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opencc-zeroJan 2022View details →

Resilience of seagrass populations to thermal stress does not reflect regional differences in ocean climate

1. The prevalence of local adaptation and phenotypic plasticity among populations is critical to accurately predicting when and where climate change impacts will occur. Currently, comparisons of thermal performance between populations are untested for most marine species or overlooked by models predicting the thermal sensitivity of species to extirpation. 2. Here we compared the ecological response and recovery of seagrass populations (Posidonia oceanica) to thermal stress throughout a year-long translocation experiment across a 2800 km gradient in ocean climate. Transplants in central and warm-edge locations experienced temperatures >29 ºC, representing thermal anomalies >5ºC above long-term maxima for cool-edge populations, 1.5ºC for central and <1ºC for warm-edge populations. 3. Cool, central and warm-edge populations differed in thermal performance when grown under common conditions, but patterns contrasted with expectations based on thermal geography. Cool-edge populations did not differ from warm-edge populations under common conditions and performed significantly better than central populations in growth and survival. 4. Our findings reveal that thermal performance does not necessarily reflect the thermal geography of a species. We demonstrate that warm-edge populations can be less sensitive to thermal stress than cooler, central populations suggesting that Mediterranean seagrasses have greater resilience to warming than current paradigms suggest.

opencc-zeroJan 2022View details →

Reproductive benefits associated with dispersal in headwater populations of Trinidadian guppies (Poecilia reticulata)

Theory suggests that the evolution of dispersal is balanced by its fitness costs and benefits, yet empirical evidence is sparse due to the difficulties of measuring dispersal and fitness in natural populations. Here, we use spatially-explicit data from a multi-generational capture-mark-recapture study of two populations of Trinidadian guppies (Poecilia reticulata) along with pedigrees to test whether there are fitness benefits correlated with dispersal. Combining these ecological and molecular datasets allows us to directly measure the relationship between movement and reproduction. Individual dispersal was measured as the total distance moved by a fish during its lifetime. We analyzed the effects of dispersal propensity and distance on a variety of reproductive metrics. We found that number of mates and number of offspring produced were positively correlated to dispersal, especially for males. Our results also reveal individual and environmental variation in dispersal, with sex, size, season, and stream acting as determining factors.

Local male breeding density affects extra‐pair paternity in a south temperate population of grass wrens Cistothorus platensis

Demographic factors can affect the frequency of extra-pair paternity (EPP) in birds, as the distribution and availability of potential mates in both space and time influence the rate of encounters between females and males. Over three breeding seasons, we intensively studied the breeding system of a south temperate population of grass wrens Cistothorus platensis by genotyping 73 broods (319 nestlings) and estimating EPP rates for those broods. Using five different radii (80, 160, 240, 320, and 400 m) around each nest with assigned paternity, we examined the effects of local breeding synchrony, male breeding density, and adult sex ratio (ASR) on the EPP rate. The majority of extra-pair offspring (~80%) were sired by neighboring males. Neither local breeding synchrony nor ASR consistently explained the EPP rate variation as their effects were only statistically significant within 320 m and 400 m. However, the EPP rate increased as the local male breeding density increased within every radius category, strongly suggesting that neighboring male abundance might play an important role in the extra-pair mating behavior in this species. Our study also highlights the relevance of using a local scale approach when studying mating behavior.

opencc-by-4.0Feb 2022View details →

Population-based, Age- and Gender- Stratified Sero-Survey Study for SARS-CoV-2 in Uganda

Results of population-based age stratified seroepidemiological investigation in Uganda

Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition

Natural landscapes are increasingly impacted by nitrogen enrichment from aquatic and airborne pollution sources. Nitrogen enrichment in the environment can eliminate the net benefits that plants gain from nitrogen-fixing microbes such as rhizobia, potentially altering host-mediated selection on nitrogen fixation. However, we know little about the long-term effects of nitrogen enrichment on this critical microbial service. Here, we sampled populations of the legume Acmispon strigosus and its associated soil microbial communities from sites spanning an anthropogenic nitrogen deposition gradient. We measured the net growth benefits plants obtained from their local soil microbial communities and quantified plant investment into nodules that house nitrogen-fixing rhizobia. We found that plant growth benefits from sympatric soil microbes did not vary in response to local soil nitrogen levels, and instead varied mainly among plant lines. Soil nitrogen levels positively predicted the number of nodules formed on sympatric plant hosts, although this was likely due to plant genotypic variation in nodule formation, rather than variation among soil microbial communities. The capacity of all the tested soil microbial communities to improve plant growth is consistent with plant populations imposing strong selection on rhizobial nitrogen fixation despite elevated soil nitrogen levels, suggesting that host control traits in A. strigosus are stable under long-term nutrient enrichment.

