Gradual Admixture Research Articles

The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences.

Koreans are thought to be an ethnic group of admixed northern and southern subgroups. However, the exact genetic origins of these two remain unclear. In addition, the past admixture is presumed to have taken place on the Korean peninsula, but there is no genomic scale analysis exploring the origin, composition, admixture, or the past migration of Koreans. Here, 88 Korean genomes compared with 91 other present-day populations showed two major genetic components of East Siberia and Southeast Asia. Additional paleogenomic analysis with 115 ancient genomes from Pleistocene hunter-gatherers to Iron Age farmers showed a gradual admixture of Tianyuan (40 ka) and Devil’s gate (8 ka) ancestries throughout East Asia and East Siberia up until the Neolithic era. Afterward, the current genetic foundation of Koreans may have been established through a rapid admixture with ancient Southern Chinese populations associated with Iron Age Cambodians. We speculate that this admixing trend initially occurred mostly outside the Korean peninsula followed by continuous spread and localization in Korea, corresponding to the general admixture trend of East Asia. Over 70% of extant Korean genetic diversity is explained to be derived from such a recent population expansion and admixture from the South.

Gene-flow from steppe individuals into Cucuteni-Trypillia associated populations indicates long-standing contacts and gradual admixture

The Cucuteni-Trypillia complex (CTC) flourished in eastern Europe for over two millennia (5100–2800 BCE) from the end of the Neolithic to the Early Bronze Age. Its vast distribution area encompassed modern-day eastern Romania, Moldova and western/central Ukraine. Due to a lack of existing burials throughout most of this time, only little is known about the people associated with this complex and their genetic composition. Here, we present genome-wide data generated from the skeletal remains of four females that were excavated from two Late CTC sites in Moldova (3500–3100 BCE). All individuals carried a large Neolithic-derived ancestry component and were genetically more closely related to Linear Pottery than to Anatolian farmers. Three of the specimens also showed considerable amounts of steppe-related ancestry, suggesting influx into the CTC gene-pool from people affiliated with, for instance, the Ukraine Mesolithic. The latter scenario is supported by archaeological evidence. Taken together, our results confirm that the steppe component arrived in eastern Europe farming communities maybe as early as 3500 BCE. In addition, they are in agreement with the hypothesis of ongoing contacts and gradual admixture between incoming steppe and local western populations.

Spin-Triplet p-Wave Superconductivity Revealed under High Pressure in UBe_{13}.

To unravel the nature of the superconducting symmetry of the enigmatic 5f heavy-fermion UBe_{13}, the pressure dependence of the upper critical field and of the normal state are studied up to 10GPa. Remarkably, the pressure evolution of the anomalous H_{c2}(T,P) over the entire pressure range up to 5.9GPa can be successfully explained by the gradual admixture of a field-pressure-induced E_{u} component in an A_{1u} spin-triplet ground state. This result provides strong evidence for parallel-spin pairing in UBe_{13}, which is also supported by the recently observed fully gapped excitation spectrum at ambient pressure. Moreover, we have also found a novel non-Fermi-liquid behavior of the resistivity, ρ(T)∼T^{n} (n≲1), which disappears with the collapse of the negative magnetoresistance behavior and the existence of a superconducting ground state around P=6 GPa, suggesting a close interplay between Kondo scattering and superconductivity.

Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping

The ancestral chromosomal segments in admixed genomes are of significant importance for both population history inference and admixture mapping, because they essentially provide the basic information for tracking genetic events. However, the distributions of the lengths of ancestral chromosomal segments (LACS) under some admixture models remain poorly understood. Here we introduced a theoretical framework on the distribution of LACS in two representative admixture models, that is, hybrid isolation (HI) model and gradual admixture (GA) model. Although the distribution of LACS in the GA model differs from that in the HI model, we demonstrated that the mean LACS in the HI model is approximately half of that in the GA model if both admixture proportion and admixture time in the two models are identical. We showed that the theoretical framework greatly facilitated the inference and understanding of population admixture history by analyzing African-American and Mexican empirical data. In addition, we found the peak of association signatures in the HI model was much narrower and sharper than that in the GA model, indicating that the identification of putative causal allele in the HI model is more efficient than that in the GA model. Thus admixture mapping with case-only data would be a reasonable and economical choice in the HI model due to the weak background noise. However, according to our previous studies, many populations are likely to be gradually admixed and have pretty high background linkage disequilibrium. Therefore, we suggest using a case-control approach rather than a case-only approach to conduct admixture mapping to retain the statistics power in recently admixed populations.

