scholarly journals A comprehensive survey of models for dissecting local ancestry deconvolution in human genome

2018 ◽  
Vol 20 (5) ◽  
pp. 1709-1724 ◽  
Author(s):  
Ephifania Geza ◽  
Jacquiline Mugo ◽  
Nicola J Mulder ◽  
Ambroise Wonkam ◽  
Emile R Chimusa ◽  
...  
Keyword(s):  
Modern Human ◽  
Human Populations ◽  
Population Admixture ◽  
Local Ancestry ◽  
The Past ◽  
Challenges And Opportunities ◽  
Adaptive Processes ◽  
Comprehensive Survey ◽  
Simulation Results ◽  
Shed Light

Abstract Over the past decade, studies of admixed populations have increasingly gained interest in both medical and population genetics. These studies have so far shed light on the patterns of genetic variation throughout modern human evolution and have improved our understanding of the demographics and adaptive processes of human populations. To date, there exist about 20 methods or tools to deconvolve local ancestry. These methods have merits and drawbacks in estimating local ancestry in multiway admixed populations. In this article, we survey existing ancestry deconvolution methods, with special emphasis on multiway admixture, and compare these methods based on simulation results reported by different studies, computational approaches used, including mathematical and statistical models, and biological challenges related to each method. This should orient users on the choice of an appropriate method or tool for given population admixture characteristics and update researchers on current advances, challenges and opportunities behind existing ancestry deconvolution methods.

FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data

2019 ◽  
Vol 21 (5) ◽  
pp. 1837-1845
Author(s):  
Ephifania Geza ◽  
Nicola J Mulder ◽  
Emile R Chimusa ◽  
Gaston K Mazandu
Keyword(s):  
Phenotypic Variability ◽  
Modern Human ◽  
Genomic Variation ◽  
Unified Framework ◽  
Local Ancestry ◽  
Human Heredity ◽  
Snp Data ◽  
Variation Patterns ◽  
Adaptive Processes ◽  
Local Ancestry Inference

Abstract Several thousand genomes have been completed with millions of variants identified in the human deoxyribonucleic acid sequences. These genomic variations, especially those introduced by admixture, significantly contribute to a remarkable phenotypic variability with medical and/or evolutionary implications. Elucidating local ancestry estimates is necessary for a better understanding of genomic variation patterns throughout modern human evolution and adaptive processes, and consequences in human heredity and health. However, existing local ancestry deconvolution tools are accessible as individual scripts, each requiring input and producing output in its own complex format. This limits the user’s ability to retrieve local ancestry estimates. We introduce a unified framework for multi-way local ancestry inference, FRANC, integrating eight existing state-of-the-art local ancestry deconvolution tools. FRANC is an adaptable, expandable and portable tool that manipulates tool-specific inputs, deconvolutes ancestry and standardizes tool-specific results. To facilitate both medical and population genetics studies, FRANC requires convenient and easy to manipulate input files and allows users to choose output formats to ease their use in further potential local ancestry deconvolution applications.

scholarly journals Limits of long-term selection against Neandertal introgression

2019 ◽  
Vol 116 (5) ◽  
pp. 1639-1644 ◽  
Author(s):  
Martin Petr ◽  
Svante Pääbo ◽  
Janet Kelso ◽  
Benjamin Vernot
Keyword(s):  
Negative Selection ◽  
Modern Human ◽  
Model Parameters ◽  
Human Populations ◽  
Modern Humans ◽  
High Coverage ◽  
Protein Coding ◽  
The Past ◽  
Wide Range

Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.

scholarly journals MITOMIX, an Algorithm to Reconstruct Population Admixture Histories Indicates Ancient European Ancestry of Modern Hungarians

2018 ◽  
Author(s):  
Zoltán Maróti ◽  
Tibor Török ◽  
Endre Neparáczki ◽  
István Raskó ◽  
István Nagy ◽  
...  
Keyword(s):  
Bronze Age ◽  
Population Level ◽  
European Ancestry ◽  
Human Populations ◽  
Population Admixture ◽  
Genetic Composition ◽  
Depth Analysis ◽  
A Minor ◽  
Past Population ◽  
Shed Light

