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.

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.

I ♥ sabbaticals

Why? Because Jerry Coyne can mention this amazing conference, I can take a look at the luminaries speaking at it, and decide at the drop of a hat that I’m going. So this weekend, I’ll be spending my Halloween at a major conference on evolution. Yay!

Look forward to lots of liveblogging (I hope…if they have wi-fi in the conference halls. If not, there will be some massive data dumps in the evenings.)

The ups and downs of radio

Yesterday, I got a brief mention of a botch of a radio show on NPR that nattered on about a “deep rift” in atheism, but this morning on MPR you could have heard Richard Dawkins talking about evolution. He got the better gig.

This interview does make clear one difference in strategy between Dawkins and myself. The interviewer tries to hammer him on being less than respectful to religious believers, and Dawkins is always polite and tries his best to downplay the conflict. In a similar situation, I’d simply say, “Yes, I am openly contemptuous of religious belief. You want to make something of it?”

I guess I’m meaner than Dawkins.

Uh-oh! Deep rift, deep rift, DEEP RIFT!

Mismatch of the decade: Thornton vs. Behe

One of my favorite examples of the step-by-step evolution of molecules has been the work coming out of Joe Thornton’s lab on glucocorticoid receptors. It’s marvelous stuff that nails down the changes, nucleotide by nucleotide.

It’s also work that Michael Behe called “piddling”, despite the fact that it directly addresses the claims of irreducible complexity. Have you ever noticed how the creationists will make grand demands (show me how a duck evolved from a crocodile!) and then reject every piece of fossil evidence you might show them because there are still “gaps”? This is the converse of that argument: when you’ve got a system where you can show each tiny molecular/genetic change, they dismiss that as trivial. You really can’t win.

Well, Thornton has been working hard and coming up with more and more details, while Behe is still sitting there, eyes clamped shut and ears stoppered, insisting that IT CAN’T HAPPEN LALALALAALALALALAAAA. Behe threw together some dreck claiming that not only didn’t Thornton’s work demonstrate evolution, but it actually supported Intelligent Design creationism!

Boy, did he make a mistake.

Remember how when the creationists started playing games with his work, it roused Richard Lenski to slap down Conservapædia hard? We’ve got a similar situation here.

Joe Thornton has written a beautiful response to Michael Behe.

Read it. Really. It’s a whole lesson in important principles in evolutionary theory all by itself. It exposes the ignorance of Behe through and through, and demolishes the premises of Behe’s latest foolish book. And it made me feel soooo gooooood.

Jonathan Wells gets everything wrong, again

I was just catching up on a few blogs, and noticed all this stuff I missed about Jonathan Wells’ visit to Oklahoma. And then I read Wells’ version of the event, and just about choked on my sweet mint tea.

The next person–apparently a professor of developmental biology–objected that the film ignored facts showing the unity of life, especially the universality of the genetic code, the remarkable similarity of about 500 housekeeping genes in all living things, the role of HOX genes in building animal body plans, and the similarity of HOX genes in all animal phyla, including sponges. 1Steve began by pointing out that the genetic code is not universal, but the questioner loudly complained that 2he was not answering her questions. I stepped up and pointed out that housekeeping genes are similar in all living things because without them life is not possible. I acknowledged that HOX gene mutations can be quite dramatic (causing a fly to sprout legs from its head in place of antennae, for example), but 3HOX genes become active midway through development, 4long after the body plan is already established. 5They are also remarkably non-specific; for example, if a fly lacks a particular HOX gene and a comparable mouse HOX gene is inserted in its place, the fly develops normal fly parts, not mouse parts. Furthermore, 6the similarity of HOX genes in so many animal phyla is actually a problem for neo-Darwinism: 7If evolutionary changes in body plans are due to changes in genes, and flies have HOX genes similar to those in a horse, why is a fly not a horse? Finally, 8the presence of HOX genes in sponges (which, everyone agrees, appeared in the pre-Cambrian) still leaves unanswered the question of how such complex specified genes evolved in the first place.

The questioner became agitated and shouted out something to the effect that HOX gene duplication explained the increase in information needed for the diversification of animal body plans. 9I replied that duplicating a gene doesn’t increase information content any more than photocopying a paper increases its information content. She obviously wanted to continue the argument, but the moderator took the microphone to someone else.

It blows my mind, man, it blows my freakin’ mind. How can this guy really be this stupid? He has a Ph.D. from UC Berkeley in developmental biology, and he either really doesn’t understand basic ideas in the field, or he’s maliciously misrepresenting them…he’s lying to the audience. He’s describing how he so adroitly fielded questions from the audience, including this one from a professor of developmental biology, who was no doubt agitated by the fact that Wells was feeding the audience steaming balls of rancid horseshit. I can’t blame her. That was an awesomely dishonest/ignorant performance, and Wells is proud of himself. People should be angry at that fraud.

