Analysis Of Genetic Differentiation Research Articles

Genetic diversity and population genetics of Schistosoma haematobium isolated from children in Lusaka and Siavonga districts, Zambia.

Urogenital schistosomiasis remains a pervasive health challenge in rural Zambian communities. This study explores the molecular epidemiology and genetic diversity of Schistosoma haematobium using mitochondrial genes (cox1 and nadh1). Urine samples from 421 children in Siavonga and Lusaka districts, Zambia, were collected between December 2020 and February 2022. Microscopy and DNA extraction facilitated the identification of S. haematobium, followed by amplification, sequencing, and phylogenetic analysis of cox1 and nadh1 genes. Phylogenetic analysis revealed clustering with samples from mainland African countries, emphasizing shared haplotypes. Both mitochondrial genes exhibited substantial diversity, with 5 haplotypes from 37 cox1 sequences and 12 haplotypes from 23 nadh1 sequences. High haplotype diversity (0.621-0.808) and low nucleotide diversity (0.00181-0.03288) were observed. Siavonga and Lusaka districts shared the majority of S. haematobium haplotypes. Molecular variance and genetic differentiation analysis indicated variations within populations rather than between populations (cox1: -0.025, nadh1: 0.01646). These findings suggest a limited differentiation between S. haematobium populations in Siavonga and Lusaka, potentially indicating gene flow. Tajima's test revealed negative values, indicating a departure from neutrality, introduction of rare alleles, and recent population expansion. This study contributes essential insights into S. haematobium population genetics, crucial for effective urogenital schistosomiasis control in Zambia.

Microsatellite analysis of genetic diversity and population differentiation of Acanthopagrus schlegelii in China

The study utilized 9 self-selected polymorphic microsatellite loci to amplify and investigate the genetic diversity and differentiation of Acanthopagrus schlegelii populations in 10 wild populations along the Chinese coast. The values of Polymorphic Information Content (PIC) ranged from 0.4433 to 0.5804, with an average value of 0.5143. The average number of alleles per locus (A) ranged from 3.0000 to 3.4444, with a mean value of 3.2333 and an overall value of 3.6667. The average number of effective alleles per locus (Ae) ranged from 2.0130 to 2.6014, with a mean value of 2.2994 and an overall value of 2.8013. The observed heterozygosity (Ho) ranged from 0.4607 to 0.5789, with an average value of 0.5278 and an overall value of 0.5261. The expected heterozygosity (He) ranged from 0.4657 to 0.5967, with an average value of 0.5183 and an overall value of 0.6224. The results of genetic differentiation showed the genetic differentiation coefficient (Fst) was 0.1806, and the gene flow (Nm) was 1.1342. The UPGMA cluster analysis indicated significant genetic differentiation among A. schlegelii populations along the Chinese coast, with the populations being divided into two groups, namely the northern and southern populations. The genetic differentiation structure of the southern population was inconsistent with its geographical distribution. This study utilized microsatellite molecular markers to investigate the genetic diversity and genetic differentiation of 10 wild A. schlegelii populations along the coast of China. The research results indicate that the genetic diversity of the 10 wild A. schlegelii populations is at a moderate level, with evidence of north-south differentiation. This provides a scientific basis for the conservation, germplasm improvement, and aquaculture of A. schlegelii resources in China. It also offers background information for recent stock enhancement and release projects and their impact on the genetic resources of A. schlegelii.

Genomic and Transcriptome Analysis Reveals the Biosynthesis Network of Cordycepin in Cordyceps militaris.

