SMBE conference: Vienna July 12-16

Exciting news: I will be giving a talk at the SMBE conference in Vienna in the "Genomic and epigenomic evolution of sex chromosomes: Broad patterns and intriguing cases" Edit: the "Speciation Genomics" symposium. I'll be presenting at 16:30 on Tuesday, 14 July in Festsaal.

Here is the title and abstract:

	Title	Disrupted imprinting, the large X-effect, and extreme hybrid overgrowth in hamsters
	Abstract	Extreme abnormal growth is a recurrent phenotype in mammalian hybrids, indicating that disruption of development may play an important role in mammalian speciation. Disrupted genomic imprinting - the parent-specific epigenetic silencing of one allele - resulting in dosage imbalances between growth factors and repressors has been hypothesized to be the predominant cause of abnormal hybrid growth in mammals. However, genetic imprinting may also expose hybrid incompatibilities through the hemizygous expression of genes. Here we combined genome-wide transcriptomic and quantitative genetic experiments to dissect the genetic underpinnings of extreme overgrowth that manifests in hybrids between two closely related species of dwarf hamsters. Specifically we tested for disrupted imprinting and differences in the expression of growth-related genes in overgrown hybrid placenta. We found that large hybrids show evidence for disrupted paternal imprinting and differential expression of imprinted genes in general. Surprisingly, the disruption of paternal imprinting is associated with reduced gene expression. As paternally imprinted genes tend to repress offspring growth, these data suggest that overgrowth is associated with a reduction in growth repressors rather than an excess of growth factors. Using QTL mapping, we have further identified the X chromosome as the predominant factor explaining hybrid placental overgrowth. However, expression and imprinting status of the X chromosome is not significantly disrupted, indicating that X-linked genetic incompatibilities are not caused by chromosome-wide misregulation. Collectively, our data underscore a central role for both disrupted epigenetic processes and the X chromosome in driving the evolution of abnormal hybrid growth in mammals.

Manuscript II - Planning part 2

In the last post I came up with a number of questions that I an address with my data set, but in the end, I have at couple compelling hypotheses that I can test which should be the focus of the paper.

Here is the first hypothesis:

Many imprinted genes are growth factors that act in a dosage-dependent manner. Abnormal growth is the result of increased expression of genes which promote or repress growth. Abnormal growth manifests in a parent-of-origin manner when one hybrid type exhibits increases in growth promoting genes and the reciprocal hybrid exhibits increases in growth repressing genes.

The common trait to all hybrids, large or small, is that genes which regulate growth show increased expression level. If these genes promote growth then the individual is large, if these genes repress growth then the individual is small. Furthermore, we predict that when imprinting is disrupted, the gene which should be expressed from a single allele is actually expressed from both alleles. This should result in a doubling of expression level.

We can test this hypothesis by looking at expression level in large hybrids and comparing it with small hybrids. If growth promoting genes are expressed from two alleles and show increased expression level in large hybrids then this hypothesis would be supported.

The second hypothesis is this:

There is ample evidence that hemizygosity is bad as it exposes things which are deleterious but recessive. This is probably most clear when we look at the X chromosome. One of the main reasons for Haldane's rule (the disproportionate affliction of incompatibilities in males) is that males have a single copy of the X while females have two X chromosomes. Thus, females are able to mask recessive deleterious things on the X but males are not. As imprinted genes are similarly expressed from a single copy, all recessive incompatabilities involving them will be exposed. Furthermore, in the reciprocal hybrid, the alternate allele is expressed which should ameliorate the incompatibility.

This hypothesis is mute with respect to dosage, and can occur whether or not the dosage of different alleles is disrupted.


I think that the paper will start by addressing these two hypothesis and set up a framework for how to test each using the growth effects in the hamster hybrids.

Manuscript II - planning

I'm about to start writing my next manuscript. It's going to deal with patterns of gene expression in the placenta of F1 hybrids. I'm stalled a bit as I try to figure out exactly what questions I will be addressing and how I will go about discussing them in the manuscript. So, I'm hoping that writing this will help me flesh out my thoughts on what questions I'll be asking, why they are important, and how to address them.

First, all the questions I can think of that I can address with my data:

Is the histology of placentas abnormal in large or small hybrids? males or females?
Is gene expression disrupted in hybrid placentas?
How many genes show differential expression (DE)?
How many genes show DE between P. campbelli and P. sungorus (evolutionary changes)?
How many genes show DE between parents and hybrids (hybrid breakdown)?
How many genes show DE between cxs and SxC hybrids (could explain POE growth)?
How many genes are DE between males and females within each parent species?
How many genes are DE between males and females with the hybrids?
Are sex-specific effects prevalent in hamster hybrids?
For all these categories: what do those genes do? / Is there any functional enrichment for DE genes?
Do imprinted genes show DE?
Is imprinting disrupted (DI) in hybrids? Large, small, or both?
Does DI correlate with POE growth?
How often does disrupted imprinting correlate with differential expression?
Does the simple model of 'disrupted imprinting=2x increase in expression' hold?
Do paternally expressed genes show higher expression in large hybrids than small hybrids?
Do paternally expressed genes show higher expression in large hybrids than the parents?
Do maternally expressed genes show lower expression in large hybrids than small hybrids?
Do maternally expressed genes show lower expression in large hybrids than the parents?
What is happening on the X chromosome in hybrids?
Is X-linked expression disrupted?
Is X-linked expression correlated with abnormal growth?
Is there imprinted X inactivation (XCI) in hybrid placentas?
Is XCI disrupted?
Do any/many genes escape XCI? Which?
Does escape of XCI seem to have anything to do with POE growth?


