Thursday, August 29, 2013

What is the survival advantage of a larger genome?

The huge variation in genome sizes.  (Note that the X-axis
 is logirithmic.) Source: Wikimedia.
The amount of genomic DNA varies at least 40000-fold across eukaryotic species. But species with a lot of nuclear DNA content do not necessarily seem more complex than those with a small genome-- for example, amoebas have genomes much larger than those of humans. What's more, sequencing data show that the DNA of organisms with large genomes does not include large numbers of "extra" protein coding genes absent in their relatives with small genomes.  Instead, the difference among closely related species is made up chiefly by DNA sequences which do not code for proteins. 


 The high degree of variability  in genome sizes among closely related species is an instance of "the C-value enigma."  It costs a lot of energy to maintain DNA, to repair it when it's damaged, and to handle it accurately during cell division and sexual reproduction, and these costs would be expected to translate into a survival disadvantage, driving species over time toward very compact genomes. And there are real costs to having large genomes. Among plants, for example, there is a strong correlation between the size of the genome and the duration of meiosis. Plants with larger genomes are also more sensitive, in aggregate, to DNA damage via radiation, and they do less well in ecosystems with heavy metal pollution.  Is there some type of counterbalancing survival advantage to having and maintaining all that extra DNA? If so, what is it?

An 2009 paper by Leitch et al.  illustrates this enigma with respect to orchids. Genome sizes in this plant family vary more than 150-fold. (For comparision, genome size variation across all mammals is about 4 fold.) Leitch et al gathered data from 300 different orchid species and crunched the numbers to see if they could discern correlations between genome size and other traits of the plants.  The first trend that Leitch et al noticed was that the genome sizes of most orchid species, across all subfamilies, clustered at a fairly small size, comparable to the sizes observed for mammals. Larger genomes were much rarer.

Genome size (reported as 1C,  or the 
DNA content of unfertilized seeds) of
orchids, separated by lifestyle:
 terrestrial (top) or epiphytic (bottom).  
Genomes larger than 15 ph are observed 
exclusively in land-dwelling orchids.
Next, Leitch et al. noticed a striking difference when genome sizes were plotted according to the plant lifestyle. All of the large genomes they observed belonged  to ground-dwelling orchids.  Epiphyte orchids in this study (which grow  on other plants for physical support) exclusively had genomes at the small end of the range for all species. This pattern held even within orchid subfamilies containing species with both lifestyles. This difference in size distributions suggests that either a large genome is selected against in plants with an ephiphytic lifestyle, or that some advantage might be available for plants with large genomes and terrestrial lifestyle. 
Referring to data from other plant studies, Leitch et al. hypothesize that having a larger genome is disadvantageous for epiphytic orchids. One possible disadvantage that they consider is the known correlation between larger genome sizes and larger plant cell sizes.  Larger cells-- specifically, larger guard cells forming the pores on the bottom of leaves-- would make larger air pores, leading to more rapid exchange of gas but also to increased water loss. Perhaps epiphytic orchids, which must conserve water, have undergone selection for smaller guard cells and thus smaller genomes. Alternatively, phosphorous-- a key component of DNA-- is scarce in the epiphytic niche, and could become a source of selective pressure. Thus the study of Leitch et al. ends up by documenting a specific instance in which larger DNA genomic content appears to be a survival disadvantage. 

The model of Frank et al. Increases
 in atmospheric CO2 levels would
 tend to favor plants with larger guard cells
on their leaves. 
Another approach to understanding the relationship between genome sizes to evolutionary processes is to examine the fossil record. There is a really fascinating example of this in a 2012 paper by  Frank et al.  Frank et al speculated that larger guard cells, by promoting gas exchange,  would be advantageous during evolutionary intervals in which atmospheric carbon dioxide was high. To evaluate this, they collected measurements of guard cell volumes from 400 million years of the fossil record, and remarkably did find a correlation between this simple geometric measure and measures of atmospheric CO2.  Since genome size correlates with guard cell size, its possible that genomic size contributed to evolutionary processes on this longer time scale.
Frank et al. are careful to add this disclaimer to their work: "Our goal is not to identify, nor does it require, a mechanism for change in or evolution of plant genome size. However, an understanding of the selective forces involved requires a model that tells us what to expect from a given set of assumptions, so to this end, we describe a simple model to accompany our findings." With this caveat, their paper provides conceptual support for large genomes as a structural, rather than strictly genetic, trait. 







