Search

Ecological limits on the population sizes and number of species a region is capable of supporting are thought to simultaneously produce spatial patterns in genetic diversity and species richness. However, we do not know the extent to which resource-based environmental limits jointly determine these patterns of biodiversity in ectotherms because of their low energy requirements compared to endotherms. Here, we adapt a framework for the ways ecological limits may shape genetic diversity and species richness previously tested in mammals for amphibians to determine whether similar processes produce continental patterns of biodiversity across both taxa. Repurposing open, raw microsatellite data from 19 species sampled at 554 sites in North America we found that spatial patterns of genetic diversity run opposite to patterns of species richness and genetic differentiation. However, while measures of resource availability and niche heterogeneity predict 89% of the variation in species richness, these landscape metrics are poor predictors of genetic diversity. Although heterogeneity appears to be an important driver of genetic and species biodiversity patterns in both amphibians and mammals, our results suggest that variation in genetic diversity both within and across species makes it difficult to infer general processes producing spatial patterns of amphibian genetic diversity.

Steady increases in human population size and resource consumption levels are driving rampant agricultural expansion and intensification in some of the world’s most pristine ecosystems. Habitat loss caused by agriculture puts the integrity of ecosystems at risk, and as a consequence, threatens the persistence of human societies that rely on ecosystem services to produce resources. Here we develop a spatially explicit model describing the coupled dynamics of an agricultural landscape and human population size to study the effect of different land-use management strategies, defined by the levels of agricultural clustering and intensification, on the sustainability of the social-ecological system. We show how gradual agricultural expansion can cause natural habitat to undergo a percolation transition leading to abrupt habitat fragmentation that feedbacks on human’s decision making, causing faster agricultural expansion and aggravating habitat loss and fragmentation. We found that agricultural intensification to spare land from conversion is a successful strategy only in highly natural landscapes and that clustering agricultural land is the most effective measure to preserve landscape connectivity and avoid severe fragmentation. Our work highlights the importance of preserving large connected natural fragments in agricultural landscapes to enhance sustainability.

Cold-adapted species escape climate warming by latitudinal and/or altitudinal range shifts, and currently occur in Southern Europe in isolated mountain ranges within "sky islands". Here, we studied the genetic structure of the Apollo butterfly in five such sky islands (above 1,000 m) in France, and infer its demographic history since the last interglacial, using single nucleotide polymorphisms (ddRADseq SNPs). The Auvergne and Alps populations show strong genetic differentiation but not alpine massifs, although separated by deep valleys. Combining three complementary demographic inference methods and species distribution models (SDMs) we show that the LIG period was highly unfavourable for Apollo that probably survived in small population in the highest summits of Auvergne. The population shifted downslope and expanded eastward between LIG and LGM throughout the large climatically suitable Rhône valley between the glaciated summits of Auvergne and Alps. The Auvergne and Alps populations started diverging before the LGM but remained largely connected till the mid-Holocene. Population decline in Auvergne was more gradual but started before (~7 kya vs. 800 ya), and was much stronger with current population size ten times lower than in the Alps. In the Alps, the low genetic structure and limited evidence for isolation by distance suggest a nonequilibrium metapopulation functioning. The core Apollo population experienced cycles of contraction-expansion with climate fluctuations with largely interconnected populations overtime according to a "metapopulation-pulsar" functioning. This study demonstrates the power of combining demographic inferences and SDMs to determine past and future evolutionary trajectories of an endangered species at a regional scale.

Summary This paper describes advances made to aerial surveys of macropods in New South Wales and Queensland. Regular aerial surveys of macropods across large areas of Australia’s arid and semi-arid rangelands were established as a response to concerns for the species’ conservation. They became integral to the harvest management of the four macropod species – Eastern Grey Kangaroo (Macropus giganteus), Western Grey Kangaroo (M. fuliginosus), Red Kangaroo (Osphranter rufus) and Common Wallaroo (O. robustus). Harvest quotas are set as a proportion of population size, requiring absolute estimates of abundance. Counts were made in strip transects from fixed-wing aircraft, but required correction for animals that are missed. In New South Wales and Queensland, counts are now made using line transect sampling, providing survey-specific correction. Helicopters are used in more rugged and timbered areas and where Common Wallaroo can be more frequently found and harvested. Mark-recapture distance sampling is used in more open country that can be surveyed using fixed-wing aircraft and improves the accuracy of density estimates by accounting for animals missed on the transect line. Macropod populations are likely to be surveyed in the future by airborne imagery and by drones, but the technology needs further development. Spatial models could usefully provide small-scale density estimates and address non-random sampling.

