Summer 2024 updates

This has been a very productive summer for the Tollis Lab!

Congratulations, Dr. Simone Gable!

Simone Gable successfully defended her dissertation, entitled “Forest for the Trees: A Genome-Wide Perspective on Reptile Evolution”! Simone is the first PhD student to graduate out of the lab, joining in Fall 2020 and completing her studies in a brisk four years. She will be moving on to Arizona State University to work on the EarthBioGenome Project as a postdoc.

PhD student Vahid Fard passed his comprehensive exam, successfully defending his literature review on cancer evolution.

CR1 Retrotransposon Paper Published

Our paper on CR1 retrotransposon evolution across reptiles with a novel focus on squamates, first-authored by Simone Gable and co-authored with NAU undergrads Jasmine Mendez, Nicholas Bushroe, and Adam Wilson, was published this summer in Genome Biology and Evolution. This was the first look at CR1 diversity and dynamics in reptiles since 2015, and in her dissertation work Simone examined 350 vertebrate genomes and discovered several new-to-science subfamilies of CR1 existed across squamate genomes, and finds supports for an extraordinarily rapid rate of genomic evolution in squamates compared to other reptiles (birds, crocodilians, and turtles).

Evolution 2024 (Montreal, Canada)

Two Tollis Lab talks were featured at the Evolution Meeting in Montreal, Canada!

The first was given by Sophie Matthews, a PhD student from the University of Galway who visited our lab in Fall 2023 to study gene duplications and cancer prevalence across mammals. She spoke about her project which we hope to publish soon. Sophie’s talk was selected to be featured in the Cancer Evolution Across Scales symposium.

Followed by Simone Gable in the Systematics II symposium, who spoke about her dissertation research on squamate phylogenomics.

New Squamate Genomics Review Paper

NAU PhD student Simone Gable has published a dissertation chapter that reviews squamate genomics and its utility for phylogenomics and genome evolution studies. The article was published in the journal Genes and is entitled “The State of Squamate Genomics: Past Present and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order”.

The coauthors include Nicholas Bushroe, Jasmine Mendez, and Adam Wilson, who are current or former NAU undergraduate students who contributed to the genomics and meta analyses in the paper, and Michael Byars, who was a research technician in the lab until 2021. Congratulations Simone and coauthors!

The Tollis Lab is NSF Funded!

The Tollis Lab is part of a $1.5 million dollar project awarded by the National Science Foundation entitled “Collaborative Research: The Genomic Basis of Evolutionary Innovations in the Squamate Tree of Life” (DEB2323124), along with collaborators Dr. Frank Burbrink at the American Museum of Natural History and Dr. Tiago Simões at Princeton University.

We will combine extensive phenotypic sampling from 370 living and fossil squamates with extensive genomic sampling of species from >90% of squamate families (including the de novo sequencing and assembly of >100 genomes), with the goal of identifying branches in the squamate phylogeny where the are observed changes in the rate of both phenotypes and genomic regions.

The project will take three years and we will be hiring postdocs for each institution (NAU, AMNH, Princeton)! More soon!

Undergraduate Research Awards for Tollis Lab Students in 2023!!!

We would like to congratulate Nicholas Bushroe and Rebecca Chavez who have both been awarded Hooper Undergraduate Research Awards (HURA) !

Nicholas will be studying the relationship between transposable element activity and phenotypic evolution in squamates, and Rebecca will be researching the relationship between transposable element activity and cancer prevalence across mammals. Way to go!

Prestigious NAU Undergraduate Research Award Goes To: Jasmine Mendez and Adam Wilson!

NAU undergraduate researchers Jasmine Mendez and Adam Wilson have been awarded the Hooper Undergraduate Research Award for their proposal The Selfish Sequences in Squamate Genomes: Evolutionary Dynamics of CR1 and LINE-1 non-LTR Retrotransposons! The award will provide financial support and software licenses to carry out their already-quite-successful research during 2022-2023. Congratulations!

Our Turtle Phylogenomics manuscript is available!

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.