Supergene origin and maintenance in Atlantic cod
Michael Matschiner,Julia Maria Isis Barth,Ole K. Tørresen,Bastiaan Star,Helle Tessand Baalsrud,Marine S. O. Brieuc,Christophe Pampoulie,Ian Bradbury,Kjetill S. Jakobsen,Sissel Jentoft +9 more
TLDR
This article investigated the origin and maintenance of four megabase-scale supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual.Abstract:
Abstract Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation. read more
Citations
More filters
Journal ArticleDOI
A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes
Emily Hager,Olivia S. Harringmeyer,Tyler Wooldridge,Shunn Theingi,Jacob T. Gable,S. McFadden,Beverly I. Neugeboren,Kyle M. Turner,Jeffrey D. Jensen,Hopi E. Hoekstra +9 more
TL;DR: A key role for a large, previously uncharacterized inversion is uncovered in the evolution and maintenance of classic mammalian ecotypes and fitness benefits that arise from suppressed recombination within the inversion.
Journal ArticleDOI
Chromosomal inversion polymorphisms shape the genomic landscape of deer mice
TL;DR: In this article , a single species of deer mouse (Peromyscus maniculatus) was found to have 21 polymorphic inversions that are large (1.5-43.8 Mb) and cause near-complete suppression of recombination when heterozygous (0.03 cM Mb −1 ).
Journal ArticleDOI
Inversions and parallel evolution
TL;DR: It is predicted that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting.
Journal ArticleDOI
How genomics can help biodiversity conservation.
Kathrin Theissinger,Carlos Fernandes,Giulio Formenti,Iliana Bista,Paul R. Berg,Christoph Bleidorn,Aureliano Bombarely,Angelica Crottini,Guido Roberto Gallo,José A. Godoy,Sissel Jentoft,Joanna Malukiewicz,Alice Mouton,Rebekah A. Oomen,Sadye Paez,Per J. Palsbøll,Christophe Pampoulie,María José Ruiz-López,Simona Secomandi,Hannes Svardal,Constantina Theofanopoulou,Jan de Vries,Ann-Marie Waldvogel,Guojie Zhang,Erich D. Jarvis,Miklós Bálint,Claudio Ciofi,Robert M. Waterhouse,Camila J. Mazzoni,Jacob Höglund +29 more
TL;DR: A survey of the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications, can be found in this paper .
Journal ArticleDOI
Rapid adaptive radiation of Darwin’s finches depends on ancestral genetic modules
Carl-Johan Rubin,Erik D Enbody,Mariya P. Dobreva,Arhat Abzhanov,Brian W. Davis,Sangeet Lamichhaney,Mats E. Pettersson,Ashley T. Sendell-Price,C. Grace Sprehn,Carlos A. Valle,Karla Vasco,Ola Wallerman,B. Rosemary Grant,Peter R. Grant,Leif Andersson +14 more
TL;DR: Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation that represent ancestral haplotype blocks with origins predating speciation events during the Darwin’s finch radiation.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Shaun Purcell,Shaun Purcell,Benjamin M. Neale,Benjamin M. Neale,Kathe Todd-Brown,Lori Thomas,Manuel A. R. Ferreira,David Bender,David Bender,Julian Maller,Julian Maller,Pamela Sklar,Pamela Sklar,Paul I.W. de Bakker,Paul I.W. de Bakker,Mark J. Daly,Mark J. Daly,Pak C. Sham +17 more
TL;DR: This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
Journal ArticleDOI
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
TL;DR: This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
Related Papers (5)
Ectopic Gene Conversions in Four Escherichia coli Genomes: Increased Recombination in Pathogenic Strains
Robert T. Morris,Guy Drouin +1 more