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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.

Objective: A genomic region associated with a particular phenotype is called quantitative trait loci (QTL). To detect the optimal F2 population size associated with QTLs in native chicken, we performed a simulation study on F2 population derived from crosses between two different breeds.Methods: A total of 15 males and 150 females were randomly selected from the last generation of each F1 population which was composed of different breed to create two different F2 populations. The progenies produced from these selected individuals were simulated for six more generations. Their marker genotypes were simulated with a density of 50K at three different heritability levels for the traits such as 0.1, 0.3, and 0.5. Our study compared 100, 500, 1,000 reference population (RP) groups to each other with three different heritability levels. And a total of 35 QTLs were used, and their locations were randomly created.Results: With a RP size of 100, no QTL was detected to satisfy Bonferroni value at three different heritability levels. In a RP size of 500, two QTLs were detected when the heritability was 0.5. With a RP size of 1,000, 0.1 heritability was detected only one QTL, and 0.5 heritability detected five QTLs. To sum up, RP size and heritability play a key role in detecting QTLs in a QTL study. The larger RP size and greater heritability value, the higher the probability of detection of QTLs.Conclusion: Our study suggests that the use of a large RP and heritability can improve QTL detection in an F2 chicken population.

Computational efficiency has become a key issue in genomic prediction (GP) owing to the massive historical datasets accumulated. We developed hereby a new super-fast GP approach (SHEAPY) combining randomized Haseman-Elston regression (RHE-reg) with a modified Algorithm for Proven and Young (APY) in an additive-effect model, using the former to estimate heritability and then the latter to invert a large genomic relationship matrix for best linear prediction. In simulation results with varied sizes of training population, GBLUP, HEAPY|A and SHEAPY showed similar predictive performance when the size of a core population was half that of a large training population and the heritability was a fixed value, and the computational speed of SHEAPY was faster than that of GBLUP and HEAPY|A. In simulation results with varied heritability, SHEAPY showed better predictive ability than GBLUP in all cases and than HEAPY|A in most cases when the size of a core population was 4/5 that of a small training population and the training population size was a fixed value. As a proof of concept, SHEAPY was applied to the analysis of two real datasets. In an Arabidopsis thaliana F2 population, the predictive performance of SHEAPY was similar to or better than that of GBLUP and HEAPY|A in most cases when the size of a core population (2 0 0) was 2/3 of that of a small training population (3 0 0). In a sorghum multiparental population, SHEAPY showed higher predictive accuracy than HEAPY|A for all of three traits, and than GBLUP for two traits. SHEAPY may become the GP method of choice for large-scale genomic data.

Mutations with large fitness benefits and mutations occurring at high rates may both cause parallel evolution, but their contribution is predicted to depend on population size. Moreover, high-rate and large-benefit mutations may have different long-term adaptive consequences. We show that small and 100-fold larger bacterial populations evolve resistance to a β-lactam antibiotic by using similar numbers, but different types of mutations. Small populations frequently substitute similar high-rate structural variants and loss-of-function point mutations, including the deletion of a low-activity β-lactamase, and evolve modest resistance levels. Large populations more often use low-rate, large-benefit point mutations affecting the same targets, including mutations activating the β-lactamase and other gain-of-function mutations, leading to much higher resistance levels. Our results demonstrate the separation by clonal interference of mutation classes with divergent adaptive consequences, causing a shift from high-rate to large-benefit mutations with increases in population size.

Hamadryas baboons, Papio hamadryas, differ from almost all other primate species in that males separate female kin by aggressively coercing females into joining their one-male units. Male behaviour thus appears to be the sole determinant of social structure, shaping patterns of relatedness. However, recent genetic studies have found that female relatedness within one-male units (OMUs) is higher than across OMUs, contrary to expected results of male behaviour. This has caused some researchers to speculate that female hamadryas baboons have some influence over dispersal. In this study, we used an agent-based model to parse how the hamadryas social system influences OMU female relatedness. We hypothesized that (1) the multilevel social structure in hamadryas baboons leads to greater-than-random relatedness in OMUs and that (2) subtle female preference leads to even higher relatedness, similar to the pattern observed in genetic data. Our agent-based model of hamadryas baboon society and dispersal was based on available field data and ran for 150 years in discrete 6-month intervals. To test hypothesis 2, we implemented manipulations mimicking female kin attraction, which increased females’ chances of being transferred into a unit containing closely related females. As output of every simulation, pedigree relatedness of adult female dyads within and across OMUs was calculated. We validated our model by comparing patterns of group size, population size, adult sex ratio and dispersal rates with available field data. The results of our simulations supported both hypotheses. Relatedness within OMUs was slightly higher than across OMUs when females had no influence over dispersal. When we implemented our scenarios of female influence on dispersal, the relatedness within OMUs increased even more, approaching the effect size of genetic data from the field. We conclude that, despite conflicting interests, a combination of male and female behaviour create a complex pattern of gene flow in this unique multilevel social system.

