scholarly journals The consequences of an introgression event

2018 ◽  
Vol 27 (24) ◽  
pp. 4973-4975 ◽  
Author(s):  
Nicholas H. Barton
Keyword(s):  
Introgression Event

scholarly journals Introgression from Gorilla caused the Human-Chimpanzee split

2018 ◽  
Author(s):  
Johan Nygren
Keyword(s):  
Common Ancestor ◽  
Nuclear Genome ◽  
Genome Project ◽  
Lineage Sorting ◽  
Chromosome 5 ◽  
Speciation Model ◽  
Introgression Event ◽  
The Common

ABSTRACT: The Gorilla Genome Project (Scally, 2012) showed that 30% of the gorilla genome introgressed into the ancestor of humans and chimpanzees, and that the two species diverged through lineage sorting with 15% ending up in Pan and another 15% in Homo. That introgression is the Pan-Homo split, hybridization, which led to speciation as the new hybrid lineages became reproductively isolated from one another. The NUMT on chromosome 5 (“ps5”) (Popadin, 2017) fits perfectly with the introgression speciation model, it was formed from mtDNA that had diverged from the common ancestor of Pan-Homo for 1.8 Myr at the time of insertion into the nuclear genome, and originated in the Gorilla lineage. The ps5 pseudogene was transferred to Pan and Homo during the introgression event that led to the Pan-Homo split, 6 million years ago.

scholarly journals Divergence-Based Introgression Polarization

2020 ◽  
Vol 12 (4) ◽  
pp. 463-478 ◽  
Author(s):  
Evan S Forsythe ◽  
Daniel B Sloan ◽  
Mark A Beilstein
Keyword(s):  
Genetic Material ◽  
Introgressive Hybridization ◽  
Sequence Divergence ◽  
Whole Genome ◽  
Major Area ◽  
Genome Data ◽  
Whole Genomes ◽  
Potential Sources ◽  
Introgression Event ◽  
Do So

Abstract Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during introgression (i.e., polarization of introgression directionality). Existing methods that do polarize introgression are often only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in introgression. Here, we present divergence-based introgression polarization (DIP), a method for polarizing introgression using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of introgression when additional taxa are not available. We use simulations to show that DIP can polarize introgression and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin introgression event.

scholarly journals The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

2020 ◽  
Author(s):  
Xinjun Zhang ◽  
Kelsey Witt ◽  
Amy Ko ◽  
Kai Yuan ◽  
Shuhua Xu ◽  
...  
Keyword(s):  
South Asians ◽  
East Asian ◽  
Ancestral Population ◽  
The Tibetan Plateau ◽  
East Asians ◽  
Adaptive Introgression ◽  
Asian Populations ◽  
Introgressed Segment ◽  
Introgression Event ◽  
Selection Event

AbstractRecent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 43,000 (15,700–60,000) years ago, and selection started 12,000 (1,925-50,000) years ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

scholarly journals The origin of domestication genes in goats

2020 ◽  
Author(s):  
Zhuqing Zheng ◽  
Xihong Wang ◽  
Ming Li ◽  
Yunjia Li ◽  
Zhirui Yang ◽  
...  
Keyword(s):  
Genetic Changes ◽  
High Frequencies ◽  
Mitochondrial Haplogroup ◽  
Animal Domestication ◽  
Strong Signal ◽  
Immune Resistance ◽  
Neural Genes ◽  
Signature Of Selection ◽  
Introgression Event ◽  
Historical Remains

AbstractGoat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here we analyze the genomes of worldwide domestic goats, wild caprid species and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7,200 and 8,100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanism of animal domestication.One Sentence SummaryGoat domestication mainly focused on immune and neural genes, with adaptive leaps driven by introgression and selection.

scholarly journals Replication of LZTFL1 gene region as a susceptibility locus for COVID-19 in Latvian population.

