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Freshwater jellyfish (= limnic medusa‐budding hydrozoans, FWJ) are a small group of cnidarians found on all continents except Antarctica in temperate to tropical latitudes. Members of this group belong primarily to three genera: Astrohydra, Craspedacusta, and Limnocnida. While Astrohydra and Limnocnida are typically restricted to the islands of Japan, Africa, and the Indian subcontinent, one species or potential species complex, Craspedacusta sowerbii, became globally invasive. Despite research going back about one‐and‐a‐half centuries, little is known about their phylogeny and ecology compared to marine jellyfish. Recent species distribution modelling, however, showed that by 2050, C. sowerbii will potentially extend their distribution ranges due to global warming to high‐latitude ecosystems and be present (medusa stage) for an extended time in the seasonal limnic production cycle. An increase in their relative ecological importance with temporal and spatial spreading is hypothesised. Only recently, it has been shown that the trophic roles of polyps and medusae and their prey overlap with other ecosystem members. In addition, medusa behaviour may cause trophic cascades and alter vertical nutrient distributions. However, polyps and other benthic life cycle stages are understudied. In globally, changing freshwater ecosystems that may become more accommodating for FWJ, an improved understanding of their population biology and ecosystem ecology is urgently needed. In this integrative review, we, therefore, explore reasons for the hampered historical research progress, contrast developments with those of marine cnidarians, compile and publish alongside an extensive and unprecedented literature database, and formulate avenues for future directions in FWJ research. [ABSTRACT FROM AUTHOR]

Recent work indicates that feralisation is not a simple reversal of domestication, and therefore raises questions about the predictability of evolution across replicated feral populations. In the present study we compare genes and traits of two independently established feral populations of chickens (Gallus gallus) that inhabit archipelagos within the Pacific and Atlantic regions to test for evolutionary parallelism and/or divergence. We find that feral populations from each region are genetically closer to one another than other domestic breeds, despite their geographical isolation and divergent colonisation histories. Next, we used genome scans to identify genomic regions selected during feralisation (selective sweeps) in two independently feral populations from Bermuda and Hawaii. Three selective sweep regions (each identified by multiple detection methods) were shared between feral populations, and this overlap is inconsistent with a null model in which selection targets are randomly distributed throughout the genome. In the case of the Bermudian population, many of the genes present within the selective sweeps were either not annotated or of unknown function. Of the nine genes that were identifiable, five were related to behaviour, with the remaining genes involved in bone metabolism, eye development and the immune system. Our findings suggest that a subset of feralisation loci (i.e. genomic targets of recent selection in feral populations) are shared across independently established populations, raising the possibility that feralisation involves some degree of parallelism or convergence and the potential for a shared feralisation 'syndrome'. [ABSTRACT FROM AUTHOR]

Species occupying dryland river ecosystems often experience "boom‐and‐bust" demographic cycles that coincide with shifts in habitat availability. Knowing whether declines are within natural thresholds versus those caused by acute human disturbance is critical for managing protected species. We investigated temporal shifts in abundance and habitat use of an endangered population of the threespine stickleback Gasterosteus aculeatus in southern California, where a Mediterranean climate leads to ephemeral habitat in one of the regions' least hydrologically modified rivers, the Santa Clara River. We conducted population surveys over a period of below‐average rainfall in the upper watershed in Soledad Canyon, with predefined reaches surveyed multiple times per year to capture different hydrologic conditions. Abundances were stable across years but varied significantly depending on location, with some reaches remaining dry and others drying seasonally to varying degrees. Occupancy models showed that the presence of stable perennial reaches, drying regime, and other site‐specific factors were important predictors of habitat use, and that certain reaches may be key to ensuring source‐sink dynamics as flow dissipates over the dry season. Low occupancy in two sections was driven by different predominant mechanisms, one by diel cycles of evapotranspiration and the other by cattails (Typha spp.), with both having greater effects during the hotter, drier parts of the year. As dryland river ecosystems are vulnerable to the effects of anthropogenic‐induced climate change, this study demonstrates how temporal monitoring can delimit dry‐state benchmarks for improving management interventions (i.e., translocation and habitat restoration) for protected species under conditions that are predicted to worsen in the coming years. [ABSTRACT FROM AUTHOR]

Cydalima perspectalis (Walker 1859) (Lepidoptera: Crambidae) is a destructive pest that has recently been reported from the ancient Hyrcanian forests feeding on leaves and shoots of Buxus hyrcana Pojarkova.To gain a deeper insight into the biology and population dynamics of C. perspectalis, a laboratory population was studied under controlled conditions. The moth was reared on B. hyrcana at 25 ± 1°C, 65 ± 10% RH and 16 h:8 h (L:D), and the data obtained were used to build a life table, adjusted to allow for the evaluation of the stage duration, for both males and females.The mean adult survival was 11.94 ± 0.26 days, the pre‐oviposition period lasted, on average, for 6.71 ± 0.18 days and the mean fecundity attained was 58.19 ± 7.81 eggs/female. Newly emerged females had a life expectancy (exj) of 14 days and males 19 days.The intrinsic rate of increase for the population was 0.05 ± 0.00 days−1, and the net reproductive rate was 24.05 ± 3.95 offspring/female. The biological and ecological data obtained allowed for the estimation of C. perspectalis biotic potential, thus contributing to the development of sustainable control methods for this pest and, consequently, to a reduction of the damage caused to box trees. [ABSTRACT FROM AUTHOR]

Close-kin mark-recapture (CKMR) is a method analogous to traditional mark-recapture but without requiring recapture of individuals. Instead, multilocus genotypes (genetic marks) are used to identify related individuals in one or more sampling occasions, which enables the opportunistic use of samples from harvested wildlife. To apply the method accurately, it is important to build appropriate CKMR models that do not violate assumptions linked to the species' and population's biology and sampling methods. In this study, we evaluated the implications of fitting overly simplistic CKMR models to populations with complex reproductive success dynamics or selective sampling. We used forward-in-time, individual-based simulations to evaluate the accuracy and precision of CKMR abundance and survival estimates in species with different longevities, mating systems, and sampling strategies. Simulated populations approximated a range of life histories among game species of North America with lethal sampling to evaluate the potential of using harvested samples to estimate population size. Our simulations show that CKMR can yield nontrivial biases in both survival and abundance estimates, unless influential life history traits and selective sampling are explicitly accounted for in the modeling framework. The number of kin pairs observed in the sample, in combination with the type of kinship used in the model (parent-offspring pairs and/or half-sibling pairs), can affect the precision and/or accuracy of the estimates. CKMR is a promising method that will likely see an increasing number of applications in the field as costs of genetic analysis continue to decline. Our work highlights the importance of applying population-specific CKMR models that consider relevant demographic parameters, individual covariates, and the protocol through which individuals were sampled. [ABSTRACT FROM AUTHOR]

The life history of insular gecarcinid crabs is divided into a marine larval and an adult phase, adapted to the terrestrial environment. As adults, individuals migrate seasonally to locations near the sea, engaging in reproductive behaviors. Therefore, identifying breeding and recruitment areas is crucial for the conservation of insular gecarcinids, especially for those endangered, such as Johngarthia lagostoma (H. Milne Edwards, 1837). We used sex ratio and sexual dimorphism analyses (body and cheliped size) as well as records of juveniles and adults to describe the population structure of J. lagostoma in the Trindade Island, Brazil. During the reproductive period, several population parameters were compared among sites with different altitudes, comprising two beaches (Andradas and Tartarugas) and two hills (Príncipe, 136 m; and Desejado, 612 m). Overall, males predominated in the population and invested more in body and cheliped growth than females. However, at Andradas Beach, it was observed a similar frequency of adult males and females as well as a small difference in the body size between the sexes. In comparison, the smallest crabs were found at Príncipe Hill. The analyzed population presented a predominance of adults, especially at Andradas Beach (93.1%). Compared to the other sites sampled, Príncipe Hill showed the highest abundance of juveniles (males: 22.2%; females: 40.8%). Thus, Andradas Beach was considered a reproductive site, while Príncipe Hill had the highest density of juveniles, which makes them priority areas for the conservation of J. lagostoma in Trindade Island. [ABSTRACT FROM AUTHOR]

