scholarly journals Genome-wide ancestry and introgression in a Zambian baboon hybrid zone

2019 ◽  
Author(s):  
Kenneth L Chiou ◽  
Christina M Bergey ◽  
Andrew S Burrell ◽  
Todd R Disotell ◽  
Jeffrey Rogers ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome ◽  
Hybrid Zone ◽  
Introgressive Hybridization ◽  
Toll Like Receptor ◽  
Genome Wide ◽  
Species Boundary ◽  
Primate System ◽  
Immune Related Genes ◽  
Coagulation Pathway

Hybridization in nature offers unique insights into the process of natural selection in incipient species and their hybrids. In order to evaluate the patterns and targets of selection, we examine a recently discovered baboon hybrid zone in the Kafue River valley of Zambia, where Kinda baboons (Papio kindae) and gray-footed chacma baboons (P. ursinus griseipes) coexist with hybridization. We genotyped baboons at 14,962 variable genome-wide autosomal markers using double-digest RADseq. We compare ancestry patterns from this genome-wide dataset to previously reported ancestry from mitochondrial-DNA and Y-chromosome sources. We also fit a Bayesian genomic cline model to scan for genes with extreme patterns of introgression. We show that the Kinda baboon Y chromosome has penetrated the species boundary to a greater extent than either mitochondrial DNA or the autosomal chromosomes. We also find evidence for overall restricted introgression in the JAK/STAT signaling pathway. Echoing results in other species including humans, we find evidence for enhanced and/or directional introgression of immune-related genes or pathways including the toll-like receptor pathway, the blood coagulation pathway, and the LY96 gene. Finally we show enhanced introgression and excess chacma baboon ancestry in the sperm tail gene ODF2. Together, our results elucidate the dynamics of introgressive hybridization in a primate system while highlighting genes and pathways under selection.

Analyse génétique de la zone d'hybridation entre les deux sous-espèces de souris Mus musculus domesticus et Mus musculus musculus en Bulgarie

Genome ◽  
1988 ◽  
Vol 30 (3) ◽  
pp. 427-437 ◽  
Author(s):  
Flavie Vanlerberghe ◽  
Pierre Boursot ◽  
Josette Catalan ◽  
Svestoslav Gerasimov ◽  
François Bonhomme ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome ◽  
Hybrid Zone ◽  
Mus Musculus ◽  
Functional Differentiation ◽  
Restriction Pattern ◽  
The Black Sea ◽  
Mus Musculus Domesticus ◽  
The Balkans ◽  
Mus Musculus Musculus

The hybrid zone between the two subspecies of mice Mus musculus domesticus and Mus musculus musculus, which has been studied extensively in Denmark, crosses Europe to the Black Sea through the Alps and the Balkans. Two hundred and seventy-nine animals were captured in 22 localities along a transect across the Balkans. The animals were characterized for seven diagnostic nuclear loci by protein electrophoresis and by restriction pattern analysis of their mitochondrial DNA. The nuclear data show a sharp transition between the two subspecies, most of the variations in allele frequencies (from 0.9 to 0.1) occurring within a 36-km section of the transect. The introgression varies from one locus to the other and is more pronounced, in terms of distance, in M. m. musculus territory. Mitochondrial DNA introgression is important but occurs in one direction only, i.e. from M. m. musculus to M. m. domesticus, while a cytoplasmic transfer from M. m. domesticus to M. m. musculus has been reported. A previous study showed that no Y chromosome introgression occurs. The different behaviour of these three types of markers could be due to the interaction between selection against hybrid genomes and meiotic recombination. Objectively, it would appear that the genes that can introgress are neutral or nearly so and have been separated from deleterious genes they were linked to by recombination. This could explain the differential introgression between autosomal loci. The mitochondrial and Y chromosomes undergo no or very little recombination and each is transmitted as a whole. Their degree of introgression is thus indicative of the intensity of selection resulting from the amount of functional differentiation between the two taxa, which seems to be strong for the Y chromosome and weak for mitochondrial DNA. We propose that the asymmetry of nuclear introgression is due to different population structures. As M. m. musculus is relatively less structured, the rapid spreading of introgressed genes would be favoured. Such a scheme, however, can hardly account for the unidirectionality of the mitochondrial flow, which could be due to sex-dependant behaviour.Key words: mice, hybrid zone, introgression, enzyme polymorphism.

Gene pool of ethnic groups of the Caucasus: Results of integrated study of the Y chromosome and mitochondrial DNA and genome-wide data

2012 ◽  
Vol 48 (6) ◽  
pp. 640-650 ◽  
Author(s):  
E. K. Khusnutdinova ◽  
S. S. Litvinov ◽  
I. A. Kutuev ◽  
B. B. Yunusbayev ◽  
R. I. Khusainova ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Ethnic Groups ◽  
Y Chromosome ◽  
Gene Pool ◽  
The Caucasus ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Integrated Study

scholarly journals Examining the effect of mitochondrial DNA variants on blood pressure in two Finnish cohorts

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jaakko Laaksonen ◽  
Pashupati P. Mishra ◽  
Ilkka Seppälä ◽  
Leo-Pekka Lyytikäinen ◽  
Emma Raitoharju ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Mitochondrial Dna ◽  
Genome Wide Association Study ◽  
Rare Variants ◽  
Meta Analysis ◽  
Noncommunicable Diseases ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Genome Wide ◽  
Mitochondrial Dna Variants

