Introducing the Black Queen Hypothesis

A paper by Morris and colleagues (2012) has generated some stir among biologists. The authors are proposing the Black Queen hypothesis to explain genomic reductions among free living interacting microbes. Rather than rehash arguments that have been made more eloquently, I’d like to just point out some informative ones

Quick summary over at the New Scientist

In depth critique by Robert T. Gonzalez

Tommy Leung also reminded me of a great review paper by Sachs et al (2011) over at TREE that is highly relevant to this debate.

Estimating dates using HIV evolution patterns

In this post we see how we can track mutation rates to estimate when people were infected with HIV and even when the virus first crossed over into humans.

HIV is an evolution machine

Its polymerase enzyme is pretty sloppy and has an error rate of about 1 mistake for every 10 thousand nucleotide bases copied.

For a virus with a genome about 10 thousand bases in length, that means that basically every time HIV replicates itself, it makes a mistake.

Sometimes these errors result in a defective virus, but sometimes they give the virus some new property its predecessor didn’t have, such as resistance to an antiretroviral agent (the drugs we use to treat HIV). The high mutation rate of HIV has also led to extensive worldwide diversity in the epidemic, leading to groupings of related viruses called clades that are named with the letters A through K, and sometimes with two letters where it looks like two clades have recombined into a spliced version of HIV. The different clades are shown in this phylogenetic tree. Also shown are how they relate to other immunodeficiency viruses that infect other primates, as well as how HIV (more precisely, HIV-1) is related to a distinct virus that also infects humans and causes AIDS, called HIV-2, which is mostly confined to west Africa.

This extensive diversity also makes it very difficult to develop an HIV vaccine.

Although the high mutation rate makes things difficult for scientific and medical advances in HIV, it does allow us to see evolution in action, and can lead to some pretty interesting discoveries.

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A post on one of biology’s most confounding riddles: the latitudinal gradient in biodiversity.

A beautiful, but comparatively species poor forest in eastern Oregon

Explaining global patterns of biodiversity is a fundamental goal in biology. Understanding how the tens of millions of species on earth have arranged themselves into populations, communities, and ecosystems, is critical for conserving them in the face of a rapidly growing human population and global climate change.

ResearchBlogging.orgThe latitudinal gradient in species diversity is perhaps the most famous such pattern, and it has confounded biologists for decades. Almost invariably across taxonomic groups, hemispheres and continents, as one moves from polar regions towards the equator, species diversity increases (see the figure for a depiction of global bird diversity). The concept of diversity here can be broken down into three parts: “alpha diversity” or the diversity of species in a single location; “beta diversity”, or the turnover of species observed when moving among locations; and “gamma diversity” or the diversity of species found in an entire region. The latitudinal diversity gradient holds true for all three elements.
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