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Research: Direct estimate of the rate of germline mutation in a bird
- Linnéa Smeds,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. September 2016 26: 1211-1218; Published in Advance July 13, 2016, doi:10.1101/gr.204669.116
...is available for this article.] The rate of mutation is one of the most central parameters in evolutionary and population genetics (Lynch 2010a) but is notoriously difficult to accurately estimate. The primary difficulty lies in that mutation rates are extremely low (Drake et al. 1998; Lynch 2010a...
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Research: Genome-wide evidence for speciation with gene flow in Heliconius butterflies
- Simon H. Martin,
- Kanchon K. Dasmahapatra,
- Nicola J. Nadeau,
- Camilo Salazar,
- James R. Walters,
- Fraser Simpson,
- Mark Blaxter,
- Andrea Manica,
- James Mallet,
- and Chris D. Jiggins
Genome Res. November 2013 23: 1817-1828; Published in Advance September 17, 2013, doi:10.1101/gr.159426.113
...to address long-standing questions regarding the extent to which divergence and speciation occurs in the face of ongoing gene flow. One prediction of models of speciation with gene flow is that the level of divergence should be heterogeneous across the . Some loci are likely to be shared between incipient...
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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
...emphasize the necessity of incorporating linked selection as a model to identify regions involved in adaptation and speciation. [Supplemental material is available for this article.] Uncovering the genetic architecture of reproductive isolation and its evolutionary history are central tasks...
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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
...a hidden Markov model that directly infers the local genealogy of the human, chimpanzee, and orangutan species to show that ILS occurswithin;1%of the .Weuse thepatterns of ILS to disentangle human–orangutan speciation from human– orangutan divergence. This allows us to estimate the population sizes...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...). With the default minimum variant length parameter L = 50 and correcting for sequencing coverage, estimated interspecies SV proportion ranged from 4.73% to 9.86% (mean, 7.11%), with smaller values within the mbuna (mean, 5.45%) and benthic (mean, 5.20%) groups. The estimated differences were much lower within...
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REVIEW: Models of Molecular Evolution and Phylogeny
- Pietro Liò and
- Nick Goldman
Genome Res. December 1, 1998 8: 1233-1244; doi:10.1101/gr.8.12.1233
...free parameters to the Jukes and Cantor (1969) model: Usually the nucleotide equilibrium frequencies can be estimated by simply analyzing base composition in the DNA sequences under study. Hasegawa and coworkers (1985) implemented transition/transversion bias in Felsenstein’s model, effectively...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...diversification, adaptation, and speciation. To better understand the changes that occurred in the different subs of a hybrid species and how they facilitate adaptation, we have completed chromosome-level de novo assemblies of all chromosomes for a recently formed hybrid yeast, Saccharomyces bayanus strain CBS380...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...regions per megabase aligned per million years diverged for different animal clades.DiscussionGenome scrambling and speciationOur study design, combined with the recent divergence times estimated for O. dioica, allowed us to study scrambling on a finer timescale than was reached by previous studies...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...comprising more than 49 megabases of DNA. Finally, we provide a list of 182 candidate genes potentially involved in gibbon diversification and speciation.A fundamental question in evolutionary biology is to establish how Hominina diverged from apes, starting from a common ancestor. It is common knowledge...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
....keightley@ed.ac.ukAbstractGenetic variation originates from several types of spontaneous mutation, including single-nucleotide substitutions, short insertions and deletions (indels), and larger structural changes. Structural mutations (SMs) drive evolution and are thought to play major roles in evolutionary adaptation, speciation...
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