scholarly journals Past and potential future population dynamics of three grouse species using ecological and whole genome coalescent modeling

2018 ◽  
Vol 8 (13) ◽  
pp. 6671-6681 ◽  
Author(s):  
Radoslav Kozma ◽  
Mette Lillie ◽  
Blas M. Benito ◽  
Jens-Christian Svenning ◽  
Jacob Höglund
Keyword(s):  
Population Dynamics ◽  
Whole Genome ◽  
Future Population

Bonobo population dynamics: Past patterns and future predictions for the Lola ya Bonobo population using demographic modelling

2018 ◽  
Author(s):  
Lisa J. Faust ◽  
Claudine André ◽  
Raphaël Belais ◽  
Fanny Minesi ◽  
Zjef Pereboom ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Pan Troglodytes ◽  
Growth Trajectories ◽  
Demographic Model ◽  
Pan African ◽  
Demographic Modelling ◽  
Projected Changes ◽  
Demographic Patterns ◽  
Future Population ◽  
Future Growth

Wildlife sanctuaries rescue, rehabilitate, reintroduce and provide life-long care for orphaned and injured animals. Understanding a sanctuary’s population dynamics—patterns in arrival, mortality and projected changes in population size—allows careful planning for future needs. Building on previous work on the population dynamics of chimpanzees (Pan troglodytes) in sanctuaries of the Pan African Sanctuary Alliance (PASA; Faust et al. 2011), this chapter extends analyses to the only PASA bonobo sanctuary. Its authors analysed historic demographic patterns and projected future population dynamics using an individual-based demographic model. The population has been growing at 6.7 per cent per year, driven by arrivals of new individuals (mean = 5.5 arrivals per year). Several model scenarios projecting varying arrival rates, releases and breeding scenarios clarify potential future growth trajectories for the sanctuary. This research illustrates how data on historic dynamics can be modelled to inform future sanctuary capacity and management needs. Les sanctuaires de faune secourent, réhabilitent, réintroduisent, et fournissent des soins pour toute la vie aux animaux orphelins et blessés. Comprendre les dynamiques de la population d’un sanctuaire—les motifs d’arrivée, mortalité, et de changements projetés de la taille de la population—permet une planification prudente pour les nécessités du futur. En se basant sur le travail déjà fait sur les dynamiques de la population chimpanzé (Pan troglodytes) dans les sanctuaires du Pan African Sanctuary Alliance (PASA; Faust et al. 2011), nous étendons notre analyse au seul sanctuaire bonobo par PASA. Nous avons analysé les motifs démographiques historiques et avons projeté les futures dynamiques de la population en utilisant un modèle démographique basé sur l’individu. La population augmente de 6.7 per cent par an, poussée par l’arrivée de nouveaux individus (moyenne = 5.5 arrivées par an). Plusieurs scénarios modèles montrent une trajectoire de potentielle croissance pour le sanctuaire. Cette recherche illustre comment modeler les données sur les dynamiques historiques pour informer la capacité future du sanctuaire et les besoins gestionnaires.

scholarly journals Compression with unified and accessible byte blocks to enhance management and analyses of UKBB-scale genotypes

2021 ◽  
Author(s):  
Miaoxin Li ◽  
Liubin Zhang ◽  
Yangyang Yuan ◽  
Wenjie Peng ◽  
Bin Tang ◽  
...  
Keyword(s):  
Data Structure ◽  
Large Scale ◽  
Fundamental Problem ◽  
Population Based ◽  
Whole Genome ◽  
Storage Space ◽  
Problem Of Time ◽  
Conventional Analysis ◽  
Time Overhead ◽  
Future Population

Abstract Whole-genome sequencing projects of millions of persons contain enormous genotypes, entailing a huge memory burden and time overhead during computation. Here, we introduce Genotype Blocking Compressor (GBC), a method for rapidly compressing large-scale genotypes into a fast-accessible and highly parallelizable format. We demonstrate that GBC has a competitive compression ratio to help save storage space. Furthermore, GBC is the fastest method to access and manage compressed large-scale genotype files (sorting, merging, splitting, etc.). Our results indicate that GBC can help resolve the fundamental problem of time- and space-consuming computation with large-scale genotypes, and conventional analysis would be substantially enhanced if integrated with GBC to access genotypes. Therefore, GBC's advanced data structure and algorithms will accelerate future population-based biomedical research involving big genomics data.

scholarly journals Ten Recommendations for Supporting Open Pathogen Genomic Analysis in Public Health Settings

2020 ◽  
Author(s):  
Allison Black ◽  
Duncan R. MacCannell ◽  
Thomas R. Sibley ◽  
Trevor Bedford
Keyword(s):  
Public Health ◽  
Population Dynamics ◽  
Large Scale ◽  
Genomic Analysis ◽  
Molecular Data ◽  
Whole Genome ◽  
Public Health Agencies ◽  
Health Agencies ◽  
Scale Population ◽  
Informatics Infrastructure

