Genetic Substructure Research Articles

Characterization of Y chromosome diversity in newfoundland and labrador: evidence for a structured founding population.

The population of Newfoundland and Labrador (NL) is largely derived from settlers who migrated primarily from England and Ireland in the 1700s-1800s. Previously described as an isolated founder population, based on historical and demographic studies, data on the genetic ancestry of this population remains fragmentary. Here we describe the largest investigation of patrilineal ancestry in NL. To determine the paternal genetic structure of the population, 1,110 Y chromosomes from an NL-based cohort were analyzed using 5,761 Y-specific SNPs. We identified 160 distinct terminal haplogroups, the majority of which (71.4%) belong to the R1b haplogroup. When compared with global reference populations, the NL population haplogroup composition and frequencies primarily resemble those observed in English and Irish ancestral source populations. There is also evidence of genetic contributions from Basque, French, Portuguese, and Spanish fishermen and early settlers who frequented NL. Interestingly, the observed population structure shows geographical and religious clustering that can be associated with the settlement of the ancestral source populations from predominantly Protestant, England, and Catholic, Ireland respectively. For example, the R1b-M222 haplogroup, seen in people of Irish descent, is found clustered in the Irish-settled Southeast region of NL. The clustering and expansion of Y haplogroups in conjunction with the geographical and religious clusters illustrate that limited subsequent in-migration, geographic isolation, and societal factors have contributed to the genetic substructure of the NL population and its designation as a founder population.

Influence of Sires on Population Substructure in Dülmen Wild Horses.

The objectives of the present study were to analyze the influence of the stallions employed in the Dülmen wild horses on the genetic diversity and population substructure using Bayesian cluster analysis. The Dülmen wild horse is maintained as a unique horse population exposed to the natural conditions all year round in the Merfelder Bruch near Dülmen in Westphalia, Germany. Stallions selected for breeding have to prove their abilities to survive under this harsh environment. We used multilocus genotypic information from a set of 29 autosomal microsatellites to determine the paternity of 185 male foals sired by nine stallions. As females could not be sampled, we could not make inferences on all yearlings and test whether there are differences in the genetic population parameters between both sexes. The mean number of progeny was 19.92 with a range of 2-32, caused by the length of the service period per stallion. The average observed and unbiased expected heterozygosity was 0.688 and 0.631, the mean number of alleles was 4.448, and Wright's FIS was -0.173. Pairwise genetic distances (FST and Nei's unbiased genetic distances) were significant and varied between 0.038 to 0.091 and 0.085 to 0.290, respectively. Neighbor-joining dendrogram plots clustered a large proportion of the paternal progeny groups in different branches. Posterior Bayesian analyses using seven paternal half-sib groups with 10-74 members supported a maximum of six clusters, with two paternal progeny groups not differing, and a median of five clusters, with two groups of two sires each falling into the same clusters. When sires were employed in non-consecutive years, progeny from these different years of the same sires were grouped in the same cluster, whereas the progeny of one sire from two consecutive years were in different clusters. We were able to distinguish male progeny from Dülmen wild horse stallions and to show the effects of stallion use on the genetic substructure in the Dülmen wild horse herd. In conclusion, the analyses showed the genetic potential of the Dülmen wild horse stallions to maintain a high genetic diversity and also the effects in which breeding seasons and for how long stallions are used to sire foals. The selection of stallions may be sensitive for the further development of genetic diversity and preserve this closed population as a valuable resource for further studies on the evolution of the horse.

Deep genetic substructure within bonobos.

Establishing the genetic and geographic structure of populations is fundamental, both to understand their evolutionary past and preserve their future. Nevertheless, the patterns of genetic population structure are unknown for most endangered species. This is the case for bonobos (Pan paniscus), which, together with chimpanzees (Pan troglodytes), are humans' closest living relatives. Chimpanzees live across equatorial Africa and are classified into four subspecies,1 with some genetic population substructure even within subspecies. Conversely, bonobos live exclusively in the Democratic Republic of Congo and are considered a homogeneous group with low genetic diversity,2 despite some population structure inferred from mtDNA. Nevertheless, mtDNA aside, their genetic structure remains unknown, hampering our understanding of the species and conservation efforts. Mapping bonobo genetic diversity in space is, however, challenging because, being endangered, only non-invasive sampling is possible for wild individuals. Here, we jointly analyze the exomes and mtDNA from 20 wild-born bonobos, the whole genomes of 10 captive bonobos, and the mtDNA of 136 wild individuals. We identify three genetically distinct bonobo groups of inferred Central, Western, and Far-Western geographic origin within the bonobo range. We estimate the split time between the central and western populations to be ∼145,000 years ago and genetic differentiation to be in the order of that of the closest chimpanzee subspecies. Furthermore, our estimated long-term Ne for Far-West (∼3,000) is among the lowest estimated for any great ape lineage. Our results highlight the need to attend to the bonobo substructure, both in terms of research and conservation.

