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.