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1,068 results for “demographic”
Data for: Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation
<p>Data for:</p> <p>Houde P, Braun EL, Zhou L. 2020. Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation. Diversity, in review</p> <p>**************************************************<br> The .tar.gz file will expand to yield a directory named "Houde_Braun_Zhou_data_files". That directory has three subdirectories:</p> <p>1. alignments<br> 2. indel_matrices<br> 3. trees</p> <p>The Houde_Braun_Zhou_data_files directory also includes a README.txt file with complete details regarding the contents of each subdirectory.</p>
Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments
<p>Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous <i>versus</i> evergreen forests and insular <i>versus</i> mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (<i>F</i><sub>ST</sub> = 0.004 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long-lasting gene flow between populations, inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (<i>F</i><sub>ST</sub> = 0.08 on average), in line with the inference of moderate ancestral migrations, followed by isolation since the end of the last glaciation. Effective population sizes were overall large, yet smaller on the island than on the mainland. Weak and non-parallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular <i>versus</i> mainland birds, and were more often found in regions of low recombination as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.</p>
Population genetic structure and demographic history of the lone star tick, Amblyomma americanum (Ixodida: Ixodidae): new evidence supporting old records
Range expansions are a potential outcome of climate change. Population genetic structure and demography can be used as tools to evaluate hypotheses on changes in geographic distribution. In this study we explored the genetic variability, population genetic structure, demographic history, and habitat suitability of Amblyomma americanum, a North American tick species that is a known vector of several pathogenic microorganisms. We used a novel double digestion restriction site-associated DNA sequencing (dd-RAD seq), and we discovered 8181 independent single nucleotide polymorphisms (SNPs) from 189 ticks from across the geographic range of the species. Overall, genetic diversity was lower than expected. Further, the edge populations did not have a statistically significant lower diversity than core populations, and hypotheses of range expansion are not supported by a test based on genetic data. Nonetheless, moderate levels of population structure were detected among geographic regions, with the northeast cluster the least variable. Demographic and species distribution models support a scenario where A. americanum was present in more northern locations in the past, underwent a bottleneck, and is now recovering. These findings highlight the importance of demographic modeling and genomic data in assessing the recent history and genetic structure of pathogen vectors.
Data from: Environmental context determines the limiting demographic processes for plant recruitment across a species' elevational range
<p>Plant recruitment is a multi-stage process determining population dynamics and species distributions. Still, we have limited understanding of how the successive demographic processes depend on the environmental context across species' distributional ranges. We conducted a large-scale transplant experiment to study recruitment of <i>Pinus cembra</i> over six years. We quantified the effects of environmental conditions on four demographic processes and identified the most limiting across and beyond the pines' elevational range over several years. Realized transition probabilities of the demographic processes varied substantially across the species' distributional range. Seed deposition decreased from the lower to the upper elevational range margin by 90 %, but this reduction was offset by increased seed germination and seedling survival. Dispersal limitation at the upper range margin potentially stems from unsuitable seed caching conditions for the animal seed disperser, whereas increased seed germination might result from enemy escape from fungal pathogens and favourable abiotic conditions at the upper range margin. Our multi-year experiment demonstrates that environmental context is decisive for the local relevance of particular demographic processes. We conclude that experimental studies identifying the limiting demographic processes controlling species distributions are key for projecting future range dynamics of plants.</p>
Demographic analysis for article Hurricane-induced demographic changes in a nonhuman primate population
<p><span><span><span><span><span><span><span><span><span><span><span>Major disturbance events can have large impacts on the demography and dynamics of animal populations. Hurricanes are one example of an extreme climatic event, predicted to increase in intensity due to climate change, and thus expected to be a considerable threat to population viability. However, <span><span>little is understood about the </span></span>underlying demographic mechanisms shaping population response following these extreme disturbances. Here, we analyze 45 years of the most comprehensive free-ranging nonhuman primate demographic dataset to determine the effects of major hurricanes on the variability and maintenance of long-term population fitness. For this, we use individual-level data to build matrix population models and perform perturbation analyses. Despite reductions in population growth rate mediated through reduced fertility, our study reveals a demographic buffering during hurricane years. As long as survival does not decrease, our study shows that hurricanes do not result in detrimental effects at the population level, demonstrating the unbalanced contribution of survival and fertility to population fitness in long-lived animal populations.</span></span></span></span></span></span></span></span></span></span></span></p>
Latitudinal gradients in population growth do not reflect demographic responses to climate
<p>Spatial gradients in population growth, such as across latitudinal or elevational gradients, are often assumed to primarily be driven by variation in climate, and are frequently used to infer species' responses to climate change. Here, we use a novel demographic, mixed model approach to dissect the contributions of climate variables vs. other latitudinal or local site effects on spatiotemporal variation in population performance in three perennial bunchgrasses. For all three species, we find that performance of local populations decreases with warmer and drier conditions, despite latitudinal trends of decreasing population growth towards the cooler and wetter northern portion of each species' range. Thus, latitudinal gradients in performance are not predictive of either local or species-wide responses to climate. This pattern could be common, as many environmental drivers, such as habitat quality or species' interactions, are likely to vary with latitude or elevation, and thus influence or oppose climate responses.</p>
Data from: Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula
The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from Approximate Bayesian Computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately 5 effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. 5 individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.
