Saturday, June 26, 2010
Phylogenetic dataset workflow literature review
I just got done with my evolution class for the summer semester and for my final project, I wrote a paper reviewing the literature about phylogenetic dataset automation. You can download it here. Enjoy!
Sunday, June 20, 2010
Natural selection
Most natural selection is purifying selection, that is it weeds out harmful random mutations. For the most part, natural selection actually keeps things simple and just maintains what is currently in place. If there are alleles in a population and 1 does not have any fitness advantage over another, then 1 eventually taking over the population can simply be explained by a random evolutionary mechanism such as genetic drift.
Natural selection on the other hand is the only mechanism for adaptive evolutionary change. The complex adaptations we see in nature such as the vertebrate eye for example, represent the accumulation of small changes such that each were more fit than another. There is no mechanism for natural selection to see ahead, each small step had to be beneficial enough on its own to be selected for, there is no perfect archetype being strived for.
Since natural selection can only work with existing variation which must necessarily arise from random variation, it is not possible for any adaptation to simply come out of nowhere. Natural selection tinkers with existing structures to give rise to new ones.
Is there a way to reconcile the fact that in general natural selection tends to be conservative rather than creative with the fact that natural selection is the only known mechanism to generate adaptive structures? I think so. Sean Carroll explained in his book Endless Forms Most Beautiful that over evolutionary time the force of natural selection tends to reduce the number of structures while at the same time increasing their specialization. For example, if a gene is duplicated several times, the resulting redundancy will loosen the constraints of natural selection on these gene sequences. As the conservative force of natural selection pares down this redundancy, new functions will be inevitably carved out from this variation.
In other words, natural selection is not a builder or an inventor. Natural selection is a sculptor.
Natural selection on the other hand is the only mechanism for adaptive evolutionary change. The complex adaptations we see in nature such as the vertebrate eye for example, represent the accumulation of small changes such that each were more fit than another. There is no mechanism for natural selection to see ahead, each small step had to be beneficial enough on its own to be selected for, there is no perfect archetype being strived for.
Since natural selection can only work with existing variation which must necessarily arise from random variation, it is not possible for any adaptation to simply come out of nowhere. Natural selection tinkers with existing structures to give rise to new ones.
Is there a way to reconcile the fact that in general natural selection tends to be conservative rather than creative with the fact that natural selection is the only known mechanism to generate adaptive structures? I think so. Sean Carroll explained in his book Endless Forms Most Beautiful that over evolutionary time the force of natural selection tends to reduce the number of structures while at the same time increasing their specialization. For example, if a gene is duplicated several times, the resulting redundancy will loosen the constraints of natural selection on these gene sequences. As the conservative force of natural selection pares down this redundancy, new functions will be inevitably carved out from this variation.
In other words, natural selection is not a builder or an inventor. Natural selection is a sculptor.
Wednesday, June 16, 2010
Endosymbiosis
According to the endosymbiotic theory the first eukaryote was formed by the merger of 2 prokaryotes. But how did this happen? The traditional idea was that a primitive eukaryote engulfed the ancestor of our mitochondria since eukaryotes are known for phagocytosis, the abilty to engulf other cells. However, this is probably not how it happened because the ability to engulf other cells requires energy. It is now known that all eukaryotes either have mitochondria or have lost them at some point. Nick Lane contends in his book Power, Sex, Suicide that this links the origin of eukaryotes with the acquisition of mitochondria. So, before the host cell acquired mitochondria, it wasn't going around engulfing other cells. Lane suggests that perhaps these two ancient prokaryotes started out their symbiotic relationship by living in close proximity and progressed over time to one cell living inside the other.
Genetic studies suggest that the host cell was most likely a methanogen archea. These cells are anaerobic meaning they survive on sulpher and stay away from oxygen. This seems unlikely because if this were true, why did eukaryotes appear just as oxygen levels were rising? As Lane points out, more oxygen means more sulphates because oxygen reacts with sulpher from volcanoes to produce sulphates. But, as we all know, most eukaryotes thrive in the presence of oxygen. Besides, what would use would a methenogen have for mitochondria which are useless without oxygen? Lane believes that the most likely answer is that the ancestor of mitochondria had a diverse genetic toolkit. Perhaps, it had the genes for utilizing hydrogen and oxygen. Once it started supplying the hydrogen for the methanogen, it would no longer be dependent on deep sea vents and could venture off into oxygenated environments. This primitive eukaryote would have had to adapt to the oxygenated environment before the mitochondria ancestor living inside it lost its oxygen utilizing genes through disuse.
