Philip Ward—What do phylogenies tell us about evolution?

A phylogeny is a statement about the evolutionary history of organisms. Cladograms give branching order only, but phylograms include branch lengths as well. They inform us about diversification of lineages, patterns and rates of trait evolution, and the ages of taxa and timing of radiations.

The tree is a model for the history of life at the macroevolutionary level. Darwin fully embraced the idea.Trees now being built with DNA sequence data, using improved phylogenetic algorithms and increased computational power. We now have many well-supported phylogenies backed up by multiple lines of evidence.

There are issues with correlating gene trees with species trees — there can be discordance because of coalescence, etc.

There is some controversy about how much lateral gene transfer confounds the tree model of evolution. Are there parts where the tree model breaks down completely? Some microbiologists argue that archaeobacteria and prokaryote phylogeny can’t be fit into a tree; the sensationalist New Scientist cover was shown. Ward thinks it is an exaggeration. Lateral gene transfer occurs, but Wu and Eisen analyzed 31 conserved protein coding genes in archaea and bacteria and a well-resolved phylogeny still emerges. This argues that lateral gene transfer was not so rampant that it obscures the central tree.

Ward showed a diagram from the Creation “Museum”, illustrating their belief in an “orchard of life”. They need to do a pseudo-phylogenetic analysis to show the “kinds” of life; much of their language has been taken from phylogenetic systematics. He calls it a cargo cult science.

What do the new molecular phylogenies tell us about evolution. Convergence is widespread; morphology can mislead us about evolutionary history. We’re seeing well-supported clades emerging, such as the afrotheria, scattered within old morphological trees. We’re also seeing a stronger biogeographic pattern in the data.

We also have tools for reconstructing ancestral states: we’re using molecular/genetic data to infer and reconstruct an ancestral form. We can use this to reconstruct ancestral protein sequences, which can then be synthesized and their biological properties measured. Ward described the work of the Thornton lab on reconstructing glucocorticoid receptors.

Phylogenies also provide new insight into concepts of higher, more inclusive taxa. Specific example is the persistence of the dinosaur clade beyond the K/T boundary in the form of birds.

Non-pc taxon names: just as the fish taxon excludes tetrapods, inscts seem to be modified crustaceans, butterflies are modified moths, ants are modified wasps.

Eric Lander—Genomics and Darwin in the 21st Century

Lander began by saying he wasn’t an evolutionist — an interestingly narrow definition of the term. He’s a fan of the research, but considers himself a biomedical geneticist, as if that was something different.

Having entire genomes of many species available for quantitative analysis is going to lead to a qualitative change in the science we can do.

He gave a pocket summary of the human genome project. Mouse genome followed, then rat and dog, and now have sequence (to varying degrees of completeness) of 44 species, out of 4600 mammals. Within Homo, there’s the hapmap project and the 1000 genomes project, so at least in us we’re going for depth and breadth of coverage.

Sequencing technology is rapidly accelerating. Exponential growth in the number of nucleotides sequenced per year. Exponentially on a log scale! We’re developing a tremendous amount of data acquisition capability. We’ll be able to address mechanisms of physiology and evolution, and learning about the particulars of history.

Lander focuses on genome-wide studies. Evolutionary conservation is a guide to extracting information from the genome. Showed synteny diagrams of mouse and human, and discussed analyses that allow you to identify highly conserved pieces, bits that might have significant function.

Number of genes is low, 20,500. Early higher numbers he admitted were inflated a bit by prior expectations; when they had a good estimate of 30,000, they decided to waffle and call it 30-40,000.

If genes are counted by homology, how do we know there aren’t many more genes that don’t have homology. If that were case, the number of genes in humans would still be close to the estimated numbers in chimp and macacque.

There are also well-conserved non-coding regions in DNA. 5% of the genome is under selection: coding 1.2%, non-coding 3.8%. Found 200 gene poor regions that contain key developmental genes, and many of the conserved non-coding regions are associated with them.

Long intergenic non-coding DNA: pretty much all of the genome is transcribed, but the vast majority of this is simply noise. There about a dozen regions known where transcription of non-coding DNA seem to be conserved evolutionarily, and have some function: they be transcriptional repressors.

Mechanism of evolutionary innovation in coding genes: examples of whole genome duplication, divergence and loss, all of which can be demonstrated by comparison with an outgroup. Outgroup comparisons can demonstrate whole genome duplications.

Mechanisms of innovation in non-coding regions: about 84% of conserved DNA is shared between marsupials and placentals, suggesting that about 16% of changes are novel. About 15% of placental specific CNEs are derived from transposons.

