المؤلفون: Igolkina, Anna A, Noujdina, Nina V, Vishnyakova, Margarita, Longcore, Travis, von Wettberg, Eric, Nuzhdin, Sergey V, Samsonova, Maria G

المصدر: Molecular Biology and Evolution. 40(6)

مصطلحات موضوعية: Cicer, Polymorphism, Single Nucleotide, Bayes Theorem, Gene Frequency, Genomics, chickpea, admixture graph, allele frequency, compositional data, domestication, Biochemistry and Cell Biology, Evolutionary Biology, Genetics

الوصف: According to archaeological records, chickpea (Cicer arietinum) was first domesticated in the Fertile Crescent about 10,000 years BP. Its subsequent diversification in Middle East, South Asia, Ethiopia, and the Western Mediterranean, however, remains obscure and cannot be resolved using only archeological and historical evidence. Moreover, chickpea has two market types: "desi" and "kabuli," for which the geographic origin is a matter of debate. To decipher chickpea history, we took the genetic data from 421 chickpea landraces unaffected by the green revolution and tested complex historical hypotheses of chickpea migration and admixture on two hierarchical spatial levels: within and between major regions of cultivation. For chickpea migration within regions, we developed popdisp, a Bayesian model of population dispersal from a regional representative center toward the sampling sites that considers geographical proximities between sites. This method confirmed that chickpea spreads within each geographical region along optimal geographical routes rather than by simple diffusion and estimated representative allele frequencies for each region. For chickpea migration between regions, we developed another model, migadmi, that takes allele frequencies of populations and evaluates multiple and nested admixture events. Applying this model to desi populations, we found both Indian and Middle Eastern traces in Ethiopian chickpea, suggesting the presence of a seaway from South Asia to Ethiopia. As for the origin of kabuli chickpeas, we found significant evidence for its origin from Turkey rather than Central Asia.

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/3r64d73d

المؤلفون: Cheng, Jade Yu, Stern, Aaron J, Racimo, Fernando, Nielsen, Rasmus

المصدر: Molecular Biology and Evolution. 39(1)

مصطلحات موضوعية: Biological Sciences, Genetics, Human Genome, Computer Simulation, Gene Frequency, Genetics, Population, Genome, Human, Genomics, Humans, Polymorphism, Single Nucleotide, Selection, Genetic, positive selection, admixture, population structure, human evolution, selective sweeps, Biochemistry and Cell Biology, Evolutionary Biology, Biochemistry and cell biology, Evolutionary biology

الوصف: One of the most powerful and commonly used approaches for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this article, we present a new maximum likelihood method for finding regions under positive selection. It is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. Using simulated data, we compare our method to related approaches, and show that it is orders of magnitude faster than the state-of-the-art, while retaining similar or higher power for most simulation scenarios. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin, and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, such as immunity, fat distribution, food intake, vision, and hair development.

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/7d18p8x1

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المؤلفون: Ai, Huashui, Zhang, Mingpeng, Yang, Bin, Goldberg, Amy, Li, Wanbo, Ma, Junwu, Brandt, Debora, Zhang, Zhiyan, Nielsen, Rasmus, Huang, Lusheng

المصدر: Molecular Biology and Evolution. 38(11)

مصطلحات موضوعية: Genetics, Biotechnology, Animals, Biological Evolution, Breeding, Haplotypes, Humans, Male, Polymorphism, Single Nucleotide, Sus scrofa, Swine, Y Chromosome, Y chromosome, admixture, selection, pig, genome sequencing, Biochemistry and Cell Biology, Evolutionary Biology

الوصف: Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We resequenced 80 Eurasian pigs from nine different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex-biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y chromosomes.

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/09j1060p

المؤلفون: Svedberg, Jesper, Shchur, Vladimir, Reinman, Solomon, Nielsen, Rasmus, Corbett-Detig, Russell

المصدر: Molecular Biology and Evolution. 38(5)

مصطلحات موضوعية: Genetics, Adaptation, Biological, Algorithms, Animals, Drosophila melanogaster, Genetic Introgression, Markov Chains, Models, Genetic, Selection, Genetic, Software, adaptive evolution, adaptive introgression, selection, admixture, hybridisation, HMM, population genomics, pesticide resistance, adaptive, evolution, Biochemistry and Cell Biology, Evolutionary Biology

الوصف: Adaptive 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 data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set 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 data sets 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/.

