LIVIVO - Search results -

Search results

Result 1 - 10 of total 27

Search options

Article ; Online: A fully integrated machine learning scan of selection in the chimpanzee genome.

Nye, Jessica / Mondal, Mayukh / Bertranpetit, Jaume / Laayouni, Hafid

NAR genomics and bioinformatics

2020 Volume 2, Issue 3, Page(s) lqaa061

Abstract: After diverging, each chimpanzee subspecies has been the target of unique selective pressures. Here, we employ a machine learning approach to classify regions as under positive selection or neutrality genome-wide. The regions determined to be under ... ...

Abstract	After diverging, each chimpanzee subspecies has been the target of unique selective pressures. Here, we employ a machine learning approach to classify regions as under positive selection or neutrality genome-wide. The regions determined to be under selection reflect the unique demographic and adaptive history of each subspecies. The results indicate that effective population size is important for determining the proportion of the genome under positive selection. The chimpanzee subspecies share signals of selection in genes associated with immunity and gene regulation. With these results, we have created a selection map for each population that can be displayed in a genome browser (www.hsb.upf.edu/chimp_browser). This study is the first to use a detailed demographic history and machine learning to map selection genome-wide in chimpanzee. The chimpanzee selection map will improve our understanding of the impact of selection on closely related subspecies and will empower future studies of chimpanzee.
Language	English
Publishing date	2020-09-03
Publishing country	England
Document type	Journal Article
ISSN	2631-9268
ISSN (online)	2631-9268
DOI	10.1093/nargab/lqaa061
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Revisiting the out of Africa event with a deep-learning approach.

Montinaro, Francesco / Pankratov, Vasili / Yelmen, Burak / Pagani, Luca / Mondal, Mayukh

American journal of human genetics

2021 Volume 108, Issue 11, Page(s) 2037–2051

Abstract: Anatomically modern humans evolved around 300 thousand years ago in Africa. They started to appear in the fossil record outside of Africa as early as 100 thousand years ago, although other hominins existed throughout Eurasia much earlier. Recently, ... ...

Abstract	Anatomically modern humans evolved around 300 thousand years ago in Africa. They started to appear in the fossil record outside of Africa as early as 100 thousand years ago, although other hominins existed throughout Eurasia much earlier. Recently, several studies argued in favor of a single out of Africa event for modern humans on the basis of whole-genome sequence analyses. However, the single out of Africa model is in contrast with some of the findings from fossil records, which support two out of Africa events, and uniparental data, which propose a back to Africa movement. Here, we used a deep-learning approach coupled with approximate Bayesian computation and sequential Monte Carlo to revisit these hypotheses from the whole-genome sequence perspective. Our results support the back to Africa model over other alternatives. We estimated that there are two sequential separations between Africa and out of African populations happening around 60-90 thousand years ago and separated by 13-15 thousand years. One of the populations resulting from the more recent split has replaced the older West African population to a large extent, while the other one has founded the out of Africa populations.
MeSH term(s)	Africa ; Algorithms ; Bayes Theorem ; Deep Learning ; Evolution, Molecular ; Fossils ; Genetic Variation ; Humans ; Monte Carlo Method ; Whole Genome Sequencing/methods
Language	English
Publishing date	2021-10-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219384-x
ISSN	1537-6605 ; 0002-9297
ISSN (online)	1537-6605
ISSN	0002-9297
DOI	10.1016/j.ajhg.2021.09.006
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 107: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania.

Mondal, Mayukh / Bertranpetit, Jaume / Lao, Oscar

Nature communications

2019 Volume 10, Issue 1, Page(s) 246

Abstract: Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient ... ...

Abstract	Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.
Language	English
Publishing date	2019-01-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-018-08089-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Improving Selection Detection with Population Branch Statistic on Admixed Populations.

Yelmen, Burak / Marnetto, Davide / Molinaro, Ludovica / Flores, Rodrigo / Mondal, Mayukh / Pagani, Luca

Genome biology and evolution

2021 Volume 13, Issue 4

Abstract: Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular ... ...

Abstract	Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.
MeSH term(s)	Asians/genetics ; Computer Simulation ; Haplotypes ; Humans ; Polymorphism, Single Nucleotide ; Selection, Genetic
Language	English
Publishing date	2021-02-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evab039
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: The genetic makings of South Asia.

Metspalu, Mait / Mondal, Mayukh / Chaubey, Gyaneshwer

Current opinion in genetics & development

2018 Volume 53, Page(s) 128–133

Abstract: South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for ...

Abstract	South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the 'Indian Cline'. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia.
MeSH term(s)	Asia ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Genetics, Population ; Genome, Human/genetics ; Human Migration ; Humans ; Iran ; Selection, Genetic/genetics
Chemical Substances	DNA, Ancient ; DNA, Mitochondrial
Language	English
Publishing date	2018-10-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1077312-5
ISSN	1879-0380 ; 0959-437X
ISSN (online)	1879-0380
ISSN	0959-437X
DOI	10.1016/j.gde.2018.09.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3240: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Chronology of natural selection in Oceanian genomes.

