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Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
.... In exemplar yeast and mammalian data sets, we demonstrate that the predictive power of ERC2.0 is improved relative to the previous method, ERC1.0, and that further improvements are obtained by using larger yeast and mammalian phylogenies. We attribute the improvements to both the larger data sets and improved...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...mammalian species to detect significant correlations between the relative evolutionary rates of genes and changes in diet. We have identified six genes—ACADSB, CLDN16, CPB1, PNLIP, SLC13A2, and SLC14A2—that experienced significant changes in evolutionary constraint alongside changes in carnivory score...
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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
.... First, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous regulatory elements and identified thousands of promoter and enhancer regions with differential epigenomic activity in mole-rats. These elements associate with known mole...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
.... The color legend is as shown in D.The inferred methylation states in ancestral species indicate an increasing proportion of hypomethylation in the orthologous along each branch of the phylogenetic tree (Fig. 2C). We estimated that HMRs made up 7.0% of the orthologous in the last common ancestor of the seven...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
...mammalian RNA-seq data have been used to study the evolution of 1:1 orthologous (single-copy) genes (Brawand et al. 2011; Warnefors and Kaessmann 2013; Necsulea and Kaessmann 2014) and some specific aspects of paralogs (Chen and Zhang 2012; Rogozin et al. 2014), the evolutionary and functional relevance...
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Research: Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals
- Yoshihito Niimura,
- Atsushi Matsui,
- and Kazushige Touhara
Genome Res. September 2014 24: 1485-1496; Published in Advance July 22, 2014, doi:10.1101/gr.169532.113
...of OR genes among multiple mammalian species is not straightforward for three main reasons. (1) The number of genes for inferring orthology and paralogy is very large. (2) Orthologous relationships between genes from two species are usually not one-to-one; they can be multiple-to-multiple or zeroto...
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RESOURCE: EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
- Albert J. Vilella,
- Jessica Severin,
- Abel Ureta-Vidal,
- Li Heng,
- Richard Durbin,
- and Ewan Birney
Genome Res. February 2009 19: 327-335; Published in Advance November 24, 2008, doi:10.1101/gr.073585.107
...-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...and Griffiths-Jones (2011) for miRNA annotation from RNA-seq data]. As a result, miRNAs in our data set are supported by 90% or more reads that map only to miRNA genes and are not enriched with repeated elements (Supplemental Table S8). Inference of miRNA clusters and families MiRNA genes within 50 kb of each...
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Research: Natural selection drives the accumulation of amino acid tandem repeats in human proteins
- Loris Mularoni,
- Alice Ledda,
- Macarena Toll-Riera,
- and M. Mar Albà
Genome Res. June 2010 20: 745-754; Published in Advance March 24, 2010, doi:10.1101/gr.101261.109
...(24 repeats) (Supplemental file 1, S5), the most recent phylogenetic group we considered was ‘‘Primata.’’ This group was composed of human repeats that were also present in chimpanzee and rhesus macaque but absent from the rest of the mammalian and vertebrate orthologous proteins (157 repeats). Given...
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Letter: Extreme variability among mammalian V1R gene families
- Janet M. Young,
- Hillary F. Massa,
- Li Hsu,
- and Barbara J. Trask
Genome Res. January 2010 20: 10-18; Published in Advance December 1, 2009, doi:10.1101/gr.098913.109
...phylogenetic inference. Our trees show that species-specific V1R subfamilies are common throughout the entire mammalian phylogeny and are especially apparent in species with large V1R repertoires. Most V1Rs we identify are the product of duplication since divergence from any other species in our study. In fact...

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