AbstractHigh blood pressure (BP) is a major risk factor for many noncommunicable diseases. The effect of mitochondrial DNA single-nucleotide polymorphisms (mtSNPs) on BP is less known than that of nuclear SNPs. We investigated the mitochondrial genetic determinants of systolic, diastolic, and mean arterial BP. MtSNPs were determined from peripheral blood by sequencing or with genome-wide association study SNP arrays in two independent Finnish cohorts, the Young Finns Study and the Finnish Cardiovascular Study, respectively. In total, over 4200 individuals were included. The effects of individual common mtSNPs, with an additional focus on sex-specificity, and aggregates of rare mtSNPs grouped by mitochondrial genes were evaluated by meta-analysis of linear regression and a sequence kernel association test, respectively. We accounted for the predicted pathogenicity of the rare variants within protein-encoding and the tRNA regions. In the meta-analysis of 87 common mtSNPs, we did not observe significant associations with any of the BP traits. Sex-specific and rare-variant analyses did not pinpoint any significant associations either. Our results are in agreement with several previous studies suggesting that mtDNA variation does not have a significant role in the regulation of BP. Future studies might need to reconsider the mechanisms thought to link mtDNA with hypertension.

scholarly journals Y Chromosome, Mitochondrial DNA and Childhood Behavioural Traits

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Laurence J. Howe ◽  
A. Mesut Erzurumluoglu ◽  
George Davey Smith ◽  
Santiago Rodriguez ◽  
Evie Stergiakouli
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome

scholarly journals Cytogenetic and molecular analysis of the Pantaneiro cattle breed

2006 ◽  
Vol 41 (11) ◽  
pp. 1609-1615 ◽  
Author(s):  
Érica Cunha Issa ◽  
Wilham Jorge ◽  
José Robson Bezerra Sereno
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome ◽  
Molecular Analysis ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Zebu Cattle ◽  
European Origin ◽  
Paternal Line

The objective of this work was to characterize Pantaneiro cattle genetically through its paternal ancestry by the morphology of the Y chromosome, whether submetacentric or acrocentric, as well as to identify the maternal ancestry through mitochondrial DNA. The karyotype and mitochondrial DNA of 12 bulls of Pantaneiro breed were analyzed. The Y chromosome was analyzed in lymphocyte metaphases and the mitochondrial DNA by diagnosing its haplotype (Bos taurus and Bos indicus). Among Pantaneiro animals analyzed three had a taurine (submetacentric) Y and nine had a zebuine (acrocentric) Y chromosome, suggesting breed contamination by Zebu cattle, once Pantaneiro is considered to be of European origin. The mitochondrial DNA was exclusively of taurine origin, indicating that the participation of zebuines in the formation of the breed occurred entirely through the paternal line.

scholarly journals Tracing the genetic history of the ‘Cañaris’ from Ecuador and Peru using uniparental DNA markers

BMC Genomics ◽  
2020 ◽  
Vol 21 (S7) ◽  
Author(s):  
José R. Sandoval ◽  
Daniela R. Lacerda ◽  
Marilza M. S. Jota ◽  
Paulo Robles-Ruiz ◽  
Pierina Danos ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome ◽  
Genetic Relationship ◽  
Tandem Repeats ◽  
Geographic Proximity ◽  
Lake Titicaca ◽  
Control Region Sequences ◽  
History Of ◽  
Historical Question ◽  
Close Genetic Relationship

Abstract Background According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including Kañaris, a Quechua-speaking community located at the highlands of the Province of Ferreñafe, Lambayeque (Peru). Other families were probably taken from the Central Andes to a place close to Kañaris, named Inkawasi. Evidence of this migration comes from the presence near the Kañaris–Inkawasi communities of a village, a former Inka camp, which persists until the present day. This scenario could explain these toponyms, but it is still controversial. To clarify this historical question, the study presented here focused on the inference of the genetic relationship between ‘Cañaris’ populations, particularly of Cañar and Ferreñafe, compared to other highland populations. We analysed native patrilineal Y chromosome haplotypes composed of 15 short tandem repeats, a set of SNPs, and maternal mitochondrial DNA haplotypes of control region sequences. Results After the genetic comparisons of local populations—three from Ecuador and seven from Peru—, Y chromosome analyses (n = 376) indicated that individuals from the Cañar region do not share Y haplotypes with the Kañaris, or even with those of the Inkawasi. However, some Y haplotypes of Ecuadorian ‘Cañaris’ were associated with haplotypes of the Peruvian populations of Cajamarca, Chivay (Arequipa), Cusco and Lake Titicaca, an observation that is congruent with colonial records. Within the Kañaris and Inkawasi communities there are at least five clans in which several individuals share haplotypes, indicating that they have recent common ancestors. Despite their relative isolation, most individuals of both communities are related to those of the Cajamarca and Chachapoyas in Peru, consistent with the spoken Quechua and their geographic proximity. With respect to mitochondrial DNA haplotypes (n = 379), with the exception of a shared haplotype of the D1 lineage between the Cañar and Kañaris, there are no genetic affinities. Conclusion Although there is no close genetic relationship between the Peruvian Kañaris (including Inkawasi) and Ecuadorian Cañar populations, our results showed some congruence with historical records.

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