Culturing Science – biology as relevant to us earthly beings

Posts Tagged ‘Evolution

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)

ResearchBlogging.org

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

The evolution of the eukaryotes and our human story

“Taxonomy and classification are funny,” my father joked recently, “because the organisms being classified really don’t care what they are. We’re the only ones who care!”

Well, at least I thought it was a good joke.  And it speaks to a certain truth: humans generally are obsessed with organizing and putting things into categories.  It is evident in the way we divide our music into genres (“Is this chillwave or witch house?”) or put our pants in a different drawer than our shirts. This may seem silly, but, with our consciousness and perception, we need to categorize in order to make sense of our world, to generalize, and, well, to help us find things.

We no longer have unicorns in our taxonomical literature. From the Ashmole Bestiary, 1504. Via BibliOdyssey.

Long before any ideas of natural selection and evolution as we know them now, people were trying to organize the natural world around them.  In 350 BCE, Aristotle published his History of Animals, which attempted to categorize the various “natures” of animals based on their characteristics.  For example, he identified what we now know as arthropods as animals that do not have blood and, “if they have feet, have many” (French 1994).  Some of his categorizations were not so on-par; for example, he placed foxes and snakes in the same category because they both burrow underground and thus have “sympathetic natures.”  Accurate or not, the effort is there: making sense of the world through categorization.

Although we’ve been at it for a long time, we are not close to being finished identifying all extant species, much less cataloging them.  Just this week it was announced that, due to double-counts, the estimate of the number of flowering plant species will be cut by 600,000.  600,000!  And those are just the plants that are living today, excluding all the known and unknown species that have gone extinct.

It would be easy to say, “whatever, who cares about the extinct ones?  If I’m categorizing to make sense of the world, I want to pay attention to the world I’m living in.  Leave the past in the past, man!”  But if people view the world as stories as I believe we do, we need this history of organisms to construct our narrative1.

A basic illustration of the 3 domain system of taxonomy. The yellowish circles indicate the 3 nodes and the 3 domains of the Bacteria, Eukarya and Archaea. The Eukarya and Archaea share a common ancestor but evolved separately from there. Not to scale in terms of time or breadth. Drawn by Hannah Waters.

And, in particular, we need to know the history of our own species: where do we fit into the puzzle?  How far back can we trace our own ancestors?  When I was 14, I was taught that we are part of the Animal Kingdom, one of the five kingdoms of life.  When I was 17, I was instead taught the three domain system: the Bacteria, the Archaea, and the Eukarya, a classification developed by the microbiologist Carl Woese in the late 1970s.  This new system organized the world based on cell type, in particular dividing the Monera, which previously described all single-celled life, into the Bacteria and the Archaea, which are each single-celled but have many differences in structure.  (See this great post by Labrat for more information on their distinction.)  No longer were we humans described as “animals” as in ancient times, but rather based on an ancient ancestor, the first to embody the type of cell that makes up our bodies.

In the three-domain system, we eukaryotes are more closely related to the archaea, but evolved separately from a common ancestor (sister lineages).  We evolved a unique nucleus composed of specific proteins, and later acquired mitochondria or plastids from bacteria through endosymbiosis.  However, a different hypothesis has arisen in the past couple of decades: the 2-domain system.  In this system, the Eukarya are even more closely related to the Archaea.  In fact, we are a subgroup, having evolved from a singular lineage within the Archaea.  A mere secondary domain, replacing Eukarya as a “primary domain” or sister lineage as put forth in the 3-domain system.

A basic illustration of the 2 domain system of taxonomy. The yellowish circles indicate the 2 nodes and the 2 domains of the Bacteria and Archaea. Of note is that the Eukarya evolved from the Archaean domain. Not to scale in terms of time or breadth. Drawn by Hannah Waters.

