Brekke, P. | bioRxiv Science

bioRxiv2023

Including the Invisible Fraction in Whole Population Studies: a Guide to the Genetic Sampling of Unhatched Bird Eggs

Early embryo mortality has recently been proven to be a significant component of avian reproductive failure. Due to the difficulty in distinguishing eggs which have suffered early embryo mortality from unfertilised eggs, this cause of reproductive failure has historically been underestimated and overlooked. We describe methods for recognising and collecting undeveloped, unhatched eggs from wild bird populations, identifying and isolating embryonic material in unhatched eggs, and efficiently extracting DNA from those samples. We test these methods on unhatched eggs collected from the field which have undergone post-mortem incubation. We obtained DNA yields from early-stage embryos that are sufficient for a wide range of molecular techniques, including microsatellite genotyping for parentage analysis and sex-typing. The type of tissue sample taken from the egg affected downstream DNA yields and microsatellite amplification rates. Species-specific microsatellite markers had higher amplification success rates than cross-species markers. We make key recommendations for each stage of the sampling and extraction process and suggest improvements potential and protocol modifications. Genetic and possibly genomic analysis of embryos that die early in development has the potential to advance many fields. The methods described here will allow a more in-depth exploration of the previously overlooked causes of early embryo mortality in wild populations of birds, including threatened species.

genetics↗

bioRxiv2022

Intergenerational effects from spatial and genetic environment predict early-life social network structure

Early independence is a crucial stage in the ontogeny of social environments, but it is often challenging to study in the wild. Genetics may structure groups if young animals associate with familiar kin, but association opportunities also develop as a by-product of environmental processes such as spatial resource distribution. The contribution of these alternate factors in initial opportunities for bonding outside direct relatives is difficult to pick apart, despite its importance in shaping later life. However, species where genetics and spatial structure are less closely coupled (for example, via extra-pair mating) provide a natural opportunity to disentangle these effects. We addressed this gap by investigating the contribution of relatedness versus spatiotemporal synchrony (natal nest-box location and fledge timing) to early-life social structure in newly-independent young hihi (Notiomystis cincta). We also investigated the contribution of inbreeding in both juveniles and their parents, to individual-level sociality, as this genetic factor has had limited focus in studies of social structure. Using a long-term genetic pedigree, detailed breeding records, and social network data collected across three cohorts, we found that juvenile social associations were predicted by natal nest-box location, irrespective of relatedness between juveniles. Therefore, the physical environment can create initial opportunities for associations to develop once young animals disperse from natal sites. Furthermore, juvenile sociability was predicted by their fathers (but not mothers) inbreeding, highlighting how genetics may have indirect and intergenerational effects on social behaviour. Overall, social structure in wild animals can emerge early in life if the natal environment determines association opportunities. These patterns may even be pre-determined across generations if breeding and settlement decisions made by parents affect the physical and social environments experienced by their offspring. Ultimately, our study highlights how influences on early life social structure may have important consequences for population dynamics and evolutionary potential.

animal behavior and cognition↗