Data from: The influence of climate variability on demographic rates of avian Afro-palearctic migrants
<p>Climate is an important driver of changes in animal population size, but its effect on the underlying demographic rates remains insufficiently understood. This is particularly true for avian long-distance migrants which are exposed to different climatic factors at different phases of their annual cycle. To fill this knowledge gap, we used data collected by a national-wide bird ringing scheme for eight migratory species wintering in sub-Saharan Africa and investigated the impact of climate variability on their breeding productivity and adult survival. While temperature at the breeding grounds could relate to the breeding productivity either positively (higher food availability in warmer springs) or negatively (food scarcity in warmer springs due to trophic mismatch), water availability at the non-breeding should limit the adult survival and the breeding productivity. Consistent with the prediction of the trophic mismatch hypothesis, we found that warmer springs at the breeding grounds were linked with lower breeding productivity, explaining 29% of temporal variance across all species. Higher water availability at the sub-Saharan non-breeding grounds was related to higher adult survival (18% temporal variance explained) but did not carry-over to breeding productivity. Our results show that climate variability at both breeding and non-breeding grounds shapes different demographic rates of long-distance migrants.</p>
Demographic Profile for Decreasing the Rate of Motorcycle Accidents in Malaysia Survey
<p>Table 2: Demographic profile of the survey</p>
Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal
<p>Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development, reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a factor-analytic approach to capture partially unobserved drivers of seasonal population dynamics. We use 40 years of individual-based demography from yellow-bellied marmots (Marmota flaviventer) to fit and project population models that account for seasonal demographic covariation using a latent variable. We show that this latent variable, by producing positive covariation among winter demographic rates, depicts a measure of environmental quality. Simultaneous, negative responses of winter survival and reproductive-status change to declining environmental quality result in a higher risk of population quasi-extinction, regardless of summer demography where recruitment takes place. We demonstrate how complex environmental processes can be summarized to understand population persistence in seasonal environments.</p>
Study on the correlation of prevalence of ocular disease to different demographic variables, medical history and concomitant diseases.
<p>Random blood sugar, cholesterol, and triglycerides were analyzed by taking the blood sample from each patient. The average of the parameters was recorded, and the standard deviation (SD) was calculated. The parameters have been presented in the study as mean± SD. Blood sample analysis revealed that the average random blood glucose level (mg/dl) was 113.3±26.9 (Mean ±SD). The average cholesterol level was 189.35± 49.7 mg/dl, and the average triglycerides level was 124.25±50.0 mg/dl. Average systolic and diastolic blood pressure was found to be 126.0 ± 15.5 mmHg and 81.43 ± 8.0 mmHg, respectively. The patients were examined by the dermatologist. The dermatologists observed the signs, and the patients were asked about the presence of the symptoms to evaluate the severity of psoriasis and psoriatic arthropathy. The patients were asked about the duration for which they had been suffering from psoriasis. On average, a patient was found to be suffering from psoriasis for 11.4 ±9.9 years (the duration ranged from a minimum of 1 year to a maximum of 45 years). The doctor screened the patients for the number of sites involved and evaluated the severity of psoriasis via psoriasis area and severity index (PASI) score. Average Psoriasis Area and Severity Index (PASI) for the patients, as recorded by the dermatologists, was found to be 5.94 ± 6.8. </p>
Demographics of Galaxies in the Nearby Universe: A case study with AGN and post-mergers
<p>Here I present a volume limited catalog of ~113,600 visually classified galaxies from SDSS and the NOAO legacy survey. The classifications include identifications of bars, rings, spiral arms, tidal tails, etc. I compare my classifications to those from other crowd sourced surveys and machine learning based catalogs to verify classification accuracy. Using this catalog, I will show results on the systematics which affect quantitative/ML classifications and implications for the Nancy Grace Roman space telescope galaxy surveys. Time permitting I will discuss (a) bar fractions in the local Universe and role of close pair interactions in triggering bars (b) the role of mergers in triggering AGN and the frequency of dual AGN in the local Universe.</p>
Data from: Demographic traits improve predictions of spatiotemporal changes in community resilience to drought