Cordycepin is the primary active compound of Cordyceps militaris. However, the definitive genetic mechanism governing cordycepin synthesis in fruiting body growth and development remains elusive, necessitating further investigation. This study consists of 64 C. militaris strains collected from northeast China. The high-yielding cordycepin strain CMS19 was selected for the analysis of cordycepin production and the genetic basis of cordycepin anabolism. First, the whole-genome sequencing of CMS19 yielded a final size of 30.96 Mb with 8 contigs and 9781 protein-coding genes. The genome component revealed the presence of four additional secondary metabolite gene clusters compared with other published genomes, suggesting the potential for the production of new natural products. The analyses of evolutionary and genetic differentiation revealed a close relationship between C. militaris and Beauveria bassiana. The population of strains distributed in northeast China exhibited the significant genetic variation. Finally, functional genes associated with cordycepin synthesis were identified using a combination of genomic and transcriptomic analyses. A large number of functional genes associated with energy and purine metabolism were significantly enriched, facilitating the reconstruction of a hypothetical cordycepin metabolic pathway. Therefore, our speculation of the cordycepin metabolism pathway involved 24 genes initiating from the glycolysis and pentose phosphate pathways, progressing through purine metabolism, and culminating in the core region of cordycepin synthesis. These findings could offer fundamental support for scientific utilizations of C. militaris germplasm resources and standardized cultivation for cordycepin production.

Differences in Albizia odoratissima genetic diversity between Hainan Island and mainland populations in China.

This study aimed at exploring unique population genetic characteristics of Albizia odoratissima (Linn. f) Benth on Hainan Island to provide a scientific basis for its rational utilization and protection. It analyzed the genetic diversity and structure of 280 individuals from 10 subpopulations of A. odoratissima from Hainan Island and Baise City using 16 expression sequence markers - simple sequence repeat markers. The genetic diversity of Hainan population (I = 0.7290, He = 0.4483) was lower than that of the Baise population (I = 0.8722, He = 0.5121). Compared with the Baise population (Nm = 2.0709, FST = 0.1077), the Hainan Island population (Nm = 1.7519, FST = 0.1249) exhibited lower gene flow and higher degree of genetic differentiation. Molecular variance and genetic differentiation analyses showed that the main variation originated from individuals within the subpopulation. There were significant differences in the genetic structure between Hainan and Baise populations. It grouped according to geographical distance, consistent with the Mantel test results (R2 = 0.77, p = 0.001). In conclusion, the genetic diversity of the island A. odoratissima population was lower than that distributed on land, the two populations exhibited obvious genetic structure differences. Both the degrees of inbreeding and genetic differentiation were higher in the island population than in the land population.

Joint application of A-InDels and miniSTRs for forensic personal, full and half sibling identifications, and genetic differentiation analyses in two populations from China

BackgroundPreviously, a novel multiplex system of 64 loci was constructed based on capillary electrophoresis platform, including 59 autosomal insertion/deletions (A-InDels), two Y-chromosome InDels, two mini short tandem repeats (miniSTRs), and an Amelogenin gene. The aim of this study is to evaluate the efficiencies of this multiplex system for individual identification, paternity testing and biogeographic ancestry inference in Chinese Hezhou Han (CHH) and Hubei Tujia (CTH) groups, providing valuable insights for forensic anthropology and population genetics research.ResultsThe cumulative values of power of discrimination (CDP) and probability of exclusion (CPE) for the 59 A-InDels and two miniSTRs were 0.99999999999999999999999999754, 0.99999905; and 0.99999999999999999999999999998, 0.99999898 in CTH and CHH groups, respectively. When the likelihood ratio thresholds were set to 1 or 10, more than 95% of the full sibling pairs could be identified from unrelated individual pairs, and the false positive rates were less than 1.2% in both CTH and CHH groups. Biogeographic ancestry inference models based on 35 populations were constructed with three algorithms: random forest, adaptive boosting and extreme gradient boosting, and then 10-fold cross-validation analyses were applied to test these three models with the average accuracies of 86.59%, 84.22% and 87.80%, respectively. In addition, we also investigated the genetic relationships between the two studied groups with 33 reference populations using population statistical methods of FST, DA, phylogenetic tree, PCA, STRUCTURE and TreeMix analyses. The present results showed that compared to other continental populations, the CTH and CHH groups had closer genetic affinities to East Asian populations.ConclusionsThis novel multiplex system has high CDP and CPE in CTH and CHH groups, which can be used as a powerful tool for individual identification and paternity testing. According to various genetic analysis methods, the genetic structures of CTH and CHH groups are relatively similar to the reference East Asian populations.