2021 ◽  
Author(s):  
Raimonds Rescenko ◽  
Raitis Peculis ◽  
Monta Ustinova ◽  
Laura Ansone ◽  
Helena Daiga Litvina ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Genetic Factors ◽  
P Values ◽  
Genome Wide ◽  
Increased Risk ◽  
Host Genetic ◽  
Introgression Event ◽  
Functional Investigation ◽  
Host Genetic Factors ◽  
Independent Cohort

The severity of COVID-19 disease is partly determined by host genetic factors that have been reported by GWAS. We evaluated nine previously reported genome-wide significant associations regardless of the disease severity in a representative sample from the population of Latvia. Our cohort consisted of 475 SARS-CoV-2 positive cases, from which 146 were hospitalized individuals and 2217 controls. We found three variants from Neanderthal introgression event at the 3p21.31 region to be significantly associated with increased risk of SARS-CoV-2 infection and hospitalization status. The strongest association was displayed by rs71325088 with Bonferroni adjusted P=0.007, OR=1.46 [95% CI 1.17-1.81]. We performed fine-mapping by exploring 1 Mb region at 3p21.31 locus and identified 9 SNPs with even lower p-values with the strongest association estimated for rs2191031 P=5e-05, OR = 1.40[CI 95% 1.19-1.64] located in the LZTFL1. We show clear replication of 3p.21.31 locus in an independent cohort which favors further functional investigation of leading variants.

scholarly journals The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

2021 ◽  
Vol 118 (22) ◽  
pp. e2020803118
Author(s):  
Xinjun Zhang ◽  
Kelsey E. Witt ◽  
Mayra M. Bañuelos ◽  
Amy Ko ◽  
Kai Yuan ◽  
...  
Keyword(s):  
South Asians ◽  
East Asian ◽  
Ancestral Population ◽  
The Tibetan Plateau ◽  
East Asians ◽  
Adaptive Introgression ◽  
Asian Populations ◽  
Introgressed Segment ◽  
Introgression Event ◽  
Selection Event

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000–59,500) y ago, and selection started around 9,000 (2,500–42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

scholarly journals A novel mouse chromosome 17 hybrid sterility locus: implications for the origin of t haplotypes.

Genetics ◽  
1991 ◽  
Vol 129 (1) ◽  
pp. 237-246
Author(s):  
S H Pilder ◽  
M F Hammer ◽  
L M Silver
Keyword(s):  
Mouse Chromosome ◽  
Genetic Background ◽  
Hybrid Sterility ◽  
Chromosome 17 ◽  
Structural Studies ◽  
Mus Spretus ◽  
Introgression Event ◽  
Different Sources ◽  
Two Hybrid ◽  
T Haplotype

Abstract The effects of heterospecific combinations of mouse chromosome 17 on male fertility and transmission ratio were investigated through a series of breeding studies. Animals were bred to carry complete chromosome 17 homologs, or portions thereof, from three different sources-Mus domesticus, Mus spretus and t haplotypes. These chromosome 17 combinations were analyzed for fertility within the context of a M. domesticus or M. spretus genetic background. Two new forms of hybrid sterility were identified. First, the heterospecific combination of M. spretus and t haplotype homologs leads to complete male sterility on both M. spretus and M. domesticus genetic backgrounds. This is an example of symmetrical hybrid sterility. Second, the presence of a single M. domesticus chromosome 17 homolog within a M. spretus background causes sterility, however, the same combination of chromosome 17 homologs does not cause sterility within the M. domesticus background. This is a case of asymmetrical hybrid sterility. Through an analysis of recombinant chromosomes, it was possible to map the M. domesticus, M. spretus and t haplotype alleles responsible for these two hybrid sterility phenotypes to the same novel locus (Hybrid sterility-4). Previous structural studies had led to the hypothesis that the ancestral t haplotype originated through an introgression event from M. spretus or a related species. If this were true, one might expect that (1) M. spretus homologs would be transmitted at a non-Mendelian ratio within the M. domesticus background, and (2) t haplotypes would be transmitted at a ratio closer to Mendelian within the M. spretus background.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals The origin of domestication genes in goats

