Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish

Reid S. Brennan, Timothy M. Healy, Heather J. Bryant, Man Van La, Patricia M. Schulte, Andrew Whitehead

Preprint posted on 27 January 2018

Article now published in Molecular Biology and Evolution at

A powerful new approach finds that adaptive divergence along a salinity gradient in an estuarine fish is driven by natural selection for genes linked to key physiological traits

Selected by Andy Turko

Key findings

Understanding the genetic underpinnings of phenotypic divergence and local adaptation is a fundamental goal of evolutionary biology. In a huge undertaking that combines morphological and physiological measurements alongside whole genome sequencing of over 300 Atlantic killifish collected from the Potomac River and Chesapeake Bay, Reid Brennan and colleagues have made major headway towards identifying the genetic basis of local adaptation along a riverine gradient. Upstream habitats were characterized by oxygen-rich freshwater, while downstream estuary sites were saltier and more hypoxic. By combining two methods of genomic analysis – an association study that links genes to phenotypes, followed by a selection scan to determine which genetic regions are favoured by natural selection – the authors identified sets of genes that were both under selection in different habitats and linked to population level differences in osmoregulation, hypoxia tolerance, and metabolic rate. Particularly interesting was the finding that the three physiological variables measured were not correlated with one another and were linked to non-overlapping sets of genes, suggesting these traits are independently under selection.

What I liked about this preprint

I was really impressed by the sheer effort required to collect a broad range of phenotypic and genomic data on several hundred individual fish. Furthermore, by working across levels of organization and linking genomic data to whole-animal physiological traits, the authors present a comprehensive picture of freshwater colonization by killifish. These results indicate selection on key pathways that have long been hypothesized to be important for adaptive divergence between fresh and brackish water habitats.

Future directions

The modularity of the three physiological traits that were measured is curious given recent reports suggesting that traits such as hypoxia tolerance and metabolic rate are often linked. Perhaps this trait independence is key to the broad environmental/geographic range (e.g. eurythermal, euryhaline) of Atlantic killifish?

I was initially surprised that “only” 16 SNPs popped out as phenotypically important and under selection, but is this really a low number to detect given that many genes of low effect are responsible for whole-animal traits? Future studies examining other environmental transitions and different species are needed before we have a sense of how many SNPs under selection would be “normal”.

Several ionoregulatory genes were found to be under selection in freshwater-adapted killifish, leading the authors to develop a hypothesized “sodium uptake metabolon” that would increase sodium ion uptake from the environment and minimize paracellular loss. Looking back, Andrew Whitehead said “I wish we had measured sodium uptake as a trait. We’ll have to save that for another study.”

Figure 5 from Brennan et al.

Tags: fundulus, gwas, ion regulation, local adaptation, mummichog, salinity tolerance

Posted on: 14 February 2018 , updated on: 23 February 2018

Read preprint (1 votes)

Have your say

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here

preLists in the evolutionary biology category:

EMBO | EMBL Symposium: The organism and its environment

This preList contains preprints discussed during the 'EMBO | EMBL Symposium: The organism and its environment', organised at EMBL Heidelberg, Germany (May 2023).


List by Girish Kale

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.


List by Martin Estermann

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.


List by Alex Eve

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.


List by Ana Dorrego-Rivas

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20


List by Maiko Kitaoka et al.

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome


List by Hiral Shah

COVID-19 / SARS-CoV-2 preprints

List of important preprints dealing with the ongoing coronavirus outbreak. See for additional resources and timeline, and for full list of bioRxiv and medRxiv preprints on this topic


List by Dey Lab, Zhang-He Goh


SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.


List by Alex Eve

Pattern formation during development

The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.


List by Alexa Sadier