Biology subjects

Foster, Y.

Publications and source records attributed to Foster, Y..

3 recordsLinked to original sources

bioRxiv2026

Elevated recessive lethal frequencies drive hatching failure following near extinction in 'Alala, the Hawaiian crow

Near-extinction events impose severe genomic bottlenecks that can have lasting fitness consequences, yet the specific mechanisms involved remain poorly understood. Alal[a], the last remaining Hawaiian crow, narrowly avoided extinction when a conservation breeding program was initiated from just eight genetic founders. Although the conservation breeding program has since recovered to [~]120 birds, it remains plagued by egg hatching failure rates >50%. To investigate the impacts of this bottleneck on hatching failure and other fitness components, we generated a chromosome-level reference genome and resequenced 175 individuals, including 78 deceased embryos. Although long runs of homozygosity (ROH) >1Mb are abundant in Alal[a] (mean FROH=0.32), associations between FROH and measures of survival and reproduction, including egg failure, were weak or nonexistent. Instead, we identify two recessive lethal haplotypes that together account for nearly all of the excess hatching failure and have persisted in the population at high frequency (15-25%), hinting at impaired purifying selection. Eco-evolutionary simulation models demonstrate that these findings are expected for a species that has endured a severe population bottleneck and exhibits modest levels of pre-bottleneck heterozygosity. Our findings suggest that elevated recessive allele frequencies may be a broadly important consequence of population bottlenecks.

evolutionary biology↗

bioRxiv2022

Species-wide genomics of kakapo provides transformational tools to accelerate recovery

The k[a]k[a]p[o] is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analyzed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size, and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values, and hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for k[a]k[a]p[o], including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.

genomics↗

bioRxiv2022

Ebony underpins Batesian mimicry in an insect melanic polymorphism

The evolution of Batesian mimicry - whereby harmless species avoid predation through their resemblance to harmful species - has long intrigued biologists. In rare cases, such mimicry systems can be highly dynamic, being maintained via frequency-dependent selection on intraspecific polymorphisms, in which only some individuals within a population resemble a noxious model. Here, we use genomic approaches to identify the genetic basis of a striking mimicry polymorphism within a widespread New Zealand stonefly complex. Specifically, highly melanised specimens of Zelandoperla closely resemble an aposematic stonefly (Austroperla cyrene) well-known for its production of hydrogen cyanide. We assess convergence in the colour pattern of these two species, compare their relative palatability to predators, and use genome-wide association mapping to elucidate the genetic basis of this mimicry polymorphism. Our analysis reveals that melanised Zelandoperla overlap significantly with Austroperla in colour space, but are significantly more palatable to predators, indicating that they are indeed Batesian mimics. Analysis of 194,773 genome-wide SNPs reveals a strong outlier locus (ebony) differentiating melanic (mimic) versus non-melanic phenotypes. As ebony has a well-documented role in insect melanin biosynthesis, our findings highlight its conserved function across deeply divergent hexapod lineages. Distributional records suggest a link between the occurrence of Zelandoperla mimics and forested ecosystems where the model Austroperla is abundant, suggesting the potential for adaptive shifts in this system underpinned by environmental change.

evolutionary biology↗