Recent estimate of Asian elephants in Borneo reveals a smaller population

Asian elephants occurring in northern Borneo form a geographically isolated and genetically distinct population. Of this, the subpopulation of Central Sabah holds the greatest opportunity for long-term survival, due to a relatively large population size and occurrence over a vast, contiguous, and protected habitat. We surveyed this subpopulation in 2015 using advanced methods to obtain a population size estimate. We used the distance-sampling framework and laid out transects following a stratified random design for counting elephant dung piles; measured dung decay following the 'retrospective' method; and used Bayesian analysis to estimate dung decay rate and dung pile density. Thus, we estimated a posterior mean dung decay rate of 212 days (95% BCI: 133–319), an overall elephant density of 0.07 per km2 (95% BCI: 0.03–0.11), and a population size of 387 elephants (95% BCI: 169–621). These estimates were far lower than the population size of 1132 individuals and density of 1.18 per km2 estimated in 2008. It is unlikely that there has been a steep population decline, as there were no drastic land-use changes between 2008 and 2015, nor were there other identifiable causes for a population decline. Therefore, it appears that the methodological and analytical flaws in the previous estimate are the most plausible reason for this observed difference. Given that the new estimate suggests a much smaller population, it is prudent and precautionary to use the new estimate as the basis for all policy decisions and conservation actions for elephants in Sabah.

Population genomic consequences of life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (common garden phenotype data)

Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200m geographical gap of no intermediate habitat. Individual inbreeding coefficients (FIS) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1km) scales. Finally, YNP adaptation does not re-use a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.

opencc-by-4.0Apr 2021View details →

A 24-hour dynamic population distribution dataset based on mobile phone data from Helsinki Metropolitan Area, Finland

Related article: Bergroth, C., Järv, O., Tenkanen, H., Manninen, M., Toivonen, T., 2022. A 24-hour population distribution dataset based on mobile phone data from Helsinki Metropolitan Area, Finland. <a href="https://www.nature.com/articles/s41597-021-01113-4">Scientific Data 9, 39</a>.   In this dataset: We present temporally dynamic population distribution data from the Helsinki Metropolitan Area, Finland, at the level of 250 m by 250 m statistical grid cells. Three hourly population distribution datasets are provided for regular workdays (Mon – Thu), Saturdays and Sundays. The data are based on aggregated mobile phone data collected by the biggest mobile network operator in Finland. Mobile phone data are assigned to statistical grid cells using an advanced dasymetric interpolation method based on ancillary data about land cover, buildings and a time use survey. The data were validated by comparing population register data from Statistics Finland for night-time hours and a daytime workplace registry. The resulting 24-hour population data can be used to reveal the temporal dynamics of the city and examine population variations relevant to for instance spatial accessibility analyses, crisis management and planning.  Please cite this dataset as: Bergroth, C., Järv, O., Tenkanen, H., Manninen, M., Toivonen, T., 2022. A 24-hour population distribution dataset based on mobile phone data from Helsinki Metropolitan Area, Finland. Scientific Data 9, 39. https://doi.org/10.1038/s41597-021-01113-4   Organization of data The dataset is packaged into a single Zipfile Helsinki_dynpop_matrix.zip which contains following files: <ol> <li> HMA_Dynamic_population_24H_workdays.csv represents the dynamic population for average workday in the study area.</li> <li> HMA_Dynamic_population_24H_sat.csv represents the dynamic population for average saturday in the study area.</li> <li> HMA_Dynamic_population_24H_sun.csv represents the dynamic population for average sunday in the study area.</li> <li>target_zones_grid250m_EPSG3067.geojson represents the statistical grid in ETRS89/ETRS-TM35FIN projection that can be used to visualize the data on a map using e.g. QGIS.</li> </ol> Column names <ol> <li>YKR_ID : a unique identifier for each statistical grid cell (n=13,231). The identifier is compatible with the statistical YKR grid cell data by Statistics Finland and Finnish Environment Institute.</li> <li>H0, H1 ... H23 : Each field represents the proportional distribution of the total population in the study area between grid cells during a one-hour period. In total, 24 fields are formatted as “Hx”, where x stands for the hour of the day (values ranging from 0-23). For example, H0 stands for the first hour of the day: 00:00 - 00:59.  The sum of all cell values for each field equals to 100 (i.e. 100% of total population for each one-hour period)</li> </ol> In order to visualize the data on a map, the result tables can be joined with the target_zones_grid250m_EPSG3067.geojson data. The data can be joined by using the field YKR_ID as a common key between the datasets. License Creative Commons Attribution 4.0 International. Related datasets <ul> <li>Järv, Olle; Tenkanen, Henrikki & Toivonen, Tuuli. (2017). Multi-temporal function-based dasymetric interpolation tool for mobile phone data. Zenodo. https://doi.org/10.5281/zenodo.252612</li> <li>Tenkanen, Henrikki, & Toivonen, Tuuli. (2019). Helsinki Region Travel Time Matrix [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3247564</li> </ul>

