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Method: Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
- Yi-Chieh Wu,
- Matthew D. Rasmussen,
- Mukul S. Bansal,
- and Manolis Kellis
Genome Res. March 2014 24: 475-486; Published in Advance December 5, 2013, doi:10.1101/gr.161968.113
...use dyFigure 2. Duplications, losses, and deep coalescence. In A–C, evolutionary events are depicted using the unified model (left), the gene tree evolving ‘‘inside’’ the locus tree (middle), and the LCT (right). (A) Gene duplication was discussed in Figure 1. Evolution within a single species tree...
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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
.... Analyses of genomic divergence therefore need to be complemented with more sensitive tests for gene flow between populations (Kulathinal et al. 2009; Ellegren et al. 2012; Garrigan et al. 2012; TheHeliconiusGenome Consortium 2012; Nosil et al. 2012). A widely used approach is to fit coalescent models...
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Method: Genome-scale coestimation of species and gene trees
- Bastien Boussau,
- Gergely J. Szöllősi,
- Laurent Duret,
- Manolo Gouy,
- Eric Tannier,
- and Vincent Daubin
Genome Res. February 2013 23: 323-330; Published in Advance November 6, 2012, doi:10.1101/gr.141978.112
...families for comparative genomics. BMC Bioinformatics (Suppl 6) 10: S3. Rasmussen M, Kellis M. 2010. A Bayesian approach for fast and accurate gene tree reconstruction. Mol Biol Evol 28: 273–290. Rasmussen MD, Kellis M. 2012. Unified modeling of gene duplication, loss, and coalescence using a locus tree...
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Method: Genealogical inference and more flexible sequence clustering using iterative PopPUNK
- Bin Zhao,
- John A. Lees,
- Hongjin Wu,
- Chao Yang,
- and Daniel Falush
Genome Res. May 30, 2023 gr.277395.122; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122
...pairwise core-distance between all isolates 196 (extracted from initial model fitting results); 197 198 When one of these cutoffs is provided, iterative-PopPUNK searches all the nodes except 199 root node in the partially resolved tree and extracts the relative similarity values (P max-cluster200 dist or P...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...not be expected in relation to Eurasian wolves, thus suggesting postdivergence gene flow between Iberian wolves and dogs.To further dissect the evolutionary history of this genomic region, we compared the population phylogenetic trees for the entire Chromosome 2 and for the 500 kb region using TreeMix (Pickrell...
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Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
- Ying Zhen,
- Christian D. Huber,
- Robert W. Davies,
- and Kirk E. Lohmueller
Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
...across different taxa as is p+s+. In the Complex models, humans have a smaller p+γ+ than do mice. However, the LL curves of p+γ+ overlap between D. melanogaster and mice and between D. melanogaster and humans, suggesting they are not significantly different (Supplemental Fig. S4).Effects of biased gene...
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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
...and invertebrate species (Oliver et al. 2009), but partial or complete gene loss has been common across the Metazoan tree of life (Baker et al. 2017). In organisms lacking a functional copy of PRDM9, the initiation of crossovers and the distribution of recombination across the must be mediated by other factors...
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Research: Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior
- Mohammed Errbii,
- Jürgen Gadau,
- Kerstin Becker,
- Lukas Schrader,
- and Jan Oettler
Genome Res. June 2024 34: 863-876; Published in Advance June 5, 2024, doi:10.1101/gr.278392.123
...) and allowing the evolution of genes important for social life.Alternative models suggested that elevated rates of recombination in social Hymenoptera may increase resistance to pathogens and facilitate behavioral and morphological differentiation by increasing genetic diversity at the colony level (Shykoff...
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Resource: The genome of the vervet (Chlorocebus aethiops sabaeus)
- Wesley C. Warren,
- Anna J. Jasinska,
- Raquel García-Pérez,
- Hannes Svardal,
- Chad Tomlinson,
- Mariano Rocchi,
- Nicoletta Archidiacono,
- Oronzo Capozzi,
- Patrick Minx,
- Michael J. Montague,
- Kim Kyung,
- LaDeana W. Hillier,
- Milinn Kremitzki,
- Tina Graves,
- Colby Chiang,
- Jennifer Hughes,
- Nam Tran,
- Yu Huang,
- Vasily Ramensky,
- Oi-wa Choi,
- Yoon J. Jung,
- Christopher A. Schmitt,
- Nikoleta Juretic,
- Jessica Wasserscheid,
- Trudy R. Turner,
- Roger W. Wiseman,
- Jennifer J. Tuscher,
- Julie A. Karl,
- Jörn E. Schmitz,
- Roland Zahn,
- David H. O'Connor,
- Eugene Redmond,
- Alex Nisbett,
- Béatrice Jacquelin,
- Michaela C. Müller-Trutwin,
- Jason M. Brenchley,
- Michel Dione,
- Martin Antonio,
- Gary P. Schroth,
- Jay R. Kaplan,
- Matthew J. Jorgensen,
- Gregg W.C. Thomas,
- Matthew W. Hahn,
- Brian J. Raney,
- Bronwen Aken,
- Rishi Nag,
- Juergen Schmitz,
- Gennady Churakov,
- Angela Noll,
- Roscoe Stanyon,
- David Webb,
- Francoise Thibaud-Nissen,
- Magnus Nordborg,
- Tomas Marques-Bonet,
- Ken Dewar,
- George M. Weinstock,
- Richard K. Wilson,
- and Nelson B. Freimer
Genome Res. December 2015 25: 1921-1933; Published in Advance September 16, 2015, doi:10.1101/gr.192922.115
...are therefore of great scientific and clinical interest as theymay include duplications or deletions of gene regulatory or protein-coding regions. To identify candidate SVs potentially contributing to vervet trait variation, we selected six vervets with 59 direct descendants (collectively) and a range...

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