Viable Population Size Research Articles

Resource-based modelling approach to studying evolutionary rescue.

In this paper, we present an in-depth investigation into the dynamics of evolutionary rescue using a resource-based modelling approach. Utilizing classical consumer-resource models, we aim to understand how species can adapt to abrupt environmental changes that alter the availability of substitutable resources. Through both analytical solutions and simulation-based techniques, we explore the conditions under which populations can recover from critical sizes and avoid extinction. Our findings highlight the importance of minimum viable population sizes, mutation rates, and the adaptive capacity of metabolic strategies in influencing population resilience. We demonstrate that while increased mutation rates can facilitate faster recovery by enabling populations to evolve new metabolic strategies suited to the altered resource landscape, populations starting with smaller sizes or facing severe reductions in resource availability are more susceptible to extinction. This study offers valuable insights into the interplay between ecological dynamics and evolutionary mechanisms, providing a comprehensive framework for predicting population persistence and informing conservation strategies under changing environmental conditions.

The US Endangered Species Act and acceptable risk

The fundamental criterion for listing or delisting species under the United States Endangered Species Act (ESA) is acceptable extinction risk. But what is the meaning of “acceptable risk”? This concept has received little attention in conservation biology, and hence, the purpose of this paper is to explain acceptable risk within the context of the ESA. All complex environmental policy decisions involve trade-offs, and hence, choosing one policy from several policy options entails a comparison of the benefits, costs, and risks of all options. Acceptable-risk problems are decision problems requiring a choice among different policy options, and an acceptable risk is defined as the risk associated with the chosen policy. In general, people will accept the risk imposed by a particular policy when that policy yields sufficient net benefits. The ESA, its legislative history, and implementing regulations clearly state that species listing determinations must be based solely on science and “without reference to possible economic or other impacts” caused by the listing of that species. If economic considerations are prohibited from influencing listing decisions, then risk reduction is not constrained by cost, and therefore, the only rational choice for acceptable extinction risk is zero risk. This outcome, known as a “stopping-point problem”, is absurd, and consequently, federal agencies responsible for listing determinations are forced to issue opaque decisions that obscure their true rationale, which in turn, lead to inconsistency and improper political influence. Illustrations of acceptable risk in null hypothesis tests, the United States Clean Air Act, and minimum viable population size are also presented.

Conservation genetics of the white-bellied pangolin in West Africa: A story of lineage admixture, declining demography, and wide sourcing by urban bushmeat markets.

During the last 40 years, the volumes of African pangolins feeding the illegal wildlife trade have dramatically increased. We conducted a conservation genetics survey of the most traded African species, the white bellied pangolin (WBP; Phataginus tricuspis), across three West African countries including Guinea, Côte d'Ivoire, and Ghana. Our study combining mitochondrial DNA sequencing and microsatellite genotyping is the first to reveal a wide pattern of admixture between two of the six mitochondrial lineages as previously delimited within WBP. We found a signature of isolation by distance but a lack of population genetic structuring, supporting the idea that WBP may have underestimated dispersal abilities. Levels of genetic diversity were low in West African lineages (WAfr and Gha) compared to Central Africa, reinforcing the picture of genetic pauperization shared by West African WBP. We observed a 85%-98% decline in the effective population size of WBP occurring c. 3200 to 400 ya, with current numbers (520-590) at the lower end of the conservative thresholds for minimum viable population size. The microsatellite markers were powerful enough to differentiate between individuals and identify replicated samples, confirming the utility of this approach in tracing the pangolin trade. Genetic diversity estimates confirmed that Yopougon, the main bushmeat market from Abidjan (Côte d'Ivoire), was fed by a large trade network as confirmed by vendors reporting 10 different sources situated 62-459 km away from the market. We conclude that WBP distributed in the Upper Guinean Block should be considered a single management unit of high conservation concern, as impacted by genetic diversity erosion, drastic decline in effective population size, and wide range sourcing for feeding urban bushmeat markets. Given the genetic admixture pattern detected within WBP from West Africa, we advocate for a multi-locus strategy to trace the international trade of the species.

