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594 results for “Demographic data”
Data from: Demographic history of an elusive carnivore: using museums to inform management
Elusive carnivores present a challenge to managers because traditional survey methods are not suitable. We applied a genetic approach using museum specimens to examine how historical and recent conditions influenced the demographic history of Puma concolor in western and southern Texas, USA. We used 10 microsatellite loci and indexed population trends by estimating historical and recent genetic diversity, genetic differentiation, and effective population size. Mountain lions in southern Texas exhibited a 10% decline in genetic diversity, whereas diversity remained stable in western Texas. Genetic differentiation between western and southern Texas was minimal historically (FST = 0.04, P < 0.01), but increased 2-2.5 times in our recent sample. An index of genetic drift for southern Texas was 7-8 times that of western Texas, presumably contributing to the current differentiation between western and southern Texas. Furthermore, southern Texas exhibited a > 50% temporal decline in effective population size, whereas western Texas showed no change. Our results illustrate that population declines and genetic drift have occurred in southern Texas, likely because of contemporary habitat loss and predator control. Population monitoring may be needed to ensure the persistence of mountain lions in the southern Texas region. This study highlights the utility of sampling museum collections to examine evolutionary processes and inform wildlife management.
Data from: Density trends and demographic signals uncover the long-term impact of transmissible cancer in Tasmanian Devils
Monitoring the response of wild mammal populations to threatening processes is fundamental to effective conservation management. This is especially true for infectious diseases, which may have dynamic and therefore unpredictable interactions with their host. We investigate the long-term impact of a transmissible cancer, devil facial tumour disease (DFTD), on the endemic Tasmanian devil. We analyse trends in devil spotlight counts and density across the area impacted by the disease. We investigate the demographic parameters which might be driving these trends, and use spatial capture-recapture models to examine whether DFTD has affected home range size. We found that devils have declined by an average of 77% in areas affected by DFTD, and that there is a congruent trend of ongoing small decline in spotlight counts and density estimates. Despite this, devils have persisted to date within each of nine monitoring sites. One site is showing as yet unexplained small increases in density 8–10 years after the emergence of DFTD. We also found the prevalence of DFTD has not abated despite large declines in density and that diseased sites continue to be dominated by young devils. The long-term impact of the disease has been partially offset by increased fecundity in the form of precocial breeding in 1-year-old females, and more pouch young per female in diseased sites. The lower densities resulting from DFTD did not affect home range size. Synthesis and applications. Transmission of devil facial tumour disease continues despite large declines in devil density over multiple generations. Plasticity in life history traits has ameliorated the impact of devil facial tumour disease, however broad-scale trends in density show ongoing decline. In light of this, devil facial tumour disease and the impact of stochastic events on the reduced densities wrought by the disease, continue to threaten devils. In the absence of methods to manage disease in wild populations, we advocate managing the low population densities resulting from disease rather than disease per se.
Data from: Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape
Aim: Climate warming is causing extensive loss of glaciers in mountainous regions, yet our understanding of how glacial recession influences evolutionary processes and genetic diversity is limited. Linking genetic structure with the influences shaping it can improve understanding of how species respond to environmental change. Here, we used genome-scale data and demographic modelling to resolve the evolutionary history of Lednia tumana, a rare, aquatic insect endemic to alpine streams. We also employed a range of widely used data filtering approaches to quantify how they influenced population structure results. Location: Alpine streams in the Rocky Mountains of Glacier National Park, Montana, USA. Taxon: Lednia tumana, a stonefly (Order Plecoptera) in the family Nemouridae. Methods: We generated single nucleotide polymorphism data through restriction-site associated DNA sequencing to assess contemporary patterns of genetic structure for 11 L. tumana populations. Using identified clusters, we assessed demographic history through model selection and parameter estimation in a coalescent framework. During population structure analyses, we filtered our data to assess the influence of singletons, missing data and total number of markers on results. Results: Contemporary patterns of population structure indicate that L. tumana exhibits a pattern of isolation-by-distance among populations within three genetic clusters that align with geography. Mean pairwise genetic differentiation (FST) among populations was 0.033. Coalescent-based demographic modelling supported divergence with gene flow among genetic clusters since the end of the Pleistocene (~13-17 kya), likely reflecting the south-to-north recession of ice sheets that accumulated during the Wisconsin glaciation. Main conclusions: We identified a link between glacial retreat, evolutionary history and patterns of genetic diversity for a range-restricted stonefly imperiled by climate change. This finding included a history of divergence with gene flow, an unexpected conclusion for a mountaintop species. Beyond L. tumana, this study demonstrates the complexity of assessing genetic structure for weakly differentiated species, shows the degree to which rare alleles and missing data may influence results, and highlights the usefulness of genome-scale data to extend population genetic inquiry in non-model species.
