scholarly journals Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec

2022 ◽  
Author(s):  
Morgan Dedato ◽  
Claude Robert ◽  
Joëlle Taillon ◽  
Aaron Shafer ◽  
Steve Cote
Keyword(s):  
Rangifer Tarandus ◽  
Demographic History ◽  
Genomic Diversity ◽  
Model Parameters ◽  
Demographic Model ◽  
Conservation Genomics ◽  
Holistic View ◽  
Census Size ◽  
Highly Correlated ◽  
Tajima’S D

The loss of genetic diversity is a challenge many species are facing, and genomics is a potential tool that can inform and prioritize decision making. Caribou populations have experienced significant recent declines throughout Québec, Canada, and some are considered threatened or endangered. We calculated the ancestral and contemporary patterns of genomic diversity of five caribou populations and applied a comparative framework to assess the interplay between demography and genomic diversity. We calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates. Whole genome re-sequencing was completed on 67 caribou and genotype likelihoods were estimated. We calculated nucleotide diversity, θπ and estimated the coalescent or ancestral Ne, which ranged from 12,030 to 15,513. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. These ratios were highly correlated with genomic signatures (i.e. Tajima’s D) and explicit demographic model parameters. Values of contemporary Ne, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary Ne:NC ratio. Importantly, conservation genetics theory would predict this population to be of less concern based on this ratio. Of note, F varied only slightly between populations, and runs of homozygosity were not abundant in the genome. Our study highlights how genomic patterns are nuanced and misleading if viewed only through a contemporary lens; a holistic view should integrate ancestral Ne and Tajima’s D into conservation decisions.

scholarly journals All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 139
Author(s):  
Marlien M. van der Merwe ◽  
Jia-Yee S. Yap ◽  
Peter D. Wilson ◽  
Helen T. Murphy ◽  
Andrew Ford
Keyword(s):  
Genetic Diversity ◽  
Allelic Variation ◽  
Germplasm Conservation ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Ex Situ ◽  
Spatial Distance ◽  
Genetic Connectivity ◽  
Conservation Genomics ◽  
Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

scholarly journals The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

2019 ◽  
Author(s):  
Lewis G. Spurgin ◽  
Mirte Bosse ◽  
Frank Adriaensen ◽  
Tamer Albayrak ◽  
Christos Barboutis ◽  
...  
Keyword(s):  
Positive Selection ◽  
Recombination Rate ◽  
Demographic History ◽  
Great Tit ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Hapmap Project ◽  
Widespread Species ◽  
Continental Scale ◽  
Genome Wide

AbstractA major aim of evolutionary biology is to understand why patterns of genomic diversity vary among populations and species. Large-scale genomic studies of widespread species are useful for studying how the environment and demographic history shape patterns of genomic divergence, and with the continually decreasing cost of sequencing and genotyping, such studies are now becoming feasible. Here, we carry out one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning almost the entire geographic range of the European great tit subspecies. We found that genome-wide variation was consistent with a recent colonisation across Europe from a single refugium in South-East Europe, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear “islands of differentiation” even among populations with very low levels of genome-wide differentiation. Low local recombination rate in the genome was a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination is a key driver of highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, most likely as a result of recent directional selection at the range edges of this species. Haplotype-based measures of selection were also related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. These regions under positive selection contained candidate genes associated with morphology, thermal adaptation and colouration, providing promising avenues for future investigation. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into evolution.

Reconciling internal and external satisfaction through probabilistic graphical models

2017 ◽  
Vol 9 (3/4) ◽  
pp. 347-370 ◽  
Author(s):  
Flaminia Musella ◽  
Roberta Guglielmetti Mugion ◽  
Hendry Raharjo ◽  
Laura Di Pietro
Keyword(s):  
Customer Satisfaction ◽  
Bayesian Networks ◽  
Graphical Models ◽  
Object Oriented ◽  
Holistic Approach ◽  
Probabilistic Graphical Models ◽  
Model Parameters ◽  
Holistic View ◽  
Content Type ◽  
External Customer

Purpose This paper aims to holistically reconcile internal and external customer satisfaction using probabilistic graphical models. The models are useful not only in the identification of the most sensitive factors for the creation of both internal and external customer satisfaction but also in the generation of improvement scenarios in a probabilistic way. Design/methodology/approach Standard Bayesian networks and object-oriented Bayesian networks are used to build probabilistic graphical models for internal and external customers. For each ward, the model is used to evaluate satisfaction drivers by category, and scenarios for the improvement of overall satisfaction variables are developed. A global model that is based on an object-oriented network is modularly built to provide a holistic view of internal and external satisfaction. The linkage is created by building a global index of internal and external satisfaction based on a linear combination. The model parameters are derived from survey data from an Italian hospital. Findings The results that were achieved with the Bayesian networks are consistent with the results of previous research, and they were obtained by using a partial least squares path modelling tool. The variable ‘Experience’ is the most relevant internal factor for the improvement of overall patient satisfaction. To improve overall employee satisfaction, the variable ‘Product/service results’ is the most important. Finally, for a given target of overall internal and external satisfaction, external satisfaction is more sensitive to improvement than internal satisfaction. Originality/value The novelty of the paper lies in the efforts to link internal and external satisfaction based on a probabilistic expert system that can generate improvement scenarios. From an academic viewpoint, this study moves the service profit chain theory (Heskett et al., 1994) forward by delivering operational guidelines for jointly managing the factors that affect internal and external customer satisfaction in service organizations using a holistic approach.