Monitoring the demographics and genetics of reintroduced populations is critical to evaluating reintroduction success, but species ecology and the landscapes that they inhabit often present challenges for accurate assessments. If suitable habitats are restricted to hierarchical dendritic networks, such as river systems, animal movements are typically constrained and may violate assumptions of methods commonly used to estimate demographic parameters. Using genetic detection data collected via fecal sampling at latrines, we demonstrate applicability of the spatial capture–recapture (SCR) network distance function for estimating the size and density of a recently reintroduced North American river otter (Lontra canadensis) population in the Upper Rio Grande River dendritic network in the southwestern United States, and we also evaluated the genetic outcomes of using a small founder group (n = 33 otters) for reintroduction. Estimated population density was 0.23–0.28 otter/km, or 1 otter/3.57–4.35 km, with weak evidence of density increasing with northerly latitude (β = 0.33). Estimated population size was 83–104 total otters in 359 km of riverine dendritic network, which corresponded to average annual exponential population growth of 1.12–1.15/year since reintroduction. Growth was ≥40% lower than most reintroduced river otter populations and strong evidence of a founder effect existed 8–10 years post‐reintroduction, including 13–21% genetic diversity loss, 84%–87% genetic effective population size decline, and rapid divergence from the source population (F ST accumulation = 0.06/generation). Consequently, genetic restoration via translocation of additional otters from other populations may be necessary to mitigate deleterious genetic effects in this small, isolated population. Combined with non‐invasive genetic sampling, the SCR network distance approach is likely widely applicable to demogenetic assessments of both reintroduced and established populations of multiple mustelid species that inhabit aquatic dendritic networks, many of which are regionally or globally imperiled and may warrant reintroduction or augmentation efforts., Monitoring the demographics and genetics of reintroduced populations is critical to evaluating reintroduction success, but species ecology and the landscapes that they inhabit often present challenges for accurate assessments. Using genetic detection data collected via fecal sampling at latrines, we demonstrate applicability of the spatial capture–recapture (SCR) network distance function for estimating the size and density of a recently reintroduced North American river otter (Lontra canadensis) population in the Upper Rio Grande River dendritic network in the southwestern United States, and we also evaluated the genetic outcomes of using a small founder group for reintroduction. Combined with noninvasive genetic sampling, the SCR network distance approach is likely widely applicable to demogenetic assessments of both reintroduced and established populations of multiple mustelid species that inhabit aquatic dendritic networks, many of which are regionally or globally imperiled and may warrant reintroduction or augmentation efforts.

Objective To estimate the numbers of COVID‐19‐related hospitalisations in Australia after re‐opening the international border. Design Population‐level deterministic compartmental epidemic modelling of eight scenarios applying various assumptions regarding SARS‐CoV‐2 transmissibility (baseline R 0 = 3.5 or 7.0), vaccine rollout speed (slow or fast), and scale of border re‐opening (mean of 2500 or 13 000 overseas arrivals per day). Setting Simulation population size, age structure, and age‐based contact rates based on recent estimates for the Australian population. We assumed that 80% vaccination coverage of people aged 16 years or more was reached in mid‐October 2021 (fast rollout) or early January 2022 (slow rollout). Main outcome measures Numbers of people admitted to hospital with COVID‐19, December 2021 ‒ December 2022. Results In scenarios assuming a highly transmissible SARS‐CoV‐2 variant (R 0 = 7.0), opening the international border on either scale was followed by surges in both infections and hospitalisations that would require public health measures beyond mask wearing and social distancing to avoid overwhelming the health system. Reducing the number of hospitalisations to manageable levels required several cycles of additional social and mobility restrictions. Conclusions If highly transmissible SARS‐CoV‐2 variants are circulating locally or overseas, large and disruptive COVID‐19 outbreaks will still be possible in Australia after 80% of people aged 16 years or more have been vaccinated. Continuing public health measures to restrict the spread of disease are likely to be necessary throughout 2022.

Endemic species distributed in fragmented habitats are highly vulnerable to extinction because they may have low genetic diversity. However, some life-history traits can mitigate the effect of genetic drift on populations. We analysed the level and distribution of genetic variation and ancestral population size of Yucca capensis, a long-lived endemic plant of the Baja California Peninsula, Mexico. Its populations are scattered across a habitat that is suffering accelerated transformation. We used six nuclear microsatellites to genotype 224 individuals from 17 locations across the entire species' geographic range. We estimated polymorphisms, heterozygosity and genetic structure. We also evaluated the ancestral and recent effective size and time since the population started to change. We found high heterozygosity, high polymorphism and low differentiation among locations, suggesting a panmictic population across the range. We also detected a large ancestral effective population size, which suffered a strong reduction in the Mid-Holocene. Despite changes in environmental conditions caused by habitat modification, the high diversity and low differentiation in Y. capensis may result from its large ancestral effective size and life-history traits, such as plant longevity, clonal growth and mating system, which reduce the rate of loss of genetic variation. However, the dependence on a specialist pollinator that displays short flight range can reduce gene flow among the plant populations and could, shortly, lead them into an extinction vortex.