Wednesday, August 28, 2013

Ramblin' man

John Hawks reviews data that Homo Erectus hominins were in China as early as 1.6 million years ago. I guess wanderlust is in our bones!  The more precise dating is obtained using paleomagnettic measures.

Many other animals dispersed from Africa in this epoch (lower Pliestocene), and it could be that the hominins were following the availability of familiar game.

Tuesday, August 27, 2013

Evidence for Neanderthal manufacture of leatherworking tools

The lissoir tool as used to burnish hides.
Credit: Abri Peyrony and Pech-de-l'Aze projects
There is considerable controversy about the social abilities and cultural achievements of Neanderthals.  In western European sites, tools and ornaments have been found in Neanderthal contexts, but it was not clear if these items were indigenous to the Neanderthals or somehow learned from anatomically modern humans. In today's PNAS, Sorressi et al.  report bone tools for burnishing hides, excavated from Neanderthal sites dating to before the arrival of anatomically modern humans. These new finds thus strengthen the the argument that Neanderthals had their own toolmaking culture.

Sequoias are used to this

Fire scars (arrows)  in a sequoia cross-section show 
that this tree survived repeated wildfires over
 its 500 year lifespan.
National Geographic has a nice write-up of how sequoias handle wildfires like the current Rim Fire near Yosemite valley. As the cross-section shows, these giants have seen it all, from droughts to wildfires.  During the Medieval Warm period, a prior very warm and dry period in the Sierras, a given sequoia would experience wildfires at intervals of 10 to 15 years.

Monday, August 26, 2013

Tame dogs-- and feral scientists

Via John Hawks, I had missed this during last summer: there are several big scientific groups interested in when and where dogs were first domesticated. It is clear that there were dogs in human society about 10,000 years ago, but more recent claims are pushing the start of domestication back to as far as 35,000 years ago. A very interesting-- but still contentious-- topic!

Saturday, August 24, 2013

Asian carp-- not (yet) in the Great Lakes

Asian Carp approaching Lake Michigan
via waterways in the greater Chicago area.
Credit:mlive
Asian carp are a group of invasive species that are working their way up tributaries of the Mississippi river and are nearing the Great Lakes.  These fish eat huge amounts of plankton  and have no established predators, and thus they could become very disruptive to the already stressed Great Lakes ecosystem.  Thus far, there have been no findings of live Asian Carp within the Great Lakes, but DNA evidence for their presence was reported last April.  It is thought to be just a matter of time before they enter the Great Lakes. Tests are continuing, especially for rivers feeding into the Great Lakes, as the fish need long rivers for breeding.

Bats as a possible reservoir for Middle Eastern Respiratory Syndrome

Middle Eastern Respiratory Syndrome , or MERS, is a lethal viral pneumonia which has only been known to epidemiologists since 2012.  The causative agent of MERS is a coronavirus, a member the same virus family responsible for Severe Acute Respiratory Syndrome (SARS) and for several animal diseases.  There have been about 100 confirmed cases of MERS so far, all clustered around the Middle East, with more than 40% mortality.  The key question for researchers of this new disease agent is whether this virus has the potential to cause an epidemic, as SARS did in 2003.

