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1,068 results for “demographic”
Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe
<p>Understanding the biological processes involved in genetic differentiation and divergence between populations within species is a pivotal aim in evolutionary biology. One particular phenomenon that requires clarification is the maintenance of genetic barriers despite the high potential for gene flow in the marine environment. Such patterns have been attributed to limited dispersal or local adaptation, and to a lesser extent to the demographic history of the species. The corkwing wrasse (<i>Symphodus melops</i>) is an example of a marine fish species where regions of particular strong divergence are observed. One such genetic break occurred at a surprisingly small spatial scale (<i>F</i><sub>ST</sub> ~0.1), over a short coastline (<60 km) in the North Sea-Skagerrak transition area in southwestern Norway. Here, we investigate the observed divergence and purported reproductive isolation using genome resequencing. Our results suggest that historical events during the post-glacial recolonization route can explain the present population structure of the corkwing wrasse in the northeast Atlantic. While the divergence across the break is strong, we detected ongoing gene flow between populations over the break suggesting recent contact or negative selection against hybrids. Moreover, we found few outlier loci and no clear genomic regions potentially being under selection. We concluded that neutral processes and random genetic drift e.g., due to founder events during colonization have shaped the population structure in this species in Northern Europe. Our findings underline the need to take into account the demographic process in studies of divergence processes.</p>
Data from: Balancing food acquisition and predation risk drives demographic changes in snowshoe hare population cycles
<p>Snowshoe hare cycles are one of the most prominent phenomena in ecology. Experimental studies point to predation as the dominant driving factor, but previous experiments combining food supplementation and predator removal produced unexplained multiplicative effects on density. We examined the potential interactive effects of food limitation and predation in causing hare cycles using an individual based food-supplementation experiment over-winter across three cycle phases that naturally varied in predation risk. Supplementation doubled over-winter survival with the largest effects occurring in the late increase phase. Although the proximate cause of mortality was predation, supplemented hares significantly decreased foraging time and selected for conifer habitat, potentially reducing their predation risk. Supplemented hares also lost less body mass which resulted in the production of larger leverets. Our results establish a mechanistic link between how foraging time, mass loss, and predation risk affect survival and reproduction, potentially driving demographic changes associated with hare cycles.</p>
Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations
<p><span>Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (<em>Pagophila eburnea</em>), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (approximately 1000 ind.), suggesting that the evolutionary potential of the species is not assured.</span></p>
Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
<p>Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to study demographic history and reduced representation (ddRAD) sequencing data to analyze spatial genetic structure in the broadnosed pipefish (<em>Syngnathus typhle</em>). Its main habitat are seagrass meadows, which along the study coast (SW Norway) have a patchy distribution. Combining the results from several analyses including scans for selection, suggests that stochastic genetic drift has shaped the observed population structure largely due to its patchy habitat distribution. The restricted gene flow is further driven by life history traits such as the presence of parental care combined with no pelagic life stages, resulting in a clear isolation-by-distance pattern spanning 100s of kilometers.</p> <p>The spatial scale of demographic connectivity was inferred from long-term (~30 year) census population counts that uncovered a sharp decline in spatial correlations in abundance with distance (37% decorrelation over 2 km). These findings were contrasted with data from two other fish species sampled along the same coastline, both having pelagic larval stages lasting ~20 days (corkwing wrasse, <em>Symphodus melops</em>, and black goby, <em>Gobus niger</em>) where the population structure is not that evident. For these species, we found a wider spatial scale of demographic connectivity (decorrelation distances of 14 and 28 km, respectively), and weaker isolation-by-distance except at one point along the coast where both species revealed a strong barrier to gene flow, seemingly due to a lack of suitable habitat. Combined, these findings suggest that habitat fragmentation and absence of a pelagic larval stage in pipefish strongly increases geographic structuring, while the pelagic larvae of wrasse and goby increase genetic and demographic connectivity, except over extensive habitat shifts.</p>
Data from: Two dimensions of demographic differentiation of species in a mountain grassland community: an experimental test
