Course Page for BIO715 (2025) taught by Brian Golding and Ian Dworkin (and maybe Ben Evans will join in for some fun)
When: Monday 2:30 - 4:30 fall semester (2025). First class will be September 8th, 2025.
Where: LSB 213A (the seminar room in LSB inside the lounge on the 2nd floor).
Instuctors: Dr. Brian Golding, Dr. Ian Dworkin and when he can find some spare time from his job as chair of the department, Dr. Ben Evans.
Topics broadly spanning "Evolutionary Genetics". See course content below.
We generally expect you to have an introductory Genetics (equivalent of BIO2C03) and introductory evolutionary biology (equivalent of BIO3FF3), we do not expect any specific knowledge of population genetics (equivalent of BIO3PG3) or Molecular Evolution (equivalent of MolBiol4DD3), but of course they will help! We will be providing both review readings as well as the primary literature readings to help everyone get up to speed. We also (below) will have some background resources if you feel they will help.
For the first 6-7 weeks, we will discussing several topics in phenotypic evolution, largely from a quantitative genetics perspective. In particular we will focus on concepts of evolvability (the propensity for a trait to evolve), evolutionary rates (how fast do traits evolve) and the predictiability of evolutionary response, in particular how well does mutational and genetic variation within species provide a prediction of divergence among species? We will cap this section of the course off with a discussion about the (dis)cordance between molecular and phenotypic rates of evolution (although we may save this for the very last week).
For the second half of the course (the remaining 6 weeks), we will focus more on molecular evolution and molecular population genetics. Among the topics we might look at include the phenomena of lateral gene transfer, low complexity sequence evolution, repetitive element evolution, sex chromosome evolution (for Prof. Evans), the evolution of new genes, and other topics to be determined.
Each week there will be a written critique of a specific paper (details to follow, but ~ 1 page in length). You are expected to attend all classes as class discussions will be another major part of the assessment. Finally, each student will be expected to write an independent, synthetic and analytical paper based on topics you will choose (but approved by Ben, Brian or Ian).
You should have access to all of these via McMaster library. If you have any problems reach out to Ian or Brian (depending on who is leading class)., as we have PDFs of all of them.
Refresh yourself (or introduce yourself) to the fundamentals of Quantitative Genetics. While the first two papers below do an admirable job, some may find a more introductory chapter or two helpful to read first. The perfect readings for this would be chapters 4-6 of Conner, J & Hartl, D. 2004. A primer of ecological genetics. This book puts everything in a very evolutionary context, which will be very useful. Unfortunately our library does not seem to have an electronic copy of it, (there is one physical copy in the library). Alternatively chapters 8 & 9 of Hartl, D. 2020. A primer of population genetics and genomics are a reasonable introduction to quantitative genetics.
However, the relevant chapter in amost any Genetics of Evolutionary Biology textbook will do just fine. It may be called "Quantitative Genetics" or "Genetics of complex traits" or something like that. I recommend reading one of these first before reading the papers below. Come prepared with lots of questions about what you don't understand about Quantitative Genetics. I will spend much of the first week helping to get everyone up to speed.
McGuigan, K. 2006. Studying phenotypic evolution using multivariate quantitative genetics
If you already read Tsuboi in detail, I suggest this alternative article, that is related, quite clear, and I think is in general a nice summary. Also by the same author (Dolph Schluter) as the primary article we are reading!
Schluter, D. 2024. Variable success in linking micro- and macroevolution
and the primary paper we are reading (and you are writing a critique of):
Schluter, D. 1996. Adaptive radiation along genetic lines of least resistance
Review article on G-matrix and how it evolves.
Arnold et al. 2008. UNDERSTANDING THE EVOLUTION AND STABILITY OF THE G-MATRIX
The primary paper we are reading (for your critique):
Mallard et al. 2023.Selection and the direction of phenotypic evolution
Houle et al. 2017. Mutation predicts 40 million years of fly wing evolution
Adventures with Lateral Gene Transfer.
This week just a review paper ... Tonkin-Hill G. 2025 NatMicrobiol Within-host bacterial evolution and the emergence of pathogenicity
Next week papers to critque.
Keeling PJ. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet. 2024 Jan 23. PMID: 38263430.
Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol. 2024 Jan;17(1):e14408. PMID: 38226780.
Gilbert C, Maumus F. Sidestepping Darwin: horizontal gene transfer from plants to insects. Curr Opin Insect Sci. 2023 Jun;57:101035. PMID: 37061183.
Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel). 2023 Feb 4;12(2):328. PMID: 36830238.
Gophna U, Altman-Price N. Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution. Annu Rev Microbiol. 2022 Sep 8;76:481-502. PMID: 35667126.
Arnold BJ, Huang IT, Hanage WP. Horizontal gene transfer and adaptive evolution in bacteria. Nat Rev Microbiol. 2022 Apr;20(4):206-218. PMID: 34773098.
Aubin E, El Baidouri M, Panaud O. Horizontal Gene Transfers in Plants. Life (Basel). 2021 Aug 21;11(8):857. PMID: 34440601.
Van Etten J, Bhattacharya D. Horizontal Gene Transfer in Eukaryotes: Not if, but How Much? Trends Genet. 2020 Dec;36(12):915-925. PMID: 33012528.
Lateral Gene Transfer Part II
This week review paper ... Arnold et al. 2022 Nature Review Microbiology Horizontal gene transfer and adaptive evolution in bacteria. and Zhaxybayeva 2025 Journam Molecular Biology Impact of Horizontal Gene Transfer on Adaptations to Extreme Environments
To be critiqued, Stepanauskas et al. 2025 ISME Net rate of lateral gene transfer in marine prokaryoplankton.
Your proposal (max 1-2 pages) and a presentation outlining your proposal.
Since Gabriela and Sarah still have their own presentations to do, to be fair to them, we will have the critique of Gluck-Thaler et al. 2022 MBE Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes and Habig et al 2024 PNAS Frequent horizontal chromosome transfer between asexual fungal insect pathogens due Nov 24.
For the 17th, I would like you to read Husnik et al. 2021 Current Biology Bacterial and archaeal symbioses with protists to provide a bit of background from a modern perspective.
For the 24th, some background material is provided in Parks et al., Chromosome Research 2019 **. For Dec 1st, please provide a critique of Gonzalez-Duran E, Kroop X, Schadach A, Bock R. Nat Plants. 2025 Jun;11(6):1154-1164. **.
No critique this week, but you will be advesaries with the other students regarding the plausibility of biological, vs artefactual explanations.
Required readings:
Rolland et al. 2023. Conceptual and empirical bridges between micro- and macroevolution
De Lisle and Svennson. 2025. Revisiting evolutionary rate–time relationships.
I also wrote a few notes (think of it like an FAQ for evolutionary rates) that may be helpful. PDF format or .Rmd format for R.
Arnold, S. 2023. Evolutionary Quantitative Genetics
Walsh, B. Lynch M. 2018. Evolution and Selection of Quantitative Traits
Gingerich, PD. 2019. Rates of Evolution: A Quantitative Synthesis
Harmon, L. 2019. Phylogenetic Comparative Methods: Learning From Trees
Cutter, A. 2019. A primer of molecular population genetics
Hartl, D. 2020. A primer of population genetics and genomics