Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish
Posted on: 14 February 2018 , updated on: 23 February 2018
Preprint posted on 27 January 2018
Article now published in Molecular Biology and Evolution at http://dx.doi.org/10.1093/molbev/msy154
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
Categories: evolutionary biology, genomics, physiology, zoology
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.”
(1 votes) Sign up to customise the site to your preferences and to receive alerts
Register hereAlso in the evolutionary biology category:
Geometric analysis of airway trees shows that lung anatomy evolved to enable explosive ventilation and prevent barotrauma in cetaceans
Sarah Young-Veenstra
Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium
Rodrigo Senovilla-Ganzo
Modular control of time and space during vertebrate axis segmentation
AND
Natural genetic variation quantitatively regulates heart rate and dimension
Girish Kale, Jennifer Ann Black
Also in the genomics category:
A fine kinetic balance of interactions directs transcription factor hubs to genes
Deevitha Balasubramanian
Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium
Rodrigo Senovilla-Ganzo
Enhancer cooperativity can compensate for loss of activity over large genomic distances
Milan Antonovic
Also in the physiology category:
Investigating Mechanically Activated Currents from Trigeminal Neurons of Non-Human Primates
Vanessa Ehlers
Geometric analysis of airway trees shows that lung anatomy evolved to enable explosive ventilation and prevent barotrauma in cetaceans
Sarah Young-Veenstra
Precision Farming in Aquaculture: Use of a non-invasive, AI-powered real-time automated behavioural monitoring approach to predict gill health and improve welfare in Atlantic salmon (Salmo salar) aquaculture farms
Jasmine Talevi
Also in the zoology category:
Geometric analysis of airway trees shows that lung anatomy evolved to enable explosive ventilation and prevent barotrauma in cetaceans
Sarah Young-Veenstra
Blue appendages and temperature acclimation increase survival during acute heat stress in the upside-down jellyfish, Cassiopea xamachana
Maitri Manjunath
How the liver contributes to stomach warming in the endothermic white shark Carcharodon carcharias
Sarah Young-Veenstra
preLists in the evolutionary biology category:
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
| List by | Alex Eve, Katherine Brown |
preLights peer support – preprints of interest
This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.
| List by | preLights peer support |
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 http://covidpreprints.com for additional resources and timeline, and https://connect.biorxiv.org/relate/content/181 for full list of bioRxiv and medRxiv preprints on this topic
| List by | Dey Lab, Zhang-He Goh |
1
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 |
Also in the genomics category:
End-of-year preprints – the genetics & genomics edition
In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) genomics 2) bioinformatics 3) gene regulation 4) epigenetics
| List by | Chee Kiang Ewe et al. |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
| List by | Reinier Prosee |
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 |
Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University
This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.
| List by | Nándor Lipták |
20th “Genetics Workshops in Hungary”, Szeged (25th, September)
In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf
| List by | Nándor Lipták |
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
| List by | Jesus Victorino |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
| List by | Shikha Nayar |
Also in the physiology category:
Fibroblasts
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
| List by | Osvaldo Contreras |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
| 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. |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
| List by | Sandra Malmgren Hill |
Cellular metabolism
A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.
| List by | Pablo Ranea Robles |