Genetic data and niche differences suggest that disjunct populations of Diglossa brunneiventris are not sister lineages

Disjunct distributions within a species are of great interest in systematics and biogeography. This separation can function as a barrier to gene flow when the distance among populations exceeds the dispersal capacity of individuals, and depending on the duration of the barrier, it may eventually lead to speciation. Here we describe patterns of geographic differentiation of two disjunct populations of Diglossa brunneiventris separated by approximately 1000 km along the Andes. Diglossa brunneiventris vuilleumieri is isolated in northern Colombia, while Diglossa brunneiventris brunneiventris has a seemingly continuous distribution across Peru, Bolivia, and Chile. We sequenced mitochondrial and nuclear DNA of the two Diglossa brunneiventris subspecies to evaluate whether they form a monophyletic clade, while including the other three species within the carbonaria complex (D. gloriosa, D. humeralis and D. carbonaria). We also constructed ecological niche models for each Diglossa brunneiventris subspecies to compare their climatic niches. We found that when using all available molecular data, the two D. brunneiventris subspecies are not sister lineages. In fact, each subspecies is more closely related to other species in the carbonaria complex. Our niche modeling analyses showed that the subspecies are occupying almost entirely different climatic niches. An additional, and not expected result was that the carbonaria complex might encompass more cryptic species than previously considered. We suggest reevaluating the taxonomic status of these brunneiventris populations, especially the northern subspecies, given its highly restricted range and potential threatened status.

Data from: Controlling trapping, overgrazing and invasive vegetation is key to saving Java's last population of the Black-winged Myna

The Black-winged Myna (Acridotheres melanopterus) is an Endangered passerine endemic to the islands of Java and Bali, Indonesia. Illegal trapping to supply the cage-bird trade has led to its near-total extinction, with the global population estimated to number fewer than 100 individuals. The only known population of Black-winged Mynas on Java occurs at Baluran National Park (BNP). These data were generated to meet the two primary aims of the linked paper: the first was to estimate the Black-winged Myna (Acridotheres melanopterus) population size and range at BNP; and the second was to use species distribution modelling to evaluate the potential suitability of areas currently unoccupied by Black-winged Mynas across BNP to identify priorities for management intervention. We carried out line-transect distance sampling following the standard distance analysis method to estimate the population size. A total of 56 detections of groups of Black-winged Mynas were recorded along line transects and are included in the dataset. These records are associated with the land cover type for that segment of the transect, the perpendicular distance of the record to the transect, and the survey effort associated with each transect. To produce the species distribution model, we used three predictor raster layers along with all Black-winged Myna presences recorded (not freely available, see below) and a generated set of pseudo-absences. The dataset contains both the raw data used to create the land cover classification as well as the final raster. The raw data used to produce the habitat classification contains classified points (n = 426) from across BNP, which were used as a training and test data for a random forest land cover classification.

opencc-zeroJun 2022View details →

Density, parasitism, and sexual reproduction are strongly correlated in lake Daphnia populations

Many organisms can reproduce both asexually and sexually. For cyclical parthenogens, periods of asexual reproduction are punctuated by bouts of sexual reproduction, and the shift from asexual to sexual reproduction has large impacts on fitness and population dynamics. We studied populations of Daphnia dentifera to determine the amount of investment in sexual reproduction as well as the factors associated with variation in investment in sex. To do so, we tracked host density, infections by nine different parasites, and sexual reproduction in 15 lake populations of D. dentifera for three years. Sexual reproduction was seasonal, with male and ephippial female production beginning as early as late September and generally increasing through November. However, there was substantial variation in the prevalence of sexual individuals across populations, with some populations remaining entirely asexual throughout the study period and others shifting almost entirely to sexual females and males. We found strong relationships between density, prevalence of infection, parasite species richness, and sexual reproduction in these populations. However, strong collinearity between density, parasitism, and sexual reproduction means that further work will be required to disentangle the causal mechanisms underlying these relationships.