Characterization of fine geographic scale population genetics in sugar kelp (Saccharina latissima) using genome-wide markers

BackgroundKelps are not only ecologically important, being primary producers and habitat forming species, they also hold substantial economic potential. Expansion of the kelp cultivation industry raises the interest for genetic improvement of kelp for cultivation, as well as concerns about genetic introgression from cultivated to wild populations. Thus, increased understanding of population genetics in natural kelp populations is crucial. Genotyping-by-sequencing (GBS) is a powerful tool for studying population genetics. Here, using Saccharina latissima (sugar kelp) as our study species, we characterize the population genetics at a fine geographic scale, while also investigating the influence of marker type (biallelic SNPs versus multi-allelic short read-backed haplotypes) and minor allele count (MAC) thresholds on estimated population genetic metrics.ResultsWe examined 150 sporophytes from 10 locations within a small area in Mid-Norway. Employing GBS, we detected 20,710 bi-allelic SNPs and 42,264 haplotype alleles at 20,297 high quality GBS loci. We used both marker types as well as two MAC filtering thresholds (3 and 15) in the analyses. Overall, higher genetic diversity, more outbreeding and stronger substructure was estimated using haplotypes compared to SNPs, and with MAC 15 compared to MAC 3. The population displayed high genetic diversity (HE ranging from 0.18–0.37) and significant outbreeding (FIS ≤ − 0.076). Construction of a genomic relationship matrix, however, revealed a few close relatives within sampling locations. The connectivity between sampling locations was high (FST ≤ 0.09), but subtle, yet significant, genetic substructure was detected, even between sampling locations separated by less than 2 km. Isolation-by-distance was significant and explained 15% of the genetic variation, while incorporation of predicted currents in an “isolation-by-oceanography” model explained a larger proportion (~ 27%).ConclusionThe studied population is diverse, significantly outbred and exhibits high connectivity, partly due to local currents. The use of genome-wide markers combined with permutation testing provides high statistical power to detect subtle population substructure and inbreeding or outbreeding. Short haplotypes extracted from GBS data and removal of rare alleles enhances the resolution. Careful consideration of marker type and filtering thresholds is crucial when comparing independent studies, as they profoundly influence numerical estimates of population genetic metrics.

FamLink2 – A comprehensive tool for likelihood computations in pedigrees analyses involving linked DNA markers accounting for genotype uncertainties

There is an increasing demand for software that can handle an arbitrary number of linked markers in forensic genetics; primarily with application to inference of relationships and direct matching but also in applications such as ancestry inference and mixture interpretation. With the emergence of sequencing technologies, denser sets of SNP markers are generated and analyzed. Additionally, sequence data of low quality and quantity DNA generate uncertainty about the underlying true genotype. We provide an efficient implementation of a general model for pedigree likelihood computations with genetic marker data using a three-layered approach. The top and first layer is the population model where allele frequencies and population substructure are accounted for. The second layer is the inheritance model which efficiently handles linked markers using an IBD model. The third and bottom layer is the observational level where we model the likelihood of the true genotype given underlying reads as well as parameters for errors. We exemplify the utility of our implementation as well as provide validation according to guidelines established by the ISFG using a combination of two published SNP panels. We demonstrate that computations are feasible for panels encompassing 10,000 markers and we argue that, due to the properties of the underlying algorithm, extending the number of markers will result in a linear increase in computation time. In addition we study the impact of parameters used in our model and suggest some guidelines pertaining to their values. The results demonstrate that a probabilistic model for low coverage sequence read data is needed instead of relying on an a threshold based genotype and applying our general model for inference of relationships on a real case can be superior, i.e. higher information content, to other methods relying on either fixed genotypes with low quality sequence data or simple pair wise relationship tests. In summary, the implementation, FamLink2 (freely available at https://famlink.se), can jointly handle genetic linkage, genotype uncertainty and population substructure for an arbitrary pedigree with data for any number of individuals. Whereas the current study will focus on calculations disregarding mutations, FamLink2 has the ability to model mutations for certain built-in pedigrees.

Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations

BackgroundNorth African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa.ResultsWe conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa.ConclusionsWe have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.

When a name changes everything: taxonomy and conservation of the Atlantic bushmaster (Lachesis Daudin, 1803) (Serpentes: Viperidae: Crotalinae)

The South American bushmaster Lachesis muta is currently considered a valid taxon with no recognized subspecies. However, its wide distribution with discontinuous populations, the restricted sampling of molecular data in previous studies, and the inherent difficulty in obtaining diagnostic data, preclude a detailed evaluation of the taxonomic status of this taxon. In this study, we use high-resolution genomics, as well as venomic, morphological, and ecological data to infer the speciation processes involved in the evolutionary history of L. muta populations. Our data recognize the Amazon populations as L. muta and the Atlantic Forest populations as L. rhombeata. Lachesis rhombeata has lower genetic diversity than L. muta and we recommend a critical evaluation to include this species in the national and international red lists of endangered species. Moreover, we propose classifying the L. rhombeata population from the Baturité massif (Ceará state) as an evolutionarily significant unit (ESU) for conservation and we also found genetic substructure within L. muta populations. We expect our results will contribute to the taxonomic stability of the Neotropical fauna and highlight the urgency of protecting Atlantic Forest populations of Lachesis species and, consequently, the landscape that this species and related biota inhabit.

Combined demographic, ecological and genetic tools reveal connectivity within a fragmented butterfly population

Protected species require targeted studies to establish population sizes, their dispersal capacity and the possible genetic bottleneck effect that could impair the future of the remaining populations. In this study, we used the genotyping-by-sequencing technique (SNP: single nucleotide polymorphism) combined with Capture-Mark-Recapture (CMR) method to measure the dispersal ability and subpopulation sizes of the protected butterfly Zerynthia polyxena in 14 sites of NW Italian Alps. The study species form a metapopulation divided into several small subpopulations (ranging from 90 to 859 estimated subpopulation sizes). The species showed low mobility, likely due to habitat fragmentation, with individuals travelling an average of 80 m from their original capture site. SNPs highlighted high observed heterozygosity, low genetic substructuring at short distances, and large genetic differentiation only for individuals found in sites located at 46 km distance, suggesting high gene flow at short distances and limited gene flow between distant populations. Although CMR data did not detect movement beyond 700 m, the genetic results revealed remarkable connectivity among nearby subpopulations. The results indicate that gene flow still exists among the subpopulations despite the fragmented habitat. Considering that the species is locally threatened by habitat loss due to the planning of a European high-speed railway, our data suggest that it is not too late to adopt conservation measures. In conclusion, combining genetic and ecological studies can be utilised to design proper conservation plans for protected and threatened insect metapopulations.

Rediscovery, systematics and conservation of an enigmatic freshwater crayfish (Parastacidae) from the Australian monsoon tropics

AbstractFreshwater wetlands are among the world's most valuable ecosystems, supporting diverse biota and critical ecological services, yet these habitats have suffered extensive and pervasive anthropogenic disturbance. Northern Australia represents a rare example of a relatively unmodified, vast wetland habitat. The freshwater crayfishes of the region are poorly documented, with one enigmatic species, the nutcracker yabby Cherax nucifraga, described from a single individual sampled opportunistically from the stomach of a predatory fish. Here we report on the rediscovery of C. nucifraga from a relatively limited distribution in semi‐permanent coastal freshwater wetlands. Field studies were conducted to inform natural resource management and conservation. Genome skimming to recover mitogenomes, 18S–28S and histone sequences demonstrated a sister relationship with two congeners from the tropics, and moderate molecular genetic substructure was apparent within C. nucifraga between mainland and Melville Island locations. Cherax nucifraga is characterised by the presence of a strawberry‐coloured soft patch on the outer margin of the claw, uniquely present in both mature males and females. Meristic and multivariate morphometric comparisons are made with the co‐occurring redclaw Cherax quadricarinatus and the allopatric whiteclaw yabby Cherax bicarinatus, with a summary of diagnostic traits developed into a visual guide and key. Programs to further understand ecology, threats and traditional ecological knowledge will help to inform the future conservation management of the species in the face of increasing development and environmental change to northern Australian coastal freshwater wetlands. Specific conservation actions include identifying and protecting refuge habitats and preventing incursions by other Cherax species.

