Population Extinction Research Articles

Dynamics of a stochastic nutrient–plankton model with regime switching

In this paper, a stochastic nutrient–plankton model with regime switching is proposed, where the regime switching plankton mortality is described by a continuous time Markov chain with different states. We study the effects of regime switching plankton mortality on the distribution of plankton biomass as well as the persistence and extinction of plankton populations. Moreover, we show that there exists a unique stationary distribution in the model, which is ergodic, indicating that the plankton populations will survive forever. By applying a sophisticated sensitivity analysis technique, we found that the phytoplankton biomass is highly sensitive to the grazing rate by zooplankton and least sensitive to the re-mineralization of dead biomass of plankton into nutrients concentration. The numerical results show that the persistence and extinction of plankton populations is sensitive to variations of nutrient input. We find that the noise can enhance the oscillations of plankton biomass and the regime switching plankton mortality has capacity to decrease the amplitudes of the oscillations in the bloom phase. Our findings emphasize that the regime switching plankton mortality contributes to the survival of plankton populations in the aquatic system.

Temperature synchronizes temporal variation in laying dates across European hole-nesting passerines.

Identifying the environmental drivers of variation in fitness-related traits is a central objective in ecology and evolutionary biology. Temporal fluctuations of these environmental drivers are often synchronized at large spatial scales. Yet, whether synchronous environmental conditions can generate spatial synchrony in fitness-related trait values (i.e., correlated temporal trait fluctuations across populations) is poorly understood. Using data from long-term monitored populations of blue tits (Cyanistes caeruleus, n = 31), great tits (Parus major, n = 35), and pied flycatchers (Ficedula hypoleuca, n = 20) across Europe, we assessed the influence of two local climatic variables (mean temperature and mean precipitation in February-May) on spatial synchrony in three fitness-related traits: laying date, clutch size, and fledgling number. We found a high degree of spatial synchrony in laying date but a lower degree in clutch size and fledgling number for each species. Temperature strongly influenced spatial synchrony in laying date for resident blue tits and great tits but not for migratory pied flycatchers. This is a relevant finding in the context of environmental impacts on populations because spatial synchrony in fitness-related trait values among populations may influence fluctuations in vital rates or population abundances. If environmentally induced spatial synchrony in fitness-related traits increases the spatial synchrony in vital rates or population abundances, this will ultimately increase the risk of extinction for populations and species. Assessing how environmental conditions influence spatiotemporal variation in trait values improves our mechanistic understanding of environmental impacts on populations.

Genetic Diversity and Population Structure Derived from Body Remains of the Endangered Flightless Longhorn Beetle Iberodorcadion fuliginator in Grassland Fragments in Central Europe

Knowledge of patterns of genetic diversity in populations of threatened species is vital for their effective conservation. However, destructive sampling should be avoided in threatened species so as not to additionally increase the risk of local population extinction. We exclusively used beetle remains and beetles collected after death to analyze local and regional patterns of genetic variation in the endangered flightless longhorn beetle Iberodorcadion fuliginator in the border region of Switzerland, France and Germany, in grassland remnants. We extracted DNA from the beetles’ remains and genotyped 243 individuals at 6 microsatellite loci. We found moderate genetic differentiation between populations, each belonging to one of two metapopulations situated on either side of the river Rhine, but distinct genetic differentiation between populations across metapopulation. The genetic distance between populations was correlated with the geographic distance between the sites sampled. Genetic structure analysis inferred the presence of two genetic clusters. The populations in the Alsace (France) represent one cluster, together with the Swiss populations near Basel, which is separated by the river Rhine from the cluster composed of the populations in southwestern Germany. Thus, the historical separation by the river Rhine surpasses more recent effects of human-induced habitat fragmentation on the genetic differentiation in I. fuliginator.

Integrating Social Forestry and Biodiversity Conservation in Indonesia

Social forestry (SF) has long been implemented in production and protected forests in Indonesia. SF is considered to be a win–win solution for occupied and cultivated forest areas. The aim of this paper was to review the implementation of social forestry in Indonesia and its strengths and challenges. The secondary purpose was to synthesize the lessons learned and recommendations for the government about designing SF that can integrate the objective of forest biodiversity conservation and the social welfare of the surrounding communities. The study used a systematic literature review (SLR) of international and national peer-reviewed articles. The results of the study indicate that SF is intended to achieve benefits in three main areas: social, economic, and ecological. However, the review found that the ecological aspects of biodiversity conservation often receive less attention compared to the social and economic goals. A strong point of SF implementation is increasing community access to forest land use, while a challenge that must be resolved is that including communities in forest management can result in fragmentation and changes to animal habitats; thus, there is the potential for population decline and extinction. This study advises policymakers to pay more attention to ecological functions to ensure forest sustainability in SF development.

