Coop lab talks from Evol2014

Our talks from Evolution are below. Much of the work is unpublished and provisional, so please contact us for updates/details if you are interested in the work.

Alisa’s talk on a Model of Genome-Wide Patterns of Ancestry in a Secondary Contact Zone
Alisa_SedghifarPresentation.pdf

Graham’s Evolution talk on adaptation to patchy environments (also given in slightly modified form at SMBE)
Coop-Evolution-2014.pdf
the first half is joint work with Peter Ralph, the second is a collaboration with Chenling, Kevin Wright, and John Willis.

Gideon’s poster on a novel method for visualizing spatial structure and admixture (given at SMBE, and as guerrilla poster at Evolution by graham):
gideon_bradburd_SMBE_poster.pdf

Simon’s talk on Exploring genome-wide signals of selection against gene flow
Simon_Aeschbacher_Evolution2014.pdf, Simon’s talk was videoed and posted to youtube.

Jeremy’s talk on testing for adaptive phenotypic divergence
Figshare

Yaniv’s talk on why sperm might evolve to help keep female meiosis fair:
yaviv_brandvain_evolution2014.pdf

Alex Cagan’s [@ATJCagan] sketch of Graham’s talk from SMBE:
Bpy0ra4CQAA9c0L.jpg_large
original tweet. All of his sketches of the talks were great!

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Coop lab at Evolution 2014

Evolution_logo

We’re looking forward to seeing old friends and meeting new folks at Evolution 2014. Here’s a list of the talks by the Coop lab at the conference.


Jeremy Berg. General extensions of Qst/Fst for detecting adaptation in quantitative traits.

2A_306A Methods for Migration. Sunday, 9:00 AM – 9:15 AM Room: 306 A

Graham Coop. Parallel evolution during local adaptation. ASN Vice Presidential Symposium:Modern approaches to local adaptation. Date: Monday, 3:15 PM – 3:45 PM. Room 402

Alisa Sedghifar. A Model of Genome-Wide Patterns of Ancestry in a Secondary Contact Zone
3C_303 Hybridization. Monday, 2:00 PM – 2:15 PM Room 303

Yaniv Brandvain. Sperm do not evolve to collaborate in female meiotic drive. 4C_306A Sex and Evolution Tuesday, 2:30 PM – 2:45 PM Room: 306 A

Simon Aeschbacher. Exploring genome-wide signals of selection against gene flow 4D_301A Genome Evolution. Tuesday, 3:15 PM – 4:30 PM. Room: 301 A

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Coop Lab T-shirt

The theme for the coop lab T-shirt this year is POPGEN IN SPACE!!! A bunch of the research interests in the lab currently focus on spatial population genetics, so it seemed like a great opportunity to bust out a homage to “pigs in space” featuring Fisher, Haldane, and Wright. Images below, we’ll post some pics of the lab in the t-shirts later.

John Novembre and I held a symposium by this name at SMBE a few years ago, we had this idea for the T-shirt then but never quite got around to it.

Slide4

Slide8

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Genomic variation in sharing between siblings

Siblings of the same sex resemble each other to varying degrees. For most traits this is mostly due to differences in the environment between them, and its effects on their development. However, siblings also subtly differ in their genomic similarity, due to the randomness of segregation and recombination. I thought I’d extend our previously discussion of genomic sharing between relatives (see here) to show how variable genomic sharing is between siblings. Again using data from real transmissions.

Below is a picture of the sharing between a pair of sibs. The parent genome is shown as 2 pairs of chromosomes, for each of 22 autosomes. These are coloured by the genomic material they transmitted to the child. The third plot of each row shows the overlap between the siblings’ genomes in light purple. So, for example, the two sibs (on page 1) share all of chromosome 21 as inherited from the father, but only the right tip of the chr21 in the mother. You can also see genomic stretches where the pair of sibs would share their both of their genotype (i.e. both alleles), e.g. the sibs share both maternal and paternal alleles for the first ~1/3 of chr22.

overlap_btwn_siblings1

Here’s a slide show illustrating this across 10 pairs of siblings.

This slideshow requires JavaScript.