Genetic substructure and host-specific natural selection trend across vaccine-candidate ORF-2 capsid protein of hepatitis-E virus.

Hepatitis E virus is a primary cause of acute hepatitis worldwide. The present study attempts to assess the genetic variability and evolutionary divergence among HEV genotypes. A vaccine promising capsid-protein coding ORF-2 gene sequences of HEV was evaluated using phylogenetics, model-based population genetic methods and principal component analysis. The analyses unveiled nine distinct clusters as subpopulations for six HEV genotypes. HEV-3 genotype samples stratified into four different subgroups, while HEV-4 stratified into three additional subclusters. Rabbit-infectious HEV-3ra samples constitute a distinct cluster. Pairwise analysis identified marked genetic distinction of HEV-4c and HEV-4i subgenotypes compared to other genotypes. Numerous admixed, inter and intragenotype recombinant strains were detected. The MEME method identified several ORF-2 codon sites under positive selection. Some selection signatures lead to amino acid substitutions within ORF-2, resulting in altered physicochemical features. Moreover, a pattern of host-specific adaptive signatures was identified among HEV genotypes. The analyses conclusively depict that recombination and episodic positive selection events have shaped the observed genetic diversity among different HEV genotypes. The significant genetic diversity and stratification of HEV-3 and HEV-4 genotypes into subgroups, as identified in the current study, are noteworthy and may have implications for the efficacy of anti-HEV vaccines.

Tracing the fine-scale demographic history and recent admixture in Hmong-Mien speakers.

The linguistic, historical, and subsistent uniqueness of Hmong-Mien (HM) speakers offers a wonderful opportunity to investigate how these factors impact the genetic structure. The genetic differentiation among HM speakers and their population history are not well characterized. Here, we generate genome-wide data from 65 Yao ethnicity samples and analyze them with published data, particularly by leveraging haplotype-based methods. We determined that the fine-scale genetic substructure of HM speakers corresponds better with linguistic classification than with geography. Particularly, parallels between serial founder events and language differentiations can be observed in West Hmongic speakers. Multiple lines of evidence indicate that ~500-year-old GaoHuaHua individuals are most closely related to West Hmongic-speaking Bunu. The strong genetic bottleneck of some HM-speaking groups, especially Bunu, could potentially be associated with their long-term practice of swidden agriculture to some degree. The inferred admixture dates for most of the HM speakers overlap with the reign of the Ming dynasty (1368-1644 CE). Besides a common genetic origin for HM speakers, their genetic ancestry is shared primarily with neighboring Han Chinese and Tai-Kadai speakers in south China. In conclusion, our analyses reveal that recent isolation and admixture events have contributed to the genetic population history of present-day HM speakers.

Genetic history of esophageal cancer group in southwestern China revealed by Y‐chromosome STRs and genomic evolutionary connection analysis

Genetic and environmental factors play crucial roles in the development of esophageal cancer (EC) and contribute uniquely or cooperatively to human cancer susceptibility. Sichuan is located in the interior of southwestern China, and the northern part of Sichuan is one of the regions with a high occurrence of EC. However, the factors influencing the high incidence rate of EC in the Sichuan Han Chinese population and its corresponding genetic background and origins are still poorly understood. Here, we utilized genome-wide single nucleotide polymorphisms (SNPs) and Y-chromosome short tandem repeats (Y-STRs) to characterize the genetic structure, connection, and origin of cancer groups and general populations. We generated Y-STR-based haplotype data from 214 Sichuan individuals, including the Han Chinese EC population and a control group of Han Chinese individuals. Our results, obtained from Y-STR-based population statistical methods (analysis of molecular variance (AMOVA), principal component analysis (PCA), and phylogenetic analysis), demonstrated that there was a genetic substructure difference between the EC population in the high-incidence area of northern Sichuan Province and the control population. Additionally, there was a strong genetic relationship between the EC population in the northern Sichuan high-incidence area and those at high risk in both the Fujian and Chaoshan areas. In addition, we obtained high-density SNP data from saliva samples of 60 healthy Han Chinese individuals from three high-prevalence areas of EC in China: Sichuan Nanchong, Fujian Quanzhou, and Henan Xinxiang. As inferred from the allele frequency of SNPs and sharing patterns of haplotype segments, the evolutionary history and admixture events suggested that the Han population from Nanchong in northern Sichuan Province shared a close genetic relationship with the Han populations from Xinxiang in Henan Province and Quanzhou in Fujian Province, both of which are regions with a high prevalence of EC. Our study illuminated the genetic profile and connection of the Northern Sichuan Han population and enriched the genomic resources and features of the Han Chinese populations in China, especially for the Y-STR genetic data of the Han Chinese EC population. Populations living in different regions with high incidences of EC may share similar genetic backgrounds, which offers new insights for further exploring the genetic mechanisms underlying EC.