Influence of abiotic factors on kinetics of viable populations of biocontrol agents in the phyllosphere of lettuce and strawberry leaves

AbstractThere is little information on the effect of temperature, relative humidity (RH) and vapour pressure deficit (VPD) on the viable populations of two commercial biocontrol strains, Bacillus subtilis QST 713 (recently classified as B. velezensis) and Gliocladium catenulatum J1446 (syn. Clonostachys rosea). The PMAxx‐qPCR molecular assay was used to quantify the viable biocontrol agent (BCA) populations on fully extended lettuce and strawberry leaves under a range of temperature and RH combinations. Overall, there was a small decline in the population size of viable cells for the two biocontrol organisms on strawberry and lettuce leaves within 10 days of application. However, for most experimental runs, which contained general UK agronomy climates, such a decline was not statistically significant. Moreover, for a few runs, the viable populations increased significantly in optimal BCA growth temperatures with high RH. Only temperature (ambient) and dew point significantly affected the rate of temporal changes in the viable biocontrol population size. Thus, an increasing temperature led to decreased daily mortality. It should be noted that much of the variability in the estimated daily mortality rates remains unaccounted for, thus unless under extreme conditions, the biocontrol efficacy in practice is less likely to be affected by the survival of biocontrol microbes but more likely by other factors that influence the density of biocontrol cells in the phyllosphere, especially dilution due to rapid host leaf expansion, spray coverage and rain wash‐off.

Public and private protected areas can work together to facilitate the long-term persistence of mammals

SummaryThe conservation performance of protected areas (PAs) is typically measured according to whether species are likely to be present within PAs. However, to attain the goal of long-term conservation it is important to consider the performance of PAs in terms of their ability to support the persistence of the species they contain. We used the concept of minimum viable population (MVP) size to examine the potential for PAs within a large national PA network to support mammal species over the long term. By developing habitat models for each species and estimating the area required to support the MVP size for each species, we identified whether each PA had sufficient habitat to meet the species’ requirements. We found that as a whole the PA network is able to support at least one viable population for all species studied. However, the extent of protection offered to species by the PA network varies considerably, with many PAs not able to support viable populations of individual species on their own. By understanding the capacity of PAs to provide long-term protection to species, our findings can guide strategies to increase the resilience of PA networks as a whole, including by improving habitat quality within and connectivity between PAs.

In Memoriam : Edward O. Wilson (1929-2021): It All Started with Ants.

In Memoriam : Edward O. Wilson (1929-2021): It All Started with Ants.

Time-lagged effects of habitat fragmentation on terrestrial mammals in Madagascar.

Biodiversity is severely threatened by habitat destruction. As a consequence of habitat destruction, the remaining habitat becomes more fragmented. This results in time-lagged population extirpations in remaining fragments when these are too small to support populations in the long term. If these time-lagged effects are ignored, the long-term impacts of habitat loss and fragmentation will be underestimated. We quantified the magnitude of time-lagged effects of habitat fragmentation for 157 nonvolant terrestrial mammal species in Madagascar, one of the biodiversity hotspots with the highest rates of habitat loss and fragmentation. We refined species' geographic ranges based on habitat preferences and elevation limits and then estimated which habitat fragments were too small to support a population for at least 100 years given stochastic population fluctuations. We also evaluated whether time-lagged effects would change the threat status of species according to the International Union for the Conservation of Nature (IUCN) Red List assessment framework. We used allometric relationships to obtain the population parameters required to simulate the population dynamics of each species, and we quantified the consequences of uncertainty in these parameter estimates by repeating the analyses with a range of plausible parameter values. Based on the median outcomes, we found that for 34 species (22% of the 157 species) at least 10% of their current habitat contained unviable populations. Eight species (5%) had a higher threat status when accounting for time-lagged effects. Based on 0.95-quantile values, following a precautionary principle, for 108 species (69%) at least 10% of their habitat contained unviable populations, and 51 species (32%) had a higher threat status. Our results highlight the need to preserve continuous habitat and improve connectivity between habitat fragments. Moreover, our findings may help to identify species for which time-lagged effects are most severe and which may thus benefit the most from conservation actions.

