Genomic Insights Into the Population History and Biological Adaptation of Southwestern Chinese Hmong–Mien People

Hmong–Mien (HM) -speaking populations, widely distributed in South China, the north of Thailand, Laos, and Vietnam, have experienced different settlement environments, dietary habits, and pathogenic exposure. However, their specific biological adaptation remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are also unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations; one localized in the HM clines, and others possessed affinity with Han Chinese. We also identified one new ancestral lineage specifically existed in HM people, which spatially distributed from Sichuan and Guizhou in the north to Thailand in the south. The sharing patterns of the newly identified homogenous ancestry component combined the estimated admixture times via the decay of linkage disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward in the historic period, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese Population Genomic Diversity Project (CPGDP), especially in the regions with rich ethnolinguistic diversity.

Population Structure and Phylogeny of Some U.S. Peach Cultivars

Peach (Prunus persica) cultivars maintained at the U.S. Department of Agriculture program at Byron, GA, have never been characterized with any molecular markers. In this study, 20 microsatellite markers were used to genotype 112 cultivars and the data were analyzed to discern their population structure and phylogenetic relationships. STRUCTURE simulations revealed four K clusters and broad genetic admixture among the cultivars. Principal coordinate analysis (PCoA) showed the cultivar groups from western, northeastern, and southeastern U.S. states were adjacent to each other except cultivars from Michigan (close to most southeastern state groups) and Florida (most distant from the other groups). Principal component analysis (PCA) showed that these cultivars had no obvious PCA partitioning boundaries. The intertwined distribution in both PCoA and PCA partitions suggested many of them were genetically closely related to each other largely because most shared same ancestral parentages. Most pairwise distance means within and between the cultivar groups were relatively low, suggesting close phylogenetic relations among those cultivars, as were demonstrated in the phylogenetic tree. Limiting factors and perspectives relevant to peach breeding are discussed.

The Genetic Structure and East-West Population Admixture in Northwest China Inferred From Genome-Wide Array Genotyping

Northwest China is a contacting region for East and West Eurasia and an important center for investigating the migration and admixture history of human populations. However, the comprehensive genetic structure and admixture history of the Altaic speaking populations and Hui group in Northwest China were still not fully characterized due to insufficient sampling and the lack of genome-wide data. Thus, We genotyped genome-wide SNPs for 140 individuals from five Chinese Mongolic, Turkic speaking groups including Dongxiang, Bonan, Yugur, and Salar, as well as the Hui group. Analysis based on allele-sharing and haplotype-sharing were used to elucidate the population history of Northwest Chinese populations, including PCA, ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave/qpAdm and ALDER, fineSTRUCTURE and GLOBETROTTER. We observed Dongxiang, Bonan, Yugur, Salar, and Hui people were admixed populations deriving ancestry from both East and West Eurasians, with the proportions of West Eurasian related contributions ranging from 9 to 15%. The genetic admixture was probably driven by male-biased migration- showing a higher frequency of West Eurasian related Y chromosomal lineages than that of mtDNA detected in Northwest China. ALDER-based admixture and haplotype-based GLOBETROTTER showed this observed West Eurasian admixture signal was introduced into East Eurasia approximately 700 ∼1,000 years ago. Generally, our findings provided supporting evidence that the flourish transcontinental communication between East and West Eurasia played a vital role in the genetic formation of northwest Chinese populations.

Subtle East–West Phylogeographic Break of Asteropyrum (Ranunculaceae) in Subtropical China and Adjacent Areas

East–west phylogeographic break is common among plant species in subtropical China. However, the estimation time of east–west phylogeographic break has always relied on inferences of calibrated phylogenies, and the contribution of environmental heterogeneity to population differentiation has largely been ignored. In this study, we estimated the divergence time of Asteropyrum populations through coalescent-based approaches based on DNA sequences of ten nuclear loci and evaluated the contribution of environmental heterogeneity to population differentiation. The results showed that there were two chloroplast clades and nuclear groups within Asteropyrum, displaying a subtle pattern of east–west differentiation. The divergence time of the two nuclear groups was dated to ~1.2 Ma, which is associated with climate changes during the Mid-Pleistocene transition. A genetic admixture event between the two genetic groups happened at ~0.46 Ma, resulting in several admixed populations. Isolation by environmental distance (IBE) explained the majority (46.32%) of population differentiation, but that isolation by geographic distance (IBD) only contributed 4.66%. The results of this study suggest that climate changes during the Pleistocene may be a major cause for the east–west phylogeographic break in subtropical China. However, the complex terrain and high environmental heterogeneity in the west of subtropical China (and adjacent regions such as the Hengduan Mountains and the Himalayan Moutains) caused by strong geological uplift may have profoundly shaped the population structure of plant species in subtropical China.

