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.

The angiogenic growth of cities.

Describing the space-time evolution of urban population is a fundamental challenge in the science of cities, yet a complete theoretical treatment of the underlying dynamics is still missing. Here, we first reconstruct the evolution of London (UK) over 180 years and show that urban growth consists of an initial phase of diffusion-limited growth, followed by the development of the railway transport network and a consequential shift from central to suburban living. Such dynamics-which are analogous to angiogenesis in biological systems-can be described by a minimalist reaction-diffusion model coupled with economic constraints and an adaptive transport network. We then test the generality of our approach by reproducing the evolution of Sydney, Australia, from 1851 to 2011. We show that the rail system coevolves with urban population, displaying hierarchical characteristics that remain constant over time unless large-scale interventions are put in place to alter the modes of transport. These results demonstrate that transport schemes are first-order controls of long-term urbanization patterns and efforts aimed at creating more sustainable and healthier cities require careful consideration of population-transport feedbacks.

Partition refinement of WorldPop population spatial distribution data method: A case study of Zhuhai, China.

Currently, the core idea of the refined method of population spatial distribution is to establish a correlation between the population and auxiliary data at the administrative-unit level and, then, refine it to the grid unit. However, this method ignores the advantages of public population spatial distribution data. Given these problems, this study proposed a partition strategy using the natural break method at the grid-unit level, which adopts the population density to constrain the land class weight and redistributes the population under the dual constraints of land class and area weights. Accordingly, we used the dasymetric method to refine the population distribution data. The study established a partition model for public population spatial distribution data and auxiliary data at the grid-unit level and, then, refined it to smaller grid units. This method effectively utilizes the public population spatial distribution data and solves the problem of the dataset being not sufficiently accurate to describe small-scale regions and low resolutions. Taking the public WorldPop population spatial distribution dataset as an example, the results indicate that the proposed method has higher accuracy than other public datasets and can also describe the actual spatial distribution characteristics of the population accurately and intuitively. Simultaneously, this provides a new concept for research on population spatial distribution refinement methods.

Genetic Structure and Diversity of Hatchery and Wild Populations of Yellow Catfish Tachysurus fulvidraco (Siluriformes: Bagridae) from Korea.

Yellow catfish Tachysurus fulvidraco is an important commercial fish species in South Korea. However, due to their current declines in its distribution area and population size, it is being released from hatchery populations into wild populations. Hatchery populations also produced from wild broodstocks are used for its captive breeding. We reported 15 new microsatellite DNA markers of T. fulvidraco to identify the genetic diversity and structure of its hatchery and wild populations, providing baseline data for useful resource development strategies. The observed heterozygosity of the hatchery populations ranged from 0.816 to 0.873, and that of the wild populations ranged from 0.771 to 0.840. Their inbreeding coefficient ranged from -0.078 to 0.024. All populations experienced a bottleneck (p < 0.05), with effective population sizes ranging from 21 to infinity. Their gene structure was divided into two groups with STRUCTURE results of K = 2. It was confirmed that each hatchery population originated from a different wild population. This study provides genetic information necessary for the future development and conservation of fishery resources for T. fulvidraco.

Infection-induced increases to population size during cycles in a discrete-time epidemic model.

One-dimensional discrete-time population models, such as those that involve Logistic or Ricker growth, can exhibit periodic and chaotic dynamics. Expanding the system by one dimension to incorporate epidemiological interactions causes an interesting complexity of new behaviors. Here, we examine a discrete-time two-dimensional susceptible-infectious (SI) model with Ricker growth and show that the introduction of infection can not only produce a distinctly different bifurcation structure than that of the underlying disease-free system but also lead to counter-intuitive increases in population size. We use numerical bifurcation analysis to determine the influence of infection on the location and types of bifurcations. In addition, we examine the appearance and extent of a phenomenon known as the 'hydra effect,' i.e., increases in total population size when factors, such as mortality, that act negatively on a population, are increased. Previous work, primarily focused on dynamics at fixed points, showed that the introduction of infection that reduces fecundity to the SI model can lead to a so-called 'infection-induced hydra effect.' Our work shows that even in such a simple two-dimensional SI model, the introduction of infection that alters fecundity or mortality can produce dynamics can lead to the appearance of a hydra effect, particularly when the disease-free population is at a cycle.

