scholarly journals Relative species abundance and population densities of the past; developing multi-species occupancy models for fossil data

2021 ◽  
Author(s):  
Trond Reitan ◽  
Torbjørn Ergon ◽  
Lee Hsiang Liow
Keyword(s):  
Species Abundance ◽  
Biased Sampling ◽  
Occupancy Models ◽  
Geological Time ◽  
Population Densities ◽  
Time Intervals ◽  
Relative Population ◽  
Modelling Framework ◽  
Wide Range ◽  
Species Occupancy

The number of individuals of species within communities varies, but estimating abundance, given incomplete and biased sampling, is challenging. Here, we describe a new occupancy model in a hierarchical Bayesian framework with random effects, where multi-species occupancy and detection are modeled as a means to estimate relative species abundance and relative population densities. The modelling framework is suited for occupancy data for temporal samples of fossil communities with repeated sampling including multiple species with similar preservation potential. We demonstrate our modelling framework using a fossil community of benthic organisms to estimate changing relative species abundance dynamics and relative population densities of focal species in 9 (geological) time-intervals over 2.3 million years. We also explored potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled time-intervals. The modelling framework is applicable across a wide range of questions on species-level dynamics in (palaeo)ecological community settings.

scholarly journals TRAMPOline: a Temporal Relative Abundance-focused multi-sPecies Occupancy model, illustrated using fossils

2021 ◽  
Author(s):  
Trond Reitan ◽  
Torbjørn Ergon ◽  
Lee Hsiang Liow
Keyword(s):  
Relative Abundance ◽  
Biased Sampling ◽  
Geological Time ◽  
Modeling Framework ◽  
Time Intervals ◽  
Occupancy Model ◽  
Focal Species ◽  
Additional Information ◽  
Wide Range ◽  
Species Occupancy

The occupancy and relative abundance of species are temporally varying. Estimating these, given incomplete and biased sampling is challenging, not least for fossilized organisms, where preservation is an additional issue. Here, we describe a relative abundance-focused multi-species occupancy model (TRAMPOline) in a hierarchical Bayesian framework. We designed our model on the basis of the need to understand the dynamics of several focal species over 2.3 million years, by drawing on additional information provided by non-focal species observed in the same fossilized community. We expanded our model by adding random effects of species and time intervals (geological formations) and explored potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled geological time intervals. Our new model, set in an occupancy modeling framework widely used in ecology but little applied in paleoecology, is applicable across a wide range of questions on species-level dynamics in contemporary and palaeoecological community settings.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

scholarly journals A Kinetic Theory Model of the Dynamics of Liquidity Profiles on Interbank Networks

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 363
Author(s):  
Marina Dolfin ◽  
Leone Leonida ◽  
Eleonora Muzzupappa
Keyword(s):  
Kinetic Theory ◽  
Network Formation ◽  
Transition Probabilities ◽  
Stochastic Game ◽  
Theory Model ◽  
Point Of View ◽  
Network Efficiency ◽  
Modelling Framework ◽  
Wide Range ◽  
Complex Adaptive

This paper adopts the Kinetic Theory for Active Particles (KTAP) approach to model the dynamics of liquidity profiles on a complex adaptive network system that mimic a stylized financial market. Individual incentives of investors to form or delete a link is driven, in our modelling framework, by stochastic game-type interactions modelling the phenomenology related to policy rules implemented under Basel III, and it is exogeneously and dynamically influenced by a measure of overnight interest rate. The strategic network formation dynamics that emerges from the introduced transition probabilities modelling individual incentives of investors to form or delete links, provides a wide range of measures using which networks might be considered “best” from the point of view of the overall welfare of the system. We use the time evolution of the aggregate degree of connectivity to measure the time evolving network efficiency in two different scenarios, suggesting a first analysis of the stability of the arising and evolving network structures.

Patterns of Evolution of the Ediacaran Soft-Bodied Biota

2014 ◽  
Vol 88 (2) ◽  
pp. 269-283 ◽  
Author(s):  
Dmitriy Grazhdankin
Keyword(s):  
High Energy ◽  
Ecosystem Engineering ◽  
Low Energy ◽  
Geological Time ◽  
Time Intervals ◽  
Inner Shelf ◽  
Sedimentary Environments ◽  
Burrowing Activity ◽  
Ecological Associations ◽  
Channel Systems

