Bodega 2017


I’ve been spending the week teaching in the Bodega Marine Lab for the 2017 Workshop in Applied Phylogenetics. It’s been a fun week of statistics, phylogenies, data analysis, and beautiful weather. This year, Jeremy Brown (@jembrown) and I put together a new day long session focusing on model selection, model performance, and the challenges of big data in phylogenetics. My slides are available over at

The Bodega Cycle

Coffee and an absurdly nice sunrise

Coffee and an absurdly nice sunrise

Lecture and practicals all day.

Lecture and practicals all day.

Brief pause for bourbon and beautiful sunset.

Brief pause for bourbon and a beautiful sunset.

Analyze all night. (rinse repeat).

Analyze all night. (…rinse repeat).

Posted in genomics, informatics, phylogenetics, teaching, travel

Spring 2017 lab meeting schedule

  • 18 January – Open
  • 25 January – Bob
  • 1 February – Laci
  • 8 February – Robyn
  • 15 February – Open
  • 22 February – Luke
  • 1 March – Anthony Laci
  • 8 March – Maya Julio
  • 15 March – Van Open Anthony
  • 22 March – Open Van
  • 29 March – Spring Break
  • 5 April – Anthony
  • 12 April – Arielle
  • 19 April – Stevie
  • 26 April – No Meeting – Tester Symposium
  • 3 May – Preston, Maya, Melissa
Posted in lab, UH

The book is out!

I’m a little late posting this, but the book is out! The author’s advance copies arrived a couple months ago and UC Press and Amazon are both now shipping copies.

Amphibians and Reptile Species of Special Concern.

Amphibians and Reptile Species of Special Concern.

Posted in conservation, herps, Natural History

Fall 2016 lab meeting schedule

Sept. 6 – ArtSci opening
Sept. 13 – Amber
Sept. 20 – no meeting (Bob out of town)
Sept. 27 – Van
Oct. 4 – Maya
Oct. 11 – Stevie
Oct. 18 – Luke
Oct. 25 – Anthony
Nov. 1 – Laci
Nov. 8 – no meeting (Election Day)
Nov. 15 – Preston
Nov. 22 – no meeting
Nov. 29 – Megan
Dec. 6 – Robyn

Posted in lab, UH

New paper highlighted in Molecular Ecology

Bob and I have a new paper out in the current issue of Molecular Ecology: Assessing the performance of DNA barcoding using posterior predictive simulations. In the same issue, our paper was highlighted in a great ‘Perspective’ piece written by Lucie Zinger and Hervé Philippe. Check them both out!

Posted in Uncategorized

Desert Oracle

I’ve got an article on the elusive California Gila monster in the Spring 2016 issue of the Desert Oracle. Check it out.

Desert Oracle backDesert Oracle Cover

Posted in conservation, herps, Natural History, outreach, travel

Tester Symposium 2016

I’m a little late getting to this, but I wanted to put up a quick post about the 2016 Tester Symposium which took place at the end of last week. This year marked the 41st year of this symposium, which supports graduate student research here at the University of Hawaii. It’s three solid days of graduate student talks, two key note lectures by Dolph Schluter (this year’s invited speaker), and capped off with a banquet at the beautiful aquarium in Waikiki.

Emilie spoke about her thesis research this year and was selected as a winner for best talk! This is great news and well deserved.

I was part of the organizational team for this symposium for the previous two years. I found it really nice to be able to kick back and enjoy the symposium a bit more this year. Organizing is fun, but inevitably comes with some stress, and less opportunity to watch the talks.

Awards Banquet at Waikiki Aquarium

Emilie Richards wins best talk award!

Emilie Richards wins best talk award!

Posted in lab, UH

Postdoctoral Position Available

We’re looking for a postdoc to join the team. Please share the ad below with any colleagues that may be interested.

Postdoctoral position in phylogenetics and bioinformatics at the University of Hawaii

The Thomson Lab is looking for a postdoctoral researcher to participate in an NSF funded project that seeks to build an archive of Bayesian phylogenetic output and examine the performance of Bayesian estimation of phylogeny for large datasets. The project is a collaboration between the Thomson Lab and the Moore Lab at UC Davis and aims to improve MCMC performance, assess goodness of fit of phylogenetic models, and contribute to the field’s ability to carry out robust Bayesian phylogenetic inference by developing new scientific resources and educational tools. The candidate should have demonstrated experience in phylogenetics and bioinformatics, including programming with SQL, R and/or Python. The selected candidate will join a lab that focuses on phylogenetics, bioinformatics, and conservation in UH’s Department of Biology. The position is based in Honolulu, a vibrant city that is consistently recognized for its diversity, outdoor recreation, and high quality of life.

The start date is flexible, but ideally will be on or before 1 August 2016. Funding is available for two years ($54,000/year, with an additional stipend for health insurance). Application review will begin 1 May. Minimum PhD in Evolutionary Biology (or related field) is required. The University of Hawaii is an Equal Opportunity/Affirmative Action employer.

To apply, please send CV and names and contact information for three reference to Bob Thomson:

Posted in informatics, lab, phylogenetics, UH

Emilie Defends

Hearty congratulations to Emilie Richards who successfully defended her masters thesis yesterday! Emilie’s work focuses on characterizing the performance of model assessment tests for phylogenomic datasets. She gave a great talk on an interesting, important project that she’ll be submitting for publication shortly, so stay tuned!

Great job Emilie!

Emilie Richards and Bob Thomson

Posted in genomics, informatics, lab, phylogenetics, UH

Summer 2016 REU at UH

There is a brand new research program for undergraduates starting this summer at UH. Get in touch with the program coordinators, or faculty sponsors with questions!
The quick advertisement follows, but see the project website here for more detail.
Participants in the Summer 2016 Research Experience for Undergraduates (REU) program will take advantage of high-throughput DNA sequencing and phylogenetic methods to study the identity and origins of Hawai?i’s native, endemic and invasive organisms. REU participants will be mentored by a diverse faculty from the departments of Biology, Botany, and Microbiology, the Hawai‘i Natural Energy Institute at the University of Hawai‘i at Manoa, and Kapi‘olani Community College in Honolulu, Hawai‘i.
The 10-week REU summer program provides participants with stipends of $5,250, and covers the costs of accommodations, food and travel to Hawaii. This unique experience allows participants to gain hands-on research experience, providing an excellent stepping stone for future graduate studies.
Applications for Summer 2016 are due March 15, 2016. Please visit the program website for further information and to apply.
Questions can be addressed to program coordinators Dr. Stuart Donachie ( and Dr. Stephanie Kraft-Terry (
Posted in lab, outreach, UH