Different Levels Of Admixture Research Articles

Development of EST-SSR Markers Related to Polyphyllin Biosynthesis Reveals Genetic Diversity and Population Structure in Paris polyphylla

Paris polyphylla is an important medicinal plant that can biosynthesize polyphyllins with multiple effective therapies, ranging from anti-inflammation to antitumor; however, the genetic diversity of Paris polyphylla is still unclear. To explore the genetic characteristics of cultivation populations in primary planting areas, we developed 10 expressed sequence tag simple sequence repeat (EST-SSR) markers related to polyphyllin backbone biosynthesis and utilized them in 136 individuals from 10 cultivated populations of P. polyphylla var. yunnanensis. The genetic diversity index showed that ten loci had relatively high genetic polymorphism levels. Shannon information of loci suggested that more information occurred within population and less information occurred among population. In addition, the overall populations exhibited a low degree of differentiation among populations, but maintained a high degree of genetic diversity among individuals, resulting in high gene flow and general hybridization. The genetic structure analysis revealed that 10 populations possibly derived from two ancestral groups and all individuals were found with different levels of admixture. The two groups were different from the cultivation groups at population level, suggesting the cross-pollination among cultivars. These findings will provide insights into the genetic diversity of the germplasm resources and facilitate marker-assisted breeding for this medicinal herb.

Shifting tree species composition affects biodiversity of multiple taxa in Central European forests

Central Europe's temperate forests are heavily shaped by centuries of human activity. Their natural vegetation, mainly consisting of beech-dominated (Fagus sylvatica) deciduous forests, has been widely replaced by more profitable species grown outside of their natural ranges. This has strongly influenced forest-dwelling communities. Necessary adaptations to changing climatic conditions and the increasing demand for forest ecosystem multifunctionality are reversing these shifts in tree species composition. Integrative approaches that seek to balance production and conservation goals promote mixed forests of beech with spruce (Picea abies), pine (Pinus sylvestris), or oak (Quercus spp.). These mixed forests more closely resemble the natural vegetation and have reduced vulnerability to disturbances compared to coniferous monocultures, but higher commercial value compared to pure beech forests. However, our understanding of how different levels of admixture of commercially relevant tree species to beech forests affect multi-trophic diversity and community composition remains limited.We investigated herbaceous plants, fungi, oribatid mites, springtails, true bugs, beetles, birds and bats in 41 mature forest stands differing in tree species composition. We assessed the effects of admixtures on abundances and alpha and gamma diversity, i.e. the total number of species per forest type, and a measure of multidiversity by comparing reference beech stands with stands containing varying proportions of admixed species. At the plot level, the proportion of admixtures was especially important regarding oak and pine. Increasing shares of oak positively affected birds, true bugs and herbivorous beetles. Increasing shares of pine benefitted herbivorous true bugs and understory plants but negatively affected other true bugs, bats, and litter-decomposing fungi. Spruce admixture resulted in higher saproxylic beetle and bird diversity. At the landscape level, admixture significantly increased gamma diversity in plants, mycorrhizal and litter decomposing fungi and herbivorous and saproxylic beetles. Only springtail gamma diversity decreased in the presence of admixture. Admixture also significantly altered community composition for six out of 13 taxa. Indicator species were found for all forest types, and seven species groups included species significantly associated with pure beech stands.Our results indicate that forestry decisions determine forest biodiversity across trophic levels via tree species composition, combining habitat heterogeneity effects and tree species-specific associations. Even low shares of admixed species affect local abundances and diversity. By displacing some species while benefitting others, admixing also alters community composition. This study provides a basis for estimating how altering tree species composition in Central European forests changes the diversity and composition of forest communities.