A phylogeny, or family tree, of coronaviruses, based on
amino acid sequences of an enzyme encoded in their
 genome. The virus which causes MERS is labeled in this figure
 with HCoV-EMC/2012 for Human Coronavirus (HCoV) and the 
case  number, and is highlighted in grey. This virus clusters very 
tightly with two coronaviruses  isolated from bats. Note that the 
SARS virus (labeled SARS-CoV) also has a close relationship to 
MERS with respect to this sequence being compared. 
The coronavirus which causes MERS has been isolated, and its genome resembles  several coronaviruses known to be present in bats. Thus the leading theory about this newly discovered virus is that it is a zoonotic virus, that is, a virus which can be transmitted from humans to non-human vertebrates or vice-versa.  Outbreaks of MERS in humans would become more likely in communities which interact frequently with nearby infected animals, and it becomes important to identify the non-human species which harbor the virus. And just this month, there has been a report of isolation of a MERS sequence from bat samples, which would be consistent with the sequence similarity of MERS coronaviruses to other bat coronaviruses.
These results are very preliminary, with a short MERS  fragment identified in only a single bat. Specifically, because bats harbor related coronaviruses, some of which are only now being discovered, researchers would like to see more genomic sequence, and isolates from more bats to be sure that virus that causes MERS is indeed harbored by bats.  Finally, since bats and humans generally avoid one another, it remains to be seen whether other animals are also part of the infection cycle.

Overall, then, MERS is a deadly infectious disease that can spread from person to person and likely from animal to person. Moreover, mutations in the virus causing MERS could change its infectious properties, and trigger an epidemic of viral pneumonia.

Update: A nice write-up of the detective work involved with these viruses is at Understanding Evolution.

Thursday, August 22, 2013

Possible therapy for people with Ebola Virus Disease


A map of historical outbreaks of  Ebola Virus 
Disease. A related virus also escaped  in Reston, 
Virginia (U.S.A.) but did not infect humans. 



Ebola Virus Disease is an often fatal hemorrhagic fever, triggered in humans and other primates by a small set of closely related viruses. This family comprises some of the most virulent infectious agents known, causing fatality rates as high as 90 percent. Thus far, this disease has only hit humans in small, but devastating, localized outbreaks. However, because of its high transmissibility, the scarcity of diagnostic tests, and the ceaseless motion of modern travelers, these viruses could conceivably trigger much larger, even international, pandemics. Finally, in addition to being a public health concern, the viruses of this family are also considered potential biological weapons.

Historically, there has been no cure for Ebola Virus Disease, and public health efforts were limited to isolating patients to prevent further transmission. But now scientists at the United States Institute for Infectious Diseases (USIID) and collaborators have announced a possible therapy for people with Ebola Virus Disease. The therapy agent, called MB-003, is a mixture of three monoclonal antibodies, each of which can bind to proteins expressed by Ebola virus. In an earlier paper, these scientists had found that MB-003 could protect rhesus macaques from the virus when the cocktail was administered 1 h postinfection,  and even  obtained significant protection if  treatment began 24 or 48 h postinfection. But new work published in Science Translational Medicine the authors extended these studies in a really exciting way.  This time, they waited until infected animals showed symptoms of disease, suggesting that the infection was already rampaging. This situation more closely resembles what a doctor would confront especially in a rural clinic,  i.e. the patient would not come in until the illness were already manifest.

The approach used to fight Ebola, a mixture of monoclonal antibodies,  is a modern take on an old therapy known as passive immunization or serum therapy. Long before the modern pharmaceutical era, doctors had realized that blood serum isolated from survivors of a disease would be very effective if given to patients suffering from the same disease. This is because the blood of the recovered patient would have lots of antibodies against that disease agent. Of course, blood will have antibodies against all sorts of other things, and the toxicity was a big reason this type of therapy was largely abandoned in favor of pharmaceuticals. Monoclonal cocktails may have fewer toxic side effects than whole blood serum therapies, and might even be used as immunizations in the future. 

Sunday, August 18, 2013

How dinosaurs were able to have such long necks

Comparison of saruopod dinosaur necks (right side) to necks of non-dinosaurs (left). Credit:  Taylor and Weidel, PeerJ 2013 )
Via National Geographic, I found this interesting analysis by Taylor and Weidel of the neck lengths of sauropod dinosaurs (apatosaurus and so forth)-- by far the longest necks of land-dwelling animals, far eclipsing necks of giraffes and other modern-day creatures.
Such a huge neck on a mammal would be extremely heavy because of the bone weight. In the case of sauropods,  the bones were not solid, but were penetrated with air sacs, so their relative weight was reduced compared to modern large mammals. These air sacs may have also contributed to breathing efficiency by making sure fresh air intake was optimized (the long necks would have made breathing like trying to breathe through a straw).
The paper also discusses the possible unique muscle anatomy of these dinosaurs. The weight (despite all the air sacs) and length of these huge necks required strong muscular attachements to lift and move. Muscles are rarely preserved in fossils, but the bones have residual marks, such as ligament scars, which can give clues about where the muscles ran. Taylor and Weidel speculate that the some of the sauropods had bones and muscles working together like a cantilevered beam, with a very strong lifting support muscle group and specializations to stabilize the neck from side-to-side.  For others such as brachiosaurus, there may have been other anatomical ways to achieve the forces necessary to operate their necks.
A really fascinating look at the mechanics demanded by a really unusual physical attribute.

