A microsatellite‐based linkage map for song sparrows (Melospiza melodia)

Abstract

Although linkage maps are important tools in evolutionary biology, their availability for wild populations is limited. The population of song sparrows ( Melospiza melodia) on Mandarte Island, Canada, is among the more intensively studied wild animal populations. Its long-term pedigree data, together with extensive genetic sampling, have allowed the study of a range of questions in evolutionary biology and ecology. However, the availability of genetic markers has been limited. We here describe 191 new microsatellite loci, including 160 high-quality polymorphic autosomal, 7 Z-linked and 1 W-linked markers. We used these markers to construct a linkage map for song sparrows with a total sex-averaged map length of 1731 cM and covering 35 linkage groups, and hence, these markers cover most of the 38-40 chromosomes. Female and male map lengths did not differ significantly. We then bioinformatically mapped these loci to the zebra finch ( Taeniopygia guttata) genome and found that linkage groups were conserved between song sparrows and zebra finches. Compared to the zebra finch, marker order within small linkage groups was well conserved, whereas the larger linkage groups showed some intrachromosomal rearrangements. Finally, we show that as expected, recombination frequency between linked loci explained the majority of variation in gametic phase disequilibrium. Yet, there was substantial overlap in gametic phase disequilibrium between pairs of linked and unlinked loci. Given that the microsatellites described here lie on 35 of the 38-40 chromosomes, these markers will be useful for studies in this species, as well as for comparative genomics studies with other species.

Direct and indirect genetic and fine‐scale location effects on breeding date in song sparrows

“…Since 1993, all ringed chicks were blood‐sampled and genotyped at ∼ 160 highly polymorphic microsatellite loci to assign genetic parentage (Nietlisbach et al . ). All genetic mothers matched those assigned from observed behaviour.…”

Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population

“…Additionally, blood sampling of all individuals at approximately 6 days after hatching since 1993 allows correcting the pedigree for extra-pair paternities and determining the sex [37][38][39][40][41]. F was calculated using the R package pedigreemm [42] for individuals with at least two (and a mean of eight) genetically verified ancestral generations plus earlier genetically not verified generations.…”

“…We calculated mean H at 160 microsatellite loci (described in [37]), covering 35 linkage groups and a sex-averaged autosomal map length of 1731 centiMorgan [37], although the latter is likely an underestimate given the number of markers used [43]. Most of the 38-40 chromosomes typically found in birds [44] were covered by at least one and maximally 20 loci.…”

The Consequences of Polyandry for Sibship Structures, Distributions of Relationships and Relatedness, and Potential for Inbreeding in a Wild Population

“…We first compiled a social pedigree linking all banded offspring to their observed mother and her socially paired male spanning 1975-2015 (Reid et al 2014(Reid et al , 2015a(Reid et al , 2015b. Since 1993, all adults and banded offspring were blood sampled and genotyped at ∼160 highly polymorphic microsatellite loci, and all offspring were assigned to genetic sires with 199% individual-level statistical confidence (Nietlisbach et al 2015(Nietlisbach et al , 2017Reid et al 2015a). We then compiled a genetic pedigree linking all banded offspring to their mother and true genetic father (Sardell et al 2010;Reid et al 2014Reid et al , 2015aReid et al , 2015bNietlisbach et al 2015).…”

“…Since 1993, all adults and banded offspring were blood sampled and genotyped at ∼160 highly polymorphic microsatellite loci, and all offspring were assigned to genetic sires with 199% individual-level statistical confidence (Nietlisbach et al 2015(Nietlisbach et al , 2017Reid et al 2015a). We then compiled a genetic pedigree linking all banded offspring to their mother and true genetic father (Sardell et al 2010;Reid et al 2014Reid et al , 2015aReid et al , 2015bNietlisbach et al 2015). We thereby generated two parallel pedigrees spanning 1993-2015 that describe sibship structures and the distributions of relationships and relatedness among all population members as they would have been had all observed breeding pairs been monogamous within broods (social pedigree) and given the realized pattern of extrapair reproduction and underlying polyandry (genetic pedigree; Lebigre et al 2012;Reid et al 2014).…”