I’ve just pulled out this small, two-paragraph fragment from his longer post, because it’s about all I can bear. I’ve flagged a few things that I’ll explain — the Meyer/Wells tag team really is a pair of smug incompetents.

1The genetic code is universal, and is one of the pieces of evidence for common descent. There are a few variants in the natural world, but they are the exceptions that prove the rule: they are slightly modified versions of the original code that are derived by evolutionary processes. For instance, we can find examples of stop codons in mitochondria that have acquired an amino acid translation. You can read more about natural variation in the genetic code here.

2That’s right, he wasn’t answering her questions. Meyer was apparently bidding for time until the big fat liar next to him could get up a good head of steam.

3This implication that Hox gene expression is irrelevant because it is “late” was a staple of Wells’ book, Icons of Evolution and the Politically Incorrect Guide to Darwinism and Intelligent Design. It’s a sham. The phylotypic stage, when the Hox genes are exhibiting their standard patterns of expression, of humans is at 4-5 weeks (out of 40 weeks), and in zebrafish it’s at 18-24 hours. These are relatively early events. The major landmarks before this period are gastrulation, when major tissue layers are established, and neurulation, when the neural tube forms. Embryos are like elongate slugs with the beginnings of a few tissues before this time.

4What? Patterned Hox gene expression is associated with the establishment of the body plan. Prior to this time, all the embryonic chordate has of a body plan is a couple of specified axes, a notochord, and a dorsal nerve tube. The pharyngula stage/phylotypic stage is the time when Hox gene expression is ordered and active, when organogenesis is ongoing, and when the hallmarks of chordate embryology, like segmental myotomes, a tailbud, and branchial arches are forming.

5Hox genes are not non-specific. They have very specific patterning roles; you can’t substitute abdominal-B for labial, for instance. They can be artificially swapped between individuals of different phyla and still function, which ought, to a rational person, be regarded as evidence of common origin, but they definitely do instigate the assembly of different structures in different species, which is not at all surprising. When you put a mouse gene in a fly, you are transplanting one gene out of the many hundreds of developmental genes needed to build an eye; the eye that is assembled is built of 99% fly genes and 1% (and a very early, general 1%) mouse genes. If it did build a mouse eye in a fly, we’d have to throw out a lot of our understanding of molecular genetics and become Intelligent Design creationists.

Hox genes are initiators or selectors; they are not the embryonic structure itself. Think of it this way: the Hox genes just mark a region of the embryo and tell other genes to get to work. It’s as if you are contracting out the building of a house, and you stand before your subcontractors and tell them to build a wall at some particular place. If you’ve got a team of carpenters, they’ll build one kind of wall; masons will build a different kind.

6No, the similarity of Hox genes is not a problem. It’s an indicator of common descent. It’s evidence for evolution.

7Good god.

Why is a fly not a horse? Because Hox genes are not the blueprint, they are not the totality of developmental events that lead to the development of an organism. You might as well complain that the people building a tarpaper shack down by the railroad tracks are using hammers and nails, while the people building a MacMansion on the lakefront are also using hammers and nails, so shouldn’t their buildings come out the same? Somebody who said that would be universally regarded as a clueless moron. Ditto for a supposed developmental biologist who thinks horses and flies should come out the same because they both have Hox genes.

8You can find homeobox-containing genes in plants. All that sequence is is a common motif that has the property of binding DNA at particular nucleotide sequences. What makes for a Hox gene, specifically, is its organization into a regulated cluster. How such genes and gene clusters could arise is simply trivial in principle, although working out the specific historical details of how it happened is more complex and interesting.

The case of sponges is enlightening, because they show us an early step in the formation of the Hox cluster. Current thinking is that sponges don’t actually have a Hox cluster (the first true Hox genes evolved in cnidarians), they have a Hox-like cluster of what are called NK genes. Apparently, grouping a set of transcription factors into a complex isn’t that uncommon in evolution.

9If you photocopy a paper, the paper doesn’t acquire more information. But if you’ve got two identical twins, A who is holding one copy of the paper, and B who is holding two copies of the same paper, B has somewhat more information. Wells’ analogy is a patent red herring.

The ancestral cnidarian proto-Hox cluster is thought to have contained four Hox genes. Humans have 39 Hox genes organized into four clusters. Which taxon contains more information in its Hox clusters? This is a trick question for Wells; people with normal intelligence, like most of you readers, would have no problem recognizing that 39 is a bigger number than 4. Jonathan Wells seems to have missed that day in his first grade arithmetic class.

It’s appalling, but this is the Discovery Institute’s style: to trot out a couple of crackpots with nice degrees, who then proceed to make crap up while pretending to be all sincere and informed and authoritative. It’s an annoying trick, and I can understand entirely why a few intelligent people with actual knowledge in the audience might find the performance infuriating. I do, too.