Justin’s News

Amatitlania siquia Amsiq_u0 editNews

Check this page regularly for updates about what Justin and his collaborators have been up to lately, including news about research progress, travel, meetings and other events.

June 23–27, 2017 – Justin and the Eckert lab are attending the Evolution 2017 Meetings (joint SSE, ASN, and SSB meetings) in Portland, OR. We look forward to learning cutting edge science, seeing friends, forging new collaborations, and giving great presentations of our hard-eared research. Justin is presenting ddRAD-seq phylogeography results from his Brazilian postdoc, as well as his new VCU pine tree postdoc, on Sunday & Monday. He tweeted out his schedule Wednesday morning, en route to Portland State University. Keep watching us on Twitter (@JBagz1, @iowensis, @evolMM) for more updates about #Evol2017!


April 1, 2017 – Justin has officially started his new job in the Eckert Lab, located in the Virginia Commonwealth University (VCU) Department of Biology!

March 29, 2017 – Justin and Flor moved the family to Richmond, VA to start new jobs at Virginia Commonwealth University. Justin was awarded a postdoctoral scholar position that is part of a ~$500,000 portion of a $4 million NSF MacroSystems Biology grant!

June 6, 2016 – Our manuscript on Amatitlania convict cichlid phylogeography and Bayesian species delimitation is now accepted at the Biological Journal of the Linnean Society!  Congrats to Justin and his co-authors Wilfredo Matamoros, Caleb McMahan, Michi Tobler, Prosanta Chakrabarty, and Jerry Johnson on the first paper stemming from their group collaboration on the phylogeography of Central American freshwater fishes. The picture at the top right of this page is a convict cichlid. Hopefully, this group will continue to collaborate on great things in the near future!

June 2, 2016 – Justin completed and submitted the revised version of our manuscript on phylogeography and species delimitation in Amatitlania ‘convict cichlids’ to BJLSFingers crossed! This has been a year-long revision process, given interruptions from Justin’s fieldwork and other activities related to his current postdoc position.

May 1-8, 2016 – Justin travelled to visit collaborators Tomas Hrbek and Izeni Farias at their LEGAL lab (Laboratório de Evolução e Genética AnimaL) at UFAM in Manaus, Amazonas, Brazil. The goal of the trip was to prep ddRAD-seq genomic libraries for Brazilian freshwater fishes he is studying during his current postdoc, and sequence them using NGS technologies (Ion Torrent platform). Justin had a very successful week and was able to prep several barcoded libraries that are now yielding data from thousands of loci across different tetra and suckermouth armored catfish genomes. These are the first data of their kind ever generated for freshwater fishes of Brazil, and they reflect a steep increase in the number of loci available for the study taxa (0-1 to 1000’s).

April 15, 2016 – Justin has been officially accepted to attend the Auburn University Bioinformatics Bootcamp this June! The bootcamp will be a week-long intensive workshop on practical approaches to designing and analyzing Next-Generation Sequencing (NGS) run and resulting datasets, including “genomic and transcriptomic assembly, annotation, differential expression, phylogenomics and more.” Justin will be traveling back to Alabama (his home state) for the workshop, which will take place June 6-10, 2016.

March 11, 2016 – Justin has officially kicked off the semester, co-teaching ZOO 397806, Tópicos em Zoologia: Taxonomia Integrativa com Ênfase em Squamata (Topics in Zoology: Integrative Taxonomy with an Emphasis on Squamata) at UnB. Co-instructors are Justin Bagley, Maria Breitman, Fabricius Domingos, and Helga Weiderhecker, all four postdocs in the Herpetology Lab at UnB (CHUNB). This is the first time this course, or anything like it (as far as we know), has ever been taught. Wish us luck on a great semester teaching the theory and practice of integrative taxonomy! Also, check out the course website in English here.

January 21, 2016 – Justin submitted his phylogenetic comparative methods paper on sperm competition, mating system, and sexual size dimorphism (SSD) evolution in Centrarchidae to Journal of Evolutionary Biology! Wow, submitting two papers in the same week! Congratulations to Justin, Mark Pyron, and Stephen Jacquemin for excellent work getting this paper ready and out to review.  

January 16, 2016 – Justin submitted his comparative phylogeography paper on testing hypotheses of Panamanian frog and fish diversification using hierarchical ABC with model averaging to Journal of Evolutionary Biology! Congrats to Justin and Jerry on the first paper resulting from their collaboration with Mike Hickerson at CUNY.

November 27, 2015 – Justin has been accepted to the European Workshop on Genomics in Cesky Krumlov, Czechoslovakia, planned for January 10-23, 2016. He hopes to attend the meeting to learn genome assembly and Rad-seq experimental design and analysis workflows under Bill Cresko and Julian Catchen.