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.

Climate and land management are important environmental drivers that affect the structure of terrestrial plant communities worldwide. Demographic studies allow a mechanistic understanding of the pathways in which environmental factors change population size. Climate and land management might interactively influence vital rates and growth rates of populations, however, demographic studies have not heretofore considered both factors in combination. We used the Global Change Experimental Facility as a platform to study the effect of climate (ambient climate conditions vs. future climate conditions) and land management (sheep grazing vs. mowing) on the demography of the common grass, Bromus erectus growing in semi-natural grassland communities. Using an integral projection model, we found positive population growth rates for B. erectus under all treatment combinations, and an interactive effect of climate and land management. Under ambient climate conditions, population growth of B. erectus was higher in mowed than grazed grassland plots, while population growth rates were similar across both management types under future climatic conditions. This interaction was primarily due to between-treatment changes in seedling recruitment, a vital rate to which the population growth rate is particularly sensitive. The interaction found in this study highlights the importance of considering multiple environmental drivers in demographic studies, to better predict future plant population dynamics and ultimately changes in community structure.

Populations of rare and restricted species are commonly challenged due to risks associated with reduced genetic diversity, environmental variation, and demographic stochasticity. Killickia grandiflora (Lamiaceae) is one of three Killickia species endemic to the Drakensberg Mountain Centre in KwaZulu-Natal, South Africa. Its confirmed distribution is restricted to a firebreak between two catchments in the Cathedral Peak region of the Ukhahlamba Drakensberg Transfrontier Park, where it is threatened by habitat transformation. In this study, we aimed to understand factors that promote or inhibit gene flow within this highly restricted K. grandiflora population, to estimate inbreeding, and to assess its status as a potentially threatened species. Exclusion and hand pollination trials indicate that K. grandiflora cannot autonomously self-pollinate and is dependent on pollinators for outcrossing. Germination trials and tetrazolium staining suggest that the seeds may have dormancy breaking requirements or are inviable. Inbreeding and genetic diversity analyses show that the K. grandiflora population nonetheless maintains a high level of genetic diversity, likely through outcrossing, despite the small population size and apparent poor reproductive success. We recommend that the IUCN conservation status of K. grandiflora be changed from Vulnerable to ‘Critically Endangered’ based on observed reductions in population size, limited extent of occurrence, small number of mature individuals, and threats by woody competitors. We strongly recommend that the known population(s) be monitored and the habitat patches be conserved regardless of size and maintained through regular burning to enable the species’ survival and conservation. Ex situ propagation and reintroduction to its historical habitat should be explored as additional conservation measures for this species.

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.

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence., Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe; 1332