1. There is remarkable variation in life histories of coexisting plant species. These 'alternative designs' for the given set of environmental conditions are likely to play a role in species niche differences and thus may underlie species coexistence, although there is no clear demonstration of it. Currently available data on within-community differentiation concern primarily easy and measurable traits that are not fully informative of life history variation. Their relevance for functional differentiation of species and species coexistence is far from clear. 2. Here we examined differentiation of coexisting species in demographic parameters and how it determines species' response to neighbors. We determined these parameters for a set of 21 co-occurring species by fitting a process-based model to a long-term (30 yrs) data series of shoot counts. We examined the functional relevance of these parameters using a field experiment. We further asked with which functional traits they are correlated. 3. Species were differentiated along two largely independent axes: (i) slow vs. fast, separating species according to instantaneous growth rate, competitive response and intraspecific density dependence; and (ii) dispersal vs. local dynamics, which separated species with strong dispersal (by seeds or vegetative) from species that tended to stay in the occupied spot. While the slow-fast axis was associated with commonly used leaf and seed traits, the dispersal axis was best predicted by lateral spreading distance. 4. Each of these two axes predicted different components of species' responses to neighbor competition: the slow-fast axis was a good predictor of the short-term response, whereas dispersal axis was a good predictor of the long-term response. 5. Synthesis. Demographic differentiation of coexisting species resembles to an important degree demographic differentiation known from large-scale comparisons. This differentiation is functionally meaningful also at the fine scale; its role in species' responses to competition implies it is involved in species niche differentiation and coexistence. While seed and leaf traits are important correlates of demographic differentiation, a hitherto underappreciated trait, viz. lateral spreading distance, is an important predictor of the dispersal axis at the fine-scale and should be more widely used.
Demographic rates and stature of tree species in 13 sub-tropical forests: annual growth, annual survival, annual recruitment >( 1 cm dbh), stature (max dbh)
<p>Organisms of all species must balance their allocation to growth, survival and recruitment. Among tree species, evolution has resulted in different life-history strategies for partitioning resources to these key demographic processes. Life-history strategies in tropical forests have often been shown to align along a trade-off between fast growth and high survival, i.e. the well-known fast-slow continuum. In addition, an orthogonal trade-off has been proposed between tall stature – resulting from fast growth and high survival – and recruitment success, i.e. a stature−recruitment trade-off. However, it is not clear if these two independent dimensions of life-history variation structure tropical forests worldwide.</p> <p>We used data from 13 large-scale and long-term tropical forest monitoring plots in three continents to explore the principal trade-offs in annual growth, survival and recruitment as well as tree stature. These forests included relatively undisturbed forests as well as typhoon-disturbed forests. Life-history variation in twelve forests was structured by two orthogonal trade-offs, the growth−survival trade-off and the stature−recruitment trade-off. Pairwise Procrustes analysis revealed a high similarity of demographic relationships among forests. The small deviations were related to differences between African and Asian plots.</p> <p><em>Synthesis</em>. The fast-slow continuum and tree stature are two independent dimensions structuring many, but not all tropical tree communities. Our discovery of the consistency of demographic trade-offs and life-history strategies across different forest types from three continents substantially improves our ability to predict tropical forest dynamics worldwide.</p>
Demographic data, anthropometric measurements, and clinical parameters
<p>Demographic data, anthropometric measurements, and clinical parameters</p>
Socio-demographic, institutional and governance factors influencing adaptive capacity of smallholder irrigation schemes
<p>Socio-demographic, institutional and governance factors influencing adaptive capacity of smallholder irrigation schemes</p>
Genomic data reveal the biogeographic and demographic history of Ammospiza sparrows in northeast tidal marshes
<p><b><i>Aim: </i></b>Shaped by both climate change and sea-level rise, tidal salt marshes represent ephemeral systems that are home to only a few, highly specialized species. The dynamic ecological histories and spatial complexities of these habitats, however, render it challenging to reconstruct the complete biogeographic histories of their endemic taxa. Here, we leverage three species of North American <i>Ammospiza </i>sparrows that inhabit tidal marshes ( <i>Ammospiza caudacuta</i>, <i>A. maritima</i>, and <i>A. n. subvirgatus</i>) and closely related freshwater species to demonstrate the utility of whole-genome data in resolving demographic and evolutionary history as it relates to divergence and dispersal events in ephemeral ecosystems. We employ a combination of demographic and biogeographic reconstructions to shed new light on the colonization history of freshwater-saline environments in this system.</p> <p><b><i>Location: </i></b>North America</p> <p><b><i>Taxon: </i></b> <i>Ammospiza Sparrows</i></p> <p><b><i>Methods: </i></b>We sequenced whole genomes from <i>Ammospiza </i>sparrows to address our objectives. We conducted phylogenomic analyses and reconstructed the demographic and biogeographic history of this clade based on 21 million SNPs from 54 total individuals.</p> <p><b><i>Results: </i></b>Phylogenies based on several million SNPs supported several well-resolved clades that predominantly corresponded to their prior species designations. Phylogenetic and biogeographic reconstructions suggest a series of saltwater to freshwater colonization events within this group, with some endemic taxa exhibiting associations with tidal marsh habitat over longer evolutionary time scales and some habitat transitions occurring as recently as 5,000 years ago. </p> <p><b><i>Main Conclusions: </i></b>Our reconstructions support a biogeographic hypothesis with fewer vicariance and dispersal events among <i>Ammospiza </i>sparrows that is in contrast with the currently supported evolutionary scenario. Biogeographic reconstructions further suggest saltwater to freshwater transitions in <i>A. n. subvirgatus </i>as opposed to the long hypothesized freshwater origin. Our results highlight the fact that reconstructing biogeographic and evolutionary dynamics in ephemeral systems poses challenges given the propensity for high turnover. This reinforces the importance of a multifaceted approach to biogeographic reconstructions in historically dynamic ecosystems.</p>
