In collaboration with the Cresko Lab at University of Oregon, we have now assembled 7 complete genomes of syngnathid fishes. The complete genomes are available from NCBI under BioProject PRJNA851781. The genomes were assembled using a combination of PacBio Sequel II Hi-Fi sequencing and Hi-C library sequencing to produce chromosome-level assemblies. These genomes are part of our goal to ensure that we have at least one high-quality genome for each major lineage within the fish family Syngnathidae. Special thanks to Balan Ramesh and Clay Small for taking the lead in assembling the genomes and to the National Science Foundation for funding this work. Many more genomes are yet to come.
New Lab Members
Fall 2021 is an exciting time for the Jones Lab, as we welcome four new lab members! Hannah Kemp is an undergraduate student working primarily on killifish. Elyse Barker and Megean Myers are new Ph.D. students in the lab. Their projects will focus on issues related to the evolution of male pregnancy, sexual selection, and microbiomes in syngnathid fishes. Dr. Balan Ramesh is a new postdoctoral scientist in the lab. He will be spearheading the bioinformatics analysis of the many new syngnathid genomes that we plan to sequence over the next several years.
New Funding
The Jones Lab has been fortunate to receive two new grants from the National Science Foundation in 2020. The first grant, “The Genomics of Sexual Selection in Pipefishes and Seahorses”, will fund a series of projects aimed at investigating the genome-level effects of sexual selection. The second grant, in collaboration with Bill Cresko’s lab at the University of Oregon, is entitled “The Evo-Devo of Male Pregnancy and Its Effects on the Brood Pouch Microbiome”. This project endeavors to understand the evolution and development of the male’s brood pouch, as well as how the evolution of the pouch shapes the male-pregnancy microbiome.
Moving On…
Simulating Evolution with C++
The C++ programming language has a reputation as tough one to learn, but the difficulty level is often exaggerated. For basic evolutionary models, a fairly modest skill set is good enough, and learning C++ prepares the mind to learn other programming languages like Perl and Python. Check out my tutorial on using C++ to build evolutionary models for a very basic introduction. The book assumes no prior programming knowledge and can be downloaded as a free pdf from my publications page.
G-matrix Simulator Note
Our new program note describing software to simulate the evolution of the additive genetic variance-covariance matrix (the G-matrix) is now online at the Journal of Heredity. Follow this link to the paper, and you too can experience, to quote one of the referees, “the magics of G-matrix evolution”!
Sarah Flanagan’s New Job
Dr. Sarah Flanagan, who earned her Ph.D. in the Jones Lab in 2016, has accepted a faculty job in the School of Biological Sciences at the University of Canterbury in Christchurch, New Zealand! After leaving the Jones Lab, Sarah spent two productive years as a postdoctoral fellow at NIMBioS (National Institute for Mathematical and Biological Synthesis). She will start her new faculty position in the fall of 2018. Congratulations on your new job, Sarah!
We’ve Moved!
The Jones Lab has moved to the University of Idaho! After 13 great years at Texas A&M University, the time came to move along and experience new opportunities. The Department of Biological Sciences will be a great home for the Jones Lab, and we’re looking forward to continuing our work in this amazing new setting! Use the internet to find out more about the Department of Biological Sciences, the University of Idaho, the town of Moscow, and the incredible Palouse region.
Syngnathid Genomes!
Seahorses and pipefish have finally entered the post-genomic era with the publication of two complete genomes in December of 2016. Lin et al. (2016) published the genome sequence of the tiger tail seahorse (Hippocampus comes) in Nature, and Small et al. (2016) published the genome sequence of the Gulf pipefish (Syngnathus scovelli) in Genome Biology. In addition to providing interesting insights about gene loss and duplications related to key adaptations in this group of fishes, these genomes open many new doors in syngnathid research.
Emily’s Seahorse Research
The research of former graduate student Emily Rose (now a Visiting Assistant Professor at University of Tampa) graced the cover of the November 2016 issue of the Journal of Heredity. She examined the phylogenetic placement of a seahorse population that inhabits an isolated, saltwater lake in the Bahamas. See the cover here.
The Jones Lab 