Managed culls mean extinction for a marine mammal population when combined with extreme climate impacts

Human actions led to the worldwide decline of marine mammal populations in the 18th–19th centuries. Global adoption of protective legislation during the 20th century has recently allowed many marine mammal populations to recover. This positive trend is particularly true of pinnipeds (e.g., seals and sea lions), whose recovering populations are increasingly in conflict with fisheries. Fisheries organisations have called for managed culls of sea lion populations to reduce competition for target fish species as well as damage to catch and fishing gear through operational interactions. However, despite widespread perceptions that sea lion populations are generally increasing, to-date, culls have often been considered or implemented without quantitative evidence of their impacts on seal lion population viability. This knowledge gap is particularly concerning given the expected increase in extreme climate conditions, such as extreme El Niño events, which together with culls could push sea lion populations in some parts of the world into the extinction vortex. Here, I develop stochastic matrix population models of the South American sea lion (Otaria flavescens) parameterised through a combination of species-specific field data and phylogenetic imputation using data from related species in the COMADRE animal matrix database. Using these models, I project the impact of (1) three cull scenarios with different intensity and temporal frequency targeting adult females, (2) extreme El Niño events whose frequency is modelled using a Markovian transition matrix, and (3) the interaction of culls and extreme climate events on population dynamics. I focus on the Chilean population of O. flavescens, where recent increases in sea lion numbers have triggered widespread conflict with small-scale fisheries, and where sea lion populations will increasingly be affected by extreme El Niño conditions. I find that sea lion populations decline below minimum viable population sizes within 16–28 years under all scenarios involving culls and extreme climate events. This research explicitly incorporates parameter uncertainty into population projections—in so doing, it illustrates the need for future research to collect stage-specific, annual population data to reduce uncertainty regarding marine mammal vital rates.

Defining performance thresholds for effective management of biodiversity within protected areas.

Performance thresholds are an important tool for determining successful conservation outcomes. They provide an objective means of defining good ecological condition and have been endorsed as an essential part of best practice in protected area (PA) management within the International Union for the Conservation of Nature Green List of Protected and Conserved Areas Standard. With a growing number of PAs attaining Green List status globally, thresholds developed by PAs on the Green List present an excellent resource with which to identify the attributes of well-defined performance thresholds. We examined 349 thresholds associated with PAs on the Green List to determine whether they were specific and measurable (i.e., factors recognized as essential for setting well-defined targets). We assessed whether thresholds were defined quantitatively and whether definitions included ambiguous terms (e.g., stable numbers). We identified six different ways thresholds were expressed and found that many thresholds were expressed as management objectives, rather than ecological condition thresholds, although this trend improved over time. Approximately one-half of the performance thresholds lacked the necessary specificity to delineate successful outcomes. Our results enabled us to develop a checklist of information required to set robust performance thresholds. Recommendations include that thresholds should be quantitatively defined, including quantitative estimates of the limits of acceptable change (LAC) around the target condition. To ensure transparency, a rationale and associated evidence should be provided to support the threshold and the LAC. When accompanied by a rationale and quantitative estimate of the current condition of the value, unambiguously defined thresholds with a quantitative LAC provide an objective means of demonstrating that successful conservation outcomes have been achieved. These recommendations will help conservation managers apply the Green List Standard and improve the measurement of conservation outcomes more broadly.