In the last five years, interest in close-kin mark-recapture (CKMR), a variant of mark-recapture that uses genetically inferred kin as 'recaptures', has grown dramatically. However, understanding the basis of CKMR, and properly implementing it, remains challenging. This paper describes an R package, CKMRpop, for simulating age-structured populations with user-specified demography, overdispersed variance in reproductive success (allowing for different ratios of effective to census size) and random sampling of individuals. Using compiled code for the simulation makes it feasible to simulate populations of millions of individuals. From the simulation output, pairs of sampled individuals related within a user-specified number of generations are found. Such pairs form the foundation for CKMR inference, and simulating them provides insight for understanding the statistical basis for CKMR and for assessing the feasibility of CKMR in different scenarios. We predict that CKMRpop will serve as an important tool for researchers contemplating CKMR estimation of population size. Furthermore, the methods presented here for identifying and categorizing relationships beyond half-siblings allow a more complete picture of the wide variety of kin pairs encountered in populations. This identifies the fraction of kin pairs that may not be the target of a CKMR experiment, but may be inadvertently mistaken for a more closely related 'target' kin pair. Additionally, as more distant kin categories will likely be accurately inferred from increasingly available and inexpensive whole genome resequencing, understanding the distributions of more distant relationships in populations is a first step towards broadening the scope of CKMR to include them.

Whole genome sequencing provides deep insights into the evolutionary history of a species, including patterns of diversity, signals of selection, and historical demography. When applied to closely related taxa with a wealth of background knowledge, population genomics provides a comparative context for interpreting population genetic summary statistics and comparing empirical results with the expectations of population genetic theory. The Galapagos giant tortoises (Chelonoidis spp.), an iconic rapid and recent radiation, offer such an opportunity. Here, we sequenced whole genomes from three individuals of the 12 extant lineages of Galapagos giant tortoise and estimate diversity measures and reconstruct changes in coalescent rate over time. We also compare the number of derived alleles in each lineage to infer how synonymous and nonsynonymous mutation accumulation rates correlate with population size and life history traits. Remarkably, we find that patterns of molecular evolution are similar within individuals of the same lineage, but can differ significantly among lineages, reinforcing the evolutionary distinctiveness of the Galapagos giant tortoise species. Notably, differences in mutation accumulation among lineages do not align with simple population genetic predictions, suggesting that the drivers of purifying selection are more complex than is currently appreciated. By integrating results from earlier population genetic and phylogeographic studies with new findings from the analysis of whole genomes, we provide the most in-depth insights to date on the evolution of Galapagos giant tortoises, and identify discrepancies between expectation from population genetic theory and empirical data that warrant further scrutiny.

Pleistocene glacial cycles influenced the diversification of high-latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger-scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20-30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre-LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high-latitude species.

Environmental risk assessment of metal mixtures is challenging due to the large number of possible mixtures and interactions. Mixture toxicity data cannot realistically be generated for all relevant scenarios. Therefore, methods for prediction of mixture toxicity from single-metal toxicity data are needed. We tested how well toxicity of Cu-Ni-Zn mixtures to Daphnia magna populations can be predicted based on the Dynamic Energy Budget theory with an individual-based model (DEB-IBM), assuming non-interactivity of metals on the physiological level. We exposed D. magna populations to Cu, Ni, and Zn and their mixture at a fixed concentration ratio. We calibrated the DEB-IBM with single-metal data and generated blind predictions of mixture toxicity (population size over time), with account for uncertainty. We compared the predictive performance of the DEB-IBM with respect to mixture effects on population density and population growth rates with that of two reference models applied on the population level, independent action and concentration addition. Our inferred physiological modes of action (pMoA) differed from literature-reported pMoAs, raising the question of whether this is a result of different model selection approaches, intraspecific variability, or whether different pMoAs might actually drive toxicity in a population context. Observed mixture effects were concentration- and endpoint-dependent. The independent action was overall more accurate than the concentration addition but concentration addition-predicted effects on population growth rate were slightly better. The DEB-IBM most accurately predicted effects on 6-week density, including antagonistic effects at high concentrations, which emerged from non-interactivity at the physiological level. Mixture effects on initial population growth rate appear to be more difficult to predict. To explain why model accuracy is endpoint-dependent, relationships between individual-level and population-level endpoints should be illuminated. Environ Toxicol Chem 2021;40:3034-3048. © 2021 SETAC.