Data from: Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history
Estimates of inbreeding and relatedness are commonly calculated using molecular markers, although the accuracy of such estimates has been questioned. As a further complication, in many situations, such estimates are required in populations with reduced genetic diversity, which is likely to affect their accuracy. We investigated the correlation between microsatellite- and pedigree-based coefficients of inbreeding and relatedness in laboratory populations of Drosophila melanogaster that had passed through bottlenecks to manipulate their genetic diversity. We also used simulations to predict expected correlations between marker- and pedigree-based estimates and to investigate the influence of linkage between loci and null alleles. Our empirical data showed lower correlations between marker- and pedigree-based estimates in our control (nonbottleneck) population than were predicted by our simulations or those found in similar studies. Correlations were weaker in bottleneck populations, confirming that extreme reductions in diversity can compromise the ability of molecular estimates to detect recent inbreeding events. However, this result was highly dependent on the strength of the bottleneck and we did not observe or predict any reduction in correlations in our population that went through a relatively severe bottleneck of N = 10 for one generation. Our results are therefore encouraging, as molecular estimates appeared robust to quite severe reductions in genetic diversity. It should also be remembered that pedigree-based estimates may not capture realized identity-by-decent and that marker-based estimates may actually be more useful in certain situations.
The unequal impact of the COVID-19 pandemic in 2020 on life expectancy across urban areas in Chile: A cross-sectional demographic study
<p>Data accompanying the paper The unequal impact of the COVID-19 pandemic in 2020 on life expectancy across urban areas in Chile: A cross-sectional demographic study, currently at https://www.medrxiv.org/content/10.1101/2021.12.08.21267475v1</p>
Data from: Harvesting has variable effects on demographic rates and population growth across three dry forest tree species
<p>Understanding how anthropogenic activities, such as harvesting, influence plant populations is important to quantify sustainable practices that conserve species of socioeconomic importance. There is limited knowledge on how harvesting of branches and non-timber forest products affect populations of trees in the dry tropics. We measure demographic vital rates of three dry tropical tree species in the presence and absence of harvesting and apply integral projection models to quantify population growth rates, which represent the mean fitness across the life cycle. Our results show that the three species vary in their demographic rates and life history. Harvesting significantly decreases the growth of two species. Current levels of harvesting only significantly decreased the population growth rate of one species that experienced both branch and main stem harvesting. Life table response experiments reveal that the negative effect of harvesting on the population growth rate of this species is primarily due to individuals being forced to re-sprout from their base. Few individuals were observed recruiting from seed, and this might be due to the presence of other threats, such as fire, soil erosion, and grazing. Our results provide knowledge on the demography and the effects of harvesting on endemic tree species of the Eastern Ghats, a region for which few demographic studies are available. These results are relevant to conserving forest biodiversity for the benefits of people and can contribute to quantitative threat assessment for IUCN red listing.</p>
Demographic data along with a comparison of α1-Antitrypsin, Interleukin-1β and Interleukin -6 levels measured in this study
<p><strong>Serum levels of α-1Antitrypsin, Interleukin-1β, and Interleukin-6 in Iraqi COVID-19 patients: A cross-Sectional Study, data set</strong></p>
Demographic responses to climate change in a threatened Arctic species
<p>The Arctic is undergoing rapid and accelerating change in response to global warming, altering biodiversity patterns and ecosystem function across the region. For Arctic endemic species, our understanding of the consequences of such change remains limited. Spectacled eiders (<i>Somateria fischeri</i>), a large Arctic sea duck, use remote regions in the Bering Sea, Arctic Russia, and Alaska throughout the annual cycle making it difficult to conduct comprehensive surveys or demographic studies. Listed as Threatened under the U.S. Endangered Species Act, understanding the species response to climate change is critical for effective conservation policy and planning. Here, we developed an integrated population model to describe spectacled eider population dynamics using capture-mark-recapture, breeding population survey, nest survey, and environmental data collected between 1992 and 2014. Our intent was to estimate abundance, population growth, and demographic rates, and quantify how changes