Relative Population Size Research Articles

Food depletion regulates the demography of invasive dreissenid mussels in a stratified lake

AbstractLake stratification produces sharp gradients in temperature and pelagic resources which have cascading effects on the traits of aquatic populations, including invasive species and their ecosystem impacts. We study the consequences of such common environmental gradients on the demography of quagga mussels, one of the world's most aggressive invasive species. Coupling a series of in situ experiments with a biophysical model of the pelagic community, we quantify mussel growth and recruitment in littoral vs. profundal benthic habitats of eastern Lake Erie. We found that both severe food depletion and cold temperatures in the hypolimnion during summer stratification cause mussels to grow twice as slowly and currently inhibit recruitment in profundal compared to littoral habitats. Together with the high biomass and large mean mussel size found in long‐term monitoring surveys in the profundal habitats, our results imply that mussels successfully colonizing profundal habitats have relatively long lifespans with low growth rates, and therefore lower productivity, compared to mussels in shallow areas. Consequently, the bulk of dreissenid biomass in Lake Erie and other Great Lakes found in the vast but resource‐poor profundal habitats may have very limited impacts on epilimnetic communities compared to mussels in littoral areas. By contrast, mussels in profundal habitats strongly reduce food availability to hypolimnetic communities throughout the year. Thus, our results explain how the ecosystem impacts of sessile freshwater invaders are likely to vary among habitats and lakes depending on the relative size of profundal populations and the extent of stratification.

A guide to calculating habitat‐quality metrics to inform conservation of highly mobile species

AbstractMany metrics exist for quantifying the relative value of habitats and pathways used by highly mobile species. Properly selecting and applying such metrics requires substantial background in mathematics and understanding the relevant management arena. To address this multidimensional challenge, we demonstrate and compare three measurements of habitat quality: graph‐, occupancy‐, and demographic‐based metrics. Each metric provides insights into system dynamics, at the expense of increasing amounts and complexity of data and models. Our descriptions and comparisons of diverse habitat‐quality metrics provide means for practitioners to overcome the modeling challenges associated with management or conservation of such highly mobile species. Whereas previous guidance for applying habitat‐quality metrics has been scattered in diversified tracks of literature, we have brought this information together into an approachable format including accessible descriptions and a modeling case study for a typical example that conservation professionals can adapt for their own decision contexts and focal populations.Considerations for Resource Managers Management objectives, proposed actions, data availability and quality, and model assumptions are all relevant considerations when applying and interpreting habitat‐quality metrics. Graph‐based metrics answer questions related to habitat centrality and connectivity, are suitable for populations with any movement pattern, quantify basic spatial and temporal patterns of occupancy and movement, and require the least data. Occupancy‐based metrics answer questions about likelihood of persistence or colonization, are suitable for populations that undergo localized extinctions, quantify spatial and temporal patterns of occupancy and movement, and require a moderate amount of data. Demographic‐based metrics answer questions about relative or absolute population size, are suitable for populations with any movement pattern, quantify demographic processes and population dynamics, and require the most data. More real‐world examples applying occupancy‐based, agent‐based, and continuous‐based metrics to seasonally migratory species are needed to better understand challenges and opportunities for applying these metrics more broadly.

Gene flow analysis method, the D-statistic, is robust in a wide parameter space

BackgroundWe evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis.ResultThe sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, {widehat{f}}_G and {widehat{f}}_{hom} , to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background.ConclusionsThe D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations.

A simplified mark–release–recapture protocol to improve the cost effectiveness of repeated population size quantification

Abstract Obtaining an accurate quantification of population size is often of prime importance in ecology and conservation biology (e.g. population viability analysis, a basic step for assessing species and population status in a given area and guiding effective conservation). When obtaining a reliable quantification of absolute (vs. relative) population size is required, Mark–Release–Recapture (MRR) is a method of choice for many organisms. This is a highly reliable but costly procedure in terms of time and potential impact on species and sites. Consequently, less costly alternatives are highly desirable for conservation and population ecologists. We present here a simplified MRR protocol to mitigate this cost of repeated MRR sampling with little compromise on the quality of the population size estimation. Using one of the largest existing butterfly MRR databases, collected on two fritillary species over a period of 20 years and >20 populations in Belgium, we assessed the possibility to reduce the effort of collecting MRR data while keeping accurate quantification of total population size. By downsampling from the full datasets and calculating a range of demographic census metrics, we specifically investigated whether marking individuals is necessary, and whether the number of sampling sessions can be reduced. We found that (1) counting individuals is not enough: some individual marking, even in a simplistic way to differentiate newly recorded from previously seen individuals, is essential for estimating population size. (2) A simple linear conversion function (number of “missed” individuals for each marked one) can be used to compute population size from the number of individuals marked over a small number of MRR sampling sessions. (3) Parameterizing this function is system specific, because it depends on detectability of individuals, but only requires an initial effort of traditional high‐effort MRR in a few populations encompassing the expected range of population size, combined with previous knowledge on the species about potential factors affecting detectability. Our simplified MRR protocol should allow scientists to obtain absolute population size estimates almost as good as with traditional high‐effort MRR, but at a cost lowered in both the marking procedure and the intensity of field visits.