I’m posting these as we are currently doing a reading group on recent advances in Quantitative Genetics. This week Gideon and Reid are leading a discussion of Visscher et al “Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings.”. In that paper they have a plot of the variation of how much of their autosomal genomes siblings share:
journal.pgen.0020041.g001
note that the distribution is centered on a half but with a small amount of scatter around that due to the randomness of mendelian segregation and the fact that chromosomes are inherited in big chunks. (I apologize for the default excel graph, but I didn’t make it ;) )

Visscher et al make really nice use of this slight variability in how much of the genome sibs share to learn about how much variation in height within a population is due to genetic variation. They use the fact that sibs who share slightly more of their genome (>0.5) should have more similar heights, than sibs who share less of their genomes (<0.5). This allows them to partition out how much of the resemblance between siblings is due to a shared environment, as opposed to shared genomes.

This is a really nice application variation in genomic sharing (although the paper is a little tough going in places). It also makes me wonder if sibs are actually unconsciously, weakly aware of these subtle genomic differences (through their similarity in a range of traits, including height etc). I could imagine doing a study where siblings (or others) are asked to assess how similar they are/feel, and then assessing whether this is weakly correlated with the fraction of the genome shared. I keep meaning to followup on this idea with some popgen theory to assess how this might play out in modifying kin-selection and altruism between sibs and other relatives. Anyone know if this has this been looked at before?

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A fond farewell to Yaniv!

The awesome Yaniv Brandvain has flown the Coop lab, and starts his evolutionary plant genomics lab at the University of Minnesota today. It’s been wonderful having Yaniv as a member of the Coop lab. Yaniv brought a wonderful sense of community to Davis, and the Coop lab and the Center for Population Biology benefited enormously from his intellectual generosity. We are sad to see him go, but we know the future holds great things for him and his lab.

You can get some sense of the diverse projects that Yaniv worked on in his time in Davis from his recent publications. We also have a more papers in the pipeline, so keep an eye out for those.

The Coop lab out for dinner:
photo-13
(Kristin, Alisa, Jeremy, Chenling, Yaniv at a dinner for Yaniv and Jeremy’s Quals exam. Gideon not present. )

As a leaving present we got Yaniv the Princeton guide to Evolution:

photo-14
It was signed by many folks at Davis, and had many messages of support from Yaniv’s many collaborators and authors of many of the chapters (who Yaniv knows). A small, but fitting, tribute to mark the evolution of a wonderful scientist.

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GC Williams and Socrates

Thought I’d pull this passage out of GC Williams’s “Adaptation and Natural selection“. I was looking for it the other day, as I’m considering using it in my Evolution class, and couldn’t find it easily via google.

“Natural selection of phenotypes cannot in itself produce cumulative change, because phenotypes are extremely temporary manifestations. They are the result of interactions between genotype and environment that produces what we recognize as an individual. Such an individual consists of genotypic information and information recorded since conception. Socrates consisted of the genes his parents gave him, the experiences they and his environment later provided, and the growth a development mediated by numerous meals. For all I know, he may have been very successful in the evolutionary sense of leaving numerous offspring. His phenotype, nevertheless, was utterly destroyed by the hemlock and has never since been duplicated. If the hemlock had not killed him, something else soon would have. So however natural selection may have been acting on Greek phenotypes in the forth century B.C., it did not of itself produce any cumulative effect.

The same argument holds also for genotypes. With Socrates’ death, not only did his phenotype disappear, but also his genotype.[...] The loss of Socrates’ genotype is not assuaged by any consideration of how prolifically he may have reproduced. Socrates’ genes may be with us yet, but not his genotype, because meiosis and recombination destroy genotypes as surely as death.”

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Coop lab hiring postdocs

The Coop lab at UC Davis (www.gcbias.org) is seeking candidates for two postdoctoral positions. These two positions will broadly focus on:
1) The evolutionary causes and consequences of recombination variation in humans.
2) understanding polygenic selection and soft sweeps.

Successful applicants would also have considerable flexibility to develop their own research program in collaboration with the Coop lab. Strong candidates for these positions would have a PhD in population genetics, statistics, or related fields, and have good backgrounds in computational and statistical approaches. The Coop lab works at the intersection of population genomics, theoretical population genetics, and methods development. We are active members of the Department of Evolution and Ecology and Center for Population Biology.

Please send Graham Coop an email gmcoop [at] ucdavis.edu. Please include
(i) your CV, (ii) a description of your previous research and future goals, (iii) contact details for three references. We will consider applications on a rolling basis starting immediately.

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