Why is the 2-domain system being considered at all?  The Archaea and Eukarya share many of the same components of their genetic information systems, such as over 30 ribosomal proteins, RNA polymerases, transciption factors, promoters to initiate transcription of the genome, and replication enzymes (Gribaldo et al. 2010).  A general tenet of constructing phylogenies, evolutionary trees through time, is that the simpler answer is usually better.  Proponents of the 2-domain system argue that it is simpler for these genetic pathways to have evolved once in the older domain, the Archaea, and been retained in the newer subdomain, the Eukarya.  Proponents of the 3-domain system hold that these systems evolved earlier before the lineages split and were preserved in both the groups over time.

Eukaryotes also share many genes with the Bacteria, even more than with the Archaea.  Do these genes “even out the score” and support the 3-domain system, or were they acquired as a remnant of bacterial endosymbiosis?  An early edition PNAS paper (2010) by James Cotton and James McInerney of the National University of Ireland argues its title: “Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function.”

The authors compared every gene in the yeast genome to bacterial and archaeal genomes, finding that 952 genes have bacterial homologues, while 216 show homology to archaeal genes.  Using these genes, they performed two main tests.  First, they examined how frequently each of these genes killed the cell when deleted from the genome – a test to see just how imperative each is to the cell’s survival.  They found that lethal genes are twice as likely to be of archaeal origin than bacterial origin, giving the Archaea one “important point” in their book.  Second, they looked at how frequently these genes were actually transcribed, or copied into a form from which they can be made into proteins.  Using RNAseq, they found that there was significantly more expression of genes with archaeal homologues than bacterial.  Another “important point” for Archaea.

This study seems to support the 2-domain hypothesis: the genes that come from Archaea are used more frequently and are more necessary for cell survival, despite being fewer in number than Bacterial genes.  But remember: both systems of taxonomy support the idea that Eukarya are more closely related to Archaea.  Importance is merely a factor of correlation, not evolutionary causation.  It provides evidence that the two domains are related, but not the direct evolution of Eukarya from the line of Archaea.

These lineages have been diverging from one another for at least 2.5 billion years – it seems like a bit of a stretch to be doing genomic studies at all!  Think of all the mutations and changes that have been made in the DNA over those 2.5 billion years, obscuring the true relationships and further separating these domains morphologically.  A review coming out next month in Nature Reviews Microbiology goes through a number of studies that attempted to analyze eukaryotic evolution and found that none drew a strong conclusion, or even found conflicting results, “despite analyzing largely overlapping data sets of universal genes.”  They conclude that “it is premature to label any one of these analyses as definitive” and that these large-scale genomic studies have “not yet yielded a resolution to this debate and ha[ve], if anything, intensified it.”

Even if we did know the truth, what would this mean for the “story of human evolution” I was babbling on about earlier?  Well, it means that we’re Archaea deep down!  Those badasses who live in hot springs and sulfur!  We had the potential to be hardy, tough organisms, but instead we’re frail and get cold really easily and get hunger pangs after just a few hours…

More than anything, the fact that this debate exists in the first place gives us a great perspective on our story.  Under 2500 years ago, Aristotle categorized foxes and snakes together.  Now, we’re splitting hairs over the type of ancient cell that foxes, snakes, and ourselves evolved from over 2.5 billion years ago.  It provides the history of our progress.  And look how far we’ve come!

1 Of course there are many applications for studying evolution beyond a desire to learn about our own history.  This 2005 interview with Massimo Pigliucci, an evolutionary biologist at SUNY Stony Brook, and the 1998 collective paper “Evolution, Science and Society: Evolutionary Biology and the National Research Agenda” are good places to start.

NOTE: Molecular evolution is incredibly hard to explain (in my opinion), and I did my best to do so in English.  If you have any questions or think some parts need clarification, please let me know in the comments or write me at hannah.waters [at] gmail.com.  I’d really appreciate it! Thanks!

ResearchBlogging.org

Cotton, J., & McInerney, J. (2010). Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1000265107

French, Roger.  Ancient Natural History.  New York: Routledge, 1994.

Gribaldo S, Poole AM, Daubin V, Forterre P, & Brochier-Armanet C (2010). The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nature reviews. Microbiology, 8 (10), 743-52 PMID: 20844558

Written by Hanner

September 29, 2010 at 7:52 am

Microbe biogeography: the distribution, dispersal and evolution of the littlest organisms

EDIT: This post was selected as a runner up for the PLoS ONE Blog Pick of the Month. Thanks, PLoS! Check out the winner: Greg Laden’s great post on how the victims of Vesuvius died.