Population Abundance and Density Estimates for Costa Rica’s Endemic Sea Snake, Hydrophis platurus xanthos

Population abundance and density estimates provide key information for conservation assessment and prioritization of efforts and management. However, data are still largely unavailable for many taxa, including sea snakes, which appear to be facing global declines. Here, we present the first quantitative abundance and density estimates for the geographically isolated sea snake Hydrophis platurus xanthos endemic to the inner basin of Golfo Dulce, Costa Rica. Using systematic distance sampling methods, we obtained and analyzed 199 snake detections from 46 transect lines covering the entire known distribution (totaling nine days and 469 km of effort). Our modeling methods accounted for (i) the probability of detecting a snake given it was available to be detected (ii) the average availability of snakes at the water surface during a 24-hr cycle, and (iii) the by-hour variance in the taxon’s activity pattern. The best estimate of population abundance was 29781 individuals (95% CI=20104–44115) with an estimated density of 76 snakes/km2. Without historical abundance estimates or minimum viable population size, it is unknown whether this number represents a healthy population. However, with all individuals inhabiting a relatively small inlet increasingly exposed to anthropogenic impacts, the long-term persistence of H. p. xanthos may be threatened by ongoing impacts (boat propeller strikes, agricultural runoff, and climate change), as well as unforeseen events in the future.

Modeling minimum viable population size with multiple genetic problems of small populations.

An important goal for conservation is to define minimum viable population (MVP) sizes for long-term persistence of a species. There is increasing evidence of the role of genetics in population extinction; thus, conservation practitioners are starting to consider the effects of deleterious mutations (DM), in particular the effects of inbreeding depression on fitness. We sought to develop methods to account for genetic problems other than inbreeding depression in MVP estimates, quantify the effect of the interaction of multiple genetic problems on MVP sizes, and find ways to reduce the arbitrariness of time and persistence probability thresholds in MVP analyses. To do so, we developed ecoevolutionary quantitative models to track population size and levels of genetic diversity. We assumed a biallelic multilocus genome with loci under single or multiple, interacting genetic forces. We included mutation-selection-drift balance (for loci with DM) and 3 forms of balancing selection for loci for which variation is lost through genetic drift. We defined MVP size as the lowest population size that avoids an ecoevolutionary extinction vortex. For populations affected by only balancing selection, MVP size decreased rapidly as mutation rates increased. For populations affected by mutation-selection-drift balance, the MVP size increased rapidly. In addition, MVP sizes increased rapidly as the number of loci increased under the same or different selection mechanisms until even arbitrarily large populations could not survive. In the case of fixed number of loci under selection, interaction of genetic problems did not always increase MVP sizes. To further enhance understanding about interaction of genetic problems, there is need for more empirical studies to reveal how different genetic processes interact in the genome.

The role of sigma factor competition in bacterial adaptation under prolonged starvation.

The study of adaptive microbial evolution in the laboratory can illuminate the genetic mechanisms of gaining fitness under a pre-defined set of selection factors. Laboratory evolution of bacteria under long-term starvation has gained importance in recent years because of its ability to uncover adaptive strategies that overcome prolonged nutrient limitation, a condition often encountered by natural microbes. In this evolutionary paradigm, bacteria are maintained in an energy-restricted environment in a growth phase called long-term stationary phase (LTSP). This phase is characterized by a stable, viable population size and highly dynamic genetic changes. Multiple independent iterations of LTSP evolution experiments have given rise to mutants that are slow-growing compared to the ancestor. Although the antagonistic regulation between rapid growth and the stress response is well-known in bacteria (especially Escherichia coli), the growth deficit of many LTSP-adapted mutants has not been explored in detail. In this review, I pinpoint the trade-off between growth and stress response as a dominant driver of evolutionary strategies under prolonged starvation. Focusing on mainly E. coli-based research, I discuss the various affectors and regulators of the competition between sigma factors to occupy their targets on the genome, and assess its effect on growth advantage in stationary phase (GASP). Finally, I comment on some crucial issues that hinder the progress of the field, including identification of novel metabolites in nutrient-depleted media, and the importance of using multidisciplinary research to resolve them.