When each of the Avalon-, Ediacara-, and Nama-type fossil assemblages are tracked through geological time, there appear to be changes in species composition and diversity, almost synchronized between different sedimentary environments, allowing a subdivision of the late Ediacaran into the Redkinian, Belomorian and Kotlinian geological time intervals. The Redkinian (580–559 Ma) is characterized by first appearance of both eumetazoan traces and macroscopic organisms (frondomorphs and vendobionts) in a form of Avalon-type communities in the inner shelf environment, whereas coeval Ediacara-type communities remained depauperate. The Belomorian (559–550 Ma) is marked by the advent of eumetazoan burrowing activity in the inner shelf, diversification of frondomorphs, migration of vendobionts from the inner shelf into higher energy environments, and appearance of tribrachiomorphs and bilateralomorphs. Ediacaran organisms formed distinctive ecological associations that coexisted in the low-energy inner shelf (Avalon-type communities), in the wave- and current-agitated shoreface (Ediacara-type communities), and in the high-energy distributary systems (Nama-type communities). The Kotlinian (550–540 Ma) witnessed an expansion of the burrowing activity into wave- and current-agitated shoreface, disappearance of vendobionts, tribrachiomorphs and bilateralomorphs in wave- and current-agitated shoreface, together with a drop in frondomorph diversity. High-energy distributary channel systems of prodeltas served as refugia for Nama-type communities that survived until the end of the Ediacaran and disappeared when the burrowing activity reached high-energy environments. This pattern is interpreted as an expression of ecosystem engineering by eumetazoans, with the Ediacaran organisms being progressively outcompeted by bilaterians.

A penalized likelihood for multi‐species occupancy models improves predictions of species interactions

Ecology ◽  
2021 ◽  
Author(s):  
Hannah L. Clipp ◽  
Amber L. Evans ◽  
Brin E. Kessinger ◽  
Kenneth Kellner ◽  
Christopher T. Rota
Keyword(s):  
Species Interactions ◽  
Penalized Likelihood ◽  
Occupancy Models ◽  
Species Occupancy

Timing of Aldicarb Applications to Control Meloidogyne arenaria in Peanut1

2001 ◽  
Vol 28 (2) ◽  
pp. 73-75 ◽  
Author(s):  
J. R. Rich ◽  
D. W. Gorbet
Keyword(s):  
Arachis Hypogaea ◽  
Chemical Treatment ◽  
Optimal Time ◽  
Meloidogyne Arenaria ◽  
Root Knot Nematode ◽  
Population Densities ◽  
Time Intervals ◽  
Yield Increase ◽  
Post Harvest ◽  
Chemical Treatments

Abstract Four fieldtrialswere conductedin northwest Florida to determine the efficacyofaldicarb appliedat varyingtime intervals after planting on peanut (Arachis hypogaea) to manage the peanut root-knot nematode, Meloidogyne arenaria. Initial treatments with aldicarb (Temik 15G), fenamiphos (Nemacur 15G), and phorate (Thimet 15G) were made at planting of peanut cv. Southern Runner. The chemicals were applied as 20-cm-wide bands over the open seed furrow using a tractor-mounted Gandy applicator. Post-plant treatments were made with a Gandy applicator at time intervals from 28 to 104 dafter planting as 36-cm-wide bands over the row centers. Post-harvest M. arenaria population densities were affected little by any chemical treatment compared to the control. The efficacy of the chemical treatments was variable and averaged onlya 295-kglha yield increase for the single at-plant applications of aldicarb compared to the control. Allat-plant + post-plant aldicarb treatments increased yield over the control by an average of712 kg¡ ha. Results from these trials did not establish a single optimal time for post-plant application of aldicarb on peanut. Data from these tests, however, indicated that a post-plant aldicarb treatment can be applied latter than previously recommended in Florida.

scholarly journals A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees

2017 ◽  
Vol 284 (1846) ◽  
pp. 20162395 ◽  
Author(s):  
Kohei Koyama ◽  
Ken Yamamoto ◽  
Masayuki Ushio
Keyword(s):  
Lognormal Distribution ◽  
Species Abundance ◽  
Self Similarity ◽  
Lognormal Distributions ◽  
Multiplicative Effect ◽  
Wide Range ◽  
Error Distributions ◽  
Species Abundance Distributions ◽  
Self Similar ◽  
Ulmus Davidiana

Lognormal distributions and self-similarity are characteristics associated with a wide range of biological systems. The sequential breakage model has established a link between lognormal distributions and self-similarity and has been used to explain species abundance distributions. To date, however, there has been no similar evidence in studies of multicellular organismal forms. We tested the hypotheses that the distribution of the lengths of terminal stems of Japanese elm trees ( Ulmus davidiana ), the end products of a self-similar branching process, approaches a lognormal distribution. We measured the length of the stem segments of three elm branches and obtained the following results: (i) each occurrence of branching caused variations or errors in the lengths of the child stems relative to their parent stems; (ii) the branches showed statistical self-similarity; the observed error distributions were similar at all scales within each branch and (iii) the multiplicative effect of these errors generated variations of the lengths of terminal twigs that were well approximated by a lognormal distribution, although some statistically significant deviations from strict lognormality were observed for one branch. Our results provide the first empirical evidence that statistical self-similarity of an organismal form generates a lognormal distribution of organ sizes.

scholarly journals A comparative survey of the impacts of extreme rainfall in two international case studies

2017 ◽  
Author(s):  
Matthieu Spekkers ◽  
Viktor Rözer ◽  
Annegret Thieken ◽  
Marie-Claire ten Veldhuis ◽  
Heidi Kreibich
Keyword(s):  
Case Studies ◽  
Online Survey ◽  
Residential Buildings ◽  
Age Groups ◽  
Extreme Rainfall ◽  
Water Levels ◽  
Economic Losses ◽  
Biased Sampling ◽  
Wide Range ◽  
Damage Data

