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Posts Tagged ‘Genetics

When adaptation doesn’t happen

“Evolutionary biology has been enriched by considering not only how adaptation happens, but also why it often does not happen,
or at least does not happen as we might naively expect.”

Douglas Futuyma (2010)

In 2005, a group of scientists from La Trobe University in Australia investigated how species will adapt to global warming by studying a species of rainforest fly, Drosophila birchii (later published in Science).  Increased temperatures may lead to drier conditions in rainforests, so the authors wanted to see how quickly this fly could adapt and develop resistance to desiccation.

As in many directed evolution experiments, they took the flies to a lab and exposed them to dry conditions, with most of the flies unable to survive the dryness.  The survivors were then bred to one another.  Thus generation after generation, only the most desiccation resistant flies would survive, resulting in a population that could survive dry conditions potentially induced by global warming.  Right?

Well, that was the idea at least.  At first, their population of flies did show a bit of increased resistance.  However, in the proceeding 28 generations of selection, there was no increased resistance to desiccation, despite that previous papers had found increased resistance in 3 other Drosophila species.  Drosophila birchii was unable to adapt to these conditions.  What went wrong?

The assumptions of natural selection

Natural selection itself is based on three assumptions in a population.  The first is that there will be variation in traits, such as multiple colors of eyes or hair.  The second is that these traits be heritable through the generations, that children will inherit the traits of their parents.  The third is that these variable traits have differential fitness, or that some versions of a trait might help you survive better than another.  Thus certain trait variants will help its carrier organism survive better, passing that trait to its offspring which will in turn bear this trait.

In order for populations to adapt by natural selection, these three requirements must be fulfilled.  When a biologist sees any population, he or she typically assumes that these they are met, and I can’t really blame them.  All cellular life we know of on this planet has a hereditary mechanism, the gene, which has differential fitness depending on the variation, thus meeting requirements two and three.

But what about requirement one, genetic variation in a population?  It has frequently been assumed to also exist in all populations.  In his 2010 review, Douglas Futuyma quotes the famous geneticist Richard Lewontin, who concluded in his 1974 book that “genetic variation relevant to all aspects of the organism’s development and physiology exists in natural populations,” for “[t]here appears to be no character—morphogenetic, behavioral, physiological or cytological—that cannot be selected in Drosophila.”

The idea here is that at any point in a healthy population, there will be many variants of genes in the population, which are replenished infrequently by new mutations.  Thus, when selective pressures come around, there is a full stock of variants to differentially survive and lead to new adaptations.  This is why small populations and inbreeding are considered such problems: the small gene pool means fewer gene variants and an increased inability to adapt to new conditions.

But why should this have to be true?  Is a lab-bred stock of Drosophila really enough to show that there is variation in natural populations, when the lab has a completely different set of selective pressures?

Selection bias in evolutionary studies

When the researchers studying the rainforest Drosophila birchii analyzed the genetic diversity of their collected populations, they found very low variation in the desiccation gene group compared to other genes in the population such as wing size.  This lack of variation prevented the flies from adapting to new conditions – though the researchers weren’t sure why.  Perhaps these dessication genes had (relatively) recently been under selective pressure, and had not had time to reconstitute the genetic diversity in the population.

Unfortunately, there are very few studies of this kind so it’s hard to draw any conclusions.  After all, people studying evolution usually want to study EVOLUTION IN ACTION and not evolution when it doesn’t happen.  I suspect that past experiments that have found low genetic diversity have been tossed simply because it seems less interesting evolutionarily – when maybe it is in fact more interesting.

This would be a form of selection bias: the choice of study populations or species unconsciously (or consciously) swayed by the desired outcome of EVOLUTION IN ACTION.  In his 1991 Croonian Lecture at the at the Royal Society, Anthony Bradshaw gave a compelling example of this sort of selection bias in evolutionary studies (published here).

In Prescot, Merseyside, a copper refinery opened up next to a meadow that had many species of grasses and wildflowers.  Over time, the soil was contaminated by copper, killing off many of the plants.  However, after 70 years, there were 5 species that were still able to thrive in these meadows!  They had adapted and developed a resistance to copper.

Even now I’m thinking to myself, “oh! cool!  How did they adapt that way?  How did that mechanism work?  How quickly did the resistance gene spread?” etc.  But what I’m forgetting is that, while five species did adapt, twenty-one species failed to adapt.  If there really was massive diversity at all genes in each population, you would think that at least one would confer some benefit to survive the copper.  But this did not happen: twenty-one species went locally extinct.

