Find research datasets worth reusing

opencc-by-4.0Nov 2015View details →

Figure 4. S in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)

Figure 4. S. gynobranchiata: А, a body fragment of an egg-carrying female; В, a 3–chaetiger larva just hatched from egg capsule; С, a 3–chaetiger larva on the 2nd day; D, a 5–chaetiger larva equipped with anal cirri; E, a 9–chaetiger larva; F, a 13–chaetiger larva making a tube. Scale: А- F – 100 µm.

opencc-by-4.0Nov 2015View details →

Figure 3 in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)

Figure 3. Distribution of polychaete worms S. gynobranchiata (density in ind.·m-2) in the Sevastopol Bay: A – in 2007; B – in 2008; C – in 2013.

Differentiation of rhizosphere fungal assemblages by host ploidy level in mixed-ploidy Larrea tridentata populations

Polyploidy—whole genome duplication—is common in plants. Studies over the last several decades have documented numerous mixed-ploidy populations. Whether arising via recurrent whole genome duplication events within a population, or from secondary contact, the persistence of mixed populations is possible by niche differentiation. Specifically, one mechanism facilitating ploidy co-occurrence is microbially-mediated niche differentiation (MMND), wherein cytotypes occupy different niches via interactions with different sets of microbes. Inherently cryptic, MMND is underexplored in polyploid plant populations. Here, we search for evidence of MMND in creosotebush (Larrea tridentata), a dominant desert shrub of the southwestern U.S. and northern Mexico. We sequenced root-associated fungal taxa in soil diploid, autotetraploid, and autohexaploid plants growing in two naturally-occurring mixed-cytotype populations. Within populations, we found substantial fungal assemblage overlap across host plant cytotypes. However, using indicator species analysis, we identified some fungi that are differentiated by host plant cytotype, satisfying a precondition for MMND. Future study is needed to determine the degree of niche differentiation conferred, if any, and whether the identified fungi play a role in the long-term persistence of multiple cytotypes within populations.

Data from: Additive genetic and environmental variation interact to shape the dynamics of seasonal migration in a wild bird population

Dissecting joint micro-evolutionary and plastic responses to environmental perturbations requires quantifying interacting components of genetic and environmental variation underlying expression of key traits. This ambition is particularly challenging for phenotypically discrete traits where multiscale decompositions are required to reveal non-linear transformations of underlying genetic and environmental variation into phenotypic variation, and when effects must be estimated from incomplete field observations. We devised a joint multistate capture-recapture and quantitative genetic animal model and fitted this model to full-annual-cycle resighting data from partially-migratory European shags (Gulosus aristotelis) to estimate key components of genetic, environmental and phenotypic variance in the ecologically critical discrete trait of seasonal migration versus residence. We demonstrate non-negligible additive genetic variance in latent liability for migration, resulting in detectable micro-evolutionary responses following two episodes of strong survival selection. Further, liability-scale additive genetic effects interacted with substantial permanent individual and temporary environmental effects to generate complex non-additive effects on expressed phenotypes, causing substantial intrinsic gene-by-environment interaction variance on the phenotypic scale. Our analyses therefore reveal how temporal dynamics of partial seasonal migration arise from combinations of instantaneous micro-evolution and within-individual phenotypic consistency, and highlight how intrinsic phenotypic plasticity could expose genetic variation underlying discrete traits to complex forms of selection.

opencc-by-4.0Jun 2023View details →

Boldness and physiological variation in round goby populations along their Baltic Sea invasion front

Data/code for the paper: Galli, A., Behrens, J. W., Gesto, M., & Moran, N. P. (2023). Boldness and physiological variation in round goby populations along their Baltic Sea invasion front. Physiology & Behavior, 114261. <a href="https://doi.org/10.1016/j.physbeh.2023.114261">https://doi.org/10.1016/j.physbeh.2023.114261</a>

Ecological interactions driving population dynamics of two tick-borne pathogens, Borrelia burgdorferi and Babesia microti

Borrelia burgdorferi (Bb) and Babesia microti (Bm) are vector-borne zoonotic pathogens commonly found co-circulating in Ixodes scapularis and Peromyscus leucopus populations. The restricted distribution and lower prevalence of Bm has been historically attributed to lower host-to-tick transmission efficiency and limited host ranges. We hypothesized that prevalence patterns are driven by coinfection dynamics and vertical transmission. We use a multi-year, multiple-location, longitudinal dataset with mathematical modelling to elucidate coinfection dynamics between Bb and Bm in natural populations of P. leucopus, the most competent reservoir host for both pathogens in the eastern USA. Our analysis indicates that, in the absence of vertical transmission, Bb is viable at lower tick numbers than Bm. However, with vertical transmission, Bm is viable at lower tick numbers than Bb. Vertical transmission has a particularly strong effect on Bm prevalence early in the active season while coinfection has an increasing role during the nymphal peak. Our analyses indicate that coinfection processes, such as facilitation of Bm infection by Bb, have relatively little influence on the persistence of either parasite. We suggest future work examines the sensitivity of Bm vertical transmission and other key processes to local environmental conditions to inform surveillance and control of tick-borne pathogens.

