Following Rob’s lead, today I am sharing my top 3 posts of 2015 based on the number of pageviews they received. I’m also throwing in one of the posts I had the most fun researching and writing. Thank you to all the readers who have read, liked, shared, and commented The Molecular Ecologist posts last year. We have some exciting things planned for the blog in 2016, and hope y’all will continue to support the site!
1. Gene expression analyses- are we doing it wrong?
Gene expression! Image from the University of Michigan
This post from June 29th, 2015 highlighted three preprints focused on potential problems with current RNA-seq/gene expression analyses. For an in-depth review on the dangers of batch effects, check out this post by my fellow TME contributor Noah Snyder-Mackler. Improvements to how we analyze transcriptomic data continue to roll out. One example is a new preprint by Soneson et al. on F1000Research showing gene-level rather than transcript-level analyses are superior in terms of performance and interpretation.
2. Next generation sequencing: more replicates or more sequence?
In my May 11th, 2015 post, I wrote about whether researchers should shoot for more replicates or more sequence depth when testing differential gene expression. Although the results may vary depending on the organism or experimental treatment of interest, and some questions still require deep sequencing (i.e. differential expression of exons, transcript-specific expression), according to the results of Liu et al., adding biological replicates is generally more powerful than adding sequencing depth for transcriptomic studies.
3. Hybrid speciation is for the birds (and plants, reptiles, fish, and insects)
The Italian sparrow, Passer italiae. Photo by Robert Parmiggiani
This post was published on Jan 5th, 2015 and I suspect it got a lot of pageviews because it was the blog’s first post back after the 2014 holidays, people were back in the office getting ready to do some science, AND because hybrid speciation is so cool! I had a lot of fun doing the background research for this post. It started with a great quote by R. A. Fisher who once called hybridization ‘‘the grossest blunder in sexual preference which we can conceive of an animal making” and focused on two papers published in 2014 (Trier et al. and Hermansen et al.) that empirically tested for intrinsic reproductive isolation among the homoploid hybrid Italian sparrow and its parental species, the Spanish and house sparrows, with which the Italian sparrow overlaps geographically.
BONUS: A love letter to sponges
The azure vase sponge, Callyspongia plicifera. Photo by S. Ong
Sponges are my primary study system but I also work on corals, brittle stars, Tigriopus copepods, and other marine invertebrates. On March 23rd, 2015 I wrote a post highlighting some of the cool ecology and evolution research focused on sponges. This year, I wrote about the controversial question of whether sponges or ctenophores are the earliest branching animal lineage. The debate continues to evolve- check out this News and Views Nature piece in which three evolutionary biologist weigh in.