1. Pollinator-mediated reproductive interference can occur when two or more plant species share the same pollinators. Recent studies have suggested that prior autonomous selfing mitigates reproductive interference, potentially facilitating coexistence even in the absence of pollination niche partitioning (i.e. the pre-emptive selfing hypothesis). However, whether the evolution of prior selfing promotes coexistence, in the context of the eco-evolutionary dynamics of population size, selfing rates and inbreeding depression, remains poorly understood. 2. We constructed an individual-based model to examine the conditions under which the evolution of prior selfing promotes coexistence in the context of mutual reproductive interference. In the model, two plant species compete by way of mutual reproductive interference, and both have the potential to evolve the capacity for prior autonomous selfing. We expected that purging of deleterious mutations might result in evolutionary rescue, assuming that the strength of inbreeding depression declines as the population selfing rate increases; this would enable inferior competitors to maintain population density through the evolution of prior selfing. 3. Our simulation demonstrated that evolution of prior selfing may promote coexistence, whereas reproductive interference in the absence of such evolution results in competitive exclusion. We found that lower pollinator availability is likely to favour rapid evolutionary shifts to higher prior selfing rates, thereby neutralising the negative effects of reproductive interference in both species. When the strength of inbreeding depression decreased with an increase in the population-level selfing rate, moderate pollinator availability resulted in long-term coexistence in which relative abundance-dependent selection on the prior selfing rate served to intermittently maintain the population density of the inferior competitor. 4. Synthesis. We demonstrate that the evolution of prior selfing may increase population growth rates of inferior competitors and may consequently promote long-term coexistence via an evolutionary rescue. This constitutes a novel mechanism explaining the co-evolutionary coexistence of closely related plant species without niche partitioning, and is consistent with recent studies reporting that closely related species with mixed mating systems can co-occur sympatrically, even under conditions of mutual reproductive interference.

Reconstructing past events of hybridization and population size changes are required to understand speciation mechanisms and current patterns of genetic diversity, and ultimately contribute to species' conservation. Sea turtles are ancient species currently facing anthropogenic threats including climate change, fisheries, and illegal hunting. Five of the seven extant sea turtle species are known to currently hybridize, especially along the Brazilian coast where some populations can have ~32%-42% of hybrids. Although frequently observed today, it is not clear what role hybridization plays in the evolutionary diversification of this group of reptiles. In this study, we generated whole genome resequencing data of the five globally distributed sea turtle species to estimate a calibrated phylogeny and the population size dynamics, and to understand the role of hybridization in shaping the genomes of these ancient species. Our results reveal discordant species divergence dates between mitochondrial and nuclear genomes, with a high frequency of conflicting trees throughout the nuclear genome suggesting that some sea turtle species frequently hybridized in the past. The reconstruction of the species' demography showed a general decline in effective population sizes with no signs of recovery, except for the leatherback sea turtle. Furthermore, we discuss the influence of reference bias in our estimates. We show long-lasting ancestral gene flow events within Chelonioidea that continued for millions of years after initial divergence. Speciation with gene flow is a common pattern in marine species, and it raises questions whether current hybridization events should be considered as a part of these species' evolutionary history or a conservation issue.

Signatures of past changes in population size have been detected in genome-wide variation in many species. However, the causes of such demographic changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely documented, it is unclear whether refugial populations of co-distributed species have experienced shared histories of population size change. We analyse whole genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). For four of these species, we find support for large changes in effective population size (Ne ) through the Pleistocene that coincide with major climate events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories in this guild are largely idiosyncratic, even at the scale of a single glacial refugium.

Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual‐based simulations under a stepping‐stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries) and heterogenicity (the genomic proportion heterozygous for ancestry) are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration rate increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones., Ancestry changes along admixed chromosomes have been used by numerous models and methods to reveal the history of admixed populations, yet these approaches are rarely applied to structured hybrid zones. In this study, we perform simulations under a stepping‐stone model, focusing on migration rate, deme size, and hybrid zone age as key parameters. We find that ancestry patterns including our novel summary—the junction frequency spectrum—are sensitive indicators of demographic history.

