Site pleiotropy of a stickleback Bmp6 enhancer

Rowley, Alyssa J.; Square, Tyler A.; Miller, Craig T.

doi:10.1016/j.ydbio.2022.09.012

Cited by 2 publications

(1 citation statement)

References 43 publications

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“…Furthermore, the strict one‐to‐one trait QTL significance method for detecting parallel evolution does not include consideration of the hierarchy and diversity of convergence and parallel evolution, which can span morphological traits, ecotypes, performance, or even fitness (James et al., 2020 ; Rosenblum et al., 2014 ; Stern, 2013 ). Ultimately, we argue that our method of quantifying parallel evolution provides a more accurate view of the process and better captures the frequency of reuse of adaptive genetic variation in nature, given the ubiquity of pleiotropy (Cerca et al., 2023 ; Rowley et al., 2022 ; Sivakumaran et al., 2011 ; Solovieff et al., 2013 ) and gene flow and introgression among rapidly radiating species in nature (Gillespie et al., 2020 ; Martin & Richards, 2019 ; Poelstra et al., 2018 ; Richards et al., 2018 , 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Parallel evolution of integrated craniofacial traits in trophic specialist pupfishes

St. John,

Dunker,

Richards

et al. 2024

Ecology and Evolution

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Populations may adapt to similar environments via parallel or non‐parallel genetic changes, but the frequency of these alternative mechanisms and underlying contributing factors are still poorly understood outside model systems. We used QTL mapping to investigate the genetic basis of highly divergent craniofacial traits between the scale‐eater (Cyprinodon desquamator) and molluscivore (C. brontotheroides) pupfish adapting to two different hypersaline lake environments on San Salvador Island, Bahamas. We lab‐reared F2 scale‐eater x molluscivore intercrosses from two different lake populations, estimated linkage maps, scanned for significant QTL for 29 skeletal and craniofacial traits, female mate preference, and sex. We compared the location of QTL between lakes to quantify parallel and non‐parallel genetic changes. We detected significant QTL for six craniofacial traits in at least one lake. However, nearly all shared QTL loci were associated with a different craniofacial trait within each lake. Therefore, our estimate of parallel evolution of craniofacial genetic architecture could range from one out of six identical trait QTL (low parallelism) to five out of six integrated trait QTL (high parallelism). We suggest that pleiotropy and trait integration can affect estimates of parallel evolution, particularly within rapid radiations. We also observed increased adaptive introgression in shared QTL regions, suggesting that gene flow contributed to parallel evolution. Overall, our results suggest that the same genomic regions may contribute to parallel adaptation across integrated suites of craniofacial traits, rather than specific traits, and highlight the need for a more expansive definition of parallel evolution.

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