Poor Access for African Researchers to African Emergency Care Publications: A Cross-sectional Study.

IntroductionBased on relative population size and burden of disease, emergency care publication outputs from low- and middle-income regions are disproportionately lower than those of high-income regions. Ironically, outputs from regions with higher publication rates are often less relevant in the African context. As a result, the dissemination of and access to local research is essential to local researchers, but the cost of this access (actual and cost-wise) remains unknown. The aim of this study was to describe access to African emergency care publications in terms of publisher-based access (open access or subscription) and alternate access (self-archived or author provided), as well as the cost of access.MethodsWe conducted a retrospective, cross-sectional study using all emergency medicine publications included in Scopus between 2011 and 2015. A sequential search strategy described access to each article, and we calculated mean article charges against the purchasing power parity index (used to describe out-of-pocket expense).ResultsWe included 666 publications from 49 journals, of which 395 (59.3%) were open access. For subscription-based articles, 106 (39.1%) were self-archived, 60 (22.1%) were author-provided, and 105 (38.8%) were inaccessible. Mean article access cost was $36.44, and mean processing charge was $2,319.34. Using the purchasing power parity index it was calculated that equivalent out-of-pocket expenditure for South African, Ghanaian and Tanzanian authors would respectively be $15.77, $10.44 and $13.04 for access, and $1,004.02, $664.36 and $830.27 for processing. Based on this, the corrected cost of a single-unit article access or process charge for South African, Ghanaian and Tanzanian authors, respectively, was 2.3, 3.5 and 2.8 times higher than the standard rate.ConclusionOne in six African emergency care publications are inaccessible outside institutional library subscriptions; additionally, the cost of access to publications in low- and middle-income countries appears prohibitive. Publishers should strongly consider revising pricing for more equitable access for researchers from low- and middle-income countries.

A probabilistic assessment of the rapidity of PETM onset

Knowledge of the onset duration of the Paleocene-Eocene Thermal Maximum—the largest known greenhouse-gas-driven global warming event of the Cenozoic—is central to drawing inferences for future climate change. Single-foraminifera measurements of the associated carbon isotope excursion from Maud Rise (South Atlantic Ocean) are controversial, as they seem to indicate geologically instantaneous carbon release and anomalously long ocean mixing. Here, we fundamentally reinterpret this record and extract the likely PETM onset duration. First, we employ an Earth system model to illustrate how the response of ocean circulation to warming does not support the interpretation of instantaneous carbon release. Instead, we use a novel sediment-mixing model to show how changes in the relative population sizes of calcareous plankton, combined with sediment mixing, can explain the observations. Furthermore, for any plausible PETM onset duration and sampling methodology, we place a probability on not sampling an intermediate, syn-excursion isotopic value. Assuming mixed-layer carbonate production continued at Maud Rise, we deduce the PETM onset was likely <5 kyr.

Global city size hierarchy: Spatial patterns, regional features, and implications for China

City size hierarchy and distribution are always at the heart of urban studies, as they have a special ability to reveal the rules of city development and urban system spatial layouts. There is however a data deficiency with regard to city size hierarchy and distribution; in particular, an absence of complete statistics and spatial differences from the global perspective. To fill this research gap, this paper investigates global city size hierarchy based on 2014 data of more than 190 countries and regions by using classic models of “rank-size” rule, the fractal theory and the law of the primate city. We analyzed the spatial patterns, regional features, and implications for China from multi-scale and multi-dimension perspectives. The results show that: (1) There is an obvious pyramid structure of global city size distribution, but differences exist among countries and regions with different economic development types, suggesting a feature of “various types with pyramid dominated”; (2) The primate feature of global city size distribution is not very obvious. However, the primacy ratios of developed countries are much higher than others, and significant differences exist among different regions; (3) The global Zipf exponent and Hausdorff dimension are 0.66 and 1.29, respectively. Cities with middle ranks are in the majority, and the monopoly power of large and super cities is effective to a certain extent, indicating a decreasing concentration tendency in the city size distribution and a convergence trend in terms of relative population size, especially with regard to the medium and small cities; (4) The medium and small cities develop swiftly with limited agglomeration effect of large cities, and Chinese cities would significantly influence global urban progress and spatial patterns. Therefore, developing 780–800 cities will be reasonable for China's urbanization efforts by 2030.

