L. Lacey Knowles
Institutional home page
lsa.umich.edu/eeb/people/faculty/knowlesl.html
Arrival and Departure
May 28 to June 6
Lecture Materials
Demo and Tutorials
No demos in class, but if your are interested in spatial coalescent simulations and iDDC modeling check out: https://becheler.github.io/quetzal-CRUMBS/index.html and https://becheler.github.io/who-am-i/ This software package includes a test for the robustness of the MSC.
If you are interested in software for incorporating a speciation process into species delimitation, check out DELINEATE https://github.com/jeetsukumaran/delineate
Lecture in Brief
Capstone lecture: Evolutionary applications of genomic data Knowles-Woodshole-2023-Lect.pdf
I will highlight some common themes for model-based analyses with examples of a variety of evoltuionary applications of genomic data (e.g., phylogenetics, adaptive evolution, phylogeography, inferences about species boundaries): namely,
- decisions/choices we make about modeul formulation
- recognizing the subjectivity of model formulation itself when making inferences
- decisions when applying to empirical data (e.g., how much data, what type of data, use of summary statistics etc)
Refereces
Here are some references for some papers I will hihglight as basckground reading.
Phylogeography
Becheler A, Knowles LL (2022) Computational resources for simulating under a spatial coalescent model across heterogeneous landscapes and testing hypotheses about the geography of genetic variation: QUETZAL-EGGS, -CRUMBS, -NEST and DECRYPT. Mol. Ecol. Res., in review. QUEZTAL__MER__submitted.pdf
Carstens et al. (2017) Objective choice of phylogeographic models. Mol. Phylog. Evol. 116: 136-140.
He Q, Prado JR, Knowles LL (2017) Inferring the geographic origin of a range expansion: latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program X-ORIGIN. Mol. Ecol. 26:6908-6920.
Massatti R, Knowles LL (2016) Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges. Mol. Ecol. 25:3974-3986. Massatti&Knowles2016-ME.pdf
Oaks, J. R., J. Sukumaran, J. A. Esselstyn, C. W. Linkem, C. D. Siler, M., T. Holder, and R. M. Brown. 2013. Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events. Evolution 67:991–1010.
Papadopoulou A, Knowles LL (2016) Towards a paradigm shift in comparative phylogeography driven by trait-based hypotheses. Proc. Natl. Academy Sci. USA 113:8018-8024. Papadopoulou&Knowles2016-PNAS.pdf
Adadptive evolution
Decimated little brown bat population show potential for adaptive change. Scientific Reports. 10:3023. doi.org/10.1038/s41598-020-59797-4 Auteri&Knowles2020.pdf
Species delimitation
Leache et al. (2018) The spectre of too many species. Syst. Biol., in press.
Jackson ND, Morales A, Carstens BC, O’Meara BC (2017) Species delimitation with gene flow. Systematic Biology 66, 799-812.
Sukumaran J, Knowles LL (2017) Multispecies coalescent delimits structure, not species. Proc. Natl. Academy Sci. USA 114:1607-1612.Sukumaran&Knowles-PNAS-2017.pdf
Sukumaran J, Holder MT, Knowles LL (2021) Incorporating the speciation process into species delimitation. PloS Comput. Biol.17(5):e1008924. https://doi.org/10.1371/journal.pcbi.1008924 Sukumaran et al.2021-PlosCompBiol.pdf
Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. PNAS 107:9264-9269.