Lacey Knowles
Lacey Knowles

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Arrival and Departure

May 28 to June 6

Lecture Materials

Lecture slides 2023

Demo and Tutorials

No demos in class, but if your are interested in spatial coalescent simulations and iDDC modeling check out: and 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

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)


Here are some references for some papers I will hihglight as basckground reading.


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. 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. Sukumaran et al.2021-PlosCompBiol.pdf

Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. PNAS 107:9264-9269.