Ok, that was more than I expected so that's good.
Now some organization.

My first thoughts are that the main question is what are patterns of expression in hybrid placentas and do they reflect a possible basis for parent-of-origin growth? This has three main sub-questions which are (1) what are the patterns of differential expression in hybrid placenta? (2) what is the pattern of imprinting in hybrid placenta? and (3) what is the overlap between DE and DI in hybrids?

So far, this sounds really descriptive and one of the strengths of my project is that I have a couple really strong a priori predictions about disrupted expression and imprinting and the size of the hybrids. Therefore, I think I should be able to motivate this in a more hypothesis-driven manner, rather than just as a simple description of expression patterns.

To do that, I need to lay out the prediction of gene expression.

To be continued...

Denver Museum of Nature and Science

K~ and I visited the Denver Museum today and were given a private tour of the collections. J. D~ was kind enough to spend his entire Friday afternoon showing us around and letting us see all the cool stuff. Fortunately, we got the grand tour despite the fact that museum is currently moving it's entire collection to a brand new housing area with fancy state-of-the-art rolling cabinets.

We spent most of the time with the bird collection and we got to see about 40 passenger pigeons (extinct), an ossified goose trachea (shout out to M. J~), and articulated skeletons of a bunch of birds including a kestrel and three different owls (which K~ identified on sight as a saw-whet, burrowing, and pygmy).

They also had two complete elephant bird eggs (these are watermelon size, the hand for scale doesn't actually do it justice). Elephant birds are from Madagascar and went extinct a couple hundred years ago. The fact that any eggs stil exist is amazing - not to mention two complete, unbroken ones.

 The Denver Museum had a collection trip to the Galapagos in 1960, one year before they stopped allowing collections, and returned with a number of Geospiza finches.

Most excitingly, they had a male and two female speciments of the infamous Ivory-Billed Woodpecker (unfortunately, the photo is a bit blurry*):

















We also got to see a bunch of the beetles, scorpions, spiders, camel scorpions (which I've never even heard of before but looked bad-ass - apparently the mouthparts for predator in the movie Predator were based on these guys) and whip scorpions (which gained fame in the movie Harry Potter and the Goblet of Fire as the spider that Moody used to demonstrate the unforgivable curses to the defense agains the dark arts class). Also we were able to see some more beetles, butterflies and moths as they were being moved to the new shelves (the staff were fantastic and took a break from moving specimens to let us look at the cool beetles).

After the birds and bugs we headed over to the fossils - there were two dire wolves (smaller than I expected), an irish elk skull (with antlers spanning further than I could reach from toe to fingertip), a bunch of mammoth and mastodon skulls, leg bones, and vertebrae, a petrified tree stump we helped move, and a Stockoceros (which is like a pronghorn with two horns).

One really cool specimen we saw was a giant ground sloth.

Then we got to the mammal cabinets and looked mainly at the chipmunks, but we got to see some lions, tigers, a gorilla, and bats too. Didn't see any Phodopus but I guess I've seen plenty of them.

All in all it was a great afternoon. Major thanks to J. D~ for showing us around and answering all our questions. Also to the staff of the Denver Museum for taking time to show us some cool biology!

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*I'm told all ivory-billed photos are blurry - it's a tradition. 

Parent-of-Origin Effects Paper is out!

http://authorservices.wiley.com/bauthor/onlineLibraryTPS.asp?DOI=10.1111/evo.12500&ArticleID=1354661

Capture design

One project that I'm working on is to map the genetic factors that cause parent-of-origin growth in dwarf hamsters. This project will end up being the final chapter in my dissertation and has a number of angles that hopefully will all come together in the end to forma  complete story. One of these angles is a mapping panel made out of ~200 backcrossed hamster individuals. I'm using a RAD-seq approach which has recently been sent for sequencing. This will use anonymous markers across the genome to find regions associated with growth. The shortcoming of this approach is that the markers are anonymous and not necessarily associated with known genes. In order to place known genes on the map I am designing a capture.

The capture will pull out ~10,000 gene regions (parts of exons) that are known to contain snps from each individual. I will be able to sequence those specific regions in a subset of individuals and then place those genes on the genetic map. In the end I will have actual genes that associate with growth.

I've never designed a custom capture before but J~ has and so with some guidance I'm figuring it out. My goal is to have a list of sequences, each around 200bp long (I should check that length - it needs to be long enough to sequence on Illumina) that have a diagnostic snp in the middle somewhere.

The first step is to find genes that have snps in them and I have done this earlier for my F1 placental transcriptome project.
Now that I have a set of genes with known snps, I need to make sure that none of these fall near exon boundaries. To do this I am using a Blat approach. Blat is nice because it will align my transcriptome to the Mesocricetus auratus genome and split up the genes into different exons. The output of a blat gives me the exact breakpoints in each gene so that I can choose snps that are far from those areas.

Then, once I have the list of genes that have snps far from breakpoints, we send that in to agilent (I think we're using agilent) who will actually design the capture for me. Then it just remains to do the labwork and sequence it.

Parent-of-Origin Effect paper was just accepted!!

My very first first-author paper has just been accepted by the journal Evolution!

It's now going through the typesetting process. They publish the pre-formated articles here and while it's not up now, it should appear soon.

They said expect ~12 weeks for the final proofs to be ready and then I expect there is a queue before it shows up in print.

Generally, it's a description of the parent-of-origin growth effects in dwarf hamsters and the first dalliances of mine to understand the genetic basis and answer the question: is imprinting involved or not?

I'm really excited. Now on to the writing of my second paper...