ResearchBlogging.orgIn any high school biology class1, we learn that isolation is key to the evolution of species.  For example, take Australia, where an array of marsupials such as koalas and kangaroos reproduce like no other animals on the planet.  Isolation on a continental island allowed ancestral marsupials to evolve gestation via pouch, a trait which was retained as these animals later evolved into multiple (cuddly) species.  In other words: an event that happened in the past resulted in the organisms we see today, or the history of a species influences its current form and life history.

We attribute the distribution of species on this planet, also known as biogeography, to these sorts of historical events.  Organisms evolved, and continue to evolve, the way they do due to historical circumstances out of their control, creating the biodiversity of our world.  The idea of biogeography is generally attributed to Lamarck, and throughout the late-18th and early-19th centuries (pre-Darwin, mind you), scientists suggested many reasons for the non-uniform distribution of organisms, with Lyell summing up these historical factors as a combination of environment and dispersal through migration, passive (e.g. seeds carried in the wind) or active (e.g. elephants walking across the plain).

It's hard to find images for these kinds of posts, ok? Cut me some slack. By the way, image (c) Hannah Waters 2010

However, not all organisms seemed to fit this pattern.  Scientists at this time observed that, while polar bears were limited to the arctic and monkeys to warm climes, organisms such as fungi, sponges, algae and lichens were far more ubiquitous.  The botanist Kurt Sprengel, in summary of a common thought, wrote that organisms of “lower organization” must have greater ability to disperse, allowing them to colonize more broadly and thrive where “circumstances propitious to their production occur.”  (For a full history, see Maureen O’Malley’s commentary in Nature Reviews Microbiology.)

In 1934, the Dutch biologist Lourens Baas-Becking revived this idea, with the thought that the typical explanations of biogeography do not fit with the world of microorganisms.  He saw the same species of microbe living in different places on the globe and in variable environments.  Thus, he posited that historical factors such as isolation and environment could not be the forces determining microbial distribution,  but rather that “everything is everywhere; the environment selects.”  The small size and abundance of many microbe species allowed them to be easily dispersed in water, on wind, on the bodies of animals, spreading them all over the planet.  Many microbes can also lie dormant for a long time until conditions improve, or until the “environment selects” them.  This would, in effect, create what’s been termed a “seed bank” of microbes, where all microbes are in all environments at the same time, lying in wait for environmental conditions to favor their proliferation.

A generic microbial community. Source: Frank Dazzo, Center for Microbial Ecology, Michigan State University

For most of the 20th century, this so-called “Bass-Becking Hypothesis” was widely accepted, but in the past few decades has been hotly debated.  In 2004, Tom Fenchel and Bland Finlay compiled a literature review in Bioscience in favor of the hypothesis, arguing that “habitat properties alone are needed to explain the presence of a given microbe, and historical factors are irrelevant.”  They reviewed studies which showed the ubiquity of microbe species with fewer habitat requirements (generalists, if you will), as well as microbe species that are environmentally specific but are found in their preferred habitats on many continents.  Of note is a 1997  Oikos study that they themselves published, wherein they found 20 living microbe species in a lake sample.  Upon altering conditions (such as food source, temperature, acidity, and oxygen levels), they were able to revive an additional 110 species – evidence supporting the idea of a “seed bank” of microbes.  The authors do note that this theory may only apply to the most common microbe species, since not all are able to dessicate and revive – but perhaps this ability is what made them so widespread in the first place.

One caveat with this study is that the authors advocate for a phenotypic analysis of microbes.  While the ability to study DNA was a huge benefit to the field of microbiology, the authors do not agree that this is useful due to the wide genetic variability even within a single microbial population, and thus rely on morphology to describe species instead of genetic analysis.  A 2006 review, including genetic analyses, found that things aren’t so cut and dry.  The authors cite a number of studies showing reproducible genetic differences within microbe species even along a 10-meter transect in a marsh.  In two hot springs thousands of kilometers apart, despite living in the same environment, two species of bacteria (Synechococcus and Sulfolobus) showed significant genetic differences.  This shows that isolation alone can affect genes, and thus ultimately species, “overwhelming any effect of environmental factors.”

