Introducing Dr. Matt Jones!

Congratulations to Matt Jones for successfully defending his PhD!

His PhD was truly inspiring research — combining extensive genome sequencing and analysis, functional characterization, detailed population genetic modeling, and simulations to understand the evolution of coat color change in snowshoe hares. His first author Science paper this summer was one of the most exciting and thorough single studies I have had the pleasure to work on, and that was just Chapter 2 of 4…

Matt is off to ASU in the spring to work with Jeff Jensen on population genomic inference from temporal samples.

The Evolution of Seasonal Camouflage in Snowshoe Hares

Our most recent work on the genetic basis of polymorphic seasonal camouflage in snowshoe hares is now out in Science. Outstanding effort by Good lab grad Matt Jones, with crucial collaborations from hare whisperer Scott Mills (UM), Zef Melo-Ferreira (CIBIO), Paulo Alves (CIBIO), Jeff Jensen (ASU/EPFL), and others.

This one was many years in the making.

The paper is available here

Also check out a companion video we produced, blog post by Liz Pennisi, and the UM press release

The Evolution of Polymorphic Hybrid Incompatibilities

We have published a new study in Genetics on the genetic underpinnings of polymorphic hybrid incompatibilities in mice. Led by recent postdoc alum Dr. Erica Larson (University of Denver), this study combines QTL mapping, phylo- & population genomics, with whole genome sperm sequencing to unravel the extent and causes of variable reproductive isolation between lineages of house mice. 

The early online version is available here

Seasonal Coat Color Paper in Science.

Very happy to say that we have a new paper in Science on mapping coat color polymorphisms across 8 species on to global environmental variation, as a means to understand evolutionary responses to climate change. This was a large collaborative study conceived of and led by Scott Mills and his awesome coat color team. 

Check our the paper here

This work received extensive press and provides a nice demonstration of the power and utility of museum collections as crucial repositories of genotypic and phenotypic diversity.

PhD Candidate Mafalda Ferreira receives research award!

Mafalda Ferreira (UPorto) was a granted a Portuguese national award for outstanding achievement during the academic year of 2013/2014, for her Masters’ thesis and defense (graded 20 out of 20). Her work focused on the transcriptional profiling of seasonal molts in snowshoe hares as published in Ferreira et al. 2017, Molecular Ecology. She is now pursing a PhD on the evolution of seasonal camouflage in white-tailed jackrabbits. Outstanding work Mafalda!

Paper in Nature Communications!

Ryan Bracewell's tour de force study showing a coupling between neo-sex chromosome evolution and incipient speciation in bark beetles has been published in Nature Communications!

Over 1,000 crosses, several years of field work, extensive whole genome & RAD sequencing, reproductive and phermonal phenotypes, functional characterizing of sex-specific transcriptomes -- this was a side project during Ryan's dissertation. Well done.

Read the open source manuscript here.

Postdoctoral position(s) available!

The Good lab is searching for 1-2 postdocs focused on the evolution of seasonal change. One of these positions will be announced in the next fews weeks. The other is open now as an exciting collaboration with Jeff Jensen at ASU to develop novel methods to analyze evolutionary change through time:

The Good Lab (University of Montana, and Jensen Lab (Arizona State University, are searching for a joint postdoc to investigate the population genetics of seasonally changing coat color in mammalian systems. This project has two years of funding, with one year being spent at UM focused upon data collection and generation, and one year being spent at ASU focused upon statistical method development and analysis. There is also potential for a third year extension. An important focal point of this work will be the development of improved methodology for the analysis of time-series data.

More details HERE

New NSF EPSCoR Grant on genome-to-phenome in natural populations.

I am pleased to announce that the University of Montana (Cheviron, Fishman, Good, et al) and the University of Nebraska (Storz, Montooth, Meiklejohn) just received a large training and research grant through the NSF EPSCoR Track II program focused on genome-to-phenome studies in natural populations. This support will allow us to establish a synergistic training and research network of evolutionary geneticists between these two groups. Research activities of the UNVEIL (Using Natural Variation to Educate, Innovate and Lead) network will center around core projects focused on adaptation to spatiotemporal environmental variation in mammalian and plant systems. There will be opportunities for graduate and postdoctoral support under this project (more announcements on this soon). Please contact me if you are interested.

Fellowships, Grants, Degrees, and Papers!

I have been seriously delinquent on sharing some terrific lab news over the last few action packed months! Our outstanding grad students have landed several grants and fellowships over the past few months. Check this out:

Emily Kopania received a prestigious Graduate Research Fellowship from the National Science Foundation to support her research on genome evolution and speciation in mice. Emily also received travel grants from the Society of Molecular Biology and Evolution and the Drollinger-Dial Foundation and a Rosemary Grant Award from the Society for the Study of Evolution. She also published her first co-authored paper in Mammalian Genome. 

Mafalda Ferreira received a Rosemary Grant Award from the Society for the Study of Evolution and published a first authored paper in Molecular Ecology.

Matt Jones received a Doctoral Dissertation Improvement Grant from the National Science Foundation in support of his research on seasonal camouflage in snowshoe hares. Matt also received travel grants from the American Society of Mammalogists and the Society for the Study of Evolution.