Brucato, Nicolas / André, Mathilde / Hudjashov, Georgi / Mondal, Mayukh / Cox, Murray P / Leavesley, Matthew / Ricaut, François-Xavier

iScience

2022 Volume 25, Issue 7, Page(s) 104583

Abstract: As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date ... ...

Abstract	As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul.
Language	English
Publishing date	2022-06-30
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.104583
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G.

Sinigaglia, Barbara / Escudero, Jorge / Biagini, Simone A / Garcia-Calleja, Jorge / Moreno, Josep / Dobon, Begoña / Acosta, Sandra / Mondal, Mayukh / Walsh, Sandra / Aguileta, Gabriela / Vallès, Mònica / Forrow, Stephen / Martin-Caballero, Juan / Migliano, Andrea Bamberg / Bertranpetit, Jaume / Muñoz, Francisco J / Bosch, Elena

Molecular biology and evolution

2024 Volume 41, Issue 2

Abstract: Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)-fat accumulation localized in the ... ...

Abstract	Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)-fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around the calcium-sensing receptor gene in Southeast Asian rainforest groups presenting the DSWS phenotype and identified the R990G substitution (rs1042636) as a putative adaptive variant for experimental follow-up. Although the calcium-sensing receptor has a critical role in calcium homeostasis by directly regulating the parathyroid hormone secretion, it is expressed in different tissues and has been described to be involved in many biological functions. Previous works have also characterized the R990G substitution as an activating polymorphism of the calcium-sensing receptor associated with hypocalcemia. Therefore, we generated a knock-in mouse for this substitution and investigated organismal phenotypes that could have become adaptive in rainforest hunter-gatherers from Southeast Asia. Interestingly, we found that mouse homozygous for the derived allele show not only lower serum calcium concentration but also greater body weight and fat accumulation, probably because of enhanced preadipocyte differentiation and lipolysis impairment resulting from the calcium-sensing receptor activation mediated by R990G. We speculate that such differential features in humans could have facilitated the survival of hunter-gatherer groups during periods of nutritional stress in the challenging conditions of the Southeast Asian tropical rainforests.
MeSH term(s)	Animals ; Humans ; Mice ; Calcium ; Phenotype ; Polymorphism, Genetic ; Receptors, Calcium-Sensing/genetics ; Selection, Genetic
Chemical Substances	Calcium (SY7Q814VUP) ; Receptors, Calcium-Sensing ; CASR protein, human
Language	English
Publishing date	2024-01-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msae015
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2137: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels.

Nature communications

2024 Volume 15, Issue 1, Page(s) 3352

Abstract: Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for ... ...

Abstract	Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count - both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.
MeSH term(s)	Papua New Guinea ; Humans ; Selection, Genetic ; Polymorphism, Single Nucleotide ; Altitude ; Linkage Disequilibrium ; Haplotypes ; Genome, Human ; Genetics, Population
Language	English
Publishing date	2024-04-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47735-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Reply to 'No evidence for unknown archaic ancestry in South Asia'.

Mondal, Mayukh / Casals, Ferran / Majumder, Partha P / Bertranpetit, Jaume

Nature genetics

2018 Volume 50, Issue 12, Page(s) 1637–1639

MeSH term(s)	Asia ; Asians/genetics ; Genetics, Population ; Genomics ; Human Migration ; Humans
Language	English
Publishing date	2018-11-16
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-018-0280-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3613: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 46: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: A Chromosome-Painting-Based Pipeline to Infer Local Ancestry under Limited Source Availability.

Molinaro, Ludovica / Marnetto, Davide / Mondal, Mayukh / Ongaro, Linda / Yelmen, Burak / Lawson, Daniel John / Montinaro, Francesco / Pagani, Luca

Genome biology and evolution

2021 Volume 13, Issue 4

Abstract: Contemporary individuals are the combination of genetic fragments inherited from ancestors belonging to multiple populations, as the result of migration and admixture. Isolating and characterizing these layers are crucial to the understanding of the ... ...

Abstract	Contemporary individuals are the combination of genetic fragments inherited from ancestors belonging to multiple populations, as the result of migration and admixture. Isolating and characterizing these layers are crucial to the understanding of the genetic history of a given population. Ancestry deconvolution approaches make use of a large amount of source individuals, therefore constraining the performance of Local Ancestry Inferences when only few genomes are available from a given population. Here we present WINC, a local ancestry framework derived from the combination of ChromoPainter and NNLS approaches, as a method to retrieve local genetic assignments when only a few reference individuals are available. The framework is aided by a score assignment based on source differentiation to maximize the amount of sequences retrieved and is capable of retrieving accurate ancestry assignments when only two individuals for source populations are used.
MeSH term(s)	Chromosome Painting/methods ; Genomics ; Humans ; Inheritance Patterns ; Least-Squares Analysis ; Software
Language	English
Publishing date	2021-01-29
Publishing country	England
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evab025
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito