been introduced to Gregor Mendel, the geneticist who first described gene inheritance, biologists today would be decades ahead of where we are in terms of research. For it is genetics, the phenomenon of traits being inherited by offspring from their parents, that provides the vessel for all evolutionary change. Charles Darwin and the biologists of his day imagined that there was a mechanism for inheritance. They thought there was a means through which the characteristics of parents can be passed on to their offspring, but they couldn't fully describe it. Darwin, in his famous On the Origin of Species, implicated genetics as the vehicle for natural selection, and thus evolution, without even knowing the word.

...owing to this struggle, variations, however slight and from whatever cause proceeding, if they be in any degree profitable to the individuals of a species in their infinitely complex relations to other organic beings and to their physical conditions of life, will tend to the preservation of such individuals and will generally be inherited by the offspring. The offspring also will thus have a better chance of surviving, for of the many individuals of any species which are periodically born, but a small number can survive I have called this principle by which each slight variation, if useful, is preserved, by the term Natural Selection in order to mark its relation to natures's power of selection...

In the decades after Darwin's death, his theory of evolution began to fall by the wayside in scientific literature. By the 1920's and 30's, many scientists thought that it was at best an interesting hypothesis, but without merit, as the mechanism for natural selection had yet to be identified and no observation had been made of a single speciation event. Darwin spoke of natural selection as the driving force behind the emergence of new species. In-fact, this was the very thesis of his book. But no one had yet been able to describe the phenomenon. The study of genetics continued to develop separately from evolutionary theory, only occasionally being referenced by biologists interested in heredity. It wasn't until the 1940's, with the publication of British Biologist Julian Huxley's Evolution: The Modern Synthesis, that a solid connection was made between genetics and evolutionary theory. Huxley and many other biologists were the proponents of a rebirth of Darwin's ideas; an intellectual movement known as "neodarwinism." It is through their synthesis of genetics and evolutionary theory that a clearer picture of the evolution we know today emerged. From Mutations to Modern Synthesis Theory -- How We See Genetics and Evolution Today The ideas surrounding Populuation Genetics presented in Chapter 6 were the bridge needed between genetics and natural selection that led to what we know as evolution today.
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