Data from: Evaluating the importance of individual heterogeneity in reproduction to Weddell seal population dynamics using integral projection models

<ol> <li>Identifying and accounting for unobserved individual heterogeneity in vital rates in demographic models is important for estimating population-level vital rates and identifying diverse life-history strategies, but much less is known about how this individual heterogeneity influences population dynamics.</li> <li>We aimed to understand how the distribution of individual heterogeneity in reproductive and survival rates influenced population dynamics using vital rates from a Weddell seal population by altering the distribution of individual heterogeneity in reproduction, which also altered the distribution of individual survival rates through the incorporation of our estimate of the correlation between the two rates and assessing resulting changes in population growth.</li> <li>We constructed an integral projection model (IPM) structured by age and reproductive state using estimates of vital rates for a long-lived mammal that has recently been shown to exhibit large individual heterogeneity in reproduction. Using output from the IPM, we evaluated how population dynamics changed with different underlying distributions of unobserved individual heterogeneity in reproduction.</li> <li>Results indicate that the changes to the underlying distribution of individual heterogeneity in reproduction cause very small changes in the population growth rate and other population metrics. The largest difference in the estimated population growth rate resulting from changes to the underlying distribution of individual heterogeneity was less than 1%.</li> <li>Our work highlights the differing importance of individual heterogeneity at the population level compared to the individual level. Although individual heterogeneity in reproduction may result in large differences in the lifetime fitness of individuals, changing the proportion of above- or below-average breeders in the population results in much smaller differences in annual population growth rate. For a long-lived mammal with stable and high adult-survival that gives birth to a single offspring, individual heterogeneity in reproduction has a limited effect on population dynamics. We posit that the limited effect of individual heterogeneity on population dynamics may be due to canalization of life-history traits.</li> </ol>

National forest inventory data for a size-structured forest population model

In forest communities, light competition is a key process for community assembly. Species' differences in seedling and sapling tolerance to shade cast by overstory trees is thought to determine species composition at late-successional stages. Most forests are distant from these late-successional equilibria, impeding a formal evaluation of their potential species composition. To extrapolate competitive equilibria from short-term data, we therefore introduce the JAB model, a parsimonious dynamic model with interacting size-structured populations, which focuses on sapling demography including the tolerance to overstory competition. We apply the JAB model to a two-"species" system from temperate European forests, i.e. the shade-tolerant species Fagus sylvatica L. and the group of all other competing species. Using Bayesian calibration with prior information from external Slovakian national forest inventory (NFI) data, we fit the JAB model to short timeseries from the German NFI. We use the posterior estimates of demographic rates to extrapolate that F. sylvatica will be the predominant species in 94% of the competitive equilibria, despite only predominating in 24% of the initial states. We further simulate counterfactual equilibria with parameters switched between species to assess the role of different demographic processes for competitive equilibria. These simulations confirm the hypothesis that the higher shade-tolerance of F. sylvatica saplings is key for its long-term predominance. Our results highlight the importance of demographic differences in early life stages for tree species assembly in forest communities.

Data for: Coupling dynamic energy budget and population dynamic models to inform stock enhancement in fisheries management

Extensive applications of fishery stock enhancement worldwide bring up broad concerns about its negative effects, creating a pivotal need for science-based assessment and planning of enhancement strategies. However, the lack of mechanistic understanding of enhanced population dynamics, particularly the density-dependent processes, leads to compromise in model development and limits the capacity in predicting enhancement effects. Here, we developed an individual-based model based on dynamic energy budget theory and full life history processes, to understand the mechanism of density dependence in population dynamics that emerge from individual-level processes. We demonstrated the utility of the model framework by applying it to an extensively enhanced species, Chinese prawn (Fenneropenaeus chinensis, Penaeidae). The model could yield projections reflecting the observed trajectory of population biomass and yields. The model also delineated the key effects of density dependence on the vital rates of growth, fecundity, and starvation mortality. Regarding the manifold effects of stock enhancement, we demonstrated a dampened shape in population biomass and yields with increasing magnitude of enhancement, and trade-offs between the ecological and economic objectives, i.e., pursuing high benefit might compromise the wild population without proper management. Furthermore, we illustrated the possibility of combining stock enhancement and harvest regulation in promoting population recovery while maintaining fisheries yields. We highlight the potential of the proposed model for understanding density dependence in enhancement program, and for designing integrated management strategies. The approach developed herein may serve as a general approach to assess the population dynamics in stock enhancement and inform enhancement management.