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-wide Distribution of Ancestral Chromosomal Segments

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations.

Assessment of Genetic Ancestry and Population Substructure in Costa Rica by Analysis of Individuals with a Familial History of Mental Disorder

The population of Costa Rica has been considered valuable for locating susceptibility genes of complex disorders because of historical events and a gradual admixture process. We present an assessment of 426 unrelated individuals with a familial history of mental disorder and with ancestors born in the Central Valley, genotyped at 730 microsatellites to evaluate genetic diversity, ancestry, and substructure at the general and regional population levels using quantitative methods. Low population substructure was found. Estimated mean ancestry proportions were 54%, 32%, and 13% for European, Amerindian, and African components, respectively, with some regional variation. The F(ST) values obtained confirm the largest genetic similarity to Europeans. Subdivision of the Amerindians into individual populations revealed strong similarity to Chibchan groups. Analysis of the African ancestry showed high similarity to West and Central African populations. Gene ancestries from other African areas were also detected, probably resulting from ancestral admixture within Africa prior to colonial times. Our analyses show, in an ethnohistorical-genetic context, that gene flow and admixture are important components of Costa Rican population history. The results confirm the need to consider the particular regional genetic structure, the effects of genetic drift and the ancestry when designing and interpreting investigations of genetic traits in this population.

The Admixture Linkage Disequilibrium and Genetic Linkage Inference on the Gradual Admixture Population

Through the theoretical analysis of the admixture linkage disequilibrium (ALD) in the gradual admixture (GA) model, in which admixture occurs in every generation, the ALD is found to be proportional to the difference in marker allele frequencies, p 1- p 2, between two subpopulations. Based on this property, we can employ a strict monotonic function (Δ ker =Δ/( p 1- p 2), where Δ denotes the linkage disequilibrium (LD)) of the recombination fraction between the marker locus and the disease locus to infer the true genetic linkage. We construct a quasi likelihood ratio test (LRT) for the case-only data utilizing the information of unlinked markers in the human genome. The simulation results show that our tests can be used to fine map a disease locus. The effects of parameter values in the ALD mapping are also discussed.

Siderophile trace elements in ALH84001, other SNC meteorites and eucrites: Evidence of heterogeneity, possibly time‐linked, in the mantle of Mars

Abstract— We report neutron activation analyses, including radiochemical determination of trace siderophile elements (Au, Ge, Ir, Ni, Os and Re), for three SNC/martian meteorites, and Os and Re results for numerous eucrites. Ratios such as Ga/Al in the SNC orthopyroxenite ALH84001 confirm its martian affinity—its many distinctive characteristics, most notably its near‐primordial age, notwithstanding. To the list of ALH84001's idiosyncrasies can now be added extraordinarily low concentrations of Au, Ni and, especially, Re (17 pg/g), for a martian meteorite. We consider several possible origins for the anomalously low Re content in ALH84001, including metasomatism or alteration. The pyroxene‐cumulate nature of this rock probably does not account for its low Re content. Other SNC meteorites are also cumulates. An examination of Re‐Nd variations among terrestrial basalts and komatiites suggests that Re is compatible with mantle minerals in general and only incompatible with olivine (however, olivine dominates the mantle residuum, especially during komatiite genesis). Our preferred model is that the ALH84001 parent melt formed in a mantle source region that was far more Re‐depleted, and/or at a substantially lower oxygen fugacity, than the sources of the young SNC meteorites. Such a contrast is consistent with models that replenish siderophile elements in planetary mantles by gradual admixture of late‐accreting matter and similarly derive most planetary water (which serves as an oxidant) very late in accretion. According to this model, ALH84001 formed before the siderophile‐rich matter and water had been mixed well into the martian interior. Possibly the martian mantle never became generally as Re‐rich and/or oxidized as the source region(s) of the younger SNCs.

