ArticleEcology and evolution2020
Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets.
Article in Ecology and evolution, 2020. 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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Who cites it
22 citing papers in PubMed.
- A Mid-Atlantic Brook Trout (Salvelinus fontinalis) genome to advance conservation and comparative genomics.G3 (Bethesda, Md.) · 2026Article
- Leveraging Next-Generation Tools for Genetic Assessment and Demographic Monitoring in Threatened and Elusive Humboldt Martens.Evolutionary applications · 2026Article
- Summer Rainfall Drives Adaptation with Gene Flow in a Widespread Butterfly.Molecular ecology · 2026Article
- Effects of Different SNP Calling and Sequence Mapping Choices on the Inference of Genetic Architecture Underlying Migration Tendency.Ecology and evolution · 2026Article
- Conspecific Scaffold-Level Genome Assembly Outperforms Heterospecific Chromosome-Level Assemblies for Assessing Genetic Indicators in a Threatened Marine Fish.Evolutionary applications · 2026Article
- Molecular Identification ofInsects · 2026Article
- Population Genomics Reveals Local Adaptation Related to Temperature Variation in Two Stream Frog Species: Implications for Vulnerability to Climate Warming.Molecular ecology · 2025Article
- Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses.Horticulture research · 2025Article
- Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects.Molecular ecology · 2025Article
- Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs.Journal of animal science and biotechnology · 2025Article
- Multiple Origins or Widespread Gene Flow in Agricultural Fields? Regional Population Genomics of Herbicide Resistance in Bromus tectorum.Molecular ecology · 2025Article
- Harnessing Genomics for BreedingInternational journal of molecular sciences · 2025Article
- Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species.BMC genomics · 2025Article
- Next-generation data filtering in the genomics era.Nature reviews. Genetics · 2024Review
- Whole Genome Analysis Reveals Evolutionary History and Introgression Events in Bale Monkeys.Genes · 2024Article
- Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing.G3 (Bethesda, Md.) · 2024Article
- Reference genome of Townsend's big-eared bat, Corynorhinus townsendii.The Journal of heredity · 2024Article
- Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals.Molecular biology and evolution · 2023Article
- Genetic Diversity and Population Structure of Doum Palm (Frontiers in genetics · 2022Article
- Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control.PloS one · 2022Article
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1 author.
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Abstract
The advent of high-throughput sequencing (HTS) has made genomic-level analyses feasible for nonmodel organisms. A critical step of many HTS pipelines involves aligning reads to a reference genome to identify variants. Despite recent initiatives, only a fraction of species has publically available reference genomes. Therefore, a common practice is to align reads to the genome of an organism related to the target species; however, this could affect read alignment and bias genotyping. In this study, I conducted an experiment using empirical RADseq datasets generated for two species of salmonids (Actinopterygii; Teleostei; Salmonidae) to address these questions. There are currently reference genomes for six salmonids of varying phylogenetic distance. I aligned the RADseq data to all six genomes and identified variants with several different genotypers, which were then fed into population genetic analyses. Increasing phylogenetic distance between target species and reference genome reduced the proportion of reads that successfully aligned and mapping quality. Reference genome also influenced the number of SNPs that were generated and depth at those SNPs, although the affect varied by genotyper. Inferences of population structure were mixed: increasing reference genome divergence reduced estimates of differentiation but similar patterns of population relationships were found across scenarios. These findings reveal how the choice of reference genome can influence the output of bioinformatic pipelines. It also emphasizes the need to identify best practices and guidelines for the burgeoning field of biodiversity genomics.
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