LECTURE                                             THE TOOLS OF EVOLUTION

In this lecture you will learn about:

SEX and 2N NUMBER
When there  is NO SEX and only a single copy of the genome each generation is identical to the parents. (Bacteria)

Good  mutations are rare.  A good mutation means that more of the progeny of that bacterial "strain"  will survive (Aor B on right)

Two good mutations will compete with each other until one is driven to extinction.  So one good mutation will always be lost. (A and B competing together)
 

However, sex changes this. For example two strains of bacteria, one for a new food source, gum, the other for motility to get to food.  IF the two strains of bacteria had "sex" then some of their progeny would get both good mutations and would be able to "walk" and chew bubble gum at the same time. This is conservation of good mutations. 

In order to take advantage of this there needs to be 1N in the gamete going to 2N in the adult. 

"The past decade of research has confirmed that sex is indeed a potent force. But it's powerful in ways that Darwin could not have appreciated. Studies in the past few years have demonstrated that the sexual preference that females have for one kind of male over another is potent enough to carve an old species apart into several new ones. In the lakes of East Africa, for instance, sexual selection has driven the origin of hundreds of new species from fish that live and breed side by side."
http://www.pbs.org/wgbh/nova/beta/evolution/ten-great-advances-evolution.html

 
 RANDOM ASSORTMENT AND MULTIPLE CHROMOSOMES 
RANDOM AKA INDEPENDENT ASSORTMENT AKA RECOMBINATION

When genes from parents are randomly and independently sorted into the germ cells it assures maximum variation.

When two germ cells fuse to make a new individual (sex) the good genes of both parents can contribute to better "fitness" and competitiveness. 

There is a big evolutionary investment in "sex" where the genes for two sexes need to evolve and and then all the genes to bring the two back together to ensure random assortment and a big mixing of genetic combinations in each generation.

For animation click here
 

IN ADDITION, the number of discrete chromosomes have a big impact on the amount of variation during random assortment. 

The more chromosomes, the more different possible combinations.  The equation is 
                2x with x = the number of chromosomes

With just 2 chromosomes the ant listed on the right has only 22 possible combinations or 4. 

With 8 chromosomes the fruit fly has 28 possible combinations or 2x2x2x2x2x2x2x2 = 256

With 23 chromos (like us) there are 223 possible combinations or 8,8388,6088.4 million different individuals.

What is the equation for 6 chromosomes? How many possible combinations? 
click here for answer 


 
MATCHING CHROMOSOMES
The number of chromosomes is important for speciation.  In GENERAL mismatch in chromosome number prevents interbreeding, like donkey and horse which produces a mule which is sterile. 

"They have trouble making sperm or eggs because their chromosomes don't match up well. And, because of their chromosome number.

A mule gets 32 horse chromosomes from mom and 31 donkey chromosomes from dad for a total of 63 chromosomes. (A horse has 64 chromosomes and a donkey has 62).

To understand why this is a problem, we need to understand how sperm and eggs are made. And to understand that, we need to go into a bit more detail about chromosomes. The mule has a set of horse chromosomes from its mom. And a set of donkey ones from its dad. These chromosomes aren't really matched sets like in a horse, a donkey, or a person. In these cases, a chromosome 1 is very similar to another chromosome 1. It looks pretty much the same and has nearly the same set of A's, G's, T's and C's.  But a donkey chromosome doesn't necessarily look like a horse one. And the poor mule even has an unmatched horse chromosome just sitting there.

To make a sperm or an egg, cells need to do something called meiosis.  At the end of meiosis, the sperm or egg has either mom's or dad's chromosome 1. Not both.
This process requires two things. First, the chromosomes have to look pretty similar, meaning they are about the same size and have the same information. This will have to do with how well they match up during meiosis. And second, at a later critical stage, there has to be four of each kind of chromosome. Neither of these can happen completely with a mule."
http://www.thetech.org/exhibits/online/ugenetics/ask.php?id=225

What they think happened click here


 
CROSSING OVER IN MEIOSIS
Crossing over increases genetic variability by swapping whole sections of moms and pops chromosomes resulting in totally new combinations of alleles. 
For animation on youtube click here
 

 


http://www.contexo.info/DNA_Basics/Meiosis.htm
UNEQUAL CROSSING OVER IN MEIOSIS AND GENE DUPLICATION
Unequal crossing over also occurs during meiosis. When this occurs it substantially CHANGES the length of the chromosomes, one is larger, one is smaller. This is a MUTATION. 