The conservation of animal populations often requires the estimation of population size. Low density and secretive behaviour usually determine scarce data sources and hampers precise abundance estimations of carnivore populations. However, joint analysis of independent scarce data sources in a common modeling framework allows unbiased and precise estimates of population parameters. We aimed to estimate the density of the European wildcat (Felis silvestris) in a protected area of Spain, by combining independent datasets in a spatially-explicit capture-recapture (SCR) framework. Data from live-capture with individual identification, camera-trapping without individual identification and radio-tracking concurrently obtained were integrated in a joint SCR and count data model. Ten live captures of five wildcats were obtained with an effort of 2034 trap-days, whereas seven wildcat independent events were recorded in camera traps with 3628 camera-days. Two wildcats were radio-tagged and telemetry information on their movements was obtained. The integration of the different data sources improved the precision obtained by the standard SCR model. The mean (± SD) density estimated with the integrated model (0.038 ± 0.017 wildcats/km2, 95% highest posterior density 0.013–0.082) is among the lowest values ever reported for this species, despite corresponding to a highly protected area. Among the likely causes of such low density, low prey availability could have triggered an extinction vortex process. We postulate that the estimated low density could represent a common situation of wildcat populations in the southern Iberia, highlighting the need for further studies and urgent conservation actions in the furthermost southwestern range of this species in Europe., Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature., Funding was provided by Organismo Autónomo Parques Nacionales, Project OAPN 352/2011. We are grateful for the support received during this study from the staff of Cabañeros National Park. We also thank the assistance received during the fieldwork from T. Oliveira, I. Vaz and J.C. Zarca, and during data processing from A. Fragoso. F. Díaz-Ruiz was supported by a Juan de la Cierva postdoctoral contract (FJCI-2015-24,949) and is currently supported by a postdoctoral contract from the University of Málaga (I Plan Propio de Investigación y Transferencia, call 2020). P. Monterroso was supported by UID/BIA/50027/2019 with funding from FCT/MCTES through national funds.

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.

Abstract The Marsh Fritillary butterfly (Euphydryas aurinia) is a Eurasian species which has suffered significant reductions in occurrence and abundance over the past century, particularly across the western side of its range, due to agricultural intensification and habitat loss. This loss has been particularly severe in the UK with extensive localised extinctions. Following sympathetic management, reintroduction was undertaken at four Cumbria (northern UK) sites in 2007 with stock from a captive admixture population descended from Cumbrian and Scottish founders. Annual population monitoring of the reintroductions was undertaken. Nine years post-reintroduction, the level of population genetic variation was assessed using microsatellites. Variation in historical Cumbrian samples was determined using museum samples and Scottish samples from current populations were assayed to characterise natural population variation. Half of the Scottish sites also served as indicators of the alleles present in the founder populations. The genetic contribution of the founder populations allied to population size data allowed patterns of genetic variation to be modelled. Alleles from Cumbrian and Scottish founders are present in the reintroduced populations. The four sites have levels of variation akin to natural populations and exhibit differentiation as predicted by statistical modelling and comparable with natural populations. This suggests that reintroduction following captive breeding can produce self-sustaining populations with natural levels of genetic diversity. These populations appear to be undergoing the same evolutionary dynamics with bottlenecks and drift as natural populations. Implications for insect conservation Reintroduction of captive bred individuals is a viable strategy for producing populations with natural levels of genetic diversity and evolutionary dynamics. Hybridisation of populations on the brink of extinction with those thriving can preserve some of the genetic distinctiveness of the declining population.

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.

The effectiveness of antibiotics against bacterial infections has been declining due to the emergence of resistance. Precisely understanding the response of bacteria to antibiotics is critical to maximizing antibiotic-induced bacterial eradication while minimizing the emergence of antibiotic resistance. Cell-to-cell heterogeneity in antibiotic susceptibility is observed across various bacterial species for a wide range of antibiotics. Heterogeneity in antibiotic susceptibility is not always due to the genetic differences. Rather, it can be caused by non-genetic mechanisms such as stochastic gene expression and biased partitioning upon cell division. Heterogeneous susceptibility leads to the stochastic growth and death of individual cells and stochastic fluctuations in population size. These fluctuations have important implications for the eradication of bacterial populations and the emergence of genotypic resistance.

Vultures are among the most threatened avian taxa in the world. When vultures aggregate in large numbers to feed, poisoned carcasses can extirpate entire populations at once. In the light of shrinking numbers worldwide, restocking and reintroduction projects, where wild or captive-bred vultures are released back into nature, constitute a crucial management tool, successfully implemented in many countries. However, reestablishment of sustainable vulture populations to their historical ranges remains a serious challenge, especially if the threat of poisoning persists, which is usually the case. In this study, we model the outcome of a restocking project where an initial colony is subject to repeated poisoning events. We use as an example the isolated population of the griffon vulture (Gyps fulvus) in Cyprus. Mathematical considerations and model simulations show that the probability of colony persistence depends on the initial population size and the intensity and frequency of the poisoning incidents. This type of scenario creates an Allee effect that requires a colony to exceed a minimum size in order to survive. Also in this scenario, a sequence of small but frequent poisoning episodes is worse on average than a few large and rare ones of the same cumulative mortality. Future population reinforcement efforts for vultures should focus on the release of adult birds in adequate numbers for the successful establishment of sustainable colonies and should involve a reduction in small but persistent sources of mortality such as the poison baiting of small canids that until now has been neglected by conservation scientists.

