Darwin's 200th: Red Queen And The Lives Of Species

Do species behave like individuals? Do they show the effects of aging reflected in an increased probability of extinction with age?

Darwin argued that natural selection acted at the level of the individual and consequently one type of individual was favored over another. According to him it was competition between individuals within a species that was the engine of evolutionary change.

“But the struggle almost invariably will be most severe between the individuals of the same species, for they frequent the same districts, require the same food, and are exposed to the same dangers.”

But he also recognized the possibility of competition between species leading potentially to species selection.

"The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life."

Species selection is analogous to natural selection acting between individuals. With species selection an evolutionary pattern develops as one type of species is favored or another. For example long lived species may give rise to more descendant species than short lived species. Longevity is a species level property, controlled by say a large versus small geographic range. Over time long lived species may become more numerous than short lived species. So, certain types of species proliferate if they have higher rates of speciation or lower rates of extinction. Darwin didn't really develop this concept. The fossil record in his days was poor and there was no way to test any theory of species selection.

I love palaeontology. I am not much of a fossil collector but I like to understand evolution through fossils. I had two paleontologists on my Ph.D committee. My major adviser who also knew a lot about carbonates and another guy who worked almost exclusively on evolution. This post is based on their work on evolutionary patterns in Mesozoic and Cenozoic planktonic foraminifera.

In the early 1970's University of Chicago paleontologist Leigh Van Valen applied survivorship analyses to fossil taxa. This type of analysis is usually done to understand mortality patterns in a population. So in a sample what fraction of individuals died at childbirth, how many as small children, how many as teenagers, and so on at successive intervals. The results are survivorship curves like the one below.


So depending upon socio-economic conditions, parasite loads and other controls a population may be categorized as type I, II or III. Type I is in which mortality rates of the elderly are high. Type III is one where juvenile mortality is high. And Type II is one where the probability of dying is not age depended. The odds of dying at any age are about the same.

Now you would intuitively expect species to show a type III sort of a curve. A newly formed species may not have developed adaptations to a changing environment. But as time goes by the fit between the individuals and the environment increases and so the probability of a longer lived species going extinct decreases. Instead Van Valen found that extinction patterns in fossil taxa follow curve II. The probability of extinction of species is age independent. This became know as Van Valen's law of constant extinction.

Remember to avoid this misunderstanding. The rate of extinction is not constant.

Obviously!

During major environmental perturbations, for example after a meteorite strike, the rate of extinction will increase precipitously. What Van Valen found was that the probability of extinction does not depend of how young or well established (old) the species is. Species of any age have the same chance of going extinct.

Enter the Red Queen. In Lewis Carroll's fantasia novel Through the Looking Glass the Red Queen says to Alice:

`Now, HERE, you see, it takes all the running YOU can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!’

Using this wonderfully quirky analogy Van Valen argued that species too are running faster and faster but stay in the same place relative to other species. This happens because species interact with other species in its environment. If a gazelle evolves a slightly faster speed of running so will its predator the cheetah. If a parasite evolved a new dodge to its host immune system, the host will evolve a new way of stopping the parasite. Species may change in an absolute sense but they remain the same relative to their competitors.

And so the extinction probability is stochastically constant with respect to species age.

My advisers along with their students have been testing the Red Queen prediction in a long drawn out study using Mesozoic and Cenozoic planktonic foraminifera. Their recent results have been published in the journal Palaios. Plantonic foraminifera are particularly well suited for survivorship analysis since they have a really good fossil record and their ranges are well known.

After crunching the numbers the results showed that extinction is usually random with respect to age except during major extinction events. There is a significant deviation from Red Queen behavior at and after the Cenomanian-Turonian extinction event and after the late Cretaceous-Tertiary extinction event (the one that did in the dinosaurs). This pattern is seen in figure below ( beta coeff. of zero is ideal Red Queen behavior) where the upward spikes around 96 mya ( C-T event) and 65 mya (K-T event) represent deviation from the Red Queen prediction of constant extinction probability.