As seen on the right, unequal crossing over can occur in both the homologous pair AND between sister chromatids.  When it occurs all or part of a gene gets DUPLICATED and on the other chromosome it is lost.  These chromatids separate into individual germ cells and may end up in an individual.  There are many possible FATES for the cells carrying a duplication or lost gene. 

1. If the lost gene is essential the fertilized egg may never develop properly and this is called a "LETHAL" mutation. 

2. The duplicated gene can be lethal. 

3. The duplicated gene can confer "selective advantage".

4. The duplicated gene can be unexpressed (called a pseudogene), collect more mutations and get activated sometime in the future that confers selective advantage. 

"The primary evidence that duplication has played a vital role in the evolution of new gene functions is the widespread existence of gene families. Members of a gene family that share a common ancestor as a result of a duplication event are denoted as being paralogous, distinguishing them from orthologous genes in different genomes, which share a common ancestor as a result of a speciation event. Paralogous genes can often be found clustered within a genome, although dispersed paralogues, often with more diverse functions, are also common." 
http://www.plosbiology.org/article/info:doi%2F10.1371%2Fjournal.pbio.0020206

Below is an example of a gene family for antibodies.  The jpg on the right shows the structure of how the proteins folds to form an active antibody. 
V stands for variable region 

 
CHROMOSOME SPLITTING AND FUSING
"All great apes apart from man have 24 pairs of chromosomes. There is therefore a hypothesis that the common ancestor of all great apes had 24 pairs of chromosomes and that the fusion of two of the ancestor's chromosomes created chromosome 2 in humans. The evidence for this hypothesis is very strong.

The Evidence

Evidence for fusing of two ancestral chromosomes to create human chromosome 2 and where there has been no fusion in other Great Apes is:

1)  The analogous chromosomes (2p and 2q) in the non-human great apes can be shown, when laid end to end, to create an identical banding structure to the human chromosome 2. (1)

2) The remains of the sequence that the chromosome has on its ends (the telomere) is found in the middle of human chromosome 2 where the ancestral chromosomes fused. (2)

3) the detail of this region (pre-telomeric sequence, telomeric sequence, reversed telomeric sequence, pre-telomeric sequence) is exactly what we would expect from a fusion. (3)

4) this telomeric region is exactly where one would expect to find it if a fusion had occurred in the middle of human chromosome 2.

5) the centromere of human chromosome 2 lines up with the chimp chromosome 2p chromosomal centromere.

6) At the place where we would expect it on the human chromosome we find the remnants of the chimp 2q centromere (4).

Not only is this strong evidence for a fusion event, but it is also strong evidence for common ancestry; in fact, it is hard to explain by any other mechanism."
http://www.evolutionpages.com/chromosome_2.htm

ANOTHER explanation is that some time after humans split there was a fusion. 

" The most common and best known chromosomal rearrangement affecting chromosome number is the Robertsonian translocation (ROB). It is named after the American geneticist W.R.B. Robertson, who first described this chromosomal rearrangement in grasshoppers in 1916. It occurs when the long arms of two acrocentric chromosomes (chromosomes with the centromere very near one end) fuse to form one metacentric chromosome (a chromosome with the centromere near the middle). The short arms of the original chromosomes are generally lost with no obvious adverse consequences.

ROBs can be associated with problems. In humans, approximately one in 1,000 babies is born with this form of translocation. Most appear normal, though they may experience fertility problems later in life. Fertility problems can arise when gametes (egg or sperm) are formed that are missing or have extra chromosomes. Gametes from ROB carriers may be normal, with one of each chromosome or balanced, with the translocated chromosome but neither of the acrocentric homologues. However, on occasion unbalanced gametes may be formed that are either missing a chromosome or have the translocated chromosome with one of its acrocentric homologues. Unbalanced gametes can give rise to embryos which fail to develop or develop with abnormalities such as Down’s syndrome. It is estimated that 5% of Down’s syndrome cases are the result of an ROB.

While it is true that chromosome numbers are generally fairly stable within a population of animals, they are by no means completely static.

Although ROBs can be associated with problems, there are times where no adverse outcomes are observed. For example, they have been observed in Saanan goats with a normal phenotype and no reported fertility problems. There are crossbreeding studies with sheep carrying up to three different translocations that showed no significant effect on phenotype or fertility for any of the combinations. In fact, the normal chromosome number of domestic sheep (Ovis aries, 2n = 54) is inferred to be the result of three different translocations relative to domestic goats (Capra hircus, 2n = 60). The variation in chromosome number in the Bovidae family (including the tsoan5 and cattle6 monobaramins) appears to be mostly due to ROBs.

