This month I’m going to two conferences: SMBE and Evolution.
At SMBE, I’ll be giving a poster in poster session #2 on Friday, June 5th. Drop by between 8–9pm and take your picture with Prof. Steve Steve.
At Evolution, I’ll be giving my talk on Tuesday, June 16th at 11am, in the “Population Genetic Modeling” section.
The final chapter of my dissertation has finally been published in Molecular Ecology. This is the project that got me involved with the software SPAGeDi. Although, none of that work remains in the final version of the paper, I have successfully collaborated with the authors of SPAGeDi to make it portable to Linux and OS X. The portable version will soon be made public.
Anyway, the citation of my paper is
Cartwright RA (2009) Antagonism between local dispersal and self-incompatibility systems in a continuous plant population. Molecular Ecology 18:2327-2336. [doi:10.1111/j.1365-294X.2009.04180.x]
Unfortunately, there is not a free version available yet online. The research was partially funded by NIH, so a copy should show up in pubmed in several months. Until then, you can email me at [Enable javascript to see this email address.] (NB this is not my usual address), and I’ll send you a reprint.
Abstract: Many self-incompatible plant species exist in continuous populations in which individuals disperse locally. Local dispersal of pollen and seeds facilitates inbreeding because pollen pools are likely to contain relatives. Self-incompatibility promotes outbreeding because relatives are likely to carry incompatible alleles. Therefore, populations can experience an antagonism between these forces. In this study, a novel computational model is used to explore the effects of this antagonism on gene flow, allelic diversity, neighborhood sizes, and identity-by-descent. I confirm that this antagonism is sensitive to dispersal levels and linkage. However, the results suggest that there is little to no difference between the effects of gametophytic and sporophytic SI on unlinked loci. More importantly both GSI and SSI affect unlinked loci in a manner similar to obligate outcrossing without mating types. This suggests that the primary evolutionary impact of self-incompatibility systems may be to prevent selfing, and prevention of biparental inbreeding might be a beneficial side effect.
Oak Toe Lichen, Carolina Beach State Park
When a novel, adaptive mutation arises in a population it is more likely to go extinct than go to fixation. This is because rare alleles can by chance be lost from the population through accidental deaths, chromosomal segregation, or other forces behind genetic drift.
In 1955 Motoo Kimura used what’s known as diffusion theory to find formulas for calculating the probability that a novel allele with selection coefficient 
goes to fixation. For example, take a haploid, Wright-Fisher population of size 
that consists of only A individuals with fitness 
. Assume that one of those individuals mutates to B, such that the 
. From this setup, Kimura found that the the probability that B will eventually become fixed in the population and A goes extinct is approximately
under the right assumptions. For diploids with fitnesses 
, 
, and 
. This is
Sella and Hirch (2005) use intuition to modify Kimura’s results and derive some better and more useful alternatives for the above equations, which we use in our work for their nice properties. Sella and Hirch give the following equation in their paper:
where 
if the population is haploid and 
if the population is diploid “with multiplicative fitness within loci. …” Unfortunately, they did not specify the diploid model that they were using because there are two different ones used in the literature.
The first one is used above, , , and .
The second one is , 
, and 
.
As you can see, is not measuring the same thing in both models. In the first approach, 
; in the second 
. This is important because accidentally mixing up the models will lead to erroneous results.
The difference between these two diploid models came up last week when we were applying Sella and Hirch (2005) to one of our projects. For diploids, we just couldn’t get their approximation to work (), and we suspected that they were using the second model, while we had read their paper to imply the first model. We looked back at their paper and realized that they neglect to specify exactly how they calculate 
and 
for diploids; we weren’t sure what they used.
I ended up working through their unspecified math to verify that in fact Sella and Hirch (2005) used the second model of diploid fitnesses, while we wanted to work with the first model. So here is a clarification of their equation, based on our way of thinking:
where 
if the population is haploid with fitnesses and , and 
if the population is diploid with fitnesses 
, 
, and 
.
Pinus palustris — Longleaf Pine “grass stage,” Carolina Beach State Park
Ardea herodias — Great Blue Heron, Sarah P. Duke Gardens
Ardea herodias — Great Blue Heron, Sarah P. Duke Gardens
Victoria amazonica — Water Lily, Sarah P. Duke Gardens
For many years now, I’ve been trying to get the final chapter of my dissertation published. Its gone to several journals, and at Molecular Ecology I finally got a really good editor, who is an expert in the topic. He provided great comments, which finally convinced me to bite the bullet and redo my simulations, updating my analysis.
I’ll post a pre-print when it comes available, but for now here is the abstract information.
Antagonism between Local Dispersal and Self-Incompatibility Systems in a Continuous Plant Population
Reed A. Cartwright
Abstract: Many self-incompatible plant species exist in continuous populations in which individuals disperse locally. Local dispersal of pollen and seeds facilitates inbreeding because pollen pools are likely to contain relatives. Self-incompatibility promotes outbreeding because relatives are likely to carry incompatible alleles. Therefore, populations can experience an antagonism between these forces. In this study, a novel computational model is used to explore the effects of this antagonism on gene flow, allelic diversity, neighborhood sizes, and identity-by-descent. I confirm that this antagonism is sensitive to dispersal levels and linkage. However, the results suggest that there is little to no difference between the effects of gametophytic and sporophytic SI on unlinked loci. More importantly both GSI and SSI affect unlinked loci in a manner similar to obligate outcrossing without mating types. This suggests that the primary evolutionary impact of self-incompatibility systems may be to prevent selfing, and prevention of biparental inbreeding might be a beneficial side effect.