AbstractBy making use of the increasing number of available mitogenomes we propose a novel population genetic distance metric, named Shared Haplogroup Distance (SHD). Unlike FST, SHD is a true mathematical distance that complies with all metric axioms, which enables our new algorithm (MITOMIX) to detect population-level admixture based on SHD minimum optimization. In order to demonstrate the effectiveness of our methodology we analyzed the relation of 62 modern and 25 ancient Eurasian human populations, and compared our results with the most widely used FST calculation. We also sequenced and performed an in-depth analysis of 272 modern Hungarian mtDNA genomes to shed light on the genetic composition of modern Hungarians. MITOMIX analysis showed that in general admixture occurred between neighboring populations, but in some cases it also indicated admixture with migrating populations. SHD and MITOMIX analysis comply with known genetic data and shows that in case of closely related and/or admixing populations, SHD gives more realistic results and provides better resolution than FST. Our results suggest that the majority of modern Hungarian maternal lineages have Late Neolith/Bronze Age European origins (partially shared also with modern Danish, Belgian/Dutch and Basque populations), and a smaller fraction originates from surrounding (Serbian, Croatian, Slovakian, Romanian) populations. However only a minor genetic contribution (<3%) was identified from the IXth Hungarian Conquerors whom are deemed to have brought Hungarians to the Carpathian Basin. Our analysis shows that SHD and MITOMIX can augment previous methods by providing novel insights into past population processes.

scholarly journals La genètica de les migracions humanes: Seguint el rastre de les migracions a través del nostre genoma

2015 ◽  
pp. 43
Author(s):  
David Comas Martínez
Keyword(s):  
Genetic Diversity ◽  
Academic Disciplines ◽  
Human Populations ◽  
The Past ◽  
Technological Advances ◽  
Scientific Disciplines ◽  
The Future ◽  
Shed Light

Various academic disciplines shed light on human migrations, helping us to reconstruct the past. Studying the genetic diversity of human populations today reveals past demographic and migratory events that have left an imprint on our genome. Armed with knowledge of migrations in prehistoric times, we can test hypotheses put forward in other scientific disciplines. Similarly, the distribution of genetic diversity in the future will largely depend on today’s extensive human migrations, facilitated by technological advances.

China’s Belt & Road Initiative in South Asia: China-Pakistan Economic Corridor: Its Components, Challenges, and Opportunities

2019 ◽  
Author(s):  
Ali Imran
Keyword(s):  
South Asia ◽  
The South ◽  
Study Find ◽  
Challenges And Opportunities ◽  
Shed Light

This study thoroughly shed light on the China's Belt-Road Initiative towards South Asia with particular focus on China-Pakistan Economic Corridor. The study find the number of issue in completion of BRI/CPEC in the South Asia.

Brain-eating Amoebae Infection: Challenges and Opportunities in Chemotherapy

2019 ◽  
Vol 19 (12) ◽  
pp. 980-987 ◽  
Author(s):  
Mohammad Ridwane Mungroo ◽  
Ayaz Anwar ◽  
Naveed Ahmed Khan ◽  
Ruqaiyyah Siddiqui
Keyword(s):  
Mortality Rate ◽  
Free Living ◽  
Outdoor Activities ◽  
The Past ◽  
Free Living Amoeba ◽  
Challenges And Opportunities ◽  
Life Threatening ◽  
The Central Nervous System ◽  
Living Nature ◽  
Treatment And Diagnosis

Pathogenic free-living amoeba are known to cause a devastating infection of the central nervous system and are often referred to as “brain-eating amoebae”. The mortality rate of more than 90% and free-living nature of these amoebae is a cause for concern. It is distressing that the mortality rate has remained the same over the past few decades, highlighting the lack of interest by the pharmaceutical industry. With the threat of global warming and increased outdoor activities of public, there is a need for renewed interest in identifying potential anti-amoebic compounds for successful prognosis. Here, we discuss the available chemotherapeutic options and opportunities for potential strategies in the treatment and diagnosis of these life-threatening infections.

