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paleoanthropology, genetics and evolution

genome structure

  • Fusing chromosomes

    Thu, 2012-07-19 15:20 -- John Hawks

    Carl Zimmer recounts recent research by Evan Eichler's group on the evolution of human chromosome 2, which represents a fusion of two separate chromosomes in ancient apes, which still remain separate in the living great apes: "The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists)". The research paper is by Mario Ventura and colleagues [1].

    The two chromosomes fused, and the cap was deleted, inclusing StSat. It could no longer spread around our genome, the way it did in chimpanzees and gorillas.

    This study is an important advance in our understanding of how human chromosomes evolved–a subject of medical significance, too, since the duplication of the DNA at the end of chromosomes can cause dangerous mutations that can cause genetic disorders. Plus, it is very cool to see how our chromosomes are, in fact, an ancient patchwork.

    People often ask me when this chromosome fusion happened in ancient hominins. I think they attribute excessive importance to this event, reasoning that chromosome fusion may have been the cause of some reproductive isolation. For example, they often ask specifically about Neandertals and modern humans, figuring that when we show Neandertals had 48 chromosomes, it will at last explain why they are extinct.

    In reality, the fusion must have happened within a population. The first person who carried it, and his immediate descendants, must have been able to mate and reproduce successfully with people who didn't carry it. This outcome is not uncommon for chromosomal rearrangements. Many create reproductive incompatibility, and those that do are very unlikely to become common within a population. Some become moderately common but create problems for homozygotes who carry two copies of them. Others seem to be neutral and do not cause noticeable problems.

    So why do related species with different chromosome numbers often have trouble producing fertile offspring, even if they can mate successfully? This is likely because many chromosomal rearrangements and other genetic changes have accumulated in each lineage after a long period of reproductive isolation. Each may have been near selectively neutral within the population where it first occurred. A few may start out deleterious in homozygotes, and later may become fixed in the population only after other genetic changes ameliorate (or "rescue") these deleterious effects. Sometimes, positive natural selection can favor changes within one population that decrease carriers' ability to reproduce with members of another population, and in these cases reproductive isolation can appear very rapidly. In other words, the evolutionary constraints on chromosome structure aren't simple.

    Whether fast or slow, as each of the emerging species becomes different from the ancestral genetic background, the potential for reproductive incompatibility increases. This evolution is not a single jump, but a series of steps that may result in gametic incompatibility, hybrid inviability, or hybrid sterility.

    The series of events leading to the fusion of human chromosome 2 are genetically very interesting, as are the repeated instances of rearrangement that Ventura and colleagues illustrate in chimpanzees. But chromosome fusion has no special magical power, and whether it was connected to ancient speciations or other events in our evolution will take a lot of creative hypothesis testing.

    References

    1. Ventura M, Catacchio CR, Sajjadian S, Vives L, Sudmant PH, Marques-Bonet T, Graves TA, Wilson RK, Eichler EE. The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. Genome research. 2012;22(6):1036-49.
    Tags: 
    genome structure
    speciation
    chimpanzees
    Neandertal DNA

  • The history of junk DNA explored

    Mon, 2008-02-25 08:51 -- John Hawks

    T. Ryan Gregory (Genomicron) has been writing a long series of posts looking into the history of junk DNA. He's focusing on what research articles were saying about repetitive and noncoding elements like Alu, LINES, SINES, minisatellites and the rest -- both at the time they were discovered and since then.

    The series arises from Gregory's irritation about the oft-heard claim that biologists are "discarding the long-held hypothesis that non-coding DNA has no function. For an example, here is the conclusion of a post about functional analysis of non-coding DNA in the 80's:

    In other words, there was no real period in which noncoding DNA was dismissed by the scientific community, though there was a much-needed shift away from strictly adaptive interpretations in the 1980s. Some individual researchers ignored noncoding regions, but there is no gap in the literature other than limits on what could be done in a methodological capacity. The "new" view of noncoding DNA as potentially important has been proclaimed regularly for at least as long as the claimed period of neglect between 1980 and 1994.

    One wonders just how long we will be told that we have long been neglecting noncoding DNA.

    The contrary-to-evolutionists'-claims-junk-DNA-has-function idea is also a staple of intelligent design creationists. As Gregory points out in one of his comments, biologists seem to be "getting their information from textbooks rather from the primary literature." As long as they remain ignorant of the history, they will be susceptible to junk claims.

    Too many scientists fail to realize that good literature review is just as important as good research design.

    The series is called "Quotes of Interest." I really like the idea -- many posts, grouped together, presenting a shotgun view of the literature on a single question. I have a couple of topics that would benefit from this kind of treatment -- and it's a very bloggy way to write!

    Tags: 
    history
    genome structure
    genomics

  • From 100,000 to 25,000, a tale

    Thu, 2007-03-22 10:24 -- John Hawks

    Larry Moran has summarized a long history of the changing estimates of human gene number over the last fifty years. The post was invoked by the supposed "surprise" at the current low estimate of human gene number -- only around 25,000 genes, genome-wide.

    People who learned about human genetics around the time I did often heard that the total human gene number was estimated at 100,000. Of course, there was no real evidence for the gene number, aside from various limiting assumptions. Moran raises several of the ways that people tried to estimate total gene number, ranging from genetic load arguments to hybridization experiments that attempted to find "unique" versus repetitive DNA fractions.

    Here's a sample:

    It was about this time that Walter Gilbert made his famous back-of-the-envelope calculation of 100,000 genes in the human genome. This was the estimate that became widely quoted when the human genome project was first proposed. It's interesting to note that Gilbert's estimate was not based on any experimental evidence; indeed, it conflicted with most of the available evidence suggesting far fewer genes. The larger number seemed less threatening to scientists who were worried that we might not have more genes than a fruit fly.

    If you ever find yourself needing to tell this story, Moran provides a good starting point.

    UPDATE (3/22/2006): Carl Zimmer notes a recent estimate that places the human gene number just above 18,000. This post is also highly recommended, especially for its consideration of just what all those genes do:

    Today scientists still don't know the function of 5898 genes in the human genome. In other words, over the past six years about 7,000 genes either have been figured out or have vanished into the land of nevermind. That's progress, of a sort. But unknown genes still represent a major slice of the human genome, because the total number of genes has fallen as well. The blue slice in the pie above represents 32.2% of all our known genes. For all the work that has poured into the genome, for all the grand announcements, we still don't know have the faintest idea of what about a third of our genes are for.

    That's a bit generous; working with functional categories you soon realize that the "function" of most genes is only "known" by observing structural similiarities with other known genes. For instance, a gene in humans might have a similar part of its amino acid sequence (or "motif") with a gene in Drosophila, which has known effects when mutated. That's pretty indirect knowledge of function, but something like this is all we have for many inferred human genes.

    That's what makes life interesting.

    Tags: 
    genome structure
    genomics
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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.