Saturday, August 17, 2013

That sinking feeling

This makes sense in retrospect, but I would not have predicted it: fish farms set up near the Yellow River delta are contributing to a faster-than-average sea rise in the area. The fish farms are using well water for their operations, at such a clip that it's lowering the water table. And the soft soils of river deltas will subside, or settle under their own weight, without that water content.  The article mentions a related phenomenon in Houston in the 1920's due to oil extraction.

Friday, August 16, 2013

It's all in the wrist

There's a famous scene early in the movie 2001: A space odyssey  in which a tribe of human ancestors learns (from a mysterious monolith ) how to use a club. They leverage this knowledge to whack their rivals--  and the rest, as they say, is history.

As it happens, the ability to grab a club and pound someone involves a complicated wrist motion that might be unique to the human lineage. Careful studies of the wrist bones of Australopithecus afarensis  (the famous Lucy skeleton) have concluded that they likely could not execute a squeeze grip.  However, their close relative Australopithecus sedibus likely did have the wrist geometry necessary for a power grip. So somewhere in between these two, the first ancestor picked up a club and whacked the first rival.
The "squeeze" grip.
Credit:Marzke et al.,
 Am. Journal of Physical Anthropology
These differences in wrist geometry are important--   not just because of the movie, but because the same wrist adaptations provide manual dexterity needed for the manufacture of precision tools, which in turn allows the construction of weapons like spears, the bringing down of larger prey, and probably a survival advantage.  So the motion of the wrist is right up there with brain size and upright posture as a defining adaptation of the human line. 
Human wristbones. The trapeoid, saphoid and capitate (discussed below) are marked with F, A, and G respectively. Credit: Wikipedia




Because of the importance of wristbones in dictating the manual abilities of primates, I was very interested to come across studies of the wristbones of the "hobbit" fossils found on the island of Flores in the Indonesian archipelago. These finds caused a sensation when they were reported in late 2004, because they suggested that very primitive hominins lived on Flores until very, very recently. The skeleton described in the 2004 report belonged to an adult only one meter tall, and with a brain size comparable to that of a human infant. The wristbones of that first specimen were also very primitive, falling somewhere between the shapes of a chimpanzee and of a modern human.  So this was not the wrist of an anatomically modern human, and probably the hobbits could not swing a club.
Specific wrist bones belonging to a chimpanzee (left), hobbit (center) and human (right), viewed in the case of each bone from the same angle for all three species.  Blue, yellow,  and green colors show surfaces where the bones form joints with adjacent bones, and pink indicates surfaces that are not part of joints. Note especially the rotated orientation of the human trapezoid (top row), relative to the hobbit and the chimpanzee This bone is highlighted in the image below. Credit for both: Matt Tocheri, Human Origins Program of the Smithsonian Institution

Excavations at Flores have continued, and there are now additional wristbones reported, which supports the original suggestion that the remains at this dig represent a population of distinct hominins, and not a pathological or damaged modern human. However, the story is not yet over-- the investigators at Flores did find tools at the site, of the sort that probably require a power grip to manufacture. It will take some time, and probably wristbone fossils from other sites and species, to clarify what these hobbits were capable of.
Wristbone arrangements of African apes (left) and modern humans (right). Credit: Matt Tochieri.



Thursday, August 15, 2013

Summary of the Curiosity rover's year on Mars

There's a nice write-up of all of the science that has come out of the Curiosity rover's time on Mars over at Wired Science. 

