Comprehensive paternity assignment: genotype, spatial location and social status in song sparrows, Melospiza Melodia

Abstract

Comprehensive, accurate paternity assignment is critical to answering numerous questions in evolutionary ecology. Yet, most studies of species with extra-pair paternity (EPP) fail to assign sires to all offspring. Common limitations include incomplete and biased sampling of offspring and males, particularly with respect to male location and social status, potentially biasing estimated patterns of paternity. Studies that achieve comprehensive sampling and paternity assignment are therefore required. Accordingly, we genotyped virtually all males and >99% of 6-day-old offspring over 16 years in a song sparrow (Melospiza melodia) population and used three complementary statistical methodologies to attempt complete paternity assignment for all 2207 offspring. Assignments were highly consistent across maximum likelihood methods that used solely genotype data, and heuristic and integrated Bayesian analyses that included data describing individual locations. Sires were assigned to >99% of all genotyped offspring with ≥95% confidence, revealing an EPP rate of c. 28%. Extra-pair sires primarily occupied territories neighbouring their extra-pair offspring; spatial location was therefore highly informative for paternity assignment. EPP was biased towards paired territorial males, although unpaired territorial and floater males sired c. 13% of extra-pair offspring. Failing to sample and include unpaired males as candidate sires would therefore substantially reduce assignment rates. These analyses demonstrate the integration of genetic and ecological information to achieve comprehensive paternity assignment and direct biological insight, illustrate the potential biases that common forms of incomplete sampling could have on estimated patterns of EPP, and provide an essential basis for understanding the evolutionary causes and consequences of EPP.

Disentangling the effect of genes, the environment and chance on sex ratio variation in a wild bird population

“…From 1993 onwards, blood samples from the complete adult population allowed us to assign offspring to their genetic parents with high statistical confidence [23]. These analyses showed that 28 per cent of offspring were sired by an extra-pair male, while all mothers were correctly assigned by behaviour [23]. Based on this, we reconstructed the pedigree for the complete population, going back to the beginning of the study in 1975 [21,22].…”

“…Circa 24 days post-hatching, when offspring begin foraging independently, territories are searched for offspring that have survived until independence from parental care. During 1993-2006, blood samples were collected from virtually all chicks that survived to ca 6 days post-hatch [23]. In 2004, nestlings were individually marked and a blood sample was taken when they were 1 day old to estimate the mortality rate between hatching and day 6.…”

“…Brood parasitism by brown-headed cowbirds (Molothrus ater), food availability and paternal song complexity have been reported to influence sex ratio at the time of fledging or independence from parental care in other song sparrow populations [21,22]. Furthermore, in song sparrows on Mandarte, variation in male reproductive success is greater than in female reproductive success, extra-pair paternity is relatively high [23], and males are slightly larger than females [24], each of which may be associated with skews in offspring sex ratio. Hence, if females have some form of control over the sex ratio of their brood, adaptive sex ratio manipulation, and hence individual variation in p, could reasonably be expected in this system.…”

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.…”

Extra-pair paternity in a long-distance migratory songbird beyond neighbors’ borders and across male age classes

“…Siring young outside a social pair bond has the ability to enhance productivity within a single breeding season and is an important component of male fitness (Griffith et al 2002, Kaiser et al 2015, but males within a population can differ considerably in their fitness gains from EPP (Sardell et al 2010;Reid et al 2014a;Kaiser et al 2015).…”