Genetic (SSRs) versus morphological differentiation of date palm cultivars: Fst versus Pst estimates

Date Palm (Phoenix dactylifera L.) is one of the oldest domesticated fruit trees. For future breeding program, knowledge on genetic structure of cultivars is necessary. Therefore, the present study was performed with the following aims: 1- To provide data on genetic diversity and genetic structure of 36 date palm cultivars, 2- To provide data on the association between fruit characteristics and the genetic features of the cultivars. We used nine SSRs and EST-SSR loci for our genetic investigation. The most of SSR loci obtained have a high Gst value (0.70), and therefore have a good discrimination power for date palm cultivar differentiation task. K-Means clustering grouped date palm cultivars either in two broad clusters, or in 16 smaller genetic groups. This was supported by delta K = 2 of the STRUCTURE analysis. AMOVA produced significant genetic difference among date palm cultivars (PhiPT = 0.70, P = 0.001). New genetic differentiation parameters estimated also produced significant difference among date palm cultivars (G’st(Nei) = 0.673, P =0.001; G’st(Hed) = 0.738, P = 0.001). Test of assignment revealed that some of the cultivars have 33-66% misassignment, probably due to genetic admixture. Heatmaps of genetic versus morphological/or agronomical characters in date palm cultivars differed from each other showing the cultivars morphological changes is not merely related to their genetic content. It points toward the potential role played either by environmental conditions or local selection practice. The new findings can be utilized in future conservation and breeding of date palms in the country.

Multivariate Characterization of Morpho-biometric Traits of Indigenous Helmeted Guinea Fowl (Numida meleagris) in Nigeria

This study was embarked upon to characterise phenotypically helmeted guinea fowls in three agro-ecologies in Nigeria using multivariate approach. Eighteen biometric characters, four morphological indices and eleven qualitative (phaneroptic) traits were investigated in a total of 569 adult birds (158 males and 411 females). Descriptive statistics, non-parametric Kruskal–Wallis H test followed by the Mann–Whitney U test for post hoc, Multiple Correspondence Analysis (MCA), General Linear Model, Canonical Discriminant Analysis, Categorical Principal Component Analysis and Decision Trees were employed to discern the effects of agro-ecological zone and sex on the morphostructural parameters. Agro-ecology had significant effect (P<0.05; P <0.01) on all the colour traits. In general, the most frequently observed colour phenotype of guinea fowl had pearl plumage colour (54.0%), pale red skin colour (94.2%), black shank colour (68.7%), brown eye colour (49.7%), white earlobe colour (54.8%) and brown helmet colour (72.6%). The frequencies of helmet shape and wattle size were significantly influenced (P <0.01) by agro-ecology and sex. Overall, birds from the Southern Guinea Savanna zone had significantly higher values (P <0.05) for most biometric traits compared to their Sudano-Sahelian and Tropical Rainforest counterparts. They were also more compact (120.83±1.61 vs. 113.96±0.97 vs. 111.33±1.19) and had lesser condition index (8.542±0.17 vs. 9.92±0.10 vs. 9.61±0.13) than their counterparts in the two other zones. The interaction between agro-ecology and sex had significant effect (P <0.05) on some quantitative variables. The MCA and discriminant analysis revealed considerable intermingling of the phaneroptic, biometric traits and body indices especially between the Sudano-Sahelian and Tropical Rainforest birds. Inspite of the high level of genetic admixture, the guinea fowl populations could best be distinguished using wing length, body length and eye colour. However, further complementary work on genomics will guide future selection and breeding programmes geared towards improving the productivity, survival and environmental adaptation of indigenous helmeted guinea fowls in the tropics.