Population dynamics can be influenced by physical and biological factors, particularly in stressful environments. Introduced species usually have great physiological plasticity, resulting in populations with different traits. Undaria pinnatifida, a macroalga originally described from northeast Asia, was introduced in Northern Patagonia, Argentina (San Matías Gulf) around 2010. To describe the spatio‐temporal variability in population structure and morphometry of U. pinnatifida, we conducted monthly field samplings for 2 years at the intertidal area of two contrasting sites in the San Matías Gulf. Individuals of U. pinnatifida were classified by developmental stage, and their morpho‐gravimetric variables were measured. In both intertidal sites juveniles were found in higher proportion during austral autumn and grew and matured during the autumn‐winter months (from May onwards), and individuals senesced during early austral summer (December and January). Conversely, density and biomass were largely different between sites, and individuals showed slight morphological variability between sites. Environmental (e.g., nutrient concentration, available substrate) and biological factors (e.g., facilitation, competition) may explain the observed differences. Since there is not a macroalga with U. pinnatifida morphometrical characteristics in the intertidal environments of San Matías Gulf, studying this recent introduction gives us a better understanding of its potential ecological effects. [ABSTRACT FROM AUTHOR]

Trophic interactions underpin the structure of ecological communities by describing the rates at which consumers exploit their resources. The rates at which predators consume their prey are influenced by prey traits, with many species inducing defensive modifications to prey traits following the threat of predation. Here we use different clonal lines of the protist Paramecium being consumed by Stenostomum predators to highlight how differences in prey traits impact rates of predation. Clonal lines differed in their body width traits, and in their ability to induce changes in body width. By using a factorial cross of predator and prey abundances for different clonal lines we demonstrate how evolutionary or induced alterations in prey traits can impact the relative threat of predation. Our experiments show how interference among predators impacts predation rate, and how increased body width increased predator handling times. Given that reductions in the strength of interspecific interactions are associated with increased levels of overall community stability, our results indicate how individual level changes may scale up to impact whole communities. [ABSTRACT FROM AUTHOR]

Estimating phenotypic distributions of populations and communities is central to many questions in ecology and evolution. These distributions can be characterized by their moments (mean, variance, skewness and kurtosis) or diversity metrics (e.g. functional richness). Typically, such moments and metrics are calculated using community‐weighted approaches (e.g. abundance‐weighted mean). We propose an alternative bootstrapping approach that allows flexibility in trait sampling and explicit incorporation of intraspecific variation, and show that this approach significantly improves estimation while allowing us to quantify uncertainty.We assess the performance of different approaches for estimating the moments of trait distributions across various sampling scenarios, taxa and datasets by comparing estimates derived from simulated samples with the true values calculated from full datasets. Simulations differ in sampling intensity (individuals per species), sampling biases (abundance, size), trait data source (local vs. global) and estimation method (two types of community‐weighting, two types of bootstrapping).We introduce the traitstrap R package, which contains a modular and extensible set of bootstrapping and weighted‐averaging functions that use community composition and trait data to estimate the moments of community trait distributions with their uncertainty. Importantly, the first function in the workflow, trait_fill, allows the user to specify hierarchical structures (e.g. plot within site, experiment vs. control, species within genus) to assign trait values to each taxon in each community sample.Across all taxa, simulations and metrics, bootstrapping approaches were more accurate and less biased than community‐weighted approaches. With bootstrapping, a sample size of 9 or more measurements per species per trait generally included the true mean within the 95% CI. It reduced average percent errors by 26%–74% relative to community‐weighting. Random sampling across all species outperformed both size‐ and abundance‐biased sampling.Our results suggest randomly sampling ~9 individuals per sampling unit and species, covering all species in the community and analysing the data using nonparametric bootstrapping generally enable reliable inference on trait distributions, including the central moments, of communities. By providing better estimates of community trait distributions, bootstrapping approaches can improve our ability to link traits to both the processes that generate them and their effects on ecosystems. [ABSTRACT FROM AUTHOR]

Biodiversity emerges from niche mechanisms, in which the combination of traits determines species performance, and populations drift because of the inherent stochasticity of community assembly processes. Population biology dictates that small and isolated communities are more prone to show stochastic assemblages. However, a reduced mass effect in isolated communities may promote trait selection. In addition, large and connected communities have a larger species pool, higher functional redundancy, lower population sizes and more random recruitment, which also fosters stochasticity in community assembly. These contradictory expectations demand empirical analyses.Plant metacommunities in temporary ponds are assembled by the action of strong environmental filters and cover wide ranges of local community sizes and connectivity, representing ideal systems for identifying determinants of trait‐selection processes. Using a deviance partition method introduced by the theory of community assembly by trait selection, we evaluated the role of plant traits in local community assemblies along 60 communities from a 14‐year plant survey of temporary ponds.Variation in pond size, hydroperiod, connectitivity and heterogeneity determined a selection gradien in traits related to drought resistance, life history and disperal strategies; and also in the strength of trait‐mediated community assembly. The taxonomic and functional diversity of a pond and its physical heterogeneity fostered stochasticity in the assembly of the community, which also presented a hump‐shaped association with connectivity. The pond area increased taxonomic richness but decreased functional diversity, determining negative and positive indirect effects on stochasticity.Synthesis. Diversity provides the raw material for trait selection putatively reducing stochasticity, but here diversity was positively related to stochasticity. Having enough functional diversity, larger redundancy and lower population sizes in diverse communities is probably fostering stochastic assemblages. The hump‐shaped association between stochasticity and connectivity supports a larger role of trait selection in isolated systems due to a weak mass effect, but also on connected communities in which a set of more optimal traits for the selection scenario could be available. In the ongoing state of ecosystem fragmentation, these empirical trends contribute to the mechanistic understanding of the connection between landscape structure and biodiversity assembly. [ABSTRACT FROM AUTHOR]

The encroachment of woody plants into grasslands is a global phenomenon with implications for biodiversity and ecosystem function. Understanding and predicting the pace of expansion and the underlying processes that control it are key challenges in the study and management of woody encroachment. Theory from spatial population biology predicts that the occurrence and speed of expansion should depend sensitively on the nature of conspecific density dependence. If fitness is maximized at the low‐density encroachment edge, then shrub expansion should be "pulled" forward. However, encroaching shrubs have been shown to exhibit positive feedbacks, whereby shrub establishment modifies the environment in ways that facilitate further shrub recruitment and survival. In this case there may be a fitness cost to shrubs at low density causing expansion to be "pushed" from behind the leading edge. We studied the spatial dynamics of creosotebush (Larrea tridentata), which has a history of encroachment into Chihuahuan Desert grasslands over the past century. We used demographic data from observational censuses and seedling transplant experiments to test the strength and direction of density dependence in shrub fitness along a gradient of shrub density at the grass–shrub ecotone. We also used seed‐drop experiments and wind data to construct a mechanistic seed‐dispersal kernel, then connected demography and dispersal data within a spatial integral projection model (SIPM) to predict the dynamics of shrub expansion. Contrary to expectations based on potential for positive feedbacks, the shrub encroachment wave is "pulled" by maximum fitness at the low‐density front. However, the predicted pace of expansion was strikingly slow (ca. 8 cm/year), and this prediction was supported by independent resurveys of the ecotone showing little to no change in the spatial extent of shrub cover over 12 years. Encroachment speed was acutely sensitive to seedling recruitment, suggesting that this population may be primed for pulses of expansion under conditions that are favorable for recruitment. Our integration of observations, experiments, and modeling reveals not only that this ecotone is effectively stalled under current conditions but also why that is so and how that may change as the environment changes. [ABSTRACT FROM AUTHOR]

