Biology subjects

Femerling, G.

Publications and source records attributed to Femerling, G..

3 recordsLinked to original sources

bioRxiv2024

Persistent genomic erosion in whooping cranes despite demographic recovery

Integrating in-situ (wild) and ex-situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane (Grus americana) experienced severe population declines in the 18th century, culminating into a collapse to 16 individuals in 1941. Legal protections and conservation actions have since increased the population to approximately 840 individuals, yet the impact on genomic diversity remains unclear. We analysed the temporal dynamics of genomic erosion by sequencing a high-quality genome reference, and re-sequencing 16 historical and 37 modern genomes, including wild individuals and four generations of captive-bred individuals. Genomic demographic reconstructions reveal a steady decline, accelerating over the past 300 years with the European settlement of North America. Temporal genomic analyses show that despite demographic recovery, the species has lost 70% of its genetic diversity and has increased their inbreeding. Although the modern population bottleneck reduced the ancestral genetic load, modern populations possess more realized load than masked load, possibly resulting in a chronic loss of fitness. Integrating pedigree and genomic data, we underscore the role of breeding management in reducing recent inbreeding. Yet ongoing heterozygosity loss, load accumulation, and background inbreeding argues against the species downlisting from their current Endangered status on the IUCN Red List and the Endangered Species Act. The presence of private genetic variation in wild and captive populations suggests that wild-captive crosses could enhance genetic diversity and reduce the realized load. Our findings emphasize the role of genomics in informing conservation management and policy.

evolutionary biology↗

bioRxiv2023

Topological stratification of continuous genetic variation in large biobanks

Biobanks now contain genetic data from millions of individuals. Dimensionality reduction, visualization and clustering are standard when exploring data at these scales; while efficient and tractable methods exist for the first two, clustering remains challenging because of uncertainty about sources of population structure. In practice, clustering is commonly performed by drawing shapes around dimensionally reduced data or assuming populations have a "type" genome. We propose a method of clustering data with topological analysis that is fast, easy to implement, and integrates with existing pipelines. The approach is robust to the presence of sub-populations of varying sizes and wide ranges of population structure patterns. We use UMAP and HDBSCAN, respectively methods of dimensionality reduction and density clustering, on data from three biobanks. We illustrate how topological genetic strata can help us understand structure within biobanks, evaluate distributions of genotypic and phenotypic data, examine polygenic score transferability, identify potential influential alleles, and perform quality control.

genomics↗

bioRxiv2022

Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction

High genetic diversity is often a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the IUCN Red List in 2020. By comparing historical, pre-bottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after the demographic recovery. We show that the proportion of severely deleterious mutations has reduced in modern individuals, but mildly deleterious mutations have remained unchanged. Computer simulations suggest that the Seychelles paradise flycatcher avoided extinction and recovered due to its long-term small Ne. This reduced the masked load and made the species more resilient to inbreeding. However, we also show that the chronically small Ne and the severe bottleneck resulted in very low genetic diversity in the modern population. Our simulations show this is likely to reduce the species adaptive potential when faced with environmental change, thereby compromising its long-term population viability. In light of rapid global rates of population decline, our work highlights the importance of considering genomic erosion and computer modelling in conservation assessments

evolutionary biology↗