There are other types of chromosomal rearrangements that have contributed to the range of chromosome numbers in animals that are monobaraminic (known to be from the same created kind). Some of these rearrangements are quite unexpected. For example, the Indian muntjac (Muntiacus muntjak, 2n = 6 in females, 7 in males) has the x-chromosome fused with one of its autosomes. The y-chromosome is separate. The male will have one of this autosomal pair fused to an x, and the other without a fused sex chromosome and a separate y, giving it an extra chromosome compared to the female. It is interesting to note that viable hybrids have been formed between this species and Reeve’s muntjac (Muntiacus reevesi, 2n = 46).7 Some species of antelope have a fused y-chromosome."

"A karyotype from an individual with Down’s 
syndrome that resulted from a Robertsonian 
translocation. One copy of chromosome 21 
is attached to one of chromosome 14 (the
translocated chromosome) and two additional 
copies of chromosome 21 are present. About 
5% of Down’s syndrome cases are the result 
of this type of translocation."
 


 
MUTATIONS
"But natural selection is far from the full story of evolution. Many mutations can spread throughout an entire species thanks not to natural selection but through lucky rolls of the genetic dice. This so-called neutral evolution has been particularly important in shaping the parts of the genome that do not contain protein-coding genes. Most of the news you read about DNA concerns protein-coding genes, so you might well think that there's not much of the genome that doesn't contain them. But just the opposite is true. Some 98.8 percent of the human genome is this so-called noncoding DNA.

Only in the past few years have scientists started to explore this genomic wilderness in great detail, and they've used evolution as their guide. In the human genome, for example, there are an estimated 11,000 so-called pseudogenes—stretches of DNA that once encoded proteins but no longer do so thanks to disabling mutations. These vestiges of genes once had important functions, such as synthesizing vitamins or allowing us to smell certain molecules. Scientists know that these pseudogenes were once full-blown protein-coding genes, because they can find related versions of them in our primate relatives, in good working order.

While some of your noncoding DNA started out as your own genes, much more of it started out in invading viruses. Certain kinds of viruses can insert their DNA into host cells in such a way that it gets carried down from one generation of host to the next. Eventually these in-house viruses mutate so much they can no longer infect a new host. But they can still make copies of themselves, which get inserted into their old host's genome. About 40 percent of the human genome is made up of this viral DNA. Scientists can trace the ancestry of this virus DNA by comparing its remnants in our own genomes to the ones left in other primates."

Much of this viral DNA has now mutated to such a degree that it has become little more than padding in the genome. But even these inert relicts hold clues to their past. All human beings carry versions of an ancient virus called HERV-K. The differences in those versions evolved after the original virus infected a single human and was then passed down to his or her descendants. French scientists compared these versions of HERV-K, tallying up the mutations in one. Based on those new mutations, the scientists estimated that the virus first infected a human ancestor a few million years ago.

To prove that it had indeed once been a full-fledged virus, the scientists then used the different versions of its DNA to infer what its original genetic sequence had been. They synthesized that piece of DNA and injected it into human cells. The synthesized DNA hijacked the cells and caused them to spew out viruses with the same genetic sequence. The scientists, in other words, had brought a dead virus back to life.


"Sprinkled among the dead virus DNA and disabled pseudogenes are 
some useful elements of noncoding DNA. Some of these elements are 
switches, where proteins can attach to turn neighboring genes on and off. 
Our genome also contains stretches of DNA that can produce RNA 
molecules, but no proteins. These RNA molecules have their own 
essential roles to play in our lives, for example as signal detectors and 
gene regulators.

Scientists rely on evolution to find these elements as well. If a piece of 
noncoding DNA has no important function, mutations to it will have little 
effect on the survival of the organism that carries it. But if it does have an 
essential function, mutations will be far more likely to cause devastating 
harm. As a result, organisms with those harmful mutations will have fewer 
offspring, and so the piece of DNA will not change as easily. Scientists 
can find these functional elements by comparing many different species 
and looking for stretches of noncoding DNA that are unusually similar 
from species to species. In many cases, they've been able to 
demonstrate that these elements do indeed play crucial roles in the 
survival of organisms. Evolution thus lets scientists find needles in the 
genomic haystack."
http://www.pbs.org/wgbh/nova/beta/evolution/ten-great-advances-evolution.html