We are meeting this semester on Wednesdays 1:30-2:30pm online. We are planning to work through selected chapters of the book “Tree thinking: an introduction to phylogenetic biology” (D. A. Baum and S. D. Smith. 2013. Roberts and Company, Publishers, Greenwood Village, Colorado), supplemented by additional papers on specific topics.

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Apr. 28, 2021

Paul suggests we finish off the semester by looking at this review of adaptive introgression in humans:

Racimo et al. 2015. Evidence for archaic adaptive introgression in humans. Nature Reviews Genetics 16:359-371.

It is not too long and revisits some of the methods we’ve already discussed this semester, so I think it will be a nice paper with which to end our exploration of introgression.

Apr. 21, 2021

Vidya and Frank will be leading the discussion on this paper exploring cryptic speciation and gene flow in red-eyed vireos:

Battey and Klicka. 2017. Cryptic speciation and gene flow in a migratory songbird species complex: insights from the Red-Eyed Vireo (Vireo olivaceus). Molecular Phylogenetics and Evolution 113:67-75.

Apr. 14, 2021

Spring Break.

Apr. 7, 2021

Nick has settled on Newton et al. 2020 to read this week - where we’ll see a much different approach to delimiting species of invertebrates.

Newton et al. 2020 Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex. Molecular Ecology 29(12):2269-2287.

Mar. 31, 2021

(From Elizabeth’s email message…) See below from Tanner for recommended reading for this week’s systematics discussion. The one to read in full (Zamani et al.) is only 4 pages long.

The Intros of Meierotto et al 2019 and Sharkey et al 2021, and all of Zamani et al 2021 should suffice to provide the necessary background for this discussion….this is a topic that I hope will ruffle feathers and generate a lively discussion in class.

Zamani et al. 2021. The omission of critical data in the pursuit of ‘revolutionary’ methods to accelerate the description of species. Systematic Entomology 46:1-4.

Sharkey et al. 2021. Minimalist revision and description of 403 new species in 11 subfamilies of Costa Rican braconid parasitoid wasps, including host records for 219 species ZooKeys 1013:1-665. (Note: 236.3 MB, 665 pages)

Meierotto et al. 2019. A revolutionary protocol to describe understudied hyperdiverse taxa and overcome the taxonomic impediment Deutsche Entomologische Zeitschrift 66:119–145.

Mar. 24, 2021

Zach recommended this book chapter as a good starting point for our discussion of species delimitation:

B Rannala and Z Yang. 2020. Species delimitation. pp.5.5:1–5.5:18 in: Phylogenetics in the genomic era. C Scornavacca, F Delsuc, N Galtier (eds.). No commercial publisher: open access book. hal-02536468

Also fodder for discussion: think about the ways in which you use species in your work (and thus ways in which it matters where/how a lineage gets subdivided into recognized species)—(why) does it matter where one draws the line saying that speciation has happened?

Mar. 17, 2021

(From Elizabeth’s email message…) Bernard will bring a bryophyte’s-eye view to our discussion about introgression, incomplete lineage sorting, and gene tree-species tree discordance, based on this recent paper:

Meleshko et al. 2021. Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting and not ongoing introgression in a rapidly radiated bryophyte genus. Molecular Biology and Evolution (early access published 03 March 2021)

As you will see, this turns out to be rather different than the bird’s-eye view.

Mar. 10, 2021

Following up on our discussion of methods for detecting introgression, Kristin will lead next week’s meeting on the role of introgression in the evolution of odonates (damselflies and dragonflies). Suvorov et al. 2021. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies BioRxiv 20 Feb, 2021.

Mar. 3, 2021

We will continue discussion on the Hibbins and Hahn paper paper from last week, but in addition please read Chapter 6 of the Baum and Smith book. Come with questions and thoughts about how introgression may impact whatever phenomena you are most interested in.

Feb. 24, 2021

Mark Stukel will lead discussion on this paper, which reviews approaches to detecting and characterizing introgression using phylogenomic data:

MS Hibbins and MW Hahn. 2021. Phylogenomic approaches to detecting and characterizing introgression EcoEvoRxiv 8 Feb 2021.

Feb. 17, 2021

Elizabeth Jockusch will lead the discussion on the following paper:

Patton et al. 2020. Hybridizing salamanders experience accelerated diversification Scientific Reports 10:6566.

Recommended background reading: Baum and Smith Ch. 10 pp. 316-322 with view to the question of what it means to apply this model of character evolution to hybridization as a trait and also Ch. 11, pp. 378-381 for a basic model of trait-associated diversification.

Feb. 10, 2021

Zach Muscavitch will lead the discussion on the following paper:

Varga et al. 2019. Megaphylogeny resolves global patterns of mushroom evolution. Nature Ecology and Evolution 3:668-678.

Ch. 11, pp. 371-381 in Baum and Smith, gives a good overview of several of the methods, so bring questions about that as well.

Feb. 3, 2021

Tanner Matsen will lead the discussion on the following paper:

Allio et al. 2021. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nature Communications 12:354.

Chapters 10 and 11 of the Baum and Smith book are also recommended background reading, especially the first part of chapter 10 (pp. 305-324), which discusses trait mapping methods.

Past discussions

Jan. 27, 2021

Elizabeth Jockush lead discussion on Chapter 4 in Baum and Smith as well as the 2019 paper by Al Sayad and Yassin.