Public health agencies are increasingly using pathogen whole genome sequencing (WGS) to support surveillance and epidemiologic investigations. As access to WGS has grown, greater amounts of molecular data have helped improve our ability to detect outbreaks, investigate transmission chains, and explore large-scale population dynamics, such as the spread of antibiotic resistance. However, the wide adoption of WGS also poses challenges due to the amount of data generated and the need to transform raw data prior to analysis. This complexity means that public health agencies may need more advanced computational infrastructure, a broader technical workforce, and new approaches to data management and stewardship. As both a guide for how this development could occur, and a place to initiate discussion, we describe ten proposals for developing and supporting an informatics infrastructure for public health.

scholarly journals Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis

2020 ◽  
Author(s):  
Ramses Gallegos-Monterrosa ◽  
Mathilde Nordgaard Christensen ◽  
Tino Barchewitz ◽  
Sonja Koppenhöfer ◽  
B. Priyadarshini ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Bacillus Subtilis ◽  
Genome Sequencing ◽  
Cell Communication ◽  
Growth Conditions ◽  
Ecological Niches ◽  
Genetic Adaptation ◽  
Whole Genome ◽  
Dna Barcodes ◽  
The Impact

AbstractMicrobes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.

scholarly journals Population Dynamics of Staphylococcus aureus in Cystic Fibrosis Patients To Determine Transmission Events by Use of Whole-Genome Sequencing

2017 ◽  
Vol 55 (7) ◽  
pp. 2143-2152 ◽  
Author(s):  
Andrea Ankrum ◽  
Barry G. Hall
Keyword(s):  
Cystic Fibrosis ◽  
Staphylococcus Aureus ◽  
Population Dynamics ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phylogenetic Trees ◽  
Hospital Environment ◽  
Snp Analysis ◽  
Whole Genome ◽  
Content Type

ABSTRACT Strict infection control practices have been implemented for health care visits by cystic fibrosis (CF) patients in an attempt to prevent transmission of important pathogens. This study used whole-genome sequencing (WGS) to determine strain relatedness and assess population dynamics of Staphylococcus aureus isolates from a cohort of CF patients as assessed by strain relatedness. A total of 311 S. aureus isolates were collected from respiratory cultures of 115 CF patients during a 22-month study period. Whole-genome sequencing was performed, and using single nucleotide polymorphism (SNP) analysis, phylogenetic trees were assembled to determine relatedness between isolates. Methicillin-resistant Staphylococcus aureus (MRSA) phenotypes were predicted using PPFS2 and compared to the observed phenotype. The accumulation of SNPs in multiple isolates obtained over time from the same patient was examined to determine if a genomic molecular clock could be calculated. Pairs of isolates with ≤71 SNP differences were considered to be the “same” strain. All of the “same” strain isolates were either from the same patient or siblings pairs. There were 47 examples of patients being superinfected with an unrelated strain. The predicted MRSA phenotype was accurate in all but three isolates. Mutation rates were unable to be determined because the branching order in the phylogenetic tree was inconsistent with the order of isolation. The observation that transmissions were identified between sibling patients shows that WGS is an effective tool for determining transmission between patients. The observation that transmission only occurred between siblings suggests that Staphylococcus aureus acquisition in our CF population occurred outside the hospital environment and indicates that current infection prevention efforts appear effective.

scholarly journals Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ramses Gallegos-Monterrosa ◽  
Mathilde Nordgaard Christensen ◽  
Tino Barchewitz ◽  
Sonja Koppenhöfer ◽  
B. Priyadarshini ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Bacillus Subtilis ◽  
Genome Sequencing ◽  
Cell Communication ◽  
Growth Conditions ◽  
Ecological Niches ◽  
Genetic Adaptation ◽  
Whole Genome ◽  
Dna Barcodes ◽  
The Impact

AbstractMicrobes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.

scholarly journals Estimates of vital rates and predictions of population dynamics change along a long-term monitoring program

2017 ◽  
Author(s):  
Simone Vincenzi ◽  
Dusan Jesensek ◽  
Alain J. Crivelli
Keyword(s):  
Population Dynamics ◽  
Salmo Trutta ◽  
Monitoring Program ◽  
Individual Growth ◽  
Vital Rates ◽  
Size Change ◽  
Marble Trout ◽  
Average Survival ◽  
Future Population

AbstractDespite the widespread recognition of the importance of monitoring, only a few studies have investigated how estimates of vital rates and predictions of population dynamics change with additional data collected along the monitoring program. We investigate how using the same models estimates of survival, individual growth, along with predictions about future population size change with additional years of monitoring and data collected, using as a model system freshwater populations of marble (Salmo marmoratus), rainbow (Oncorhynchus mykiss), and brown trout (Salmo trutta L.) living in Western Slovenian streams. Fish were sampled twice a year between 2004 and 2015. We found that in 3 out of 4 populations, a few years of data (3 or 4 sampling occasions, between 300 and 500 tagged individuals for survival, 100 to 200 for growth) provided the same estimates of average survival and growth as those obtained with data from more than 15 sampling occasions, while the estimation of the range of survival required more sampling occasions (up to 22 for marble trout), with little reduction of uncertainty around the point estimates. Predictions of mean density and variation in density over time did not change with more data collected after the first 5 years (i.e., 10 sampling occasions) and overall were within 10% of the observed mean and variation in density over the whole monitoring program.

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