Just as interesting a question as “How did these 5 adapt?” is “Why did these 21 fail to adapt?”  But it’s a question that’s only begun to be reconsidered.  Death and extinction are far more powerful forces in shaping the whole of biodiversity on our planet than successful adaptation, but these evolutionary failures that occur all around us are little studied.  Especially as we anticipate global climate change causing unknown impacts on species worldwide, we should be studying non-evolution to get a better sense of what natural genetic variation actually looks like and what we may be facing in the future.

Literature Cited

Bradshaw, A. (1991). The Croonian Lecture, 1991: Genostasis and the Limits to Evolution Philosophical Transactions of the Royal Society B: Biological Sciences, 333 (1267), 289-305 DOI: 10.1098/rstb.1991.0079

Futuyma, D. (2010). EVOLUTIONARY CONSTRAINT AND ECOLOGICAL CONSEQUENCES Evolution, 64 (7), 1865-1884 DOI: 10.1111/j.1558-5646.2010.00960.x

Hoffmann, A. (2003). Low Potential for Climatic Stress Adaptation in a Rainforest Drosophila Species Science, 301 (5629), 100-102 DOI: 10.1126/science.1084296

Written by Hanner

January 5, 2011 at 10:58 am

Why evolution is right, and your headline is wrong

On Friday, the Guardian published an article by Oliver Burkeman called “Why everything you ever learned about evolution is wrong.”  Pieces have been written against the article already so I won’t go into too much detail (well, a little maybe) – most notably by Jerry Coyne and the Guardian’s own response by Adam Rutherford.

The gist of the article?  Natural selection is more complicated than Darwin thought.  But put in more belligerent terms.

And it certainly is complicated.  As the article brings up, non-Darwinian forces have played a part in evolution in the past.  Microbiologist Carl Woese suggests that early microbial evolution was driven not by Darwinian evolution, but by horizontal gene transfer, where genes are traded between organisms and not passed down vertically through generations.  Burkeman also describes the phenomenon of linked genes, but does not explain the genetics.  Sometimes when two genes are next to one another on the genome, they will be passed along together as a package, even if only one is selected for.  Thus sometimes genes can be “selected” without being “selected for,” to put it in Burkeman’s terms.  But this effect can still be explained by Darwinian evolution.

The bulk of the article is about epigenetics – or how physical modifications to DNA, usually the binding of proteins, can turn a gene “on” or “off,” or change its expression level.  (See here for a primer.)  The article cites several incidents where changes in the epigenome (the full picture of an organism’s epigenetic character) caused by environmental factors affected the grandchildren of the organisms.  For example, a study where researchers confused the night/day internal clock of chickens by altering their lighting conditions found changes in their epigenetic profiles, and also found that their offspring had trouble locating food.  Thus – environmental changes are heritable?  Was Lamarck right about his giraffe necks?

Beyond the fact that most of these studies see their effects lost after a few generations – couldn’t one just argue that this is an issue of nurture?  That when you mess up a chicken’s internal clock, maybe it might have trouble raising its chicks, so that they have trouble surviving on their own?  Bottom line – I am not convinced.

What is most infuriating is the idea that because maybe there are exceptions to Darwinian evolution, it negates his theory.  I don’t think we know everything about evolution.  I don’t think that Darwin is right 100% of the time.  But I do think he is right 99% of the time.  And that’s what’s important.  As scientists, we’re seeking the patterns to life – patterns that can be applied large-scale to many organisms.  Study after study has shown that Darwinian evolution explains changes in organisms through generations most of the time.

We also should seek the abnormal – the horizontal gene transfers, the other forces at work that differ from our patterns.  But to take a field like epigenetics – which is still developing and which we barely understand, trust me, I study epigenetics for a living – and say that it somehow proves Darwin wrong?  That is absurd.  This isn’t a war.  Darwin is right.  Someone else may be right as well.  There are many forces at work here, people.

Which brings me to my final point: how could you ever publish an article called “Why everything you ever learned about evolution is wrong???”  This drives me insane.  If scientists are going to stand up and say, “we are objective, we are empirical, you can believe whatever we say because we are skeptical of ourselves and only seek truth,” we need to hold our science journalists up to the same standards.  I don’t know the credentials of the Guardian piece’s writer, but he clearly is not a trained biologist. As science becomes increasingly important in the daily lives of ever person on this planet, why is the field of science journalism and science writing shrinking?

Science writing should not be using grabber-headlines to gain readership.  I know, everyone wants their attention, every university press release wants the world to believe that they have discovered the cure to cancer or climate change or whatever else.  But, let’s face it: you haven’t.  Those problems will not be solved unless the scientific universe can form some semblance of a community.

Stop using headlines that are lies just to get attention.  Impatient internet users don’t even read the first paragraph of articles anymore, so even if your first line negates your headline, that is not good enough.  Just don’t do it.  Everything you ever learned about evolution is not wrong.  But as we learn more about how biology makes each of us who we are, our view of evolution may change.  And there’s nothing wrong with that.