Now the pattern of deviation was peculiar in that it showed that the extinction probability increased with species age . It resembled the Type 1 survivorship curve I put up above. Just like individuals, species seem to be going through senescence.

That doesn't make sense. Species don't senescence. An individual exists between the time of birth and the time of death. A species too exists between times of its origin and extinction. But at any one time of its historical range a species is made up of populations of individuals who age and die and are replaced by the next generation of individuals, an unbroken ancestor descendant series.

Yet planktonic foraminifera species after mass extinctions were behaving like individuals, going extinct as they grew older.

The most likely explanation is that during mass extinctions certain types of species were more likely to adapt and survive and the subsequent evolutionary pattern of these survivors was showing up as age dependence of extinction. Postmassextinction species tend to be made up of small sized individuals. Small size is an indicator of early sexual maturity. So these species are characterized by adults who reach sexual maturity early in life and stop growing.

These types of species are rapid evolving taxa. This is because individuals have short generation time. The rate of evolution depends on generation time and not absolute time (bacteria evolve quicker than elephants). During times of environmental disturbances it is these rapid evolvers that can keep adapting to the changing environment and make it through. Using the Red Queen metaphor, if species keep running to stay atop a moving adaptive peak, during times of crises only the sprinters among them keep pace with the rapidly changing conditions.

If you want to get somewhere else, you must run at least twice as fast as that!

As conditions improve after the mass extinction the survivor species retain their rapid response characteristic and keep evolving quickly and eventually get transformed into new morphospecies. It appears that they have gone extinct. So the pattern of increase probability of extinction with species age results from populations of post extinction species evolving rapidly into new species, a process known as pseudoextinction.

How do we understand this in terms of selection acting at different levels of biological organization?

Here again selection is acting on two levels. During environmental crises there is selection for early sexual maturity at the level of the individual. So individuals who reach sexual maturity early are favored over individuals who reach sexual maturity late in life. Early maturer's due to their shorter generation time will become more numerous in the population over time. At the same time species with early maturing individuals are also fitter than species without such characteristics. Because the former are made up of individuals with short generation times, they tend to evolve rapidly and bud off new species. This type of species then becomes more numerous with time. Selection processes acting at the two levels, are complimentary. Unlike the earlier example I gave of the selfish gene where selection was favoring the cell containing the mutant gene but opposing the individual containing that gene.

After mass extinctions the nature and patterns of biotic recovery may depend on the characteristics of the survivor species. Selection can take place above the level of the individual. This species selection or species sorting as many people like to call it may lead to the establishment of long term macro-evolutionary patterns of the sort I described.

Darwin's 200th: Evolution Within Individuals

Do individuals evolve during their lifetime or at least do parts of them evolve? The picture below left of the Tasmanian devil with a facial tumor is an example of evolution within individuals.

Well, I had to write something about evolution on Darwin's 200th birth anniversary coming up February 12. I am going to be writing two posts on evolution and evolutionary patterns that may occur at a biological level of organization below and above that of an individual. Darwin didn't address evolution at these levels of biological organization. I am not taking pot shots at any perceived inadequacies in Darwin's thinking but rather trying to highlight how successful his theory really is.

Darwin's contribution is huge because his theory of natural selection is a general explanation that is scalable to all levels of life. It provides us with the intellectual tools to expand the theory beyond what he used it for and explain life's patterns at the level of cells, individuals and species. You have to say that is a pretty powerful idea. As Richard Dawkins put it, his theory has an extraordinarily high explanatory bang for the buck!



Alright so part 1 is about evolution below the level of the individual.

Darwin didn't know anything about genes or even what causes variation. So his theory of evolution didn't address evolution at the level of molecules or cells. His great obsession was to explain how diversity arises and how organisms acquire adaptations or rather evolve a state of adaptedness to their environment over time. To this effect he argued that natural selection acts at the level of the individual. Birds may evolve smaller or larger beaks over time depending of the food available, butterflies may evolve patterns mimicking a poisonous relative, peppered moths may evolve a dark color that acts as a camouflage. Individuals vary and natural selection filters this variation, retaining traits that help individuals survive and reproduce and eliminating traits that are harmful.