Drift is the process by which gene frequency changes erratically in a population. Random sampling of gametes at reproduction is the main cause of drift, and therefore the population size of a species is most important, that is often measured by the effective size. Homozygosity and inbreeding may increase by drift. The significance of drift has become clear in studies of population genetics and evolution at the molecular level by the expansion of genome data. The effects of drift are estimated by statistical analyses of molecular data on polymorphisms and divergence among related species. In particular, the interplay of drift and selection is most important in understanding the evolution of interaction systems at various levels. Epigenetic mechanisms have significant influences on the interplay. Drift, selection, environmental factors, and epigenetics are thought to work together here. Key Concepts: Random sampling of gametes at reproduction is the major cause of drift in a finite population. Interplay of drift and selection is essential for evolution of complex systems, and the two become inseparable. Robust genetic systems enhance the effects of drift. Epigenetics gives opportunities for drift and selection to respond to environmental changes. Keywords: stochastic process; selective neutrality and near-neutrality; effective population size; interplay of drift and selection; evolution of complex systems

The Southern Ocean has been disproportionately affected by climate change and is therefore an ideal place to study the influence of changing environmental conditions on ecosystems. Changes in the demography of predator populations are indicators of broader shifts in food web structure, but long‐term data are required to study these effects. Southern elephant seals (Mirounga leonina) from Macquarie Island have consistently decreased in population size while all other major populations across the Southern Ocean have recently stabilized or are increasing. Two long‐term mark‐recapture studies (1956–1967 and 1993–2009) have monitored this population, which provides an opportunity to investigate demographic performance over a range of climatic conditions. Using a 9‐state matrix population model, we estimated climate influences on female survival by incorporating two major climatic indices into our model: The Southern Annular Mode (SAM) and the Southern Oscillation Index (SOI). Our best model included a 1 year lagged effect of SAM and an unlagged SOI as covariates. A positive relationship with SAM1 (lagged) related the previous year's SAM with juvenile survival, potentially due to changes in local prey availability surrounding Macquarie Island. The unlagged SOI had a negative effect on both juvenile and adult seals, indicating that sea ice dynamics and access to foraging grounds on the East Antarctic continental shelf could explain the different contributions of ENSO events on the survival of females in this population., This research investigated the influence of large‐scale climate modes (SAM and SOI) on female southern elephant seal survival (φ) by creating demographic models from historic capture‐mark‐recapture data. Map of the Southern Ocean from Tasmania (top) to East Antarctica and the Ross Sea (bottom) with Macquarie Island location marked by a small circle. Surrounding Antarctica, the Polar Front (blue line), 60th parallel south, (gray circle) and winter sea ice extent (white) are overlaid. Top right: Vegetation map of Macquarie Island (adapted from the Australian Antarctic Data Centre map no. 13106) and stylized illustration of a female southern elephant seal, Mirounga leonina (artwork by: Sophia Volzke).

Genotype-by-environment interaction (GEI) is one of the major factors affecting the prediction accuracy of genomic selection (GS) models. Standard models have low power to model complex GEI and they fail to predict phenotypes in unobserved environments. Here, we developed a novel prediction model that account for GEI, named 3GS, that combines genotype plus genotype × environment (GGE) analysis with genomic selection. The model calculates the principal components (PCs) of the environmental phenotypes using GGE analysis and predict the performance of these PCs using standard GS models before converting the GEBVs of these PCs (pcGEBVs) back to the original phenotypes. We demonstrated three advantages of the new model. First, 3GS showed significantly higher prediction accuracy primarily for deviated environments that have low to negative correlations to other environments. Second, 3GS can predict new genotypes in unobserved environments with high accuracy. Third, the computational complexity of 3GS increases linearly with increasing the number of environments and the population size, unlike the standard models that exhibit exponential increase, making it hundreds of times faster than the standard models for large datasets. 3GS can improve prediction accuracy with minimal resources in modern breeding programs in which massive populations get multi-environment phenotypes with high-throughput techniques. This article is protected by copyright. All rights reserved.

Until last year, North Battleford, Saskatchewan has held the title for the “crime capital of Canada” with the highest crime severity index in the country. While the crime severity index is considered a better measure of crime seriousness compared to crime rates, it is still largely influenced by population size. As a result, the small municipality of North Battleford, with a population of approximately 14,000 people, may be inappropriately labelled as the crime capital. The current study compares the crime severity index and crime rates against the location quotient: a geographical measure. The location quotient calculates an area's crime specialization, compared to surrounding areas. In the period 2006 to 2018, findings indicate that North Battleford did not specialize in violent crime compared to other municipal police jurisdictions in Saskatchewan. Implications for policy and practice, as well as local narratives and stigmatization, are discussed.

Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbor very low genetic diversity compared with their parental populations. The present study addresses how population size and within‐population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment and then imposed a one‐individual‐size population bottleneck on those surviving the antibiotic stress. During the subsequent compensatory evolution, population size increased and leveled off very rapidly. The increase of diversity was of slower paces and persisted longer. In the very early stage of compensatory evolution, populations of large sizes had a greater chance to diversify; however, this productivity–diversification relationship was not observed in later stages. Population size and diversity from the end of the compensatory evolution was not contingent on initial population growth performance. We discussed the possibility that our results be explained by the emergence of a “holey” fitness landscape under the antibiotic stress., Bacterial populations lost diversity and showed reduced growth performance after an evolutionary rescue from environmental stress. During the subsequent compensatory adaptation, improvement of growth performance preceded ecological diversification, and the final population size and diversity were not contingent on initial population growth performance. The mode and pace of adaptation and diversification may be explained by a holey fitness landscape under environmental stress.

