Taking a random walk

Up front, sorry again for the delay.  Life keeps on interfering with getting things done.

Today I'm going to talk about genetic drift.  And as usual, there's new vocabulary to learn.  So we've talked about genes before and the fact that in most animals, there are two copies of any one gene in any given individual.  Now the sequence of those two copies doesn't have to be exactly the same.  There can be differences.  Slightly different variations of the same gene are called alleles.  A common example is blood type.  ABO blood type is based on a single gene, and there are A, B, and O alleles.  

Now what about genetic drift?  What does it have to do with alleles?  In a field called population genetics, scientists study the genetic makeup of entire populations of organisms, and a common measure of this genetic makeup is allele frequency - how common some alleles are compared to other alleles.  In humans, you can think about this in terms of how common blue eyes are compared to brown eyes, or attached ear lobes versus unattached ear lobes.  On the scale of populations, evolution can be defined as change in allele frequencies over time.  Genetic drift is one explanation scientists have for why allele frequencies change over time.

Genetic drift is why increasing the population size of endangered organisms is important.  Whenever genes are passed from one generation to the next, there is some level of randomness as to which allele in an given individual will be passed on to the next generation (during sexual reproduction, each individual in a mating pair only passes on a single allele for each gene).  So how close allele frequencies stay the same over the course of multiple generations is dependent on the population size.  Why?  Take this completely abiotic example.  You flip a coin.  If you flip the coin only once, then the frequency of tails is either going to be 1 or 0.  If you flip the coin ten times, then the frequency of tails might be something more like .7 or .3.  The more times you flip the coin, the more likely that the frequency of tails will end up to be 0.5.  Genetic drift works the same way - the larger the population, the less variation in allele frequencies from generation to generation.  Conversely, the smaller the population, the more variation in allele frequencies.  If a population is small enough, you can even lose alleles from the population, because they just didn't make it into the next generation.  

Genetic drift is part of neutral theory, because what the allele does is of no consequence to the effect genetic drift has on it.  

If you want to play around with some simulations that illustrate the principle of genetic drift, here are some links:

http://darwin.eed.uconn.edu/simulations/jdk1.0/drift.html

Creating monsters

Sorry for the two week holiday.  Now that the commitments of the holidays are past, I can get back on my weekly posting.

So last time I talked about the meaning of the word evolution, and introduced a couple other topics such as mutation, recombination, genetic drift, natural selection.  So today's topic is mutation.

The genetic material within a cell is composed of DNA - deoxyribonucleic acid.  In eukaryotic cells like ours and other animals, DNA is found wrapped around a protein scaffold and forms chromosomes.  Chromosomes are typically found in matching pairs (except for sex chromosomes).  Genetic material is compartmentalized in eukaryotic cells - most of the genetic material is located in the nucleus, where chromosomes reside.  All of the genetic material belonging to a given compartment is called a genome.  In most eukaryotes, there are two genomes - the nuclear genome and the mitochondrial genome.  I'm just going to focus on the nuclear genome, because the mitochondrial genome is special (as well as the chloroplast genome in plants).  The nuclear genome in most eukaryotes is diploid, meaning that each chromosome is a member of a paired set.  In gametes (specialized cells for sexual reproduction such as eggs and sperm), only a single member from each paired set is present. So back to this whole mutation thing.  There are variety of different ways mutations can occur.  A mutation is basically a change in the genetic material.

DNA is a double helix - this means that simply put, it consists of two strings of individual "letters" running in opposite directions and additionally those strings are complementary in such a way that if you know the sequence of one string, you can deduce the sequence of the other string.  These letters are nucleotides, and there are only four of them - A (Adenine), T (Thymine), G (Guanine), and C (Cytosine).  A and T are paired together in a complementary set, and G and C make up the other complementary set.  

There are several types of mutations.  I am going to discuss the following types: 1) point mutations; 2) insertions/deletions; 3) duplications; and 4) rearrangements.

A point mutation describes a change in one of the letters to one of the other letters.  Sometimes this makes a difference in what the DNA codes for, and sometimes it has no effect at all.  In a protein-coding region (typically known as a gene), mutations that change the protein the gene codes for are called nonsynonymous mutations and mutations that don't change the protein are called synonymous mutations.  An example of a point mutation is the disease sickle cell anemia, which is caused by a single point mutation.  This point mutation changes the hemoglobin protein, which carries oxygen in red blood cells.  The mutation causes the hemoglobin proteins to attach to one another, changing the shape of the red blood cells, and causing them to create traffic jams in certain parts of the body.  Point mutations may also cause changes in when a gene is turned on (the protein is made) or turned off (the protein isn't made).

Insertions/deletions (commonly referred to as indels) are simply instances in which a single letter or a series of letters have been either inserted or deleted from the DNA.  Indels will always change the makeup of the protein that a gene codes for if the indel occurs in a gene.  Since DNA is written in a three-letter code, indels of three, or multiples of three letters, usually have the least impact since they will disrupt the rest of the code minimally.  However indels of other sizes will change essentially what every letter downstream of that indel means.  But these are generalities.  

Duplications come in a wide variety of sizes and mechanisms by which they occur.  Basically a duplication means that some pre-existing piece of DNA is copied and added to the genome.  Duplications can involve a single letter, large segments of DNA, entire chromosomes, and even entire genomes.  Excessive duplications of a three letter segment of the huntingtin gene causes Huntington's disease.  Extra copies of chromosomes in humans usually causes miscarriage, but Trisomy 21 (having three copies of chromosome 21 instead of 2) causes Down's syndrome.  Whole genome duplication is rare in animals, but we can detect episodes of whole genome duplication in fish and frogs.  Whole genome duplication is a very important part of the evolution of flowering plants (a lot of my PhD dissertation was on this topic).  Duplication basically enables other mutations to occur that change expression and function, while still maintaining what's needed to keep things running.  We'll talk more about duplication at another time.

And there's rearrangement - you don't change anything about the DNA except where it's located and maybe what direction it's in.  The most common type of rearrangement is recombination.  During meiosis (the process during which haploid (single set of chromosomes) cells are formed), chromosomes interact with their partner and swap some genetic material.  On average, one part of the chromosome is swapped with its partner during meiosis.  This only happens when sex is involved (meiosis).  But it means that there's a chance for new genetic combinations to form when the next generation is formed.

So there's a listing of all the changes that can occur.  When it comes to evolution, the only mutations that matter are those that occur in sex cells (for sexually reproducing organisms) since those are the only changes that will be passed onto the next generation and are heritable changes.  Now how mutations spread throughout a population of organisms will be the next thing I discuss - natural selection and genetic drift.