ArticleMolecular ecology2014
A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.
Article in Molecular ecology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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112 citing papers in PubMed, 266 citations in OpenAlex.
- Genomic erosion in the assessment of species' extinction risk and recovery potential.The Journal of heredity · 2026Article
- Selective Regimes and Evolutionary Dynamics of Z and W Gametologs Across an Expanded Avian Neo-Sex Chromosome.Genome biology and evolution · 2026Article
- Historically Small Population Size Limits Purging of Deleterious Mutations in a Conservation-Reliant Species, the Kirtland's Warbler.bioRxiv : the preprint server for biology · 2026Article
- Combining Population Genomics With Ancient DNA to Understand Island Colonisation History of the Madagascar Turtle Dove.Molecular ecology · 2026Article
- Genome wide data recover hierarchical genetic structure and help define conservation units for the threatened Asian Houbara.Scientific reports · 2026Article
- Improved genome assembly of whale shark, the world's biggest fish: revealing intragenomic heterogeneity in molecular evolution.GigaScience · 2026Article
- DNA Methylation Reflects Cis-Genetic Differentiation Across the European Crow Hybrid Zone.Molecular ecology · 2025Article
- Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers.Molecular ecology · 2025Article
- Lepidopteran Genomes Have Denser Transposable Elements in Smaller Chromosomes, Likely Driven by Non-allelic Homologous Recombination.Genome biology and evolution · 2025Article
- High-recombining genomic regions affect demography inference based on ancestral recombination graphs.Genetics · 2025Article
- Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.Proceedings. Biological sciences · 2025Article
- Article
- Recently Delisted Songbird Harbors Extensive Genomic Evidence of Inbreeding, Potentially Complicating Future Recovery.Evolutionary applications · 2024Article
- Inheritance of Material Wealth in a Natural Population.Ecology letters · 2024Article
- A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta).Heredity · 2024Article
- A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes.Scientific reports · 2024Article
- The Genetic Architecture of Recombination Rates is Polygenic and Differs Between the Sexes in Wild House Sparrows (Passer domesticus).Molecular biology and evolution · 2024Article
- Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions.G3 (Bethesda, Md.) · 2024Article
- Improved assembly of the Pungitius pungitius reference genome.G3 (Bethesda, Md.) · 2024Article
- Temporal challenges in detecting balancing selection from population genomic data.G3 (Bethesda, Md.) · 2024Article
52 more citing papers are in PubMed but not listed here.
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8 authors at 1 institution in 1 country.
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Abstract
Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cM and a mean genetic distance between markers of 0.12 cM. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5-2.0 event (6.6-7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cM/Mb and correlated closely with chromosome size, from 2 cM/Mb for chromosomes >100 Mb to >10 cM/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cM was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.
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