This chain of events is just one way eukaryotes could have evolved. The lesson here is that there were enough contingencies that the ascent beyond bacteria only happened once on earth in the billions of years that bacteria have populated the earth. We are truly lucky to have made it through this bottleneck. The biggest gulf in all of life is the divide between prokaryotes and eukaryotes. This gulf is much vaster than even the chasm between no life and life. We have more in common with a humble yeast cell than it does with a bacterium.
Mitochondria are the powerhouses, of the cell and without them, complex life may not even be possible. Bacteria have been around for billions of years yet, they are eternally bacteria. There are many disadvantages to maintaining mitochondria. Their genes evolve about 20 times faster than nuclear genes as they are more susceptible to mutation. Also, the genetic machinery must be maintained in each of the hundreds of mitochondria in each cell. Over time, in difference lineages, genes have migrated from the mitochondria to the nucleus. But, there is not even 1 example of a eukaryote losing all of its mitochondrial genes, therefore there must be a huge advantage to these genetic outposts. Lane argues that local control of energy production is absolutely essential. If mitochondria didn't have their own genomes, they would not be able to individually regulate energy production. Regulating hundreds of mitochondria from the nucleus would be extremely complex and it may not even be possible for such a mechanism to evolve.
Endosymbiotic theory is a beautiful illustration of the fact that the way nature solves problems aren’t always the most straightforward but reflect phylogenetic contingencies inherent to particular lineages. The merger of 2 simple prokaryotes, despite some of the disadvantages may have been the only way for complex life to evolve on earth. According to Lane, it is also why we are most likely alone in a universe full of bacteria.
Genetic studies suggest that the host cell was most likely a methanogen archea. These cells are anaerobic meaning they survive on sulpher and stay away from oxygen. This seems unlikely because if this were true, why did eukaryotes appear just as oxygen levels were rising? As Lane points out, more oxygen means more sulphates because oxygen reacts with sulpher from volcanoes to produce sulphates. But, as we all know, most eukaryotes thrive in the presence of oxygen. Besides, what would use would a methenogen have for mitochondria which are useless without oxygen? Lane believes that the most likely answer is that the ancestor of mitochondria had a diverse genetic toolkit. Perhaps, it had the genes for utilizing hydrogen and oxygen. Once it started supplying the hydrogen for the methanogen, it would no longer be dependent on deep sea vents and could venture off into oxygenated environments. This primitive eukaryote would have had to adapt to the oxygenated environment before the mitochondria ancestor living inside it lost its oxygen utilizing genes through disuse.
This chain of events is just one way eukaryotes could have evolved. The lesson here is that there were enough contingencies that the ascent beyond bacteria only happened once on earth in the billions of years that bacteria have populated the earth. We are truly lucky to have made it through this bottleneck. The biggest gulf in all of life is the divide between prokaryotes and eukaryotes. This gulf is much vaster than even the chasm between no life and life. We have more in common with a humble yeast cell than it does with a bacterium.
Mitochondria are the powerhouses, of the cell and without them, complex life may not even be possible. Bacteria have been around for billions of years yet, they are eternally bacteria. There are many disadvantages to maintaining mitochondria. Their genes evolve about 20 times faster than nuclear genes as they are more susceptible to mutation. Also, the genetic machinery must be maintained in each of the hundreds of mitochondria in each cell. Over time, in difference lineages, genes have migrated from the mitochondria to the nucleus. But, there is not even 1 example of a eukaryote losing all of its mitochondrial genes, therefore there must be a huge advantage to these genetic outposts. Lane argues that local control of energy production is absolutely essential. If mitochondria didn't have their own genomes, they would not be able to individually regulate energy production. Regulating hundreds of mitochondria from the nucleus would be extremely complex and it may not even be possible for such a mechanism to evolve.
Endosymbiotic theory is a beautiful illustration of the fact that the way nature solves problems aren’t always the most straightforward but reflect phylogenetic contingencies inherent to particular lineages. The merger of 2 simple prokaryotes, despite some of the disadvantages may have been the only way for complex life to evolve on earth. According to Lane, it is also why we are most likely alone in a universe full of bacteria.
Friday, June 4, 2010
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