Reputation and Gossip in Game Theory

2019 ◽  
pp. 213-229
Author(s):  
Charles Roddie
Keyword(s):  
Game Theory ◽  
Strategic Behavior ◽  
Third Party ◽  
The Past ◽  
Past Behavior ◽  
Future Behavior ◽  
The Game Theory ◽  
Shed Light

When interacting with others, it is often important for you to know what they have done in similar situations in the past: to know their reputation. One reason is that their past behavior may be a guide to their future behavior. A second reason is that their past behavior may have qualified them for reward and cooperation, or for punishment and revenge. The fact that you respond positively or negatively to the reputation of others then generates incentives for them to maintain good reputations. This article surveys the game theory literature which analyses the mechanisms and incentives involved in reputation. It also discusses how experiments have shed light on strategic behavior involved in maintaining reputations, and the adequacy of unreliable and third party information (gossip) for maintaining incentives for cooperation.

scholarly journals The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Dagmar Waltemath ◽  
Martin Golebiewski ◽  
Michael L Blinov ◽  
Padraig Gleeson ◽  
Henning Hermjakob ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Data Model ◽  
Computational Models ◽  
Life Sciences ◽  
The Past ◽  
Challenges And Opportunities ◽  
Stakeholder Workshop ◽  
Software Engineers ◽  
Future Work ◽  
Modeling In Biology

AbstractThis paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

scholarly journals A review on the electric vehicle routing problems: Variants and algorithms

2021 ◽  
Author(s):  
Hu Qin ◽  
Xinxin Su ◽  
Teng Ren ◽  
Zhixing Luo
Keyword(s):  
Vehicle Routing ◽  
Vehicle Routing Problems ◽  
Location Routing Problem ◽  
Routing Problems ◽  
Routing Problem ◽  
Delivery Problem ◽  
Pickup And Delivery Problem ◽  
The Past ◽  
Location Routing ◽  
Comprehensive Survey

AbstractOver the past decade, electric vehicles (EVs) have been considered in a growing number of models and methods for vehicle routing problems (VRPs). This study presents a comprehensive survey of EV routing problems and their many variants. We only consider the problems in which each vehicle may visit multiple vertices and be recharged during the trip. The related literature can be roughly divided into nine classes: Electric traveling salesman problem, green VRP, electric VRP, mixed electric VRP, electric location routing problem, hybrid electric VRP, electric dial-a-ride problem, electric two-echelon VRP, and electric pickup and delivery problem. For each of these nine classes, we focus on reviewing the settings of problem variants and the algorithms used to obtain their solutions.

scholarly journals 3D Insights into the Effects of Captivity on Wolf Mastication and Their Tooth Marks; Implications in Ecological Studies of Both the Past and Present

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2323
Author(s):  
Lloyd A. Courtenay ◽  
Darío Herranz-Rodrigo ◽  
José Yravedra ◽  
José Mª Vázquez-Rodríguez ◽  
Rosa Huguet ◽  
...  
Keyword(s):  
Data Science ◽  
Surface Modifications ◽  
Human Populations ◽  
Ecological Studies ◽  
The Past ◽  
Carnivore Species ◽  
Different Populations ◽  
Complex Relationships ◽  
As Stress ◽  
Tooth Marks

Human populations have been known to develop complex relationships with large carnivore species throughout time, with evidence of both competition and collaboration to obtain resources throughout the Pleistocene. From this perspective, many archaeological and palaeontological sites present evidence of carnivore modifications to bone. In response to this, specialists in the study of microscopic bone surface modifications have resorted to the use of 3D modeling and data science techniques for the inspection of these elements, reaching novel limits for the discerning of carnivore agencies. The present research analyzes the tooth mark variability produced by multiple Iberian wolf individuals, with the aim of studying how captivity may affect the nature of tooth marks left on bone. In addition to this, four different populations of both wild and captive Iberian wolves are also compared for a more in-depth comparison of intra-species variability. This research statistically shows that large canid tooth pits are the least affected by captivity, while tooth scores appear more superficial when produced by captive wolves. The superficial nature of captive wolf tooth scores is additionally seen to correlate with other metric features, thus influencing overall mark morphologies. In light of this, the present study opens a new dialogue on the reasons behind this, advising caution when using tooth scores for carnivore identification and contemplating how elements such as stress may be affecting the wolves under study.

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