We are pleased to announce our manuscript describing a study of phylogenomic heterogeneity across turtle evolution is available on bioRxiv. We used complete genome assemblies and next generation sequences to build a large database of genes and sites to investigate patterns underlying gene tree-species tree discordance in the phylogenomic estimation of turtles. NAU SICCS Ph.D. student Simone Gable is the first author of this manuscript. Congratulations, Simone!
Summer Update
The lab has been working remotely since March, but there are still a lot of updates!
1) Our Mammalian Cancer Gene manuscript was published in Molecular Biology and Evolution and is available open access. We looked at duplication patterns in 548 human cancer genes across 63 mammalian genome assemblies and found that across mammals longevity predicts the copy numbers of tumor suppressor genes that contain both somatic and germline mutations in human cancers. This suggests that the evolution of long lifespans is accompanied by strong selection against both sporadic and hereditary cancers in mammals.
2) The tuatara genome paper was published in Nature! This was a multi-year internationally collaborative effort led by Dr. Neil Gemmell from University of Otago in New Zealand. The Tollis Lab played a large role in this consortium, and led the phylogenomic and molecular clock analyses. We used full-scale comparative genomic data for the first time to determine that the closest relatives of the tuatara are lizards and snakes (squamates), and that these groups last shared a common ancestor ~250 million years ago. We also show that contrary to previous claims, the tuatara has evolved quite slowly at the molecular level, lending at least some evidence to the idea that it is indeed a “living fossil”. In addition to publishing the manuscript, Nature produced a very nice News and Notes piece that describes the effort and results of this project.
3) We have a new preprint available, that using elephant genomics to understand why elephant species are differentially susceptible to many types of diseases, including herpesvirus, tuberculosis, and cancer. The manuscript is in review now.
4) Another manuscript we worked on is currently available as a preprint as well, which describes the genome assembly of the eastern fence lizard (Sceloporus undulatus). Our contribution to this work included sequencing the transcriptome of this lizard, which was used to annotate the highly contiguous and high quality genome assembly. This manuscript is in review now.
New Mammalian Cancer Gene Duplications preprint available!
Our manuscript that looks at cancer gene duplications across mammals is available on bioRxiv.
Tuatara genome preprint now available
The manuscript describing the genome of the tuatara can now be accessed on bioRxiv.
Payton Smith = First Prize!
Freshman undergraduate researcher Payton Smith, an Interns 2 Scholars recipient, was also awarded first place in the Research Category for poster presentations within the College of Engineering, Informatics, and Applied Sciences at the NAU-wide Undergraduate Symposium!
Her poster is entitled: “Phylogenomics of Squamates using Many High-Confidence Single Copy Orthologs”. We are so proud of her!
Whale genomes paper now available!
Our paper “Return to the Sea, Get Huge, Beat Cancer” has been published in Molecular Biology and Evolution. The paper is open access and can be read by anybody.
You can read the press release from NAU here.
Image of Salt, an adult female humpback whale, taken by the Center for Coastal Studies under NOAA research permit 16325.
Humpback whale genome!
The humpback whale genome paper, which includes comparative analysis with 10 cetacean and 28 placental mammalian genomes, with a focus on the evolution of cancer suppression, has been accepted by Molecular Biology and Evolution!
We present the first published genome sequence for one of Earth’s most loved giants. The genome sequence can be downloaded from NCBI.