With 29 mammalian genomes compared, they have 4 substitutions per site, a detection limit of about 10 bp, and 2.8 million features detected. We have a lot of detail that can be extracted from the data sets.

We can find evidence of positive selection. Using chicken as an outgroup, we can identify genes that have undergone major changes in humans but not chimps. Comparision across 29 mammals shows even more. What we’re finding is that these evolutionarily significant genes are enriched for developmental genes.

Analysis within the human species shows that we are a young population that expanded rapidly from a small initial population of 10,000 individuals. Can now screen for associations between single-nucleotide polymorphisms and disease. We can now screen for 2 million polymorphisms in a single pass on a chip. Have now identified 500 loci associated with common traits. Most have very modest effects and only contribute to a small part of the heritability of the trait. Where is all the missing heritability? Missing loci, missing alleles, and non-additive effects of loci.

Positive selection in human history: can use hapmap data to find 300 regions with outlier distributions that suggest they have been the target of selection. Combining statistical tests narrows the specificity of identification to a size roughly equal to a single gene making it possible to identify specific genes with an interesting selective history (work in press by Pardis Sabeti). There are themes: many of these genes are involved in resisting infectious disease.

Genomics is experiencing an explosion of data that represents a huge opportunity for future discovery.

Jerry Coyne—Speciation: Problems and Prospects

Earlier today, Jerry mentioned to me that he noticed my earlier blog posts on the meeting, and thought I wasn’t being critical enough. So I think that means I’m supposed to let my inner beast out for this one. (Nah, actually, it’s because I’m in note-taking transcription mode while listening to these talks. I have to digest them for a bit before I can do any synthesis.)

What is the biogeography of speciation? Can one species split into two while splitting into two? Allopatric speciation: no gene exchange; Parapatric: limited exchange; Sympatric: free gene exchange. Allopatric is sort of the dogma of evolutionary biology. Everybody assumes gene flow and biogeography are the same thing, but they really aren’t.

Nobody contests whether allopatric speciation happens, the question is simply how often it happens. Species concept Coyne uses: groups of interbreeding populations that show substantial reproductive isolation from other forms.

Why is there a controversy about biogeography? Darwin’s concept was largely sympatric. The existence of species in the same area implies that they arose in the same area (clearly not necessarily true). The environment is regarded as important. There haven’t been enough opportunities for allopatric speciation — not that many barriers in the history of the world. Speciation is relatively difficulty with gene flow. Biologists opinions about geography have been conditioned by their own histories.

Can we estimate the frequencies of these different kinds of speciation? We have so many indubitable examples of allopatric speciation. Conditions are present everywhere.

Parapatric speciation: conditions are fairly easy, but data from nature is sparse and hard to get. Need evidence of clinal differentiation or evidence that allopatry never happened (which would be very hard to do). One example given: cave salamanders, two species, that abut a surface species, enabling a path for gene flow. Can’t entirely rule out the possibility of an allopatric speciation event in their history, however.

It’s easier to find evidence for the most controversial pattern, sympatric speciation. Theoretically supportable, and there are also experiments that demonstrate in the lab (with unlikely requirements, such as the complete lethality of intermediates).

    Criteria for verifying sympatric speciation:

  • Complete or substantial sympatry
  • True sister taxa not based on hybridization
  • Substantial reproductive isolation
  • History of taxa must make allopatry unlikely

Special examples:

  • Polyploidy. Up to 70% of angiosperm species have a polyploidization event somewhere in their ancestry. May still require allopatry to keep hybrids from being diluted out.
  • Homoploid hybrid speciation.
  • Parasitic indigobirds imprint on the song of the father, so laying eggs in different host yields individuals that only breed with individuals with similar stepparents.
  • Palms on Lord Howe Island: very small island, so necessarily sympatric. Reproductive isolation by flowering time depending on soil type offers an alternative explanation, though: it reduces gene flow

Coyne doesn’t regard this as true sympatric speciation because there was some kind of trickery that set up a reproductive barrier.

What about cases that satisfy the case of gene flow while speciation occurs? Under these stringent criteria, Coyne thinks 5 cases satisfy. The best cases are cichlids in crater lakes in Cameroon and Nicaragua. Littorina, banded molluscs that live in different tidal zones. Rhagoletis, the apple maggot fly, may not be the best case; they eclose at different times depending on the fruit on which they are laid, which represents a reproductive barrier.


  • There is no doubt that allopatric and peripatrica speciation occur
  • Parapatric speciation may occur, but evidence is hard to come by
  • Sympatric speciation is theoretically feasible, but…
  • The few studies that suggest sympatic speciation occurs suggest that it only occurs rarely

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.