Figures of Incomplete Lineage Sorting

I find figures really useful for explaining concepts like drift, differentiation, and incomplete lineage sorting. However, I often find textbook figures are not super helpful (although the Tree thinking book by Smith and Baum is good for this). So for my undergrad teaching this quarter I set myself the task of generating R code and figures. In the last post I described simple simulations of drift in single populations. In these figures each generation is a vertical column, with each diploid individual having two alleles. In each offspring generation, two random parents are chosen from each offspring, and one of each parents alleles are chosen at random.

My R code to produce these figures, and ones like them is on github here. Feel free to reuse/repurpose the figures and code. If you find them useful leave a comment, or suggest ways they could be improved. I’ll integrate these ILS figures into my popgen notes in the next month or two [pdf here].

In the figures below there are no new mutations during the simulation, so we can just track alleles over the generations.

Figure of drift causing differentiation of an ancestral polymorphism between two separated populations:

drift_split

More simulations here.

Below are three figures of complete and incomplete lineage sorting as a result of random drift of ancestral polymorphism in ancestral populations (e.g. Human-Chimp-Gorilla). All of the initial alleles are given distinct colours so their path can be tracked over time.

A different allele/lineage has fixed in all three species (e.g. human, chimp, & gorilla lineages haven’t traced back to a common ancestor yet)
completed_lineage_sorting

An allele has fixed in the two sister species (e.g. human and chimp) to the exclusion of the third (Gorilla).
completed_lineage_sorting_2

An ancestral allele has differentially fixed/lost in the two sister species (e.g. human and chimp) making one of them more related to the outgroup (e.g. humans and gorillas sharing an allele) than its sister species (chimp) at this locus.
incomplete_lineage_sorting

I’ve simulated many more figures of ancestral lineage sorting here.

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Figures of Genetic Drift

Figures are really useful for explaining concepts like drift, however, I often find textbook figures are not super helpful. Pictures of hands reaching into jam jars of beans etc are useful metaphors but don’t really depict the process of transmission (also drift is sampling with replacement, so I’m never sure what process is really being depicted by a handful of beans). In addition it helps to be able to show multiple realizations of drift to show the randomness of drift, so multiple simulations help. Dor my undergrad teaching this quarter I set myself the task of generating R code and figures to better depict drift in diploid populations. In these figures each generation is a vertical column, with each diploid individual having a two of alleles. All of the alleles are neutral with respect to each other. In each offspring generation, two random parents are chosen for each offspring, and one of each parents alleles are chosen at random.

My R code to produce these figures, and ones like them is on github here. Feel free to reuse/repurpose the figures and code. If you find them useful leave a comment, or suggest ways they could be improved. I’ve already started to integrate figures like them into my popgen notes [pdf here].

In the first set of simulations I show the loss of heterozygosity over time, in the absence of new mutations
Loss_of_het_2_alleles
(in the figures below I use grey lines to show descent, but they don’t show up well on projectors in class, so I’ve included a link to a bunch more with black lines in a pdf below).

Tracking different alleles with colours
Loss_of_het_2

Genetic drift during bottlenecks leads to the rapid loss of genetic diveristy, particularly rare alleles, but can also by chance increase the frequency of rare alleles.
Loss_of_het_col_alleles_varying_pop

Repeated bottlenecks (fluctuating population size) speed the rate of genetic drift, and even large populations can have a fast rate of drift (i.e. a smaller effective population size) if they sometimes under go bottlenecks
Loss_of_het_col_alleles_varying_pop_2

Depiction of the fact that high variance on reproductive success increases the rate of genetic drift (decrease the effective population size). The circled individuals are randomly chosen individuals who have much higher reproductive success than other individuals (contribution to 25% of offspring each). Note the large number of descendent lines originating from there:
Loss_of_het_col_alleles_varying_RS

Mutation-drift equilibrium, mutations new colours are introduced in the transmission in 10% of transmissions (a unrealistically high mutation rate, but given the small population size it illustrates the point). Initially the population has only one type of allele but mutation is constantly introducing new alleles, which drift up and down in frequency, leading to an equilibrium level of diversity in the population
Loss_of_het_2_alleles

Mutation-Drift equilibrium tracking the frequency of alleles over time:
drift_freqs
Note that many newly mutated alleles drift into the population but are quickly lost.

A bunch more simulations of these types are in this pdf.

Trevor Bedford also has a nice set of simulation figures as well.

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Lab trip to 23 & me

We took a trip down to visit 23 & me’s research group. Graham gave a talk on Alisa and Gideon’s work. Thanks to Kasia Bryc for the invitation.

23_and_me_pic
Vince, Graham, Gideon, Alisa, Kristin, Chenling and Ivan (Simon and Jeremy not pictured).

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Some photos and slides from BAPG

We had a great BAPG meeting. The tweets from the meeting are storified here.
Thanks to everyone who attended (over 100 people). Thanks to Ancestry.com and the Population Biology group at Davis for sponsorship.
Also thanks to all of the speakers (listed here). Some of them have kindly shared there slides
Lee. Genome evolution of malaria vectors in response to the increased usage of insecticide-treated bed nets
Beissinger.Patterns of demography and selection since maize domestication
Harris. Recent evolution of the mutation rate and spectrum in Europeans
Bradburd. The Geography of Genetic Admixture

A few pics between talks.
BAPG_XI_2

BAPG_XI_1

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Coop lab pics

Pic of Coop lab 2014 (minus Chenling)
Coop_lab_2014_minus_chenling
We’re trying (and likely failing) to make a normal distribution.

