Multiple life-stage inbreeding depression impacts demography and extinction risk in an extinct-in-the-wild species

The genetic status and rescue measure for a geographically isolated population of Amur tigers

The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population's genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers.

No evidence of inbreeding depression despite a historical severe bottleneck in the endangered Bermuda petrel (Pterodroma cahow)

The Bermuda petrel Pterodroma cahow is an island endemic seabird that belongs to the Procellariiformes, one of the most endangered orders of birds. Historical records suggest a significant population size decline following human settlement in Bermuda, bringing the species to near extinction. Since the 1950s, the population has been recovering aided by the implementation of an ongoing conservation plan. However, it still faces several threats, and negative genetic effects resulting from that drastic decline are to be expected, including inbreeding and genetic drift. We studied genetic diversity and levels of inbreeding, and their effects on individual fitness and mating choice. We also tested for a genetic signature of the recent demographic bottleneck. For this, we analyzed variation in thousands of nuclear single-nucleotide polymorphisms derived from double digest restriction site-associated DNA sequencing and 1 mitochondrial gene (cytochrome oxidase I). The results revealed that the Bermuda petrel suffered a recent genetic bottleneck and shows low mitochondrial diversity compared with other petrel species. Conversely, nuclear diversity was similar to that of other endangered petrels. Inbreeding levels were not high overall, although some individuals were highly inbred. However, we found no evidence that individual inbreeding or relatedness between mates affected hatching success, or that mate choice is influenced by kinship in this very small population.

Extinct in the wild: The precarious state of Earth's most threatened group of species

Extinct in the Wild (EW) species are placed at the highest risk of extinction under the International Union for Conservation of Nature Red List, but the extent and variation in this risk have never been evaluated. Harnessing global databases of ex situ animal and plant holdings, we report on the perilous state of EW species. Most EW animal species-already compromised by their small number of founders-are maintained at population sizes far below the thresholds necessary to ensure demographic security. Most EW plant species depend on live propagation by a small number of botanic gardens, with a minority secured at seed bank institutions. Both extinctions and recoveries are possible fates for EW species. We urgently call for international effort to enable the latter.

Addressing Threats and Ecosystem Intactness to Enable Action for Extinct in the Wild Species

The species listed as Extinct in the Wild (EW) in the IUCN Red List of Threatened Species consist of 84 plants and animals that have been lost from their indigenous range. EW species are therefore restricted to ex situ conservation facilities and often have populations founded with few individuals. Our analysis demonstrates that 60% of EW species are associated with ecoregions that have very low proportions of intact habitat. Furthermore, threats such as invasive species, pollution, and climate change affect just over half of EW species and compound the obstacles facing their reinstatement to the wild. Despite these bleak assessments, there are various options for EW recovery. We present five scenarios that encapsulate the circumstances facing EW species and suggest potential conservation action for each of these situations. We illustrate these scenarios using case studies of EW species that demonstrate how the various options of ex situ management, reintroduction, and assisted colonisation to new habitat can be used to address the very exacting requirements of EW species. Our aim is to present a broad review of the obstacles facing the recovery of EW species whilst inspiring action to prevent the extinction of the most imperilled species on the planet.

Ex situ breeding programs benefit from science-based cooperative management

Science-based management confers a variety of benefits to wildlife populations that are cooperatively managed by zoos and aquariums, including those managed through the Association of Zoos and Aquariums. Briefly, when management strategies are successful, they result in reproductively robust populations that better retain genetic diversity and limit inbreeding than unmanaged populations. Although the benefits of demographic and genetic management have been well documented throughout both the scientific and popular literature, it has also been established that the majority of managed populations in zoos and aquariums are not meeting the minimum criteria believed to convey long-term biological viability. For most of these populations, an inability to meet viability criteria is not an inherent failure of how cooperative management is implemented. Furthermore, in recent years, we have perceived that the need to meet specific viability goals sometimes has obscured the benefits that these populations receive from rigorous, science-based management. To better clarify the conversation surrounding population viability in zoos and aquariums, we seek to decouple viability measures and how they predict population persistence from the benefits conferred to populations through science-based management. A primary goal of population management is to facilitate the persistence of priority species for longer than would be expected if no such management were implemented. Although current viability measures and future projections of viability are important tools for assessing the likelihood of population persistence, they are not indicators of which populations may most benefit from science-based management. Here, we review the history and purpose of applying science-based management to zoo and aquarium populations, describe measures of population viability and caution against confusing those measures of viability with population management goals or long-term population sustainability, and clearly articulate the benefits conferred to zoo and aquarium populations by science-based management.

Predation thresholds for reintroduction of native avifauna following suppression of invasive Brown Treesnakes on Guam

The brown treesnake (BTS) (Boiga irregularis) invasion on Guåhan (in English, Guam) led to the extirpation of nearly all native forest birds. In recent years, methods have been developed to reduce BTS abundance on a landscape scale. To help assess the prospects for the successful reintroduction of native birds to Guåhan following BTS suppression, we modeled bird population persistence based on their life history characteristics and relative sensitivity to BTS predation. We constructed individual-based models and simulated BTS predation in hypothetical founding populations for each of seven candidate bird species. We represented BTS predation risk in two steps: risk of being encountered and risk of mortality if encountered. We link encounter risk from the bird's perspective to snake contact rates at camera traps with live animal lures, the most direct practical means of estimating BTS predation risk. Our simulations support the well-documented fact that Guåhan's birds cannot persist with an uncontrolled population of BTS but do indicate that bird persistence in Guåhan's forests is possible with suppression short of total eradication. We estimate threshold BTS contact rates would need to be below 0.0002-0.0006 snake contacts per bird per night for these birds to persist on the landscape, which translates to an annual encounter probability of 0.07-0.20. We simulated the effects of snake-proof nest boxes for Sihek (Todiramphus cinnamominus) and Såli (Aplonis opaca), but the benefits were small relative to the overall variation in contact rate thresholds among species. This variation among focal bird species in sustainable predation levels can be used to prioritize species for reintroduction in a BTS-suppressed landscape, but variation among these species is narrow relative to the required reduction from current BTS levels, which may be four orders of magnitude higher (>0.18). Our modeling indicates that the required predation thresholds may need to be lower than have yet been demonstrated with current BTS management. Our predation threshold metric provides an important management tool to help estimate target BTS suppression levels that can be used to determine when bird reintroduction campaigns might begin and serves as a model for other systems to match predator control with reintroduction efforts.

African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity

African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.

Distilling Professional Opinion to Gauge Vulnerability of Guam Avifauna to Brown Treesnake Predation

The avifauna of Guam was devastated by the introduction of the Brown Treesnake, and the restoration of native birds would need to address the problem with eradication or suppression of BTS. With eradication of the snake unlikely in the near term, and suppression capabilities limited to specific finite areas, key information for reintroductions is how low BTS abundance will likely need to be for each bird species to be re-established based on their vulnerability to BTS predation. Here, we estimate vulnerability, which can no longer be measured directly, so biologists who are familiar with one or more of seven Guam birds were surveyed to obtain their knowledge and produce quantitative vulnerability estimates. As is typical of birds adapted to islands devoid of predators, respondents judged that our focal species exhibit few predator avoidance and tolerance traits, leaving body size as the prime determinant of vulnerability. Respondent opinion also holds that any behavior that reduces the likelihood of an encounter by BTS, e.g., roosting/nesting in palm crowns, cavity nesting, and in particular urban dwelling, substantially reduces vulnerability. Our results can help inform species-specific decisions about when it may be safe to consider the release of birds on Guam depending on the relative vulnerability of each species to predation by BTS.