2020 ◽  
Vol 6 (21) ◽  
pp. eaaz5216 ◽  
Author(s):  
Zhuqing Zheng ◽  
Xihong Wang ◽  
Ming Li ◽  
Yunjia Li ◽  
Zhirui Yang ◽  
...  
Keyword(s):  
Genetic Changes ◽  
High Frequencies ◽  
Mitochondrial Haplogroup ◽  
Animal Domestication ◽  
Strong Signal ◽  
Immune Resistance ◽  
Gastrointestinal Pathogens ◽  
Signature Of Selection ◽  
Introgression Event ◽  
Historical Remains

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene, which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7200 and 8100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanisms of animal domestication.

scholarly journals Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites

2019 ◽  
Vol 36 (10) ◽  
pp. 2127-2142 ◽  
Author(s):  
Roy N Platt ◽  
Marina McDew-White ◽  
Winka Le Clec’h ◽  
Frédéric D Chevalier ◽  
Fiona Allan ◽  
...  
Keyword(s):  
High Frequency ◽  
Parasite Species ◽  
Single Gene ◽  
Sub Saharan Africa ◽  
Species Boundaries ◽  
Urogenital Schistosomiasis ◽  
Adaptive Introgression ◽  
Introgression Event ◽  
Sub Saharan ◽  
Ancient Hybridization

Abstract Introgression among parasite species has the potential to transfer traits of biomedical importance across species boundaries. The parasitic blood fluke Schistosoma haematobium causes urogenital schistosomiasis in humans across sub-Saharan Africa. Hybridization with other schistosome species is assumed to occur commonly, because genetic crosses between S. haematobium and livestock schistosomes, including S. bovis, can be staged in the laboratory, and sequencing of mtDNA and rDNA amplified from microscopic miracidia larvae frequently reveals markers from different species. However, the frequency, direction, age, and genomic consequences of hybridization are unknown. We hatched miracidia from eggs and sequenced the exomes from 96 individual S. haematobium miracidia from infected patients from Niger and the Zanzibar archipelago. These data revealed no evidence for contemporary hybridization between S. bovis and S. haematobium in our samples. However, all Nigerien S. haematobium genomes sampled show hybrid ancestry, with 3.3–8.2% of their nuclear genomes derived from S. bovis, providing evidence of an ancient introgression event that occurred at least 108–613 generations ago. Some S. bovis-derived alleles have spread to high frequency or reached fixation and show strong signatures of directional selection; the strongest signal spans a single gene in the invadolysin gene family (Chr. 4). Our results suggest that S. bovis/S. haematobium hybridization occurs rarely but demonstrate profound consequences of ancient introgression from a livestock parasite into the genome of S. haematobium, the most prevalent schistosome species infecting humans.

scholarly journals Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 497-509 ◽  
Author(s):  
Ozgur Taskent ◽  
Yen Lung Lin ◽  
Ioannis Patramanis ◽  
Pavlos Pavlidis ◽  
Omer Gokcumen
Keyword(s):  
Human Populations ◽  
Human Genetic Variation ◽  
The Past ◽  
Genetics Research ◽  
Asian Populations ◽  
Specific Analysis ◽  
Specific Manner ◽  
Introgression Event ◽  
Archaic Introgression ◽  
Evolutionary Consequences

The time, extent, and genomic effect of the introgressions from archaic humans into ancestors of extant human populations remain some of the most exciting venues of population genetics research in the past decade. Several studies have shown population-specific signatures of introgression events from Neanderthals, Denisovans, and potentially other unknown hominin populations in different human groups. Moreover, it was shown that these introgression events may have contributed to phenotypic variation in extant humans, with biomedical and evolutionary consequences. In this study, we present a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and show that they can be traced back to multiple introgression events. In parallel, we document hundreds of deletion polymorphisms shared with Neanderthals. A locus-specific analysis of one such shared deletion suggests the existence of a direct introgression event from the Altai Neanderthal lineage into the ancestors of extant East Asian populations. Overall, our study is in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.

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