Brachyuran crabs are considered one of the most representative groups in mangroves, being recognised as mangrove engineers. However, species that present commercial interest may have their population structure and spatial distribution affected by human activities, such as crab capture. Therefore, monitoring populations over time is essential. We investigated the population biology, size‐weight relationship, condition factor and spatial distribution of Ucides cordatus in a mangrove ecosystem from southern Brazil, providing information for population status assessment. Males and females differed in abundance and frequency, body size, size‐weight relationship and condition factor. Nonetheless, they presented the same spatial distribution pattern. Abundance, sex ratio and body size also revealed a possible influence of anthropised areas in the configuration and distribution of the species. Our results indicate a possible increase in the exploitation of the species, mainly due to the decrease of the largest male size classes' frequency. Interspecific competition seems to be a possible biotic factor influencing its condition factor. The spatial species distribution highlighted the importance of sites with less anthropogenic influence for the maintenance of the species that can be considered as key areas for the conservation of the U. cordatus in Babitonga Bay. [ABSTRACT FROM AUTHOR]

Centropages typicus is a temperate calanoid copepod occurring in Atlantic and Mediterranean coastal waters, where its reproductive biology and population dynamics are well‐known. C. typicus has also been suggested as a key species for monitoring the impact of environmental changes on copepod secondary production. The aim of this study is to investigate the seasonal and interannual reproductive (egg production and egg hatching success) and feeding (fecal pellet production) traits, population abundance and structure (sex ratio) of C. typicus over a 20‐year period at the Long‐Term Ecological Research site MareChiara (LTER‐MC) in the Gulf of Naples (Central Tyrrhenian Sea, Western Mediterranean Sea), identifying specific trends and patterns. At a seasonal scale, egg production and hatching success were tightly linked with maxima in February–March, driving the juvenile and adult springtime population peaks but showing a poor correlation with phytoplankton abundance, pointing to an omnivorous diet. At a multiannual scale, an observed decrease in the population is backed up by a reduction in egg production, despite an increase in hatching success. The results of this study provide new elements to comprehend the links between C. typicus functional traits, population dynamics, and environmental factors and highlight the importance of running LTER series to monitor the trends in natural environments. [ABSTRACT FROM AUTHOR]

Whole‐genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics. [ABSTRACT FROM AUTHOR]

Variations in the reproductive and survival abilities of individuals within a population are ubiquitous in nature, key to individual fitness, and affect population dynamics, which leads to strong interest in understanding causes and consequences of vital‐rate variation. For long‐lived species, long‐term studies of large samples of known‐age individuals are ideal for evaluating vital‐rate variation.A population of Weddell seals in Erebus Bay, Antarctica, has been studied each Austral spring since the 1960s. Since 1982, all newborns have been tagged each year and multiple capture‐mark‐recapture (CMR) surveys have been conducted annually.Over the past 20 years, a series of analyses have built on results of earlier research by taking advantage of steady improvements in the project's long‐term CMR data and available analytical methods. Here, I summarize progress made on four major topics related to variation in age‐specific vital rates for females: early‐life survival and age at first reproduction, costs of reproduction, demographic buffering, and demographic senescence.Multistate modelling found that age at first reproduction varies widely (4–14 years of age) and identified contrasting influences of maternal age on survival and recruitment rates of offspring. Subsequent analyses of data for females after recruitment revealed costs of reproduction to both survival and future reproduction and provided strong evidence of demographic buffering. Recent results indicated that important levels of among‐individual variation exist in vital rates and revealed contrasting patterns for senescence in reproduction and survival.Sources of variation in vital rates include age, reproductive state, year, and individual. The combination of luck and individual quality results in strong variation in individual fitness outcomes: ~80% of females born in the population produce no offspring, and the remaining 20% vary strongly in lifetime reproductive output (range: 1–23 pups).Further research is needed to identify the specific environmental conditions that lead to annual variation in vital rates and to better understand the origins of individual heterogeneity. Work is also needed to better quantify the relative roles of luck, maternal effects, and environmental conditions on variation in vital rates and to learn the importance of such variation to demographic performance of offspring and on overall population dynamics. [ABSTRACT FROM AUTHOR]

Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long‐term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception – a class of MGE termed REPIN. REPINs are non‐autonomous MGEs whose duplication depends on non‐jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria. [ABSTRACT FROM AUTHOR]

Organisms that undergo a shift in ontogeny and habitat type often change their spatial distribution throughout their life cycle, but how this affects population dynamics remains poorly understood.We examined spatial and temporal patterns in Aedes nigripes abundance, a widespread univoltine Arctic mosquito species (Diptera: Culicidae), hypothesizing that the spatial distribution of adults would be closely tied to aquatic habitat.We tracked adult densities of A. nigripes near Kangerlussuaq, Greenland using emergence traps, CO2‐baited traps, and sweep‐nets.In back‐to‐back years of sampling (2017 and 2018) we found two‐fold variation in overall abundance.Adults were spatially patchy when first emerging from aquatic habitats but within a week, mean capture rates for host‐seeking adult females were similar across locations, even in places far from larval habitat.Daily variation in mosquito captures was primarily explained by weather, with virtually no mosquito activity when temperatures averaged less than 8°C or wind speeds exceeded 6 m/s. Gravid females (3% of resting adults) were spatially patchy on the landscape, but not always in the same places where most adults emerged.The spatial distribution of adults is quickly uncoupled from the spatial distribution of larvae because A. nigripes females may disperse far from their natal habitats in search of a blood‐meal and high‐quality oviposition habitat. 8. This research highlights the value of studying ecological processes that act at disparate life stages for understanding the population biology of organisms with complex life cycles. [ABSTRACT FROM AUTHOR]

Over the past several decades, biomarkers have become indispensable tools in human biology, allowing researchers to investigate biocultural and evolutionary questions and to generate basic data on health and well‐being. Human biologists are central players in biomarker methods development, pioneering the creation of "field friendly," minimally invasively collected biomarker approaches, as well as leading the innovative use of biomarkers, most notably to map the complex pathways from social and environmental conditions to altered physiology to health effects. This special issue, Part 2 of a collection focused on minimally invasively collected biomarkers, is comprised of nine papers that jointly contribute to driving the science of biomarker methods development and application. This compilation of papers engages with topics such as biological normalcy, ecoimmunology, and the ethics of working with vulnerable and underserved populations. It also focuses attention on research areas at present not emphasized in human biology such as bone turnover markers as a window onto osteoporosis and osteoarthritis and the use of cancer‐related biomarkers in population screening and epidemiology. Taken together, these papers help draw the roadmap for future biomarker work, emphasizing: (1) the need for systematic and transparent approaches to assay validation, with open access publication; (2) simultaneous measurement of multiple biomarkers and expanded use of instrument platforms that increase the range of physiological, genomics, and omics markers available to researchers; and, (3) increased attention to ethics and researcher responsibilities, encouraging a mindset that recognizes our obligation to provide benefits to individuals and communities and to help redress past abuses. [ABSTRACT FROM AUTHOR]

Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two‐dimensional stepping stone models under a wide range of scenarios with spatio‐temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio‐temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real‐world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio‐temporal variation in deme size. [ABSTRACT FROM AUTHOR]

Biotropica, the flagship journal of the Association for Tropical Biology and Conservation, has announced its first open call for editorial service. The journal focuses on original research on the ecology, conservation, and management of tropical ecosystems, as well as the evolution, behavior, and population biology of tropical organisms. The aim is to provide timely, fair, transparent, and constructive reviews and editorial decisions. The journal values a geographically diverse Editorial Board with expertise in tropical taxa and research, reflecting the diverse authorship and readership. In response to the open call, 14 new Subject Editors have been selected from a qualified pool, and the call for editorial service will be an annual occurrence. [Extracted from the article]

