We are meeting this semester (Spring 2025) on Fridays from 11:15-12:05 in TLS 171b (i.e. the Bamford Conference Room).

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January 24, 2025

This first meeting, those who are registered will sign up for a date to lead.

You should also read the following paper for the first meeting:

R Hunt, JL Reyes-Hernández, JJ Shaw, A Solodovnikov, and KS Pedersen. 2025. Integrating Deep Learning Derived Morphological Traits and Molecular Data for Total-Evidence Phylogenetics: Lessons from Digitized Collections. Systematic Biology (accepted manuscript). DOI:10.1093/sysbio/syae072

January 31, 2025

Nick Van Gilder will lead discussion on phylogenomic discordance in rattlesnakes:

EA Myers, RM Rautsaw, M Borja, J Jones, CI Grünwald, ML Holding, FG Grazziotin, CL Parkinson. 2024. Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (viperidae: Crotalus and Sistrurus). Systematic Biology 73(4):722-741. DOI:10.1093/sysbio/syae018

February 7, 2025

Analisa Milkey will lead discussion on the following paper:

C Zhang, R Nielsen, and S Mirarab. 2025. CASTER: Direct species tree inference from whole-genome alignments. Science (early access) DOI:10.1126/science.adk9688

February 14, 2025

We will revisit the Zhang et al. CASTER paper again this week, focussing on the analyses of empirical data sets.

February 21 2025

No meeting this week due to overlap with the Graduate Mental Health Workshop.

February 28, 2025

Meghan Myles chose this paper for this week:

JB Thompson, T Hernández-Hernándex, G Keeling, M Vásquez-Cruz, and NK Priest. 2024. Identifying the multiple driveers of cactus diversifiction. Nature Communications 15:7282. DOI:10.1126/science.adk9688

March 7, 2025

Jeremy Quirõs-Navarro will discuss the following paper:

LJ Revell, LJ Harmon, and DC Collar. 2008. Phylogenetic signal, evolutionary process, and rate. Systematic Biology 57(4): 591-601. DOI:10.1080/10635150802302427

March 14, 2025

Noah Manuel will lead discussion on this paper:

K Mark, L Saag, SD Leavitt, S Will-Wolf, MP Nelsen, T Tõrra, A Saag, T Randlane, and HT Lumbsch. 2016. Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset. Organisms, Diversity, and Evolution 16:497-524. DOI:10.1007/s13127-016-0273-7

March 21, 2025

SPRING BREAK WEEK

March 28, 2025

Zach Muscavitch will lead discussion on this paper:

Benoît Perez-Lamarque & Hélène Morlon. 2024. Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions. Systematic Biology 73(3):613–622, DOI:10.1093/sysbio/syae013

April 4, 2025

Paul chose the following paper for this week:

JF Walker, SA Smith, RGJ Hodel, and E Moyroud. 2022. Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets. Syst. Biol. 71(4):943–958. DOI:10.1093/sysbio/syab052

April 11, 2025

Chelsea Kintz will lead discussion on this paper:

DM Casali, FV Freitas, and FA Perini. 2023. Evaluating the impact of anatomical partitioning on summary topologies obtained with Bayesian phylogenetic analyses of morphological data. Systematic Biology 72(1):62–77. DOI:10.1093/sysbio/syac076

April 18, 2025

Combined Systematics Seminar and Plant Lunch visit with Pam and Doug Soltis.

Note: we are beginning at 11am this week because Pam and Doug must depart for the airport at noon.

April 25, 2025

Noah Manuel will lead discussion on the following paper:

P Resl et al. 2022. Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts. Nature Communications 13:2634. DOI:10.1038/s41467-022-30218-6

May 2, 2025

Meghan Myles will lead discussion on the following paper:

L Guo, X Wang, DH Ayhan, et al. 2025. Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement. Nature Genetics 57:741–753 DOI:10.1038/s41588-025-02111-7