Ionizing radiation affects the demography and the evolution of Caenorhabditis elegans populations

Ionizing radiation can reduce survival, reproduction and affect development, and lead to the extinction of populations if their evolutionary response is insufficient. However, demographic and evolutionary studies on the effects of ionizing radiation are still scarce. Using an experimental evolution approach, we analyzed population growth rate and associated change in life history traits across generations in Caenorhabditis elegans populations exposed to 0, 1.4, and 50.0 mGy.h−1 of ionizing radiation (gamma external irradiation). We found a higher population growth rate in the 1.4 mGy.h−1 treatment and a lower in the 50.0 mGy.h−1 treatment compared to the control. Realized fecundity was lower in both 1.4 and 50.0 mGy.h−1 than control treatment. High irradiation levels decreased brood size from self-fertilized hermaphrodites, specifically early brood size. Finally, high irradiation levels decreased hatching success compared to the control condition. In reciprocal-transplant experiments, we found that life in low irradiation conditions led to the evolution of higher hatching success and late brood size. These changes could provide better tolerance against ionizing radiation, investing more in self-maintenance than in reproduction. These evolutionary changes were with some costs of adaptation. This study shows that ionizing radiation has both demographic and evolutionary consequences on populations.

Mate Perception and Gene Networks Regulating the Early Phase of Sex in Pseudo-nitzschia multistriata

Diatoms are photosynthetic microorganisms playing a key role in the functioning of aquatic ecosystems; they are at the base of the food web and are the main drivers of biogeochemical processes. These microalgae have a unique diplontic life cycle in which the vegetative phase entails a cell size reduction that would lead to the extinction of the cell population if the size was not restored, usually by sexual reproduction. The switch from asexual to sexual reproduction needs to be finely synchronized and regulated to ensure its success; to this aim, cells evolved complex chemical crosstalk that mediates mating. We focused our attention on the marine diatom Pseudo-nitzschia multistriata, investigating the reciprocal perception of the opposite mating type (MT) and the genes and signaling molecules putatively involved in the process. From previously available transcriptomic data, we selected a panel of genes deregulated during the early phase of sexual reproduction, confirming for some of them a role during mate perception and establishing a hierarchy governing their behavior. Moreover, we explored the nature of the molecules controlling sexual reproduction in this species, unveiling that the signaling is mediated by the secretion of protein and non-protein cues from the MT− and MT+, respectively. Our results point to a model in which the two MTs stimulate each other, but the stimulation by the MT− is amplified after MT+ perception in a positive feedback manner.

Modeling and Analysis of Predator-Prey Model with Fear Effect in Prey and Hunting Cooperation among Predators and Harvesting

In this paper, we present and analyze predator-prey system where prey population is linearly harvested and affected by fear and the prey population has grown logistically in the absence of predators. The predator population follows hunting cooperation, and it predates the prey population in the Holling type II functional responses. Based on those assumptions, a two-dimensional mathematical model is derived. The positivity, boundedness, and extinction of both prey and predator populations of the solution of the system are discussed. The existence, stability (local and global), and the Hopf bifurcation analysis of the biologically feasible equilibrium points are investigated. The aim of this research is to explore the effect of fear on the prey population and hunting cooperation on the predator population, and both prey and predator populations are harvested linearly and taken as control parameters of the model. If the values of c 1 > 1 , then both prey and predator populations are extinct and also fear parameter has a stabilizing effect on system 4. From the numerical simulation, it was found that the fear effect, hunting cooperation, prey harvesting, and predator harvesting change the dynamics of system 4.

Temporal variation in the peregrine falcons (Falco peregrinus) diet after the extinction of the original population and the emergence of a new population in Slovakia