Характеристика микрогаплотипа гена FADS2 у коренного населения Сибири

Our study of the FADS2 gene polymorphism in the indigenous populations of Siberia resulted in finding a microhaplotype of 150 nucleotides in length, represented by various combinations of polymorphism variants in four loci (rs174609, rs174610, rs174611, rs74771917). By these loci, 5 microhaplotype variants were identifie d in the studied populations of the northeastern (Chukchi, Koryak, Even) and southeastern (Buryat) parts of Siberia, the effective numbe r of which (Ae) varies from 2.16 in Buryats to 3.89 in Koryaks. Heterozygosity values in the populations vary from 0.624 in Buryats to 0.805 in Evens. The analysis of genetic differentiation showed highly authentic differences between the northern and southern populations of Siberia's eastern part in the distribution of the FADS2 gene microhaplotype variants. Thus, this microhaplotype has a sufficiently high informativity for detecting genetic differences between Siberian indigenous populations and can, therefore, be used in panels of markers designed for genetic identification at the population and individual level.

Genetic diversity and differentiation analysis reveals geographical structure characteristics of Dermatophagoides farinae (Acari: Pyroglyphidae).

Dermatophagoides farinae (Acari: Pyroglyphidae) has been reported as one of the major sources of indoor allergens that trigger allergic disease in humans. In this study, the genetic diversity and differentiation of nine geographic populations of D. farinae were investigated by analyzing mitochondrial and nuclear genes (COI, Cytb, COI+Cytb, and ITS). The results showed high genetic diversity across the D. farinae populations. The BX (Benxi) population showed the lowest genetic diversity, possibly due to climatic causes. Significant genetic differentiation was observed among D. farinae populations based on mitochondrial genes. The analysis of molecular variance (AMOVA) results elucidated that the contribution to the rate of variation was primarily from among populations. Phylogenetic analysis and haplotype network based on mitochondrial genes both indicated significant geographic structure among D. farinae populations. The nine geographic populations of D. farinae were divided into two groups with the Qinling Mountains-Huai River Line serving as the boundary for spatial analysis of molecular variance analysis (SAMOVA). However, the Mantel test analysis showed no association between genetic differentiation and geographic distance because of the high level of gene flow among some populations through the transportation of stored food. Overall, these results indicate both significant genetic differentiation among D. farinae populations, but also significant gene exchange between them. Results from the analysis of the nuclear gene ITS differed from the mitochondrial genes due to differences in molecular markers between mitochondrial genes and nuclear genes. These observations improve our understanding of the genetic diversity and structure of D. farinae populations.

Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain.

The genetic variation and population structure of gene N (nucleocapsid) and part of gene L (replicase) from 13 eggplant mottle dwarf virus (EMDV) isolates from Spain were evaluated and compared with sequences of EMDV isolates from other countries retrieved from GenBank. Phylogenetic inference of part of gene L showed three main clades, one containing an EMDV isolate from Australia and the other two containing isolates from Iran and Europe, as well as four subclades. EMDV isolates from Spain were genetically very similar and grouped in a subclade together with one isolate from Germany and one from the UK. No new recombination events were detected in addition to one recombination previously reported, suggesting that recombination is rare for EMDV. The comparison of synonymous and non-synonymous rates showed that negative selection played an important role, and only two codons were under positive selection. Genetic differentiation (Fst test), phylogenetic and nucleotide diversity analyses suggest a unique introduction of EMDV to Spain and low gene flow with other countries. In contrast, Greece and Italy showed diverse populations with high gene flow between both.

Genetic diversity and population structure of the Asian citrus psyllid in China.