<ol> <li>Communities are increasingly threatened by extreme weather events. The cumulative effects of such events are typically investigated by assessing community resilience,<i> i.e.</i>, the extent to which affected communities can achieve pre-event states. However, a mechanistic understanding of the processes underlying resilience is frequently lacking and requires linking various measures of resilience to demographic responses within natural communities.</li> <li>Using 13 years of data from a shrub community that experienced a severe drought in 2005, we use generalized additive models to investigate temporal changes in three measures of resilience. We assess whether community-weighted, species-specific demographic traits such as longevity and reproductive output can predict changes in resilience and how the performance of these traits compares to more commonly used plant functional traits such as leaf area or root dry-matter content.</li> <li>We find significant spatiotemporal variation in community dynamics after the drought. Overall, demographic traits are better at predicting absolute and relative resilience in total plant cover, but functional traits outperform demographic traits when resilience in community composition is assessed. All resilience measures show non-linear and context-specific responses to demographic and functional traits; and these responses depend strongly on the severity of initial drought impact.</li> <li> <i>Synthesis</i>: Our work demonstrates that a full picture of the mechanisms underlying community responses to drought requires the assessment of numerous species-specific characteristics (including demographic and functional traits) and how these characteristics differentially affect complementary measures of community changes through time. </li> </ol>
Data from: What makes a leaf tough? Patterns of correlated evolution between leaf toughness traits and demographic rates among 197 shade-tolerant woody species in a neotropical forest
Slow-growing juveniles of shade-tolerant plant species are predicted to have tough leaves because of the high cost of leaf replacement in shade relative to potential carbon gain. We assessed the degree of correlated evolution among eight traits associated with leaf toughness and their relationships with growth and mortality rates of 197 tree and shrub species from the understory of the 50-hectare forest dynamics plot on Barro Colorado Island, Panama. Path analysis with phylogenetically independent contrasts revealed that leaves attained material toughness (resistance to fracture per unit fracture area) through increases in tissue density, percent cellulose per unit dry mass, and vein fracture toughness. Lamina density and cellulose content evolved independently, and thus represent different paths to material toughness. Structural toughness (resistance to fracture per unit fracture length) depended on material toughness and lamina thickness. Mortality rates of individuals 1-10 cm in stem diameter were negatively correlated with material toughness and lamina density, but were independent of structural toughness and cell wall fiber contents. Leaf toughness traits were uncorrelated with relative growth rates. These results imply that material toughness enhances resistance to natural enemies, which increases survival and offsets the biomass allocation cost of producing tough leaves in the shaded understory.
Data from: Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig-pollinating wasp mutualism
Historical abiotic factors such as climatic oscillations and extreme climatic events as well as biotic factors have shaped the structuring of species' genetic diversity. In obligate species-specific mutualisms, the biogeographic histories of the interacting species are tightly linked. This could be particularly true for nuclear genes in the Ficus-pollinating wasp mutualistic association as the insects disperse pollen from their natal tree. In this study we compare spatial genetic structure of plant and pollinator for the Ficus hirta-Valisia javana association throughout South-East China including Hainan Island, for both nuclear and cytoplasmic markers. We show that dispersal of the insect leads to plant and insect presenting similar signatures of lack of genetic isolation by distance for nuclear genes on the continent over a distance of 1000 km. But we also show that the demographic histories of plant and insect are strikingly different. This is in agreement with extreme climatic events leading to transient regional extinctions of the insects, associated with local survival of the plants. We also evidence genetic differentiation for both wasps and fig-tree between the continent and Hainan Island, although the Qiongzhou Strait is only on average 30 km wide suggesting that geographic isolation by itself has not been sufficient to generate this differentiation. Hence, our results suggest that in highly dispersive mutualistic systems, isolation by dispersal limitation across a geographic barrier could be supplemented by isolation by adaptation, and maybe by coevolution, allowing further genetic divergence. In such systems, species may frequently be composed of a single population.