But natural selection doesn't only act at the level of the organism. It can act on any entities which shows certain properties. If entities vary in certain traits, if these traits are heritable and if these traits affect "fitness" i.e. they enable one variant to reproduce more than the other then natural selection is off and running. In the natural world these conditions are most familiarly met by whole organisms but in principal they can be met by cells or genes within cells.

Our cells contains two copies of each gene. During cell reproduction a fair system would ensure that each gene has a 50% chance of being passed down to the next generation. But there is scope of this system being subverted. If a mutant gene acquires the ability to increase its chance of being passed down to more than 50% by copying itself and proliferating inside the cell or by killing its sister gene, natural selection will favor it. Genes might then engage in a war among themselves to increase their own reproduction at the expense of the body. In fact complex bodies will not evolve if such genomic conflict is the norm. Mark Ridley has written an engrossing book on how evolution has come up with ingenious solutions to minimize this conflict enabling complex life to emerge.

Still evolution has not done a perfect job of prevention. Whole organisms - and I am talking about multicellular entities- are made up of populations of cells. During development these cells divide and establish cell lineages that perform different functions in the body. Each cell division comes with a probability of a copying error as 4 billion bases get read and a copy of the genome is assembled. Over time as somatic cells divide differences might arise between cells and natural selection might then act on those differences.

The most well know example of this is cancer, where a mutant somatic cell arises and increases in frequency relative to the "normal" cell type. This happens even though the change is harmful to the body. The birth and death rate of cells is a faster process than the birth and death rates of individuals and so natural selection will favor any mutant cell that concentrates on its own reproduction even if it is to the detriment of the body.

Evolution of cells within an organism that confer benefits to the individual also occurs and a recent paper- Evolution of Highly Polymorphic T Cell Populations in Siblings with the Wiskott-Aldrich Syndrome - in PLoS One describes this. The paper reports on a case of two brothers who have both inherited a disease causing allele. But the researchers found that over time in this cell population there have been multiple corrective somatic mutations. These corrective mutations confer an advantage to the host cell and consequently it occurs at higher frequency in that cell population than the diseased cell type. The researchers found that corrective mutants have been positively selected for and the diseased cells selected against.

The development, function and life cycle of somatic cells is part of a great co-operative venture that make bodies work. But population level evolutionary processes can occur in these cell lines within an individual. This is evolution, though not in a form we are familiar with.

By familiar evolution I mean a form where one type of individual is favored over another. That is what Darwin tried to explain. Darwin didn't know about the genes part. He understood something was passed from parent to child and his theory of natural selection worked just as well with this notion and explained the origin of adaptations. We know now that those adaptations develop and change over time through the flow of genes from the passage of germ line cells.

Somatic cell genes don't flow across generational times of whole organisms. The evolutionary histories of somatic cell lineages are short lived and are terminated as these cell lines go extinct with the death of the organism.

But just when you start getting comfortable with the idea of a well established evolutionary pattern, nature or rather evolution itself finds a way to get around it. A facial tumor that has spread and nearly decimated the Tasmanian devil - a marsupial carnivore - shows that somatic cells can sometimes develop an evolutionary history that can extend beyond the lifetime of an individual. Olivia Judson wrote a nice essay about this tumor and its effect on the Tasmanian Devils. The cancerous cell initially arose through a mutation. Devils are aggressive creatures and they often bite each other especially during mating. The cancer cells graft themselves on facial tissue of the other individual and grow and spread.The tumor gene thus spread from animal to animal by bypassing the normal channels of reproduction.

The mutant gene that produced this cancer is a good example of a selfish gene. This is a concept made famous by Richard Dawkins and represents a way of thinking about natural selection. A selfish gene is a mutant gene that enhances its own reproduction relative to the other copy of the gene or other genes in the cell often to the detriment of the body. So it is not just any old mutation. Most copying accidents or mutations harm the gene as well as the body. But "selfish genes" are mutations that natural selection favors at the level of the gene or the cell and opposes at the level of the individual.