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

BackgroundGenetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding.ResultsGenotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2.ConclusionsPopulation genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

APOL 1 and kidney disease

APOL1 gene variants have been described to offer higher risk to develop hypertension, collapsing nephropthy and end stage kidney disease. The prevalence of mutations of the APOL1 gene among afro-descendant patients with chronic kidney disease for the G1 and the G2 variants can be of 20–22% and 13–15%, respectively [1]. Moreover this can be a greater problem in afrodescendante based populations, for instance, in Colombia, the genetic background of the populations was shaped by different levels of admixture between Natives, European, and Africans. Approximately 35.363 patients have diagnosed chronic kidney disease and according to population studies, 10.4% of these patients are Afro-descendant, and these frecuency can be as high as 90% in some áreas of this country. Given the importance that accounts on this area in the last years, the purpose of this review is to highlight the majors improvements in the understanding on the biology, pathophysiology and kidney disease development on patients affected with this genetic high risk variants.

Prevalence of APOL1 Risk Variants in Afro-Descendant Patients with Chronic Kidney Disease in a Latin American Country.

Introduction In Colombia, the genetic background of the populations was shaped by different levels of admixture between Natives, European, and Africans. Approximately 35.363 patients have diagnosed chronic kidney disease and according to population studies, 10.4% of these patients are Afro-descendant. We aim to assess the frequency of APOL1 variants G1 and G2 in Afro-descendant patients with ESRD treated at la Fundacion Valle del Lili University Hospital in Cali, Colombia. Methods This is an observational cross-sectional study. Afro-descendant patients with ESRD in waitlist or recipients of kidney transplant were evaluated. Clinical data were collected from the electronic medical records. Genotyping was carried out by amplification of the exon 7 of the APOL1 gene. For the identification of risk genotypes, the bioinformatics tool BLAST was used. Results We enrolled 102 participants. The frequency of APOL1 risk variants was 67.2%, in which 24.5% (n = 25) were G1 heterozygous and 5.8% (n = 6) were G2 heterozygous and 37% of the patients had high-risk status with two alleles in homozygous (G1/G1 = 21 and G2/G2 = 3) or compound heterozygote (G1/G2 = 14) form.

Genetic diversity and phylogenetic relationship among araucana creole sheep and Spanish sheep breeds

Knowledge of genetic diversity and relationship among domestic animals is important for sustainable strategies and conservation plans evaluating genetic diversity within and across breeds. Due to the lack of studies focusing on the genetic relationship between the European and South American creole populations, we performed comprehensive genetic analyses of nine sheep breeds raised in Spain compared with Araucana creole sheep. The Araucana creole sheep is an autochthonous breed raised in the south of Chile and represents an important zoogenetic resource for the local economy. The aim of this research was to characterize the genetic variability and structure based on individual genotypes. A total of 179 individuals were analyzed (Ile de France, IF n = 18, Merino Español, ME n = 18, Merino de Grazalema, MG n = 16, Merino Negro, MN n = 18, Montesina, MO n = 19, Merino Precoz, MP n = 18, Segureña, SE n = 17, Churra Lebrijana, CL n = 14, Fleischschaf, FL n = 13, Araucana, AR n = 28) by using 19 microsatellite markers. In total, 281 alleles were observed, and the value of average polymorphic information content was 0.81. The estimated diversity parameters indicated that populations retained high levels of genetic diversity (0.69 ± 0.06) and revealed the existence of genetic differentiation among the groups (FST = 10.1%). We found that the highest inbreeding coefficient was in the MP (FIS = 0.121). The study also proved the short genetic distance between ME and MG, whereas MO and MP were the most distant populations. Finally, AR presented a short genetic distance with the SE breed. The STRUCTURE analyses revealed that the populations have a particular genetic background and presented different levels of admixture. The most appropriate cluster number was K = 7. This work is the first report to confirm historical information about the genetic origin of the domestic creole population in Chile and its relationship with European breeds. Overall, the population parameters reported here provide useful information for establishing support in terms of decision-making about their conservation.

A genomic Neolithic time transect of hunter-farmer admixture in central Poland

Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times.

Admixture and genetic diversity distribution patterns of non-recombining lineages of Native American ancestry in Colombian populations.

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.

Association between Y haplogroups and autosomal AIMs reveals intra-population substructure in Bolivian populations.