[Edit: Thanks for the write-up, Genomeweb Daily Scan!)

Written by Hanner

March 21, 2010 at 11:49 am

How Genetics Works [Photo]

[via Flowing Data]

Written by Hanner

March 12, 2010 at 7:40 am

Posted in Uncategorized

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Invasive species corrupt DNA, not just ecosystems (Fitzpatrick et al., PNAS 2010)

I rarely think about how invasive species affect genetics.  It’s always in terms of ecosystems or species: invasive brown tree snakes gobbling up birds and lizards in Guam, or zebra mussels overwhelming and altering the environment of the Great Lakes.  How one species outcompetes and replaces another, changing the natural system.  This is partly because many of the common examples are of predator-prey relationships, where the two species are very distantly related and could never breed, thus keeping genetics out of the picture.  But what about situations where the introduced animal and native animal are similar?

This gets us into the muddy waters of what defines a species.  For sexually reproducing organisms, a species is the group of animals with whom one can exchange genetic material via reproduction, or, in other words, can produce fertile offspring.  To distinguish one species from another under this definition, a scientist would need a pretty wide worldview.  How else could he know that a squirrel from England could not mate with a US squirrel if it tried?  And the honest answer is: he can’t.  (Unless he collected squirrels from around the world and tried to mate them all with one another… but that’s a lot of work.)  Thus, species are often also defined based on location or geography, despite the fact that maybe they could mate if they had access to one another.  But what are the chances that a squirrel will swim across the Atlantic for a new girlfriend?

And there’s where invasive species fit in.  In a paper published this week in PNAS out of Knoxville, TN, Lexington, KY, and UC Davis, scientists studied the Salinas Valley in central California, where salamanders from Texas and New Mexico had been introduced in the 1950s for use as bait by fisherman.  These salamanders, the Barred Tiger Salamanders (Ambystoma tigrinum mavortium) had been defined as a separate species from the threatened native California Tiger Salamanders (Ambystoma californiense), as their populations had been living apart for 3-10 million years, and thus it was unlikely that they were still genetically similar enough to mate.  But – alas – this assumption was wrong.  The invasive salamanders have been mating with the native species for the last 50 years, producing hybrids which are able to mate with either species and one another.  The question: is this hybridization significantly changing the DNA of the native species?

To investigate this question, the researchers identified an introduction site at a pond in central California, and took samples of over 200 salamanders (by clipping the end of their tail and immediately releasing them) at this site and others within a region 200 km north.  Using salamanders of each species from non-invaded ranges, they determined the baseline genetic makeup of each species.

They scanned the genomes of the sampled salamanders (say it 10 times fast) for 68 genetic markers to see if any of the invasive genes had “taken over” the native genes.  They saw no real difference in 65 of these species — that is, the salamanders retained their native genes.  However, they saw a drastic increase in 3 of the genes.  In the figure below, taken from their paper (click on image for larger size),  the little “thermometers” measure the DNA differences at different sites, native in white and invasive in black, with the introduction site indicated by the red arrow.  The upper left (A) shows the big picture: of the 68 gene markers studied total, invasive genes are only apparent at the introduction site.  The other 3 boxes (B, C, D) show the three genes that have spread — and as you can see, they have spread far and deep, despite their invisibility overall (A).  The authors were thorough: they tested whether this pattern was due to either sampling error or random genetic drift without natural selection, and neither of these biases accounted for the pattern of these 3 genes.

The function of these genes is unknown.  However, by studying the behavior of the animals, it seems they are related to reproduction.  The hybrids have larger larvae with greater survival and develop more quickly, ever hastening their dispersal.  This raises a few questions:

1.  If these invasive genes are helping survival, then who cares if they invaded?  It is easy to look at this as actually beneficial to the threatened native salamanders.  However, it has unknown impacts on the surrounding ecosystem.  These bigger larvae eat a lot more, impacting the populations of their prey species through indirect effects of the invasion.  A change in the abundance of one species affects all others – what seems to be an immediate benefit can be incredibly harmful in the long run.

2.  How do we define a species?  The native salamanders are a threatened species.  If they have received genes that increase their numbers through hybridization, is this a comeback?  Are they still A. californiense?  Do these 3 genes alone make them A. mavortium?  Are they an entirely new species?  Is it possible to stop the invasion of these genes throughout the state without killing off a threatened species?

I don’t have the answers to these questions.  We human beings are drawn to classification: we want to put all of the animals in neat little piles and call it fin.  But the truth is that species are eternally evolving — as Peter and Rosemary Grant have shown with their Galapagos finches, most recently in November 2009.  The monkeys that live on one side of a jungle can have a different genetic makeup than the ones on the other side even if they can still mate.