Genetic structure in the nonbreeding range of rufa Red Knots suggests distinct Arctic breeding populations

An understanding of the migratory connectivity between breeding and nonbreeding areas is fundamental to the management of long-distance migrants under pressure from habitat change along their flyways. Here we describe evidence for genetic structure within the nonbreeding range of the endangered Arctic-Canadian rufa subspecies of Red Knots (Calidris canutus). Using blood and tissue samples from the major nonbreeding regions in Argentina (Tierra del Fuego and Río Negro), northern Brazil (Maranhão), and southeastern USA (Florida), we estimated genetic structure in 514 amplified fragment length polymorphism (AFLP) loci, applying cluster assignment analyses in DAPC, assignPOP, and STRUCTURE. Using a priori location information, individuals could be correctly re-assigned to their nonbreeding regions, which validated that the assignment accuracy of the data was sufficient. Without using a priori location information, we detected 3–5 genotype clusters, and posterior assignment probabilities of samples to these genotype clusters varied among the three regions. Lastly a chi-square test confirmed that allele frequencies varied significantly among nonbreeding regions, rejecting the hypothesis that samples were drawn from a single gene pool. Our findings hint at undescribed structure within the Red Knot rufa breeding range in the Canadian Arctic and indicate that each rufa nonbreeding area in this study hosts a different subsample of these breeding populations. The observation that nonbreeding sites of rufa Red Knots contain different genetic pools argues for separate conservation management of these sites.

Population structure, patterns of natal dispersal, and demographic history in a declining aerial insectivore, the purple martin Progne subis

Genetic variation is a fundamental component of biodiversity, and studying population structure, gene flow, and demographic history can help guide conservation strategies for many species. Like other aerial insectivores, the purple martin (Progne subis) is in decline, and yet their genetic background remains largely unknown. To address this knowledge gap, we assessed population structure in the nominate eastern subspecies (P. s. subis) with relation to natal dispersal and examined historical genetic patterns in all three subspecies (P. s. subis, P. s. arboricola, P. s. hesperia) across their North American breeding range by estimating effective population sizes over time. We used next-generation sequencing strategies for genomic analyses, integrating whole-genome resequencing data with continent-wide band encounter records to examine natal dispersal. We documented population structure across P. s. subis, with the highest differentiation between the northern (Alberta) and more southern colonies and following patterns of isolation-by-distance. Consistent with spatial patterns of genetic differentiation, we also found greater longitudinal than latitudinal natal dispersal distances, signifying potential latitudinal constraints on gene flow. Earlier contractions in effective population sizes in the western P. s. arboricola and P. s. hesperia compared to the eastern P. s. subis subspecies suggest these subspecies originated from two different glacial refugia. Together, these findings support latitudinal distinction in P. s. subis, and elucidate the origin of subspecies differentiation, highlighting the importance to conserve populations across the range to maximize genetic diversity and adaptive potential in the purple martin.

opencc-zeroDec 2021View details →

Data from: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution

The study "Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution" by Schenk et al. explores the phenotypic and genotypic changes in Escherichia coli after 500 generations of laboratory adaptation to increasing concentrations of an antibiotic (CTX). The source data files and scripts pertaining to the figures in the main manuscript and the extended data are available on the publishers webiste. Here we provide the source data files and scripts pertaining to the supplementary materials, organized according the figures in the supplementary material. Data are provided for Figures S2-S4, S6-S8, and S10-S12.

