scholarly journals Bayesian inference of population expansions in domestic bovines

2007 ◽  
Vol 3 (4) ◽  
pp. 449-452 ◽  
Author(s):  
E.K Finlay ◽  
C Gaillard ◽  
S.M.F Vahidi ◽  
S.Z Mirhoseini ◽  
H Jianlin ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Demographic History ◽  
Population Expansion ◽  
Parametric Model ◽  
African Buffalo ◽  
Domestic Species ◽  
The Past ◽  
In The Wild ◽  
Past Population ◽  
Bayesian Skyline Plots

The past population dynamics of four domestic and one wild species of bovine were estimated using Bayesian skyline plots, a coalescent Markov chain Monte Carlo method that does not require an assumed parametric model of demographic history. Four domestic species share a recent rapid population expansion not visible in the wild African buffalo ( Syncerus caffer ). The estimated timings of the expansions are consistent with the archaeological records of domestication.

Beyond Deep Learning: An Econometric Example

2020 ◽  
Vol 28 (Supp01) ◽  
pp. 31-38 ◽  
Author(s):  
Ruofan Liao ◽  
Paravee Maneejuk ◽  
Songsak Sriboonchitta
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Prediction Models ◽  
Original Data ◽  
Parametric Model ◽  
Parametric Models ◽  
The Past ◽  
Currency Exchange ◽  
Currency Exchange Rate ◽  
Linear And Nonlinear

In the past, in many areas, the best prediction models were linear and nonlinear parametric models. In the last decade, in many application areas, deep learning has shown to lead to more accurate predictions than the parametric models. Deep learning-based predictions are reasonably accurate, but not perfect. How can we achieve better accuracy? To achieve this objective, we propose to combine neural networks with parametric model: namely, to train neural networks not on the original data, but on the differences between the actual data and the predictions of the parametric model. On the example of predicting currency exchange rate, we show that this idea indeed leads to more accurate predictions.

scholarly journals Temporal fluctuations of Y-chromosomal variation in Bos taurus

2008 ◽  
Vol 4 (6) ◽  
pp. 752-754 ◽  
Author(s):  
Emma Svensson ◽  
Anders Götherström
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Demographic History ◽  
Northern Europe ◽  
Chromosomal Gene ◽  
Chromosomal Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Domestic Species ◽  
History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

scholarly journals Reef development and Sea level changes drive Acanthaster Population Expansion in the Indo-Pacific region

2020 ◽  
Author(s):  
P.C. Pretorius ◽  
T.B. Hoareau
Keyword(s):  
Population Size ◽  
Sea Level ◽  
Environmental Changes ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Population Level ◽  
Sea Level Changes ◽  
Reef Development ◽  
Curve Fitting Method

AbstractMolecular clock calibration is central in population genetics as it provides an accurate inference of demographic history, whereby helping with the identification of driving factors of population changes in an ecosystem. This is particularly important for coral reef species that are seriously threatened globally and in need of conservation. Biogeographic events and fossils are the main source of calibration, but these are known to overestimate timing and parameters at population level, which leads to a disconnection between environmental changes and inferred reconstructions. Here, we propose the Last Glacial Maximum (LGM) calibration that is based on the assumptions that reef species went through a bottleneck during the LGM, which was followed by an early yet marginal increase in population size. We validated the LGM calibration using simulations and genetic inferences based on Extended Bayesian Skyline Plots. Applying it to mitochondrial sequence data of crown-of-thorns starfish Acanthaster spp., we obtained mutation rates that were higher than phylogenetically based calibrations and varied among populations. The timing of the greatest increase in population size differed slightly among populations, but all started between 10 and 20 kya. Using a curve-fitting method, we showed that Acanthaster populations were more influenced by sea-level changes in the Indian Ocean and by reef development in the Pacific Ocean. Our results illustrate that the LGM calibration is robust and can probably provide accurate demographic inferences in many reef species. Application of this calibration has the potential to help identify population drivers that are central for the conservation and management of these threatened ecosystems.

scholarly journals Population Dynamics in Pre-Modern China

2013 ◽  
Author(s):  
Zhongwei Zhao
Keyword(s):  
Economic Development ◽  
Population Growth ◽  
Chinese Population ◽  
Environmental Changes ◽  
Demographic History ◽  
Social Institutions ◽  
Population History ◽  
Chinese History ◽  
Population Changes ◽  
The Past

China constituted one of the earliest civilizations in the world. During most of the past two millennia, China was also one of the most advanced economies and the home of around a quarter of the world’s population. By the start of the first millennium, the Chinese population was already about sixty million. In the next two thousand years, China’s population growth and economic development significantly influenced the world’s population changes and history. Partly for these reasons, in the study of population and social history, China’s historical population growth, demographic regimes, marriage patterns, and household formation systems are frequently used as examples in the discussion of population changes, microsocial structure, and their relationships with natural resources and economic development in past times. Population changes were one of the key components of Chinese history. The size and density of the population, the rise and fall of fertility and mortality, and the increase and decrease of population movements were not only related to demographic factors such as age structure. They were also strongly affected by political and economic conditions, social institutions and cultural traditions, and natural and social environments. Therefore, studies of demographic history, those conducted recently in particular, often shed new light on economic, political, social, and environmental changes in the past. This bibliography, through reviewing major works published in Chinese and English, provides an introduction to China’s main historical population data sources, major research questions, and debates in the study of Chinese population history. It also introduces recent advances in Chinese historical demography and important research findings made by these developments.

