A place to put the lab meeting schedule, and perhaps some associated docs
| Date | Leader | Topic | Notes |
|---|---|---|---|
| May 2 | Puneeth | research update | |
| May 9 | Mete | journal club | https://www.biorxiv.org/content/10.1101/2025.04.03.646616v1 |
| May 16 | - | - | holiday |
| May 23 | - | - | Rebekah committee meeting |
| May 30 | Rebekah/Puneeth/Mete | SMTPB practice | |
| June 6 | - | - | SMTPB |
| June 13 | Kuangyi/Mete | Evolution practice | |
| June 20 | Puneeth | Rescue mtg practice | |
| June 27 | - | - | matt away |
| July 4 | - | - | matt away |
| July 11 | Matt | ||
| July 18 | Mete | ||
| July 25 | Rebekah | ||
| Aug 1 | - | - | holiday |
| Aug 8 | Raghav | research update | |
| Aug 15 | - | DSI symposium | |
| Aug 22 | Kuangyi | journal club | https://academic.oup.com/evolut/article-abstract/71/1/23/6725958, https://rethinkingecology.pensoft.net/article/31992 |
| Aug 29 | Matt | journal club | https://www.biorxiv.org/content/10.1101/2025.08.04.668505v1.abstract |
| Date | Leader | Topic | Notes |
|---|---|---|---|
| Jan 10 | Matt | mimulus rescue paper | https://www.biorxiv.org/content/10.1101/2024.10.24.619808v1 |
| Jan 17 | Kuangyi | job talk practice | Matt away |
| Jan 24 | Puneeth | rescue with mate limitation manuscript | Matt away |
| Jan 31 | Chris | coop ch 3 | |
| Feb 7 | Mete | update on recombination landscape model | |
| Feb 14 | Rebekah | msc manuscript feedback | |
| Feb 21 | - | - | reading week |
| Feb 28 | Puneeth | Human Pop Gen of India | https://www.biorxiv.org/content/10.1101/2024.02.15.580575v2 |
| Mar 7 | Chris | feedback in coevo models | https://www.biorxiv.org/content/10.1101/2025.02.28.640831v1.full.pdf+html |
| Mar 14 | Mete | evol eqns from demo stochasticity | https://www.journals.uchicago.edu/doi/abs/10.1086/733196?journalCode=an! |
| Mar 21 | Rebekah | ||
| Mar 28 | Tabris | 397 project talk | |
| Apr 4 | international day of evolutionary rescue! | ||
| Apr 11 | - | - | Atwood |
| Apr 18 | - | - | holiday |
| Apr 25 | Matt | Langdon et al 2024 | https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002742 |
| Date | Leader | Topic | Notes |
|---|---|---|---|
| Sept 9 | Chris | Coevo rescue | |
| Sept 16 | Kuangyi | Drift in Fisher's runaway model | |
| Sept 23 | Mete | Recombination modifiers | https://www.pnas.org/doi/full/10.1073/pnas.2022805118 |
| Sept 30 | - | - | http://www.fields.utoronto.ca/activities/24-25/oncology-evolution |
| Oct 7 | Puneeth | multivariate rescue ideas | |
| Oct 14 | - | - | holiday |
| Oct 21 | David McLeod | triple LD | joint with Mideo lab |
| Oct 28 | Chris | Appraisal Practice | |
| Nov 4 | - | - | Chris appraisal |
| Nov 11 | Mete | appraisal practice | |
| Nov 18 | Puneeth | ARGs | |
| Nov 25 | Kuangyi | job talk practice | |
| Dec 2 | Kuangyi | job talk practice part 2 | |
| Dec 9 | Rebekah | stochasticity in the moving optimum model | |
| Dec 16 | - | - | faculty retreat |
| Date | Leader | Topic | Notes |
|---|---|---|---|
| May 28 | Matt | Bocce! | |
| June 5 | Mete | Gillespie Ch1 | |
| June 12 | Puneeth | Gillespie Ch2 | |
| June 19 | Matt | Gillespie Ch3 | |
| June 26 | Chris | Gillespie Ch4 | |
| July 3 | Kuangyi | Gillespie Ch5 | |
| July 10 | Matt | Gillespie Ch6 | |
| July 17 | Puneeth | Gillespie Ch7 | |
| July 24 | - | Evolution practice talks | |
| July 31 | - | cancel for Evolution | |
| August 7 | - | Evolution summary | cancelled due to fever |
| August 14 | Matt | paper | https://www.biorxiv.org/content/10.1101/2021.11.01.466728v4 |
| August 19 | Tabris | practice talk | special Monday edition |
| August 22 | Catherine | project presentation | |
| August 28 | - | taking a break before fall |
| Date | Leader | Topic | Notes |
|---|---|---|---|
| Jan 16 | Puneeth | Coevolution Paper (https://www.sciencedirect.com/science/article/pii/S0022519323002850?via%3Dihub) | |
| Jan 23 | Chris | ||
| Jan 30 | Mete | Gillespie 1984: https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.1984.tb00380.x | matt out of town |
| Feb 6 | Kuangyi | matt out of town | |
| Feb 13 | Puneeth | ||
| Feb 20 | Chris | Elevator Pitch Practice | |