For the correct evaluation of the weight of genetic evidence in a forensic context, databases must reflect the structure of the population, with all possible groups being represented. Countries with a recent history of admixture between strongly differentiated populations are usually highly heterogeneous and sub-structured. Bolivia is one of these countries, with a high diversity of ethnic groups and different levels of admixture (among Native Americans, Europeans and Africans) across the territory. For a better characterization of the male lineages in Bolivia, 17 Y-STR and 42 Y-SNP loci were genotyped in samples from La Paz and Chuquisaca. Only European and Native American Y-haplogroups were detected, and no sub-Saharan African chromosomes were found. Significant differences were observed between the two samples, with a higher frequency of European lineages in Chuquisaca than in La Paz. A sample belonging to haplogroup Q1a3a1a1-M19 was detected in La Paz, in a haplotype background different from those previously found in Argentina. This result supports an old M19 North-south dispersion in South America, possibly via two routes. When comparing the ancestry of each individual assessed through his Y chromosome with the one estimated using autosomal AIMs, (a) increased European ancestry in individuals with European Y chromosomes and (b) higher Native American ancestry in the carriers of Native American Y-haplogroups were observed, revealing an association between autosomal and Y-chromosomal markers. The results of this study demonstrate that a sub-structure does exist in Bolivia at both inter- and intrapopulation levels, a fact which must be taken into account in the evaluation of forensic genetic evidence.

Genetic Substructure of Kuwaiti Population Reveals Migration History

The State of Kuwait is characterized by settlers from Saudi Arabia, Iran, and other regions of the Arabian Peninsula. The settlements and subsequent admixtures have shaped the genetics of Kuwait. High prevalence of recessive disorders and metabolic syndromes (that increase risk of diabetes) is seen in the peninsula. Understanding the genetic structure of its population will aid studies designed to decipher the underlying causes of these disorders. In this study, we analyzed 572,366 SNP markers from 273 Kuwaiti natives genotyped using the illumina HumanOmniExpress BeadChip. Model-based clustering identified three genetic subgroups with different levels of admixture. A high level of concordance (Mantel test, p=0.0001 for 9999 repeats) was observed between the derived genetic clusters and the surname-based ancestries. Use of Human Genome Diversity Project (HGDP) data to understand admixtures in each group reveals the following: the first group (Kuwait P) is largely of West Asian ancestry, representing Persians with European admixture; the second group (Kuwait S) is predominantly of city-dwelling Saudi Arabian tribe ancestry, and the third group (Kuwait B) includes most of the tent-dwelling Bedouin surnames and is characterized by the presence of 17% African ancestry. Identity by Descent and Homozygosity analyses find Kuwait’s population to be heterogeneous (placed between populations that have large amount of ROH and the ones with low ROH) with Kuwait S as highly endogamous, and Kuwait B as diverse. Population differentiation FST estimates place Kuwait P near Asian populations, Kuwait S near Negev Bedouin tribes, and Kuwait B near the Mozabite population. FST distances between the groups are in the range of 0.005 to 0.008; distances of this magnitude are known to cause false positives in disease association studies. Results of analysis for genetic features such as linkage disequilibrium decay patterns conform to Kuwait’s geographical location at the nexus of Africa, Europe, and Asia.

Admixture Patterns and Genetic Differentiation in Negrito Groups from West Malaysia Estimated from Genome-wide SNP Data

Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the "negritos" who are believed to be descendants of the earliest settlers of Southeast Asia. Here we report patterns of genetic substructure and admixture in two Malaysian negrito populations (Jehai and Kensiu), using ~50,000 genome-wide single-nucleotide polymorphism (SNP) data. We found traces of recent admixture in both the negrito populations, particularly in the Jehai, with the Malay through principal component analysis and STRUCTURE analysis software, which suggested that the admixture was as recent as one generation ago. We also identified significantly differentiated nonsynonymous SNPs and haplotype blocks related to intracellular transport, metabolic processes, and detection of stimulus. These results highlight the different levels of admixture experienced by the two Malaysian negritos. Delineating admixture and differentiated genomic regions should be of importance in designing and interpretation of molecular anthropology and disease association studies.