Abstract. Flooding is assessed as the most important natural hazard in Europe, causing thousands of deaths, affecting millions of people and accounting for large economic losses in the past decade. Little is known about the damage processes associated with extreme rainfall in cities, due to a lack of accurate, comparable and consistent damage data. The objective of this study is to investigate the impacts of extreme rainfall on residential buildings and how affected households coped with these impacts in terms of precautionary and emergency actions. Analyses are based on a unique dataset of damage characteristics and a wide range of potential damage explaining variables at the household level, collected through computer-aided telephone interviews (CATI) and an online survey. Exploratory data analyses based on a total of 859 completed questionnaires in the cities of Münster (Germany) and Amsterdam (the Netherlands) revealed that the uptake of emergency measures is related to characteristics of the hazardous event. In case of high water levels, more efforts are made to reduce damage, while emergency response that aims to prevent damage is less likely to be effective. The difference in magnitude of the events in Münster and Amsterdam in terms of rainfall intensity and water depth, is probably also the most important cause for the differences between the cities in terms of the suffered financial losses. Factors that significantly contributed to damage in at least one of the case studies are water contamination, the presence of a basement in the building and people's awareness of the upcoming event. Moreover, this study confirms conclusions by previous studies that people's experience with damaging events positively correlates with precautionary behaviour. For improving future damage data acquisition, we recommend to include cell-phones in a CATI survey to avoid biased sampling towards certain age groups.

scholarly journals SEAMUS (v1.0): a Δ<sup>14</sup>C-enabled, single-specimen sediment accumulation simulator

2019 ◽  
Author(s):  
Bryan C. Lougheed
Keyword(s):  
Sediment Core ◽  
Accumulation Rate ◽  
Sediment Accumulation ◽  
Species Abundance ◽  
Depth Interval ◽  
Single Specimen ◽  
14C Dating ◽  
Deep Sea Sediment ◽  
Wide Range ◽  
History Of

Abstract. The systematic bioturbation of single particles (such as foraminifera) within deep-sea sediment archives leads to the apparent smoothing of any temporal signal as record by the downcore, discrete-depth mean signal. This smoothing is the result of the systematic mixing of particles from a wide range of depositional ages into the same discrete depth interval. Previous sediment models that simulate bioturbation have specifically produced an output in the form of a downcore, discrete-depth mean signal. Palaeoceanographers analysing the distribution of single foraminifera specimens from sediment core intervals would be assisted by a model that specifically evaluates the effect of bioturbation upon single specimen populations. Taking advantage of recent increases in computer memory, the single-specimen SEdiment AccuMUlation Simulator (SEAMUS) was created in Matlab, whereby large arrays of single specimens are simulated. This simulation allows researchers to analyse the post-bioturbation age heterogeneity of single specimens contained within discrete-depth sediment core intervals, and how this heterogeneity is influenced by changes in sediment accumulation rate (SAR), bioturbation depth (BD) and species abundance. The simulation also assigns a realistic 14C activity to each specimen, by considering the dynamic Δ14C history of the Earth and temporal changes in reservoir age. This approach allows for the quantification of possible significant artefacts arising when 14C dating multi-specimen samples with heterogeneous 14C activity. Users may also assign additional desired carrier signals to specimens (e.g., stable isotopes, trace elements, temperature, etc.) and consider a second species with an independent abundance. Finally, the model can simulate a virtual palaeoceanographer by randomly picking whole specimens (whereby the user can set the percentage of older, broken specimens) of a prescribed sample size from discrete depths, after which virtual laboratory 14C dating and 14C calibration is carried out within the model.

scholarly journals Quantitative analysis of tumour spheroid structure

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alexander P Browning ◽  
Jesse A Sharp ◽  
Ryan J Murphy ◽  
Gency Gunasingh ◽  
Brodie Lawson ◽  
...  
Keyword(s):  
Cell Lines ◽  
Tumour Microenvironment ◽  
Culture Conditions ◽  
Experimental Models ◽  
Seeding Density ◽  
Modelling Framework ◽  
Tumour Spheroid ◽  
Tumour Spheroids ◽  
Wide Range

Tumour spheroids are common in vitro experimental models of avascular tumour growth. Compared with traditional two-dimensional culture, tumour spheroids more closely mimic the avascular tumour microenvironment where spatial differences in nutrient availability strongly influence growth. We show that spheroids initiated using significantly different numbers of cells grow to similar limiting sizes, suggesting that avascular tumours have a limiting structure; in agreement with untested predictions of classical mathematical models of tumour spheroids. We develop a novel mathematical and statistical framework to study the structure of tumour spheroids seeded from cells transduced with fluorescent cell cycle indicators, enabling us to discriminate between arrested and cycling cells and identify an arrested region. Our analysis shows that transient spheroid structure is independent of initial spheroid size, and the limiting structure can be independent of seeding density. Standard experimental protocols compare spheroid size as a function of time; however, our analysis suggests that comparing spheroid structure as a function of overall size produces results that are relatively insensitive to variability in spheroid size. Our experimental observations are made using two melanoma cell lines, but our modelling framework applies across a wide range of spheroid culture conditions and cell lines.

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