Frederick Cohan—the Origins of Ecological Diversity in Prokaryotes

How do we distinguish bacterial species? Cohan shows us some nice diagrams of phenotypic and molecular clusters, and they show groups separated by gaps — therefore, species. Unfortunately the species defined thereby are big and contain considerable diversity within them. Darwin defined species as divergent forms between which one finds morphological gaps. Mayr: cohesive set of organisms whose divergence is constrained by genetic exchange. Speciation requires a breakdown of that exchange.

Mallet has developed a version of Darwin’s species definition that includes molecular characters. Under Mayr, speciation is tough, under Mallet, speciation is easy. The two models differ in the frequency of cladogenesis.

How do bacterial species maintain cohesion? Periodic selection purges divergent populations. Diversity within ecotypes is maintained by selective purges, but ecotypes that found new populations in new environments will not face the same selective effects.

Why doesn’t the free(er) exchange of genetic material between bacterial species lead to a convergence or fusion of species? One reason is the rarity of genetic exchange. If two ecotypes have a suite of niche-specifying genes, low frequency of interchange will not be sufficient to prevent divergence.This does not prevent free exchange of niche-transcending genes, genes that are useful in different environments.

Lots of details from Cohan’s work followed, and I confess to being a bit lost in places. He’s looking at different soil bacteria that are found in different ecotypes—for instance, having different characteristic fatty acid content depending on whether they are found on a north-facing or south-facing slope. He argues that speciation is easy because genetic exchange doesn’t prevent speciation. They’re working on finding and confirming ecotypes with whole genome sequencing.

There is cohesion with local populations in one niche, but there is also niche-specifying divergence that is in defiance of cohesion. In animals and plants, niche-transcending genes are only shared between close relatives; in bacteria, they can be shared by the most distant relatives. This sharing doesn’t interfere with divergence.

Paul Sereno— Dinosaurs: Phylogenetic reconstruction from Darwin to the present

Oops, missed the first part of this talk due to the distractions of Lunch. Walked in as he was talking about tree vs. ladder thinking (people have a hard time conceptualizing trees) and history as a chronicle — barebones description of events — or a narrative — events linked by causal explanations.

It took a century for biologists to use systematics to make testable hypotheses about evolution. Darwin himself talked at length about all kinds of evidence for evolution, but strangely neglected fossils and dinosaurs altogether. Sereno blames this on rivalry with Richard Owen, who was the big dinosaur man of the day. One fossil Darwin was pleased with was Archaeopteryx, and Huxley in particular made the link between Archy and birds. Sereno brought in fossil of Confuciusornis — very cool.

We have begun to separate out the chronology from the narrative; chronology is a limiting factor in our hypotheses. We are interested in the trajectory of change over time, and Sereno confesses to baldly exploiting that to get a publication in nature of Raptorex, but he carefully omitted any causal discussion in the paper, trusting readers to infer a narrative from the story, because that’s what we do.

Deplores the thinness of work in the philosophy of phylogeny.

History: Darwin crystallized many of the pieces of an existing chronology into an evolutionary narrative. The next big breakthrough was Hennig (1950) who atomized morphological transformations and branching patterns, defining specific terms to describe phenomena important for understanding trees. Quantitative cladistics (1969) put it on a solid empirical foundation. Character states were coded as mathematical variables.

Problem: everyone has a different matrix for the analysis of characters for each phylogeny examined. The matrix is a black box. We are searching for a methodology that will link everything together. A modern comparative cladistics would open up the black box for universal analysis. Need to figure out what the characters are, and need to be able to do comparative analysis. There is no global understanding of what a character or character state are. There is currently a movement to develop a universal character ontology.

He makes a strong case that we have a serious problem with different investigators studying the same phylogenies, but using different characters and even scoring them differently. We need to standardize to enable full comparisons of multiple data sets.

Douglas Schemske—Ecological Factors in the Origin of Species

How do different varieties become species? Darwin credited selection. What are the details of this process? Speciation is a booming topic in the science literature, with 25,000 titles last year. Need to define a species to begin. Uses Mayr’s biological species concept, which focuses on the importance of reproductive isolating factors.

