Nucleotide Diversity Indices Research Articles

Genetic Diversity and Relationship of Native Phalaenopsis Orchids: A Case Study of Indonesian Archipelago

The native Phalaenopsis is valuable germplasm for future orchid breeding programs and for its conservation because it provides many beneficial traits or genes. This study aimed to determine and analyze the molecular diversity and phylogeny of Indonesian native Phalaenopsis by a DNA barcoding (matK) marker. A total of 19 samples of Phalaenopsis orchids were used in this study. All leaf samples of orchid were extracted and purified using a commercial DNA isolation kit from Geneaid Biotech Ltd., Taiwan (GP100). The DNAs were then amplified by specific matK primers: Forward (5’-CGTACAGTACTTTTGTGTTTACGAG-3’) and Reverse (5’-ACCCAGTCCATCTGGAAATCTTGGTTC-3’). The DNA targets or products (matK) were purified and sequenced by the Sanger-bidirectional method at 1st Base Ltd., Malaysia. Before further analysis, the matK sequences of Phalaenopsis were edited, reconstructed, and aligned with the assistance of Clustal W in the MEGA 11 software. Its genetic diversity was determined using the nucleotide diversity index (π%), and the phylogenetic analysis was performed using the maximum likelihood (ML) method with a statistical bootstrap. The phylogenetic relationship was also assessed using principal component analysis (PCA). Based on this marker, the native Phalaenopsis has a high genetic diversity (π% = 1.70). In addition, the phylogenetic analysis revealed that this germplasm was separated into seven clades, where P. pantherina has the closest relation to P. cornu-cervi and P. gigantea. Conversely, the highest genetic distance was to P. amabilis from South Kalimantan and to P. celebensis from Sulawesi, at a coefficient divergence of 0.084. Our findings provide an essential foundation for supporting future orchid breeding practices, including conservation, on local and global scales.

Extensive transcriptome data providing great efficacy in genetic research and adaptive gene discovery: a case study of Elymus sibiricus L. (Poaceae, Triticeae).

Genetic markers play a central role in understanding genetic diversity, speciation, evolutionary processes, and how species respond to environmental stresses. However, conventional molecular markers are less effective when studying polyploid species with large genomes. In this study, we compared gene expression levels in 101 accessions of Elymus sibiricus, a widely distributed allotetraploid forage species across the Eurasian continent. A total of 20,273 high quality transcriptomic SNPs were identified. In addition, 72,344 evolutionary information loci of these accessions of E. sibiricus were identified using genome skimming data in conjunction with the assembled composite genome. The population structure results suggest that transcriptome SNPs were more effective than SNPs derived from genome skimming data in revealing the population structure of E. sibiricus from different locations, and also outperformed gene expression levels. Compared with transcriptome SNPs, the investigation of population-specifically-expressed genes (PSEGs) using expression levels revealed a larger number of locally adapted genes mainly involved in the ion response process in the Sichuan, Inner Mongolia, and Xizang geographical groups. Furthermore, we performed the weighted gene co-expression network analysis (WGCNA) and successfully identified potential regulators of PSEGs. Therefore, for species lacking genomic information, the use of transcriptome SNPs is an efficient approach to perform population structure analysis. In addition, analyzing genes under selection through nucleotide diversity and genetic differentiation index analysis based on transcriptome SNPs, and exploring PSEG through expression levels is an effective method for analyzing locally adaptive genes.

Haplotype Diversity in mtDNA of Honeybee in the Czech Republic Confirms Complete Replacement of Autochthonous Population with the C Lineage.

The study aimed to analyze the genetic diversity in the Czech population of Apis mellifera using mitochondrial DNA markers, tRNAleu-cox2 intergenic region and cox1 gene. A total of 308 samples of bees were collected from the entire Czech Republic (from colonies and flowers in 13 different regions). Following sequencing, several polymorphisms and haplotypes were identified. Analysis of tRNAleu-cox2 sequences revealed three DraI haplotypes (C, A1, and A4). The tRNAleu-cox2 region yielded 10 C lineage haplotypes, one of which is a newly described variant. Three A lineage haplotypes were identified, two of which were novel. A similar analysis of cox1 sequences yielded 16 distinct haplotypes (7 new) within the population. The most prevalent tRNAleu-cox2 haplotype identified was C1a, followed by C2a, C2c, C2l, and C2d. For the cox1 locus, the most frequent haplotypes were HpB02, HpB01, HpB03, and HpB04. The haplotype and nucleotide diversity indices were high in both loci, in tRNAleu-cox2 with values of 0.682 and 0.00172, respectively, and in cox1 0.789 and 0.00203, respectively. The Tajima's D values were negative and lower in tRNAleu-cox2 than in cox1. The most frequent haplotypes were uniformly distributed across all regions of the Czech Republic. No haplotype of the indigenous M lineage was identified. High diversity and the occurrence of rare haplotypes indicate population expansion and continuous import of tribal material of the C lineage.