Admixture Patterns and Genetic Differentiation in Negrito Groups from West Malaysia Estimated from Genome-wide SNP Data

Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the “negritos” who are believed to be descendants of the earliest settlers of Southeast Asia. Here we report patterns of genetic substructure and admixture in two Malaysian negrito populations (Jehai and Kensiu), using ~50,000 genome-wide single-nucleotide polymorphism (SNP) data. We found traces of recent admixture in both the negrito populations, particularly in the Jehai, with the Malay through principal component analysis and STRUCTURE analysis software, which suggested that the admixture was as recent as one generation ago. We also identified significantly differentiated nonsynonymous SNPs and haplotype blocks related to intracellular transport, metabolic processes, and detection of stimulus. These results highlight the different levels of admixture experienced by the two Malaysian negritos. Delineating admixture and differentiated genomic regions should be of importance in designing and interpretation of molecular anthropology and disease association studies.

Phylogeographic analysis of paternal lineages in NE Portuguese Jewish communities

The establishment of Jewish communities in the territory of contemporary Portugal is archaeologically documented since the 3rd century CE, but their settlement in Trás-os-Montes (NE Portugal) has not been proved before the 12th century. The Decree of Expulsion followed by the establishment of the Inquisition, both around the beginning of the 16th century, accounted for a significant exodus, as well as the establishment of crypto-Jewish communities. Previous Y chromosome studies have shown that different Jewish communities share a common origin in the Near East, although they can be quite heterogeneous as a consequence of genetic drift and different levels of admixture with their respective host populations. To characterize the genetic composition of the Portuguese Jewish communities from Trás-os-Montes, we have examined 57 unrelated Jewish males, with a high-resolution Y-chromosome typing strategy, comprising 16 STRs and 23 SNPs. A high lineage diversity was found, at both haplotype and haplogroup levels (98.74 and 82.83%, respectively), demonstrating the absence of either strong drift or founder effects. A deeper and more detailed investigation is required to clarify how these communities avoided the expected inbreeding caused by over four centuries of religious repression. Concerning haplogroup lineages, we detected some admixture with the Western European non-Jewish populations (R1b1b2-M269, approximately 28%), along with a strong ancestral component reflecting their origin in the Middle East [J1(xJ1a-M267), approximately 12%; J2-M172, approximately 25%; T-M70, approximately 16%] and in consequence Trás-os-Montes Jews were found to be more closely related with other Jewish groups, rather than with the Portuguese non-Jewish population.

A Perspective on the History of the Iberian Gypsies Provided by Phylogeographic Analysis of Y‐Chromosome Lineages

The European Gypsies, commonly referred to as Roma, are represented by a vast number of groups spread across many countries. Although sharing a common origin, the Gypsy groups are highly heterogeneous as a consequence of genetic drift and different levels of admixture with surrounding populations. With this study we aimed at contributing to the knowledge of the Roma history by studying 17 Y-STR and 34 Y-SNP loci in a sample of 126 Portuguese Gypsies. Distinct genetic hallmarks of their past and migration route were detected, namely: an ancestral component, shared by all Roma groups, that reflects their origin in India (H1a-M82; approximately 17%); an influence from their long permanence in the Balkans/Middle-East region (J2a1b-M67, J2a1b1-M92, I-M170, Q-M242; approximately 31%); traces of contacts with European populations preceding the entrance in the Iberian Peninsula (R1b1c-M269, J2b1a-M241; approximately 10%); and a high proportion of admixture with the non-Gypsy population from Iberia (R1b1c-M269, R1-M173/del.M269, J2a-M410, I1b1b-M26, E3b1b-M81; approximately 37%). Among the Portuguese Gypsies the proportion of introgression from host populations is higher than observed in other groups, a fact which is somewhat unexpected since the arrival of the Roma to Portugal is documented to be more recent than in Central or East Europe.