The Asian citrus psyllid (ACP) is the main vector of Citrus Huanglongbing, the most damaging citrus disease, causing significant financial losses in the citrus industry. Global warming has expanded the habitat of this pest, allowing it to continue its northward migration to China. Population genetic information of ACP is fundamentally essential for species management. This study investigated the genetic diversity and population structure of Chinese ACP using the mitochondrial cytochrome oxidase subunit I gene by dataset comprised 721 sequences from 27 geographic sites in China. Low haplotype diversity (0.323 ± 0.022) and low nucleotide diversity (0.00071 ± 0.00007) were observed in the entire population, which may indicate recent founder events. Twenty-three haplotypes were identified and clustered into 2 haplogroups: haplogroup I and haplogroup II. Haplogroup II included only 2 unique haplotypes, which occurred exclusively in the Southwest China ACP population. Genetic differentiation analyses were also indicative of Southwest China population was significantly differentiated from the remaining populations. Demographic history analysis showed that ACP population in China has experienced demographic expansion. Our results provided a better understanding of the genetic distribution patterns and structures of ACP populations in China.

Genetic polymorphism and natural selection of the erythrocyte binding antigen 175 region II in Plasmodium falciparum populations from Myanmar and Vietnam

Plasmodium falciparum erythrocyte binding antigen 175 (PfEBA-175) plays essential role in erythrocyte invasion by the parasite and is a leading vaccine candidate. However, its genetic diversity in global isolates is a concern in developing an universal vaccine incorporating this protein. This study aimed to investigate genetic polymorphisms and natural selection of pfeba-175 region II (RII) in Myanmar and Vietnam P. falciparum isolates. Vietnam pfeba-175 RII displayed a low genetic polymorphism, while Myanmar pfeba-175 RII showed high levels of genetic diversity across the region. Point mutations, deletion, and recombinations were main factors contributing to genetic diversities in P. falciparum populations. Global pfeba-175 RII revealed similar, but not identical, genetic polymorphisms and natural selection profiles. Despite profiles of amino acid substitutions differed among populations, five major amino acid changes (K279E, E403K, K481I, Q584K, and R664) were commonly detected in global pfeba-175 RII populations. Haplotype network and genetic differentiation analyses of global pfeba-175 RII populations demonstrated no geographical relationships. Non-neglectable level of genetic diversity was observed in global pfeba-175 RII populations, emphasizing the need to consider this when designing an effective vaccine based on this protein. This study underscores the importance of the continuous monitoring of genetic diversity of pfeba-175 RII in the global P. falciparum populations.

Genetic analysis of phenotypic plasticity identifies BBX6 as the candidate gene for maize adaptation to temperate regions.

Climate changes pose a significant threat to crop adaptation and production. Dissecting the genetic basis of phenotypic plasticity and uncovering the responsiveness of regulatory genes to environmental factors can significantly contribute to the improvement of climate- resilience in crops. We established a BC1F3:4 population using the elite inbred lines Zheng58 and PH4CV and evaluated plant height (PH) across four environments characterized by substantial variations in environmental factors. Then, we quantified the correlation between the environmental mean of PH (the mean performance in each environment) and the environmental parameters within a specific growth window. Furthermore, we performed GWAS analysis of phenotypic plasticity, and identified QTLs and candidate gene that respond to key environment index. After that, we constructed the coexpression network involving the candidate gene, and performed selective sweep analysis of the candidate gene. We found that the environmental parameters demonstrated substantial variation across the environments, and genotype by environment interaction contributed to the variations of PH. Then, we identified PTT(35-48) (PTT is the abbreviation for photothermal units), the mean PTT from 35 to 48 days after planting, as the pivotal environmental index that closely correlated with environmental mean of PH. Leveraging the slopes of the response of PH to both the environmental mean and PTT(35-48), we successfully pinpointed QTLs for phenotypic plasticity on chromosomes 1 and 2. Notably, the PH4CV genotypes at these two QTLs exhibited positive contributions to phenotypic plasticity. Furthermore, our analysis demonstrated a direct correlation between the additive effects of each QTL and PTT(35-48). By analyzing transcriptome data of the parental lines in two environments, we found that the 1009 genes responding to PTT(35-48) were enriched in the biological processes related to environmental sensitivity. BBX6 was the prime candidate gene among the 13 genes in the two QTL regions. The coexpression network of BBX6 contained other genes related to flowering time and photoperiod sensitivity. Our investigation, including selective sweep analysis and genetic differentiation analysis, suggested that BBX6 underwent selection during maize domestication. Th is research substantially advances our understanding of critical environmental factors influencing maize adaptation while simultaneously provides an invaluable gene resource for the development of climate-resilient maize hybrid varieties.