Both reviews note that there is not enough data out there to draw strong conclusions; the 2006 study was relying on 10 articles alone to determine distance and environmental signficance.  To me the differences in these studies come down to how one defines a “species.”  Typically, we differentiate species based on an organism’s ability to produce fertile offspring with another – if they can, they are the same species.  (There are many caveats to the “species problem” beyond my scope right now.  For a really thorough write-up, see this post from the Wild Muse.)  However, most microbes reproduce via cell division, and genes can be transferred horizontally despite “species” boundaries.  So how do we even define a microbial species in the first place?  If we’re looking at evolution alone, it would seem that genetic differences even within microbes that are commonly described as the same species morphologically would be meaningful, as these genetic differences put them on the path to become novel species.

One major question that the idea of “everything is everywhere” brings up is: how do microbes evolve in the first place?  If these organisms are relatively free from the external pressures of isolation and environment, going locally extinct or reviving based on their surrounding conditions, evolution must take an incredibly long time.

I could not find a paper on biogeography and microbial evolution; however, a paper in PLoS published in April 2010 looked at the biogeography and large-scale evolution of phytoplankton in the ocean.   In light of questions I’m asking here, oceanic plankton and microbe communities are very similar.  They are both small organisms  primarily dispersed passively, by ocean currents in the case of plankton.  The ocean hosts a wide variety of environments, and plankton are also generally considered to be everywhere at once.  While it is not ideal, I will use this planktonic model to look at biogeography and evolution in a more specific system.  (Well, as specific as you can get with the ocean…)

A generic planktonic community.

Just as the determinants of microbial biogeography haven’t been concluded, the same is true of plankton.  In this study, the authors sampled planktonic communities in two very different ocean environments: subtropical/tropical oceans, characterized by similar conditions throughout a wide geographical range, highly stratified ocean layers, and nutrient-poor surface waters, and sub-Arctic waters, characterized by high vertical mixing and high nutrient levels across the water column.  They compared 250-ml samples pairwise from each of the oceanic habitats and found that the planktonic communities were “strikingly dissimilar.”  However, when they increased their sample size 100-fold to 25 liters, they found that these contrasting ocean environments shared 76% of their total species pool!  This effect is surely found in many microbial studies: when comparing diversity between smaller plots, you are more likely to find a difference.  But an increase in plot size, even within the same environment, will find more similarities.  (Which is a more meaningful measurement is another question… I’d be happy to hear your comments on that one.)

To look at the evolution of phytoplankton, the authors took core samples from four distinct geographic environments and then identified fossil diatom species within from 240 million years ago to the present, generating “community assemblages” of diatoms through time.  They then compared these communities assemblages with environmental factors: global CO2 concentrations and oceanic upwelling strength.  The authors found that, despite “local determinants such as regional current systems, terrestrial nutrient inputs, atmospheric deposition, physical mixing, etc.,” global climate measures largely predicted the diatom community assemblage, with many species recovering after local extinction.  That’s right: even after the extinction of a species, when preferable environmental conditions returned, so did the diatom.

This study provides a clue regarding the importance of environmental conditions to the global distribution of abundant, passively dispersed organisms.  What is also interesting is that the same diatom species were found again and again over the course of 240 million years.  Their ability for high dispersal and recovery of species enables planktonic communities to evolve “slowly and gradually” over time.

But clearly they have evolved: plankton (and microbes) are incredibly diverse clades.  The question to look at now is how is evolution driven in highly dispersed organisms?

And thus, as usual, they are the tiniest organisms that force us to broaden our view on basic tenets of biology.  Just as horizontal gene transfer did for traditional natural selection, now microbial dispersal does for the evolution of species.

It does give me a great deal of hope regarding life on this planet: the possibility that there is a cache of microbes waiting around for the perfect conditions, even ones not suitable for us.  As my father, Dennis P. Waters (who needs a blog), once put it, “As long as there’s bacteria, there’s hope.”