So, selection is operating at two levels here. At a lower level cells which contain the mutant gene are fitter than cells that don't contain this gene. But at a higher level individuals that don't contain this mutant gene are fitter than individuals that do. The gene spreads even though it is harmful to the body since cellular reproduction is faster than the generation times of individuals.

The cancer is spreading rapidly in the Tasmanian Devils. Their populations have crashed in some areas by nearly 90% since the inception of this infectious cancer. It is possible that the devils may become extinct.

Natural selection operates on the immediate advantage. It has no long terms plans.

Our bodies are collections of tightly integrated cells. This fantastic example of co-operation has evolved through natural selection over hundreds of millions of years. We don't think of somatic cells as a separate life form. The cells that make up our bodies are us. But occasionally as in the case of the facial cancer in the Tasmanian devils the us can morph into the other. A cell which was part of the Tasmanian devil is evolving into a parasite.

Natural selection is an unsentimental process. It doesn't care for a billion years of co-operative evolution. If the opportunity arises, cells will just as easily rebel against our elaborate body politic and develop lives of their own.

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Tomorrow's post will be on the effect of species selection or species sorting on biotic recovery during and after mass extinctions.

Darwin: Quote Of The Week

Of all the articles, blogs, rants and talks going around in celebration of the 150th anniversary of The Origin of Species and of Darwin's 200th birth anniversary I enjoyed this piece the most so far:

After 200 Years, Darwin's Legacy Still Evolving

Ira Flatow talks to Matthew Chapman, Charles Darwin's great great grandson.

Matthew Chapman: Ya..there was a certain amount of pressure to be academically successful... most people as they grow up imagine they will do better than their father.. or better than their grandfather and certainly better than their great great grandfather and I figured that was not going to happen in the academic sphere... So I kind of dropped out..

Talk about high expectations.

Son when you grow up you need to come up with something better than The Theory of Natural Selection

It's a refreshingly humorous talk, one that takes a look at America's reluctance to embrace evolution.

Listen!

Community Science In India Using Web Maps

After my earlier preview of Bhuvan, a Web Map service to be launched in March 09 by the Indian Space Research Organization, a reader alerted me to a web mapping portal catering to the biology community of India. The name of this service is India Biodiversity Portal and it has been built on a foundation of Google Maps imaging service.

I looked through the site to find out who built this stuff. Apparently a group of NGO's, research organizations and Universities approached the National Knowledge Commission for permission to setup this interactive portal. So, this web service can be thought of as a map based wiki where users can not only view and browse and query data but add to it as well.

Here is the Portal Charter:

It will provide a platform for aggregating and sharing data and information on biodiversity by allowing wide-spread community participation.

It will leverage the intelligence of the crowd in generating, soliciting and aggregating biodiversity information.

It will provide free and open access to biodiversity information. All contributed information will be accessible under the Creative Commons license. The license regimes under which each bit of information is shared will be clearly specified.

It will provide explicit and unambiguous attribution and credit the source of the information.

It will facilitate social networking and build an open community of amateurs, naturalists, professionals, scientists, and others who are interested in the biodiversity of India.

We will build mechanisms for aggregating and validating information by the community, inspired by the large scale success of the wiki.

We believe in building a positive, respectful and trustful participatory environment that benefits science and society, and contributes to a sustainable future.

The language is frankly shocking, even seditious. Open and free access.... sharing data and information...... social networking and open community....... trustful participatory environment. I am not used to hearing this!

A few years ago all these terms were an oxymoron as far as spatial data was concerned. I mean how dare you share data and maps with someone else without the government's permission?!

My experience has been more like....no you cannot have that data....... security concerns..........access delayed....Ministry of Defence clearance required........

.....but I just want to map the distribution of amphibians along riverine habitats.....what?.... no I don't think that poses a threat to national security.

.......project cancelled.