Plant-ant interactions mediate herbivore-induced conspecific negative density dependence in a subtropical forest.

The early growth stage of plants is vital to community diversity and community regeneration. The Janzen-Connell hypothesis predicts that conspecific density dependence lowers the survival of conspecific seedlings by attracting specialist natural enemies, promoting the recruitment and performance of heterospecific neighbors. Recent work has underscored how this conspecific negative density dependence may be mediated by mutualists - such as how mycorrhizal fungi may mediate the accrual of host-specific pathogens beneath the crown of conspecific adult trees. Aboveground mutualist and enemy interactions exist as well, however, and may provide useful insight into density dependence that are as of yet unexplored. Using a long-term seedling demographic dataset in a subtropical forest plot in central China, we confirmed that conspecific neighborhoods had a significant negative effect on seedling survival in this subtropical forest. Furthermore, although we detected more leaf damage in species that were closely related to ants, we found that the presence of ants had significant positive effects on seedling survival. Beside this, we also found a negative effect of ant appearance on seedling growth which may reflect a trade-off between survival and growth. Overall, our findings suggested that ants and conspecific neighborhoods played important but inverse roles on seedling survival and growth. Our results suggest ants may mediate the influence of conspecific negative density dependence on seedling survival at community level.

The influence of gene flow on population viability in an isolated urban caracal population.

Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.

Neotropical mammal responses to megafires in the Brazilian Pantanal.

The increasing frequency and severity of human-caused fires likely have deleterious effects on species distribution and persistence. In 2020, megafires in the Brazilian Pantanal burned 43% of the biome's unburned area and resulted in mass mortality of wildlife. We investigated changes in habitat use or occupancy for an assemblage of eight mammal species in Serra do Amolar, Brazil, following the 2020 fires using a pre- and post-fire camera trap dataset. Additionally, we estimated the density for two naturally marked species, jaguars Panthera onca and ocelots Leopardus pardalis. Of the eight species, six (ocelots, collared peccaries Dicotyles tajacu, giant armadillos Priodontes maximus, Azara's agouti Dasyprocta azarae, red brocket deer Mazama americana, and tapirs Tapirus terrestris) had declining occupancy following fires, and one had stable habitat use (pumas Puma concolor). Giant armadillo experienced the most precipitous decline in occupancy from 0.431 ± 0.171 to 0.077 ± 0.044 after the fires. Jaguars were the only species with increasing habitat use, from 0.393 ± 0.127 to 0.753 ± 0.085. Jaguar density remained stable across years (2.8 ± 1.3, 3.7 ± 1.3, 2.6 ± 0.85/100 km2), while ocelot density increased from 13.9 ± 3.2 to 16.1 ± 5.2/100 km2. However, the low number of both jaguars and ocelots recaptured after the fire period suggests that immigration may have sustained the population. Our results indicate that the megafires will have significant consequences for species occupancy and fitness in fire-affected areas. The scale of megafires may inhibit successful recolonization, thus wider studies are needed to investigate population trends.

A crescente frequência e gravidade dos incêndios causados pelo homem provavelmente terão efeitos deletérios na distribuição e persistência das espécies. Em 2020, mega incêndios no Pantanal brasileiro queimaram 43% do bioma e resultaram na mortalidade em massa da vida selvagem. Nós investigamos mudanças no uso ou ocupação do habitat para uma comunidade de oito espécies de mamíferos na Serra do Amolar, Brasil, após os incêndios de 2020, usando um conjunto de dados de armadilhas fotográficas instaladas no período pré e pós­fogo. Além disso, estimamos a densidade de duas espécies naturalmente marcadas, a onça­pintada Panthera onca e a jaguatirica Leopardus pardalis. Das oito espécies, seis (a jaguatirica, o cateto Dicotyles tajacu, o tatu­canastra Priodontes maximus, a cutia Dasyprocta azarae, o veado mateiro Mazama americana e a anta Tapirus terrestris) tiveram ocupação reduzida após os incêndios, e uma teve uso de habitat estável (a onça­parda, Puma concolor). O tatu­canastra apresentou o declínio mais acentuado na ocupação após os incêndios de 0,431 ± 0,171 para 0,077 ± 0,044. A onça­pintada foi a única espécie com uso crescente de habitat, de 0,393 ± 0,127 para 0,753 ± 0,085. A densidade da onça­pintada permaneceu estável ao longo dos anos (2,8 ± 1,3, 3,7 ± 1,3, 2,6 ± 0,85/100 km2), enquanto a densidade da jaguatirica aumentou de 13,9 ± 3,2 para 16,1 ± 5,2/100 km2. No entanto, o baixo número de onças­pintadas e jaguatiricas recapturadas após o período do fogo sugere que a imigração pode ter sustentado as populações. Nossos resultados indicam que os mega incêndios terão consequências significativas para a ocupação e resiliência das espécies nas áreas afetadas pelo fogo. A escala dos mega incêndios pode inibir uma recolonização bem­sucedida, pelo que são necessários estudos mais amplos para investigar as tendências populacionais.

Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck.

Studies have found a pronounced decline in male effective population sizes worldwide around 3000-5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.

Habitat alteration or climate: What drives the densities of an invading ungulate?

Anthropogenic habitat alteration and climate change are two well-known contributors to biodiversity loss through changes to species distribution and abundance; yet, disentangling the effects of these two factors is often hindered by their inherent confound across both space and time. We leveraged a contrast in habitat alteration associated with the jurisdictional boundary between two Canadian provinces to evaluate the relative effects of spatial variation in habitat alteration and climate on white-tailed deer (Odocoileus virginianus) densities. White-tailed deer are an invading ungulate across much of North America, whose expansion into Canada's boreal forest is implicated in the decline of boreal caribou (Rangifer tarandus caribou), a species listed as Threatened in Canada. We estimated white-tailed deer densities using 300 remote cameras across 12 replicated 50 km2 landscapes over 5 years. White-tailed deer densities were significantly lower in areas where winter severity was higher. For example, predicted deer densities declined from 1.83 to 0.35 deer/km2 when winter severity increased from the lowest value to the median value. There was a tendency for densities to increase with increasing habitat alteration; however, the magnitude of this effect was approximately half that of climate. Our findings suggest that climate is the primary driver of white-tailed deer populations; however, understanding the mechanisms underpinning this relationship requires further study of over-winter survival and fecundity. Long-term monitoring at the invasion front is needed to evaluate the drivers of abundance over time, particularly given the unpredictability of climate change and increasing prevalence of extreme weather events.

Three decades of nearshore surveys reveal long-term patterns in gray whale habitat use, distribution, and abundance in the Northern California Current.

The nearshore waters of the Northern California Current support an important seasonal foraging ground for Pacific Coast Feeding Group (PCFG) gray whales. We examine gray whale distribution, habitat use, and abundance over 31 years (1992-2022) using standardized nearshore (< 5 km from shore) surveys spanning a large swath of the PCFG foraging range. Specifically, we generated density surface models, which incorporate detection probability into generalized additive models to assess environmental correlates of gray whale distribution and predict abundance over time. We illustrate the importance of coastal upwelling dynamics, whereby increased upwelling only yields higher gray whale density if interspersed with relaxation events, likely because this combination optimizes influx and retention of nutrients to support recruitment and aggregation of gray whale prey. Several habitat features influence gray whale distribution, including substrate, shelf width, prominent capes, and river estuaries. However, the influence of these features differs between regions, revealing heterogeneity in habitat preferences throughout the PCFG foraging range. Predicted gray whale abundance fluctuated throughout our study period, but without clear directional trends, unlike previous abundance estimates based on mark-recapture models. This study highlights the value of long-term monitoring, shedding light on the impacts of variable environmental conditions on an iconic nearshore marine predator.

Quantitative Metrics in Mass-Gathering Studies: A Comprehensive Systematic Review.