1That is, in one where evolution is taught at all…

Cermeño, P., de Vargas, C., Abrantes, F., & Falkowski, P. (2010). Phytoplankton Biogeography and Community Stability in the Ocean PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010037

Fenchel, T., & Finlay, B. (2004). The Ubiquity of Small Species: Patterns of Local and Global Diversity BioScience, 54 (8) DOI: 10.1641/0006-3568(2004)054[0777:TUOSSP]2.0.CO;2

Martiny, J., Bohannan, B., Brown, J., Colwell, R., Fuhrman, J., Green, J., Horner-Devine, M., Kane, M., Krumins, J., Kuske, C., Morin, P., Naeem, S., Øvreås, L., Reysenbach, A., Smith, V., & Staley, J. (2006). Microbial biogeography: putting microorganisms on the map Nature Reviews Microbiology, 4 (2), 102-112 DOI: 10.1038/nrmicro1341

O’Malley, M. (2007). The nineteenth century roots of ‘everything is everywhere’ Nature Reviews Microbiology, 5 (8), 647-651 DOI: 10.1038/nrmicro1711

Written by Hanner

June 18, 2010 at 10:41 am

Animals without oxygen and their implications for the evolution of life

ResearchBlogging.orgIt’s been a slow few weeks around here at Culturing Science.  It’s due to a little bit of writer’s block, but mainly it’s just the beautiful weather keeping me outdoors and away from the computer.  Hopefully you’ve been outside so much that you haven’t noticed.

But today my dream article was published: microorganisms, extreme environments, evolution, and daydreaming all rolled into one.  I couldn’t resist but write it up in an excitement-driven fury.  (The 90 degree weather in Philadelphia is also a little too hot for my taste.)

Are you sitting down?  Today scientists from the Polytechnic University of Marche (Ancona, Italy) and the Natural History Museum of Denmark published their discovery of the first multi-cellular animals found to survive without oxygen.  You’ve probably heard of Archaea or Bacteria species which are able to survive in extreme temperatures, acid, or sulfur-rich environments – places we wouldn’t dream of living.  And the world at large is fascinated by them for this reason.

For this study, the scientists collected sediment core samples from the L’Atalante basin in the Mediterranean.  This basin is completely anoxic (oxygen-free), with a salty layer of brine above forming a physical barrier preventing any oxygen from reaching the area.  In the sediment, they found traces of animals from three phyla:  Nematoda, Arthropoda and Loricifera.

However, as all the animals were dead upon analysis, they had to confirm that these animals were in fact living in the sediment, and hadn’t simply settled there in a “rain of cadavers”  (What poetry!) from oxygenated areas of the sea.  They treated the specimens with a stain that binds to proteins – presumably dead animals would have fewer proteins due to decomposition.  In the figure to the right, we see little protein in the Arthropoda (a) and Nematoda (b) images.  However, the Loricifera (c) specimen is bright pink, indicating protein.  The arthropod and nematode species are thus probably dead bodies or shed exoskeletons – but the Loriciferan (unstained in f) shows promise of actual life in the oxygen-free sediment.

After staining more specimens, the researchers also noticed eggs (d and e) within the bodies of the Loriciferans.  This is a novel find because it suggests that these animals do not just spend part of their lifecycle in the anoxic sediment, but live without oxygen for their entire lives, including reproduction.  They additionally found exoskeletons from young Loriciferans (g) suggesting that these eggs grow up in the sediment as well.  While it would still be a new discovery to science if we found animals that live part of their lives in anoxic conditions, the fact that they spend their entire lifecycles down there raises many more questions and expands our definition of life on this planet.

To further confirm that these bugs are living in the sediment, the team gathered fresh sediment samples and added radioactive protein to see if the Loriciferans would eat it.  They traced this radioactivity and found that the animals had incorporated the radioactive substrate into their bodies providing final evidence that these guys are in fact living without oxygen.