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.

Geographical variation in the likelihood of biological invasions can be affected by propagule pressure and habitat suitability, which are driven by ecological and social processes. Past studies have empirically quantified the role of drivers by comparing geographical variation in numbers of invading species with variation in candidate factors; however, lack of data has limited empirical studies for individual species. Lymantria dispar (L.), a nonnative forest pest formerly known as gypsy moth, is an exemplar species for exploring invasion drivers because of extensive records on its spread. Since its establishment in eastern United States in 1869, it has been repeatedly introduced into outlying areas, prompting 325 eradication programs from 1972 to 2014. We used these eradication programs as proxies for new establishment events, with the assumption that populations would have established in the absence of eradication treatments. These proxy events were used to quantify the effects of socio-environmental factors on the probability of L. dispar arrival and establishment. Establishment probability was significantly affected by propagule pressure (distance to the previously invaded area, human population size, and the area of source outbreaks) and habitat suitability (climate and availability of host trees). The statistical model developed here can be used to predict invasions and inform surveillance strategies to more efficiently manage these invasions.

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.

Assessing the risk to threatened species of population decline from anthropogenic disturbances is challenging when there are issues with species identification, and little is known of their biology, distribution, population size, and habitat preference. The bare-rumped sheath-tailed bat (Saccolaimus saccolaimus) is one such species that has a poorly defined distribution over two broad areas of northern Australia. Environmental impact assessments are expected to consider the possibility of its presence in intervening areas outside the known distributions. Our study presents new empirical data that can assist with detection of S. saccolaimus across the entire expanse of northern Australia, provides a critical analysis of acoustics-based identification of the species, and assessed presence within the potentially high value habitat of tall Eucalyptus tetrodonta-dominated forest on the western side of Cape York Peninsula using a combination of trapping and acoustic recordings. Capture of other Saccolaimus species was the greatest of any survey conducted to date in Australia, demonstrating that the capture of these high-flying bat species in tall forest habitats can be relatively effective with mist net arrays hoisted into the tree canopy. In addition, reference echolocation call collections from the focal trapping area plus other locations across northern Australia allowed characterisation and comparison of the calls of most low-frequency-emitting (LFE) echolocating bat species of northern Australia. In addition to separation of species-specific search phase call types using multivariate statistics, a compilation of features from search phase, approach phase and feeding buzz echolocation calls will help distinguish S. saccolaimus from most other LFE species. However, the similarity of the echolocation calls of S. mixtus and S. saccolaimus prevented them from being distinguished from one another. A multi-method approach that emulates the present study and incorporates our recommendations and cautions will lead to robustness in ecological studies and greater clarity in environmental impact assessments.

Cerberiopsis candelabra Vieill. is a long-lived, monocarpic (= semelparous) and mass-flowering rain-forest tree, endemic to New Caledonia. Population size structures suggest establishment has been episodic, followed by a recruitment gap that might signal population decline. Here, we use age structures based on tree rings to better assess population dynamics and persistence, and investigate influences of tree size, age and growth rate on flowering. Age structures of populations surveyed in 2007–2008 were unimodal, with establishment over c. 15–81 y, followed by a recruitment gap of c. 23–79 y. Seedling mortality was generally high. High densities of flowering trees or large-scale exogenous disturbances may be necessary for in-situ regeneration. There was no evidence of a simple flowering threshold: flowering in 2017 occurred across a wide range of tree size, age and growth rate. Instead, evidence suggested that size and age at flowering may vary among plants depending on their growth trajectory. Environmental triggers of flowering were not identified by dating tree establishment, but the last three mass-flowering events occurred in years of tropical cyclones. Regeneration and persistence might be facilitated if large-scale disturbances trigger flowering, improving reproductive efficiency by synchronising flowering and linking reproduction with environmental conditions that enhance seedling recruitment.

