Molecular Evolution
evolgen | April 20, 2007It seems like everything is coming in twos the past couple of days. Yesterday we mentioned two books on the evolution of genomes and two stories involving either Wolbachia or sex determination. Today, we have two stories involving criticisms of scientific papers. One deals with the evolution of the bacterial flagellum, and the other addresses natural selection on the brain expressed gene ASPM in humans.
The first story involves everyone's favorite irreducibly complex cellular apparatus: the bacterial flagellum. During the Kitzmiller v. Dover trial, Nick Matzke worked with the plaintiffs (the…
evolgen | April 19, 2007Oxford University Press will be releasing a new book in June entitled Darwinian Detectives: Revealing the Natural History of Genes and Genomes. From the OUP description of the book:
Molecular scientists exploring newly sequenced genomes have stumbled upon quite a few surprises, including that only one to ten percent of the genetic material of animals actually codes for genes. What does the remaining 90-99% of the genome do? Why do some organisms have a much lower genome size than their close relatives? What were the genetic changes that were associated with us becoming human?
Ignoring the…
evolgen | April 12, 2007Sex chromosomes are cool. Because they're cool, I've written about them before. It's cool to trace the origins of sex chromosomes. It's cool to study how they evolve. And it's cool to compare similarities and differences of sex chromosomes within and between taxa. In organisms that use sex chromosomes to determine sex (eg, mammals, Drosophila, and birds), there is a big honking chromosome that looks like most autosomes and a piddly little chromosome that doesn't even recombine. In some organisms, males have one copy of the dinky chromosome (which we call a Y chromosome) and one copy of the…
evolgen | March 29, 2007Last week, I linked to an article in Seed about synonymous mutations with deleterious effects in humans. It's heavy with errors, but I didn't linger too much on them. Larry Moran, on the other hand, got a bit more riled up than I did, and John Logsdon (whose blog has the potential to be something cool) agrees with Larry. And I agree with both of them.
The issue here is with the neutral theory, which Larry describes quite well (see also the coverage in this primer to population genetics). Many people misinterpret the neutral theory and think that it claims that all mutations in some class (non…
evolgen | March 20, 2007Darwinian evolution means different things to different people. To me, and many other population geneticists, it refers to positive selection. To Jeffrey Schwartz, an anthropologist at the University of Pittsburgh, Darwinian evolution means gradual change. By the way, Schwartz also thinks humans are more closely related to orangutans than they are to chimps and gorillas.
I'm having a hard time making heads or tails of Schwartz. He seems hypercritical of all molecular evolution -- to the point where one wonders whether he even understands the field. He appears to not understand that evolution…
evolgen | March 19, 2007In the comments of my dinosaur genome size post, Shelley asked:
So do ALL birds have equally small genomes or is there variation among species?
I don't think she was looking for a trite response along the lines of: "Of course there's variation among species." What she was asking, I presume, is how much variation in genome size do we see in birds? As you can see in this phylogeny, all birds (and nearly all theropods) have small genomes. But that tree only presents data from a few species.
To get a better idea of genome size variation within birds, I downloaded C-values (amount of DNA in a…
evolgen | March 17, 2007Genome size can be measured in a variety of ways. Classically, the haploid content of a genome was measured in picograms and represented as the C-value. People began to realize that the C-value was not correlated with any measures of organismal complexity and seemed to vary unpredictably between taxa. This was known as the C-value paradox, and it confused geneticists for quite a while. With an increased understanding of genome structure, however, came the resolution of the paradox: this measure of genome size does not correlate with gene content. The majority of many eukaryotic genomes…
evolgen | February 15, 2007Some bio-bloggers are atwitter over an article by Wojciech Makalowski on Scientific American's website about Junk DNA. I'm a little late to the game because, well, I've been really busy looking at sequences to determine if they are junk DNA. Is it irony? Is it coincidence? Who cares? It's an opportunity to discuss semantics, and I love semantics.
Those of you who have hung around here for a while know this topic often comes up at evolgen (remember this, this, and this . . . hell, here's what a search for Junk DNA turns up). Long story short, I can't stand the term junk DNA, but I do agree…
evolgen | February 6, 2007Where the variation comes from.
Evolution proceeds by the action of many different evolutionary forces on heritable variation. Natural selection leads to the increase in frequency of variation that allows individuals to produce more offspring who, themselves, produce offspring. Genetic drift changes the frequency of variation through random sampling of individuals from one generation to the next. Population subdivision divides the variation into isolated groups where other forces (selection, drift, etc) act upon it. But where does all this variation come from?
