In some eukaryotes, germline and somatic genomes differ dramatically in their composition. Here we characterise a major germline-soma dissimilarity caused by a germline-restricted chromosome (GRC) in songbirds. We show that the zebra finch GRC contains >115 genes paralogous to single-copy genes on 18 autosomes and the Z chromosome, and is enriched in genes involved in female gonad development. Many genes are likely functional, evidenced by expression in testes and ovaries at the RNA and protein level. Using comparative genomics, we show that genes have been added to the GRC over millions of years of evolution, with embryonic development genes bicc1 and trim71 dating to the ancestor of songbirds and dozens of other genes added very recently. The somatic elimination of this evolutionarily dynamic chromosome in songbirds implies a unique mechanism to minimise genetic conflict between germline and soma, relevant to antagonistic pleiotropy, an evolutionary process underlying ageing and sexual traits.

Supplementary information: 4 tables, 6 figuresSupplementary materials: Two Excel files for GWAS, eQTL and eigenGWAS, and summary of gene expression analysis. One .mpg file that contains videos of motile sperm of alternative karyomorphs. 2Sperm competition is an important selective force in many organisms. As a result, sperm have evolved to be among the most diverse cells in the animal kingdom. However, the relationship between sperm morphology, sperm motility and fertilisation success is only partially understood. The extent to which between-male variation is heritable is largely unknown, and remarkably few studies have investigated the genetic architecture of sperm traits, especially sperm morphology. Here we use high-density genotyping and gene expression profiling to explore the considerable sperm trait variation that exists in the zebra finch Taeniopygia guttata.We show that nearly all of the genetic variation in sperm morphology is caused by an inversion polymorphism on the Z chromosome acting as a 'supergene'. These results provide a striking example of two evolutionary genetic predictions. First, that in species where females are the heterogametic sex, genetic variation affecting sexually dimorphic traits will accumulate on the Z chromosome. Second, recombination suppression at the inversion allows beneficial dominant alleles to become fixed on whichever haplotype they first arise, without being exchanged onto other haplotypes. Finally, we show that the inversion polymorphism will be stably maintained by heterozygote advantage, because heterozygous males have the fastest and most successful sperm.Sperm are perhaps the most diverse cells in the animal kingdom, with enormous morphological variation between taxa, between species, between males and within an ejaculate 1 .Considerable interest in sperm diversity has arisen following the realisation that sperm competition (post-copulatory sexual selection) is a powerful selective force in many organisms 2 , and that sperm morphology has co-evolved with female reproductive tract morphology 3 . The zebra finch is a model species for studies of sperm biology. Sperm length is repeatable within an ejaculate, yet variable between different males; most morphological traits (head, midpiece, tail and total length) are highly heritable 4 . Furthermore, there is a documented phenotypic and genetic correlation between morphology and sperm swimming velocity ('motility') 5 . In artificially selected lines, pronounced differences in total sperm length are apparent after just three generations of divergent selection, and males with long sperm have the greatest probability of fertilisation success in sperm competition 3 trials 6 . Additionally, the zebra finch has its genome sequenced, assembled and annotated 7 , and so the toolkit to explore the genetics of phenotypic variation is available.In this study we set out to understand the genetic architecture of sperm morphology and motility in the zebra finch. Our aim was to combine genome wide association mapping with analyses of ...

Sperm competition, in which the ejaculates of multiple males compete to fertilize a female's ova, results in strong selection on sperm traits. Although sperm size and swimming velocity are known to independently affect fertilization success in certain species, exploring the relationship between sperm length, swimming velocity and fertilization success still remains a challenge. Here, we use the zebra finch (Taeniopygia guttata), where sperm size influences sperm swimming velocity, to determine the effect of sperm total length on fertilization success. Sperm competition experiments, in which pairs of males whose sperm differed only in length and swimming speed, revealed that males producing long sperm were more successful in terms of (i) the number of sperm reaching the ova and (ii) fertilizing those ova. Our results reveal that although sperm length is the main factor determining the outcome of sperm competition, complex interactions between male and female reproductive traits may also be important. The mechanisms underlying these interactions are poorly understood, but we suggest that differences in sperm storage and utilization by females may contribute to the outcome of sperm competition.

Unhatched eggs are a common phenomenon in birds and are often referred to as being ‘infertile’, which (confusingly) can mean at least two things: (1) that the ovum has not been fertilized or (2) that the embryo has died during development. These two broad categories of hatching failure can be difficult to distinguish, particularly in the early stages of embryo development. We describe methods to distinguish between infertility (due to insufficient sperm) and early embryo mortality in passerine eggs using the Zebra Finch Taeniopygia guttata as a model. We also describe how we successfully adapted these methods for use on eggs from a wild species, the Tree Sparrow Passer montanus, collected after the incubation period, and show that sperm can be visualized on the perivitelline layer of unhatched eggs even several weeks after laying.

The duration of the developmental period represents a fundamental axis of life-history variation, yet broad insights regarding the drivers of this diversity are currently lacking. Here, we test mechanistic and ecological explanations for the evolution of developmental duration using embryological data and information on incubation and fledging for 3096 avian species. Developmental phases associated primarily with growth are the longest and most variable, consistent with a role for allometric constraint in determining the duration of development. In addition, developmental durations retain a strong imprint of deep evolutionary history and body size differences among species explain less variation than previously thought. Finally, we reveal ecological correlates of developmental durations, including variables associated with the relative safety of the developmental environment and pressures of breeding phenology. Overall, our results provide broad-scale insight into the relative importance of mechanistic, ecological and evolutionary constraints in shaping the diversification of this key life-history trait.