Brain-eating amoebas

While on the topic of amoebas, there have been a few cases of kids getting meningitis after inhaling amoebas while swimming in freshwater lakes. Click though the link for an image of the infectious amoeba-- definitely nightmare fuel!

And here, the same species of amoeba can get into neti pots used to clear out sinuses.

Friday, August 09, 2013

Giant viruses and the amoebas they live in: a bizarre community

Comparision of relative sizes of viruses to that of  E. Coli, a common bacterium. Credit: New Scientist

Most of the viruses that we study, such as influenza or herpes, are really minuscule, far smaller than bacteria, for instance. In addition to tiny physical size, their genome is also very small compared to free living organisms. But over the last decade, French scientists have isolated viruses which totally break this pattern. Mimivirus, first reported in 2002, was found infecting amoebas in a water tank. This virus is almost four times the size of influenza and comparable to some bacteria. In the last month, scientists report two instances of even bigger viruses-- the so call Pandoravirus family.  The genomes of these viruses are physically larger even than some parasitic eukaryotes. 
In all of that DNA are lots of genes which are unlike any so far identified. The discoverers suggest that this category of viruses may be heirs to a fourth domain of life, outside of eukaryotes, bacteria, and archaea. Importantly, these are bona fide viruses, lacking the genes encoding the ribosomal machinery and other key features of bacteria.
These viruses are so different from what is commonly encountered that there must be something unusual about their lifestyle. While I was reading about this discovery, I came across some interesting commentary from some of the scientists who had made the earlier Mimivirus discovery, that it's no coincidence that these viruses were all found in amoebas. Amoebas are free-dwelling eukaryotes which ingest just about anything large enough. For example, if they are exposed to latex particles of about 0.5 microns, they will take them up, even though they are indigestible. 
A lot of what amoebas internalize in the real world--such as bacteria-- serve as food. But many microbes don't get eaten after ingestion. They seem to persist, in a symbiotic relationship with the amoeba. The scientists were able to demonstrate that a single amoeba could be host to two different bacteria and a virus-- all at the same time. In such an complex and possibly competitive environment, having many genes might be necessary to defend against unexpected visitors. In support of this idea, bacterial strains which can live inside amoebas also have larger genomes than their close relatives which do not. And amoebas themselves can have enormous genomes: one species has a genome of 670,000 megabases-- more than 200x the human genome of 2,900 megabases! 
So something about the amoebas and the microbes which infect them allows or even requires them to have very big genomes. The physical size of these giant viruses may be a function of needing to fit all that DNA into a package, or might be a separate phenomenon. For example, the Mimivirus is already right at the threshold of the latex beads that the amoeba will ingest. Could their size help the viruses to get ingested into their preferred home? That might explain why thus far these really big viruses have only been found in environments favored by amoebas. 

Wednesday, August 07, 2013

Gerald Joyce on the work of defining and searching for life

Astrobiology.net has a lengthy interview with Gerald Joyce describing his contributions to the search for exobiology-- i.e. life outside of Earth. Joyce was on a group selected to define what was being searched for-- he's careful to clarify that they did not try to "define" life in the scientific sense , which would be a whole topic in itself- but instead to extrapolate from properties of Earch life to define what they would search for outside of earth. As the old adage goes, "the universe is not only stranger than we imagine, it's stranger than we can imagine." Their search is going to have constraints, and constraints will exclude some phenomena even from consideration.  I think it's an important habit of scientific investigations to be as explicit as possible, right at the outset, about constraints.


Monday, August 05, 2013

Symposium on human origins

Dienekes links to a series of You Tube videos from a symposium on human origins from earlier this year. Looks really fascinating!

Saturday, August 03, 2013

University of California moving to make its research open-access

A very internet moment-- I just saw on my Feedly Reader feed of Techmeme  (itself an aggregator site) that the University of California senate has approved open-access rules for research performed by UC faculty. Published research  will be available to the public at no charge.  The link to the UC announcement is here. I agree with Gregory Ferenstein of TechCrunch (see first link) that it will be great for people who are interested in reading about all types of science.  I also really agree with the principle that the public has already paid for this research and should have access to the results.