Jokes apart this portal shows that scientists and other users of spatial data in India desperately want an open and transparent environment that enables them to quickly acquire, value add, share data and set up collaborative projects that engage as wide a user base as possible. This portal is a reflection of a new mind set which has been missing for so long in this country.

There are collateral benefits of projects such at this one. You often wonder, ..how do you get the public at large interested in science? How do you get people who are not involved in science professionally to inculcate the scientific outlook? Applications like this map wiki is an example of how it can be done. Anyone can come here, browse through biology and environment data layers, get curious about the world around them, ask critical questions about the state of the environment in the location they live, start a project and contribute to building a database (you have to be a registered user) and start feeling more connected with science and the scientific way of thinking. A virtual meeting place that allows citizens ranging from professional users of spatial data to high school students to initiate a much needed and long overdue conversation with the Indian scientific community. I feel one of the most effective ways to raise public awareness and support for science is through interactive projects like this one.

The makers of Bhuvan would do well to take a long look at such emerging applications. I want to stress again that it will not be the quality of images or the technology itself that will decide whether Bhuvan will succeed in grabbing a significant share of users away from Google Maps, but whether users will be able to access the Bhuvan API and customize Bhuvan to their needs and build innovative location data based applications on top of ISRO's images.

It is the openness and participatory nature of applications like this Biodiversity portal that Bhuvan will be competing against.

More power to them.

New Metazoan Tree of Life

PLoS Biology has an interesting paper (open access) on early metazoan evolution and the nature of the common ancestor of all metazoans.

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis:

Author Summary:

Following one of the basic principles in evolutionary biology that complex life forms derive from more primitive ancestors, it has long been believed that the higher animals, the Bilateria, arose from simpler (diploblastic) organisms such as the cnidarians (corals, polyps, and jellyfishes). A large number of studies, using different datasets and different methods, have tried to determine the most ancestral animal group as well as the ancestor of the higher animals. Here, we use “total evidence” analysis, which incorporates all available data (including morphology, genome, and gene expression data) and come to a surprising conclusion. The Bilateria and Cnidaria (together with the other diploblastic animals) are in fact sister groups: that is, they evolved in parallel from a very simple common ancestor. We conclude that the higher animals (Bilateria) and lower animals (diploblasts), probably separated very early, at the very beginning of metazoan animal evolution and independently evolved their complex body plans, including body axes, nervous system, sensory organs, and other characteristics. The striking similarities in several complex characters (such as the eyes) resulted from both lineages using the same basic genetic tool kit, which was already present in the common ancestor. The study identifies Placozoa as the most basal diploblast group and thus a living fossil genome that nicely demonstrates, not only that complex genetic tool kits arise before morphological complexity, but also that these kits may form similar morphological structures in parallel.

The study proposes that we used to think like this:


Source: Pharyngula

Now we need to think like this:



Credit: American Museum of Natural History

Triploblasts (Bilaterans) did not branch out from within an already flourishing diploblastic tree. Rather both lineages diverged from a common ancestor very early in the history of metazoan evolution and evolved similar complex characters in parallel.

I am not really qualified to comment on the research and how sound the conclusions of this study are but if this study holds up my question is what does this do to our understanding of homology? The evolution literature is full of definitions of homology. I like to think of it as the same feature modified differently in related species. So that feature was present in the most recent common ancestor of the two species. You can apply it to any feature of biological organization; bones, genes and behavior as well.

This study proposes that several similar morphological features like body axis patterning, nervous system, sensory organs were not present in the common ancestor of Bilaterans and diploblasts. So they are not homologous. They evolved independently in these two lineages. But these morphological features developed from the same ancestral genetic toolkit. Which means that these genes should be considered homologous. Off course these genetic toolkits would have evolved different expression patterns in the two lineages as well as differentiated in other ways particularly by gene duplication events, more so in the Bilaterans.

But can we consider the ancestral genetic toolkit inherited by Bilaterans and the diploblasts to be a case of molecular homology which does not translate to homology at another level (morphology)? Can we call the same gene but which is regulated differently in two species and which may control the development of similar or different features homologous or not?