Data from: Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial-nuclear comparison
Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.
Data from: Linking genetic kinship and demographic analyses to characterize dispersal: methods and application to Blanding's turtle
Characterizing how frequently, and at what life stages and spatial scales, dispersal occurs can be difficult, especially for species with cryptic juvenile periods and long reproductive life spans. Using a combination of mark–recapture information, microsatellite genetic data, and demographic simulations, we characterize natal and breeding dispersal patterns in the long-lived, slow-maturing, and endangered Blanding's turtle (Emydoidea blandingii), focusing on nesting females. We captured and genotyped 310 individual Blanding's turtles (including 220 nesting females) in a central Wisconsin population from 2010 to 2013, with additional information on movements among 3 focal nesting areas within this population available from carapace-marking conducted from 2001 to 2009. Mark–recapture analyses indicated that dispersal among the 3 focal nesting areas was infrequent (<0.03 annual probability). Dyads of females with inferred first-order relationships were more likely to be found within the same nesting area than split between areas, and the proportion of related dyads declined with increasing distance among nesting areas. The observed distribution of related dyads for nesting females was consistent with a probability of natal dispersal at first breeding between nearby nesting areas of approximately 0.1 based on demographic simulations. Our simulation-based estimates of infrequent female dispersal were corroborated by significant spatial genetic autocorrelation among nesting females at scales of <500 m. Nevertheless, a lack of spatial genetic autocorrelation among non-nesting turtles (males and females) suggested extensive local connectivity, possibly mediated by male movements or long-distance movements made by females between terrestrial nesting areas and aquatic habitats. We show here that coupling genetic and demographic information with simulations of individual-based population models can be an effective approach for untangling the contributions of natal and breeding dispersal to spatial ecology.
Data from: Demographic stimulation of the obligate understorey herb, Panax quinquefolius L., in response to natural forest canopy disturbances
1.Natural and anthropogenic forest canopy disturbances significantly alter forest dynamics and lead to multi-dimensional shifts in the forest understorey. An understorey plant's ability to exploit alterations to the light environment caused by canopy disturbance leads to changes in population dynamics. The purpose of this work was to determine if population growth of a species adapted to low light increases in response to additional light inputs caused by canopy disturbance, or alternatively, declines due to long-term selection under low light conditions. 2.To address this question, we quantified the demographic response of an understorey herb to three contrasting forest canopy disturbances (ice storms, tent caterpillar defoliation and lightning strikes) that encompass a broad range of disturbance severity. We used a model shade-adapted understorey species, Panax quinquefolius, to parameterize stage-based matrix models. Asymptotic growth rates, stochastic growth rates and simulations of transient dynamics were used to quantify the population-level response to canopy disturbance. Life table response experiments were used to partition the underlying controls over differences in population growth rates. 3.Population growth rates at all three disturbed sites increased in the transition period immediately after the canopy disturbance relative to the transition period prior to disturbance. Stochastic population models revealed that growth rates increased significantly in simulations that included disturbance matrices relative to those simulations that excluded disturbance. Additionally, transient models indicated that population size (n) was larger for all three populations when the respective disturbance matrix was included in the model. 4.Synthesis Obligate shade species are most likely to be pre-adapted to take advantage of canopy gaps and light influx to a degree, and this pre-adaptation may be due to long-term selection under dynamic old growth forest canopies. We propose a model whereby population performance is represented by a parabolic curve where performance is maximized under intermediate levels of canopy disturbance. This study provides new evidence to aid our understanding of the population-level response of understorey herbs to disturbances whose frequency and intensity are predicted to increase as global climates continue to shift.
Data from: Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear
The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.
Data from: Demographic and spatiotemporal patterns of avian influenza infection at the continental scale, and in relation to annual life cycle of a migratory host
Since the spread of highly pathogenic avian influenza (HPAI) H5N1 in the eastern hemisphere, numerous surveillance programs and studies have been undertaken to detect the occurrence, distribution, or spread of avian influenza viruses (AIV) in wild bird populations worldwide. To identify demographic determinants and spatiotemporal patterns of AIV infection in long distance migratory waterfowl in North America, we fitted generalized linear models with binominal distribution to analyze results from 13,574 blue-winged teal (Anas discors, BWTE) sampled in 2007 to 2010 year round during AIV surveillance programs in Canada and the United States. Our analyses revealed that during late summer staging (July-August) and fall migration (September-October), hatch year (HY) birds were more likely to be infected than after hatch year (AHY) birds, however there was no difference between age categories for the remainder of the year (winter, spring migration, and breeding period), likely due to maturing immune systems and newly acquired immunity of HY birds. Probability of infection increased non-linearly with latitude, and was highest in late summer prior to fall migration when densities of birds and the proportion of susceptible HY birds in the population are highest. Birds in the Central and Mississippi flyways were more likely to be infected compared to those in the Atlantic flyway. Seasonal cycles and spatial variation of AIV infection were largely driven by the dynamics of AIV infection in HY birds, which had more prominent cycles and spatial variation in infection compared to AHY birds. Our results demonstrate demographic as well as seasonal, latitudinal and flyway trends across Canada and the US, while illustrating the importance of migratory host life cycle and age in driving cyclical patterns of prevalence.