My latest paper has now been published by MBE. You can grab your free reprint by following this link. I earlier blogged about some of the implications of this research, which you can see here.
Abstract:
Insertions and deletions (indels) are fundamental but understudied components of molecular evolution. Here we present an expectation-maximization algorithm built on a pair hidden Markov model that is able to properly handle indels in neutrally evolving DNA sequences. From a data set of orthologous introns, we estimate relative rates and length distributions of indels among primates and rodents. This technique has the advantage of potentially handling large genomic data sets. We find that a zeta power-law model of indel lengths provides a much better fit than the traditional geometric model and that indel processes are conserved between our taxa. The estimated relative rates are about 12-16 indels per 100 substitutions, and the estimated power-law magnitudes are about 1.6-1.7. More significantly, we find that using the traditional geometric/affine model of indel lengths introduces artifacts into evolutionary analysis, casting doubt on studies of the evolution and diversity of indel formation using traditional models and invalidating measures of species divergence that include indel lengths.
Reference: Cartwright RA (2009) Problems and solutions for estimating indel rates and length distributions. Molecular Biology and Evolution. 26(7):473–480
I recently became aware of an October paper from Ian Holmes’s group at UC Berkeley describing a rich genome simulation toolset: “Tools for simulating evolution of aligned genomic regions with integrated parameter estimation” Besides their programs, what’s interesting about the paper is that they judged the quality of their work by comparing it to my own research. I have much respect for Holmes and to have him compete against a program from my dissertation research is an honor. Here is a choice quote from their paper:
We also compared our simulation methods, GSIMULATOR and SIMGENOME, to DAWG, a widely cited program for simulation of neutral substitution and indel events. We chose DAWG because it most closely exemplifies the goals we have identified here: it is clearly based on an underlying evolutionary model and provides tools for estimating the parameters of the indel model directly from sequence data. It appears to be the leading general-purpose simulator at the time of writing. Other simulators (such as PSPE) are richer, but do not provide the parameter-estimation functionality that DAWG does. (internal citations removed)
In other citation news, there is a new paper out in Genetics discussing the “hothead” mutation in Arabidopsis thaliana that made this blog semi-famous. This paper follows up on arguments that hothead’s revertant phenotype is due to unexpected outcrossing. They confirm that hothead does have a high outcrossing rate and that revertant phenotypes are due to outcrossed seeds.
When I first heard this argument, I kicked myself for not thinking about it first. What first characterized hothead plants was the lack of fusion in their flowers. Wild-type A. thaliana plants are complete selfers because their flowers are fused shut, preventing external pollen from reaching the stigma. This way, only pollen produced internally will pollinate A. thaliana. However, when the flower fails to close completely, external pollen is no longer excluded and outcrossing can occur. Duh!
Admittedly, this would have been hard to argue without having the actual plants because some observations reported in Lolle’s original paper conflict with outcrossing, but it appears that these observations cannot be replicated. Perhaps they were just artifacts.
Some of you may remember that several years ago that Britten (2002) argued that human-chimp divergence was 5% not ~1.2%. (See this press release for a refresher.) Of course, creationists jumped on this research and began harping that the more scientists looked, the more distant humans and chimps were. This is important to them because the number one rule of creationism is “no matter what, humans are not related to any other living creatures,” which is so difficult to maintain in our age of science and education.—Amusingly, humans and chimps are so similar to one another that creationists cannot create a consistent definition of “created kinds” that makes humans special and lumps all the boring animals together.
Britten (2002) derived his 5% divergence metric by considering the lengths of insertions and deletions (indels) along with point substitutions between human and chimp genomes. This is unlike other estimates that just consider the number of point substitutions that have occurred between the two species and find ~1.2% divergence. At the time I commented that these two numbers—1.2% and 5%—could not be compared because they are different metrics. Additionally, Britten’s metric is probably unfairly upweighting the contribution of indels because a single event can add or remove multiple residues at a time.
A recent study of mine, which was not directed at Bitten’s work, has found that it is actually worse than that. Simply put, the total length of indels separating humans and chimps is unrelated to the evolutionary divergence between them. This arises because the variance of indel length is “nearly-infinite”, which causes nonconservation of average indel length. Therefore, two pairs of species, equally divergent evolutionarily, can and probably will have very different proportions of nucleotides belonging to indels. One pair might be 5% divergent and the other 1.5% divergent, including indels, without any underlying change in the evolutionary process or time since speciation.
The upside is that traditional substitution based evolutionary distances are unaffected and can still be used to properly estimate the evolutionary divergence between species.
Well I’ve sent my stuff off to the publisher, so I figure that I’ll share the abstract with y’all.
