scholarly journals Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 506 ◽  
Author(s):  
Catarina Branco ◽  
Miguel Arenas
Keyword(s):  
Human Evolution ◽  
Simulated Data ◽  
Real Data ◽  
Population Admixture ◽  
Evolutionary Processes ◽  
Long Distance ◽  
History Of ◽  
Pros And Cons ◽  
Alternative Scenarios ◽  
And Migration

Selecting among alternative scenarios of human evolution is nowadays a common methodology to investigate the history of our species. This strategy is usually based on computer simulations of genetic data under different evolutionary scenarios, followed by a fitting of the simulated data with the real data. A recent trend in the investigation of ancestral evolutionary processes of modern humans is the application of genetic gradients as a measure of fitting, since evolutionary processes such as range expansions, range contractions, and population admixture (among others) can lead to different genetic gradients. In addition, this strategy allows the analysis of the genetic causes of the observed genetic gradients. Here, we review recent findings on the selection among alternative scenarios of human evolution based on simulated genetic gradients, including pros and cons. First, we describe common methodologies to simulate genetic gradients and apply them to select among alternative scenarios of human evolution. Next, we review previous studies on the influence of range expansions, population admixture, last glacial period, and migration with long-distance dispersal on genetic gradients for some regions of the world. Finally, we discuss this analytical approach, including technical limitations, required improvements, and advice. Although here we focus on human evolution, this approach could be extended to study other species.

Getting Beyond the Apemen

2021 ◽  
pp. 1-18
Author(s):  
Lesley Newson ◽  
Peter J. Richerson
Keyword(s):  
At Risk ◽  
Natural Selection ◽  
Human Evolution ◽  
Evolutionary Process ◽  
Adult Males ◽  
Evolutionary Processes ◽  
Complex Information ◽  
History Of ◽  
Evolution By Natural Selection

This introductory chapter explains why a new story of human evolution is needed, and also lays the foundations of the story told in this book. One of the reasons we need a new story is that previous stories have concentrated on what our male ancestors were doing. Since survival is most at risk in the first years of life, it makes much more sense to concentrate on children and their mothers than on adult males. A brief account of the history of ideas in evolution by natural selection and human evolution provides readers with a background in evolutionary processes. Humans are a product of evolution, but we are not like other animals, because we are connected and readily share complex information. We are unique and our evolution was the result of a unique evolutionary process. To understand ourselves in evolutionary terms, it’s necessary to consider two intertwined evolutionary processes—genes and culture.

scholarly journals Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bin Huang ◽  
Guozheng Wei ◽  
Bing Wang ◽  
Fusong Ju ◽  
Yi Zhong ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Simulated Data ◽  
Real Data ◽  
Long Distance ◽  
Distance Information ◽  
Evaluation Strategy ◽  
Evaluation Procedures ◽  
Optical Maps ◽  
Improved Accuracy ◽  
Enzyme Recognition

Abstract Background Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be “searching followed by evaluation”, which is infeasible for long gaps, or “searching by evaluation”, which heavily relies on heuristics and thus usually yields unreliable contig paths. Results We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds. Conclusion Our approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing “searching by evaluation” strategy that relies on heuristics. Furthermore, unlike the “searching followed by evaluation” strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency.

scholarly journals Modeling Continuous Admixture

2015 ◽  
Author(s):  
Ying Zhou ◽  
Hongxiang Qiu ◽  
Shuhua Xu
Keyword(s):  
Computer Simulation ◽  
Gene Flow ◽  
Driving Forces ◽  
Real Data ◽  
Modern Human ◽  
Human Migration ◽  
Population Admixture ◽  
Medical Studies ◽  
Isolated Populations ◽  
History Of

Human migration and human isolation serve as the driving forces of modern human civilization. Recent migrations of long isolated populations has resulted in genetically admixed populations. The history of population admixture is generally complex; however, understanding the admixture process is critical to both evolutionary and medical studies. Here, we utilized admixture induced linkage disequilibrium (LD) to infer occurrence of continuous admixture events, which is common for most existing admixed populations. Unlike previous studies, we expanded the typical continuous admixture model to a more general admixture scenario with isolation after a certain duration of continuous gene flow, and we demonstrated that such treatment significantly improved the accuracy of inference under complex admixture scenarios. Based on the extended models, we developed a method based on weighted LD to infer the admixture history considering continuous and complex demographic process of gene flow between populations. We evaluated the performance of the method by computer simulation and applied our method to real data analysis of a few well-known admixed populations.

scholarly journals Distribution and migration of saithe (Pollachius virens) around Iceland inferred from mark-recapture studies

