Schedule
We are meeting this semester (Fall 2024) on Fridays from 1:20 to 2:20 in PBB 303 (i.e. BioPharm 3rd. floor fishbowl). Subscribe to systematics listserv to receive emails containing connection information (or write to someone listed in Contact Info).
August 30, 2024
This first meeting, those who are registered will sign up for a date to lead, and we’ll have an informal discussion of what everyone’s working on and what kind of seminar they want this to be this semester.
September 6, 2024
This week we will start working on our minitheme of species delimitation by reading this chapter from a recently published book:
ML Smith and BC Carstens. 2022. Species delimitation using molecular data. Chapter 7 in: JS Wilkins, FE Zachos, and IY Pavlinov (eds.), Species problems and beyond: contemporary issues in philosophy and practice, 1st ed. CRC Press ISBN 9780367855604.
September 13, 2024
We will discuss this paper, which is one of the few methods that does not require many loci.
N Puillandre, A Lambert, S Brouillet, and G Achaz. 2012. ABGD, automatic barcode gap discovery for primary species delimitation. Molecular Ecology 21:1864–1877. DOI:10.1111/j.1365-294X.2011.05239.x
September 20, 2024
Nick chose the paper below to discuss this week. He says “This paper will examine the difference in results between 5 different delimitation methods, including ABGD. It also is on the more digestible side as it only involves one mitochondrial locus, which should offer us more chances for discussion about barcoding.”
C Blair and RW Bryson Jr. 2017. Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma). Molecular Ecology Resources 17:1168–1182. DOI:10.1111/1755-0998.12658
Discussion of this paper was postponed until October 4 because we did not have a quorum.
September 27, 2024
Mark Stukel selected this paper introducing SPEEDEMON:
J Douglas and R Bouckaert. 2022. Quantitatively defining species boundaries with more efficiency and more biological realism. Communications Biology 5:755. DOI:10.1038/s42003-022-03723-z
October 4, 2024
This week we are going to discuss the paper (Blair and Bryson 2017) that Nick chose for Sep. 20.
October 11, 2024
Zach suggests the following two papers related to GDI (Genealogical Divergence Index).
AD Leaché, T Zhu, B Rannala, Z Yang. 2019. The spectre of too many species. Systematic Biology 68(1):168-181. DOI:10.1093/sysbio/syy051
ND Jackson, BC Carstens, AE Morales, BC O’Meara. 2017. Species delimitation with gene flow. Systematic Biology 66(5):799-812. DOI:10.1093/sysbio/syw117
Zach suggests we read the Jackson et al. paper first and save Leaché et al. for later.
October 18, 2024
This is a follow-up paper to the one we read last week, presenting the BPP perspective:
AD Leaché, T Zhu, B Rannala, Z Yang. 2019. The spectre of too many species. Systematic Biology 68(1):168-181. DOI:10.1093/sysbio/syy051
October 25, 2024
Given that Mark will be defending Oct. 25 at 4pm, let’s read his first chapter for Systematics Seminar this week:
M Stukel, AE Porczak, ERL Gordon, J Vailionis, D Haji, TR Buckley, AR Lemmon, RM Lemmon, C Simon. 2023. Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito-nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation. Systematic Entomology 49:237-257. DOI: 10.1111/syen.12613
November 1, 2024
Chelsea would like to discuss this paper:
PL McInerney, MSY Lee, AM Clement and TH Worthy. 2019. The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the southern cassowary, Casuarius casuarius (Aves, Palaeognathae). BMC Evol. Biol. 19: 233. DOI:10.1186/s12862-019-1544-7
November 8, 2024
Analisa chose the following paper, which explains how the local posterior probabilities reported by the program ASTRAL are calculated:
E Sayyari and S Mirarab. 2016. Fast coalescent-based computation of local branch support from quartet frequencies. Molecular Biology and Evolution 33(7):1654-1668. DOI:10.1093/molbev/msw079
November 15, 2024
Paul chose the following paper for this week:
N. Koch. 2021. Phylogenomic subsampling and the search for phylogenetically reliable loci. Molecular Biology and Evolution 38(9):4025-4038. DOI:10.1093/molbev/msab151
November 22, 2024
Bernard chose the following 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 Advance Access. DOI:10.1093/molbev/msab063
November 29, 2024
No Class: Thanksgiving Break Week