Cartwright RA. Problems and solutions for estimating indel rates and length distributions. Molecular Biology and Evolution. (in press)
Insertions and deletions (indels) are fundamental but understudied components of molecular evolution. Here we present an expectation-maximization algorithm built on a pair hidden Markov model that is able to properly handle indels in neutrally evolving DNA sequences. From a dataset of orthologous introns, we estimate relative rates and length distributions of indels among primates and rodents. This technique has the advantage of potentially handling large genomic datasets. We find that a zeta power-law model of indel lengths provides a much better fit than the traditional geometric model and that indel processes are conserved between our taxa. The estimated relative rates are about 12–16 indels per 100 substitutions, and the estimated power-law magnitudes are about 1.6–1.7. More significantly, we find that using the traditional geometric/affine model of indel lengths introduces artifacts into evolutionary analysis, casting doubt on studies of the evolution and diversity of indel formation using traditional models and invalidating measures of species divergence that include indel lengths.
Sarracenia leucophylla — Crimson Pitcher Plant, Duke Gardens
A couple weeks ago, tree surgeons working out side of a hospital in Wake county, discovered that there was a large hive of bees living in large oak that needed to come down. Due to the decline of wild and domestic honey bees, the state and county governments sent beekeepers to save the hive. The story was popular in the local news and made the NY Times as well.
Volunteers with the Wake County Beekeepers Association and state bee specialists squirted smoke from smoldering canisters into the opening of the giant oak to calm the bees, then moved eight large chunks of honeycomb from the trunk to a new bee box.
“We got them a good home,” said Danny Jaynes, president of the Wake County Beekeepers Association and hobby beekeeper. “It’s one of the most rewarding days of my beekeeping life.”
The combs, containing thousands of adult bees, juveniles and eggs, were placed inside wooden frames. The frames hang vertically like files inside the bee box. By moving the combs, beekeepers expect most of the bees will relocate to raise the young bees and make a new home.
Mailund on the Internet: Heads or tails and reliable alignments
In this paper they analyse the quality of multiple sequence alignments in an extremely simple manner: They first align the sequences left to right, then reverse them to essentially align them right to left. Unless the alignment algorithm has a preferred order of symbols, you’d expect to get the same alignment going left to right as right to left.
Not always, of course: if the algorithm is based on oligonucleotides or such, then the order matters, but in many cases it doesn’t.
Greg Laden: Genetics of Behavior: Fire Ants
Solenopsis invicta, a fire ant, can have colonies with a single reproductive queen (these are called mongyne colonies) or a colony wit multiple reproductive queens (called polygyne colonies).
In mongyne colonies, all individuals have a particular allele for one gene. The gene is General Protein-9 (Gp-9), and the allele is the B-like allele.
Polygyne colonies contain individuals with both the B-like allele and the b-like allele (case matters!). This has led to the suggestion that the presence of b-like is necessary and sufficient for the rise of polygyne colonies.
Below is an email that I received from NESCent:
Please disseminate this announcement widely to appropriate students at your institution
The National Evolutionary Synthesis Center (NESCent) is participating in 2008 for the second year as a mentoring organization in the Google Summer of Code. Through this program, Google provides undergraduate, masters, and PhD students with a unique opportunity to obtain hands-on experience writing and extending open-source software under the mentorship of experienced developers from around the world.
Our goal in participating is to train future researchers and developers to not only have awareness and understanding of the value of open-source and collaboratively developed software, but also to gain the programming and remote collaboration skills needed to successfully contribute to such projects. Students will receive a stipend from Google, and may work from their home, or home institution, for the duration of the 3 month program. Students will each have one or more dedicated mentors with expertise in phylogenetic methods and open-source software development.
NESCent is particularly targeting students interested in both evolutionary biology and software development. Project ideas (see URL below) range from visualizing phylogenetic data in R, to development of a Mesquite module, web-services for phylogenetic data providers or geophylogeny mashups, implementing phyloXML support, navigating databases of networks, topology queries for PhyloCode registries, to phylogenetic tree mining in a MapReduce framework, and more.
The project ideas are flexible and many can be adjusted in scope to match the skills of the student. If the program sounds interesting to you but you are unsure whether you have the necessary skills, please email the mentors at the address below. We will work with you to find a project that fits your interests and skills.
Email any questions, including self-proposed project ideas, to [Enable javascript to see this email address.].
Apply on-line at the Google Summer of Code website, where you will also find GSoC program rules and eligibility requirements. The 1-week application period for students opens on Monday March 24th and runs through Monday, March 31st, 2008.
Hilmar Lapp and Todd Vision US National Evolutionary Synthesis Center
Dr. Anne Yoder and her group at the Duke Lemur Center have produced lemur family tree tree. Greg Laden has the goods.
Note: Prof. Steve Steve was not involved in the study.
Last month, one of the fellow postdocs in our lab went back home to Denmark and began professoring again. So it’s nice to find out that one of his collaborators in Denmark is a blogger and has a really cool post about Estimating local ancestry. He even connects the post to some research that was done in our lab, which makes it double plus one good.