INTRODUCTION: Mass gatherings are events where many people come together at a specific location for a specific purpose, such as concerts, sports events, or religious gatherings, within a certain period of time. In mass-gathering studies, many rates and ratios are used to assess the demand for medical resources. Understanding such metrics is crucial for effective planning and intervention efforts. Therefore, this systematic review aims to investigate the usage of rates and ratios reported in mass-gathering studies. METHODS: In this systematic review, the PRISMA guidelines were followed. Articles published through December 2023 were searched on Web of Science, Scopus, Cochrane, and PubMed using the specified keywords. Subsequently, articles were screened based on titles, abstracts, and full texts to determine their eligibility for inclusion in the study. Finally, the articles that were related to the study's aim were evaluated. RESULTS: Out of 745 articles screened, 55 were deemed relevant for inclusion in the study. These included 45 original research articles, three special reports, three case presentations, two brief reports, one short paper, and one field report. A total of 15 metrics were identified, which were subsequently classified into three categories: assessment of population density, assessment of in-event health services, and assessment of out-of-event health services. CONCLUSION: The findings of this study revealed notable inconsistencies in the reporting of rates and ratios in mass-gathering studies. To address these inconsistencies and to standardize the information reported in mass-gathering studies, a Metrics and Essential Ratios for Gathering Events (MERGE) table was proposed. Future research should promote consistency in terminology and adopt standardized methods for presenting rates and ratios. This would not only enhance comparability but would also contribute to a more nuanced understanding of the dynamics associated with mass gatherings.

Survival in nunatak and peripheral glacial refugia of three alpine plant species is partly predicted by altitudinal segregation.

Mountain biota survived the Quaternary cold stages most probably in peripheral refugia and/or ice-free peaks within ice-sheets (nunataks). While survival in peripheral refugia has been broadly demonstrated, evidence for nunatak refugia is still scarce. We generated RADseq data from three mountain plant species occurring at different elevations in the southeastern European Alps to investigate the role of different glacial refugia during the Last Glacial Maximum (LGM). We tested the following hypotheses. (i) The deep Piave Valley forms the deepest genetic split in the species distributed across it, delimiting two peripheral refugia. (ii) The montane to alpine species Campanula morettiana and Primula tyrolensis survived the LGM in peripheral refugia, while high-alpine to subnival Saxifraga facchinii likely survived in several nunatak refugia. (iii) The lower elevation species suffered a strong population decline during the LGM. By contrast, the higher elevation species shows long-term stability of population sizes due to survival on permanently ice-free peaks and small population sizes at present. We found peripheral refugia on both sides of the Piave Valley, which acted as a major genetic barrier. Demographic modelling confirmed nunatak survival not only for S. facchinii but also for montane to alpine C. morettiana. Altitudinal segregation influenced the species' demographic fluctuations, with the lower elevation species showing a significant population increase at the end of the LGM, and the higher elevation species either showing decrease towards the present or stable population sizes with a short bottleneck. Our results highlight the role of nunatak survival and species ecology in the demographic history of mountain species.

Estimating the size of populations at risk for malaria: a case study in cattle herders and agricultural workers in Northern Namibia.

Cattle herders and agricultural workers have been identified has key high-risk populations for malaria in northern Namibia. Population size estimates for these groups are lacking but are important for planning, monitoring and evaluating the effectiveness of targeted strategies towards malaria elimination in the region. In this analysis, we extend population size estimation methods routinely used in HIV research, specifically social mapping and multiple source capture-recapture, to the context of malaria to estimate how many cattle herders and agricultural workers lived in two regions of northern Namibia over the course of the 2019-2020 malaria season. Both methods estimated two to three times more agricultural workers than cattle herders but size estimates based on the multiple source capture-recapture method were two to three times greater than the mapping-based, highlighting important methodological considerations to apply such methods to these highly mobile populations. In particular, we compared open versus closed populations assumptions for the capture-recapture method and assessed the impact of sensitivity analyses on the procedure to link records across multiple data sources on population size estimates. Our results are important for national control programs to target their resources and consider integrating routine population size estimation of high risk populations in their surveillance activities.

Estimating the size of a closed population by modeling latent and observed heterogeneity.

The paper extends the empirical likelihood (EL) approach of Liu et al. to a new and very flexible family of latent class models for capture-recapture data also allowing for serial dependence on previous capture history, conditionally on latent type and covariates. The EL approach allows to estimate the overall population size directly rather than by adding estimates conditional to covariate configurations. A Fisher-scoring algorithm for maximum likelihood estimation is proposed and a more efficient alternative to the traditional EL approach for estimating the non-parametric component is introduced; this allows us to show that the mapping between the non-parametric distribution of the covariates and the probabilities of being never captured is one-to-one and strictly increasing. Asymptotic results are outlined, and a procedure for constructing profile likelihood confidence intervals for the population size is presented. Two examples based on real data are used to illustrate the proposed approach and a simulation study indicates that, when estimating the overall undercount, the method proposed here is substantially more efficient than the one based on conditional maximum likelihood estimation, especially when the sample size is not sufficiently large.