Effects of Acremonium terricola culture supplementation on apparent digestibility, rumen fermentation, and blood parameters in dairy cows

This study was conducted to examine the effects of Acrermonium terricola culture (ATC) on feed digestibility, rumen fermentation, and blood parameters in dairy cows. Six non-lactating ruminally and duodenally fistulated cows were evaluated in a replicated 3×3 Latin square design, with each period lasting 27 d. The cows were randomly assigned into three treatment groups: (1) basal diet (no additive); (2) basal diet plus 15g/cow per day ATC; and (3) basal diet plus 30g/cow per day ATC. Cows supplemented with ATC had a higher total-tract apparent digestibility of dry matter and crude protein, production of ammonia nitrogen and volatile fatty acids, and relative population size of proteolytic bacteria than did unsupplemented cows. ATC supplementation decreased ruminal pH, concentration of urea nitrogen, aspartate transaminase, non-esterified fatty acids, and beta-hydroxybutyric acid in plasma and improved ruminal disappearance of roughage and blood glucose content. Overall, ATC is an effective feed additive and regulates apparent digestibility, rumen fermentation, and blood metabolism for dairy cows.

Computer extracted features of gland morphology on H&amp;E surgically resected tissue images as predictive of biochemical recurrence and rate of expression in African American compared to Caucasian American men.

e16559 Background: Prostate cancer (PCa) is 1.7 times more prevalent and 2.3 times more lethal in African American (AA) men than in Caucasian American (CA) men. Additionally there is a higher incidence (when controlling for relative population size) of more aggressive PCa in the AA compared to the CA population which has led a number of groups to investigate whether there are molecular differences in the disease phenotype between the two groups. In this work we investigate whether computer extracted features of glandular morphology from digitized pathology images of surgical specimens identified as predictive of biochemical recurrence are also differentially expressed between AA and CA patients. Methods: Two cohorts were gathered. Cohort 1 (C1) contained digitized whole mount Gleason 7 radical prostatectomy specimens (RPS) from 72 patients (46 CA, 26 AA). Cohort 2 (C2) comprising quarter and whole mount RPS from 145 patients (135 CA, 10 AA), who either had biochemical recurrence in 5 years (47) or did not (98). A pathologist annotated each image in both cohorts for a representative cancerous region. Glands were automatically segmented and 216 features describing gland arrangement, shape, and disorder were extracted from every image. Features were tested for significance by Wilcoxon rank sum test at p &lt; .05. Results: 8 features of gland morphology were significantly different between AA and CA groups and also predictive of biochemical recurrence (Table). Conclusions: We identified 8 computer extracted features of gland morphology that were both differentially expressed between AA and CA men and predictive of biochemical recurrence, suggesting that there are histomorphometric differences in prostate cancer appearance between AA and CA men. [Table: see text]

Changes in the relative population size of selected ruminal bacteria following an induced episode of acidosis in beef heifers receiving viable and non-viable active dried yeast.

To characterize the changes in the relative population size (RPS) of select ruminal bacteria and rumen fermentation variables in beef heifers supplemented with a strain of Saccharomyces cerevisiae as viable active dried (ADY) or killed dried (KDY) yeast following an induced episode of ruminal acidosis. Six ruminally cannulated beef heifers fed a diet consisting of 50% forage and 50% grain (dry matter basis) were used in a replicated 3×3 Latin square design with three 28-day periods. Treatments were: (i) control (CTRL; no yeast); (ii) ADY (4gday-1 providing 1010 CFU per g; AB Vista, UK); and (iii) KDY (4gday-1 autoclaved ADY). The acidosis challenge was induced on day 22 and rumen samples were collected on day 15 (baseline; BASE), day 22 (challenge day; CHAL), and on day 29 (168th hour post acid challenge or recovery, REC) of each period. Over the study, duration of pH <5·8 (indicative of subacute ruminal acidosis) was less for ADY and KDY than CTRL, with ADY less than KDY. No treatment effects were observed on relative abundance of ruminal bacteria, but the day effect was significant. The RPS of lactate producers and utilizers was greater while RPS of fibrolytic bacteria was lower during CHAL than BASE and REC. Yeast supplementation, irrespective of its viability, showed beneficial effects on ruminal pH variables in animals more susceptible to acidosis. Rumen microbial population was altered with the induction of severe acidosis. Most of the changes reverted back to baseline values during the recovery phase. Yeast supplementation reduced subacute rumen acidosis in the most susceptible cattle, but failed to attenuate severe acidosis induced by a grain challenge. The study provided valuable insight into the mechanism by which acidosis affects cattle performance. Individual animal variation in ruminal fermentation partly explained the variability in response to yeast supplementation in the study.

