Category Archives: Genetics

Mutation Patterns in the Human Genome are More Variable Than Expected

I want to bring your attention to a somewhat dense and possibly inconclusive (but important) paper accompanied by a very informative overview in PLoS Biology, concerning mutations in the human genome.

ResearchBlogging.orgMutation rates and patterns of mutation are important for a number of reasons. For one thing, the genome itself is a data set that is both broad and deep. There is a lot of information in a given individual genome (a haploid set of genes from a person, for instance) but there is a wide range of variation in that information. So, inferences or assertions regarding the nature and distribution of genes or their variants cannot really refer to a single version of the genome, but must also take into account the variation in DNA sequences.

A very obvious area where variation is important is in reconstructing phylogenies. “Family trees” of populations or species can be reconstructed by estimating the genetic difference between pairs of samples, and from this, estimating the amount of time that has passed between a Last Common Ancestor and each of two later populations. These dyads (or triads, depending on how you count them) can then be pieced together to get a phylogeny … a graph representing the historical divergence of populations or species … that tells us a particular version of history. Obviously, the rate of mutation must be known or assumed to make this work. Variation in mutation across the genome, or across a population, or across the structure of the family tree itself will cause incorrect inferences.

The research paper is “Cryptic Variation in the Human Mutation Rate” by Hodgkinson et al. Here’s the key finding:

Continue reading Mutation Patterns in the Human Genome are More Variable Than Expected

The Perfect Bird Family Tree…

… is certainly still in the future. But we have seen a step in that direction in a new paper, coming out this week in Science. This research applies intensive and extensive genomic analysis to the avian phylogenetic tree. The results are interesting.ResearchBlogging.orgThis paper is summarized in a number of locations, most notably here on Living the Scientific Life. Here, I will summarize it only very briefly. However, there are two observations I would like to make about this paper and its apparent meaning. One has to do with the nature of science, and the other has to do with the nature of evolution in particular. I’ll argue that we can quantify (almost non-trivially) the number of times science is wrong. I’ll also argue that Stephen Jay Gould was wrong (not totally, but not trivially) about one of his most important assertions (other than his musings about the myth of vaginal orgasms … we’ll talk about that another time). Continue reading The Perfect Bird Family Tree…

Genome Size and Flight in Bats

i-68efa548cdb44e33126c5936c96fe3ed-evolution_2008.jpgContinuing with our discussion of the Evolution 2008 conference, I was hoping to meet T. Ryan Gregory yesterday. He is listed on the Evolution 2008 program as an author of a talk on genome size. Goodnews/badnews: Gregory did not show, but the talk, given by his coauthor working in his lab, was excellent, so we didn’t need him.The research was done, and the paper delivered, by Jillian Smith. The title of the paper was “Genome size evolution in mammals” but it was more focused on specific results Jillian had come up with regarding bats.i-3117c0a3e6ded7c6ab8d12c4393c42c2-bat.jpg

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The bottom line is this: Genome size does not have a lot of function or interest other than simply knowing the size of the genome you are about to delve into on a research project (so it’s like knowing how far away your field site is so you can budget travel, or how big your grocery store run is so you can decide if you can walk to the store or drive, etc.). But there are a couple of ways in which genome size might be interesting in a way that relates to adaptation and/or evolution. Continue reading Genome Size and Flight in Bats

Biology Will Never Be the Same Again: Scott Lanyon

i-68efa548cdb44e33126c5936c96fe3ed-evolution_2008.jpgThe Evolution 2008 conference started out today with a special program for K-12 teachers (mainly life science teachers) organized by the Minnesota Citizens for Science Education (MNCSE). The opening speaker was Scott Lanyon, director of the Bell Museum of Natural History. (The Bell hosted this event.)i-360cbb04fb3ca5b4766c7598e92870d3-Scott_Lanyon.jpgScott’s objective was to outline several areas of evolutionary biology where fundamental changes had occurred over recent years. This was to provide perspective and food for thought for the Life Sciences teachers attending the event, and Scott was very successful in this effort.In each case, Scott described a similar trope … “Not so many years ago, understanding [this or that thing] was thought nearly impossible…. but today, look what we have….”Specifically, Scott, a bird phylogeny expert, outlined four areas of research corresponding to four major areas of evolutionary biology: Continue reading Biology Will Never Be the Same Again: Scott Lanyon

“US government gene guru to resign”

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Photograph of Francis S. Collins
Just passing along the details from Associated Press:

WASHINGTON (AP) — The government is losing its gene guru: Dr. Francis Collins, who helped lead the breakthrough unraveling of the human genetic code — and found common ground between the belief in God and science — is resigning.Collins, arguably the nation’s most influential geneticist, announced Wednesday that he will leave the National Institutes of Health this summer, to write a book and explore other opportunities.The folksy geneticist helped translate the complexities of DNA into everyday vernacular. Collins led the Human Genome Project that, along with a competing private company, mapped the genetic code — or “the book of human life,” as he famously called it…..

Read the rest here.Here is part of an email from Collins: Continue reading “US government gene guru to resign”

Resurrection of DNA Function from an Extinct Genome

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Could even this bird be reanimated, gene by gene?
When you are extinct you’re extinct. Everything about you is dead and gone. There are no more of you, every individual in your species is kaput, non existent, used up, as the Pima Indians would say, you are hokum (like a car with a flat tire). In fact, you are hohokum (like a car with no tires). Your existence is erased. You are as blotto as a budgie in Burbank.Indeed, every bit of your being, every gene in your genome, every base pair in your DNA, is no longer extant….Or is it? Continue reading Resurrection of DNA Function from an Extinct Genome