Genomic diversity and Demographic History of the Dromiciops genus (Marsupialia: Microbiotheriidae)

2022 ◽  
pp. 107405
Author(s):  
Julian F. Quintero-Galvis ◽  
Pablo Saenz-Agudelo ◽  
Guillermo C. Amico ◽  
Soledad Vazquez ◽  
Aaron B.A. Shafer ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Diversity ◽  
History Of

scholarly journals Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Sara Lado ◽  
Jean Pierre Elbers ◽  
Angela Doskocil ◽  
Davide Scaglione ◽  
Emiliano Trucchi ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Diversity ◽  
Phylogeographic Structure ◽  
Arid Environments ◽  
Migration Patterns ◽  
Migration Rates ◽  
Global Migration ◽  
Genome Wide ◽  
A Genome ◽  
Scale Population

AbstractDromedaries have been essential for the prosperity of civilizations in arid environments and the dispersal of humans, goods and cultures along ancient, cross-continental trading routes. With increasing desertification their importance as livestock species is rising rapidly, but little is known about their genome-wide diversity and demographic history. As previous studies using few nuclear markers found weak phylogeographic structure, here we detected fine-scale population differentiation in dromedaries across Asia and Africa by adopting a genome-wide approach. Global patterns of effective migration rates revealed pathways of dispersal after domestication, following historic caravan routes like the Silk and Incense Roads. Our results show that a Pleistocene bottleneck and Medieval expansions during the rise of the Ottoman empire have shaped genome-wide diversity in modern dromedaries. By understanding subtle population structure we recognize the value of small, locally adapted populations and appeal for securing genomic diversity for a sustainable utilization of this key desert species.

scholarly journals Design and Simulation of MEMS Moisture Sensor Using COMSOL Multiphysics Software

2018 ◽  
Vol 7 (4.26) ◽  
pp. 141
Author(s):  
Muhamad Nazrin Ismail ◽  
Noriah Yusoff ◽  
Nor Hayati Saad ◽  
Amirul Abd Rashid
Keyword(s):  
Cost Effective ◽  
Micro Electro Mechanical System ◽  
Experimental Result ◽  
Comsol Multiphysics ◽  
Model Parameters ◽  
Moisture Sensor ◽  
Sensor Sensitivity ◽  
Sensor Devices ◽  
Major Application ◽  
Highly Correlated

Micro-electro-mechanical system (MEMS) is a hybrid technology that combines electronic, electric and mechanical technology in a micron-size system. This allowed for higher performance and multifunction devices fabricated at much lighter weight and cost effective. One of the major application of MEMS is in sensor devices area. This paper highlight the simulation study of a typical moisture sensor fabricated from Tungsten Interdigitated (IDE) MEMS device. Using COMSOL Multiphysics software, the moisture sensor was modelled based on the current material and physical dimension and layout. The model then go through validation proses to its sensitivity performance against the experimental result. Subsequently, the optimization on sensor sensitivity was carried out by varying the model parameters including the sensor physical dimension, working temperature and humidity. The simulation result suggest that the sensor sensitivity is highly correlated to the electrode distance value. The average sensitivity of the sensor improved to ~48% better when the distance between reduced to 50% from 6 micron to 3 micron tested at temperature between 25 ̊ C to 45 ̊ C. This information is valuable as the input to the sensor designer in finalizing the MEMS physical layout in producing highly sensitive moisture sensor devices.  

Dissolved Oxygen Dynamics of a Stream: Model Discrimination and Estimation of Parameter Variability Using an Extended Kalman Filter

1984 ◽  
Vol 16 (5-7) ◽  
pp. 561-569 ◽  
Author(s):  
B J Cosby
Keyword(s):  
Model Identification ◽  
Model Parameters ◽  
Low Light ◽  
Short Period ◽  
Kaiman Filter ◽  
Short And Long Term ◽  
Highly Correlated ◽  
Oxygen Dynamics ◽  
Stream Model

A model identification procedure is presented based on an extended Kaiman filter (EKF) applied to the oxygen mass balance equation of a stream. The procedure is used with data from a small Danish stream to discriminate among eight mathematical models of the photosynthesis-light (P-I) response of macrophytes in the stream. Each model was tested for adequacy using objective criteria based on the expected behavior of the innovations sequence (the time series of differences between predicted and observed oxygen concentrations) derived from the EKF. Temporal variation of the model parameters was also examined using the EKF. The maximum photosynthetic rate (Pm) varied slowly over the year but was essentially stationary within any three to six day period. The low light efficiency of photosynthesis (Eo) varied from day to day within any short period, but three to six day means of Eo were essentially stationary over the year. The ratio (Ik = Pm/Eo) was highly correlated with both short and long term variations in daily mean light intensity.