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/760770j8

المؤلفون: Barbieri, Chiara, Barquera, Rodrigo, Arias, Leonardo, Sandoval, José R, Acosta, Oscar, Zurita, Camilo, Aguilar-Campos, Abraham, Tito-Álvarez, Ana M, Serrano-Osuna, Ricardo, Gray, Russell D, Mafessoni, Fabrizio, Heggarty, Paul, Shimizu, Kentaro K, Fujita, Ricardo, Stoneking, Mark, Pugach, Irina, Fehren-Schmitz, Lars

المصدر: Molecular biology and evolution. 36(12)

مصطلحات موضوعية: Humans, Language, Genome, Human, History, Ancient, Peru, Phylogeography, Human Migration, Native American population genetics, South American prehistory, admixture, human migration, runs of homozygosity, Genome, Human, History, Ancient, Biochemistry and Cell Biology, Evolutionary Biology, Genetics

الوصف: Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/060957ds

المؤلفون: Semo, Armando, Gaya-Vidal, Magdalena, Fortes-Lima, Cesar A., Alard, Berenice, Oliveira, Sandra, Almeida, Joao, Prista, Antonio, Damasceno, Albertino, Fehn, Anne-Maria, Schlebusch, Carina, 1977, Rocha, Jorge

المصدر: Molecular biology and evolution. 37(2):406-416

مصطلحات موضوعية: Mozambique, Bantu expansion, population structure, migration, admixture

الوصف: The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using similar to 1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a "late split" between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-408113
https://doi.org/10.1093/molbev/msz224
https://uu.diva-portal.org/smash/get/diva2:1421681/FULLTEXT01.pdf

المؤلفون: Racimo, Fernando, Gokhman, David, Fumagalli, Matteo, Ko, Amy, Hansen, Torben, Moltke, Ida, Albrechtsen, Anders, Carmel, Liran, Huerta-Sánchez, Emilia, Nielsen, Rasmus

المصدر: Molecular Biology and Evolution. 34(3)

مصطلحات موضوعية: Human Genome, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Adaptation, Biological, Adipose Tissue, Alleles, Animals, DNA Methylation, DNA, Ancient, Greenland, Haplotypes, Humans, Inuit, Models, Genetic, Neanderthals, Polymorphism, Single Nucleotide, Selection, Genetic, Sequence Analysis, DNA, T-Box Domain Proteins, adaptive introgression, Denisova, positive selection, Native Americans, methylation, admixture, admixture., Biochemistry and Cell Biology, Evolutionary Biology

الوصف: A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/4nk8v86h

المؤلفون: Mendoza-Revilla, Javier, Chacón-Duque, J. Camilo, Fuentes-Guajardo, Macarena, Ormond, Louise, Wang, Ke, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Acuña-Alonzo, Victor, Jaramillo, Claudia, Arias, William, Barquera, Rodrigo, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, de Cerqueira, Caio C. Silva, Rivera, Keyla M. Badillo, Nieves-Colón, Maria A., Gignoux, Christopher R., Wojcik, Genevieve L., Moreno-Estrada, Andrés, Hünemeier, Tábita, Ramallo, Virginia, Schuler-Faccini, Lavinia, Gonzalez-José, Rolando, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Balding, David, Fumagalli, Matteo, Adhikari, Kaustubh, Ruiz-Linares, Andrés, Hellenthal, Garrett

المصدر: Molecular biology and evolution. 39(4)

مصطلحات موضوعية: natural selection, Latin Americans, Native Americans, admixture

الوصف: Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

وصف الملف: print

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-204383
https://doi.org/10.1093/molbev/msac076

المؤلفون: Cahill, James A, Heintzman, Peter D, Harris, Kelley, Teasdale, Matthew D, Kapp, Joshua, Soares, Andre ER, Stirling, Ian, Bradley, Daniel, Edwards, Ceiridwen J, Graim, Kiley, Kisleika, Aliaksandr A, Malev, Alexander V, Monaghan, Nigel, Green, Richard E, Shapiro, Beth

المصدر: Molecular Biology and Evolution. 35(5)

مصطلحات موضوعية: Biological Sciences, Genetics, Human Genome, Animals, Climate Change, Fossils, Gene Flow, Hybridization, Genetic, Ice Cover, Ursidae, genomics, hybridization, ancient DNA, ursus, paleogenomics, admixture, Biochemistry and Cell Biology, Evolutionary Biology, Biochemistry and cell biology, Evolutionary biology

الوصف: Recent genomic analyses have provided substantial evidence for past periods of gene flow from polar bears (Ursus maritimus) into Alaskan brown bears (Ursus arctos), with some analyses suggesting a link between climate change and genomic introgression. However, because it has mainly been possible to sample bears from the present day, the timing, frequency, and evolutionary significance of this admixture remains unknown. Here, we analyze genomic DNA from three additional and geographically distinct brown bear populations, including two that lived temporally close to the peak of the last ice age. We find evidence of admixture in all three populations, suggesting that admixture between these species has been common in their recent evolutionary history. In addition, analyses of ten fossil bears from the now-extinct Irish population indicate that admixture peaked during the last ice age, whereas brown bear and polar bear ranges overlapped. Following this peak, the proportion of polar bear ancestry in Irish brown bears declined rapidly until their extinction. Our results support a model in which ice age climate change created geographically widespread conditions conducive to admixture between polar bears and brown bears, as is again occurring today. We postulate that this model will be informative for many admixing species pairs impacted by climate change. Our results highlight the power of paleogenomics to reveal patterns of evolutionary change that are otherwise masked in contemporary data.

URL الوصول: https://escholarship.org/uc/item/0p7239rx