Darwin on speciation: recommends Stauffer’s compilation of Darwin’s notes as much more thorough and specific than the Origin. Darwin explained speciation as a consequence of selection, divergence, and extinction. Mayr thought Darwin considered geographic isolation to be unimportant; the big book does infer that “some degree of geographical isolation would be indispensible”. Darwin had much more sophisticated views of speciation than Mayr ascribed to him.

What are reproductive barriers in nature? Case study of monkeyflowers (Mimulus) that show very different morphologies and different pollinators (bees vs. hummingbirds). Ecogeographic barriers, premating isolation, postmating prefertilization barriers, hybrid unfitness. In Mimulus, species separated by elevation with a very narrow band of sympatry. Reciprocal translocation showed that the two species are highly adapted to their native ranges.

Premating isolation imposed by bees/hummingbirds that very rarely feed on different flowers.

Postmating isolation: artificially pollinated with cross-species gametes. One species can produce hybrids, but the other does so only at low frequency.

Hybrid fitness: F1 hybrids are not as viable.

Cited Coyne’s work on how these factors work sequentially. Each step in isolation has different degree of contribution, but ecogeographic isolation is the most important component.

What traits contribute to reproductive isolation? They made hybrid F1s, crossed them to produce F2 hybrids that vary widely in morphology. Transplanted them to Yosemite, where they kept records of what pollinators visited which hybrids. Key factors were nectar production (hummingbirds favor lots of nectar); bees shunned hybrids rich in carotenoids — reds were invisible to bees.

Now looking at QTLs (quantitative trait loci) that affect reproductive isolation, and those genes that affect carotenoid production seem to be important. Isolated strains that only carried trans-specific carotenoid genes. This single gene has dramatic differences in visitations by bees vs. hummingbirds.

A single gene substitution seems to be responsible for the reproductive isolation. It takes a long period of time for post-zygotic barriers to evolve, and the most important barriers are in the habitat. Comparative studies of other species were cited to show that ecogeo barriers are the main agents of speciation.

Peter & Rosemary Grant—Natural Selection, Speciation, and Darwin’s Finches

How do we explain the diversity of species in the world? The core process is speciation, a splitting of a lineage into two divergent lines that at the end, cannot interbreed. What do we know about speciation in Darwin’s finches?

They evolved from a common ancestor in 2-3 million years into 14 different species, filling different ecological niches in the Galapagos, largely free of human interference. Showed us photos of four different species with very different beaks.

Developed predictions of population density from things like available biomass, and worked out relationship of expected density to beak size. It seems to have worked, with good correlations between where the environment provides the best opportunities and the kinds of species that are actually present.

Different birds in different environments have different characters, presumably generated by adaptive processes. They frequently observe matches between species present and available food supplies. This is a historical interpretation: what is needed is direct observation of morphological changes in response to changes in the environment.

How much genetic variation is extant in a population? They assessed this in bird populations on Daphne Major, measuring heritability of beak size (value = 0.74, about the same as heritability of height in human populations).

How much genetic difference is present between species? Two genes show consistent graded pattern that correlate with beak shape: BMP4 and calmodulin. Inserting finch BMP4 genes in chickens produces chickens with larger beaks. Most of the variation is thought to be not in structure of genes, but in their regulation.

Describe size-dependent mortality in birds during drought — large birds survived better. Used r=h2s to predict what the average beak size in subsequent generation, tested it, and found a very good fit.

Later rainy year led to a second evolutionary shift, back to favoring smaller birds. They now have a body of data describing almost 30 years of evolutionary responses to 5 drought years. Mean trait values are changing over these years. The birds are not the same morphologically now as they were at the start of their study. Have seen an identical drought condition in 2005 to drought in 1983, but in this recent drought, saw a different reaction. Now, there is a substantial population of magnirostris on the island, so the response to drought is decline in beak size: they are seeing character displacement to increase differences between two species.

Rosemary Grant took the lectern to talk about courtship. Finches can recognize conspecifics by both morphology and song. THere are individual differences, but also larger species differences. Song is learned early by young birds, mainly from the father, and once learned, it is retained for life. Song is learned in a Lorenzian fashion by imprinting, forming a pre-mating species barrier. Sometimes, males will take over a nest of another species and fail to toss out all the chicks, so you sometimes (1%) get individuals that learn a foster-father’s song, of a different species…so you get hybrids later in life.

Hybrids were not seen to survive any of the drought years. Hybrids had intermediate sized beaks that did not thrive when only large, tough seeds were present, but could do well in wet years with abundant small seeds. In those cases, hybrids survived as well as parental types, so their death is not a result of genetic incompatibility.

These hybrids trickle cross-species genes into the foster parents’ species. Will this lead to fusion of the two species? Maybe not, because drought reinforces differences.

Also, some hybrids with magnirostris seen — they don’t breed back into the population. They can’t compete with the purebred magnirostris, and the purebreds also beat up the hybrids.

Douglas Futuyma—Evolutionary Ecology and the Question of Constraints

I have wireless access in the lecture hall today, so I’m going to try liveblogging these talks. This may get choppy! What it will lack in editing will be compensated for by more timely and regular updates. I hope. At least I’ll be able to dump something to the site every 40-60 minutes.

He summarizes the idea that there is a wealth of genetic diversity in populations to allow for effective selection. Lack of mutations should not limit a straightforward selection response. This raises a paradox, however: organisms have phylogenetic niche conservatism. Many species are evolutionarily unadventurous. He works on clades of herbivorous insect species that are sticking to the same plant groups since the Miocene.

May be many niches in nature that are unfilled: example: fish-catching bats have only one species. Where are the nocturnal aerial fish-feeders in other environments? Species don’t just liberally fill every possibility.

Futuyma introduces Gould/Eldredge’s concept of stasis. We need to acknowledge the existence of constraints that are limiting factors on evolutionary possibilities.

Genetic constraints:

In some cases, a “character” doesn’t exist — there aren’t genes or developmental pathways that specify it. For example, thoracic bristle number in flies may not be defined by simple genetic programs. Haldane said humans will not evolve into angels because we lack the required genetic diversity in wings or moral character.

Little or no genetic variance in a character or combination of characters. Looked at Ophraella beetles, asking whether genetic predispositions might limit which species of plants they can feed on. Screened for genetic variation; in about half the cases they found no evidence of genetic variation that would allow for expansion into distantly related plant species. Discussed Bradshaw’s work on genostasis in evolution, which found little genetic variance in heavy metal tolerance in grasses, dessication resistance in rainforest flies, locomotor and life history traits in Hyla. Adaptation observed in some fly species may have been facilitated by hybridization, which introduces the needed variation.

Species evolve along lines of genetic least resistance, where variation is present in the population. Other directions may not be easily followed.

Successful genetic change may require correlated change in multiple other traits, so genetic diversity may hinder evolutionary change by making the optimal combinations rare in the population. Demanding simultaneous changes in larval and adult characters, for instance, might limit rates of change.

Major issue: how much evolutionary novelty is due to new mutations vs. recombination of standing variation in a population?

What accounts for stasis? Most adaptive novelties are associated with shifts to new niches. Because of recombination, new constellations of characters are likely to be ephemeral and not appear in the fossil record — we don’t see them because of issues in population structure. Adaptive gene combinations will be diluted by interbreeding with individuals that lack the combination, so novelties are unlikely to spread very far (unless it’s also associated with reproductive isolation).

During the glacial periods, most species did not adapt to new environments — they used habitat tracking to follow favorable environments. Recombination with more abundant ancestral genotypes leads to collaps of population structures that might favor new forms. Subpopulations lose their character when merged with larger populations, so reproductive isolation is important.

Interesting prediction: ought to be more stasis in times of environmental fluctuation, and more expansion of novelties in subpopulations in times of environmental stability.. Adaptation to rapid environmental change may fail, especially if multiple character changes are required, and extinction is not unllkely. Climate change may simply doom many species. Adaptation to other invasive species is also going to be slow. And many adaptations may be unlikely and evolve only rarely.

Once upon a time, biologists like the idea of convergence — that similar populations might arise in similar environments (I’m thinking of Simon Conway Morris here), but communities are dependent on contingency in evolutionary history, and a deterministic, equilibrial view of ecological “communities” can no longer be supported.

We are seeing a major shift in the discipline to the importance of constraint and evolvability, and the origin of variation. History is important. and there’s increasing integration of disciplines to cover micro- and macro-evolution.

Marc Hauser— where do morals come from? NOT religion.

Whoa. This was a data-rich talk, and my ability to transcribe it was over-whelmed by all the stuff Hauser was tossing out. Unfortunately, I think the talk also suffered from excess and a lack of a good overview of the material. But it was thought-provoking anyway.

One of the themes was how people resolve moral dilemmas. He began with a real world example, the story of an overweight woman in South Africa who insisted on joining a tour exploring a cave, and got stuck in the exit tunnel, trapping 22 people behind her. Do you sacrifice one to save many? One of the trapped people was a diabetic who needed to get out—should they have blown up the woman so the others could escape? This was presented as a kind of philosophical trolley problem, and the audience was asked what was best to do…but I don’t think it works, because unlike those philosophical dilemmas, in the real world we pursue different strategies, and it’s rarely a black and white situation where one has to choose between precisely two possibilities — as in this case, which was resolved by greasing her up with paraffin and pulling her out.

Hauser gave an overview of the philosophical explanations for making moral decisions.

  • Hume: morality intuitive, unconscious, emotional

  • Kant: rational, conscious, justified principles

  • Theist: divine inspiration, explicit within scripture

  • Rawls: intuitive, unconscious, grammar of action: not emotional, built on principles

He’s going to side with Rawls. The key difference between a Rawlsian morality and the others is that a moral decision is made unconsciously, and THEN emotional and rational justifications are made for it. This is testable if you have a way to remove the emotional component of decision; a Rawlsian moral agent will still make the same moral judgments. Studies of brain damaged patients with loss of emotional affect support the idea so far.

He analogized this to linguistics, in which we make abstract, content-free computations to determine, for instance, whether a particular sentence is grammatical. This computation is obligatory and impenetrable; we can’t explain the process of making the decision as we’re doing it, although we can construct rules after the fact.

For instance, he summarized three principles that seem to be general rules in moral judgments.

  • Harm intended as the means to a goal is worse than harm seen as a side-effect.

  • Harm caused by action is morally worse than harm caused by omission.

  • Harm caused by contact is morally worse than equivalent harm caused by non-contact

We don’t judge morality purely on the basis of reasonable outcomes, but also on intent. He suggested that judging only on the basis of whether an outcome is bad or good is a primitive and simplistic strategy, that as people mature they add nuance by considering intentionality — someone who poisons a person accidentally is less morally culpable than someone who does it intentionally.

One example he gave that I found a bit dubious is the use of Transcranial Magnetic Stimulation to shut down regions of brain, in particular the right temporal/parietal junction (which seems to be a locus of intent judgment). In subjects that have that region zapped (a temporary effect!) all that matters is outcome. These studies bother me a bit; I don’t know if I really trust the methodology of TMS, since it may be affecting much more in complex and undefined ways.

Does knowledge ofthe law affect moral judgments? Holland no longer makes a legal distinction betwwen active and passive euthanasia, and many Dutch people are able to articulate a belief that passive euthanasia is less human than active euthanasia. Do the Dutch no longer percieve the action/omission distinction in Hauser’s 3 rules? In a dilemma test, they still make the same distinctions on active and passive stories as others do — actively killing someone to save others is morally worse than simply allowing someone to die by inaction to have the same effect — which again suggests that the underlying mechanisms of making moral decisions are unchanged.

In these same dilemma tests, they’ve correlated outcomes with demographic data. The effects of religion, sex, etc. are negligible on how people make moral decisions.

He makes an important distinction: These are effects on judgment, not behavior. How does behavior connect with judgment?

Hauser describe Mischel’s longitudinal studies of kids given a simple test: they were given a cookie, and told they’d get more if they could hold off on eating it for some unspecified length of time. Kids varied; some had to have that cookie right away, others held off for longer periods of time. The interesting thing about this experiment is that the investigator looked at these same kids as adults 40 years later, and found that restraint in a 3 year old was correlated with greater marital stability, for instance, later in life. The idea is that these kinds of personal/moral capacities are fixed fairly early in people and don’t seem to be affected much by experience or education.

There were some interesting ideas here, and I would have liked to have seen more depth of discussion of individual points. The end of the talk, in particular, was a flurry of data and completely different experiments that weren’t tied in well with the thesis of the talk, and there weren’t opportunities for questions in these evening talks, so it was a bit difficult to sort everything out.

Ron Numbers—Anti-evolution in America, from creation science to Intelligent Design

Ron Numbers gave a brief history of creationism, reminding us that perhaps a majority of the people in the world reject Darwin, and he also emphasized a few facts in that history that many would find surprising.

There was no organized opposition to evolution until the 1920s, when it was marshalled by William Jennings Bryan, who was most concerned about the ethical implications of evolution. He made the point that the popular movie about the Scopes trial, Inherit the Wind, was historically inaccurate. One of the most memorable moments in the movie was when Darrow pinned Bryan down on the date of the creation to 4004 BC…but Bryan had no such preconception. The primary strain of creationism at that time had absolutely no problem with the age of the Earth, and Bryan plainly stated in interviews and speeches that he was a proponent of the day-age theory, in which the “days” of creation week were not required to be 24-hour modern days.

These early creationists had no bone to pick with geology at all, and were unperturbed at the thought that the world was hundreds of millions of years old. The two dominant explanations were the day-age theory, which stretched out the time-span of creation week to cover the whole of geological time, and gap theory, which argued that between the creation of the world mentioned at the beginning of Genesis, and the account of the 6 creation days, there was a long undocumented period of time in which geological history occurred. The latter model was also popular because it was presented in the Scofield Reference Bible, which specifically placed the geological column in a ‘gap’ in the account, and stated that the 6 days referred to the creation of Eden.

The dissenters from this position were a tiny minority, the Seventh Day Adventists, who were regarded as weird by the majority of fundamentalists. The Seventh Day Adventists credited a source of divine information other than the Bible, the prophecies and visions of their founder, Ellen White, who was the source of the idea that Genesis had to be describing a literal six 24-hour day creation occurring 6000 years ago. Her disciple, George MacReady Price, came up with the idea of wedging all of geology into the Noachian Flood. These were not popular ideas.

The mainstreaming of literalist creationism occurred in the 1960s, when John Whitcomb and Henry Morris wrote The Genesis Flood. It’s basically the same nonsense he Seventh Day Adventists were peddling, but Whitcomb and Morris were not SDAs, making it possible for conservative Christians, who regarded Seventh Day Adventism as a freaky cult, to coalesce in the formation of the Creation Research Society. These people had no ambition to convert the research community, but instead wanted to wean bible-believers away from what they considered the compromises of day-age and gap theory.

Another consequence of this shift was that it opened up hard-core creationists to a kind of hyper-evolution: they had to explain how a small ark of fixed size could contain all the animals in the world, so they had to postulate a small number of created “kinds” that diversified into new species after the flood, at a pace evolutionary biologists consider absurd.

In the early 1980s, these new, literal creationists got ambitious and started trying to push into classrooms by legislation, efforts that got stymied by major court decisions in Arkansas and Louisiana, which ruled that mandatory teaching of creationism was unconstitutional. One consequence of the Arkansas decision was that, when the creationists had been anticipating victory, they had begun assembling a creationist textbook. When they lost instead, they had to rewrite to remove the word “creationism” and replace it with “intelligent design”.