November 1-14, 2015 – Justin and Flor traveled to Manaus, situated in the heart of the Amazon forest, to conduct two weeks of molecular laboratory work at LEGAL / UFAM (Universidade Federal do Amazonas) and INPA (Instituto Nacional de Pesquisas da Amazônia). We successfully extracted and sequenced DNA from samples for our two ongoing postdoctoral research projects on Cerrado-Amazon phylogeography. This work conducted as part of collaborations with Tomas Hrbek & Izeni Farias (LEGAL) and Fernanda Werneck (INPA), who provided fun times and support during our trip.

September 2015 – Justin welcomes his first Brazilian undergraduate fellow, Ingrid Pinheiro, to the lab/BJT Project (Postdoc Project). Welcome Ingrid! After dreaming of becoming a marine biologist since childhood, Ingrid is now a Biology major at UnB with aspirations to develop a career as a professional organismal biologist. Despite having mainly microbiology lab experience under her belt, Ingrid has “hit the ground running” during her first weeks on the BJT Project. She has already started learning how to identify and process riverine fish samples, and she had a successful experience during her first field outing sampling fishes with Justin and Pedro in the southern DF region. 

June 20-27, 2015 – Flor and Justin went to Boulder, Colorado for the Mountain West Summer Institute, where Flor was a facilitator in the National Academies’ annual workshop on Scientific Teaching! Flor was able to take a leadership role in mentoring other professors (also with backgrounds and experience in teaching evolution) in active learning techniques and other ways of effectively teaching science at the university level.

May 22, 2015 – Our paper on phylogeography and species limits in Amatitlania convict cichlids (like the one shown above right) from Central America is now under review at Biological Journal of the Linnean Society! This paper presents findings based on new data that provide a novel perspective on the biogeography, morphological evolution, and taxonomy of these cichlids. This work is also awesome because is the direct result of a collaboration between the Johnson Lab (BYU), the Chakrabarty Lab (LSUMZ, Ichthyology Division), and the Tobler Lab (K-State), started during Justin’s PhD. 

March 5, 2015 – Our paper on multilocus coalescent-based species delimitation in the Poecilia sphenops species complex was formally accepted in PLoS OneCongrats to Justin, Fernando, Flor, Jerry and other co-authors for getting this paper, which was Justin’s 3rd dissertation chapter, out in a fine open-access journal!  Look for this paper to come out soon online, and for the data to be publicly available on Dryad.

December 19, 2014 – Justin’s electronic dissertation (ETD) has obtained final approval from the BYU Department of Biology and College of Life Sciences!  Justin’s dissertation PDF has now cleared all hoops to obtain final approval for being accepted at the library and disseminated across the world through BYU’s Electronic Theses & Dissertations system, as well as the ProQuest/UMI Dissertation Publishing system.

December 6, 2014 – Justin & Flor moved to Brasília to prepare for 2015-2017 postdocs at the University of Brasília (Universidade de Brasília), which is located in the Federal District (capital) of Brazil.  Many thanks to our family and friends in the US and to our Brazilian colleagues, but especially to Roger Ledo (and Rebecca) and Pedro Aquino, for help with the move!

November 26, 2014 – Justin was awarded a prestigious 3-year Science Without Borders (Ciências Sem Fronteiras) postdoctoral fellowship in Brazil based on his grant proposal to the Young Talent grant program.  The Young Talent program is funded by the Brazilian government, including CNPq (the Brazilian NSF analog), and is aimed in part at attracting talented young scientists to conduct 2- to 3-year research projects in Brazil in collaboration with a Brazilian host lab.  Starting in 2015, Dr. Bagley will be funded to conduct an integrative research project combining comparative phylogeography and phylogenetic community ecology of freshwater fishes of the Brazilian Cerrado, in collaboration with Francisco “Kiko” Langeani at UNESP, and Guarino Colli and Pedro De Podestà Uchôa de Aquino from UnB.  Wish Justin and Flor luck as they move to Brazil in December!

October 31, 2014 – Justin successfully defended his dissertation before the public and passed his final PhD oral examination without qualifications!!  Congrats!!!  Many thanks to advisor Jerry Johnson, and to the rest of the PhD committee including Byron Adams, Mark Belk, Keith Crandall, and Duke Rogers, for guidance, moral support, discussions, and comments on manuscripts.  There’s a new PhD in the lab/house!!

October 1, 2014 – Our manuscript on lizard reproductive mode evolution is now accepted at the Journal of Evolutionary Biology!  Congrats to Matt Watson, Rob Makowsky, and Justin for this, the first paper from their collaboration on phylogenetic comparative evolution of squamate lizards.