Making the Most of What We Have: A Practical Application of Multidimensional Item Response Theory in Test Scoring

2005 ◽  
Vol 30 (3) ◽  
pp. 295-311 ◽  
Author(s):  
Jimmy de la Torre ◽  
Richard J. Patz
Keyword(s):  
Item Response ◽  
Practical Method ◽  
Multidimensional Item Response Theory ◽  
Model Parameters ◽  
Practical Application ◽  
Multidimensional Item Response ◽  
Multiple Tests ◽  
Monte Carlo Techniques ◽  
Estimation Of Model Parameters ◽  
Highly Correlated

This article proposes a practical method that capitalizes on the availability of information from multiple tests measuring correlated abilities given in a single test administration. By simultaneously estimating different abilities with the use of a hierarchical Bayesian framework, more precise estimates for each ability dimension are obtained. The efficiency of the proposed method is most pronounced when highly correlated abilities are estimated from multiple short tests. Employing Markov chain Monte Carlo techniques allows for straightforward estimation of model parameters.

scholarly journals Conservation genomics of an Australian orchid complex with implications for the taxonomic and conservation status of Corybas dowlingii

2020 ◽  
Author(s):  
Natascha D. Wagner ◽  
Mark A. Clements ◽  
Lalita Simpson ◽  
Katharina Nargar
Keyword(s):  
Species Complex ◽  
Conservation Status ◽  
Taxonomic Status ◽  
Genomic Diversity ◽  
Hybrid Origin ◽  
Genetic Admixture ◽  
Conservation Genomics ◽  
Closely Related Species ◽  
Genomic Signatures ◽  
Genetic Position

AbstractThis study assessed genomic diversity in an Australian species complex in the helmet orchids to clarify taxonomic delimitation and conservation status of the threatened species Corybas dowlingii, a narrow endemic from southeast Australia. Taxonomic delimitation between the three closely related species C. aconitiflorus, C. barbarae, and C. dowlingii has been mainly based on floral traits which exhibit varying degrees of overlap, rendering species delimitation in the complex difficult. Genomic data for the species complex was generated using double-digest restriction-site associated DNA (ddRAD) sequencing. Maximum likelihood, NeighborNet, and Bayesian structure analyses showed genetic differentiation within the species complex and retrieved genomic signatures consistent with hybridisation and introgression between C. aconitiflorus and C. barbarae, and an intermediate genetic position of C. dowlingii indicating a hybrid origin of the species. The genetic structure analysis showed varying levels of genetic admixture for several C. aconitiflorus, C. barbarae, and C. dowlingii samples, thus further corroborating the presence of hybridisation and introgression within the species complex. The taxonomic status of C. dowlingii D.L.Jones was revised to C. × dowlingii D.L.Jones stat. nov. to reflect its hybrid origin. The conservation status of C. × dowlingii was assessed based on key ecological and ethical aspects, and recommendations made regarding its conservation status in Australian conservation legislation.

scholarly journals GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Ekaterina Noskova ◽  
Vladimir Ulyantsev ◽  
Klaus-Peter Koepfli ◽  
Stephen J O’Brien ◽  
Pavel Dobrynin
Keyword(s):  
Genetic Algorithm ◽  
Allele Frequency ◽  
Frequency Spectrum ◽  
Demographic History ◽  
Model Organisms ◽  
Demographic Model ◽  
Multiple Populations ◽  
Demographic Models ◽  
Allele Frequency Spectrum ◽  
History Of

Abstract Background The demographic history of any population is imprinted in the genomes of the individuals that make up the population. One of the most popular and convenient representations of genetic information is the allele frequency spectrum (AFS), the distribution of allele frequencies in populations. The joint AFS is commonly used to reconstruct the demographic history of multiple populations, and several methods based on diffusion approximation (e.g., ∂a∂i) and ordinary differential equations (e.g., moments) have been developed and applied for demographic inference. These methods provide an opportunity to simulate AFS under a variety of researcher-specified demographic models and to estimate the best model and associated parameters using likelihood-based local optimizations. However, there are no known algorithms to perform global searches of demographic models with a given AFS. Results Here, we introduce a new method that implements a global search using a genetic algorithm for the automatic and unsupervised inference of demographic history from joint AFS data. Our method is implemented in the software GADMA (Genetic Algorithm for Demographic Model Analysis, https://github.com/ctlab/GADMA). Conclusions We demonstrate the performance of GADMA by applying it to sequence data from humans and non-model organisms and show that it is able to automatically infer a demographic model close to or even better than the one that was previously obtained manually. Moreover, GADMA is able to infer multiple demographic models at different local optima close to the global one, providing a larger set of possible scenarios to further explore demographic history.

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