Data from: Mitochondrial introgressive hybridization following a demographic expansion in the tomato frogs of Madagascar, genus Dyscophus
Madagascar is a biodiversity hotspot with a unique fauna and flora largely endemic at the species level and highly threatened by habitat destruction. The processes underlying population-level differentiation in Madagascar's biota are poorly understood and have been proposed to be related to Pleistocene climatic cycles, yet the levels of genetic divergence observed are often suggestive of ancient events. We combined molecular markers of different variability to assess the phylogeography of Madagascar's emblematic tomato frogs (Dyscophus guineti and D. antongilii) and interpret the observed pattern as resulting from ancient and recent processes. Our results suggest that the initial divergence between these taxa is probably old as reflected by protein-coding nuclear genes and by a strong mitochondrial differentiation of the southernmost population. Dramatic changes in their demography appear to have been triggered by the end of the last glacial period and possibly by the short return of glacial conditions known as the 8K event. This dramatic change resulted in an approximately 50-fold reduction of the effective population size in various populations of both species. We hypothesize these species' current mitochondrial DNA diversity distribution reflects a swamping of the mitochondrial genetic diversity of D. guineti by that of D. antongilii previous to the populations' bottlenecks during the Holocene, and probably as a consequence of D. antongilii demographic expansion approximately 1 million years ago. Our data support the continued recognition of D. antongilii and D. guineti as separate species and flag D. guineti as the more vulnerable species to past and probably also future environmental changes.
Data from: Maintenance of genetic diversity in an introduced island population of Guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation
Fifteen Guanacos were introduced to Staats Island in Falklands/Malvinas archipelago from Patagonia in the 1930s. After introduction, the Guanaco population increased to almost 400 animals that retained a footprint of the founding effect and bottleneck reflected in the genetic status of this isolated population. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulation, and (ii) assess the likely source population of the introduced Guanacos. Genetic variation estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci were compared among 154 Guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variation on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island Guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation.
Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern
The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using Isolation-with-Migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The Likelihood Ratio Test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia, and define this species as a single evolutionarily significant unit for conservation purposes.
Data from: Demographic history inferred from genome-wide data reveals two lineages of sheldgeese endemic to a glacial refugium in the southern Atlantic
Aim: The Malvinas/Falkland Islands (MFI) constitute the largest archipelago in the southern Atlantic, and harbour endemic lineages that presumably evolved after sea-level rise, associated with glacial periods, isolated ancestral populations. We investigate the role of the MFI in isolating populations from continental counterparts of two highly vagile species: the sheldgeese Chloephaga picta and Chloephaga rubidiceps. Location: Patagonia and the Malvinas/Falkland Islands. Methods: We sampled C. picta and C. rubidiceps on the continent and MFI. Using a reduced-representation genomic approach, we quantified the genetic differentiation between insular and continental populations of both species, and used coalescent-based analyses to model their demography. Results: The MFI harbour independently evolving lineages of C. picta and C. rubidiceps, which diverged from their continental counterparts during the Middle-Late Pleistocene and have since experienced negligible gene flow. Main conclusions: The c. 450 km that separate the archipelago from the continent are sufficient to isolate populations of these putatively highly vagile species. Ancestral lineages may have reached the MFI refugium during glacial cycles. Without conservation measures, the drastic decline of the morphologically, behaviourally and ecologically distinct continental population of C. rubidiceps, to < 1000 individuals, may lead to the extinction of an independently evolving taxon.
Data from: Environmental and demographic drivers of male mating success vary across sequential reproductive episodes in a polygynous breeder
Ecological and social factors underpinning the inequality of male mating success in animal societies can be related to sex ratio, sexual conflict between breeders, effects of non-breeders, resource dispersion, climatic conditions, and the various sequential stages of mating competition that constitute the sexual selection process. Here, we conducted an individual-based study to investigate how local resource availability and demography interact with annual climate conditions to determine the degree of male mating inequality, and thus opportunity for sexual selection across two sequential reproductive episodes (harem and subsequent mate acquisition) in a naturally regulated (feral) horse population in Sable Island National Park Preserve, Canada. Using a 5-year, spatially explicit, mark-resight dataset and hierarchical mixed-effects linear modelling, we evaluated the influence of adult sex ratio (ASR) on mating success, and then tested for effects of freshwater availability, density, unpaired male abundance, and precipitation during each breeding season. Unpaired male abundance, freshwater availability, and ASR differed in their effects on male mating success according to year and selection episode. Opportunity for sexual selection in males associated with harem acquisition increased with ASR, and unpaired male abundance further explained weather-related inter-annual variation after accounting for ASR. In contrast, once a harem was secured, ASR had little effect on male mating inequality in regards to acquiring additional females, while inter-annual variation in mating inequality increased with decreasing freshwater availability. Our findings show that local demography, resource availability, and weather effect opportunity for sexual selection in males differently depending on selection episode, and can attenuate or accentuate effects of ASR.
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Allen Brain Atlas
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