in the environment influenced population dynamics. Abundance of spectacled eiders breeding in western Alaska has increased since listing in 1993 and responded more strongly to annual variation in first year survival than adult survival or productivity. We found both adult survival and nest success were highest in years following intermediate sea ice conditions during the wintering period, and both demographic rates declined when sea ice conditions were above or below average. In recent years sea ice extent has reached new record lows and has remained below average throughout the winter for multiple years in a row. Sea ice persistence is expected to further decline in the Bering Sea. Our results indicate spectacled eiders may be vulnerable to climate change and the increasingly variable sea ice conditions throughout their wintering range with potentially deleterious effects on population dynamics. Importantly, we identified that different demographic rates responded similarly to changes in sea ice conditions, emphasizing the need for integrated analyses to understand population dynamics.</p>
Demographics for all four breeds of broiler chickens
<p><span>In 2018, over nine billion chickens were slaughtered in the United States. As the demand for chickens increases, so too have concerns regarding the welfare of the chickens in these systems and the damage such practices cause to the surrounding ecosystems. To address welfare concerns, there is large-scale interest in raising chickens on pasture and switching to slower-growing, higher-welfare breeds as soon as 2024. We created a box model of US chicken demographics to characterize aggregate broiler chicken welfare and land use consequences at the country scale for US shifts to slower-growing chickens, housing with outdoor access, and pasture management. The US produces roughly 20 million metric tons of chicken meat annually. Maintaining this level of consumption entirely with a slower-growing breed would require a 44.6%–86.8% larger population of chickens and a 19.2% – 27.2% higher annual slaughter rate, relative to the current demographics of primarily "Ross 308" chickens that are slaughtered at a rate of 9.25 billion per year. Generating this quantity of slower-growing breeds in conventional concentrated animal feeding operations (CAFO) would require 90,582-98,687 km2, an increase of 19.9-30.6% over the 75,577 km2 of land used for current production of Ross 308. Housing slower-growing breeds on pasture, the more individually welfare-friendly option, would require </span><span>108,642-121,019 km2, a 43.8-60.1% increase over current land use. Allowing slower-growing breeds occasional outdoor access is an intermediate approach that would require 90,691-98,811 km2, an increase of 20-30.7% of the current land use, a very minor increase of land relative to managing slower-growing breeds in CAFOs. In sum, without a drastic reduction in consumption, switching to alternative breeds will lead to a substantial increase in the number of individuals killed each year, an untenable increase in land use, and a possible decrease in aggregate chicken welfare at the country-level scale. Pasture-based management requires substantial additional land use. These results demonstrate constraints and trade-offs in animal welfare, environmental conservation, and food animal consumption, while highlighting opportunities for policies to mitigate impacts in an integrated manner using a One Health approach.</span></p>
Data from: Genome-wide analysis reveals demographic and life history patterns associated with habitat modification in land-locked, deep-spawning sockeye salmon (Oncorhynchus nerka)
<p>Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography and life history of native biota, while disrupting the behaviour of species that are dependent on spatial connectivity to complete their life cycles. In the Alouette River system (British Columbia, Canada), dam construction in 1928 impacted passage of anadromous sockeye salmon (<i>Oncorhynchus nerka</i>), with the last records of migrants occurring in the 1930's. Since that time, <i>O. nerka</i> persisted as a resident population in Alouette Reservoir until experimental water releases beginning in 2005 created conditions for migration; two years later, returning migrants were observed for the first time in ~70 years, raising important basic and applied questions regarding life history variation and population structure in this system. Here, we investigated the genetic distinctiveness and population history of Alouette Reservoir <i>O. nerka</i> using genome-wide SNP data (n=7,709 loci) collected for resident and migrant individuals, as well as for neighbouring anadromous sockeye salmon and resident kokanee populations within the Fraser River drainage (n=312 individuals). Bayesian clustering and principal components analyses based on neutral loci revealed five distinct clusters, largely associated with geography, and clearly demonstrated that Alouette Reservoir resident and migrant individuals are genetically distinct from other <i>O. nerka</i> populations in the Fraser River drainage. At a finer-level, there was no clear evidence for differentiation between Alouette Reservoir residents and migrants; although we detected eight high-confidence outlier loci, they all mapped to sex chromosomes suggesting that differences were likely due to uneven sex ratios rather than life history. Taken together, these data suggest that contemporary Alouette Reservoir <i>O. nerka</i> represents a landlocked sockeye salmon population, constituting the first reported instance of deep-water spawning behaviour associated with this life history form. This finding punctuates the need for re-assessment of conservation status and supports on-going fisheries management activities in Alouette Reservoir. </p>
Data from: How do functional traits influence tree demographic properties in a subtropical monsoon forest?