So what’s the big deal about a multicellular organism living without oxygen?  Why am I nearly peeing myself over this?  We already know about single-celled organisms can live in extreme conditions.  Why is this so exciting?

It makes sense that single-celled organisms would be more likely to survive in weird places because they can adapt to environments more easily.  They only have one cell to take care of, so if that one cell is viable, they’re fine.  In addition, single-celled organisms are more likely to transfer genes between one another, allowing adaptations to spread more quickly.  But it was assumed that we don’t find multicellular life in extreme conditions because more complex life simply could not exist there.

But now we have found a multicellular animal that can survive without oxygen.  And the million dollar question: how did it evolve that way?  In their findings, Danovaro et al. mention that the Loriciferans don’t appear to have mitochondria, which are found in oxygen-consuming animals, but rather hydrogenosomes, which are found in some single-celled organisms living in extreme environments.  This presents the possibility of endosymbiosis – or the incorporation of one organism into the other.  Endosymbiotic theory is widely accepted to explain mitochondria and chloroplasts in cells; perhaps this occurred another time for the hydrogenosomes of the Loriciferans.  This suggests that maybe this is not as rare of an event as we thought – who knows what other organelles have evolved this way, including ones we haven’t identified yet.

This finding has implications for how we think about the evolution of life on earth.  We humans are obsessed with ourselves; since we breathe oxygen, it’s often assumed that life on earth evolved once oxygen was around.  The discovery of these non-oxygen-breathing animals provides evidence that multicellular life could have risen prior to oxygen, supporting evidence that early life evolved in highly acidic conditions.  (For more on this, see Marek Mantel and William Martin’s commentary on this paper.)

But let’s get down to the real business: let’s talk about space and aliens.  Thus far, we have been primarily searching for alien life based on oxygen because we have lacked proof that complex life can exist that isn’t oxygen based.  The only life we know – us – is oxygen based, providing no other models of life besides planets with oxygen.  The prior knowledge of only single-celled organisms living in non-oxygen based environments suggested that intelligent life cannot exist in those systems.  And while I wouldn’t consider Loriciferans (also known as “brush-heads”) intelligent, they do suggest that non-oxygen substrates can support higher life.  So when looking for aliens, let’s stop being so anthropocentric.  Life can survive without oxygen.

Danovaro, R., Dell’Anno, A., Pusceddu, A., Gambi, C., Heiner, I., & Kristensen, R. (2010). The first metazoa living in permanently anoxic conditions BMC Biology, 8 (1) DOI: 10.1186/1741-7007-8-30

Written by Hanner

April 7, 2010 at 2:41 pm

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

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

ResearchBlogging.org

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

Nature-inspired network design: recent studies in slime mold and leaf veins

This post was chosen as an Editor's Selection for ResearchBlogging.org Nature-inspired design:  this phrase makes me think of shark-skin swimsuits, velcro, and an endless assortment of coffee tables using natural knots and tree branches.  There is logic behind design reliant upon natural elements.  After all, organisms have been undergoing evolution for millions of years for the sake of efficiency.  If anyone knows how to cut through the water cleanly, it would be a shark, wouldn’t it?

When thinking about designing human networks, it thus seems “natural” to turn to nature, which certainly has expertise in the subject.  Every organism has to have a way of transporting nutrients and water around its body, systems which become more complicated as the organisms do.  Think about your circulatory system: all those veins and arteries and capillaries seemingly spread through your skin and innards at random.  But this network of transport tubes has gone through great evolution in order to be so intricate that it seems random to us.

Three recent papers have highlighted the use of organisms to help plan civilized networks: that is, highways and train systems.  The first two papers feature one of my father’s favorite organisms, the slime mold, while the third looks at leaf vein systems.  (For my post on leaf veins as drivers of plant evolution, click here.)

