Evolution of Biological Diversity

Part 12 of my BIO101 lecture notes. As always, click on the web-spider icon to see the original post (from June 04, 2006). Correct errors and make suggestions to make this better. Perhaps this entire series can be included in the "Basic Concepts" series.

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BIO101 - Bora Zivkovic - Lecture 4, Part 2

In the previous segment of the lecture, we looked at the Origin of Life and the beginnings of the evolution of biological diversity. Now we move to explanations of the mechanisms by which diversity arises.

Although traits can be inherited by non-DNA ways, and DNA sequence does not neccessarily translate directly onto the traits, in the long term the differences between species tend to be recorded in the genome. Thus, differences between genomes of different species are most important differences between them. How do differences between genomes arise? There are six major (and some minor) ways this happens:

Mutations are small changes in the sequences of DNA. Some of the changes are just substitutions of one nucleotide with another, others are deletions, insertions and duplications of single nucleotides or small strings of nucleotides within a gene, or within a non-coding regulatory sequence. Such small changes may alter the function of the gene-product (protein) which may translate into changes in traits which may be selected for by natural or sexual selection.

Gene duplication occurs quite often due to errors in DNA replication during cell division, or due to errors in 'crossing-over' phase of meiosis. Instead of a single copy of a gene, the offspring have two copies of that same gene. As long as one copy remains unaltered and functions properly, the other gene is free to mutate (i.e., there will stabilizing selection on the first copy, and no selection for the preservation of the sequence of the second copy). The second gene may transiently become non-functional, but as it keep mutating it may beging coding for a completely novel protein which will start interacting with other molecules in the cell. If this new interaction confers increased fitness on the organism, this new gene sequence will become selected for and fine-tuned by natural (or sexual) selection for its new function.

Chromosome duplication may also occur due to errors in DNA replication during cell division. Instead of just one gene being duplicated, a large number of genes now exist in two copies, each pair of copies consisting of one copy that is preserved by stabilizing selection and another copy that is free to mutate and thus potentially evolve novel traits.

Genome duplication has occured many times, especially in plants. The whole genome doubles, i.e., all of the chromosomes are duplicated. The resulting state is called polyploidy. This provides a very large amount of genetic material for natural selection to tinker with and, over time, produce novel traits.

Rearrangement of segments of the DNA along the same chromosome, or between chromosomes, places different genes that were once far from each other into closer proximity. Thus, genes that were previously quite independent from each other may now be expressed together or may start influencing each other's expression. Thus, the genes become linked together (or unlinked from each other), restructuring the batteries of genes that work together in a common function. This may free some genes to evolve independently, while tying some genes together and thus constraining the direction in which development of traits may evolve.

Lateral transfer (sometimes called 'horizontal transfer') is an exchange of DNA sequences between individuals of the same species or of different species. While vertical transfer moves genes from parents to offspring, lateral transfer moves genes between unrelated individuals. Such transfer is very common in microorganisms. Some species of Bacteria, Archaea and Protista routinely engage in gene swapping, which results in increase of genetic diversity of the species and thus provides raw material for evolution to build new traits. Gene swapping between organisms of different species may transfer a complete function from one species to another. Sometimes viruses act as carriers of genes from one species to another. For instance, a virus may take a piece of a bacterial genome and later insert it into a genome of a plant or a mammal. Some key genes involved in the development of the placenta originated as bacterial genes inserted into early mammalian genomes via viruses.

One important thing to bear in mind is that evolution has to ensure the survival of the individual at all stages of its life-cycle, not just the adult. Thus, evolution of new traits can occur only if it does not disrupt the viability of eggs, larvae, immature adults and mature adults.

Another important thing to keep in mind is that traits arise through embryonic and post-embryonic development. Thus, evolution of traits is really evolution of development. Evolution of genomes, thus, is not evolution of random grab-bags of many genes, but evolution of complexes of genes involved in development of particular traits.

A product of a gene is a protein. A protein that is capable of binding to DNA and thus regulating the expression of other genes is called a transcription factor. When bound to a gene, a transcription factor may induce its expression, block its expression, or increase or decrease the rate of its expression. The patterns of gene expression are key to embryonic development and cell differentiation, so it is not surprising that transcription factors play a large role in evolution of new traits via development.

A novel pattern of gene expression may arise in two ways. First, by mutation of a transcription factor (so-called trans-factors), it changes which genes it affects and the way it affects them. Second, by mutations in regulatory regions (so-called cis-factors) of the target genes, the transcription factors may or may not bind to them, or a different transcription factor may bind to them, or the effect of the binding on transcription of the gene may change.