Can DNA help trace the local trade of pangolins? Conservation genetics of white-bellied pangolins from the Dahomey Gap (West Africa)

BackgroundAfrican pangolins are currently experiencing unprecedented levels of harvesting, feeding both local demands and the illegal international trade. So far, the lack of knowledge on the population genetics of African pangolins has hampered any attempts at assessing their demographic status and tracing their trade at the local scale. We conducted a pioneer study on the genetic tracing of the African pangolin trade in the Dahomey Gap (DG). We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellite loci.ResultsTree-based assignment procedure showed that the pangolin trade is endemic to the DG region, as it was strictly fed by the the Dahomey Gap lineage (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, important inbreeding levels, and lack of geographic structure. We identified a 92–98% decline in DGL effective population size 200–500 ya—concomitant with major political transformations along the ‘Slave Coast’—leading to contemporaneous estimates being inferior to minimum viable population size (< 500). Genetic tracing suggested that wildlife markets from the DG sourced pangolins through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of a same individual on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies with cross-validation of observed data that traced five traded pangolins to their forest origin, c. 200–300 km away from the markets.ConclusionsAlthough the genetic toolkit that we designed from traditional markers can prove helpful to trace the illegal trade in pangolins, our tracing ability was limited by the lack of population structure within the DGL. Given the deleterious combination of genetic, demographic, and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated.

A Noninvasive Genetic Insight into the Spatial and Social Organization of an Endangered Population of the Eurasian Otter (Lutra lutra, Mustelidae, Carnivora)

The Eurasian otter is endangered in Italy, only surviving in southern river basins. The spatial and social structure of a population living at the border of the current range was explored through a noninvasive genetic study along 174 km of the Sangro river. Sampling was conducted in 2011 and 2012, collecting spraints and anal jellies at 62 marking sites. Samples were successfully genotyped at 13 nuclear microsatellites and the ZFX/ZFY locus for molecular sexing, resulting in 14 distinct genotypes (4 females, 2 possible females, 8 males), from 35 marking sites. Mean captures/recaptures rate was 3.8 captures/individual, with males being recaptured more frequently than females. Spatial overlap among individuals was analyzed through a linear regression model fitted against sibship categories and sex pairing. Nine out of the fourteen genotyped individuals belonged to three full-sib clusters, while five individuals had no full-sibs in the population. Full-sibs overlapped more than half-sibs, while male–male pairs showed significantly higher spatial overlap than both male–female and female–female pairs. Estimated mean density was 0.152 otters/km and 2.4 individuals/10 × 10 km grid cell. Accordingly, the 3440 grid cells of otter occurrence in Italy could likely host about 8000 otters, suggesting the current population has become larger than the minimum viable population size.

Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population

Transboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.

Connections to the Deep: Deep Vertical Migrations, an Important Part of the Life Cycle of Apherusa glacialis, an Arctic Ice-Associated Amphipod

Arctic sea ice contains a substantial amount of living biota of which part is lost through melt and export out of the Arctic Ocean every year. It is unclear how populations can be maintained within the Arctic Ocean. A representative ice inhabitant, the amphipodApherusa glacialiswas previously assumed to spend its entire life in the sea ice habitat, hence being dependent on sea ice to complete its life cycle. However, several recent studies report pelagic occurrences and suggest that seasonal vertical migrations might be an adaptive life history trait enabling a viable population size in the Arctic Ocean. In this study we use a particle-tracking model to investigate to what extent vertical migration might affect the species’ retention in the Arctic Ocean and the sea ice habitat. The modeled trajectories ofA. glacialiswere calculated based on ice drift and ocean currents from a coupled ocean – sea ice model covering the Arctic Ocean. We test two scenarios: (1) trajectories ofA. glacialisthat stay attached to the ice or follow the surface currents if they melt out of the ice and (2) trajectories ofA. glacialisthat undertake a seasonal vertical migration to drift with the currents at depth for parts of the year. In the multi-year model simulations it is assumed that after an initial period of 2 yearsA. glacialisthat are located outside sea-ice cover each spring will perish while those located within the ice-covered region will reproduce. The model results show that a seasonal vertical migration both increases the total number of individuals and leads to a population distribution within the Arctic Ocean more in line with previous findings than the results from the non-migratingA. glacialis. Our results support the hypothesis that a seasonal migration may be an adaptive life history strategy in this species.