Coop Lab Holiday dinner
Holiday_dinner_2014

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Evolutionary Classics Reading Group 2014

For our Monday reading group we chose to read a series of classic papers in Evolutionary Biology. Each week the discussion leaders chose their paper/book excerpt and often chose to add a companion paper. Below is a complete list of the papers read. Thanks to all of the discussion leaders and everyone who attended. Thanks also to Leslie Turner and others for the conversation that sparked the idea for revisiting the classics (see here for more of the twitter discussion, and this Mendeley group by Leslie).

1. Kreitman’83 Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. see also this post by Casey Bergman on 30th anniversary of paper. Alisa Sedghifar.
2. Price 1970 Selection and Covariance & Queller 1992 Quantitative Genetics, Inclusive Fitness, and Group Selection. Jeremy Berg.
3. Mayr ’47 Ecological factors in speciation . Moria Robinson & Meredith Cenzer
4. Kettlewell 1955 SELECTION EXPERIMENTS ON INDUSTRIAL
MELANISM IN THE LEPIDOPTERA
accompanied by Majerus 2009 Industrial Melanism in the Peppered Moth, Biston betularia: An Excellent Teaching Example of Darwinian Evolution in Action . Reid Brennan & Ryan Baldini
5. excerpts from Waddington’s “The strategy of the genes” 1957 on the epigenetic landscape & genetic assimilation Judy Wexler & David Luecke
6. Excerpt of Clausen, Keck, & Hiesey 1940 Experimental studies on the nature of species. I. Effects of varied environments on western North American plants. & their “Concept of Species Based on Experiment” 1939. Michelle Stitzer & Mark Taylor.
7. On the origins of reinforcement,Dobzhansky 1940 Speciation as a Stage in Evolutionary Divergence paired with Noor’s Reinforcement and other consequences of sympatry. 1999 Kristin Lee, Micah Freedman, & Philipp Brand.
8. Felsenstein 1985 Phylogenies and the Comparative Method paired with Pennell’s Models and meanings in comparative biology book review. Jiansi Gao & Chenling Antelope
9. Charlesworth, Lande, & Slatkin 1982 A Neo-Darwinian Commentary on Macroevolution. Vince buffalo & Serena Caplins.
10. Dobzhansky ’47 Adaptive Changes Induced by Natural Selection in Wild Populations of Drosophila paired with Grant & Grant 2002 Unpredictable Evolution in a 30-Year Study of Darwin’s Finches. Chris Griesemer,Gideon Bradburd and Jaime Ashander.

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Bay Area Population Genomics Meeting XI

Dear population genomicists of the Bay Area,

The tenth Bay Area Population genomics meeting was great, thanks to CEHG Stanford for hosting it. We will be hosting BAPG XI at UC Davis (Storer Hall) on December 6, 2014, and we hope to see you all there!

9.30am-10am Breakfast (Storer Hall)

10am-11am Session 1
10.00am Gideon Bradburd (UC Davis)
The Geography of Genetic Admixture
10.20am Rajiv McCoy (Stanford)
Causes and consequences of aneuploidy in human embryos
10.40am Laurie Stevison (UCSF)
Time-scale of recombination rate evolution in great apes

11am-11.30am Coffee

11.30am-12.30pm  Session 2
11.30am Kelley Harris (UC Berkeley)    
Recent evolution of the mutation rate and spectrum in Europeans
11.50am Tim Beissinger (UC Davis)       
Patterns of demography and selection since maize domestication
12.10pm Yoosook Lee (UC Davis)            
Genome evolution of malaria vectors in response to the increased usage of insecticide-treated bed nets

12.30-1.30 pm Lunch

1.30pm Session 3
1.30pm Daniel Weissman (UC Berkeley)
Minimal-assumption inference from genomic data
1.50pm Sandeep Venkataram (Stanford)
The adaptive mutation spectrum from yeast experimental evolution
2.10pm Chris Ellison (UC Berkeley)          
Transposable elements have rewired and fine-tuned the dosage compensation gene regulatory network in Drosophila miranda
2.30pm Andres Moreno (Stanford)           
Native American genomics and beyond

2.50pm Posters/Social

Thanks to Ancestry.com and the Population Biology group at Davis for sponsorship.

Registration is free but required, so we can make sure we order enough food and get a big enough room. Registration is now closed (as of November 22nd). Registration list here: google doc.

The Coop Lab: Simon Aeschbacher, Chenling Antelope, Jeremy Berg, Gideon Bradburd, Vince Buffalo, Graham Coop, Ivan Juric, Kristin Lee, Alisa Sedghifar
P.S. the twitter hashtag will be #BAPGXI.

Posters
For those bringing posters, there will be wallspace provided on the first two floors of Storer Hall, as well as bluetack and tape for hanging your posters. Posters should be no wider than 48″ (~1.2m), and those bringing posters should try to have their posters set up by 10am (so they can be viewed from the first coffee break). Please contact Gideon Bradburd (gbradburd@ucdavis.edu) with all poster-related questions.

TRANSPORTATION

DRIVING From Bay area

Take the I-80 East, merge onto the 113N (to Woodland) at exit 70 (one after Kidwell rd exit)

Take exit 27 to UC Davis, turn right onto Hutchison Rd. Turn left onto Kleiber Hall drive. As you approach the gate, Storer Hall will be to your right.

Parking will be free in the lot to your left (parking structure P27, visible on the campus map after checking the box “Permit Parking”)

Storer hall on a campus map:

http://campusmap.ucdavis.edu/?b=145

AMTRAK to Davis (Bikes are permitted.)

http://www.capitolcorridor.org/

Morning: Eastward bound Weekend schedule, the best train is #720:

8.04am Berkeley (University and 4th st)

8.12am Richmond (next to BART)

arrives in Davis at 9.22am

Storer Hall is just a ~15 min walk from the train station: down 2nd and straight on through campus, by the Quad, then just across California Ave, behind Hutchinson.

Return: 3.50pm or 4.55 train from Davis,

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