Long‐term population declines have elevated recovery of grassland avifauna to among the highest conservation priorities in North America. Because most of the Great Plains is privately owned, recovery of grassland bird populations depends on voluntary conservation with strong partnerships between private landowners and resource professionals. Despite large areas enrolled in voluntary practices through U.S. Department of Agriculture's Lesser Prairie‐chicken (Tympanuchus pallidicinctus) Initiative (LPCI), the effectiveness of Farm Bill investments for meeting wildlife conservation goals remains an open question. Our objectives were to evaluate extents to which Conservation Reserve Program (CRP) and LPCI‐grazing practices influence population densities of grassland birds; estimate relative contributions of practices to regional bird populations; and evaluate percentages of populations conserved relative to vulnerability of species. We designed a large‐scale impact‐reference study and used the Integrated Monitoring in Bird Conservation Regions program to evaluate bird population targets of the Playa Lakes Joint Venture. We used point transect distance sampling to estimate density and population size for 35 species of grassland birds on private lands enrolled in native or introduced CRP plantings and LPCI‐prescribed grazing. Treatment effects indicated CRP plantings increased densities of three grassland obligates vulnerable to habitat loss, and LPCI grazing increased densities of four species requiring heterogeneity in dense, tall‐grass structure (α = 0.1). Population estimates in 2016 indicated the practices conserved breeding habitat for 4.5 million birds (90% CI: 4.0–5.1), and increased population sizes of 16 species , totaling 1.8 million birds (CI: 1.4–2.4). Conservation practices on private land benefited the most vulnerable grassland obligate species (AICc weight = 0.53). By addressing habitat loss and degradation in agricultural landscapes, conservation on private land provides a solution to declining avifauna of North America and scales up to meet population recovery goals for the most imperiled grassland birds., Article impact statement: Voluntary conservation on private land addressing critical habitat needs provides an emerging solution to the decline of grassland birds.

Theoretical models of ecological specialisation commonly assume that adaptation to one environment leads to fitness reductions (costs) in others. However, experiments often fail to detect such costs. We addressed this conundrum using experimental evolution with Escherichia coli in several constant and fluctuating environments at multiple population sizes. We found that in fluctuating environments, smaller populations paid significant costs, but larger ones avoided them altogether. Contrastingly, in constant environments, larger populations paid more costs than the smaller ones. Overall, large population sizes and fluctuating environments led to cost avoidance only when present together. Mutational frequency distributions obtained from whole-genome whole-population sequencing revealed that the primary mechanism of cost avoidance was the enrichment of multiple beneficial mutations within the same lineage. Since the conditions revealed by our study for avoiding costs are widespread, it provides a novel explanation of the conundrum of why the costs expected in theory are rarely detected in experiments.

Age is a fundamental parameter in wildlife management as it is used to determine the risk of extinction, manage invasive species, and regulate sustainable harvest. In a broad variety of vertebrates species, age can be determined by measuring DNA methylation. Animals with known ages are initially required during development, calibration, and validation of these epigenetic clocks. However, wild animals with known ages are frequently difficult to obtain. Here, we perform Monte‐Carlo simulations to determine the optimal sample size required to create an accurate calibration model for age estimation by elastic net regression modelling of cytosine‐phosphate‐guanine methylation data. Our results suggest a minimum calibration population size of 70, but ideally 134 individuals or more for accurate and precise models. We also provide estimates to the extent a model can be extrapolated beyond a distribution of ages that was used during calibration. The findings can assist researchers to better design age estimation models and decide if their model is adequate for determining key population attributes.

In longitudinal event data, a crude rate is a simple quantification of the event rate, defined as the number of events during an evaluation window, divided by the at-risk population size at the beginning or mid-time point of that window. The crude rate recently received revitalizing interest from medical researchers who aimed to improve measurement of misdiagnosis-related harms using administrative or billing data by tracking unexpected adverse events following a "benign" diagnosis. The simplicity of these measures makes them attractive for implementation and routine operational monitoring at hospital or health system level. However, relevant statistical inference procedures have not been systematically summarized. Moreover, it is unclear to what extent the temporal changes of the at-risk population size would bias analyses and affect important conclusions concerning misdiagnosis-related harms. In this article, we present statistical inference tools for using crude-rate based harm measures, as well as formulas and simulation results that quantify the deviation of such measures from those based on the more sophisticated Nelson-Aalen estimator. Moreover, we present results for a generalized multibin version of the crude rate, for which the usual crude rate is a single-bin special case. The generalized multibin crude rate is more straightforward to compute than the Nelson-Aalen estimator and can reduce potential biases of the single-bin crude rate. For studies that seek to use multibin measures, we provide simulations to guide the choice regarding number of bins. We further bolster these results using a worked example of stroke after "benign" dizziness from a large data set.

