University of Oulu

Hagen, IJ, Lien, S, Billing, AM, et al. A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome. Mol Ecol Resour. 2020; 20: 544– 559.

A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome

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Author: Hagen, Ingerid J.1,2; Lien, Sigbjørn3; Billing, Anna M.1;
Organizations: 1Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
2Norwegian Institute for Nature Research (NINA), Trondheim, Norway
3Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
4Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
5Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
6Department of Biology, Lund University, Lund, Sweden
7Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 2.7 MB)
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Language: English
Published: John Wiley & Sons, 2020
Publish Date: 2020-04-06


The house sparrow is an important model species for studying physiological, ecological and evolutionary processes in wild populations. Here, we present a medium density, genome wide linkage map for house sparrow (Passer domesticus) that has aided the assembly of the house sparrow reference genome, and that will provide an important resource for ongoing mapping of genes controlling important traits in the ecology and evolution of this species. Using a custom house sparrow 10 K iSelect Illumina SNP chip we have assigned 6,498 SNPs to 29 autosomal linkage groups, based on a mean of 430 informative meioses per SNP. The map was constructed by combining the information from linkage with that of the physical position of SNPs within scaffold sequences in an iterative process. Averaged between the sexes; the linkage map had a total length of 2,004 cM, with a longer map for females (2,240 cM) than males (1,801 cM). Additionally, recombination rates also varied along the chromosomes. Comparison of the linkage map to the reference genomes of zebra finch, collared flycatcher and chicken, showed a chromosome fusion of the two avian chromosomes 8 and 4A in house sparrow. Lastly, information from the linkage map was utilized to conduct analysis of linkage disequilibrium (LD) in eight populations with different effective population sizes (Ne) in order to quantify the background level LD. Together, these results aid the design of future association studies, facilitate the development of new genomic tools and support the body of research that describes the evolution of the avian genome.

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Series: Molecular ecology resources
ISSN: 1755-098X
ISSN-E: 1755-0998
ISSN-L: 1755-098X
Volume: 20
Issue: 2
Pages: 544 - 559
DOI: 10.1111/1755-0998.13134
Type of Publication: A1 Journal article – refereed
Field of Science: 1184 Genetics, developmental biology, physiology
Funding: This study was supported by grants from NTNU, The Norwegian Research Council (programmes STORFORSK, Strategic University Program in Conservation Biology, projects 191847 and 221956) The Norwegian Directorate for Nature Management, and The EU‐commission (project METABIRD). This work was also partly supported by the Research Council of Norway through its Centres of Excellence funding scheme, project 223257).
Copyright information: © 2020 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.