| Feb 27 | Mete | coalescent estimation of recomb. rate: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207867/pdf/ge1453833.pdf | |
| Mar 05 | Kuangyi | practice for departmental seminar | |
| Mar 12 | Puneeth | effect of epigenetic and genetic architecture on the U-shape of rescue | |
| Mar 19 | Chris | SLiM co-evolutionary model: https://www.biorxiv.org/content/10.1101/2023.12.07.570693v2.full | matt out of town |
| Mar 26 | Mete | crossover covariation: https://www.sciencedirect.com/science/article/pii/S009286741930203X?via%3Dihub | |
| Apr 02 | Kuangyi | ||
| Apr 09 | Puneeth | ||
| Apr 17 | Chris | ||
| Apr 23 | Mete |
| date | leader | topic | notes |
|---|---|---|---|
| Sep 11 | Matt | planning | with bocce |
| Sep 18 | Litong & Mete | shiny app | |
| Sep 25 | Matt | practice presentation | on spacetrees, for Holt lab mtg |
| Oct 2 | Iain Mathieson | Using ancient DNA to learn about human health and evolution | register: https://canssiontario.utoronto.ca/event/ares-iain-mathieson/?mc_cid=5bbf2bf8c2&mc_eid=a22a443224 |
| Oct 9 | - | - | university holiday |
| Oct 16 | Kuangyi | PhD review | good chance matt is home with newborn |
| Oct 23 | Chris | Research Update | good chance matt is home with newborn |
| Oct 30 | Mete | evolution of epistasis: https://academic.oup.com/genetics/article/177/2/1001/6064448 | |
| Nov 6 | Puneeth | Research Update : Phylogenetic Networks-Distinguishability of Networks and Tree Sequences to infer Networks | |
| Nov 13 | - | - | canceled |
| Nov 20 | Kuangyi | the infinitesimal model: https://www.sciencedirect.com/science/article/pii/S0040580917300886 | 9am |
| Nov 27 | Chris | coevolutionary arms races in mutualisms: https://www.journals.uchicago.edu/doi/pdfplus/10.1086%2F714274 | |
| Dec 4 | Puneeth | demographic inference under the coalescent in a spatial continuum: https://www.sciencedirect.com/science/article/abs/pii/S0040580916300181?via%3Dihub | |
| Dec 11 | Mete | host-pathogen GWAS: https://www.nature.com/articles/s41467-019-10724-w | |
| Dec 18 | Matt |
| date | leader | type | topic | notes |
|---|---|---|---|---|
| May 4 | scarborough bluffs | |||
| May 11 | Puneeth | update | Appraisal Draft 1 | |
| May 16 | Matt | book reading | Ewens ch1 | note this is a tuesday (mete out of town May 17-25) |
| May 25 | Puneeth | update | Appraisal Draft 3 | mete and luna out of town for EEID |
| June 1 | Puneeth | book reading | Ewens ch2 | |
| June 8 | - | - | - | matt and puneeth out of town for rescue workshop |
| June 15 | Chris | book reading | Ewens ch3 | |
| June 22 | Mete | book reading | Ewens ch4 | matt out of town |
| June 29 | Puneeth | book reading | Ewens ch5 | |
| July 6 | Matt | book reading | Ewens ch6 | |
| July 13 | Mete | book reading | Ewens ch7 | |
| July 20 | Tam | book reading | Ewens ch8 | mete out of town |
| July 27 | Puneeth | book reading | Ewens ch9 | mete out of town |
| August 3 | Matt | book reading | Ewens ch10 | |
| August 10 | Mete | book reading | Ewens ch11 | |
| August 17 | Puneeth | book reading | Ewens ch12 | |
| August 24 | Tam | presentation | density-dependence in the moving optimum model | |
| August 31 | - | - | - | break |
| date | leader | type | topic | notes |
|---|---|---|---|---|
| Jan 13 | - | - | the year in review | |
| Jan 19 | Matt | update | writing equilibrium allele frequency in terms of invasion criteria | |
| Jan 26 | Mete | paper | fitness valley crossing: https://www.sciencedirect.com/science/article/pii/S0040580909000264?via%3Dihub, https://academic.oup.com/genetics/article/186/4/1389/6063653?login=true | |
| Feb 2 | - | - | cancelled | matt out of town |
| Feb 9 | - | discussion | Duncan Dauvergne - asst. prof in math, random growth models | |
| Feb 16 | Puneeth | update | Infering dispersal history from linked loci using ancestral recombination graphs | |
| Feb 23 | Mete | paper | coalescent under recurrent mutation: https://www.biorxiv.org/content/10.1101/2022.08.18.504427v1 | |
| Mar 2 | Mark Hibbins | - | brownian motion on phylogenetic networks | |
| Mar 9 | - | - | cancelled | matt and puneeth out of town |
