Supplementary material from "Genetic consequence of rapid demographic collapses suggested by population genomics of the black-necked cranes"

Many plant and animal species face rapid demographic declines, requiring an examination of the genetic consequences. The small population paradigm suggests such declines increase genetic load and extinction risk. However, some species recover rapidly from severe bottlenecks, indicating possible alternative outcomes. To investigate, we compared population genomic characteristics of the black-necked crane before and after a recent bottleneck. Modern genomes showed reduced diversity, intensified inbreeding, and a greater realized genetic load compared to historical genomes, confirming the impact of an abrupt bottleneck during the 1980s. Our analyses also revealed that purifying selection remained efficient during this period, as indicated by the relative purging of highly deleterious alleles within runs of homozygosity and a consistent signal of strong evolutionary constraint at highly conserved homozygous sites. This persistence of purifying selection may have mitigated the severity of inbreeding depression. Thus, rapid demographic recovery can coincide with ongoing purifying selection, potentially preventing a short-term extinction vortex. However, the overall increased genetic load will likely impair long-term evolutionary potential. These findings highlight complex microevolutionary responses to population collapse and underscore the urgency of active conservation to reverse declines before genetic erosion becomes irreversible.