Biology subjects

Lee, K. G. L.

Publications and source records attributed to Lee, K. G. L..

4 recordsLinked to original sources

bioRxiv2026

Genomic quantification of inbreeding depression in wild vertebrate populations

Inbreeding depression is a critical driver of extinction risk in fragmented populations, yet its magnitude in the wild has historically been estimated using sparse pedigrees or low-resolution molecular markers. The transition to genomic metrics of inbreeding offers unprecedented precision in quantifying realized homozygosity and its fitness costs. We conducted a systematic review and multi-level meta-analysis of 91 effect sizes from 20 wild vertebrate populations to provide a global benchmark for genomic inbreeding depression. Our results confirm a pervasive and significant negative relationship between fitness and genomic inbreeding. Males exhibited significantly stronger inbreeding depression than females. Fitness costs were consistent across life stages (developmental, adult and lifetime) and across types of fitness traits (survival vs. reproduction). We found no significant association between the magnitude of inbreeding depression and IUCN conservation status or historical isolation (discretely measured as "isolated" or "non-isolated"). As we enter a genomics era that will provide realised estimates of inbreeding, future studies can be added to this meta-analysis to provide a more comprehensive view of inbreeding depression and potentially identify patterns pertinent to evolutionary biology and conservation science.

evolutionary biology↗

bioRxiv2026

Inbreeding depression by polygenic load following a severe population bottleneck

It is poorly understood how populations survive extreme bottlenecks despite severe inbreeding. We investigate the genomic architecture of inbreeding in the once critically endangered Seychelles warbler (Acrocephalus sechellensis) using 37 years of individual-based monitoring and 1.8 million SNPs. Linkage disequilibrium patterns reveal a historical effective population size of [~]270 that plummeted to [~]13 coinciding with human colonisation events of the Seychelles archipelago. Contemporary genomes are over one-third inbred from recent inbreeding measured by runs of homozygosity (ROH) formed since human colonisation of the Seychelles, 50 generations ago (mean FROH < 50 generations ago = 0.38), and we identify significant inbreeding depression across cross key fitness traits. On average, a 17.9% reduction in lifespan and a 15.1% reduction in lifetime offspring production were associated with each 10% increase in individual inbreeding. Genome-wide scans reveal this depression is caused by a polygenic load. Our results suggest that a history of small population size could have facilitated the selective purging of severe genetic load, while mildly deleterious alleles escaped selection via drift. A partitioned genetic load architecture potentially enabled species recovery despite the inbreeding depression that followed near-extinction.

evolutionary biology↗

bioRxiv2026

A Seychelles warbler genomic toolkit

Understanding evolutionary processes is greatly facilitated by high-quality data on genetic variation. We report the development of a genomic toolkit for a recently bottlenecked, long-term studied species, the Seychelles warbler (Ptimerl dezil; Acrocephalus sechellensis). This toolkit comprises a reference genome assembled into 31 chromosomes, together with functional annotations and reference-panel-free imputation of whole-genome sequences from 1,935 individuals. The genomic data have been used to assign the sequenced individuals into a genetic pedigree. Individual genomic data are associated with a suite of phenotypic metadata, amassed from three decades of fieldwork in this closed, long-term monitored population. We compared sex and parentage assigned using the genomic data with the previously recorded sex and parentage metadata to identify and correct 41 sample DNA samples labelled with the wrong identity. This population resource enables a wide range of analyses, that include, but are not limited to phylogenetics, metabarcoding, recombination rates, linkage patterns, adaptation, heritability, demographic history, selection, and inbreeding estimates. We wish to encourage interest from researchers seeking to collaborate on future analyses and data collection. Overall, our methods demonstrate the potential of next generation sequencing and statistical tools to provide dense genomic datasets at large sample sizes for wild populations.

genomics↗

bioRxiv2024

A path analysis disentangling determinants of natal dispersal in a cooperatively breeding bird

Delayed offspring dispersal is an important aspect of the evolution of cooperative breeding. By applying a path-analysis approach to the long-term Seychelles warbler (Acrocephalus sechellensis) dataset, we studied whether and how delayed dispersal is affected by territory quality, the presence of helpers and non-helping subordinates, maternal breeding status, age and fecundity, and offspring sex ratio. We found that offspring are more likely to disperse when their genetic mothers are co-breeders, helpers are absent and territory quality is high. In contrast to earlier findings, our analysis does not support the idea that offspring sex ratio is affected by territory quality and helper presence. Our findings suggest that a complex interplay of ecological and social factors shapes dispersal decisions. Our study underscores the importance of considering proximate factors in understanding cooperative breeding dynamics, and it shows that path analyses offer valuable insights into dissecting the intricate relationships influencing dispersal in wild populations.

ecology↗