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

Hagen, Ingerid Julie; Lien, Sigbjørn; Billing, Anna Maria; Elgvin, Tore O.; Trier, Cassandra Nicole; Niskanen, Alina K.; Tarka, Maja; Slate, Jon; Sætre, Glenn‐Peter; Jensen, Henrik

doi:10.1111/1755-0998.13134

Cited by 17 publications

(18 citation statements)

References 64 publications

(127 reference statements)

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“…While we do not explicitly model LD between loci, we thus implicitly account for differences in LD across groups through the group‐specific allele effects. Hagen et al (2020) indeed found that the levels of LD in house sparrows were generally higher and remained higher over longer distances along the chromosomes on islands in our study system with smaller effective population sizes (generally outer islands, which recently went through a strong population bottleneck, see Baalsrud et al, 2014). Group‐specific allele effects can also be caused by QTL having epistatic interactions with loci whose allele frequencies differ between groups (Rio, Mary‐Huard, et al, 2020).…”

Section: Discussionsupporting

confidence: 68%

Genomic estimation of quantitative genetic parameters in wild admixed populations

2022

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Heritable genetic variation among free‐living animals or plants is essential for populations to respond to selection and adapt. It is therefore important to be able to estimate additive genetic variance VA, which can be obtained using a GLMM known as the animal model. An underlying assumption of the standard animal model is that the study population is genetically unstructured, which is often unrealistic. In fact, admixture might be the norm rather than the exception in the wild, like in geographically structured populations, in the presence of (im)migration or in reintroduction and conservation contexts. Unfortunately, animal model estimators may be biased in such cases. The so‐called genetic group animal models that account for genetically differentiated subpopulations have recently become popular, but methodology is currently only available for cases where relatedness among individuals can be estimated from pedigrees. To ensure that genetic group animal models with heterogeneous VA remain applicable to populations with genomic data but no pedigrees, there is a clear need to generalize these models to the case when exclusively genomic data are available. We therefore introduce such methodology for wild admixed systems by extending methods that were recently suggested in the context of plant breeding. Our extension relaxes the limiting assumptions that currently restrict their use to artificial breeding set‐ups. We illustrate the usefulness of the extended genomic genetic group animal model on a wild admixed population of house sparrows resident in an island system in Northern Norway, where genome‐wide data on more than 180,000 single nucleotide polymorphisms (SNPs) are available to derive genomic relatedness. We compare our estimates of quantitative genetic parameters to those derived from a corresponding pedigree‐based genetic group animal model. The satisfactory agreement indicates that the new method works as expected. Our extension of the very popular animal model ensures that the upcoming challenges with increasing availability of genomic data for quantitative genetic studies of wild admixed populations can be handled. To make the method widely available to the scientific community, we offer guidance in the form of a tutorial including step‐by‐step instructions to facilitate implementation.

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Section: Discussionsupporting

confidence: 68%

Genomic estimation of quantitative genetic parameters in wild admixed populations

2022

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“…While we do not explicitly model LD between loci, we thus implicitly account for differences in LD across groups through the groupspecific allele effects. Hagen et al (2020) indeed found that levels of LD in house sparrows were generally higher and remained higher over longer distances along the chromosomes on islands in our study system with smaller effective population sizes (generally outer islands, which recently went through a strong population bottleneck, see Baalsrud et al, 2014). Group-specific allele effects can also be caused by QTL having epistatic interactions with loci whose allele frequencies differ between groups (Rio et al, 2020a).…”

Section: Wing Length Body Mass Tarsus Lengthsupporting

confidence: 64%

Genomic estimation of quantitative genetic parameters in wild admixed populations

Aase

Jensen

Muff

2021

Preprint

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Heritable genetic variation among free-living animals or plants is essential for populations to respond to selection and adapt. It is therefore important to be able to estimate additive genetic variance VA, which can be obtained using a generalized linear mixed model known as the animal model. An underlying assumption of the standard animal model is that the study population is genetically unstructured, which is often unrealistic. In fact, admixture might be the norm rather than the exception in the wild, like in geographically structured populations, in the presence of (im)migration, or in re-introduction and conservation contexts. Unfortunately, animal model estimators may be biased in such cases. So-called genetic group animal models that account for genetically differentiated subpopulations have recently become popular, but methodology is currently only available for cases where relatedness among individuals can be estimated from pedigrees. To ensure that the animal model remains useful in future applications, there is a clear need to generalize genetic group animal models with heterogeneous VA to the case when exclusively genomic data is available. We therefore introduce such methodology for wild admixed systems by extending methods that were recently suggested in the context of plant breeding. Our extension relaxes the limiting assumptions that currently restrict their use to artificial breeding setups. We illustrate the usefulness of the extended genomic genetic groups animal model on a wild admixed population of house sparrows resident in an island system in Northern Norway, where genome-wide data on more than 180 000 single nucleotide polymorphisms (SNPs) is available to derive genomic relatedness. We compare our estimates of quantitative genetic parameters to those derived from a corresponding pedigree-based genetic groups animal model. The satisfactory agreement indicates that the new method works as expected. Our extension of the very popular animal model ensures that the upcoming challenges with increasing availability of genomic data for quantitative genetic studies of wild admixed populations can be handled. To make the method widely available to the scientific community, we offer guidance in the form of a tutorial including step-by-step instructions to facilitate implementation.

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“…This fission was not observed in the superb fairy-wren, the sole other species from the Meliphagoidea superfamily with a chromosome-length genome that allows large-scale synteny analyses, and the high-density linkage map necessary to confirm within-chromosome linkage [ 1 ]. Neither has it been reported for other passerine birds with both resources available (i.e., great tit, collared flycatcher, and house sparrow) [ 11 , 13 , 14 ].…”

Section: Data Descriptionmentioning

confidence: 99%

Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

et al. 2022

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Background The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. Results We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. Conclusions The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.

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

Cited by 17 publications

References 64 publications

Genomic estimation of quantitative genetic parameters in wild admixed populations

Genomic estimation of quantitative genetic parameters in wild admixed populations

Genomic estimation of quantitative genetic parameters in wild admixed populations

Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

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