Abstract We made an analysis of the osteological remains of prey that had been captured by the peregrine falcon (Falco peregrinus) and was collected from eyries perched high in rocky cliffs of Slovakia. Birds dominated the 7,233 vertebrates identified (class Aves, with minimum of 98 species and 97.2% of the total). Bones from mammals (class Mammalia, 24 species, 2.5%) were rarely found, and sporadic remains from lower vertebrate species (classes Amphibia, Reptilia, Pisces, 0.3%) were also noted. The collected specimens were divided over three distinct periods. Before domestic pigeons became a major component in the juvenile peregrine falcon diet (Period A), wild pigeons and doves were the most common prey; specifically stock doves (Columba oenas) caught at lower elevations, and wood pigeons (Columba palumbus) in mountainous areas. The Eurasian woodcock (Scolopax rusticola) was a frequent prey . The diversity of peregrine falcon diet reached its maximum between the 1930s and the 1950s (Period B), with the domestic pigeon (Columba livia domestica) present in the diet at a similar abundance (16.1%) to wild pigeons and doves. The peregrine falcon population tailed off in the 1960s as pesticides became more commonly used in agriculture. A new population started expanding from Western Europe during the 1990s and has stabilised at around 150 breeding pairs in recent years. Since the turn of the millennium (Period C), domestic pigeons have become the dominant prey (51.1%) along with smaller songbirds such as hawfinches (Coccothraustes coccothraustes) and common starlings (Sturnus vulgaris), at 15.5% and 14.6% of total osteological remains collected, respectively.

Analysis of a microfluidic chemostat model with random dilution ratios

In this paper, we first construct a microfluidic chemostat model for the growth of biofilms and planktonic populations with random dilution ratios and then investigate its dynamical behavior. Using the theory of monotone dynamical systems and the Multiplicative Ergodic Theorem, we show the existence of random attractors and stationary measures, and present Lyapunov exponents for the linearized cocycle with respect to the random model. Further on, if the top Lyapunov exponent is negative, we give the extinction of microbial populations, including the forward and pull-back trajectories.

Range expansion and first observation of Tridacna noae (Cardiidae: Tridacninae) in American Sāmoa.

Giant clams are ecologically important, benefitting species of all trophic levels. But numerous populations have declined drastically in numbers due to past intensive exploitation that led to their listing in both CITES Appendix II and IUCN Red List of Threatened Species. However, giant clams are notoriously difficult to identify, and recent molecular work has revealed that morphological misidentification of giant clams have confounded current population assessments and extinction risk. The most recent study of the status of giant clams in the Samoan Archipelago was published in a journal over 20 years ago, without molecular corroboration of visual identifications. Using morphologic characteristics and ezRAD genetic techniques, we identify the existence of Tridacna noae in the Samoan Archipelago, presenting the first observation and a resulting range expansion. Accurately identifying the extant species in the archipelago is the first step toward a much-needed population status assessment to effectively manage these long-lived species.

Anthropogenic threats to the Vulnerable Andean Condor in northern South America.

Vultures comprise one of the most threatened groups of birds worldwide. With a total population not exceeding 6700 mature individuals, and in rapid decline across its range, the Andean Condor (Vultur gryphus) is listed as a Vulnerable species in the IUCN red list. Local population extinctions and decline are of particular concern in northern South America, where no more than 340 condors may exist at present. Despite this, no quantitative assessments exist in Ecuador, Colombia, and Venezuela regarding the threats affecting Andean Condor populations. To address this, we compiled records of Andean Condors injured, or killed, between 1979 and 2021. We obtained data of 164 condors affected by different causes of injury, of which 83.5% were reported in Ecuador, 15.2% in Colombia, and 1.2% in Venezuela. Of the total number, 84.7% of the injured individuals died. Between 1979 and 2021, in Ecuador, Colombia and Venezuela, at least 103 Andean Condors were presumably poisoned, 22 were shot, and 39 individuals were affected by other causes. The total number of individuals affected by different causes represents between 48% and 72% of the total population estimated in northern South America. Of great concern is the fact that, between 2007 and 2021, poisoning and shooting together caused the loss of 19-31% of the estimated population of condors in Ecuador, and 7-21% of the estimated population in Colombia. Given the important mortality induced by humans, environmental education programs, socio-ecological research, application of environmental laws, and management strategies based on scientific evidence to prevent and mitigate human-wildlife conflicts are urgently required for effective Andean Condor conservation in northern South America.

Dynamics of a spatiotemporal model on populations in a polluted river

In this paper, we investigate the dynamics for a reaction–diffusion–advection system which models populations in a polluted river. More precisely, we study the stability of steady states, which yields sufficient conditions that lead to population persistence or extinction. Furthermore, some dependence of the stability of the toxicant-only steady state and the population-toxicant coexistence steady state on the model parameters are given.