Numbers talked a bit about Intelligent Design, and argued that it was different from the previous version of creationism…but not in a good way, or in a milder way. The brainchild of Philip Johnson, Intelligent Design was far more radical than the previous iterations — Johnson opposed methodological materialism, and specifically wants to incorporate god into science. While arguing that ID is something new, though, he also made it clear that it is not because ID is a secular theory — it’s an extraordinarily religious idea, backed by religious proponents, and funded by theocratic extremists like Howard Ahmanson.

He ended by giving us the discouraging news that 65.5% of Americans believe in creationism, and that the movement is expanding beyond US borders to the Islamic and Jewish world, too. Bummer, man. He could have at least offered some hope for the future.

Richard Lewontin—Genetic Determination and Adaptation: Two Bad Metaphors

It was a fine evening here in Chicago, with all these superstars of evolutionary biology in attendance. It was also an information-dense evening — I tried to keep up on my little laptop, but I know I missed a lot. Fortunately, I’m not alone: Rob Mitchum and Jeremy Manier were also covering the event, and have a play-by-play available. I’ll just dump what I’ve got here tonight. I do have wi-fi passwords so I can get things up a little more promptly tomorrow and Saturday.

Richard Lewontin opened up with a few deprecatory comments about the religiosity of our surroundings (the talks were given in a chapel) and our purpose, the reverence given to Saint Darwin. He was there to talk about the importance and danger of metaphors, and addressed two of them. The New Testament metaphor of genes make organisms, and the Old Testament metaphor that organisms adapt to the environment.

It’s not true that genes make organisms. Organisms are consequence of interactions between inside and outside, genes and molecules, and the phenotype is not predictable from the genotype. He discussed the classic example of norms of reaction in Achillea, showing growth of clones in different environments. Cloned plants taken from cuttings — so they’re genetically identical — and grown in different environments show different patterns of growth, and, for instance, don’t show a simple relationship between morphology and the elevation at which they’re grown. Another example is bristle number in Drosophila which show similar unpredictable pattern of response to temperature. Another thing to think about: look at the fingerprints on your left and right index fingers. They’re not identical, but they have the same genes and formed in the same environment at the same time. Living organisms are the outcome of developmental and physiological processes influenced four factors: genes, non-genic molecules in the embryo, environment, and random variation.
Biologists have known this for years but have fallen prey to the metaphor of genetic determinism. (He also mentioned another bad metaphor as an aside: the cell as a machine.)

The other bad bad metaphor is the idea that organisms adapt to ecological niches. Organisms do not fit into preexisting niches. You can’t look at “niches” in the environment…there are an infinity of them. The organism determines the niche. A better idea is the concept of niche construction, in which niches change as organisms evolve. Organisms take whats available and integrate it with their biology, and the life activities of organisms determine what is relevant. When did living in water become the niche of the ancestral seal?

Organisms seek out appropriate environments, the idea of microclimate. Put mesic (adapted to environments with a moderate amount of moisture) and xeric (dry or desert) flies in evironments with different zones of humidity, one surprising result is that the xeric flies move most quickly and determinedly to moist areas, more so than mesic flies. It’s not that dry-adapted flies can handle dryness better…it’s that they’re better at finding damp microenvironments.

Lewontin gave several other examples of organisms that respond in sophisticated ways to confound simple interpretations of adaptation: that we all produce shells of altered microenvironments around us by our metabolic activity; that trees can count the number of days of a certain temperature to trigger flowering; that Daphnia measure the rate of environmental change to determine whether to reproduce sexually or asexually; that organisms modulate the statistical properties of their environment by storage.

He suggested that we need to set aside the bad metaphor of adaptation for a less bad metaphor of construction. Unfortunately, this creates a difficult situation for scientists interested in selection, because, for instance, frequency dependent selection means that the addition of new genotypes to the gene pool (which happens constantly) causes fitness to change in unpredictable ways. It’s a game of rock-paper-scissors with a lot more than just three possibilities. He closed by saying that addressing this kind of problem should be the goal of the next generation of evolutionary biologists.