Cancer‐associated fibroblasts (CAFs) have conflicting roles in the suppression and promotion of cancer. Current research focuses on targeting the undesirable properties of CAFs, while attempting to maintain tumour‐suppressive roles. CAFs have been widely associated with primary or secondary therapeutic resistance, and strategies to modify CAF function have therefore largely focussed on their combination with existing therapies. Despite significant progress in preclinical studies, clinical translation of CAF targeted therapies has achieved limited success. Here we will review our emerging understanding of heterogeneous CAF populations in tumour biology and use examples from pancreatic ductal adenocarcinoma to explore why successful clinical targeting of protumourigenic CAF functions remains elusive. Single‐cell technologies have allowed the identification of CAF subtypes with a differential impact on prognosis and response to therapy, but currently without clear consensus. Identification and pharmacological targeting of CAF subtypes associated with immunotherapy response offers new hope to expand clinical options for pancreatic cancer. Various CAF subtype markers may represent biomarkers for patient stratification, to obtain enhanced response with existing and emerging combinatorial therapeutic strategies. Thus, CAF subtyping is the next frontier in understanding and exploiting the tumour microenvironment for therapeutic benefit. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Factors shaping the distribution and abundance of species include life‐history traits, population structure, and stochastic colonization–extinction dynamics. Field studies of model species groups help reveal the roles of these factors. Species of Caenorhabditis nematodes are highly divergent at the sequence level but exhibit highly conserved morphology, and many of these species live in sympatry on microbe‐rich patches of rotten material. Here, we use field experiments and large‐scale opportunistic collections to investigate species composition, abundance, and colonization efficiency of Caenorhabditis species in two of the world's best‐studied lowland tropical field sites: Barro Colorado Island in Panamá and La Selva in Sarapiquí, Costa Rica. We observed seven species of Caenorhabditis, four of them known only from these collections. We formally describe two species and place them within the Caenorhabditis phylogeny. While these localities contain species from many parts of the phylogeny, both localities were dominated by globally distributed androdiecious species. We found that Caenorhabditis individuals were able to colonize baits accessible only through phoresy and preferentially colonized baits that were in direct contact with the ground. We estimate the number of colonization events per patch to be low. [ABSTRACT FROM AUTHOR]

Facultative sexual organisms combine sexual and asexual reproduction within a single life cycle, often switching between reproductive modes depending on environmental conditions. These organisms frequently inhabit variable seasonal environments, where favorable periods alternate with unfavorable periods, generating temporally varying selection pressures that strongly influence life history decisions and hence population dynamics. Due to the rapidly accelerating changes in our global environment today, understanding the population dynamics and genetic changes in facultative sexual populations inhabiting seasonal environments is critical to assess and prepare for additional challenges that will affect such ecosystems. In this study, we aimed at obtaining insights into the seasonal population dynamics of the facultative sexual freshwater cnidarian Hydra oligactis through a combination of restriction site‐associated sequencing (RAD‐Seq) genotyping and the collection of phenotypic data on the reproductive strategy of field‐collected hydra strains in a standard laboratory environment. We reliably detected 42 MlGs from the 121 collected hydra strains. Most of MLGs (N = 35, 83.3%) were detected in only one season. Five MLGs (11.9%) were detected in two seasons, one (2.4%) in three seasons and one (2.4%) in all four seasons. We found no significant genetic change during the 2 years in the study population. Clone lines were detected between seasons and even years, suggesting that clonal lineages can persist for a long time in a natural population. We also found that distinct genotypes differ in sexual reproduction frequency, but these differences did not affect whether genotypes reappeared across samplings. Our study provides key insights into the biology of natural hydra populations, while also contributing to understanding the population biology of facultative sexual species inhabiting freshwater ecosystems. [ABSTRACT FROM AUTHOR]

Species distribution models (SDMs) are widely used in ecology. In theory, SDMs capture (at least part of) species' ecological niches and can be used to make inferences about the distribution of suitable habitat for species of interest. Because habitat suitability is expected to influence population demography, SDMs have been used to estimate a variety of population parameters, from occurrence to genetic diversity. However, a critical look at the ability of SDMs to predict independent data across different aspects of population biology is lacking. Here, we systematically reviewed the literature, retrieving 201 studies that tested predictions from SDMs against independent assessments of occurrence, abundance, population performance, and genetic diversity. Although there is some support for the ability of SDMs to predict occurrence (~53% of studies depending on how support was assessed), the predictive performance of these models declines progressively from occurrence to abundance, to population mean fitness, to genetic diversity. At the same time, we observed higher success among studies that evaluated performance for single versus multiple species, pointing to a possible publication bias. Thus, the limited accuracy of SDMs reported here may reflect the best‐case scenario. We discuss the limitations of these models and provide specific recommendations for their use for different applications going forward. However, we emphasize that predictions from SDMs, especially when used to inform conservation decisions, should be treated as hypotheses to be tested with independent data rather than as stand‐ins for the population parameters we seek to know. [ABSTRACT FROM AUTHOR]

Scab (Venturia effusa) is the major cause of economic loss in pecan in the south‐eastern USA. We explored population genetic diversity and structure among orchards of cv. Desirable and native seedlings, and within‐orchard variability among trees of all cultivars sampled. We compared the ability of 30, 15 and 7 previously developed microsatellites to characterize the population genetic diversity and structure of V. effusa. Analyses of molecular variance (AMOVA) provided little evidence of structure dependent on cultivar, but there was some evidence of structure between orchards of a cultivar based on distance. Individual orchard AMOVA showed that three of 11 orchards had between‐tree population structure. Among six populations from cv. Desirable, a Mantel test showed that geographic distance was related to the pairwise genetic divergence (R2 = 0.84). Among 11 orchards of various cultivars there was little difference in diversity using 30, 15 or 7 markers, or population structure based on AMOVA. Some minor differences in population structure were seen based on discriminant analysis of principal components, or dendrograms. Thus, depending on the objectives, future studies may use as few as 15 or 7 markers without losing ability to discern population genetic diversity or structure. More populations exhibited linkage disequilibrium when using 15 or 30 markers compared to when using seven markers. Knowledge of population genetics of V. effusa in relation to host genotype is needed to understand pathogen population interactions and gene flow, knowledge that will help underpin future breeding efforts to develop durable resistance in this long‐lived orchard tree. [ABSTRACT FROM AUTHOR]

In the 1960s, scientists fascinated by the behavior of free‐living animals founded research projects that expanded into multi‐generation investigations. This paper charts the history of three scientists' projects to uncover the varied reasons for investing in a "long‐term" perspective when studying animal behavior: Kenneth Armitage's study of marmots in the Rocky Mountains, Jeanne Altmann's analysis of baboons in Kenya, and Timothy Hugh Clutton‐Brock's studies (among others) of red deer on the island of Rhum and meerkats in the Kalahari. The desire to study the behavior of the same group of animals over extended periods of time, I argue, came from different methodological traditions – population biology, primatology, and sociobiology – even as each saw themselves as contributing to the legacy of ethology. As scientists embraced and combined these approaches, a small number of long‐running behavioral ecology projects like these grew from short pilot projects into decades‐long centers of intellectual gravity within behavioral ecology as a discipline. By attending to time as well as place, we can see how this long‐term perspective was crucial to their success; they measured evolutionary changes over generations of animals and their data provided insights into how the animals they studied were adapting (or not) to changing local and global environmental factors. [ABSTRACT FROM AUTHOR]