The current status of the elasmobranchs’ populations and distribution in the Canary Islands is uncertain. Here we investigate the abundance and distribution patterns of coastal elasmobranchs of Tenerife, with a special attention on the Aetomylaeus bovinus population using a photo-identification methodology. A total of 35 visual surveys were conducted in 5 coastal areas, in which pictures were taken every time an elasmobranch individual was sighted to conduct further biometry analyses. For A. bovinus sightings, pictures were used to identify each individual. Relative abundances and sex-ratios of the elasmobranchs recorded were calculated. The Western Coastline of the island was more diverse, showing 8 species out of the 9-total observed. The photo-identification technique allowed a preliminary estimation of the population size of A. bovinus in El Palmar area with 10 individuals identified and 10 re-sightings over a period of 12 months. This study provides the first relevant information regarding broad distribution, abundance and diversity of coastal elasmobranchs around Tenerife. The study also provides information regarding site fidelity of 3 mature individuals of Aetomylaeus bovinus in the South West area.

Population size, group composition and feeding ecology of the endemic and endangered Black-and-White Colobus Monkey (Colobus guereza gallarum) was investigated in Harenna Forest, South East Ethiopia by using the line-transect method in 10 selected blocks. During the dry and wet seasons, a mean number of 212 and 246 C. g. gallarum individuals was recorded, respectively. Also, the number of groups of the animal was higher in wet (36) than dry (31) season, but statistically insignificant (P= 0.447). Out of the recorded C. g. gallarum, 25.98% were adult males; 32.53% adult females; 14.85% sub-adult male, 11.14% sub-adult female and 15.50% were juveniles/young. Young leaves were the largest (35.1%) contributor to the diet of guereza followed by shoots (22.1%) in both seasons. Other common items were included mature leaves (20.6 %), bark (17.7%), fruit (2.8%) and flower (1.7%). C. g. gallarum were observed feeding on 19 plant species belonging to 12 families. The highest contribution of the diet was from the family Rosaceae (41.67%), while family Fabaceae, Moraceae and Myrsinaceae were contributing 50% of the diet. Schefflera volkensii was the most consumed plant species which accounted for 7.96%, followed by Urera hypselodendron (7.83%) and Dombeya torrida (7.06%). Moreover, C.g.gallarum mainly forage on leaves particularly young leaves, and their foraging activities depend inside the forest. Thus, to maintain sustainable conservation of the endemic C.g.gallarum in the area, their habitats should be properly protected, and appropriate monitoring strategies should be designed.

Demographic noise, the change in the composition of a population due to random birth and death events, is an important driving force in evolution because it reduces the efficacy of natural selection. Demographic noise is typically thought to be set by the population size and the environment, but recent experiments with microbial range expansions have revealed substantial strain-level differences in demographic noise under the same growth conditions. Many genetic and phenotypic differences exist between strains; to what extent do single mutations change the strength of demographic noise? To investigate this question, we developed a high-throughput method for measuring demographic noise in colonies without the need for genetic manipulation. By applying this method to 191 randomly-selected single gene deletion strains from theE. coliKeio collection, we find that a typical single gene deletion mutation decreases demographic noise by 8% (maximal decrease: 81%). We find that the strength of demographic noise is an emergent trait at the population level that can be predicted by colony-level traits but not cell-level traits. The observed differences in demographic noise from single gene deletions can increase the establishment probability of beneficial mutations by almost an order of magnitude (compared to in the wild type). Our results show that single mutations can substantially alter adaptation through their effects on demographic noise and suggest that demographic noise can be an evolvable trait of a population.

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.

The ability of tree species to adapt to water stress and increased frequency of bark beetle outbreaks with climate change may increase with population size and standing genetic variation, calling into question the resilience of small, rare plant populations. The Torrey pine (Pinus torreyana) is a rare, genetically depauperate conifer that occurs naturally in a mainland and island population in southern California. Due to recent declines in the mainland population coinciding with drought and Ips paraconfusus bark beetle outbreaks, the species would benefit from an assessment of adaptive genetic diversity. Here, we use RNA-Seq to survey gene-coding diversity across 40 individuals to (1) characterize patterns of genetic diversity in the species and (2) test for genetic differentiation between trees that succumbed to beetle attack or survived following an outbreak. Consistent with previous studies, we found few genetic variants, with most SNPs occurring as fixed differences between populations. However, we found structure within the mainland and polymorphisms segregating in both populations. Interestingly, we found differentiation in genotypes between attacked and surviving trees and 11 SNPs associated with survival status, several of which had defense-related functions. While low diversity suggests limited adaptive capacity, genetic associations with survival in functionally relevant genes suggest adaptive potential for bark beetle defense. This initial study prompts future research to explore the genetic basis of putative resistance and suggests conservation efforts should protect surviving genotypes and the full spectrum of genetic diversity across populations to preserve the evolutionary potential of the species.

Key message The deep scoping method incorporates the use of a gene bank together with different population layers to reintroduce genetic variation into the breeding population, thus maximizing the long-term genetic gain without reducing the short-term genetic gain or increasing the total financial cost. Abstract Genomic prediction is often combined with truncation selection to identify superior parental individuals that can pass on favorable quantitative trait locus (QTL) alleles to their offspring. However, truncation selection reduces genetic variation within the breeding population, causing a premature convergence to a sub-optimal genetic value. In order to also increase genetic gain in the long term, different methods have been proposed that better preserve genetic variation. However, when the genetic variation of the breeding population has already been reduced as a result of prior intensive selection, even those methods will not be able to avert such premature convergence. Pre-breeding provides a solution for this problem by reintroducing genetic variation into the breeding population. Unfortunately, as pre-breeding often relies on a separate breeding population to increase the genetic value of wild specimens before introducing them in the elite population, it comes with an increased financial cost. In this paper, on the basis of a simulation study, we propose a new method that reintroduces genetic variation in the breeding population on a continuous basis without the need for a separate pre-breeding program or a larger population size. This way, we are able to introduce favorable QTL alleles into an elite population and maximize the genetic gain in the short as well as in the long term without increasing the financial cost.

New Zealand fur seals (Arctocephalus forsteri) are expanding in numbers and distribution throughout New Zealand. The exception is the West Coast of the South Island, where there is documented decli...

Distribution patterns of species are affected by resource availability, dispersal, disturbance and population dynamics. The smaller population size and range of the native Eurasian beaver (Castor fiber) compared to the non-native North American beaver (Castor canadensis) in Finland raise questions on reasons for the slower range expansion of the native species. We compared the population growth rates and the spread of both species from their release sites. We also studied the factors possibly affecting the spread of the Eurasian beaver in South western Finland in more detail. We found that the North American beaver has spread longer distances than the Eurasian beaver, but we did not find evidence for movement barriers constraining the expansion rate of the native species. Lack of high-quality habitats does not seem to constrain the expansion to nearby areas either. Despite this, the Eurasian beaver population has grown to a high density close to its reintroduction site, and it has started to spread to novel areas only recently. We conclude that the expansion of the native beaver in Finland seems to be controlled by factors other than those related to barriers for movement: movement behavior and population dynamics, which require further investigation.

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.

Aleutian mink disease virus (AMDV) is one the most relevant pathogens of domestic mink, where it can cause significant economic losses, and wild species, which are considered a threat to mink farms. Despite their relevance, many aspects of the origin, evolution, and geographic and host spreading patterns of AMDV have never been investigated on a global scale using a comprehensive biostatistical approach. The present study, benefitting from a large dataset of sequences collected worldwide and several phylodynamic-based approaches, demonstrates the ancient origin of AMDV and its broad, unconstrained circulation from the initial intercontinental spread to the massive among-country circulation, especially within Europe, combined with local persistence and evolution. Clear expansion of the viral population size occurred over time until more effective control measures started to be applied. The role of frequent changes in epidemiological niches, including different hosts, in driving the high nucleotide and amino acid evolutionary rates was also explored by comparing the strengths of selective pressures acting on different populations. The obtained results suggest that the viral passage among locations and between wild and domesticated animals poses a double threat to farm profitability and animal welfare and health, which is particularly relevant for endangered species. Therefore, further efforts must be made to limit viral circulation and to refine our knowledge of factors enhancing AMDV spread, particularly at the wild-domestic interface.