Freshwater Reservoir, Ecological Traps and Source-Sink Dynamics

Odonata are biodiversity indicators that adequately represent many aquatic and semi-aquatic animal species. We recorded over two field seasons a rich lentic community of Odonata (18 species) in a large artificial freshwater reservoir (ca. 55 ha) built 40 years ago. The release of water from the dam in summer for crop irrigation leads to the desiccation of large parts of the reservoir, which prevents the reproduction of half of the species of this Odonata community. We identify two adaptations that allow eight species to cope with desiccation, i.e., a precocious breeding period allowing the emergence of adults before the retreat of water, or a delayed adult emergence due to egg diapause from oviposition to the end of winter. The reservoir acts thus as an ecological trap for individuals of 10 species that developed elsewhere and were attracted to the site without successfully breeding there. As consequence of the local population extinction at each generation, the presence of individuals of these 10 species at the reservoir depends on source-sink population dynamics in the landscape. In the context of global warming that encourages the creation of artificial freshwater reservoirs, the multiplication of such sinks could threaten the persistence in the landscape of species maladapted to desiccation.

Responses of germination strategy of Agriophyllum squarrosum to rainfall pattern in the Tengger desert.

Agriophyllum squarrosum (L.) Moq. (Chenopodiaceae) is an annual pioneer psammophyte that is strictly distributed along desert margins. However, little is known about how this species adapts to shifting dunes. In this study, seeds bank was selected and germination behaviors of A. squarrosum were tested in laboratory. In addition, the effects of rainfall patterns on population dynamics were observed in field at the southeastern edge of the Tengger Desert. Soil seed bank density was significantly different in different depth of sand dunes. Under adequate water in Petri dishes, seeds began to germinate in less than 3 h and the germination peak was reached in seven days after watering. It showed that there is no innate dormancy of A. squarrosum. The buried experiments showed that the germination percentage decreased with increasing buried depth, and deeply buried seeds (10 cm) remained ungerminated. Population dynamics in different rainfall pattern of three years in field showed that germination, survival and deaths of A. squarrosum were extremely sensitive to rainfall variation. Our results suggest that precipitation is the key factor in determining population of A. squarrosum. The germination strategy of A. squarrosum ensures the efficiency use of unpredicted and scarce precipitation. The high disturbance of moving sand endowed persistence seed bank of A. squarrosum, which is essential for population continuation, avoiding population extinction under unpredicted precipitation.

Contrasting population genetic responses to migration barriers in two native and an invasive freshwater fish.

Habitat fragmentation impacts the distribution of genetic diversity and population genetic structure. Therefore, protecting the evolutionary potential of species, especially in the context of the current rate of human-induced environmental change, is an important goal. In riverine ecosystems, migration barriers affect the genetic structure of native species, while also influencing the spread of invasive species. In this study, we compare genetic patterns of two native and one highly invasive riverine fish species in a Belgian river basin, namely the native three-spined stickleback (Gasterosteus aculeatus) and stone loach (Barbatula barbatula), and the non-native and invasive topmouth gudgeon (Pseudorasbora parva). We aimed to characterize both natural and anthropogenic determinants of genetic diversity and population genetic connectivity. Genetic diversity was highest in topmouth gudgeon, followed by stone loach and three-spined stickleback. The correlation between downstream distance and genetic diversity, a pattern often observed in riverine systems, was only marginally significant in stone loach and three-spined stickleback, while genetic diversity strongly declined with increasing number of barriers in topmouth gudgeon. An Isolation-By-Distance pattern characterizes the population genetic structure of each species. Population differentiation was only associated with migration barriers in the invasive topmouth gudgeon, while genetic composition of all species seemed at least partially determined by the presence of migration barriers. Among the six barrier types considered (watermills, sluices, tunnels, weirs, riverbed obstructions, and others), the presence of watermills was the strongest driver of genetic structure and composition. Our results indicate that conservation and restoration actions, focusing on conserving genetic patterns, cannot be generalized across species. Moreover, measures might target either on restoring connectivity, while risking a rapid spread of the invasive topmouth gudgeon, or not restoring connectivity, while risking native species extinction in upstream populations.

Humid tropical vertebrates are at lower risk of extinction and population decline in forests with higher structural integrity.

Reducing deforestation underpins global biodiversity conservation efforts. However, this focus on retaining forest cover overlooks the multitude of anthropogenic pressures that can degrade forest quality and imperil biodiversity. We use remotely sensed indices of tropical rainforest structural condition and associated human pressures to quantify the relative importance of forest cover, structural condition and integrity (the cumulative effect of condition and pressures) on vertebrate species extinction risk and population trends across the global humid tropics. We found that tropical rainforests of high integrity (structurally intact and under low pressures) were associated with lower likelihood of species being threatened and having declining populations, compared with forest cover alone (without consideration of condition and pressures). Further, species were more likely to be threatened or have declining populations if their geographic ranges contained high proportions of degraded forest than if their ranges contained lower proportions of forest cover but of high quality. Our work suggests that biodiversity conservation policies to preserve forest integrity are now urgently required alongside ongoing efforts to halt deforestation in the hyperdiverse humid tropics.