Chance plays a critical but underappreciated role in determining mating success. In many cases, we tend to think of chance as background noise that can be ignored in studies of mating dynamics. When the influence of chance is consistent across contexts, chance can be thought of as background noise; in other cases, however, the impact of chance on mating success can influence our understanding of how mates are acquired and how sexual selection operates. In particular, when the importance of chance covaries with biological or ecological factors in a systematic manner—that is, when chance becomes consistently more or less important under certain conditions—then chance is important to consider if we want to fully understand the operation of mate acquisition and sexual selection. Here, we present a model that explores how chance covaries with factors such as sex ratio, adult population size, and mating regime in determining variation in mating success. We find that in some cases, chance covaries with adult population size and the operational sex ratio to create variation in mating success. We discuss how chance can influence our more general understanding of the operation of mating dynamics and sexual selection., The effect of chance on mating success can covary with biological factors of interest and influence our understanding of sexual selection. In such cases, chance becomes more than just noise, and considering chance is key to understanding fully the operation of sexual selection.

Daily activity in herbivores reflects a balance between finding food and safety. The safety‐in‐numbers theory predicts that living in higher population densities increases safety, which should affect this balance. High‐density populations are thus expected to show a more even distribution of activity—that is, spread—and higher activity levels across the day. We tested these predictions for three ungulate species; red deer (Cervus elaphus), roe deer (Capreolus capreolus), and wild boar (Sus scrofa). We used camera traps to measure the level and spread of activity across ten forest sites at the Veluwe, the Netherlands, that widely range in ungulate density. Food availability and hunting levels were included as covariates. Daily activity was more evenly distributed when population density was higher for all three species. Both deer species showed relatively more feeding activity in broad daylight and wild boar during dusk. Activity level increased with population density only for wild boar. Food availability and hunting showed no correlation with activity patterns. These findings indicate that ungulate activity is to some degree density dependent. However, while these patterns might result from larger populations feeling safer as the safety‐in‐numbers theory states, we cannot rule out that they are the outcome of greater intraspecific competition for food, forcing animals to forage during suboptimal times of the day. Overall, this study demonstrates that wild ungulates adjust their activity spread and level based on their population size., Daily activity of three ungulate species is density dependent across ten temperate forest sites. Activity spread and level increases with ungulate population size. Suggesting that future research should account for population size as a driver of ungulate activity.

In human‐dominated landscapes, connectivity is crucial for maintaining demographically stable mammalian populations. Here, we provide a comprehensive noninvasive genetic study for the brown bear population in the Hellenic Peninsula. We analyze its population structuring and connectivity, estimate its population size throughout its distribution, and describe its phylogeography in detail for the first time. Our results, based on 150 multilocus genotypes and on 244‐bp sequences of the mtDNA control region, show the population is comprised by three highly differentiated genetic clusters, consistent with geographical populations of Pindos, Peristeri, and Rhodope. By detecting two male bears with Rhodopean ancestry in the western demes, we provide strong evidence for the ongoing genetic connectivity of the geographically fragmented eastern and western distributions, which suggests connectivity of the larger East Balkan and Pindos‐Dinara populations. Total effective population size (Ne) was estimated to be 199 individuals, and total combined population size (NC) was 499, with each cluster showing a relatively high level of genetic variability, suggesting that migration has been sufficient to counteract genetic erosion. The mtNDA results were congruent with the microsatellite data, and the three genetic clusters were matched predominantly with an equal number of mtDNA haplotypes that belong to the brown bear Western mitochondrial lineage (Clade 1), with two haplotypes being globally new and endemic. The detection of a fourth haplotype that belongs to the Eastern lineage (Clade 3a1) in three bears from the western distribution places the southernmost secondary contact zone between the Eastern and Western lineages in Greece and generates new hypotheses about postglacial maxima migration routes. This work indicates that the genetic composition and diversity of Europe's low‐latitude fringe population are the outcome of ancient and historical events and highlight its importance for the connectivity and long‐term persistence of the species in the Balkans.

