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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...recombination rate is expected to lead to reduced genetic variation via background selection (loss of neutral variants linked to deleterious mutations during purifying selection) (Charlesworth 1994; Comeron 2017) and selective sweeps/hitch-hiking (haplotypes around advantageous mutations increase in frequency...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
..., we used a Bayesian binomial linear mixed model to analyze variation in the mutation rate, fitting sex and population as fixed effects and parental identity as a random effect. Some mutations could not be attributed to one parent or the other, and we chose to assign half of these to males and half...
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Research: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
- Fan Han,
- Sangeet Lamichhaney,
- B. Rosemary Grant,
- Peter R. Grant,
- Leif Andersson,
- and Matthew T. Webster
Genome Res. June 2017 27: 1004-1015; Published in Advance April 25, 2017, doi:10.1101/gr.212522.116
...of differential gene flow, or (4) recurrent hitchhiking/background selection acting across the with effects on genetic variation modulated by recombination rate. Whereas all of these models generate genomic islands of relative divergence (FST), the main difference is that dXY is above average in islands caused...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes...
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Research: Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
- Reto Burri,
- Alexander Nater,
- Takeshi Kawakami,
- Carina F. Mugal,
- Pall I. Olason,
- Linnea Smeds,
- Alexander Suh,
- Ludovic Dutoit,
- Stanislav Bureš,
- Laszlo Z. Garamszegi,
- Silje Hogner,
- Juan Moreno,
- Anna Qvarnström,
- Milan Ružić,
- Stein-Are Sæther,
- Glenn-Peter Sætre,
- Janos Török,
- and Hans Ellegren
Genome Res. November 2015 25: 1656-1665; Published in Advance September 9, 2015, doi:10.1101/gr.196485.115
...from gene flow, patterns of sequence divergence (dxy and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, -wide variation in diversity and differentiation can...
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Research: Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
- Asher D. Cutter and
- Jae Young Choi
Genome Res. August 2010 20: 1103-1111; Published in Advance May 27, 2010, doi:10.1101/gr.104331.109
..., Charlesworth B, Morgan MT. 1995. The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619–1632. Charlesworth B, Bartolome C, Noel V. 2005. The detection of shared and ancestral polymorphisms. Genet Res 86: 149–157. Cutter AD. 2008. Divergence times in Caenorhabditis...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
...is the correlation between recombination and diversity, which was originally observed in D. melanogaster (Begun and Aquadro 1992), and suggested the influence of linked selection. While such a correlation could result from ‘‘background selection’’ against linked deleterious variation (Charlesworth et al. 1993...
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Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
- Viola Nolte,
- Ram Vinay Pandey,
- Robert Kofler,
- and Christian Schlötterer
Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
...divergence (number of sex comb teeth) between the two sister species Figure 2. Nucleotide diversity (p) along the major chromosomal arms in D. mauritiana (red line) and D. melanogaster (gray line). The sliding window analysis was performed using 500-kb windows with a step size of 100 kb; chromosomal...
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LETTER: Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations
- Penelope R. Haddrill,
- Kevin R. Thornton,
- Brian Charlesworth,
- and Peter Andolfatto
Genome Res. June 2005 15: 790-799; doi:10.1101/gr.3541005
...of nucleotide polymorphism and divergence and the spatial patterning of this variation across the (e.g., Hudson et al. 1987 ; Tajima 1989 ; McDonald and Kreitman 1991 ; Fay and Wu 2000 ; Kim and Stephan 2002 ; Przeworski 2003 ). These approaches hold promise for detecting specific targets of natural selection...
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Research: Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
- Asger Hobolth,
- Julien Y. Dutheil,
- John Hawks,
- Mikkel H. Schierup,
- and Thomas Mailund
Genome Res. March 2011 21: 349-356; Published in Advance January 26, 2011, doi:10.1101/gr.114751.110
...the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS was found to be reduced in exons and gene-dense regions when we control for confounding factors such as GC content and recombination rate. Finally, we find...

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