Paternal genetic structure analysis of the modern Han populations based on Y-SNP and Y-STR.

The Han populations represent the largest ethnic group in China. Previous studies have primarily focused on investigating their genetic origins, migration and integration, as well as paternal genetic relationships within specific regional Han populations. However, a comprehensive analysis of the global paternal genetic structure of Han populations is lacking. In this study, we performed Y-chromosome sequencing on 362 unrelated male samples from Chinese Han individuals collected from Qinghai, Sichuan and Liaoning provinces. We then integrated relevant data from reported studies. Our final dataset comprised 1830 samples from 16 Han populations across 15 provinces in China, encompassing information on 89 Y-SNPs and 16 Y-STRs. Statistical analyses were conducted to assess Y-STR haplotype diversity (HD) and Y-SNP haplogroup frequencies. Additionally, we employed principal component analysis (PCA), phylogenetic tree and haplotype network to explore genetic differentiation within Han populations and the genetic relationships between Han populations and ethnic minorities surrounding them. Our results demonstrated that the O-M175 haplogroup represents the predominant paternal lineage in Han populations, with frequencies ranging from 60.53% (Qinghai Han) to 92.7% (Guangdong Han). Moreover, the subclades downstream of O-M175 showed distinct regional variations in their distribution patterns. The O2-M122 haplogroup was prevalent in all Han populations and demonstrated a gradual decline in frequency from north to south. Conversely, the distribution frequency of the O1b-M268 haplogroup decreased from south to north, particularly showed significant presence among Han populations in the Lingnan region. Haplogroup O1a-M119 distributed more frequently in the central Han populations. Our findings revealed that Chinese Han populations can be categorized into three subgroups: northern, central, and southern. Notably, there were significant differences among Han in Qinghai and other regions. Regarding the genetic relationships between Han populations and surrounding ethnic minorities, we observed a closer genetic affinity between different Han populations, but northern Han demonstrated a stronger relationship with the Hui ethnic group, while southern Han exhibited a closer connection with the Gelao and Li ethnic groups. In summary, this study presented a systematic analysis of haplogroup distribution, genetic substructure of Han populations and genetic relationships between Han populations and surrounding ethnic minorities based on 89 Y-SNPs and 16 Y-STRs systematically. Our research supplemented valuable insights into population genetics and forensic genetics, and provided data support for the forensic application of Y chromosome. The integration of Y-SNP haplogroups with Y-STR haplotypes offers enhanced understanding of the genetic substructure within Han populations, which holds significance for both population genetics research and forensic science applications.

Blood donor biobank as a resource in personalised biomedical genetic research.

Health questionnaires and donation criteria result in accumulation of highly selected individuals in ablood donor population. To understand better the usefulness of ablood donor-based biobank in personalised disease-associated genetic studies, and for possible personalised blood donation policies, we evaluated the occurrence and distributions of common and rare disease-associated genetic variants in Finnish Blood Service Biobank. We analysed among 31,880 blood donors the occurrence and geographical distribution of (i) 53 rare Finnish-enriched disease-associated variants, (ii) mutations assumed to influence blood donation: four Bernard-Soulier syndrome and two hemochromatosis mutations, (iii) type I diabetes risk genotype HLA-DQ2/DQ8. In addition, we analysed the level of consanguinity in Blood Service Biobank. 80.3% of blood donors carried at least one (range 0-9 per donor) of the rare variants, many in homozygous form, as well. Donors carrying multiple rare variants were enriched in Eastern Finland. Haemochromatosis mutation HFE C282Y homozygosity was 43.8% higher than expected, whereas mutations leading to Bernard-Soulier thrombocytopenia were rare. The frequency of HLA-DQ2/DQ8 genotype was slightly lower than expected. First-degree consanguinity was higher in Blood Service Biobank than in the general population. We demonstrate that despite donor selection, the Blood Service Biobank is a valuable resource for personalised medical research and for genotype-selected samples from unaffected individuals. The geographical genetic substructure of Finland enables efficient recruitment of donors carrying rare variants. Furthermore, we show that blood donor biobank material can be utilised for personalised blood donation policies.