The Nile tilapia (Oreochromis niloticus), Redbelly tilapia (Coptodon zillii) and Blue spotted tilapia (Oreochromis leucostictus) were introduced into Lake Naivasha in the 1950s to diversify and boost the lake fisheries. These species have since been exploited in the commercial gillnet fishery. The fish stocks, however, are currently facing problems of pollution, wetland degradation and intense fishing pressures. Accordingly, the present study investigated some aspects of the biology and population structure of the three tilapiine species in light of changing lake conditions. Fish samples were collected from January to December 2019 using multifilament gillnets of 2.0‐to‐6.0‐inch mesh sizes. Immediately after their capture, the fish specimens were transported to the lab for morphometric measurements and analysis of maturity. The highest and lowest mean (±SD) total length (TL) were exhibited by O. niloticus (22.9 ± 5.2 cm) and C. zillii (14.5 ± 2.1 cm), respectively. Similarly, O. niloticus exhibited a higher mean weight (268.4 ± 18.0 g) and body depth (7.6 ± 2.5 cm), compared to the other species. O. niloticus exhibited an isometric growth pattern, while C. zillii and O. leucostictus exhibited negative allometric growth. The fish species were in good condition, with mean condition factors of 1.59 ± 0.07, 1.51 ± 0.06 and 1.23 ± 0.03 for C. zillii, O. leucostictus and O. niloticus, respectively. Furthermore, the condition factors for O. leucostictus and O. niloticus varied by size class, exhibiting a decreasing trend with increased fish size. The male:female sex ratio revealed significantly more males than females for O. niloticus (2.30:1.0) and O. leucostictus (2.36:1.0), although not for C. zillii (1.15:1.0). O. niloticus (28.0–29.0 cm TL) matured at a larger size, followed by O. leucostictus (21.0–26.0 cm TL), and C. zillii (15.0–17.0 cm TL). In comparison, values of length‐weight parameters, condition factor, sex ratio and size at first maturity of the studied fishes varied in Lake Naivasha, Victoria, Albert and George. The gillnet mesh ≤3.0″ mainly targeted small‐sized immature fish, while mesh ≥4″ targeted mature fish, particularly O. niloticus. It was concluded that gillnets with ≥4.0″ mesh could safely be applied for this fishery in Lake Naivasha, whereas the use of smaller mesh should be controlled to protect the juveniles as a means of maintaining sustainable fisheries. Furthermore, the present study also provided useful information, including size at maturity that is vital for setting mesh size for managing the lake fishery. [ABSTRACT FROM AUTHOR]

Objectives: The long history of contact between Latin America, the Caribbean, and Asia extending back to the 16th century has only recently been focused upon in the literature, documenting the intersection of their population histories. Specifically, Chinese laborers immigrated to work in a variety of occupations in the region, along with Japanese workers and those of other Asian nationalities. In this study, we seek to uncover these hidden relationships and hypothesize that Latin American and Caribbean populations will show a close affinity to Asian populations due to a shared population history extending from the 16th century and later. Materials and methods: Using a population structure approach with craniometrics, we analyzed samples of modern individuals from Panamá, Cuba, China, and Japan, using Mahalanobis D2, principal coordinates analysis (PCoA), canonical variates analysis (CVA), minimum Fst, and an R matrix. Results: The results from the population structure analyses are consistent with more recent contact between Latin America, the Caribbean, and Asia as they cluster together on 3D plots and population genetics parameters align with knowledge of contact among these populations. Conclusions: Transpacific contact between Latin America, the Caribbean, and Asia in the 16th–20th centuries is detailed, showing an extensive trade network and evidence of Asian migrations into Latin America and the Caribbean that may be under‐enumerated in the censuses. The population signal in the craniometric data closely follow documented events with Asian populations in Panamá and Cuba in the 19th and 20th centuries, as well as the construction of the Asian Latina/o identity. [ABSTRACT FROM AUTHOR]

Late blight caused by the oomycete Phytophthora infestans is a disease of potato and tomato of worldwide relevance and is widespread throughout Europe and the Mediterranean region. While pathogen populations in northern Europe have been sampled and characterized for many years, the genetic structure of populations from southern Europe, including Italy, has been less studied. Between 2018 and 2019, we collected 91 samples of P. infestans from potato and tomato crops in Italy, Algeria, and Tunisia on FTA cards and genotyped them using 12‐plex microsatellites. These samples were compared to genotypes of P. infestans previously collected within the framework of the EuroBlight network and from published sources. Four clonal lineages were identified: 13_A2 (Blue 13), 2_A1, 23_A1, and 36_A2. Two other isolates collected could not be matched to any currently known clonal lineage. The 13_A2 and 36_A2 lineages were found exclusively in southern Italy and Algeria, while 2_A1 was only found in Algeria. This is the first report of the 36_A2 lineage in Italy. Two isolates from Solanum nigrum were 13_A2, suggesting this weed host could be a reservoir of inoculum. The 23_A1 lineage was found widely on infected tomato crops in Italy and is the same as the lineage US‐23 that is widespread in North America. Differences in genotypes across the country suggests that there may be different sources of introduction into Italy, possibly via infected seed tubers from other countries in Europe, tubers for consumption from North Africa, or tomatoes. [ABSTRACT FROM AUTHOR]

Little is known of dinosaur population biology due to insufficient information on age‐dependent fecundities and mortalities. So far, survivorship curves (SC) of only six dinosaurs (four tyrannosaurs, one ceratopsian, one hadrosaur) have been erected from bone assemblages of aged specimens. They indicate high survival throughout most of their life with presumably higher mortalities after hatching and increasing mortalities towards its end. However, none of these studies recognized that to infer a reliable SC for a taxon, the assemblage must preserve a stationary age distribution (i.e. one which is stable, with constant population size over time as overall fecundities match mortalities, hereafter SAD population). To assess SCs of these dinosaurs, I built a simple population model with age‐dependent fecundities and survival rates. Its three input parameters are maximum longevity, age at sexual maturation and maximum annual offspring number, for which information exists on these dinosaurs. As bone histological studies and scaling relationships provide estimates on these parameters, my model is also applicable to other extinct taxa. Modelling suggests that bone assemblages did not preserve SAD populations. SCs determined for SAD populations of Albertosaurus sarcophagus, Gorgosaurus libratus, Dasplatosaurus torosus and Tyrannosaurus rex indicated that low mortalities followed high mortalities in early life or that mortality rates were rather constant throughout their life. In Psittacosaurus lujiatuensis, modelling suggests low mortalities throughout most of its life that increase towards its end. Due to its simplicity, my model was unable to render composite SCs, specifically the sigmoidal shape previously predicted for Maiasaura peeblesorum. [ABSTRACT FROM AUTHOR]

Montane animals require different adaptations than lowland species because of more severe conditions. Proctoporus lizards of the Andes Mountains experience cold temperatures year‐round, which may affect their activity. Two species of this poorly known genus, P. unsaacae and P. sucullucu, have similar morphology and ecology, but had never been studied in detail. The purpose of this project was to compare the population biology of the two species and to ascertain whether they were more likely to share ecological similarities with phylogenetic relatives or with other unrelated lizards of the Andes. We established two permanent plots in the Sacred Valley of the Incas in Cusco region, Peru, and examined the thermal ecology, movement, sex ratio, longevity, population sizes, growth patterns, reproduction and other factors over a period of 4 years. Proctoporus unsaacae and P. sucullucu were similar in most aspects of their ecology except that P. sucullcu was larger, had smaller population sizes, and fewer recaptures. Both species live exclusively under rocks and are strict thermoconformers who do not actively thermoregulate their body temperatures by basking, as other high Andean lizards do. The two species have reverse sexual dimorphism with P. unsaacae having larger females and P. sucullcu having larger males. The species are highly philopatric with average movement of less than 7 m in a lifetime. Both appear to be relatively long‐lived with an individual P. unsaacae living longer than 2 years 8 months. At both sites, populations age structures had few juveniles and we detected a declining population of P. unsaacae in Urubamba. This project lays the groundwork for more in‐depth studies of the ecology of both species and their high‐elevation habitats. [ABSTRACT FROM AUTHOR]

