Shifting the paradigm in Evolve and Resequence studies: From analysis of single nucleotide polymorphisms to selected haplotype blocks

Molecular Ecology
Neda Barghi, Christian Schlötterer

Abstract

For almost a decade the combination of whole genome sequencing with experimental evolution (Evolve and Resequence, E&R; Turner, Stewart, Fields, Rice, & Tarone, ) has been used to study adaptation in outcrossing organisms. However, complications caused by inversions and hitchhiking variants have prevented this powerful approach from living up to its potential. In this issue of Molecular Ecology, Michalak, Kang, Schou, Garner, and Loeschke (), provide an important step ahead by using a population of Drosophila melanogaster devoid of segregating inversions to identify the genetic basis of resistance to five environmental stressors. They further address the challenge of hitchhiking variants by reconstructing selected haplotype blocks. While it is apparent that the haplotype block reconstruction needs further refinements, their work underpins the potential of E&R studies in Drosophila to address fundamental questions in evolutionary biology.

References

Sep 17, 2010·Nature·Molly K BurkeAnthony D Long
Feb 10, 2012·Nature·Trudy F C MackayRichard A Gibbs
Oct 17, 2012·PLoS Genetics·Josep M ComeronSamuel Bailin
Feb 1, 2013·Molecular Biology and Evolution·Darren KessnerJohn Novembre
Nov 19, 2013·Current Opinion in Genetics & Development·Sergey V Nuzhdin, Thomas L Turner
Nov 22, 2014·Molecular Biology and Evolution·Susanne U FranssenChristian Schlötterer
Mar 2, 2016·Molecular Ecology Resources·Marek BukowickiChristian Schlötterer
Oct 1, 2016·Molecular Biology and Evolution·Justin B LackJohn E Pool
Oct 6, 2016·Molecular Biology and Evolution·Susanne U FranssenChristian Schlötterer
May 27, 2017·G3 : Genes - Genomes - Genetics·Neda BarghiChristian Schlötterer
Aug 17, 2018·PLoS Computational Biology·Christos Vlachos, Robert Kofler
Oct 31, 2018·Molecular Ecology·Pawel MichalakVolker Loeschcke
Feb 5, 2019·PLoS Biology·Neda BarghiChristian Schlötterer

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Citations

Aug 19, 2020·Molecular Ecology Resources·Kathrin A Otte, Christian Schlötterer
Aug 30, 2020·Molecular Ecology·Katherine E RobertsMike Boots
Feb 14, 2021·Nature Communications·Arya IranmehrGabriel G Haddad
Jun 18, 2021·Evolution Letters·R Axel W WibergMichael G Ritchie

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Software Mentioned

MimicrEE2
Evolve

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