2007 ◽  
Vol 64 (5) ◽  
pp. 1006-1016 ◽  
Author(s):  
Hlynur Armannsson ◽  
Sigurdur Th. Jonsson ◽  
John D. Neilson ◽  
Gudrun Marteinsdottir
Keyword(s):  
Large Scale ◽  
Population Based ◽  
Fishing Effort ◽  
Stock Structure ◽  
Population Parameters ◽  
Long Distance ◽  
Mark Recapture ◽  
History Of ◽  
Migratory Routes ◽  
And Migration

Abstract Armannsson, H., Jonsson, S. Th., Neilson, J. D., and Marteinsdottir, G. 2007. Distribution and migration of saithe (Pollachius virens) around Iceland inferred from mark-recapture studies. – ICES Journal of Marine Science, 64: 1006–1016. Knowledge of the distribution and migration of populations is necessary to identify and conserve stock components and therefore genetic variability. Compared with other gadoid species, little is known about the life history of saithe (Pollachius virens) (known as pollock in the Northwest Atlantic) or its stock components. About 15 800 saithe were tagged near Iceland from 2000 to 2004 to estimate population parameters, to describe saithe dynamics on the Icelandic shelf, and to monitor long-distance migrations, should they occur. A multiplicative model was used to standardize fishing effort to describe the distribution of the tagged population, based on tag returns from the fishery. Saithe have a high affinity to their tagging area, but move considerably within that area. Because of variability in fishing effort among areas, tagged fish exhibit different area-specific catchabilities. The results also indicate seasonal offshore–inshore migrations during summer and variability in migratory routes among different tagging areas related to affinities to different feeding grounds. This could indicate a more complex stock structure than previously thought. Finally, results to date do not indicate large-scale emigration of saithe from Icelandic fishing grounds.

scholarly journals Haplotype Threading: Accurate Polyploid Phasing from Long Reads

2020 ◽  
Author(s):  
Sven D. Schrinner ◽  
Rebecca Serra Mari ◽  
Jana Ebler ◽  
Mikko Rautiainen ◽  
Lancelot Seillier ◽  
...  
Keyword(s):  
Scoring Function ◽  
Simulated Data ◽  
Real Data ◽  
Error Rates ◽  
Sequencing Data ◽  
Data Set ◽  
Current State ◽  
Long Reads ◽  
History Of ◽  
Genomic Regions

AbstractResolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. As a highly complex computational problem, polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WhatsHap polyphase, a novel two-stage approach that addresses these challenges by (i) clustering reads using a position-dependent scoring function and (ii) threading the haplotypes through the clusters by dynamic programming. We demonstrate on a simulated data set that this results in accurate haplotypes with switch error rates that are around three times lower than those obtainable by the current state-of-the-art and even around seven times lower in regions of collapsing haplotypes. Using a real data set comprising long and short read tetraploid potato sequencing data we show that WhatsHap polyphase is able to phase the majority of the potato genes after error correction, which enables the assembly of local genomic regions of interest at haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap and ready to be included in production settings.

scholarly journals The global sphere reconstruction (GSR)

2018 ◽  
Vol 620 ◽  
pp. A40
Author(s):  
A. Vecchiato ◽  
B. Bucciarelli ◽  
M. G. Lattanzi ◽  
U. Becciani ◽  
L. Bianchi ◽  
...  
Keyword(s):  
Data Reduction ◽  
Simulated Data ◽  
Real Data ◽  
Iterative Solution ◽  
Lessons Learned ◽  
Reconstruction Method ◽  
History Of Astronomy ◽  
Software Modules ◽  
History Of ◽  
Absolute Measurements

Context.TheGaiaESA mission will estimate the astrometric and physical data of more than one billion objects, providing the largest and most precise catalog of absolute astrometry in the history of astronomy. The core of this process, the so-called global sphere reconstruction, is represented by the reduction of a subset of these objects which will be used to define the celestial reference frame. As the HIPPARCOSmission showed, and as is inherent to all kinds of absolute measurements, possible errors in the data reduction can hardly be identified from the catalog, thus potentially introducing systematic errors in all derived work.Aims.Following up on the lessons learned from HIPPARCOS, our aim is thus to develop an independent sphere reconstruction method that contributes to guarantee the quality of the astrometric results without fully reproducing the main processing chain.Methods.Indeed, given the unfeasibility of a complete replica of the data reduction pipeline, an astrometric verification unit (AVU) was instituted by theGaiaData Processing and Analysis Consortium (DPAC). One of its jobs is to implement and operate an independent global sphere reconstruction (GSR), parallel to the baseline one (AGIS, namely Astrometric Global Iterative Solution) but limited to the primary stars and for validation purposes, to compare the two results, and to report on any significant differences.Results.Tests performed on simulated data show that GSR is able to reproduce at the sub-μas level the results of the AGIS demonstration run.Conclusions.Further development is ongoing to improve on the treatment of real data and on the software modules that compare the AGIS and GSR solutions to identify possible discrepancies above the tolerance level set by the accuracy of theGaiacatalog.