Recovery rates for baleen whales that were decimated by exploitation vary between species and populations. Age determination is critical for the understanding of recovery trends and population structure, but determining age in free‐ranging individuals remains challenging. Recent research has suggested that the methylation level of some genes in skin samples may provide age determinations with accuracy. We selected nine CpG sites from three genes (TET2, CDKN2A, and GRIA2) and analyzed them in 40 skin samples from known‐age individuals pertaining to two different populations of fin whales from the North Atlantic. We observed significant correlations with age in five CpG sites. We used three of these CpG sites to perform an epigenetic age estimation. Predictions had a standard deviation of 2.94, but regression between observed and predicted ages showed a clear underestimation for older fin whales. For further development, we suggest: (1) screening for new CpG sites associated with age that exhibit higher variability between individuals, and (2) including older animals whenever the sampling allows it. We also observed subtle, but significant differences between the two populations studied in one of the CpG sites (TET2_CpG + 21). We attributed these differences to genetic differences or to the dissimilar environments that affect both populations. [ABSTRACT FROM AUTHOR]

Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is one of the most economically important diseases of wheat. Recently, both factors of a gene‐for‐gene interaction between Z. tritici and wheat, the wheat receptor‐like kinase Stb6 and the Z. tritici secreted effector protein AvrStb6, have been identified. Previous analyses revealed a high diversity of AvrStb6 haplotypes present in earlier Z. tritici isolate collections, with up to c.18% of analysed isolates possessing the avirulence isoform of AvrStb6 identical to that originally identified in the reference isolate IPO323. With Stb6 present in many commercial wheat cultivars globally, we aimed to assess potential changes in AvrStb6 genetic diversity and the incidence of haplotypes allowing evasion of Stb6‐mediated resistance in more recent Z. tritici populations. Here we show, using targeted resequencing of AvrStb6, that this gene is universally present in field isolates sampled from major wheat‐growing regions of the world in 2013–2017. However, in contrast to the data from previous AvrStb6 population studies, we report a complete absence of the originally described avirulence isoform of AvrStb6 amongst modern Z. tritici isolates. Moreover, a remarkably small number of haplotypes, each encoding AvrStb6 protein isoforms conditioning virulence on Stb6‐containing wheat, were found to predominate among modern Z. tritici isolates. A single virulence isoform of AvrStb6 was found to be particularly abundant throughout the global population. These findings indicate that, despite the ability of Z. tritici to sexually reproduce on resistant hosts, AvrStb6 avirulence haplotypes tend to be eliminated in subsequent populations. [ABSTRACT FROM AUTHOR]

Modularity is now generally recognized as a fundamental feature of organisms, one that may have profound consequences for evolution. Modularity has recently become a major focus of research in organismal biology across multiple disciplines including genetics, developmental biology, functional morphology, population and evolutionary biology. While the wealth of new data, and also new theory, has provided exciting and novel insights, the concept of modularity has become increasingly ambiguous. That ambiguity is underlain by diverse intuitions about what modularity means, and the ambiguity is not merely about the meaning of the word—the metrics of modularity are measuring different properties and the methods for delimiting modules delimit them by different, sometimes conflicting criteria. The many definitions, metrics and methods can lead to substantial confusion not just about what modularity means as a word but also about what it means for evolution. Here we review various concepts, using graphical depictions of modules. We then review some of the metrics and methods for analyzing modularity at different levels. To place these in theoretical context, we briefly review theories about the origins and evolutionary consequences of modularity. Finally, we show how mismatches between concepts, metrics and methods can produce theoretical confusion, and how potentially illogical interpretations can be made sensible by a better match between definitions, metrics, and methods. Highlights: Modularity is a fundamental features of organisms, with potentially profound consequences for evolution. However, with expansion to new systems and scales of study, the concept of modularity has become increasing ambiguous. Here we map intuitions, metrics, and methods regarding modularity, discuss how their mismatch can create incoherence, and demonstrate how to untangle the confusion surrounding this core concept in organismal and evolutionary biology. [ABSTRACT FROM AUTHOR]

Due to its central importance to many aspects of evolutionary biology and population genetics, the long‐term effective population size (Ne) has been estimated for numerous species and populations. However, estimating contemporary Ne is difficult and in practice this parameter is often unknown. In principle, contemporary Ne can be estimated using either analyses of temporal changes in allele frequencies, or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches to estimate contemporary Ne of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and applied several temporal methods to estimate Ne at a few thousand (4000–7000). The approach based on LD provided higher estimates of Ne (20,000–32,000) and was associated with high variance, often resulting in infinite Ne. We conclude that whole‐genome sequencing data offers new possibilities to estimate high (>1000) contemporary Ne, but also note that such estimates remain challenging, in particular for LD‐based methods for contemporary Ne estimation. [ABSTRACT FROM AUTHOR]

Premise: Researchers adopting target‐enrichment approaches often struggle with the decision of whether to use universal or lineage‐specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage‐specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. Methods and Results: Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24–31%) and Brassicaceae (35–59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%). Conclusions: High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole. [ABSTRACT FROM AUTHOR]

Populations are typically defined as spatially contiguous sets of individuals, but large populations of social species can be composed of discrete social communities that often overlap in space. Masai giraffes (Giraffa camelopardalis tippelskirchi) of Tanzania live in distinct social subpopulations that overlap spatially, enabling us to simultaneously explore environmental and social factors correlated with demographic variation in a metapopulation of >1,400 adult females and calves. We considered statistically distinct communities in the social network as subpopulations and tested for variation among the 10 subpopulations in adult female survival, calf survival, and reproductive rate (calf‐to‐adult female ratio). We then related variation in demographic rates among subpopulations to differences in vegetation, soil type, proximity to 2 types of human settlements, local giraffe population density, and social metrics of relationship strength and exclusivity among adult females. We did not find any among‐subpopulation effects on adult female survival, suggesting adult female survival is buffered against environmental heterogeneity among subpopulations. Variation in calf demographic rates among subpopulations were correlated with vegetation, soils, anthropogenic factors, and giraffe population density but not with adult female relationship metrics, despite substantial spatial overlap. Subpopulations with more dense bushlands in their ranges had lower calf survival probabilities, and those closer to human settlements had higher reproductive rates, possibly because of spatial gradients in natural predation. Reproductive rates were higher in subpopulations with more volcanic soils, and calf survival probabilities were greater in subpopulations with higher local adult female densities, possibly related to higher‐quality habitat associated with fertile soils or lower predation risk, or to greater competitive ability. The variation in fitness among subpopulations suggests that giraffes do not move unhindered among resource patches to equalize reproductive success, as expected according to an ideal free distribution. The differences in calf survival and reproductive rates could rather indicate intercommunity differences in competitive ability, perception, learning, or experience. Our approach of comparing demography among spatially overlapping yet distinct socially defined subpopulations provides a biologically meaningful way to quantify environmental and social factors influencing fine‐scale demographic variation for social species. © 2021 The Wildlife Society. : We compared adult female survival, calf survival, and reproductive rates among spatially overlapping yet socially distinct subpopulations to quantify fine‐scale environmental and social factors that influence demographic variation. Adult female survival was high and constant across subpopulations, but reproductive rates were higher in subpopulations with more volcanic soils and closer to human settlements, and calf survival was greater in subpopulations with higher local adult female densities and with less dense bushlands. [ABSTRACT FROM AUTHOR]

Parasites can harm hosts and influence populations, communities, and ecosystems. However, parasites are reciprocally affected by population‐ and community‐level dynamics. Understanding feedbacks between infection dynamics and larger‐scale epidemiological and ecological processes could improve predictions and reveal novel control methods. We evaluated how exploitative resource competition among hosts, a fundamental aspect of population biology, influences within‐host infection dynamics of the widespread human parasite Schistosoma mansoni in its intermediate host, Biomphalaria glabrata. We added size‐dependent consumption of shared resources to a parameterized bioenergetics model to predict a priori the growth, parasite production, and survival of an infected focal host coexisting with an uninfected conspecific competitor in an experiment that varied competitor size. The model quantitatively anticipated that competitors disrupt growth and parasite production and that these effects increase with competitor size. Fitting the model to these data improved its match to host survivorship. Thus, resource competition alters infection dynamics, there are strong size asymmetries in these effects, and size‐asymmetric resource competition effects on infection dynamics can be accurately predicted by bioenergetics theory. More broadly, this framework can assess parasite transmission and control in other contexts, such as in resource competitive host communities, or in response to eutrophication, food supplementation, or culling. [ABSTRACT FROM AUTHOR]