Clearly the introduction of these salamanders, which was just an innocent attempt to raise some bait locally, has had unforeseen impacts on the ecosystem.  Humans’ ability to travel has meant that we are bringing animals together that have not evolved to live together, or have evolved apart millions of years ago.  In some ways it feels like what is done is done — and I am not enough of an expert on habitat restoration to tell you otherwise.  But try little things: wash the mud off of your boots before you go hiking in another state or country, don’t release your foreign pets locally (as my roommate Erinrose and I have been tempted to do with our pet turtle, Nicolas Cage), volunteer at your local wildlife refuge.  Biodiversity is important.

How can we save our planet?

Fitzpatrick, B., Johnson, J., Kump, D., Smith, J., Voss, S., & Shaffer, H. (2010). Rapid spread of invasive genes into a threatened native species Proceedings of the National Academy of Sciences, 107 (8), 3606-3610 DOI: 10.1073/pnas.0911802107

Written by Hanner

March 2, 2010 at 9:43 pm

Autism and schizophrenia: two sides of the same coin? (Crespi et al. 2009, PNAS)

ResearchBlogging.orgAutism and schizophrenia are two disorders that I wouldn’t think to compare to each other.  Autism is usually evident by the time a child turns three years old, and is normally characterized by a lack of social and communication skills.  Schizophrenia, on the other hand, is typically later-onset, in the teens and twenties, and stereotyped by imaginary friends and thus talking to oneself.

In 1943, Leo Kanner theorized a connection between the two, and placed autism as a type of very early-onset schizophrenia.  (Imagine the Venn diagram with the little autism circle inside of the big schizophrenia circle.)  He later renounced this theory, putting them in separate, unrelated circles.

A new study from Simon Fraser University in British Columbia by Bernard Crespi, Philip Stead, and Michael Elliot has brought these two disorders back together again in their PNAS (Proceedings from the National Academy of Sciences) paper, “Comparative genomics of autism and schizophrenia,” published early online on November 30, 2009 (doi: 10.1073/pnas.0906080106).  The authors, however, argue for a new model: that they are actually diametric, or opposite, conditions.

As with many genetic disorders, there are often many different mutations that can occur at the DNA level which show the same symptoms.  (For a review of DNA and mutations, check out my DNA Basics Primer.)  The authors of this study did a genome-wide scan, collected the most common mutations associated with these disorders, and used data from a public database to compare rates of these specific mutations between autism- and schizophrenia- diagnoses to determine whether these disorders are related, and how.

Frankly, their results are astounding.  First of all, they found 20 gene mutations which are common to both disorders, “results inconsistent with a separate and independent relationship of autism and schizophrenia.”  They also found several genes that were common to autism but not schizophrenia, rejecting Kanner’s original model of autism being a subset of schizophrenia.  They thus conclude that these disorders are related in some way.

Here’s the amazing part — at 4 different gene loci, they found opposite results for autism and schizophrenia.  That is, where a duplication of a gene section was  associated with autism, a deletion of  the same gene was associated with schizophrenia.  Their statistical work places these negative associations far from the realm of chance.

This means that autism overproduces 2 proteins which are non-functional in schizophrenics, and schizophrenics overproduce 2 proteins that are absent in autistic individuals.  Previous studies have found that both disorders are associated with improper regulation of genes involved in cell growth-signaling pathways (PI3K, Akt, and mTOR), activating or deactivating the growth, proliferation, differentiation, and death of cells (apoptosis).  Autism has excess signaling while schizophrenia has reduced signaling, especially in the brain.  Further supporting this is the collected evidence from multiple studies that autistic individuals often have increased brain size in childhood, while schizophrenic individuals have reduced brain size.

If these results hold with future tests, which I’m sure will come, it could mean a lot for both diagnosis and treatment of these disorders.  For example, a treatment for autism could lead to immediate research into a related treatment for schizophrenia, if the relationship between these disorders becomes clear.

Let’s not get our panties in a twist just yet.  While these 4 genes have very strong diametric associations and the authors’ work should be applauded, there are hundreds of genes associated with each of these disorders and the causes of autism and schizophrenia are each unclear.  It’s easy to get excited over clear patterns in scientific study — I’m guilty of it on a regular basis.  But one study doesn’t prove a theory; much more work needs to be done to fully clarify this relationship.

Crespi, B., Stead, P., & Elliot, M. (2009). Comparative genomics of autism and schizophrenia Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0906080106

Written by Hanner

December 9, 2009 at 8:59 pm

Posted in Journal Article

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