August 2014 – Justin submitted his first manuscript on the evolution of CA Poecilia to PLoS OneThis ms, his 3rd dissertation chapter, is focused on coalescent-based species delimitation in the P. sphenops species complex and has implications for taxonomy and conservation of Central American mollies.  The manuscript is presently going out for review.

April 2014 – Justin was recently hired as an Adjunct Instructor in the Utah Valley University Department of Biology.  He is scheduled to teach his first course, General Ecology, during the first block of Summer 2014.  This course includes lecture, active-learning techniques, and a field trip to learn about ecology first hand.

March 25, 2014 – Justin presented his work on species delimitation in mollies of the Poecilia sphenops species complex at the BYU Grad Expo.  Justin was honored to be selected to represent the BYU Department of Biology at the event.  He showed off an awesome poster, a tank of live P. sphenops molly breeds (related to silver mollies, lyretail mollies), and collecting gear, and told stories about field trips to Central America and new species discovered by his team and collaborators.

March 14, 2014 – Comparative phylogeography paper now moving forward at Ecology and Evolution, Johnson Lab making plans for Evolution 2014 in Raleigh.
The Editors of Ecology and Evolution have handed down a final acceptance decision on Justin and Jerry’s poeciliid comparative phylogeography paper, which is now in process/in press.  Also Justin and other members of the Johnson Lab are making travel, lodging and registration plans for the Evolution 2014 meeting this summer, from June 20-24–here we come Raleigh, NC!

February 27, 2014 – Comparative phylogeography paper now accepted at Ecology and Evolution pending minor revisions!
The Editor of Ecology and Evolution has decided to accept Justin and Jerry’s paper on the comparative phylogeography of three livebearing fish species (Alfaro cultratusPoecilia gillii, and Xenophallus umbratilis) in the lower Nicaraguan depression. This paper provides evidence for phylogeographic pseudoincongruence among these taxa, consistent with multiple independent evolutionary responses to biogeographical context in this region.

February 3, 2014 – Review paper now published online
The LCA phylogeography review is now published online for the first time in Biological Reviews.  Check it out here.

December 3, 2013 – Lower Central American phylogeography review is now accepted at Biological Reviews!
The fine journal Biological Reviews has now accepted Justin and Jerry’s manuscript entitled “Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas.”  It is a great privilege to have this dissertation manuscript (1st chapter) published in the second-highest ranking journal in Biology (impact factor=10.256)!  This paper will increase the visibility of Central America as a study system for phylogeography and historical biogeography.

Week of October 27, 2013 – finished another paper!
Justin and Ph.D. advisor Jerry Johnson have completed the final draft of Justin’s 2nd dissertation chapter manuscript on the comparative phylogeography of three Central American freshwater fishes, which they are presently preparing for Ecology and Evolution.

September 13, 2013 – Heterandria paper accepted at BMC Evolutionary Biology!
The journal BMC Evolutionary Biology has accepted Justin’s manuscript entitled, “Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota”, co-authored with Mike Sandel, Joe Travis, Maria de Lourdes Lozano-Vilano and Jerry Johnson.

August 16, 2013 – Hickerson lab training experience in NYC!
Justin traveled with Flor to New York to visit the laboratory of Mike Hickerson for a one-week training experience in multi-taxon multi-locus analysis using approximate Bayesian computation as implemented in MTML-msBayes.  Flor and Justin both enjoyed meeting and barbequing with all the members of the Hickerson lab!  New York was fantastic and they hope to travel there again soon!

July 2013 – Off to Albuquerque for the annual Joint Meeting of Ichthyologists and Herpetologists
Flor and Justin traveled with Jack Sites, Jr. and other colleagues and collaborators from BYU to Albuquerque, New Mexico to attend the JMIH meeting.  Justin and Flor gave talks on their dissertation research.  Justin particularly enjoyed seeing the “Fish Out of Water” Symposium,  collaborators from LSU and Auburn, and colleague Adam Leache, and meeting Mike Douglas.

June 2013 – Evolution meeting at Snowbird!
Justin and Flor traveled to Snowbird resort in Salt Lake City, Utah, along with the rest of the Johnson Lab and students from several other BYU Biology labs to participate in the international Evolution meeting.  Justin presented a poster to colleagues showcasing his work on the phylogeography of Heterandria formosa, while Flor presented a lightning talk on her work on Patagonian Liolaemus lizards.  Justin and Flor particularly enjoyed Dolph Schluter’s address to the ASN, and talking with colleagues Adam Leache, Brittany Barker, Daniel Ruzzante, and Rebecca Fuller.