<p><span>1. </span><span>Functional traits are good predictors of plant responses and adaptations to ever-changing environments. However, forecasting forest community dynamics is challenging because the relationships among different tree demographic properties (growth, mortality, and recruitment) and how functional traits are associated with tree demography remain largely unknown.</span></p> <p><span>2. </span><span>Here, in a 20-ha subtropical forest permanent plot, we quantified the rates of tree growth, mortality, and recruitment across 53 dominant tree species (diameter at breast height; DBH </span>≥<span> 1 cm) from 2005 to 2020. Functional traits that are closely related to plant photosynthesis, nutrients, hydraulics, and drought tolerance were measured. </span></p> <p><span>3. </span><span>We found that tree growth rate (GR) varied independently from rates of tree mortality and recruitment. Hydraulic conductivity was positively correlated with GR (explaining 27% variation – the strongest relationship observed) whereas wood density was negatively correlated with GR. Leaf life span was negatively related to tree mortality. Species with high carbon assimilation rate, nutrient concentration and hydraulic conductivity had high recruitment rates. Leaf turgor loss point was unrelated to plant demography. Principal component analysis revealed that species with quick resource-acquisition rates had high rates of growth and recruitment. </span></p> <p><span>4. </span><span>Our results illustrate that the correlations among tree demographic properties were weak in this subtropical forest with monsoonal climate. Most notably, against expectations there was no observed tradeoff between growth and mortality. Individual functional traits explained up to 27% of each demographic rate. Variation in recruitment rate was aligned with traits indexing the leaf economic spectrum and also plant hydraulic variation. A better understanding of the role of disturbances on trait-demography relationships would help build a deeper and more nuanced understanding of the ecology of subtropical monsoon forests.</span></p>
Fig. 7 in Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper
Fig. 7. Demographic history of the studied populations of Pantel's grasshopper (Omocestus panteli) inferred using STAIRWAY PLOT. Panels show the median of effective population size (N) over time, estimated assuming a mutation rate of 2.8 × 10−9 and a 1-yr generation time (both axes in a logarithmic scale). Vertical e dashed lines indicate the Last Glacial Maximum (LGM; ca. 21 ka). Number of polymorphic SNPs used to calculate the site frequency spectrum (SFS) indicated in parentheses. Colors correspond to the main genetic cluster at which populations were predominantly assigned according to STRUCTURE analyses for K = 6 (Fig. 3). Population codes as described inTable 1.
Fig. 6 in Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper
Fig. 6. Relationships (A) between genetic diversity (π) and latitude and (B) between long-term effective population size (Ne) and environmental suitability during the last glacial maximum (LGM) inferred by projecting the species-specific environmental niche model (ENM) to LGM bioclimatic conditions under the CCSM4 general atmospheric circulation model.
Fig. 5 in Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper
Fig. 5. Relationship between genetic differentiation (FST) and resistance distances based on environmental suitability during the LGM inferred by projecting the species-specific environmental niche model (ENM) to LGM bioclimatic conditions under the CCSM4 general atmospheric circulation model.
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Annotated Behaviour and Observability Dataset (ABODe)
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