Given the title of the post, the…
evolgen | January 16, 2007To the uninitiated, chromosome number may appear to reflect genome size -- more chromosomes would mean a larger genome. This is not necessarily the case if we measure genome size by the number of base pairs in a genome. There are two primary ways to change chromosome number: chromosomal duplications and chromosomal fusions/fissions. Chromosomal duplications (either through polyploidization or aneuploidy) do change the size of the genome, either by creating a second copy of a single chromosome or duplicating an entire genome. Fusions and fissions, on the other hand, merely rearrange the…
evolgen | January 13, 2007Larry Moran has been writing about olfactory receptors (1, 2, 3). The last two focus on work that has come out of Masatoshi Nei's group on the evolution of gene families -- OR genes being a archetype of gene family evolution.
evolgen | January 10, 2007Mutations are the fuel that drives the engine of evolution. Without mutations there would be no variation upon which natural selection and other evolutionary forces could act. Furthermore, much of the theoretical results regarding evolutionary genetics depend on estimates of mutation rates. For example, Kimura showed that the rate of fixation of neutral mutations is equal to the neutral mutation rate. Additionally, many models to explain the evolution of sex and recombination depend on the amount of deleterious mutations per genome per generation (U).
A group led by Peter Keightly (DOI) have…
evolgen | January 8, 2007Phenotypic differences between populations, species, or any other taxonomic classification can be attributed to genetic and environmental causes. The genetic differences can be divided into sequence divergence of transcribed regions, copy number divergence, and expression divergence. These categories are hardly independent -- expression divergence results from the evolution of the protein coding sequences of transcription factors and cis regulatory regions of transcribed sequences.
An article in press in Nature Genetics (news item here) reports on differences in expression of 4,197 genes…
evolgen | January 3, 2007Pim van Meurs has a blog post at The Panda's Thumb about the recent paper on translational selection on a synonymous polymorphic site in a eukaryotic gene (DOI link). He points out that this was predicted in a paper from 1987. In short, the rate of translation depends on the tRNA pool -- amino acids encoded by more abundant tRNA anti-codons will be incorporated more quickly than amino acids with rare tRNAs. Because protein folding begins during translation, codon usage can influence protein secondary structure. That's because rare codons could stall translation, allowing for protein…
evolgen | December 29, 2006The rift in the biological sciences may lie between computational biologists and wet labs, but when we look at individual fields, we see other divisions. In an essay in PLoS Computational Biology Carl Zimmer describes the divide amongst evolutionary biologists. On one side are researchers who like to get their hands dirty -- ecologists, paleontologists, and others that fall under the label 'naturalist'. And on the other side we have the people that prefer to work with molecular tools; Zimmer calls these guys computational biologists, but they also generate their own data, so that label isn't…
evolgen | December 21, 2006As we all know, the genetic code is redundant. Within protein coding regions, substitutions at silent sites do not affect the amino acid sequence of the encoded protein. Because of this property, these synonymous substitutions (so-called because they result in the same amino acid) are often used to estimate the neutral rate of evolution -- they should not be under selection. But there is evidence for natural selection operating on silent sites. That's because, even though different codons encode the same amino acid, the tRNAs for the synonymous codons are found at different frequencies within…
evolgen | December 20, 2006This past summer, Matt Hahn presented a talk at the Society for Molecular Biology Evolution meeting and Evolution 2006 entitled "The 17% Solution: Gene Family Divergence Between Human And Chimpanzee". The basic premise was that, even though humans and chimps are ~99% identical at the DNA sequence level, they differ substantially in copy number variants. That is, the two species have different amounts of genes from certain gene families, which Hahn estimated as a 17% difference in genes between them. Given the amount of copy number polymorphism within humans, it should come as no surprise that…
evolgen | December 18, 2006Since my last report on Nature's copy number polymorphism (CNP) papers, a couple other journals have published studies of human structural polymorphisms:
Genome Research has two papers on detecting CNPs using oligonucleotide microarrays. The strategy here is to develop a microarray that contains all the unique regions of the genome (divided into ~20 nucleotide pieces). You can quantify the amount of DNA hybridized to the array. So, when you test genomic DNA, regions of single copy DNA will have a certain intensity, whereas regions that are present at multiple copies will have higher…
evolgen | December 7, 2006The five nurses and one doctor (the Tripoli Six) accused of infecting hundreds of patients with HIV in Libya are awaiting the verdict of their trial, expected to be handed down on December 19. The second trial concluded on November 4 -- the original guilty verdict was overturned. I previously mentioned that the molecular evidence (DNA sequences from HIV taken from the patients) did not support a guilty verdict. Nature has published the results of an analysis of those DNA sequences that suggests the doctors were not responsible for the HIV infection. A description of that evidence is below the…
evolgen | December 5, 2006A few weeks ago PNAS published a paper on the evolution of snake sex chromosomes. The authors compare snake sex chromosome evolution with that of mammals and birds. Given my passing interest in sex chromosome evolution, I decided to check it out.
Snakes use sex chromosomes to determine the sex of their progeny. Sex in other reptiles, such as crocodiles, is determined by the temperature at which the eggs are incubated. There are two main types of sex chromosome systems in vertebrates: XY and ZW. Most mammals, some fish, some reptiles, and some amphibians use the XY system -- males are…