Slime molds are plasmodial protists — their cellular structure is undefinable.  While a slime mold can live as a unicellular and uninuclear organism, if it runs into another of its own species, the two will join by their cellular membranes.  If there are many around, the organism can potentially become a huge amorphous sac with many nuclei, spreading over a surface foraging for food.  (The question is: is it the singular cell membrane or the singular nucleus that makes an organism “unicellular?”)  Here’s a quick video by John Bonner, a Princeton slime mold specialist, showing the beauty of this unfortunately-named creature:

Edit: A commenter pointed out that John Bonner’s “slime molds” are different than the ones used in the research discussed below.  The slime molds in this video, Dictyostelium discoideum, do in fact form a multicellular organism and don’t exhibit the same sort of networking behavior.  The video is still worth watching, but be aware of these differences!  (Thanks, Iain and class!)

When foraging, the blob spreads over a surface looking for sugar.  Once food is located, it will redirect most of its mass elsewhere, leaving a vein behind leading to the food source.  After millions of years of evolution, one would expect that this vein would be the most efficient path between the two points.

Independently, two groups of researchers took advantage of this assumption to use slime mold to compare its foraging network between food sources to our networks connecting cities.  (For the record: one of the papers was published in the International Journal of Bifurcation and Chaos, which is an obsession-worthy title.)  Each team laid out oat flakes simulating the layout of major cities (one oat flake each!) in their region of choice – the UK and Tokyo metro areas.  The question: will the slime mold trails emulate our own systems, thought out by our grand human brains for efficiency?

Slime mold networks compared to actual city planning. Image maniputed; see papers for original figures

The answer: for the most part, yes!  As you can see in the above figures, the authors of each paper saw very similar networks to our own.  However, the slime mold lacked a more circular structure, connecting the outer hotspots to one another.  And why would it have these:  due to its impermanent nature, a slime mold does not need the forethought to create multiple connections to the same spot.  If one is broken, they can simply create a new line leading straight through.

If we’re trying to use these organisms to help us plan transportation networks, obviously this is not a perfect fit, as weather and technical problems cause blocked lines frequently.  We do need this sort of forethought when laying out our cities!  But we are not the only ones.  A paper published last week in Physical Review Letters (open access here) looked at branching patterns in leaf venation.

Just like in our own circulatory system, the network of veins bringing nutrients and water throughout a leaf cannot be simply retracted and reformed, but is a permanent structure.  With herbivores knawing holes all the time, you betcha that plants have evolved “looping networks,” as the authors put it, to ensure that a blockage in one pathway doesn’t deprive the entire leaf of nutrients.  Traditionally modelling has shown these looping networks to be inefficient compared to non-circular, tree-like networks.  Do you think these authors believed that?

As support for their premise, they punched a hole through the central vein of a lemon leaf (see image above) and injected fluorescent dye below.  And behold!  The dye was able to spread throughout the leaf despite this disruption.  They then created a model that incorporated the network’s (a) resilience to damage and (b) variation in load.  Separately and together, the models agreed: looping networks are actually more efficient in the long run.

What do these studies put together show us?  That neither alone is good enough.  We need our slime-mold, treelike networks for basic structure, with some excess leaf-vein looping for support during damage control and tourist influx.  (You never know when you’ll host the Olympics.)  The circularity might seem excessive, but when bad times hit, it will be worth it.  (The citizens will appreciate it too.)

This may seem like second nature to many of you.  But sometimes it’s nice to get some support from “first nature,” amiright?

(Endnote:  I really am curious about the grammar for slime mold.  Are slime mold(s) awesome or is a slime mold awesome?  Guesses/answers in the comments, if you are so inclined.)

Andrew Adamatzky, & Jeff Jones (2009). Road planning with slime mould: If Physarum built motorways it would
route M6/M74 through Newcastle International Journal of Bifurcation and Chaos arXiv: 0912.3967v1

Katifori, E., Szöllősi, G., & Magnasco, M. (2010). Damage and Fluctuations Induce Loops in Optimal Transport Networks Physical Review Letters, 104 (4) DOI: 10.1103/PhysRevLett.104.048704

Tero A, Takagi S, Saigusa T, Ito K, Bebber DP, Fricker MD, Yumiki K, Kobayashi R, & Nakagaki T (2010). Rules for biologically inspired adaptive network design. Science (New York, N.Y.), 327 (5964), 439-42 PMID: 20093467

Written by Hanner

February 11, 2010 at 5:55 am