Variation in behavioural traits is especially important in novel habitats where selection forces determine successful colonizers. Prey species must constantly balance the risk versus reward of remaining in an area with threats while gaining possible fitness benefits. Flight initiation distance, the distance at which an animal flees when approached by a human, is a common metric used to assess habituation to stressors and risk behaviour. Here we examine the flight initiation distance of 519 feral pigeons (Columba livia) across New York City, U.S.A. We examined this behavioural response across the metropolitan landscape with respect to multiple urbanization factors related to human activity, the abiotic environment and the ecological community. We used principal component analysis (PCA) to transform landcover characters and then liner models to test various anthropogenic variables including landcover, pedestrian traffic and human population size. We found that flight initiation distance in pigeons decreased with increased human activity (measured by pedestrian traffic and human population size) and more urban landcover (specifically longer road length and greater amounts of impervious surface). We also found that flight initiation distance was shorter in areas with more peregrine falcon, Falco peregrinus, sightings, but longer in areas with more red-tailed hawk, Buteo jamaicensis, sightings. Overall, this research demonstrates that feral pigeon behaviour varies with urbanization, human activity and ecological attributes. Since behavioural changes are often the most rapid phenotypic response to change, this study demonstrates that pigeons are responding to anthropogenic stressors, which may set the stage for adaptive changes.

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.

Gnathopogon caerulescens is an endangered but commercially important fish in Lake Biwa, Japan. The population size of G. caerulescens has drastically reduced in the past decades, and there is a strong need to develop effective resource management frameworks for the sustainable use of this species. In the management of endangered species, it is important to monitor and grasp their distribution and abundance. Although catch-based methods have generally been employed for this purpose, these methods require more labor and time and can damage the populations of endangered species. In this study, we aimed to develop a rapid and non-invasive monitoring tool for G. caerulescens using an environmental DNA-based approach. We developed a real-time PCR assay that specifically detects and quantifies G. caerulescens DNA and applied the developed assay to monitor the concentrations of G. caerulescens DNA in water in Lake Biwa. The dynamics of G. caerulescens DNA concentrations well reproduced the main characteristics of life history of G. caerulescens, suggesting the promising use of environmental DNA-based methods for monitoring the distribution and abundance of this species.

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 conservation of genetic diversity requires a deeper understanding of the processes shaping intraspecific variation. In recent decades, numerous studies identified various drivers of genetic diversity. However, the interpretation of these drivers remains inconsistent, since their strength and balance may differ between species and habitats. Therefore, we analyzed potential drivers of genetic diversity in a comparative multispecies approach across different semi-natural grassland types. We used molecular markers to detect genetic diversity in populations of nine typical grassland plant species from dry calcareous grasslands, mesic hay meadows, and wet litter meadows in Central Europe. Additionally, we collected data on potential drivers of genetic diversity, which were assigned to four categories describing habitat age, landscape structure, habitat quality, and population size. Subsequently, we applied multiple linear regression models and variation partitioning analyses to identify the most influential drivers of genetic diversity in semi-natural grassland plant populations. Our study revealed clear differences in drivers of genetic diversity between grassland types. In calcareous grasslands genetic diversity depended almost completely on landscape structure. However, we identified habitat age and habitat quality as additional drivers in hay meadows, while population size was another driver in litter meadows. The strong variation in drivers of genetic diversity in hay and litter meadows can be ascribed to higher levels of environmental variation among these sites and due to their more recent origin than calcareous grassland sites. We conclude that different drivers of genetic diversity must be considered to maintain high levels of intraspecific diversity in different grassland types.

Waterbird populations in eastern Australia have been declining over the past 35 years primarily due to water resource development and resultant changes to natural river flows and flooding. To mitigate these impacts there is an increased allocation of water for the environment, including waterbird populations. We used population viability models to identify the frequency of breeding events required to reverse the trend and achieve long-term species’ management objectives. We found that the population size of straw-necked ibis was primarily dictated by the frequency of large breeding events and to a lesser extent by adult annual survival and the frequency of small breeding events. We identified combinations of small and large breeding events over the next 10 years required for increased population growth. We also assessed the likelihood of current water management policies increasing populations and thereby reversing the decline in eastern Australia’s waterbird populations.