Note that the Species Delimitation Workshop is still planned for March 13; however, the 16th Annual Early Career Scientists Symposium “Natural History Collections: Drivers of Innovation” that was to be held on March 14-15 has been postponed until Fall 2020.
The workshop will be held in East Hall (EH) 1324 on Friday, from 9am-12pm, and the Undergraduate Science Building (USB) 1230 on Friday from 2pm-5pm. A searchable campus map is available at https://maps.studentlife.umich.edu/. We will live stream the lecture for those that registered and cannot attend (stay tuned for the live link).
For information on the software packages DELINEATE and DECRYPT, please visit the github sites. Workshop participants will run the programs from a University of Michigan server; however, you can download the program DELINEATE on your personal computer (instructions on website, including dependencies).
Note the methods and associated documentation are freely available as the software packages DELINEATE and DECRYPT. Please visit these links for background information on the respective programs that will be taught during the computer tutorials.
https://github.com/jeetsukumaran/delineate
https://becheler.github.io/pages/applications.html
In preparation of the workshop, please download FigTree on your personal computer and have R studio installed. You might also find a unix tutorial helpful; e.g. see: https://evomics.org/learnig/unix tutorial
Background reading for the species delimitation workshop:
Sukumaran J, Knowles LL (2017) Multispecies coalescent delimits structure, not species. Proc. Natl. Academy Sci. USA 114:1607-1612.
Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. PNAS 107:9264-9269; https://doi.org/10.1073/pnas.0913022107
Leache et al. (2018) The spectre of too many species. Syst. Biol., in press. https://doi.org/10.1093/sysbio/syy051
Species Delimitation Background. The resolution in genomic data makes it possible to not only detect divergent lineages, but also local population structure within them. Yet, these conflated boundaries have received little attention from those developing genetic-based species delimitation methods, potentially leading to mass over-splitting as genomic data become more widely employed. These challenges have profound implications for not only understanding the generation and dynamics of biodiversity, but also for conserving this diversity.
In this workshop, we will cover the foundations upon which genetic-based inference of species boundaries are built. In particular, we will review the history that lead to a reliance on the multispecies coalescent (MSC) as the primary model for species delimitation. Despite the appeal of genome-based species discovery, we will explain how misidentification of population structure as putative species is an emerging key issue for applications of the MSC for species delimitation, as well as the implications of divergence of gene flow for identifying species boundaries.
We will then present two recently developed approaches to address the misidentifications of species that occurs from confounding the structure within species with the divergence that accumulates between species. One approach, implemented in the program DELINEATE, takes a phylogenetic lineage-based perspective to delimit species where for the first time speciation is modeled as an extended process in the context of species delimitation analyses, as opposed to being treated as an instantaneous event. The other approach, implemented in the program DECRYPT, employs a spatially explicit coalescent model to characterize the geography of divergence to test competing hypotheses regarding the detection of cryptic diversity. Participants in the workshop will also receive hands-on training with both programs, completing a series of computer demonstrations and exercises.
These newly developed method should reduce the errors with genome-based species delimitation, while also providing a framework for gaining insights about the speciation process itself. Note the methods and associated documentation are freely available as the software packages DELINEATE and DECRYPT.
The workshop will be held at the University of Michigan, Ann Arbor, MI on March 13, 2020; the workshop is free but limited to 65 participants, and participants must apply to attend, with review of applications beginning Feb. 18. Note that the 16th Annual Early Career Scientists Symposium “Natural History Collections: Drivers of Innovation” that was to be held on March 14-15 has been postponed until Fall 2020.
Note that through the generous support of the National Science Foundation (DEB 16-55607) we will be offering travel scholarship to increase the representation from interested participants that who otherwise would not be able to attend. Priority will be given to graduate students and postdocs. Send a brief description of fit of the workshop and scholarship need (no more than 150 words) by Feb. 18.
Please address questions and application for travel scholarships to L. Lacey Knowles (knowlesl@umich.edu) and see you in March!
Workshop Committee | Lacey Knowles | Jeet Sukumaran | Arnaud Becheler
