Author Correction: Puma genomes from North and South America provide insights into the genomic consequences of inbreeding

Genomic trajectories of a near-extinction event in the Chatham Island black robin

BACKGROUND

Understanding the micro--evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.

RESULTS

We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.

CONCLUSION

Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.

“I Did, I Did Taw a Puddy Tat!” Pumas in Urban Ecosystems of Latin America: A Review of the Mediatic Information

The concentration of people living in small areas has increased in the last decade, with more than half of the world's population living in cities. This is particularly true for Latin America, a region with no particular high contribution to the world total population, but hosts several large cities. The increase in urbanization causes several threats to wildlife that face the loss of their habitat and novel environmental pressures. As the number of wildlife entering cities seems to have increased in the last year, we characterize the temporal and geographical events of a widely distributed carnivore, the puma, Puma concolor. We performed an exhaustive search for media news regarding the sighting, capture, and/or killing of pumas within human settlement areas, and tried to relate them with potential explanatory variables. We found a total of 162 events in Latin America in a period of the last 10 years, particularly concentrated in the year 2020. Most records came from Brazil, followed by Argentina, Chile, and Mexico. Of the total, 41% were only sightings, 58% were captures, and a minor percentage were considered as mascotism. Almost the same number of records came from highly populated areas (cities) than from low populated areas (rural) but with important differences between countries. The countries with more records in urban areas (Brazil and Mexico) showed a larger surface occupied by cities. The countries with most records in rural areas (Argentina and Chile) present the opposite pattern of occupied surface. This might indicate that different percentages of areas dedicated to cities or urban spaces might explain the differences among countries. The most important variable related to puma events in the populated areas was sky brightness, while human density and cattle density explained minor parts. The “anthropause” due to the COVID-19 pandemic might explain the larger number of records from 2020, while the absence of high-quality habitats due to fragmentation and high cattle density, might force the pumas to enter populated areas searching for food. Minor values of night lights could be related to a facilitation of efficiency of foraging behavior. Although some bias might exist in the data, the results should be taken into account as general statements for all analyzed countries.

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.