scholarly journals Modeling Continuous Admixture

2015 ◽  
Author(s):  
Ying Zhou ◽  
Hongxiang Qiu ◽  
Shuhua Xu
Keyword(s):  
Computer Simulation ◽  
Gene Flow ◽  
Driving Forces ◽  
Real Data ◽  
Modern Human ◽  
Human Migration ◽  
Population Admixture ◽  
Medical Studies ◽  
Isolated Populations ◽  
History Of

Human migration and human isolation serve as the driving forces of modern human civilization. Recent migrations of long isolated populations have resulted in genetically admixed populations. The history of population admixture is generally complex; however, understanding the admixture process is critical to both evolutionary and medical studies. Here, we utilized admixture induced linkage disequilibrium (LD) to infer occurrence of continuous admixture events, which is common for most existing admixed populations. Unlike previous studies, we expanded the typical continuous admixture model to a more general admixture scenario with isolation after a certain duration of continuous gene flow. Based on the extended models, we developed a method based on weighted LD to infer the admixture history considering continuous and complex demographic process of gene flow between populations. We evaluated the performance of the method by computer simulation and applied our method to real data analysis of a few well-known admixed populations.

Intraocular tuberculosis, a challenge in diagnosis and treatment

2020 ◽  
Vol 3 ◽  
pp. 4
Author(s):  
Martina Larroude ◽  
Gustavo Ariel Budmann
Keyword(s):  
Developing Countries ◽  
Clinical Signs ◽  
Steady Increase ◽  
Ocular Tuberculosis ◽  
Industrial Countries ◽  
Choroidal Granuloma ◽  
History Of ◽  
And Migration ◽  
Ocular Tb

Ocular tuberculosis (TB) is an extrapulmonary tuberculous condition and has variable manifestations. The incidence of TB is still high in developing countries, and a steady increase in new cases has been observed in industrial countries as a result of the growing number of immunodeficient patients and migration from developing countries. Choroidal granuloma is a rare and atypical location of TB. We present a case of a presumptive choroidal granuloma. This case exposes that diagnosis can be remarkably challenging when there is no history of pulmonary TB. The recognition of clinical signs of ocular TB is extremely important since it provides a clinical pathway toward tailored investigations and decision making for initiating anti-TB therapy and to ensure a close follow-up to detect the development of any complication.

Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

2019 ◽  
Vol 104 (1) ◽  
pp. 33-48 ◽  
Author(s):  
Alejandro Zuluaga ◽  
Martin Llano ◽  
Ken Cameron
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
R Package ◽  
Morphological Characters ◽  
Ancestral State ◽  
Seed Shape ◽  
Long Distance ◽  
The Pacific ◽  
And Migration ◽  
The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

Herbal Medicine: Clinical Perspective & Regulatory Status

2020 ◽  
Vol 23 ◽  
Author(s):  
Md Abul Barkat ◽  
Anjali Goyal ◽  
Harshita Abul Barkat ◽  
Mohammad Salauddin ◽  
Faheem Hyder Pottoo ◽  
...  
Keyword(s):  
Herbal Medicine ◽  
Herbal Medicines ◽  
New Drugs ◽  
Herbal Drugs ◽  
Clinical Perspective ◽  
Regulatory Status ◽  
Novel Drugs ◽  
History Of ◽  
Pros And Cons ◽  
Health Complications

Abstract:: Herbal medicines pays an important in treating the vaious diseases mainly due to the their potentially high therapeutic values and also due to the better acceptance of vaioruspatient under different health complications. The herbal medicine practice involves use of part of plant, entire plant or the selectctive isolated phytomedicineand the use and practices based on these has its pros and cons and has been greatly affected during the dawn. The search of new drugs during scientific era revives the interest in discovery of herbal drugs from different natural resources during 20th century. The present modern healthcare system invovlves utilization drugs and 50% of them are of ofnaural origin. Herbal drug disocovery found to be highly costly affair with low success rate and it hinders the further progress in utilizting the phytomedicine in treating the various deseases. But in recent years there is an increase in the search interest of herbal drugs mainly by the pharmaceutical industry and those invoves in the search of novel drugs from the herbs. Discovery of such new novel phytomedicines has to overcomes various challenges in indentification of active extracts and their toxicity, advereffects, herb drug interaction and importantly their regulatory requirments. The present review mainly focused on the history of herbal medicine, current clinical perspective, pharmaceutical, and regulatory challenges as well as its clinical presentation. Moreover, problems encountered in drug discovery from herbal resources and its possible solutions are delineated.

Sign in / Sign up

Export Citation Format

Share Document