Data from: Lions and leopards coexist without spatial, temporal or demographic effects of interspecific competition
1. Although interspecific competition plays a principle role in shaping species behaviour and demography, little is known about the population-level outcomes of competition between large carnivores, and the mechanisms that facilitate coexistence. 2. We conducted a multi-landscape analysis of two widely distributed, threatened large carnivore competitors to offer insight into coexistence strategies and assist with species-level conservation. 3. We evaluated how interference competition affects occupancy, temporal activity and population density of a dominant competitor, the lion (Panthera leo), and its subordinate competitor, the leopard (Panthera pardus). We collected camera-trap data over three years in ten study sites covering 5,070 km2. We used multispecies occupancy modelling to assess spatial responses in varying environmental and prey conditions and competitor presence, and examined temporal overlap and the relationship between lion and leopard densities across sites and years. 4. Results showed that both lion and leopard occupancy was independent of – rather than conditional on – their competitor's presence across all environmental covariates. Marginal occupancy probability for leopard was higher in areas with more bushy, 'hideable' habitat, human (tourist) activity and topographic ruggedness, whereas lion occupancy decreased with increasing hideable habitat and increased with higher abundance of very large prey. Temporal overlap was high between carnivores and there was no detectable relationship between species densities. 4. Lions pose a threat to the survival of individual leopards, but they exerted no tractable influence on leopard spatial or temporal dynamics. Furthermore, lions did not appear to suppress leopard populations, suggesting that intraguild competitors can coexist in the same areas without population decline. Aligned conservation strategies that promote functioning ecosystems, rather than target individual species, are therefore advised to achieve cost- and space-effective conservation.
Data from: Asynchronous changes in abundance over large scales are explained by demographic variation rather than environmental stochasticity in an invasive flagellate
Environmental stochasticity is important in explaining the persistence and establishment of invasive species, but the simultaneous effects of environmental and demographic factors are difficult to separate. Understanding how demography and environmental factors affect invasive species abundance over large temporal and spatial scales is essential to anticipate populations at risk of becoming established and setting appropriate management measures. Using a hierarchical mixed modeling approach we analyzed the spatial and interannual dynamics of the invasive raphidophyte Gonyostomum semen, a noxious flagellate which is spreading in northern Europe, in response to demographic and environmental variation. We used data from 76 lakes distributed across two biogeographical regions in Sweden (Central Plains in the south and Fennoscandian region in the north) and sampled during 14 years. We found a strong asynchrony in the density dynamics of G. semen populations between the two regions. G. semen showed positive trends (i.e. increasing frequency of high density peaks) in most southern lakes, forming established populations with recurrent blooms in successive years in some of them. In contrast, G. semen populations were smaller and more stochastic in the north. G. semen previous year's abundance, a proxy for cyst production and recruitment, had a strong control on the dynamics, likely contributing to the stability of high density populations in southern lakes. Conversely, the effects of climate and habitat were weaker and their influence varied across regions. Temperature was the limiting factor in the north whereas local habitat was more important in the south. Synthesis: A full understanding of the mechanisms driving abundance changes across large scales can only be gained if endogenous and environmental factors are analyzed together. For phytoplankton species, and specially, noxious microalgae, this implies that proxies for cyst production and recruitment, which are the inoculum for next year population, should be included in e.g. distribution, bloom formation and climate models, as these may modify establishment and population response to environmental variation. Asynchronous changes in abundance across regions also indicate that management plans should be developed for small regions, as inference at a large scale may obscure the mechanisms driving local population changes.
Data from: Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization
Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.
Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise
Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from pre-bottleneck historical (c.1906) and post-bottleneck contemporary (c.2014) samples of Pinzón giant tortoises (Chelonoidis duncanensis; n=25 and 149 individuals, respectively) endemic to a single island in the Galapagos. Pinzón giant tortoises had a historically large population size that was reduced to just 150-200 individuals in the mid 20th century. Since then, Pinzón's tortoise population has recovered through an ex situ head-start program in which eggs or pre-emergent individuals were collected from natural nests on the island, reared ex situ in captivity until they were 4-5 years old, and subsequently repatriated. We found that the extent and distribution of genetic variation in the historical and contemporary samples was very similar, with the latter group not exhibiting the characteristic genetic patterns of recent population decline. No population structure was detected either spatially or temporally. We estimated an effective population size (Ne) of 58 (95% CI = 50-69) for the post-bottleneck population; no pre-bottleneck Ne point estimate was attainable (95% CI = 39-infinity) likely due to the sample size being lower than the true Ne. Overall, the historical sample provided a valuable benchmark for evaluating the head-start captive breeding program, revealing high retention of genetic variation and no skew in representation despite the documented bottleneck event. Moreover, this work demonstrates the effectiveness of head-starting in rescuing the Pinzón giant tortoise from almost certain extinction.
Long-term demographic data on the red-cockaded woodpecker
<p>In cooperative breeding systems, inclusive fitness theory predicts that non-breeding helpers more closely related to the breeders should be more willing to provide costly alloparental care, and thus have more impact on breeder fitness. In the red-cockaded woodpecker (<em>Dryobates borealis</em>), most helpers are the breeders' earlier offspring, but helpers do vary within groups in both relatedness to the breeders (some even being unrelated) and sex, and it can be difficult to parse their separate impacts on breeder fitness. Moreover, most support for inclusive fitness theory has been positive associations between relatedness and behavior, rather than actual fitness consequences. We used functional linear models to evaluate the per capita effects of helpers of different relatedness on eight breeder fitness components measured for up to 41 years at three sites. In support of inclusive fitness theory, helpers more related to the breeding pair made greater contributions to six fitness components. However, male helpers made equal contributions to increasing pre-fledging survival regardless of relatedness. These findings suggest that both inclusive fitness benefits and other, direct benefits may underlie helping behaviors in the red-cockaded woodpecker. Our results also demonstrate the application of an underused statistical approach to disentangle a complex ecological phenomenon.</p>
Data from: Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age
We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, emographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the Last Glacial Maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human-related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink-footed geese (2) the decline inferred during the Middle Ages is due to human persecution and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.
Fig. 10 in Demographic data on a stag beetle (Lucanus cervus) population self-established in an artificial suburban habitat
Fig. 10. Yearly number of stag beetles found dead by predation at the Jagersveld CMR site during the period 2001- 2023. Areas in grey refer to predation by Corvids, areas in yellow to predation by hedgehogs. The annual sex-ratio measured on these beetle remains is indicated, as is the yearly total number of beetles killed by predators and the total number of natural deaths.
Fig. 9 in Demographic data on a stag beetle (Lucanus cervus) population self-established in an artificial suburban habitat
Fig. 9. Variation, as a function of year, of the mean and standard error of head width (KB) of males found dead at the Jagersveld CMR site. Numbers indicate the size of the samples, and letters and colors indicate samples not significantly differing in size from each other at the P = 0.05 threshold, by using the non-parametric Kruskal-Wallis test for multiple comparisons. Samples of years 1924 and 2021 were excluded from the K-W analysis.
Fig. 8 in Demographic data on a stag beetle (Lucanus cervus) population self-established in an artificial suburban habitat
Fig. 8. Box plots of total length (TL) of stag beetles measured in the order of their first appearance at the Jagersveld site during the capture-mark-recapture exercise of 2007. Median, quartiles and extremes of male sizes over successive weeks and of female sizes over successive ten-day periods.
Fig. 6 A-B in Demographic data on a stag beetle (Lucanus cervus) population self-established in an artificial suburban habitat
Fig. 6 A-B. Survivorship curves of marked male stag beetles during (A) the 2001 and (B) 2007 CMR exercises, in function of death as end event. Kaplan-Meyer step-curves with 95% upper and lower confidence bounds. The arrows indicate the medians of the known life span. A Weibull curve is drawn over the K-M curve. C: illustrating the lack of statistical difference between the 2001 and 2007 K-M curves.
Fig. 4 in Demographic data on a stag beetle (Lucanus cervus) population self-established in an artificial suburban habitat
Fig. 4. Cumulative number of new individuals at the Jagersveld site during the CMR sessions of 2001 and 2007. (a): appearance of the first males. (b): geometric increase of new individuals during a short period. The graphs in the right insets show this increase in semi-logarithmic coordinates. (i): inflection point. (c): more regular increase of new individuals until reaching (d) a plateau (p). The increase of new females was more progressive.
Fig. 3 in Demographic data on a stag beetle (Lucanus cervus) population self-established in an artificial suburban habitat
Fig. 3. Calendar of male capture and recapture histories at the Jagersveld site. The marked individuals are sorted by date of first capture and by known duration of longevity. 1: captured. 0: not encountered in the interval where the individual was known to be alive. +: found dead by predation on the sampling site. *: natural death. MNA: minimum number known alive.
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