Community genomics: a community-wide perspective on within-species genetic diversity.

Community genomics: a community-wide perspective on within-species genetic diversity.

Effect of Aeration on Yeast Community Structure and Volatile Composition in Uninoculated Chardonnay Wines

Uninoculated wines are regarded as having improved mouthfeel and texture and more complex flavor profiles when compared to wines inoculated with commercial S. cerevisiae strains. Uninoculated fermentation involves a complex microbial succession of yeasts and bacteria during fermentation. Microbial population dynamics are affected by several factors that can ultimately determine if a particular species or strain contributes to wine aroma and flavor. In this work, we have studied the effect of aeration, a common winemaking practice, on the yeast microbiota during uninoculated Chardonnay wine fermentation. The timing of aeration and then aeration intensity were evaluated across two successive vintages. While the timing of aeration significantly impacted fermentation efficiency across oxygen treatments, different levels of aeration intensity only differed when compared to the non-aerated control ferments. Air addition increased the viable cell population size of yeast from the genera Hanseniaspora, Lachancea, Metschnikowia and Torulaspora in both vintages. While in 2019, a high relative abundance was found for Hanseniaspora species in aerated ferments, in 2020, T. delbrueckii was visibly more abundant than other species in response to aeration. Accompanying the observed differences in yeast community structure, the chemical profile of the finished wines was also different across the various aeration treatments. However, excessive aeration resulted in elevated concentrations of ethyl acetate and acetic acid, which would likely have a detrimental effect on wine quality. This work demonstrates the role of aeration in shaping yeast population dynamics and modulating a volatile profile in uninoculated wines, and highlights the need for careful air addition to avoid a negative sensory impact on wine flavor and aroma.

Editorial: Green or red: Challenges for fish and freshwater biodiversity conservation related to hydropower

Editorial: Green or red: Challenges for fish and freshwater biodiversity conservation related to hydropower

Looking for indicator bird species in the context of forest fragmentation and isolation in West Kalimantan, Indonesia

In the context of Borneo’s drastic landscape fragmentation, we assessed the role of diverse forest and land uses—swidden agriculture, mixed garden, smallholder rubber and oil palm plantations—in determining (1) diversity levels and composition of bird species in different vegetation types; (2) the potential for bird species to act as indicators of habitat quality; and (3) the agricultural matrix’s contribution to preserving forest-dependent species. Field campaigns across West Kalimantan sites were conducted during both rainy and dry seasons, using mist nets and 10-min point count recordings along transects. We used four diversity indices, non-metric multidimensional scaling (NMDS) and the Indicator Value index (IndVal) for our analysis. Our results endorsed the general trend found across the tropics of a significant reduction in bird species richness, from the complex natural and old secondary forest structures to the simplified monoculture habitats. We recorded 10,519 individuals across 214 bird species, representing almost 90% of Borneo’s lowland forest species. NMDS differentiated intact forest from forest fragments and land under different agriculture uses. Eighty percent of the bird species preferred an intact forest environment. Industrial oil palm sites were the most ‘avoided’ vegetation type. Using IndVal, we found six indicator species significantly associated with forest, three indicator species for depleted forest, one for mixed garden, and none for oil palm plantation. Farm-dependent species richness was strikingly low, and species had little conservation value as per IUCN standards; industrial oil palm plantations were poorest in bird species. Notable exceptions were traditional mixed gardens and old fallows associated with swidden agriculture, when in proximity to forest. These traditional agroforestry systems have higher conservation value than industrial and smallholder monoculture plantations, however, their long-term preservation is uncertain, and monitoring programs are lacking that can contribute to long-term biodiversity conservation and ecosystem service maintenance. More data are needed to determine the viable population sizes for the bird indicator species identified in our study. Such knowledge on population trends can be used to monitor habitat quality and health of forest agriculture landscape mosaics and improve the effectiveness of management, conservation and monitoring in future.