opencc-by-4.0May 2023View details →

Analysis - Threatened North African seagrass meadows have supported green turtle populations for millennia

Scripts and data to run bagplots and discriminant analysis associated with the paper: Threatened North African seagrass meadows have supported green turtle populations for millennia, de Kock et al.

Life on the edge: A new toolbox for population-level climate change vulnerability assessments

Global change is impacting biodiversity across all habitats on earth. New selection pressures from changing climatic conditions and other anthropogenic activities are creating heterogeneous ecological and evolutionary responses across many species' geographic ranges. Yet we currently lack standardised and reproducible tools to effectively predict the resulting patterns in species vulnerability to declines or range changes. We developed an informatic toolbox that integrates ecological, environmental and genomic data and analyses (environmental dissimilarity, species distribution models, landscape connectivity, neutral and adaptive genetic diversity and Genotype-Environment Associations) to estimate population vulnerability. In our toolbox, functions and data structures are coded in a standardised way so that it is applicable to any species or geographic region where appropriate data are available, for example individual or population sampling and genomic datasets (e.g. RAD-seq, ddRAD-seq, whole genome sequencing data) representing environmental variation across the species geographic range. We apply our toolbox to a georeferenced genomic dataset for the East African spiny reed frog (Afrixalus fornasini) to predict population vulnerability, as well as demonstrating that range loss projections based on adaptive variation can be accurately reproduced using data for two European bat species (Myotis escalerai, and M. crypticus). Our framework sets the stage for large scale, multi-species genomic datasets to be leveraged in a novel climate change vulnerability framework to quantify intraspecific differences in genetic diversity, local adaptation, range shifts and population vulnerability based on exposure, sensitivity, and range shift potential.

Figure 5 Nav kdr 1016 and 1534 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 5 Nav kdr 1016 and 1534 site allele frequencies in UEL. Collection site locations were distributed in the three regions of the campus.

Figure 4 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 4 Allele frequencies of Nav kdr 1016 and 1534 genotyping distributed in the five different regions of Londrina.

Figure 3 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 3 Haplotypic network obtained through specimens collected in UEL. The circles are proportional to the number of specimens observed in each haplotype.

Figure 2 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 2 Haplotype network observed in five regions of Londrina. The circles are proportional to the number of specimens observed in each haplotype. The haplotypes observed are in bold. The numbers represent nucleotide change positions.

Figure 1 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 1 Collection sites in Londrina. The red line is a boundary between the five regions of the city. The yellow ones represent the streets and avenues of the city. Only the urban area was evaluated in the study.

opencc-by-4.0Jan 2020View details →

Figure 1 in Molecular characterization of Bacillus thuringiensis strains to control Spodoptera eridania (Cramer) (Lepidoptera: Noctuidae) population

Figure 1 Mortality of S. eridania caterpillars caused by different B. thuringiensis (Bt) strains with a concentration of 108 spores/mL after 7 days of bioassay.Means followed by the same letter did not differ statistically by Scott-Knott test at 1% significance (p <0.01).

opencc-by-4.0Jan 2020View details →

Figure 2 in Molecular characterization of Bacillus thuringiensis strains to control Spodoptera eridania (Cramer) (Lepidoptera: Noctuidae) population

Figure 2 Fingerprint patterns for ERIC-PCR (A) and REP-PCR (B) fragments of selected B. thuringiensis strains isolated in different locations. M = 1 kb Plus DNA ladder.

opencc-by-4.0Dec 2023View details →

Fig. 3 in Reduction Of The Breeding Population Of The Rook, Corvus Frugilegus (Aves, Corvidae), In Ukraine: The Example Of The Eastern Part Of The Kyiv Region

Fig. 3. Kernel Density Estimation of number of the rook breeding group in the research area in 1983–1985 (A), and in 2021 (B). The highest density areas are highlighted in red; the lowest density areas are green.