Adversarial Top- $K$ Ranking

We study the top- $K$ ranking problem where the goal is to recover the set of top- $K$ ranked items out of a large collection of items based on partially revealed preferences. We consider an adversarial crowdsourced setting where there are two population sets, and pairwise comparison samples drawn from one of the populations follow the standard Bradley-Terry-Luce model (i.e., the chance of item $i$ beating item $j$ is proportional to the relative score of item $i$ to item $j$ ), while in the other population, the corresponding chance is inversely proportional to the relative score. When the relative size of the two populations is known, we characterize the minimax limit on the sample size required (up to a constant) for reliably identifying the top- $K$ items, and demonstrate how it scales with the relative size. Moreover, by leveraging a tensor decomposition method for disambiguating mixture distributions, we extend our result to the more realistic scenario, in which the relative population size is unknown, thus establishing an upper bound on the fundamental limit of the sample size for recovering the top- $K$ set.

The value of museums in the production, sharing, and use of entomological data to document hyperdiversity of the changing North

If the current rate of climate change continues, the composition, distribution, and relative population sizes of species in the higher latitudes of the Northern Hemisphere are likely to change considerably. Understanding the magnitude of this change requires a well- documented baseline against which to compare. Although specimen-less observations can help augment such a baseline for the minority of organisms that can be confidently identified in the field or from photographs, the vast majority of species are small-bodied invertebrates, primarily arthropods, that can only be identified from preserved specimens and (or) their tissues. Museum staff archive specimens and make them and their data available for research. This paper describes a number of challenges to the goal of thorough documentation of high-latitude arthropod biodiversity and their potential solutions. Examples are provided from ongoing and recently completed research that demonstrates the value of museum specimens and the sharing of their data via global portals like GBIF.org.

Population dynamics, social resilience strategies, and Adaptive Cycles in early farming societies of SW Central Europe

Inferred European Holocene population size exhibits large fluctuations, particularly around the onset of farming. We attempt to find explanations for these fluctuations by employing the concept of cycling, especially that of the Adaptive Cycle. We base our analysis on chronologically and chorologically highly resolved ceramic and site data from the Linear Pottery culture (Germ. Linearbandkermik) of the early Neolithic of southwestern Central Europe. Typological seriation with dendrochronological anchor dates provides the age model for these data. Ceramic motifs are analysed with respect to the temporally changing diversity in decoration. The temporal sequence of major decoration motifs is interpreted as an indicator of social diversity: when stylistic diversity is low, social diversity is low and vice versa. The sequence of secondary decoration motifs is interpreted in terms of individual lineage emphasis: when this diversity is low, there is strong emphasis on individual lineage and vice versa. The diversity time series are complemented by a relative population size indicator derived from the count of occupational features. Diversity and population size share a shape that is typical for (part of) an Adaptive Cycle, and they differ in their positioning on the time axis — they are time-lagged. By relating the different curves to the (metaphorical) stages of the Adaptive Cycle, we find that these cycles progress at non-identical speed in different aspects of a social system. By relating the social dynamics to well-dated and highly resolved climate fluctuation records, we find evidence that severe climate excursions shaped the location of tipping points in the social system and that these social tipping points precede inferred population decline by several generations.

Plausibility Structures, Status Threats, and the Establishment of Anti-Abortion Pregnancy Centers

The authors offer a theoretical framework that resolves conflicting ideas found in extant theory pertaining to moral reform movements. The framework focuses on how community attributes, particularly the relative size of populations affiliated with supportive belief systems, shape moral reform activism by affecting both the convictions and motivations of potential supporters. The theory is applied in an analysis of county-level variation in the presence of antiabortion pregnancy centers (PCs). The authors find that the proportion of individuals affiliated with Roman Catholicism or evangelical denominations has a curvilinear relationship with PC establishment, reflecting the way in which group size can affirm convictions that are the lifeblood of moral reform but can also reduce motivation to act when the size of the group surpasses majority status. The authors also find that PCs are more likely to be found in communities where gender roles are relatively egalitarian.