High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue

Copy number alterations (CNAs) are pervasive in advanced human cancers, but their prevalence in early-stage, localized tumors and their surrounding normal tissues is poorly characterized. To investigate this phenomenon, here we developed a method for spatially resolved single-cell CNA profiling and applied it to characterize the CNA landscape in 10,007 nuclei extracted from 70 tumor and normal tissue regions (~125 mm3 tissue cubes) from prostatectomies performed in six patients with localized prostate cancer. We identified two distinct groups of cells with abnormal karyotype, one mainly consisting of sparse alterations (‘pseudo-diploid’ cells) and the other characterized by genome-wide karyotypic changes (‘monster’ cells). Pseudo-diploid cells displayed high clonal diversity and formed numerous small sized clones ranging from highly spatially localized to broadly spread clones, whereas monster cells were singular events detected throughout the prostate. We observed a remarkable correlation between the fraction of the genome affected by CNAs and the number of tissue regions in which pseudo-diploid cells were found. Highly localized pseudo-diploid clones were enriched in tumor regions and carried deletions of known or putative tumor suppressors, including APC, CDKN1B, FOXO1, FOXP1, and RB1. Spatially resolved targeted deep sequencing of 523 cancer genes detected non-synonymous mutations in both normal and tumor regions, including mutations in FOXA1, FOXP1, and SPOP genes previously implicated in prostate cancer. Strikingly, in two regions in which targeted deep sequencing detected a point mutation affecting the DNA-binding activity of the FOXA1 transcription factor, we also found a co-deletion of FOXO1 and FOXO3 genes in cells from two different pseudo-diploid clones, implicating combinatorial perturbations of Forkhead transcription factors as an early driver of prostate carcinogenesis. Our study reveals that CNAs and mutations are widespread across normal and tumor regions in the prostate glands of patients with localized prostate cancer and suggests that a subset of alterations—most likely small deletions causing the loss of key tumor suppressors—confer a fitness advantage and channel cells towards tumorigenesis.

Genome analyses revealed genetic admixture and selection signatures in Bos indicus

The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.

Demographic model and biological adaptation inferred from the genome-wide SNP data reveal tripartite origins of southernmost Chinese Huis

The culturally unique Sanya Hui (SYH) people are regarded as the descendants of ancient Cham people in Central Vietnam (CV) and exhibit a scenario of complex migration and admixture history, who were likely to first migrate from Central and South Asia (CSA) to CV and then to South Hainan and finally assimilated with indigenous populations and resided in the tropical island environments since then. A long-standing hypothesis posits that SYH derives from different genetic and cultural origins, which hypothesizes that SYH people are different from the genetically attested admixture history of northern Hui people possessing major Han-related ancestry and minor western Eurasian ancestry. However, the effect of the cultural admixture from CSA and East Asia (EA) on the genetic admixture of SYH people remains unclear. Here, we reported the first batch of genome-wide SNP data from 94 SYH people from Hainan and comprehensively characterized their genetic structure, origin, and admixture history. Our results found that SYH people were genetically different from the northern Chinese Hui people and harbored a close genomic affinity with indigenous Vietnamese but a distinct relationship with Cham, which confirmed the hypothesis of documented recent historical migration from CV and assimilation with Hainan indigenous people. The fitted admixture models and reconstructed demographic frameworks revealed an additional influx of CSA and EA ancestries during the historical period, consisting of the frequent cultural communication along the Southern Maritime Silk Road and extensive interaction with EA. Analyses focused on natural-selected signatures of SYH people revealed a similar pattern with mainland East Asians, which further confirmed the possibility of admixture-induced biological adaptation of island environments. Generally, three genetically attested ancestries from CV, EA, and CSA in modern SYH people supported their tripartite model of genomic origins.

Genomic insights into the population history and biological adaptation of Southwestern Chinese Hmong-Mien people

Hmong-Mien-speaking (HM) populations, widely distributed in South China, North of Thailand, Laos and Vietnam, have experienced different settlement environments, dietary habits and pathogen exposure. However, their specific biological adaptation also remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations and also identified one new ancestral lineage specifically exited in HM people, which spatially distributed from Sichuan and Guizhou in the North to Thailand in the South and temporally dated to at least 500 years. The sharing patterns of the newly-identified homogeneous ancestry component combined the estimated admixture times via the decay of Linkage Disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward recently, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically-informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese population genomic diversity project (CPGDP), especially in the ethnolinguistic regions.