Tumor containment: a more general mathematical analysis.

Clinical and pre-clinical data suggest that treating some tumors at a mild, patient-specific dose might delay resistance to treatment and increase survival time. A recent mathematical model with sensitive and resistant tumor cells identified conditions under which a treatment aiming at tumor containment rather than eradication is indeed optimal. This model however neglected mutations from sensitive to resistant cells, and assumed that the growth-rate of sensitive cells is non-increasing in the size of the resistant population. The latter is not true in standard models of chemotherapy. This article shows how to dispense with this assumption and allow for mutations from sensitive to resistant cells. This is achieved by a novel mathematical analysis comparing tumor sizes across treatments not as a function of time, but as a function of the resistant population size.

An approximation of populations on a habitat with large carrying capacity.

We consider stochastic dynamics of a population which starts from a small colony on a habitat with large but limited carrying capacity. A common heuristics suggests that such population grows initially as a Galton-Watson branching process and then its size follows an almost deterministic path until reaching its maximum, sustainable by the habitat. In this paper we put forward an alternative and, in fact, more accurate approximation which suggests that the population size behaves as a special nonlinear transformation of the Galton-Watson process from the very beginning.

Paradoxical Exception to Island Tameness: Increased Defensiveness in an Insular Population of Rattlesnakes.

Island tameness results largely from a lack of natural predators. Because some insular rattlesnake populations lack functional rattles, presumably the consequence of relaxed selection from reduced predation, we hypothesized that the Santa Catalina Island, California, USA, population of the southern Pacific rattlesnake (Crotalus helleri, which possesses a functional rattle), would exhibit a decrement in defensive behavior relative to their mainland counterparts. Contrary to our prediction, rattlesnakes from the island not only lacked tameness compared to mainland snakes, but instead exhibited measurably greater levels of defensiveness. Island snakes attempted to bite 4.7 times more frequently as we endeavored to secure them by hand, and required 2.1-fold more time to be pinned and captured. When induced to bite a beaker after being grasped, the island snakes also delivered 2.1-fold greater quantities of venom when controlling for body size. The additional venom resulted from 2.1-fold larger pulses of venom ejected from the fangs. We found no effects of duration in captivity (2-36 months), which suggests an absence of long-term habituation of antipredator behaviors. Breeding bird surveys and Christmas bird counts indicated reduced population densities of avian predators on Catalina compared to the mainland. However, historical estimates confirmed that populations of foxes and introduced mammalian predators (cats and pigs) and antagonists (herbivorous ungulates) substantially exceeded those on the mainland in recent centuries, and therefore best explain the paradoxically exaggerated defensive behaviors exhibited by Catalina's rattlesnakes. These findings augment our understanding of anthropogenic effects on the behaviors of island animals and underscore how these effects can negatively affect human safety.

Restoring spatiotemporal variability to enhance the capacity for dispersal-limited species to track climate change.

Climate refugia are areas where species can persist through climate change with little to no movement. Among the factors associated with climate refugia are high spatial heterogeneity, such that there is only a short distance between current and future optimal climates, as well as biotic or abiotic environmental factors that buffer against variability in time. However, these types of climate refugia may be declining due to anthropogenic homogenization of environments and degradation of environmental buffers. To quantify the potential for restoration of refugia-like environmental conditions to increase population persistence under climate change, we simulated a population's capacity to track their temperature over space and time given different levels of spatial and temporal variability in temperature. To determine how species traits affected the efficacy of restoring heterogeneity, we explored an array of values for species' dispersal ability, thermal tolerance, and fecundity. We found that species were more likely to persist in environments with higher spatial heterogeneity and lower environmental stochasticity. When simulating a management action that increased the spatial heterogeneity of a previously homogenized environment, species were more likely to persist through climate change, and population sizes were generally higher, but there was little effect with mild temperature change. The benefits of heterogeneity restoration were greatest for species with limited dispersal ability. In contrast, species with longer dispersal but lower fecundity were more likely to benefit from a reduction in environmental stochasticity than an increase in spatial heterogeneity. Our results suggest that restoring environments to refugia-like conditions could promote species' persistence under the influence of climate change in addition to conservation strategies such as assisted migration, corridors, and increased protection.