Threespine Stickleback: A Model System For Evolutionary Genomics

Abstract

The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host–microbiome and host–parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Chromosomal inversions can limit adaptation to new environments

“…For instance, QTL underlying trait variation that is important for adaptive divergence across a major habitat transition have been mapped to chromosomal inversions in populations of threespine stickleback fish and littorina snails (stickleback: Peichel & Marques 2017; Liu et al 2021; littorina: Koch et al 2021). However, both of these species have recently been exposed to new niches imposing novel selection pressures, possibly favoring novel combinations of these inversion-linked QTL (stickleback: e.g., Bell & Foster 1994; Reid et al 2021; littorina: Morales et al 2019).…”

Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

“…Here, we show that ScISOr-Seq in the context of a scRNAseq experiment allows rapid 3′-UTR annotation in threespine stickleback fish ( Gasterosteus aculeatus ). This fish has long been a focus of study in behavior, ecology, and evolution ( Bell and Foster 1994 ; Colosimo et al 2004 ; Cresko et al 2004 , 2007 ; Shapiro et al 2004 ; Hohenlohe et al 2010 ; Reid et al 2021 ), and is now a nascent system for biomedical research ( Miller et al 2007 ; Gardell et al 2017 ; Small et al 2017 ; Beck et al 2020 , 2021 ; Fuess et al 2021 ). Although stickleback has a well-assembled genome, its 3′-UTR annotations are incomplete which limits scRNAseq’s utility.…”

Gene expression in male and female stickleback from populations with convergent and divergent throat coloration

“…The subject of the present work, the threespine stickleback, is an important evolutionary model (McKinnon et al, 2019 ; McKinnon & Rundle, 2002 ; Reid et al, 2021 ). Stickleback color pattern evolution has been investigated with regard to the closely related topics of sexual selection (e.g., Milinski & Bakker, 1990 ; Tinghitella et al, 2018 ; Wright et al, 2015 ), parental care (Candolin & Tukiainen, 2015 ), and speciation (e.g., Blouw & Hagen, 1990 ; Boughman, 2001 ; Marques et al, 2017 ), as well as crypsis (e.g., Greenwood et al, 2012 ; Gygax et al, 2018 ).…”