The recovery of overexploited populations is likely to reveal behaviours that may have been present prior to harvest but are only now reappearing as the population size increases. The east Australian humpback whale (Megaptera novaeangliae) population (group V, stock E1) has recovered well from past exploitation and is now estimated to be close to the pre-whaling population size. Humpback whales were thought to follow a ‘feast and famine’ model historically, feeding intensively in high-latitude feeding grounds and then fasting while migrating and in calving grounds; however, there is growing evidence that animals may feed outside of known foraging grounds. This short article reports on the first photographically documented evidence of bubble-net feeding by humpback whales in Australian coastal waters (n = 10 groups observed) and provides the first evidence of a second site in the southern hemisphere for the formation of ‘super-groups’ (n = 6 super-groups at discrete locations). The formation of super-groups may be linked to changes in the type or density of prey available, either along the migratory route or in the feeding grounds of the previous summer. It is also possible that the increased population size following recovery make large group sizes while feeding more common. These findings strongly support evidence that feeding behaviour is not restricted to high-latitude foraging grounds in the Southern Ocean, and that prey consumption prior to leaving the coastal waters of Australia may be a significant component of the migratory ecology of this population. Understanding how environmental variation influences the extent to which humpback whales depend on foraging opportunities along their migratory route, and where feeding occurs, will help to predict how future changes in the ocean will influence whale populations. This will also allow for more effective management measures to reduce the impact of threats during this important period of energy consumption.

Aim: Globally distributed pelagic fishes are typified by very low to negligible genetic differentiation at oceanic scales arising from high gene flow and (or) large population sizes. However, genomic approaches employing thousands of loci to characterise genetic variation can illuminate subtle patterns of genetic structure and facilitate demographic inference, such that effects arising from gene flow and population size can be partially decoupled. We used a population genomics approach to identify putative stocks in a circumtropical pelagic fish, wahoo, and to assess global connectivity in this species. Location: Indo-Pacific and Atlantic Oceans. Taxon: Wahoo, Acanthocybium solandri (Cuvier, 1832). Methods: Globally distributed wahoo samples from 11 locations (representing a total of 296 individuals) were sequenced using a pool-seq ezRAD approach to obtain 1289–9825 genome-wide SNP loci per population pair for analyses of genetic structure at a minor allele frequency (MAF) >0.05. Demographic inference using a diffusion approximation method (∂a∂i) was performed using 11,495–12,812 SNPs per population pair at a MAF >0.02. Results: Genetic structure, measured as F , was overall low, suggesting very little heterogeneity amongst sample pairs (pairwise F ≤ 0.021). However, there was a clear signal of regional genetic structuring between ocean basins. A principal coordinate analysis separated samples from the Indo-Pacific with those from the Atlantic and an analysis of molecular variance suggested that ~77% of variation in genetic structure was amongst regions. Our demographic analyses found greater support for models including migration over simple models of isolation. Main conclusions: Our study provides the most thorough genetic investigation of wahoo to date. We provide evidence for global connectivity of wahoo populations over their evolutionary history, but we also provide the first indication of subtle regional structure between the Indo-Pacific and Atlantic Oceans, which occurs against a background of high gene flow. The identification of regional stocks will inform new management strategies and guide future investigations in wahoo, an increasingly important species in global fisheries. ST ST

Understanding how anthropogenic disturbances affect plant–pollinator systems has important implications for the conservation of biodiversity and ecosystem functioning. Previous laboratory studies show that pesticides and pathogens, which have been implicated in the rapid global decline of pollinators over recent years, can impair behavioral processes needed for pollinators to adaptively exploit floral resources and effectively transfer pollen among plants. However, the potential for these sublethal stressor effects on pollinator–plant interactions at the individual level to scale up into changes to the dynamics of wild plant and pollinator populations at the system level remains unclear. We developed an empirically parameterized agent‐based model of a bumblebee pollination system called SimBee to test for effects of stressor‐induced decreases in the memory capacity and information processing speed of individual foragers on bee abundance (scenario 1), plant diversity (scenario 2), and bee–plant system stability (scenario 3) over 20 virtual seasons. Modeling of a simple pollination network of a bumblebee and four co‐flowering bee‐pollinated plant species indicated that bee decline and plant species extinction events could occur when only 25% of the forager population showed cognitive impairment. Higher percentages of impairment caused 50% bee loss in just five virtual seasons and system‐wide extinction events in less than 20 virtual seasons under some conditions. Plant species extinctions occurred regardless of bee population size, indicating that stressor‐induced changes to pollinator behavior alone could drive species loss from plant communities. These findings indicate that sublethal stressor effects on pollinator behavioral mechanisms, although seemingly insignificant at the level of individuals, have the cumulative potential in principle to degrade plant–pollinator species interactions at the system level. Our work highlights the importance of an agent‐based modeling approach for the identification and mitigation of anthropogenic impacts on plant–pollinator systems., Article impact statement: Sublethal effects of pesticides and disease on pollinator foraging behavior threaten the stability of pollination systems.