Information on the population biology of alien species in non‐natural areas is essential to understanding their impacts on native species. Here, we investigated the life‐history traits, the propagule pressure and the supply potential of Athanasnitescens in a non‐native area. Sampling was monthly performed from April 2015 to March 2016 in an inter‐tidal estuary in the south‐eastern Brazilian coast. The population had a female‐biased sex ratio with a predominance of ovigerous females. Sexual dimorphism was evidenced by the mean body size and the positive allometry of chelipeds in males and of the second pleonal pleuron in females, evidencing an energy allocation to weaponry body structures and reproduction, respectively. The estimated size at which 50% of females reach functional sexual maturity was 3.3 mm of carapace length. The mean fecundity, 117 ± 40.03 eggs/female (53–263), had a positive correlation with the carapace length. The egg volume increased (83%) from the initial to the final stage of development. The presence of females carrying eggs in different stages of development indicates that A. nitescens is completing its life cycle in the studied region and shows a high propagule pressure. We provided the first insights into the biology of A. nitescens in Brazilian waters after the first record in 2009 in São Paulo coast, contributing to a better understanding of its biology and ecology in non‐natural areas. [ABSTRACT FROM AUTHOR]

1. Geographically widespread species provide excellent opportunities to investigate how phenotypes change across large‐scale environmental gradients. Temperature is a fundamental environmental variable and an important determinant of insect fitness. However, field research is often geographically restricted, and typically concentrated in northern latitudes. Basic population biology and phenotypic clines in relation to temperature therefore remain poorly known across the entire geographic range, even in otherwise well‐studied taxa. 2. We surveyed populations of the trimorphic damselfly Ischnura elegans in Cyprus, which is the southern range limit in Europe of this widespread insect species. Females of I. elegans occur in three discrete and heritable colour morphs, which vary in suites of phenotypic traits. One of these female morphs is a male‐mimic that avoids excessive male‐mating harassment by its male‐like appearance, and which is more cold‐tolerant than the two other morphs. 3. In contrast to the situation in northern Europe, these male‐mimicking females are the minority morph in Cyprus, representing only about 5% of all females. Male mimics also have lower mating rates than alternative female morphs. 4. Individuals in Cyprus are relatively small in comparison to the reported European range for body size, consistent with Bergman's rule. 5. Finally, populations of I. elegans on the island have the longest flight period known in Europe, and there is only partial evidence for seasonality in flight activity. 6. These results underscore the benefits of considering the entire range of environmental conditions encountered by insect species when conducting evolutionary ecology research. [ABSTRACT FROM AUTHOR]

Structured demographic models are among the most common and useful tools in population biology. However, the introduction of integral projection models (IPMs) has caused a profound shift in the way many demographic models are conceptualized. Some researchers have argued that IPMs, by explicitly representing demographic processes as continuous functions of state variables such as size, are more statistically efficient, biologically realistic, and accurate than classic matrix projection models, calling into question the usefulness of the many studies based on matrix models. Here, we evaluate how IPMs and matrix models differ, as well as the extent to which these differences matter for estimation of key model outputs, including population growth rates, sensitivity patterns, and life spans. First, we detail the steps in constructing and using each type of model. Second, we present a review of published demographic models, concentrating on size‐based studies, which shows significant overlap in the way IPMs and matrix models are constructed and analyzed. Third, to assess the impact of various modeling decisions on demographic predictions, we ran a series of simulations based on size‐based demographic data sets for five biologically diverse species. We found little evidence that discrete vital rate estimation is less accurate than continuous functions across a wide range of sample sizes or size classes (equivalently bin numbers or mesh points). Most model outputs quickly converged with modest class numbers (≥10), regardless of most other modeling decisions. Another surprising result was that the most commonly used method to discretize growth rates for IPM analyses can introduce substantial error into model outputs. Finally, we show that empirical sample sizes generally matter more than modeling approach for the accuracy of demographic outputs. Based on these results, we provide specific recommendations to those constructing and evaluating structured population models. Both our literature review and simulations question the treatment of IPMs as a clearly distinct modeling approach or one that is inherently more accurate than classic matrix models. Importantly, this suggests that matrix models, representing the vast majority of past demographic analyses available for comparative and conservation work, continue to be useful and important sources of demographic information. [ABSTRACT FROM AUTHOR]

The North Georgia Mountains are the southernmost region along the United States East Coast where European wine grapes (Vitis vinifera) are grown commercially. Epidemics of downy mildew, caused by Plasmopara viticola, are frequent and severe, but little is known about the epidemiology and population biology of the pathogen in this region. Disease monitoring in an experimental vineyard from 2015 to 2017 indicated that times of disease onset and progress rates were highly variable across years and cultivars. Oospores were observed microscopically, and simulation with a process‐based model indicated presence of conditions favourable for oospore germination in the spring and early summer each year. A total of 409 P. viticola isolates collected over three years were genotyped with seven microsatellite markers, revealing very high genotypic diversity, which when combined with the observation of oospores is indicative of a sexually reproducing population. Among the 409 isolates, 225 multilocus genotypes (MLGs) were identified, of which 164 were detected only once and 61 were repeated (clonal). Eight MLGs (represented by 28 isolates) were detected across years, suggesting the possibility of asexual overwintering of P. viticola in this region. Across sampling dates, the percentage of isolates belonging to nonrepeated (unique) MLGs ranged from 27.3% to 63.2%. Even towards the end of the annual epidemic, the percentage of isolates in nonrepeated MLGs was still relatively high, around 30%. These MLGs may have originated from oospores germinating late during the growing season, although incomplete sampling at earlier dates and contribution by immigration cannot be fully excluded. [ABSTRACT FROM AUTHOR]

The great scallop (Pecten maximus) is a commercially important bivalve in Europe, particularly in the English Channel, where fisheries are managed at regional and local scales through the regulation of fishing effort. In the long term, knowledge about larval dispersal and gene flow between populations is essential to ensure proper stock management. Yet, previous population genetic studies have reported contradictory results.In this study, scallop samples collected across the main fishing grounds along the French and English coasts of the English Channel (20 samples with temporal replicates for three sites, n = 1059 individuals), and the population genetic structure was analysed using 13 microsatellite loci. Coupling empirical genetic data with demogenetic modelling based on a biophysical model simulating larval exchanges among scallop beds revealed a subtle genetic differentiation between south‐west English populations and the rest of the English Channel, which was consistent with larval dispersal simulations.The present study provides a step forward in the understanding of great scallop population biology in the English Channel, underlining the fact that even in a context of potentially high gene flow and recent divergence times since the end of the last glacial maximum, weak but significant spatial genetic structure can be identified at a regional scale. [ABSTRACT FROM AUTHOR]

