ArticleGenome biology and evolution2017
Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach.
Article in Genome biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 63 citations in OpenAlex.
- Adaptation across an extreme elevational gradient in Andean leaf-eared mice, the world's highest-dwelling mammal.Science (New York, N.Y.) · 2026Article
- The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.Genome biology and evolution · 2025Article
- Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents.Evolution; international journal of organic evolution · 2024Article
- Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group.Molecular biology and evolution · 2024Article
- Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.Systematic biology · 2024Article
- The Utilization of Reference-Guided Assembly and In Silico Libraries Improves the Draft Genome of Clarias batrachus and Culter alburnus.Marine biotechnology (New York, N.Y.) · 2023Article
- The Evolution of Widespread Recombination Suppression on the Dwarf Hamster (Phodopus) X Chromosome.Genome biology and evolution · 2022Article
- Molecular Evolution across Mouse Spermatogenesis.Molecular biology and evolution · 2022Article
- The dynamics of introgression across an avian radiation.Evolution letters · 2021Article
- Evolutionary, proteomic, and experimental investigations suggest the extracellular matrix of cumulus cells mediates fertilization outcomes†.Biology of reproduction · 2021Article
- Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents.Genome biology and evolution · 2021Article
- The Legacy of Recurrent Introgression during the Radiation of Hares.Systematic biology · 2021Article
- How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies.BMC microbiology · 2020Article
- Transcriptomic resources for evolutionary studies in flat periwinkles and related species.Scientific data · 2020Article
- Instability of the Pseudoautosomal Boundary in House Mice.Genetics · 2019Article
- The genomic impact of historical hybridization with massive mitochondrial DNA introgression.Genome biology · 2018Article
- A High Quality Genome forG3 (Bethesda, Md.) · 2018Article
- Article
- Sequence and Structural Diversity of Mouse Y Chromosomes.Molecular biology and evolution · 2017Article
- Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample. Here, we develop a scalable pseudoreference approach to iteratively incorporate sample-specific variation into a genome reference and reduce the effects of systematic mapping bias in downstream analyses. To characterize this framework, we used targeted capture to sequence whole exomes (∼54 Mbp) in 12 lineages (ten species) of mice spanning the Mus radiation. We generated whole exome pseudoreferences for all species and show that this iterative reference-based approach improved basic genomic analyses that depend on mapping accuracy while preserving the associated annotations of the mouse reference genome. We then use these pseudoreferences to resolve evolutionary relationships among these lineages while accounting for phylogenetic discordance across the genome, contributing an important resource for comparative studies in the mouse system. We also describe patterns of genomic introgression among lineages and compare our results to previous studies. Our general approach can be applied to whole or partitioned genomic data and is easily portable to any system with sufficient genomic resources, providing a useful framework for phylogenomic studies in mice and other taxa.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.