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Biomedical subjects

Samuel A Speak

Publications and source records attributed to Samuel A Speak.

2 recordsLinked to original sources

Genomic erosion in the assessment of species' extinction risk and recovery potential.

Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the International Union for Conservation of Nature Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the International Union for Conservation of Nature Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.

Extinction, Biological

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 in a collapse to ~20 individuals by 1944. Legal protections and conservation actions have since increased the census population from a stock of 16 individuals 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 reference genome, and re-sequencing 16 historical (years 1867-1893) and 37 modern (2007-2020) 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 historical genetic diversity and has increased its inbreeding. Although the modern population bottleneck reduced the ancestral genetic load, modern populations possess more realised 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 persistent effects of historical inbreeding (i.e., background inbreeding) argue against the species' downlisting from its 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 realised load. Our findings emphasise the role of genomics in informing conservation management and policy.

Animals