The common carp (Cyprinus carpio) is an exotic fish, being one of the commercially important species in Lake Naivasha. The present study investigated its growth, mortality, maturity, condition and exploitation. Sampling was done monthly from January to December 2017 with gillnets of 2–5 inches mesh size. Each individual fish was measured (cm) and weighed (g) in the field. The specimens were preserved in ice and transported to the laboratory for analysis of maturity. The fish lengths ranged from 12.0 to 69.0 cm TL, and weighed between 32 and 6,840 g. The overall population sex ratio was 1:1.66 (female:male). The length at first maturity (Lm50) was calculated to be 54.0 and 49.0 cm for females and males, respectively. The length at first capture (23.9 cm) was lower than its length at first maturity, suggesting the capture of immature fish. The mean condition factor for all fish was 1.05. The peak condition values were observed during April (1.35), September (1.59) and October (1.80). The highest (1.377) mean condition was observed for size class 56–60 and the lowest (0.933) in class 26–30. The asymptotic length (L∞) was 73.5 cm, and the growth curvature (K) was 1.05 year‐1, with a growth performance index (Ф) of 3.72. The total (Z), natural (M) and fishing (F) mortality coefficients were 2.85, 1.34 and 1.78 year‐1, respectively. The exploitation rate (E) of 0.57 year‐1 was higher than the optimum sustainable yield (E0.5) of 0.32, but was not different from the maximum sustainable yields (Emax) 0.54 and economic yield (E0.1) 0.46. The results of the present study provide parameters of fish biology and population that should prove useful in managing the fishery of Lake Naivasha. [ABSTRACT FROM AUTHOR]

This study documented the parasite faunas of the spiral valves of blue sharks Prionace glauca (L. 1758) and common thresher sharks Alopias vulpinus (Bonnaterre, 1788) caught in the California Current Large Marine Ecosystem (CCLME) north of the Mexican border. The spiral valves of 18 blue and 19 thresher sharks caught in the CCLME from 2009 to 2013 were examined for parasites. Seven parasite taxa were found in blue sharks and nine in threshers. The tetraphyllidean cestode Anthobothrium sp. (78% prevalence) was the most common parasite in blue sharks, and the phyllobothriid cestode Paraorygmatobothrium sp. (90% prevalence) was the most common in threshers. An adult nematode of the genus Piscicapillaria was found in threshers for the first time and may be a new species. Adult individuals of Hysterothylacium sp. were found in both shark species. The adult acanthocephalan Rhadinorhynchus cololabis and remains of the parasitic copepod Pennella sp. – both parasites of Pacific saury, Cololabis saira – were found in the intestines of threshers, indicating recent feeding on saury. This study paves the way for a more comprehensive examination, including more samples and a wider variety of shark species, to provide a greater understanding of shark feeding behaviour and possibly provide information on shark population biology. [ABSTRACT FROM AUTHOR]

Ecologists and oceanographers inform population and ecosystem management by identifying the physical drivers of ecological dynamics. However, different research communities use different analytical tools where, for example, physical oceanographers often apply rank‐reduction techniques (a.k.a. empirical orthogonal functions [EOF]) to identify indicators that represent dominant modes of physical variability, whereas population ecologists use dynamical models that incorporate physical indicators as covariates. Simultaneously modeling physical and biological processes would have several benefits, including improved communication across sub‐fields; more efficient use of limited data; and the ability to compare importance of physical and biological drivers for population dynamics. Here, we develop a new statistical technique, EOF regression, which jointly models population‐scale dynamics and spatially distributed physical dynamics. EOF regression is fitted using maximum‐likelihood techniques and applies a generalized EOF analysis to environmental measurements, estimates one or more time series representing modes of environmental variability, and simultaneously estimates the association of this time series with biological measurements. By doing so, it identifies a spatial map of environmental conditions that are best correlated with annual variability in the biological process. We demonstrate this method using a linear (Ricker) model for early‐life survival ("recruitment") of three groundfish species in the eastern Bering Sea from 1982 to 2016, combined with measurements and end‐of‐century projections for bottom and sea surface temperature. Results suggest that (a) we can forecast biological dynamics while applying delta‐correction and statistical downscaling to calibrate measurements and projected physical variables, (b) physical drivers are statistically significant for Pacific cod and walleye pollock recruitment, (c) separately analyzing physical and biological variables fails to identify the significant association for walleye pollock, and (d) cod and pollock will likely have reduced recruitment given forecasted temperatures over future decades. [ABSTRACT FROM AUTHOR]

Aims: Floral traits are frequently studied in population biology and evolutionary ecology but are rarely considered in functional trait‐based studies focusing on the assembly of communities. We address this gap in trait‐based community assembly by synthesizing the existing literature on processes driving floral and pollination‐related trait patterns at community scales. We highlight limitations of the field due to lack of data and suggest potential directions of future research. Methods: We conducted a systematic literature search collating studies that investigated floral traits in the context of plant community assembly, which allowed us to synthesize the current state of the art and point out important gaps in our knowledge. Conclusions: The literature review shows that including pollination‐related traits in community assembly studies can shed new light on species coexistence patterns not accounted for by other types of traits. The synthesis presented here shows the diversity of approaches and existing techniques which can generate a step forward in this open field of research. What currently seems to hinder comprehensive analyses of floral traits at community levels is the lack of data, particularly in existing large repositories for traits worldwide, as well as a gap in linking modern coexistence theory with floral traits. [ABSTRACT FROM AUTHOR]

The ability to accurately gauge the body condition of free‐swimming cetaceans is invaluable in population and conservation biology, due to the direct implications that this measure has on individual fitness, survival, and reproductive success. Furthermore, monitoring temporal change in body condition offers insight into foraging success over time, and therefore the health of the supporting ecosystem, as well as a species' resilience. These parameters are particularly relevant in the context of widespread and accelerated, climate‐induced habitat change. There are, however, significant logistical challenges involved with research and monitoring of large cetaceans, which often preclude direct measure of body condition of live individuals. Consequently, a wide variety of indirect approaches, or proxies, for estimating energetic stores have been proposed over past decades. To date, no single, standardized, approach has been shown to serve as a robust estimation of body condition across species, age categories, and in both live and dead individuals. Nonetheless, it is clear that streamlining and advancing body condition measures would carry significant benefits for diverse areas of cetacean research and management. Here, we review traditional approaches and new applications for the evaluation of cetacean energetic reserves. Specific attention is given to the criteria of measure performance (sensitivity and accuracy), level of invasiveness, cost and effort required for implementation, as well as versatility e.g. applicability across different species, age groups, as well as living versus deceased animals. Measures have been benchmarked against these criteria in an effort to identify key candidates for further development, and key research priorities in the field. [ABSTRACT FROM AUTHOR]

The Nile tilapia (Oreochromis niloticus) was introduced into Lake Naivasha to provide exploitable fisheries, being one of the commercially important fish providing livelihoods to communities around the lake. Its stocks in the lake have been declining, however, because of intense fishing, ecological changes and effects of other exotic species. The present study was undertaken to investigate the population and biological parameters of Oreochromis niloticus. Fish samples (1,021) were caught monthly from January to December 2017, collecting a total of 1,021 O. niloticus, with an overall sex ratio of 2.21:1.0 (male: female). The length of the fish ranged from 9.0 to 40.0 cmTL and weighed between 20 and 1,220 g. The mean length and weight for all fish was 22.6 cm and 272.6 g. The slope b of length–weight relationship was 2.86 for all fish, indicating negative allometry. The mean condition factors were 0.99, 1.04 and 1.01 for male, female and all fish, respectively. The length at first maturity (Lm50) was estimated to be 28.0 cmTL for all sexes, indicating the fish matures at smaller sizes. The length at first capture (Lc50) was calculated to be 19.38 cm, a value much lower than its Lm50, reflecting the capture of juvenile fish. The asymptotic length (L∞) was 42 cm, the growth coefficient (K) was 0.21/year, and the growth performance index (Ф) was 2.57. The natural (M), fishing (F) and total mortality (Z) coefficients were estimated to be 0.55, 0.26 and 0.80/year, respectively. The optimum sustainable yield (E0.5), maximum sustainable yield (Emax) and maximum economic yield (E0.1) indices of 0.23, 0.35 and 0.26, respectively, imply an optimal exploitation of O. niloticus. The results of the present study provided some important insights into the biology and management needs of the O. niloticus fishery in Lake Naivasha, as well as revealing a gap for further research on its reproductive biology. [ABSTRACT FROM AUTHOR]