PT  - JOURNAL ARTICLE
AU  - Joseph A. McGirr
AU  - Christopher H. Martin
TI  - Unique genetic variants underlie parallel gene expression within a young adaptive radiation despite specialization on highly divergent resources
AID  - 10.1101/180190
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 180190
4099  - http://biorxiv.org/content/early/2017/08/24/180190.short
4100  - http://biorxiv.org/content/early/2017/08/24/180190.full
AB  - There are many cases of parallel gene expression underlying the evolution of convergent niche specialization, but parallel expression could also underlie divergent specialization. We investigated divergence in gene expression and genetic variation across three sympatric Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist and two derived specialists adapted to novel niches – a ‘scale-eater’ and a ‘snaileater.’ We sampled total mRNA from all three species at two early developmental stages and compared gene expression with whole-genome genetic differentiation between all three species. 82% of genes that were differentially expressed between snail-eaters and generalists were up or downregulated in the same direction between scale-eaters and generalists; however, there were no shared fixed variants underlying this parallel expression. These genes showing parallel expression did not exhibit increased developmental constraints, but were enriched for effects on metabolic processes. Alternatively, genes showing divergent expression were enriched for effects on cranial skeleton development and pigment biosynthesis, reflecting the most divergent phenotypes observed between specialist species. Our findings reveal that convergent adaptation to higher trophic levels between divergent niche specialists through shared genetic pathways is governed by unique genetic variants.