scholarly journals The projection of a test genome onto a reference population and applications to humans and archaic hominins

2014 ◽  
Author(s):  
Melinda A Yang ◽  
Kelley Harris ◽  
Montgomery Slatkin
Keyword(s):  
Numerical Analysis ◽  
Population Size ◽  
Demographic History ◽  
Reference Population ◽  
Average Weight ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Test Genome ◽  
History Of ◽  
Past Population

We introduce a method for comparing a test genome with numerous genomes from a reference population. Sites in the test genome are given a weight w that depends on the allele frequency x in the reference population. The projection of the test genome onto the reference population is the average weight for each x, w(x). The weight is assigned in such a way that if the test genome is a random sample from the reference population, w(x)=1. Using analytic theory, numerical analysis, and simulations, we show how the projection depends on the time of population splitting, the history of admixture and changes in past population size. The projection is sensitive to small amounts of past admixture, the direction of admixture and admixture from a population not sampled (a ghost population). We compute the projection of several human and two archaic genomes onto three reference populations from the 1000 Genomes project, Europeans (CEU), Han Chinese (CHB) and Yoruba (YRI) and discuss the consistency of our analysis with previously published results for European and Yoruba demographic history. Including higher amounts of admixture between Europeans and Yoruba soon after their separation and low amounts of admixture more recently can resolve discrepancies between the projections and demographic inferences from some previous studies.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

Genome-wide Assessment Elucidates Connectivity and the Evolutionary History of the Highly Dispersive Marine Invertebrate Littoraria Flava (Littorinidae:Gastropoda)

2020 ◽  
Author(s):  
Thainá Cortez ◽  
Rafael Viana Amaral ◽  
Thadeu Sobral-Souza ◽  
Sonia Andrade
Keyword(s):  
Population Dynamics ◽  
Species Distribution ◽  
Marine Invertebrate ◽  
Demographic History ◽  
Population Expansion ◽  
Marine Ecosystems ◽  
Assignment Test ◽  
Niche Modelling ◽  
Marine Gastropod ◽  
Haplotype Networks

Abstract Background: An important goal of population genetics studies in marine ecosystems is understanding how connectivity patterns, both spatial and temporal, are influenced by historical and evolutionary factors. When it comes to dispersion and connectivity in marine ecosystems, the role of historical and evolutionary factors over population dynamics andstructure still remains enigmatic. We evaluated the demographic history and population structure of Littoraria flava, a highly dispersive and widely distributed marine gastropod on the Brazilian intertidal zone, to predict the effects of such factors on intrapopulation divergence. To test the hypotheses that (1) the species has historically high levels of geneflow on a macrogeographic spatial scale and (2) the species distribution in rocky shores consists of subpopulations due to high degrees of environmental heterogeneity, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, nuclear internal transcribed spacer 2, and single nucleotide polymorphisms) with niche-based modeling to predict species paleodistribution.Results: Low genetic structure was observed along the coastline, and all clustering and migration analyses supported the high gene flow over long distances hypothesis (> 3,000 km). Three genetic clusters were identified by the assignment test, each mostly composed of individuals from the three sampled regions. No fine-scale variation was observed for any location. The neutrality tests and the haplotype networks suggest that L. flava had experienced population bottleneck followed by population expansion. Both paleodistribution and coalescent simulations highlight that expansion events occurred in the Southeastern coastline during the Pleistocene interglacial cycles (21 kya).Conclusions: This is the first study on the South American coast that highlights the demographic history on a marine gastropod based on genomic markers associated with niche modelling. We found that climatic changes since the interglacial periods are potentially relevant drivers for the species distribution in the past. Our findings could enhance the understanding of the population dynamics under an evolutionary view for widely distributed non-model marine organisms.

The Over-estimation of the Flux Density of Weak Radio Sources

1969 ◽  
Vol 1 (5) ◽  
pp. 233-234
Author(s):  
H. S. Murdoch
Keyword(s):  
Monte Carlo ◽  
Flux Density ◽  
Lower Limit ◽  
Error Distribution ◽  
Radio Sources ◽  
Systematic Bias ◽  
Digital Recording ◽  
Analysis Techniques ◽  
Monte Carlo Techniques ◽  
The Past

The over-estimation of the flux density of radio sources near the lower limit of a survey has often been considered in the past. The use of digital recording and analysis techniques now enables a quantitative approach to the problem. Monte Carlo techniques may be used to determine the error distribution, including any systematic bias.

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