A while back, we were invited by Molecular Ecology to write a mini review for a special issue on the ecology gene expression. We chose to focus on how recently developed technologies and tools for assembling genomes and quantifying gene expression at single-cell resolution offer great potential for researchers conducting evolutionary ecology studies in non-model organisms. The paper is now published and can be found here

and … here it is, on early view at Genome Research: https://genome.cshlp.org/content/early/2025/04/10/gr.280377.124.abstract

Our paper comprehensively assessing the performance of genome annotation methods, “Building better genome annotations across the tree of life” has officially been accepted at Genome Research. It should go live in about a month

With genome assembly becoming relatively straightforward and affordable, the biggest challenge for conducting evolutionary and functional analyses with a new genome is annotating that genome. There are many different tools to choose from, but … given that most past performance assessments (or descriptions of new annotation methods) have only been tested on a few (mostly model) organisms, it is difficult to know whether a method will work well for “my genome.” To being tackling that problem, we evaluated the performance of several genome annotation methods across 21 species spanning a large swath of the tree of life. The results of this project have turned into a manuscript that is now available on bioRxiv at: https://www.biorxiv.org/content/10.1101/2024.04.12.589245v1 . Feedback is welcome!

Our paper using genomic data to demonstrate ecotone speciation in an African rainforest lizard is officially out in Molecular Ecology. In it, we demonstrate that gene flow between rainforest and rainforest-savanna mosaic (ecotone) populations has ceased, paralleling morphological and physiological divergence. You can find it [here]

The “gold standard” for gene-level expression analysis for genome-enabled species has been almost exclusively moderate-sized single end (SE) reads … just see how many mouse studies have used 1×75 as an RNA-seq strategy. @timsackton and I had an intuition that short paired-end (PE) reads should achieve greater alignment specificity than the SE, and that should lead to more robust expression estimates. As the costs of sequencing on current Illumina insruments are per base … that means that PE 2×40 reads could be achieved at a cost identical to SE 1×75. So, we pulled down sequencing data for SRA from 12 different projects with long paired-end reads, spanning a variety of model organisms with well-annotated genomes. We then evaluated the ability of 1×75 and 2×40 (as well as 1×125) to reproduce expression estimates and downstream differential expression results relative to the 2×125 “gold standard.” Lo and behold, 2×40 consistent outperformed 1×75 and in many cases outperformed 1×125. This paper came out at the end of 2020 in BMC Bioinformatics, with help from our co-author John Gaspar. [link]