Unravelling processes between phenotypic plasticity and population dynamics in migratory birds

Populations can rapidly respond to environmental change via adaptive phenotypic plasticity, which can also modify interactions between individuals and their environment, affecting population dynamics. Bird migration is a highly plastic resource-tracking tactic in seasonal environments. However, the link between the population dynamics of migratory birds and migration tactic plasticity is not well understood. The quality of staging habitats affects individuals' migration timing and energy budgets in the course of migration, and can consequently affect individuals' breeding and overwintering performance, and impact population dynamics. Given staging habitats being lost in many parts of the world, our goal is to investigate responses of individual migration tactics and population dynamics in the face of loss of staging habitat, and to identify the key processes connecting them. We started by constructing and analysing a general full-annual-cycle individual-based model with a stylized migratory population to generate hypotheses on how changes in the size of staging habitat might drive changes in individual stopover duration and population dynamics. Next, through the interrogation of survey data, we tested these hypotheses by analysing population trends and stopover duration of migratory waterbirds experiencing loss of staging habitat. Our modelling exercise led to us posing the following hypotheses: the loss of staging habitat generates plasticity in migration tactics, with individuals remaining on the staging habitat for longer to obtain food due to a reduction in per capita food availability. The subsequent increasing population density on the staging habitat has knock on effects on population dynamics in the breeding and overwintering stage. Our empirical results were consistent with the modelling predictions. Our results demonstrate how environmental change that impacts one energetically costly life history stage in migratory birds can have population dynamics impacts across the entire annual cycle via phenotypic plasticity.

From nature reserve to mosaic management: improving matrix survival, not permeability, benefits regional populations under habitat loss and fragmentation

Although matrix improvement in fragmented landscapes is a promising conservation measure, matrix permeability (willingness of an organism to enter the matrix) and movement survival in the matrix are usually aggregated. Consequently, it is unknown which matrix property needs to be improved. It also remains unclear whether matrix upgrading from dispersal passage to providing reproduction opportunities has large conservation benefits and whether there are interactive effects between habitat and matrix management. We examined matrix effects on regional populations across a gradient of habitat loss and fragmentation using simulation experiments that integrated demographic processes and movement modeling based on circuit theory. We separately modified the levels of matrix permeability and movement survival to evaluate their individual effects. We also altered the amount and configuration of not only habitat but also improved matrix to assess their effects on population vital rates (size, survival and density). In binary landscapes comprising habitat and unimproved matrix, matrix movement survival had larger effects on population vital rates than matrix permeability. Increasing movement survival increased vital rates, yet, increasing matrix permeability decreased vital rates. Increased permeability required corresponding increased movement survival to offset potential negative population outcomes. When subsets of the matrix functioning as dispersal passage only (where no reproduction opportunities existed) were improved, increasing matrix permeability but holding movement survival constant reduced all vital rates, especially with increasing habitat fragmentation. In contrast, when movement survival increased, vital rates increased given strong habitat fragmentation. The benefits of upgrading dispersal passage to provide reproduction opportunities for population survival were greatest when habitat amount was moderate. We also found synergetic effects between amounts of habitat and improved matrix, and the benefits of matrix improvement were promoted when improvement was achieved in a spatially aggregated manner. Synthesis and applications: Matrix improvement and connectivity modeling aimed at increasing movement survival will likely bring larger conservation benefits than those for improving permeability alone. Buffering and connecting habitat remnants with improved matrix could provide benefits as long as movement survival is increased. Simultaneous implementation of habitat management and matrix improvement would yield synergistic conservation benefits.

opencc-by-4.0Dec 2021View details →

The population genetics of adaptation through copy-number variation in a fungal plant pathogen

Supplementary Tables S1-S8 for the manuscript "The population genetics of adaptation through copy-number variation in a fungal plant pathogen"

Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.

Data from: Demographic correction – a tool for inference from individuals to populations

Estimation of responses of organisms to their environment using experimental manipulations, and comparison of such responses across sets of species, is one of the primary tools in ecology research. The most common approach is to compare response of a single life stage of species to an environmental factor and use this information to draw conclusions about population dynamics of these species. Such approach ignores the fact that interspecific fitness differences measured at a single life stage are not directly comparable and cannot be extrapolated to lifetime fitness of individuals and thus species' population dynamics. Comparison of one life stage only while omitting demographic information can strongly bias conclusions, both in experimental studies with a few species, and in large comparative studies. We illustrate the effect of this omission using both an exaggerated fictitious example, and biological data on congeneric species differing in their demography. We are showing, taking simple assumptions, that different demography can completely revert conclusions reached by a comparison based on an experiment focusing on a single life stage. We show that a "demographic correction", namely translating observed effects into differences in outcomes of demographic models, is a solution to this problem. It requires turning the detected effects from the experiment into changes of transition probabilities of projection matrix models. Although such solution is limited by the low number of species with demographic data available, we believe that existing data (and data likely to be collected in the near future) permit at least approximate handling of this problem.