Nathanael Herrera received travel grants from the Drollinger-Dial Foundation and American Society of Mammalogists.

Zak Clare-Salzler defended his Master's Thesis on the evolution of seasonal change in dwarf hamsters. Hard work and perseverance!   

Tremendous work everyone!



New GBE paper on pseudoreferences!

We have a new paper in the March issue of GBE on developing pseudoreference approaches to facilitate comparative genomic studies between species with and without established references genomes. The work was led by former lab postdoc Brice Sarver (now at Amby Genetics) and includes both the development of flexible analytical pipelines to generate pseudoreferences (available on Github as pseudo-it), and the generation of new whole exome sequence data from 11 species of mice (Mus) which we used to examine the evolutionary history of this group.

The methods can be implemented through the pseudo-it package available here

Check out the paper here.


New papers in MBE, GBE, and Evolution!

We have published three new studies related to hybridization and speciation. 

Our study on the disruption of gene expression during spermatogenesis in mice led by postdoc Erica Larson has been accepted in Molecular Biology and Evolution. We present the most detailed assessment of hybrid gene expression across mouse spermatogenesis to date. Aided by novel FACS cell-specific expression data, we find evidence for disruption of X chromosome regulation at multiple stages of spermatogenesis.

Our study on the disruption of gene expression during placental development in hamsters led by recent PhD graduate Tom Brekke has been published in Evolution. In this work we present evidence for extensive disruption of genomic imprinting associated with placental and embryonic overgrowth in hybrid dwarf hamsters. 

Finally, a collaborative study examining the dynamics of mitochondrial introgression in chipmunks has been published in Genome Biology and Evolution. This work was led by lab postdoc Brice Sarver as part of his dissertation work with Jack Sullivan at Idaho. 

So three papers (in three of our favorite journals), focusing on three different rodent systems, integrating functional genomics, population genetics, and developmental biology. Fun stuff!

Genetics paper!

Our study on the evolution of gene expression, protein sequence, and methylation during spermatogenesis led by postdoc Erica Larson in my lab has been published in Genetics. We present the most developmentally detailed assessment of molecular evolution across mouse spermatogenesis to date, aided by our novel FACS cell-specific expression data and genome-wide sperm methylome data led by our collaborators Matt Dean and Andrew Smith at USC.

Genomics of Hybridization

Molecular Ecology has published a special issue on the Genomics of Hybridization, edited by Richard Abbott, Nick Barton, and myself. I thank all of the authors for their contributions and I am very proud of this collection of papers. We have dedicated to the memory of Rick Harrison, who contributed a review with Erica Larson to the issue.


In fond memory of two outstanding and influential scientists.

In April we lost two outstanding scientists and tremendous role models.

Rick Harrison (Cornell University) was a true giant in evolutionary biology, and his ties and influence on my career and lab were diverse and profound. In my opinion, there is no one in the field of speciation over the past several decades whose voice has resonated more clearly and consistently than Rick's.  His insights, thoughtfulness, and friendship will be missed. 

We were in the final editing stages of a special issue on the Genomics of Hybridization (see post above) when Rick suddenly passed away. We have dedicated this issue to his memory. At the last minute, we were also able to include a beautiful and touching In Memorium dedicated to Rick's legacy. This pretty much says it all:

Paul Joyce (University of Idaho) was a gifted mathematician and teacher who made substantial contributions to the genetics of adaptation, population genetics, phylogenetics, and microbial ecology. Paul had more recently taken an active leadership role in administration, serving as the Dean of the College of Science at the University of Idaho. Through all of this Paul remained a gifted and committed teacher, and was set to receive the honor of University of Idaho Distinguished Professor. Paul was a valued member of my MS committee and one of the most gracious and humble people that I have ever had the privilege to know. He will be greatly missed.


Congratulations to Dr. Brekke!

Founding lab member Tom Brekke has defended his PhD on hybrid inviability, genomic imprinting, and speciation in dwarf hamsters! His dissertation combines a very impressive series of genetic and transcriptomic studies on placental overgrowth and genomic imprinting. Tom dove into the Phodopus system and made a number of substantial insights into the evolution of imprinting and the genetics of speciation. His first chapter was published in Evolution (Brekke and Good, 2014) with two subsequent papers near submission. His impressive work is everything that a speciation genetics dissertation should be: using diverse cutting-edge approaches to dive deep into the genetic basis of an important and unresolved issue in evolution. Within the last two months Tom has defended his PhD, submitted his dissertation, got married, moved to England to start a post doc, and presented his work as a finalist in the Evolution 2016 - WD Hamilton Award Symposium. Wow!

Dr. Bracewell!

Ryan Bracewell has defended his PhD! Ryan has moved on to UC Berkeley to work with Doris Bachtrog. His dissertation ranks among the more impressive that I have seen, including substantial interdisciplinary work (genomics, quantitative genetics, ecological experiments, etc) on speciation and symbiosis in bark beetles. To (loosely) quote Graham Coop,  "Chainsaws and genetics, brilliant!". Stay tuned for forthcoming publications.