Genetic diversity and phylogenetic relationship estimation of Shanxi indigenous goat breeds using microsatellite markers

The objective of this study was to assess the genetic diversity, phylogenetic relationship and population structure of five goat breeds in Shanxi, China. High genetic diversities were found in the five populations, among which, Licheng big green goat (LCBG) has the highest genetic diversity, while Jinlan cashmere goat (JLCG) population has the lowest genetic diversity. Bottleneck analysis showed the absence of recent genetic bottlenecks in the five goat populations. Genetic differentiation analysis shows that the closest genetic relationship between LCBG and LLBG (Lvliang black goat) was found, and the genetic distance between JLCG and the other four populations is the largest. The population structure of JLCG is different from the other four populations with K = 2, while LCBG and LLBG have high similarity population structure as the K value changes. Knowledge about genetic diversity and population structure of indigenous goats is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of goat breeds.

Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India.

Crop wild relatives (CWRs) are vital sources of variation for genetic improvement, but their populations are few in genebanks, eroded in natural habitats and inadequately characterized. With a view to explore genetic diversity in CWRs of AA genome rice (Oryza sativa L.) species in India, we analyzed 96 accessions of 10 Oryza species by using 17 quantitative traits and 45 microsatellite markers. The morpho-quantitative traits revealed a high extent of phenotypic variation in the germplasm. Diversity index (H') revealed a high level of within-species variability in O. nivara (H' = 1.09) and O. rufipogon (H' = 1.12). Principal component (PC) analysis explained 79.22% variance with five PCs. Among the traits related to phenology, morphology, and yield, days to heading showed strong positive association with days to 50% flowering (r = 0.99). However, filled grains per panicle revealed positive association with spikelet fertility (0.71) but negative with awn length (- 0.58) and panicle bearing tillers (- 0.39). Cluster analysis grouped all the accessions into three major clusters. Microsatellite analysis revealed 676 alleles with 15.02 alleles per locus. High polymorphism information content (PIC = 0.83) and Shannon's information index (I = 2.31) indicated a high level of genetic variation in the CWRs. Structure analysis revealed four subpopulations; first and second subpopulations comprised only of O. nivara accessions, while the third subpopulation included both O. nivara and O. rufipogon accessions. Population statistics revealed a moderate level of genetic differentiation (FST = 0.14), high gene diversity (HE = 0.87), and high gene flow (Nm = 1.53) among the subpopulations. We found a high level of molecular variance among the genotypes (70%) and low among populations (11%) and within genotypes (19%). The high level of molecular and morphological variability detected in the germplasm of CWRs could be utilized for the improvement of cultivated rice.

Microsatellite-based analysis deciphers the uniqueness of three lesser-known Indian cattle populations

Indian cattle genetic resources constitute an important global gene pool. A majority of these (59.3%) are still not characterized. Identifying unique populations can ensure their inclusion in national policies of improvement and conservation. The present research describes the uniqueness of three lesser-known cattle populations (Jhari, Kamma, and Vandharvi) of Deccan Plateau region of India. These are known for draught power but are on the decline due to changing socio-agricultural scenario. Comprehensive genetic diversity and differentiation analyses using 25 FAOrecommended microsatellite markers identified high variability in all three populations with mean allelic diversity (Na) ranging between 9.32-9.80. Similarly, high genetic variability was recorded in all three populations (Ho=0.67 to 0.71). Random mating in the populations was indicated by the small positive F value. A low but significant genetic differentiation, pairwise Nei’s genetic distance, phylogenetic relationship, and genetic assignment substantiated theirseparate genetic identity. The phylogenetic analysis reflected the closeness of Vandharvi and Kamma populations. Substantial gene flow was evidenced by the effective number of migrants per generation (Nm=16.31±2.69 >1). Bayesian-based clustering indicated the germplasm exchange between Vandharvi and Kamma, whereas, Jhari comes out to be a separate gene pool. None of these have suffered demographic bottlenecks in the recent past. Findings arevaluable for the scientific management, recognition, and conservation of the three populations that contribute to the livelihood, and economic sustainability of agro-pastoral communities.