Introgression as an Important Driver of Geographic Genetic Differentiation within European White Oaks

The genetic composition of 5797 white oaks assigned in forest inventories as Quercus robur (3342), Quercus petraea (2090), Quercus pubescens (170), or as unspecified Quercus. spp. (195) sampled all over Europe were genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria. The sampling had a focus on Central and Eastern Europe, as well as the Black Sea and Caucasus region. Using a sparse nonnegative matrix factorization (snmf) algorithm, the nuclear genetic information was best represented by K = 4 different genetic clusters, whereas a principal component analysis visualized three different groups. The snmf run with K = 3 corresponded, for most individuals with the assignment in the forest inventories, to the three different species. The majority of the samples (88%) had an admixture coefficient q > 0.8 for one of the three species clusters, underlining the species integrity with a minor level of admixture. In contrast to Q. petraea, Q. robur and Q. pubescens showed a clear geographic genetic substructure. These large-scale within-species genetic structures were correlated to regionally variable levels of introgression between the species. For Q. petraea, introgression from Q. robur and Q. pubescens was less focused to particular regions, and this widespread inter-specific gene flow reduced the geographic genetic differentiation. The genetic variation at the maternally inherited SNPs led to 12 different haplotypes with a clear cross-species geographic pattern, further supporting the observation of significant hybridization and introgression among the species.

Genetic variation of annual and biennial caraway (Carum carvi) germplasm offers diverse opportunities for breeding

Caraway (Carum carvi) is an important aromatic plant of the Apiaceae family. Fruits and essential oil are used as spice, pharmaceutical and for various industrial purposes. Cultivation is endangered by on-going climatic changes so that new breeding projects are necessary to secure future cultivation of caraway. However, the initialization of new breeding programs is hampered by poor availability of phenotypic data. To close this gap, 64 annual and 68 biennial caraway accessions were phenotyped under field conditions in two years. We determined the beginning of flowering, the end of flowering, maturity, plant height, thousand-grain weight, stalk attachment rate, shattering rate, limonene, carvone and total essential oil content. Best linear unbiased estimates (BLUEs) and broad sense heritability were computed using linear mixed-effects models. We observed a high variability for all traits with medium to high heritability (h2 = 0.52 – 0.95). Merely for the carvone to limonene ratio, heritability was lower (0.17–0.25). Thus, the observed phenotypic diversity is applicable to breeding. Insights into correlations between traits may ease selection processes in breeding projects. The distribution of the phenotypic variation of some traits was partially associated with the genetic substructure detected by genotyping by sequencing (GBS) data. This could be explained by selections in former breeding programs.

The genetic diversity in the ancient human population of Upper Xiajiadian culture

AbstractThe West Liao River (WLR) and Yellow River (YR) basins are two major centers of millet farming in northern China. The result from flotation analyses and the spatial distribution of archeological sites indicate that two distinct survival strategies—agriculture and pastoralism were adopted in the southern and western regions of the WLR. Previous studies of ancient populations from the western area of the WLR suggested a correlation between a pastoral economy in the Bronze Age Upper Xiajiadian culture with a decreased genetic affinity with YR farmers. However, the population history of the southern WLR is unknown mainly due to the lack of ancient genetic data. Here we report the genomic data of an ancient individual from the Majiazishan site from the Late Bronze Age southern WLR region associated with Upper Xiajiadian culture. Unlike individuals from western WLR, this individual derived ancestry entirely from Late Neolithic YR farmers. We found a genetic substructure of the ancient human population of Upper Xiajiadian culture, which is consistent with the differences in the subsistence strategies of western and southern WLR. Climate deterioration led to different populations occupying the west and the south, respectively, in the WLR: the nomadic population from the Amur River (AR) in the west and the agricultural population from the YR in the south.

