Close-kin mark-recapture informs critically endangered terrestrial mammal status.

Reliable information on population size is fundamental to the management of threatened species. For wild species, mark-recapture methods are a cornerstone of abundance estimation. Here, we show the first application of the close-kin mark-recapture (CKMR) method to a terrestrial species of high conservation value; the Christmas Island flying-fox (CIFF). The CIFF is the island's last remaining native terrestrial mammal and was recently listed as critically endangered. CKMR is a powerful tool for estimating the demographic parameters central to CIFF management and circumvents the complications arising from the species' cryptic nature, mobility, and difficult-to-survey habitat. To this end, we used genetic data from 450 CIFFs captured between 2015 and 2019 to detect kin pairs. We implemented a novel CKMR model that estimates sex-specific abundance, trend, and mortality and accommodates observations from the kin-pair distribution of male reproductive skew and mate persistence. CKMR estimated CIFF total adult female abundance to be approximately 2050 individuals (95% CI (950, 4300)). We showed that on average only 23% of the adult male population contributed to annual reproduction and strong evidence for between-year mate fidelity, an observation not previously quantified for a Pteropus species in the wild. Critically, our population estimates provide the most robust understanding of the status of this critically endangered population, informing immediate and future conservation initiatives.

Implications of past and present genetic connectivity for management of the saltwater crocodile (Crocodylus porosus).

Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life-history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long-distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey ≈ 3000 high-quality genome-wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present-day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second-degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state-wide scales.

Low levels of sibship encourage use of larvae in western Atlantic bluefin tuna abundance estimation by close-kin mark-recapture.

Globally, tunas are among the most valuable fish stocks, but are also inherently difficult to monitor and assess. Samples of larvae of Western Atlantic bluefin tuna Thunnus thynnus (Linnaeus, 1758) from standardized annual surveys in the northern Gulf of Mexico provide a potential source of "offspring" for close-kin mark-recapture (CKMR) estimates of abundance. However, the spatial patchiness and highly skewed numbers of larvae per tow suggest sampled larvae may come from a small number of parents, compromising the precision of CKMR. We used high throughput genomic profiling to study sibship within and among larval tows from the 2016 standardized Gulf-wide survey compared to targeted sampling carried out in 2017. Full- and half-siblings were found within both years, with 12% of 156 samples in 2016 and 56% of 317 samples in 2017 having at least one sibling. There were also two pairs of cross cohort half-siblings. Targeted sampling increased the number of larvae collected per sampling event but resulted in a higher proportion of siblings. The combined effective sample size across both years was about 75% of the nominal size, indicating that Gulf of Mexico larval collections could be a suitable source of juveniles for CKMR in Western Atlantic bluefin tuna.

Robustness of close-kin mark-recapture estimators to dispersal limitation and spatially varying sampling probabilities.

Close-kin mark-recapture (CKMR) is a method for estimating abundance and vital rates from kinship relationships observed in genetic samples. CKMR inference only requires animals to be sampled once (e.g., lethally), potentially widening the scope of population-level inference relative to traditional monitoring programs.One assumption of CKMR is that, conditional on individual covariates like age, all animals have an equal probability of being sampled. However, if genetic data are collected opportunistically (e.g., via hunters or fishers), there is potential for spatial variation in sampling probability that can bias CKMR estimators, particularly when genetically related individuals stay in close proximity.We used individual-based simulation to investigate consequences of dispersal limitation and spatially biased sampling on performance of naive (nonspatial) CKMR estimators of abundance, fecundity, and adult survival. Population dynamics approximated that of a long-lived mammal species subject to lethal sampling.Naive CKMR abundance estimators were relatively unbiased when dispersal was unconstrained (i.e., complete mixing) or when sampling was random or subject to moderate levels of spatial variation. When dispersal was limited, extreme variation in spatial sampling probabilities negatively biased abundance estimates. Reproductive schedules and survival were well estimated, except for survival when adults could emigrate out of the sampled area. Incomplete mixing was readily detected using Kolmogorov-Smirnov tests.Although CKMR appears promising for estimating abundance and vital rates with opportunistically collected genetic data, care is needed when dispersal limitation is coupled with spatially biased sampling. Fortunately, incomplete mixing is easily detected with adequate sample sizes. In principle, it is possible to devise and fit spatially explicit CKMR models to avoid bias under dispersal limitation, but development of such models necessitates additional complexity (and possibly additional data). We suggest using simulation studies to examine potential bias and precision of proposed modeling approaches prior to implementing a CKMR program.

The influence of petroleum oil films on the feather structure of tropical and temperate seabird species.

Feather fouling is a primary cause of seabird mortality during marine hydrocarbon oil spills. Understanding how oils interact with feathers is an important step in mitigating this threat. Seabird feathers from 12 taxa, representing most seabird families from the tropics and southern latitudes, were exposed to crude and condensate oil films under laboratory settings. Feathers were measured for changes in mass proportional to feather size, and for barbule clumping. Seabird feathers from six distinct families exposed to very thin oil sheens (<0.3 µm) showed no significant change in proportional mass relative to control treatments, and 10 of the 12 species exposed to these films revealed no significant difference in barbule clumping. By contrast, exposure to both crude and condensate oil films ≥3 µm resulted in significant increases in feather mass and clumping. Our findings highlight the importance of considering the influence of oil on feather structure when compiling threat assessments involving seabirds.

Precision wildlife monitoring using unmanned aerial vehicles.

Unmanned aerial vehicles (UAVs) represent a new frontier in environmental research. Their use has the potential to revolutionise the field if they prove capable of improving data quality or the ease with which data are collected beyond traditional methods. We apply UAV technology to wildlife monitoring in tropical and polar environments and demonstrate that UAV-derived counts of colony nesting birds are an order of magnitude more precise than traditional ground counts. The increased count precision afforded by UAVs, along with their ability to survey hard-to-reach populations and places, will likely drive many wildlife monitoring projects that rely on population counts to transition from traditional methods to UAV technology. Careful consideration will be required to ensure the coherence of historic data sets with new UAV-derived data and we propose a method for determining the number of duplicated (concurrent UAV and ground counts) sampling points needed to achieve data compatibility.