Most important genes in evolution of development are transcription factors. Often, they work in batteries (or complexes or toolkits), where one gene induces transcription of the second gene which in turn induces transcription of the third gene, and so on. Such batteries tend to be strongly preserved in many species of living organisms, though the genes that act as final targets of action of such complexes differ between species. Such complexes may determine what is up and what is down in an early embryo, or what is forward and what is bakward in an embryo. Such complexes are used over and over in evolution to produce protruding structures, like limbs. Another such complex has been used in 40 different groups of animals for the construction of 40 quite different types of eyes.

Possibly the most important such complex in animals is the complex of Hox genes that regulates segmentation. Most animals are segmented. While this is obvious in earthworms where all segments look alike, in many other animals segments are formed in the early embryo and each segment then develops unique structures on it. Thus, an insect will develop jaws and antennae on its head segment, wings and legs on its thoracic segment, and reproductive structures and stings on its abdominal segment. You will need to carefully read the handout "A Brief Overview of Hox Genes" (http://scienceblogs.com/pharyngula/2006/04/a_brief_overview_of_hox_gene…) and be able to define Homeotic genes, Homeobox (DNA sequence), Homeodomain (protein structure) and Hox genes. Interestingly, non-segmented Cnidarians (corals and jellyfish) do not have true Hox genes, though they do have scatterings of Hox-like genes, which may be evolutionary precusors of true Hox genes.

Thus, evolution of diversity can be thought of in terms of changes in the way developmental toolkits are applied in each species. The same toolkits are used over and over for development of similar traits. The sequences of the genes within the toolkits will vary somewhat between species, and the sequences of genes that are final targets of action of toolkits will vary much more.

Thus, with quite a limited number of genetic toolkits, nature can develop a myriad different forms, from cabbages and sponges to honeybees and humans. This also explains why we do not need more than 30,000 genes to develop a human, as well as why our genome is about 99% identital to the chimpanzee genome. It is not the sequence of genes, but the combinatorics of the way the genes are turned on and off during the development that results in the final phenotype.

The common theme, then, is that evolution keeps tinkering with the same genetic toolkits over and over again. It is not neccessary to evolve thousands of completely new genes in order to have a new species spring up out of its ancestral species. A little tweak in developmental patterns of gene expression is all that is needed. The same genes may be expressed at a different place in the embryo in two different species (heterotopy), or may be expressed at a different time during development (heterochrony), or may result in expression of other final-target genes (heterotypy). Such changes account for most of the evolution of diversity of life on Earth.

Of course, such changes take a long time. It took about 3.6 billion years for life to evolve from the first primitive bacteria-like cells to the current diversity of millions of species of Bacteria, Archaea, Protista, Fungi, Plants and Animals. Our brains have never before needed to be able to comprehend such vastness of time. We do qute well with durations of seconds, minutes, hours and days. We are pretty good at mentally picturing the duration of weeks, months and years. A decade is probably the longest duration of time that our brains can correctly imagine. Already our perception of a century is distorted. Perception of a thousand years is impossible for human brains. Now try to imagine how long 10,000 years is? Any luck? Now try 100,000. How about 1.000,000 years? Add another zero and try comprehending 10.000,000 years. Multiply by ten again and try 100.000,000 years. Now try 1,000.000,000 years. Now try four times more - 4 billion years.

It is not surprising that some people, unable to comprehend 4 billion years, just plainly refuse to acknowledge that this amount of time actually passed and stick to a shorter, emotionally more pleasing yet incorrect number of about 6,000 years for the age of the Universe. Such people, of course, cannot believe that evolution actually happened, although mountains of evidence show us not just that it happened, but exactly how it happened. You can see exactly what happened when if you take your time and do this animation. You'll notice how the whole of human history is too short to be visible on a line representing billions of years. Given such enormous amount of time, the evolution of amazing diversity of life is not surprising. Actually, if such diversity did not arise - that would be a surprise.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 24 and 27

Watch Animation:

http://www.johnkyrk.com/evolution.html

Handouts:

A Brief Overview of Hox Genes (http://scienceblogs.com/pharyngula/2006/04/a_brief_overview_of_hox_gene…)
Bat Development (http://scienceblogs.com/pharyngula/2006/04/bat_development.php)
How To Make A Bat (http://scienceblogs.com/pharyngula/2006/04/how_to_make_a_bat.php)

Additional Readings:

Jellyfish Lack True Hox Genes (http://scienceblogs.com/pharyngula/2006/05/jellyfish_lack_true_hox_gene…)

Previously in this series:

Biology and the Scientific Method
Cell Structure
Protein Synthesis: Transcription and Translation
Cell-Cell Interactions
Cell Division and DNA Replication
From Two Cells To Many: Cell Differentiation and Embryonic Development
From Genes To Traits: How Genotype Affects Phenotype
From Genes To Species: A Primer on Evolution
What Creatures Do: Animal Behavior
Organisms In Time and Space: Ecology
Origin of Biological Diversity