Several attempts have been made to understand the population dynamics of fishery resources, such as tuna species using an integrated analysis model with multiple data sources. However, estimating absolute abundance levels in practical stock assessments remains a challenge. Close-kin mark–recapture (CKMR) methods provide information about the number of adults in a population using close-kinship pairs identified by genetic markers and statistical methods. In this study, we compared three methods for kinship identification using different algorithms in samples of wild Pacific bluefin tuna genotyped across 5,029 genome-wide single nucleotide polymorphisms in 4,108 samples. The fraRF method we developed employs pairwise identity-by-descent values as inputs for random-forest classification. The other two methods were CKMRsim and COLONY, which have been published and applied in several studies. These three methods were applied to the actual genotyping data with moderate missing genotypes, in addition to the pseudo-generated genotyping data for the simulation test. The simulation test mimicked genotyping data with physical linkage as well as genetic characteristics similar to those of actual samples. The three methods resulted in different numbers of inferred kinship pairs for both generated and actual data. Particularly for the half-sibling pairs, considerable number of false-positive and false-negative existed in the identification results. The differences in kinship identification results were interpreted based on a simulation test. This study may promote the understanding of behavior in each software when applying the software to SNP data with moderate missing genotypes as in the case of this study.

In the context of initiatives focused on captive breeding and reintroduction of endangered animal species, it is crucial to minimize any bias in reproductive success during the reintroduction phase in order to preserve genetic diversity. One population of Tachysurus ichikawai, a critically endangered bagrid catfish endemic to Japan, faces a threat from the construction of a dam. To address this, a captive breeding program followed by translocation is being implemented. Multiple breeding families are involved in this process; however, if there is a bias in reproductive success among them after release, it will result in a decline in genetic diversity. To identify potential biases in breeding lineages, we conducted kinship analysis between individuals born at the release site and breeding individuals. Because there were no samples available from the released individuals themselves, we examined distant kinship relationships, such as grandparent–grandchild and uncle–aunt–nephew–niece relationships, using a substantial number of single-nucleotide polymorphisms obtained from the whole genome re-sequence. Our findings indicate no bias between lineages in the first year after reintroduction, but a significant bias in the second year, emphasizing the need for continuous management and monitoring of reintroduced populations. This study demonstrates that monitoring kinship after reintroduction can correct lineage bias, which is critical for the prompt restoration of genetic diversity.

Globally, around half of all tropical forests are secondary communities which are recovering from previous disturbances. In these communities, dominant pioneers play a critical role in the successional dynamics due their ability to modify the environment, and thus to facilitate or hinder the performance of other species. In this study, we examined the population dynamics of the dominant pioneer species, Mimosa acantholoba var. eurycarpa, in a tropical dry forest during the process of secondary succession. We collected data from permanent plots over a period of 13 years and used integral projection models to analyze the vital rates and changes in population size. Most vital rates were negatively related to successional age, with resprouting, survival and recruitment of individuals responding more strongly, and individual growth rate more weakly. These vital-rate trends translated into significant variation of population size over succession, with a maximum size at year four and a rapid decline thereafter. Overall, our findings suggest that this species benefits from its ability to display a large number of resprouts in very early stages of succession, contributing to the rapid increase in population density. However, as succession unfolds, a lack of resprouting and a decline in survival reduce its population size, to the point of local extinction. These results highlight the importance of resprouting in the early dynamics of tropical dry forest communities recovering from disturbance.

The recovery of mammalian species in the US Midwest through natural recolonization constitutes a conservation success story, yet management remains challenging due to many unknowns related to population dynamics and abundance. Abundance is a critical parameter for management decisions, and estimating the density and abundance of elusive species, such as terrestrial carnivores, remains challenging despite recent technological advances. In this study, we evaluated density and abundance of a recovering carnivore species, the bobcat (Lynx rufus) in two areas of Ohio using non-invasive DNA from scat. The target areas in eastern and southern Ohio have been shown to have uneven dynamics and recolonization success and we expected that this would be reflected in differences in density and abundance. We collected 298 bobcat scats between July 2018 and April 2019 on 150 km of repeated transects. Of these, 102 scats were successfully genotyped, and 55 individuals were identified (33 in eastern Ohio and 22 in southern Ohio). Using Spatially Explicit Capture-Recapture models, we estimated 17.9 ± 4.3 and 11.3 ± 2.9 bobcats/100 km2 in eastern and southern Ohio study areas, respectively. Our results support prior telemetry data which indicated that bobcats in eastern Ohio had smaller home-ranges than bobcats in southern Ohio, and thus could support a higher density of individuals. The higher densities were similar to other eastern US populations and are much higher than other Midwestern recovering populations. Our results provide a snapshot of the population status and can be used to determine sustainable management strategies for Ohio’s bobcat population