The appropriateness of ignorance in the inverse kinetic Ising model

We develop efficient ways to consider and correct for the effects of hidden units for the paradigmatic case of the inverse kinetic Ising model with fully asymmetric couplings. We identify two sources of error in reconstructing the connectivity among the observed units while ignoring part of the network. One leads to a systematic bias in the inferred parameters, whereas the other involves correlations between the visible and hidden populations and has a magnitude that depends on the coupling strength. We estimate these two terms using a mean field approach and derive self-consistent equations for the couplings accounting for the systematic bias. Through application of these methods on simple networks of varying relative population size and connectivity strength, we assess how and under what conditions the hidden portion can influence inference and to what degree it can be crudely estimated. We find that for weak to moderately coupled systems, the effects of the hidden units is a simple rotation that can be easily corrected for. For strongly coupled systems, the non-systematic term becomes large and can no longer be safely ignored, further highlighting the importance of understanding the average strength of couplings for a given system of interest.

Country Size, Specialization Patterns and Secular Demand Stagnation

Using a dynamic two-country two-commodity Ricardian model where preference for money (or wealth) leads to aggregate demand deficiency, this paper examines the relationship between the two countries’ relative population size and their specialization patterns, employment and consumption. When the countries have similar population sizes, they specialize in respective commodities with comparative advantage. In this case a larger foreign, or a smaller home, population raises the relative price of the home commodity. It raises home real income and consumption per capita if full employment prevails in the home country. If unemployment appears, however, home employment and consumption per capita decrease.

Country Size, Specialization Patterns and Secular Demand Stagnation

Using a dynamic two-country two-commodity Ricardian model where preference for money (or wealth) leads to aggregate demand deficiency, this paper examines the relationship between the two countries’ relative population size and their specialization patterns, employment and consumption. When the countries have similar population sizes, they specialize in respective commodities with comparative advantage. In this case a larger foreign, or a smaller home, population raises the relative price of the home commodity. It raises home real income and consumption per capita if full employment prevails in the home country. If unemployment appears, however, home employment and consumption per capita decrease.

Differences in the effective population sizes of males and females do not require differences in their distribution of offspring number

Difference in male and female effective population sizes has, at times, been attributed to both sexes having unequal variance in their number of offspring. Such difference is paralleled by the relative effective sizes of autosomes, sex chromosomes, and mitochondrial DNA. I develop a simple framework to calculate the inbreeding effective population sizes for loci with different modes of inheritance. In this framework, I separate the effects due to mating strategy and those due to genetic transmission. I then show that, in addition to differences in the variance in offspring number, skew in the male/female effective sizes can also be caused by family composition. This approach can be used to illustrate the effect of induced behaviors on the relative male and female effective population sizes. In particular, I show the impact of the one-child policy formerly implemented in the People’s Republic of China on the relative male and female effective population sizes. Furthermore, I argue that, under some strong constraints on family structure, the concepts of male and female effective population sizes are invalid.

Characterization of Aspergillus section Nigri species populations in vineyard soil using droplet digital PCR.

This is the first study to demonstrate the utility of ddPCR as a means to quantify species of Aspergillus section Nigri in soil. This method eliminates the need for isolation and sequence identification of individual fungal isolates, and allows for greater throughput in measuring relative population sizes of important (i.e. mycotoxigenic) Aspergillus species within a population of morphologically indistinguishable species.

Decline of recent seabirds inferred from a composite 1000-year record of population dynamics.

Based on three ornithogenic sediment profiles and seabird subfossils therein from the Xisha Islands, South China Sea, the relative population size of seabirds over the past 1000 years was reconstructed using reflectance spectrum. Here we present an apparent increase and subsequent decline of seabirds on these islands in the South China Sea. Seabird populations peaked during the Little Ice Age (LIA, 1400–1850 AD), implying that the cool climate during the LIA appears to have been more favorable to seabirds on the Xisha Islands in the South China Sea. Climate change partly explains the recent decrease in seabird populations over the past 150 years, but the significant decline and almost complete disappearance thereof on most of the Xisha Islands is probably attributable to human disturbance. Our study reveals the increasing impact of anthropogenic activities on seabird population in recent times.