scholarly journals Learning the properties of adaptive regions with functional data analysis

2019 ◽  
Author(s):  
Mehreen R. Mughal ◽  
Hillary Koch ◽  
Jinguo Huang ◽  
Francesca Chiaromonte ◽  
Michael DeGiorgio
Keyword(s):  
Functional Data ◽  
Human Population ◽  
Genomic Data ◽  
Continuous Functions ◽  
Modern Human ◽  
Beneficial Mutation ◽  
Adaptive Introgression ◽  
Complex Modes ◽  
Data Points ◽  
Selection Parameters

AbstractIdentifying regions of positive selection in genomic data remains a challenge in population genetics. Most current approaches rely on comparing values of summary statistics calculated in windows. We present an approach termed SURFDAWave, which translates measures of genetic diversity calculated in genomic windows to functional data. By transforming our discrete data points to be outputs of continuous functions defined over genomic space, we are able to learn the features of these functions that signify selection. This enables us to confidently identify complex modes of natural selection, including adaptive introgression. We are also able to predict important selection parameters that are responsible for shaping the inferred selection events. By applying our model to human population-genomic data, we recapitulate previously identified regions of selective sweeps, such as OCA2 in Europeans, and predict that its beneficial mutation reached a frequency of 0.02 before it swept 1,802 generations ago, a time when humans were relatively new to Europe. In addition, we identify BNC2 in Europeans as a target of adaptive introgression, and predict that it harbors a beneficial mutation that arose in an archaic human population that split from modern humans within the hypothesized modern human-Neanderthal divergence range.

scholarly journals Inferring Adaptive Introgression Using Hidden Markov Models

2020 ◽  
Author(s):  
Jesper Svedberg ◽  
Vladimir Shchur ◽  
Solomon Reinman ◽  
Rasmus Nielsen ◽  
Russell Corbett-Detig
Keyword(s):  
Markov Models ◽  
Hidden Markov ◽  
Genomic Data ◽  
Diverse Populations ◽  
Powerful Method ◽  
Adaptive Genetic Variation ◽  
Adaptive Introgression ◽  
Population Genomic ◽  
Significant Interest ◽  
Selection Parameters

AbstractAdaptive introgression - the flow of adaptive genetic variation between species or populations - has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a Hidden Markov Model based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized datasets for realistic population and selection parameters. We apply Ancestry_HMM-S to a dataset of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in datasets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.

scholarly journals Functional Data Analysis in Sport Science: Example of Swimmers’ Progression Curves Clustering

2018 ◽  
Vol 8 (10) ◽  
pp. 1766 ◽  
Author(s):  
Arthur Leroy ◽  
Andy MARC ◽  
Olivier DUPAS ◽  
Jean Lionel REY ◽  
Servane Gey
Keyword(s):  
Data Analysis ◽  
Functional Data Analysis ◽  
Functional Data ◽  
Clustering Algorithms ◽  
Principal Component ◽  
Continuous Functions ◽  
Functional Principal Component Analysis ◽  
Data Set ◽  
Functional Clustering ◽  
Sport Science

Many data collected in sport science come from time dependent phenomenon. This article focuses on Functional Data Analysis (FDA), which study longitudinal data by modelling them as continuous functions. After a brief review of several FDA methods, some useful practical tools such as Functional Principal Component Analysis (FPCA) or functional clustering algorithms are presented and compared on simulated data. Finally, the problem of the detection of promising young swimmers is addressed through a curve clustering procedure on a real data set of performance progression curves. This study reveals that the fastest improvement of young swimmers generally appears before 16 years old. Moreover, several patterns of improvement are identified and the functional clustering procedure provides a useful detection tool.

scholarly journals An ecocultural model predicts Neanderthal extinction through competition with modern humans

2016 ◽  
Vol 113 (8) ◽  
pp. 2134-2139 ◽  
Author(s):  
William Gilpin ◽  
Marcus W. Feldman ◽  
Kenichi Aoki
Keyword(s):  
Cultural Change ◽  
Human Population ◽  
Competitive Exclusion ◽  
Modern Human ◽  
Learning Ability ◽  
Volterra Model ◽  
Modern Humans ◽  
Interacting Species ◽  
The Difference ◽  
Cultural Competition

Archaeologists argue that the replacement of Neanderthals by modern humans was driven by interspecific competition due to a difference in culture level. To assess the cogency of this argument, we construct and analyze an interspecific cultural competition model based on the Lotka−Volterra model, which is widely used in ecology, but which incorporates the culture level of a species as a variable interacting with population size. We investigate the conditions under which a difference in culture level between cognitively equivalent species, or alternatively a difference in underlying learning ability, may produce competitive exclusion of a comparatively (although not absolutely) large local Neanderthal population by an initially smaller modern human population. We find, in particular, that this competitive exclusion is more likely to occur when population growth occurs on a shorter timescale than cultural change, or when the competition coefficients of the Lotka−Volterra model depend on the difference in the culture levels of the interacting species.

scholarly journals Denisovan ancestry and population history of early East Asians

2020 ◽  
Author(s):  
Diyendo Massilani ◽  
Laurits Skov ◽  
Mateja Hajdinjak ◽  
Byambaa Gunchinsuren ◽  
Damdinsuren Tseveendorj ◽  
...  
Keyword(s):  
Gene Flow ◽  
Human Population ◽  
Modern Human ◽  
Population History ◽  
East Asians ◽  
Aboriginal Australians ◽  
North East ◽  
History Of ◽  
Female Member ◽  
Admixture Event

AbstractWe present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in North East Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

Prevalence and Adaptive Impact of Introgression

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Nathaniel B. Edelman ◽  
James Mallet
Keyword(s):  
Genetic Variation ◽  
Adaptive Evolution ◽  
Genetic Variants ◽  
Genomic Data ◽  
Annual Review ◽  
Publication Date ◽  
Adaptive Introgression ◽  
Changing Environments ◽  
Potential Benefits

Alleles that introgressed between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Skulls That Speak

2017 ◽  
Vol 3 (2) ◽  
Author(s):  
Antoine Balzeau
Keyword(s):  
Human Population ◽  
Modern Human ◽  
Population History ◽  
Human Language ◽  
Human Skull

Antoine Balzeau critically reviews a recent paper by Hugo Reyes-Centeno, Katerina Harvati, and Gerhard Jäger, “Tracking Modern Human Population History from Linguistic and Cranial Phenotype” that argues for a link between the development of human language and the evolving shape of the human skull.

scholarly journals Denisovan ancestry and population history of early East Asians

Science ◽  
2020 ◽  
Vol 370 (6516) ◽  
pp. 579-583
Author(s):  
Diyendo Massilani ◽  
Laurits Skov ◽  
Mateja Hajdinjak ◽  
Byambaa Gunchinsuren ◽  
Damdinsuren Tseveendorj ◽  
...  
Keyword(s):  
Gene Flow ◽  
Human Population ◽  
Modern Human ◽  
Population History ◽  
East Asians ◽  
Aboriginal Australians ◽  
History Of ◽  
East And West ◽  
Female Member ◽  
Admixture Event

We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in northeastern Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

Frontal sinus ontogeny and covariation with bone structures in a modern human population

2018 ◽  
Vol 279 (7) ◽  
pp. 871-882
Author(s):  
Marina L. Sardi ◽  
G. Germán Joosten ◽  
Cynthia D. Pandiani ◽  
María Mercedes Gould ◽  
Marisol Anzelmo ◽  
...  
Keyword(s):  
Frontal Sinus ◽  
Human Population ◽  
Modern Human ◽  
Bone Structures
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