Molecular insight into genetic differentiation, population structure and banding pattern analysis of Bambara groundnut (Vigna subterranea [L.] Verdc.) linked with inter simple sequence repeats (ISSR).

A set of 44 selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions was sampled from 11 distinct populations of four geographical zones to assess the genetic drift, population structure, phylogenetic relationship, and genetic differentiation linked with ISSR primers. The amplification of genomic DNA with 32 ISSR markers detected an average of 97.64% polymorphism while 35.15% and 51.08% polymorphism per population and geographical zone, respectively. Analysis of molecular variance revealed significant variation within population 75% and between population 25% whereas within region 84% and between region 16%. The Bidillali exposed greater number of locally common band i.e., NLCB (≤ 25%) = 25 and NLCB (≤ 50%) = 115 were shown by Cancaraki while the lowest was recorded as NLCB (≤ 25%) = 6 and NLCB (≤ 50%) = 72 for Roko and Maibergo, accordingly. The highest PhiPT value was noted between Roko and Katawa (0.405*) whereas Nei's genetic distance was maximum between Roko and Karu (0.124). Based on Nei's genetic distance, a radial phylogenetic tree was constructed that assembled the entire accessions into 3 major clusters for further confirmation unrooted NJ vs NNet split tree analysis based on uncorrected P distance exposed the similar result. Principal coordinate analysis showed variation as PC1 (15.04%) > PC2 (5.81%). The current study leads to prompting the genetic improvement and future breeding program by maximum utilization and better conservation of existing accessions. The accessions under Cancaraki and Jatau are population documented for future breeding program due to their higher genetic divergence and homozygosity.

Analysis of genetic mutation in dilated cardiomyopathy

BackgroundCardiomyopathies (CM) are heterogeneous group of genetic disorders, specifically damage the heart muscles that leads to the progression of many clinical symptoms such as congestive heart failure (CHF). Dilated Cardiomyopathy (DCM) is the most common cause of heart failure. This study focuses on genetic variations in DCM, which is chronic, generally nonreversible heart muscles disease characterized by heart chamber dilation mostly left ventricle and decreased systolic efficiency. MethodologyThis study includes two parts, First we identified 100 genes associated with DCM using deep literature survey. Genetic variants were extracted from 1000 Genome Project (1000 GP), ExAC and Simon Genome Diversity project, for the identification of deleterious variants using in silico prediction tools followed by population genetic differentiation. In Second part, we examined 21,469 patients related to cardiac diseases. Of these, 100 DCM patients were recruited for the identification of rare pathogenic variants rs143187236 in MYOM3 and an INDEL rs36212066 in MYBPC3 using ARMS-PCR and validation through Sanger sequencing. ResultsWe identified 1658, 15,058 and 461 deleterious variants in 1000 GP, ExAC and Simon Genomes project respectively predicted by both SIFT and PolyPhen2 prediction tools. Clinvar database revealed 10, 69 and one pathogenic and likely pathogenic variants associated with DCM in 1000 GP, ExAC and Simon genome. Population genetic differentiation analysis revealed South Asian populations are closely related to European and American while highly differentiated to East Asian and African populations. ARMS-PCR and Sanger sequencing data of enlisted DCM patients showed that rs143187236 in MYOM3 was found in heterozygous state in three patients while rs36212066 in MYBPC3 was not detected in studied patients. ConclusionBased on bioinformatics analysis and investigation of deleterious variants through Sanger sequencing, it is deduced that large sample size is necessary for further detection of variants that will aid in the early diagnosis of DCM.