Tigers on the edge: mortality and landscape change dominate individual-based spatially-explicit simulations of a small tiger population

ContextReductions in the tiger’s (Panthera tigris) range in Southeast Asia have been concurrent with large infrastructure expansion and landscape change. Thailand’s Dong Phayayen-Khao Yai Forest Complex (DPKY), a landscape of tiger conservation priority, may be particularly vulnerable to such changes, necessitating investigations into effects on population dynamics.ObjectivesEvaluate relative effects of landscape change scenarios on the probability of tiger persistence in DPKY and sensitivity of predictions to spatially-explicit mortality risk, landscape resistance, and tiger population density.MethodsWe utilize individual-based, spatially-explicit population modelling to evaluate the trajectory of tiger population dynamics across 11 landscape change scenarios. Concurrently, we evaluate sensitivity of predictions to landscape resistance transformation, maximum population density, and spatially-explicit mortality across 20 generations.ResultsSpatially-explicit mortality risk dominated predictions of population persistence, frequently resulting in population declines/extinction. Adjustment of moderate mortality risk to slightly convex and concave forms shifted extinction rates from 46 to 12% and 85%, respectively. Holding mortality constant at moderate levels, strong negative effects were predicted in landscape change scenarios incorporating road expansion (46%-74% extinction) and construction of dams (52%). Strong negative effects of combined development persisted even when habitat restoration measures were applied (96% extinction). Adjusting resistance and maximum population density had marginal effects.ConclusionsThe high sensitivity and variability of predictions to spatial patterns of mortality risk suggest a population on a proverbial knife’s edge. Our results underscore the importance of incorporating spatial patterns of mortality risk in population modelling, highlighting their potentially dominating influence on population dynamics and extinction risk.

Development of Malaysian Mammal Online Database

Malaysia is one of 17 mega diverse countries in the world. Despite this fact, there is still no online standalone database that focuses on Malaysian mammals. Creation of a mammalian database would allow researchers and conservationists to utilize the database for research, policy making and to answer broad scale of biodiversity questions. Human development has contribute to the depleting of mammal population and species extinction rate is faster than the effort of cataloguing them. The aim of this study is to 1) identify online database features and the type of data required for mammal database, 2) collect and populate database from existing mammal data to assist the said database and 3) to test the acceptance of the database by user of this study. The secondary data from existing database such as Global Biodiversity Information Facility (GBIF), Animal Diversity Web (ADW) and Malaysia Biodiversity Information System (MyBIS) was collected to determine the required features needed in the database. The database adhered to TDWG standard that facilitates exchange of biological information. Examination on GBIF have been made to observe their data presentation since GBIF used TDWG Standard. Rapid Prototype Model was utilized as development method and Omeka Classic was used as platform of Content Management System. The mammal data was collected online and populate into the database. The acceptance testing in form of questionnaire were distributed to verify whether the database is function properly and meet the requirement of the study. We present MYMODS, a comprehensive mammal database with 361 mammal species in Malaysia deposited in the database. The development of this database will enable the researcher and conservationist to seek and identify mammal information based on species’ scientific name, description and IUCN Red List. We believe that MYMODS will contribute to the digital knowledge that provide tools for mammal research and contributes in management of biodiversity and conservation in Malaysia. MYMODS is available at https://cercom.uthm.edu.my/mymods/

Analysis of an avian influenza model with Allee effect and stochasticity

In this paper, we investigate a two-dimensional avian influenza model with Allee effect and stochasticity. We first show that a unique global positive solution always exists to the stochastic system for any positive initial value. Then, under certain conditions, this solution is proved to be stochastically ultimately bounded. Furthermore, by constructing a suitable Lyapunov function, we obtain sufficient conditions for the existence of stationary distribution with ergodicity. The conditions for the extinction of infected avian population are also analytically studied. These theoretical results are conformed by computational simulations. We numerically show that the environmental noise can bring different dynamical outcomes to the stochastic model. By scanning different noise intensities, we observe that large noise can cause extinction of infected avian population, which suggests the repression of noise on the spread of avian virus.

Lessons from extinctions of dugong populations

Lessons from extinctions of dugong populations