Spatial genetic structure and seed quality of a southernmost Abies nephrolepis population

Abies nephrolepis (Trautv. ex Maxim.) Maxim. has its southernmost populations in South Korea and they are expected to decline under climate change. To establish a strategic conservation plan, this study aimed to investigate the spatial genetic structure and seed characteristics of A. nephrolepis. We used nine microsatellite markers on 165 individuals of A. nephrolepis and sampled seeds in a southernmost population at Mt. Hambaeksan, South Korea. We observed a high level of heterozygosity, and a simulation study found that sampling 20 individuals was enough to secure sufficient genetic diversity on average. Spatial autocorrelation analysis revealed that individuals had a positive genetic relationship until 30 m. Bayesian clustering models, STRUCTURE and GENELAND, failed to achieve a consensus in the optimal number of population (K), estimating K = 1 and K = 2, respectively. Principal coordinate analysis supported the absence of genetic substructure within the study population. There was a large variance in seed production among mother trees. On average, seeds of A. nephrolepis from Mt. Hambaeksan had a purity of 70.4% and a germination percentage of 32.2%. We found that seed weight was the most effective indicator of seed quality. Mother trees at higher altitudes had poorer purity which is threatening to A. nephrolepis considering the upslope retreat of subalpine species under climate change. Our results provide insights into the interactions among spatial processes, genetic structure, and seed quality within a population of A. nephrolepis.

Genetic diversity and ancestry of the Khmuic-speaking ethnic groups in Thailand: a genome-wide perspective

The Khmuic-speaking populations are believed to be the descendants of one of the earliest groups to settle in Mainland Southeast Asia. In Thailand, there are two agricultural Khmuic-speaking ethnic groups, the Khamu and Lua (Htin). These peoples primarily reside in scattered locations along the mountainous Thailand–Laos border in Nan province. In this study, we conducted genome-wide SNP analysis on 81 individuals from three Khamu and two Lua villages in northern Thailand. Our findings revealed that both the Khamu and Lua groups possess genetic structures that are distinct from other ethnicities in Southeast Asia, indicating a unique history of migration and settlement. Within the Khmuic group, the Khamu populations living in different locations exhibited similar genetic structures and displayed genetic affinities only with some hill-tribes and Tai-Kadai (Kra-Dai)-speaking groups in Thailand, suggesting potential intermixing or cultural exchange. Furthermore, the Lua people displayed a distinctive population structure, which could be attributed to the founder effect and endogamous marriage practices. Additionally, we discovered a relationship between the Khmuic-speaking populations in Thailand and a Neolithic ancient sample obtained from the Tham Pha Ling archaeological site in Laos. This study provides new insight into genetic substructure within the Khmuic-speaking people and their potential relationship to the indigenous inhabitants of Mainland Southeast Asia.

Pleistocene-dated genomic divergence of avocado trees supports cryptic diversity in the Colombian germplasm

Genomic characterization of ex situ plant collections optimizes the utilization of genetic resources by identifying redundancies among accessions, capturing cryptic variation, establishing reference collections, and ultimately assisting pre-breeding and breeding efforts. Yet, the integration of evolutionary genomic analyses is often lacking when studying the biodiversity of crop gene pools. Such is the case in the avocado, Persea americana Mill., an iconic American fruit tree crop that has seen an unprecedented expansion worldwide because of its nutritional properties. However, given a very restricted number of commercial clones, avocado plantations are becoming more vulnerable to diseases and climate change. Therefore, exploring new sources of evolutionary novelty and genetic diversity beyond the commercial varieties derived from traditional genetic pools in Mexico and Central America is imperative. To fill this gap, we aimed to characterize the genomic diversity of Colombian avocado trees. Specifically, we constructed reduced representation genomic libraries to genotype by sequencing 144 accessions from the Colombian National genebank and 240 materials from local commercial orchards in the Colombian northwest Andes. We merged the resulting reads with available sequences of reference genotypes from known avocado groups (also named as races), Mexican, Guatemalan, and West Indian, to discover 4931 SNPs. We then analyzed the population structure and phylogenetic diversity, and reconstructed evolutionary scenarios, possibly leading to new genetic groups in Colombian germplasm. We detected demographic stratification despite evidence of intergroup gene flow. Besides the classical three avocado groups, we found an exclusive Colombian group with a possible genetic substructure related to the geographical origin (Andean and Caribbean). Phylogenetic and ABC demographic modeling suggested that the Colombian group evolved in the Pleistocene before human agriculture started, and its closest relative from the three recognized races would be the West Indian group. We conclude that northwest South America offers a cryptic source of allelic novelty capable of boosting avocado pre-breeding strategies to select rootstock candidates well adapted to specific eco-geographical regions in Colombia and abroad.