THE RESULTS OF WORK PROJECT TCP/RER/3604 “CONSERVATION AND DEVELOPMENT OF DUAL-PURPOSE CATTLE BREEDS IN EASTERN EUROPE”

THE RESULTS OF WORK PROJECT TCP/RER/3604 “CONSERVATION AND DEVELOPMENT OF DUAL-PURPOSE CATTLE BREEDS IN EASTERN EUROPE”

Parallel anagenetic patterns in endemic Artemisia species from three Macaronesian archipelagos.

Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely related species of Artemisia (i.e. A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e. Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns-showing comparable genetic structuring among groups of islands-were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.

Population genetics of Nelumbo lutea (American lotus) near its northwestern range limit

Nelumbo lutea Wild. (American lotus) has a broad and changing geographical distribution that is influenced by human transplanting and changes to climate, hydrology, and habitat. Populations vary from extensive stands where the species appears to be an effective colonizer, to sites where the species has declined or appears to have been extirpated. Previous studies in apparently stable populations from central and southern United States revealed low genetic diversity within and between populations. In this study, we assess genetic diversity at the northern edge of N. lutea’s range where it is often imperiled. A total of 489 individuals in 25 populations collected in Upper Mississippi River regions in Minnesota and Wisconsin were amplified in 12 microsatellite loci. Ten microsatellite loci indicated significant deviation from Hardy-Weinberg principal and were utilized for further analysis. Generally, genetic diversity was low compared to the genetic studies from southern North America. Despite low levels of genetic differentiation (Fst range; 0.003–0.059), structure and UPGMA analysis indicated the possibility of two distinct clusters and slight admixture in some populations. Initial low genetic diversity in populations was likely caused by founder effect if few individuals were established at each site. Limited migration and clonal growth contribute to the continued low diversity. We provide recommendations and research suggestions for the conservation of this species.

Genetic Diversity of Durum Wheat (Triticum turgidum L. ssp. durum, Desf) Germplasm as Revealed by Morphological and SSR Markers.

Ethiopia is considered a center of origin and diversity for durum wheat and is endowed with many diverse landraces. This research aimed to estimate the extent and pattern of genetic diversity in Ethiopian durum wheat germplasm. Thus, 104 durum wheat genotypes representing thirteen populations, three regions, and four altitudinal classes were investigated for their genetic diversity, using 10 grain quality- and grain yield-related phenotypic traits and 14 simple sequence repeat (SSR) makers. The analysis of the phenotypic traits revealed a high mean Shannon diversity index (H' = 0.78) among the genotypes and indicated a high level of phenotypic variation. The principal component analysis (PCA) classified the genotypes into three groups. The SSR markers showed a high mean value of polymorphic information content (PIC = 0.50) and gene diversity (h = 0.56), and a moderate number of alleles per locus (Na = 4). Analysis of molecular variance (AMOVA) revealed a high level of variation within populations, regions, and altitudinal classes, accounting for 88%, 97%, and 97% of the total variation, respectively. Pairwise genetic differentiation and Nei's genetic distance analyses identified that the cultivars are distinct from the landrace populations. The distance-based (Discriminant Analysis of Principal Component (DAPC) and Minimum Spanning Network (MSN)) and model-based population stratification (STRUCTURE) methods of clustering grouped the genotypes into two clusters. Both the phenotypic data-based PCA and the molecular data-based DAPC and MSN analyses defined distinct groupings of cultivars and landraces. The phenotypic and molecular diversity analyses highlighted the high genetic variation in the Ethiopian durum wheat gene pool. The investigated SSRs showed significant associations with one or more target phenotypic traits. The markers identify landraces with high grain yield and quality traits. This study highlights the usefulness of Ethiopian landraces for cultivar development, contributing to food security in the region and beyond.