| Mar 16 | Mete | paper | birth-death models in epidemiology & macroevolution: https://academic.oup.com/sysbio/article/71/1/172/6308956 | |
| Mar 23 | - | - | matt out of town | |
| Mar 30 | Puneeth | paper | recombination and triplet-based species tree inference: https://www.biorxiv.org/content/10.1101/2021.11.06.467557v1 | |
| Apr 6 | - | - | matt out of town | |
| Apr 13 | - | bocce! | ||
| Apr 20 | - | Atwood practice |
| date | leader | topic | ||
|---|---|---|---|---|
| Sep 20 | Puneeth | Some more Evolutionary Rescue! | ||
| Sep 27 | Mete | Gore papers | ||
| Oct 4 | - | catch-up | ||
| Oct 11 | Felix Beaudry | career paths in genomics/medicine | ||
| Oct 18 | Mete | gene expression: https://onlinelibrary.wiley.com/doi/10.1111/evo.12732 | ||
| Oct 25 | Puneeth | microbe inheritance: https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-022-02029-2 | ||
| Nov 1 | Mete | ancestral selection graphs: https://www.sciencedirect.com/science/article/abs/pii/S0040580997912995, https://academic.oup.com/genetics/article/145/2/519/6018087 | ||
| Nov 8 | Puneeth | Ancestral Recombination Graphs | ||
| Nov 15 | Mete | structured coalescent | ||
| Nov 22 | Puneeth | Lambda/Xi Coalescent | ||
| Nov 29 | Puneeth | Diffusion, Coalescent and Duality | ||
| Dec 6 | Sydney | Practice Defence talk | ||
| Dec 13 | Sydney | THESIS DEFENSE!!! | ||
| Dec 20 | - | - |
| date | edi update | leader | presentation topic | |
|---|---|---|---|---|
| May 2 | Madeline | Rice, p. 1-17 | ||
| May 9 | Madeline | Puneeth | Rice, p. 17-39 | |
| May 16 | Matt | Matt | Rice, ch 2 | |
| May 23 | Puneeth | Sydney | My lattice model of fragmentation modes // optional reading: https://www.sciencedirect.com/science/article/pii/S0378437100005161 and https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005860#:~:text=Fragmentation%20modes%20that%20maximise%20growth,a%20wide%20range%20of%20conditions. | |
| May 30 | Sydney | Mete | Rice, ch 3 | |
| June 6 | Tom | Tom | Rice, ch 4 | |
| June 13 | Chris | Puneeth | Practice - Comittee Meeting | |
| June 20 | Matt | Ali Tafreshi | selfish supergenes | |
| June 27 | Madeline | Chris | Rice, ch 5 | |
| July 4 | Puneeth | Madeline | Rice, ch 6 | |
| July 11 | Sydney | Madeline | final thesis chapter! | |
| July 18 | Tom | Matt | Rice, ch 7 | |
| July 25 | Chris | Puneeth | Rice, ch 8 | |
| August 1 | Madeline | Sydney | Group Selection: 'A Theory of Group Selection' by Wilson: https://www.pnas.org/doi/pdf/10.1073/pnas.72.1.143 and 'Social Semantics' by West et al. (only pages 423-425 are required) https://pubmed.ncbi.nlm.nih.gov/17305808/ | |
| August 8 | Matt | Tom | Rice, ch 9 | |
| August 15 | Puneeth | Sydney | Rice, ch 10 | |
| August 22 | Sydney | Puneeth | Spatial Rescue Models | |
| August 29 | Tom | Mete | using methylation data to infer cancer phylogenies & test for selection | |
| Tuesday Sept 6 - monday is a holiday | Jahin | slendr model of Arabidopsis thaliana |
| date | topic |
|---|---|
| Jan 7 | check-in |
| Jan 10 | wakeley chapter 4 part 1 (pages 91-97) |
| Jan 17 | cancelled - matt out of town |
| Jan 24 | wakeley chapter 4 part 2 (pages 97-106) |
| Jan 31 | Dr. Maria Abou Chakra - Talk |
| Feb 7 | wakeley chapter 4 part 3 (pages 106-113) |
| Feb 14 | Madeline |
| Feb 21 | family day |
| Feb 28 | wakeley chapter 4 part 4 (pages 113-129) |
| Mar 7 | wakeley chapter 5 part 1 (pages 131 - 148) |
| Mar 14 | Sydney - also maybe a project update? |
| Mar 21 | Puneeth - An update of my project (hopefully!) |
| Mar 28 | Madeline - feedback on some analysis using a v simple structured coalescent |
| Apr 4 | Anthony - project presentation |
| Apr 11 | Matt - what is evolutionary rescue? |
| Apr 18 | practice Atwood talks |
| Apr 25 | bocce! |
| date | topic |
|---|---|
| Sep 14 | Planning |
| Sep 21 | Puneeth |
| Sep 28 | Wakeley Chapter 1 |
| Oct 5 | Chris |
| Oct 12 | Wakeley Chapter 2 |
| Oct 19 | Sydney |
| Oct 26 | Wakeley Chapter 3 part 1 |
| Nov 2 | Puneeth |
| Nov 9 | Wakeley Chapter 3 part 2 |
| Nov 16 | Tom Ouellette |
| Nov 23 | Sydney (practice committee meeting talk) |
| Nov 30 | Pam Alamilla |
| Dec 7 | Puneeth |
| Dec 14 | Matt |