Maximum Likelihood Fit of a Gradual Admixture Model to Clines of Gene Frequencies in the Main Islands of Japan.

The hypothesis was tested that the observed clines of gene frequencies in the main islands of Japan (Kyushu, Shikoku, and Honshu) were produced by a two-phase episode of immigration and admixture. In the first phase, an intrusive population occupies the western part of the main islands, causing a temporary discontinuity in the geographical distribution of the gene frequency at each locus. In the second phase, gradual admixture occurs by the random migration of both immigrants and indigenes, leading to the formation of a cline. Under the assumption that the population density is uniform in space at all times, the process is modelled mathematically as a simple diffusion on a finite linear habitat with reflecting boundaries. The discontinuous gene frequency distribution is approximated by a step function. Maximum likelihood estimates of the parameters of the model are obtained by Marquardt's method, and the chisquare statistic is used to test goodness-of-fit. The model does not give a satisfactory fit at the ABO blood group locus. It does give an acceptable fit at the group-specific component and haptoglobin loci, whether the model fitting is done at each locus separately, or at both loci simultaneously. Moreover, the maximum likelihood estimates of the elapsed time since beginning of admixture are compatible with the proposal that the immigrants arrived at the end of the Jomon period. On the other hand, the maximum likelihood estimates of the eastern limit of initial occupation appear to be too large.

Radiocarbon and stable isotopes in water and dissolved constituents, Milk River aquifer, Alberta, Canada

Origin and age of groundwater in the Milk River aquifer (Alberta, Canada) was the focal point of the present study. To answer related questions, wells in this aquifer were sampled and 2H and 18O in water, 13C and 2H in methane, 34S and 18O in SO 4, 13C and 14C in dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC), and tritium contents determined. Stable isotope analyses on ground-water permitted the recognition of at least three different zones within the aquifer: starting at the recharge zone modern-type groundwaters are encountered for the first few kilometers. These are followed by groundwater with slightly higher 18O and 2H contents, i.e. waters which do not show a glacial signature and were probably recharged under warmer climatic conditions. Groundwater in the third zone is characterized by higher salinities and a pronounced oxygen isotope shift. They show the gradual admixture of far more saline formation waters from the Alberta Basin. Sulphate-S and sulphate-O isotope values indicate a till source for the SO 4. However, SO 4 in wells close to the area where SO 4 virtually disappears show isotopic values which suggest that SO 4-reduction is occurring, although other studies could not find bacterial populations of SO 4 reducers. Methane is present in most wells and, based on C and H isotope data, has a biogenic origin. Methane production occurs close to some wells and/or it diffuses from the confining shales into the aquifer. Radiocarbon is measurable only in the first 20 km from the recharge zone, however, transformation of measured concentrations to “water ages” is very difficult because of the complexity of the geochemical system. Comparison with 14C data on DOC was, therefore, very interesting and this new technique may complement the DIC radiocarbon dating. Two wells near the recharge zone yielded DIC, DOC-High Molecular Weight (HMW) and DOC-Low Molecular Weight (LMW) results. The DIC dates were much older than DOC dates but the differenve in years between the wells for all three types of C were within 1000 a of each other. The DOC dates led to the conclusion that the initial DIC radiocarbon content was as low as 30% modern when the water entered the aquifer. The age of the water 20 km from the recharge zone was assessed at ∼20,000 a, resulting in a velocity of ∼1 m/a. This result is much higher than estimates by other techniques.