Assessment of Durian Diversity and Its Wild Relatives (Durio spp.) Based on Leaf Morphology and Molecular Marker

Durian (Durio spp.) is native to Southeast Asia and has potential for development. However, some species are threatened due to deforestation and extensive land conversion. This study aimed to determine the genetic diversity and relationships of durian and wild relatives (Durio spp.) on the Indonesia Island Borneo using a leaf morphology and DNA barcoding (matK) marker. In this study, 15 durian samples from this region were used, excluding ‘Monthong’ (Durio zibethinus) and ‘Bengang’ (Neesia strigosa) as the outgroups from the GenBank database. The leaf morphology was analyzed descriptively, whereas the genetic diversity was by the nucleotide diversity index (π%). The relationship of durians was revealed by the maximum likelihood (ML) method and examined with the bootstrap statistics for 1000 replicates, also confirmed by the PCA (principal component analysis). Based on the leaf morphology, the durians are divided into five forms, i.e., obovate-lanceolate, elliptic, ovate, oblong, and linear-oblong. ‘Pampaken’ and ‘Pampaken Burung Kecil’ indicated the earliest form (obovate-lanceolate), whereas the linear-oblong was by ‘Kamundai.’ Following the molecular marker, it was seen that the durians have low genetic diversity (π%) with only 0.015. However, phylogenetically, the durians were separated into four similar clades or groups for ML and PCA. In this instance, it has appeared that most of the durians evaluated in the current study have close relationships, except for the taxa with the farthest relationship. The results provide valuable information for the local and global durian conservation mission, including future breeding programs.

Diversity and abundance of archaeal amoA genes in the permanent and temporary oxygen minimum zones of Indian Ocean

Oxygen minimum zones are results of oxygen consumption exceeding the oxygen availability in stratified water columns of the marine environment. We compared the ammonia monooxygenase subunit A (amoA) gene abundance and the diversity of ammonia-oxidising archaea (AOA) in the Arabian Sea (AS) with those of the Bay of Bengal (BoB). Three primer pairs targeting amoA genes of water column A (WCA), water column B (WCB) and total AOA (amoAt) captured different densities of gene copy numbers in both marginal seas. Water column A (WCA) ecotypes were more abundant in the AS than in the BoB. Core-OMZ depths of the BoB contained 10 times lower amoA copy numbers than those of the AS. Along with sampling depth, concentration of ammonia shapes the WCA/WCB ecotypes in AS/BoB. Among the total AOA populations, WCB ecotypes were more abundant. The amoA gene sequences were either of Nitrosopumilales or Ca. Nitrosotaleales members and belonged to NP-γ, NP-δ, NS-β, NS-γ and NS-ε sub-clades. Pairwise distance and nucleotide diversity index analysis reveals that BoB nurtures two times more diverse amoA sequences than the AS. The core OMZ region of the BoB contains a two-fold higher diversity of amoA gene sequences compared to the AS, whereas the AS contains 13 times more abundant amoA copies than the BoB.

Genetic characteristics of Blastocystis sp. in cattle from Hebei Province, China

Blastocystis sp. is a protozoan parasite that infects the intestines of humans and animals, causing chronic diseases such as skin rashes, abdominal pain, and irritable bowel syndrome. A survey was conducted to determine the prevalence and genetic diversity of Blastocystis sp. infection in cattle, in Hebei Province, China. 2746 cattle fecal samples were collected from 11 cities in Hebei Province and analyzed using polymerase chain reaction targeting the Blastocystis sp. barcoding gene. MEGA, PhyloSuite, and PopART were used to analyze the subtype, sequence signature, pairwise genetic distance, and genetic diversity indices. The results showed that the Blastocystis sp. detection rate was 12.60% (346/2746). The infection rate in different herds was affected by region, age, breeding mode, and variety; that is, the infection rates in areas of southern Hebei, cattle under one year old, intensive raising, and dairy cattle were higher than the infection rates in northern Hebei, cattle over one year old, scatter feeding, and beef cattle. Seven Blastocystis subtypes were identified, namely, ST1, ST2, ST5, ST10, ST14, ST21, and ST26; ST10 was the dominant subtype, and ST14 was the second most common subtype. A total of 374 polymorphic and conserved sites were obtained, including 273 invariable (monomorphic) sites and 101 variable (polymorphic) sites, accounting for 27.01% of all nucleotides. The nucleotide diversity index (Pi) was 0.07749, and the haplotype (gene) diversity index (Hd) was 0.946. This study provides the first comprehensive information on the epidemiological situation of Blastocystis sp. infection in cattle from Hebei Province, China, and revealed rich genetic diversity of Blastocystis sp.

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( Plectropomus leopardus).

The leopard coral grouper ( Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ) and fixation index ( F ST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.

Genetic Variation among Three Species of Genus <i>Erythroculter</i>

The genus Erythroculter (Cypriniformes, Cyprinidae, Abramidinae) is one of the most commercially important freshwater fish species inhabiting China. However, very limited information is available regarding genetic variation among Erythroculter species, therefore hindering their effective management. In this regard, microsatellite markers and sequences of mitochondrial COII and D-loop were analyzed to investigate the genetic variation among three species of genus Erythroculter. Results demonstrated that 11 microsatellite loci were amplified effectually, and the size of allele was 110–350, 94–338 and 86–384 bps in E. ilishaeformis, E. dabryi and E. mongolicus respectively. Average number of allele was 5.82, 5.73 and 6.45 per locus for E. ilishaeformis, E. dabryi and E. mongolicus respectively. Fragments of COII and D-loop was 675 and 929 bps respectively. On the basis of Shannon’s information index, heterozygosity, polymorphic information content and nucleotide diversity index (P), the microsatellite and nucleotide diversity of E. ilishaeformis was most abundant, and that of E. mongolicus was least abundant. Based on the haplotype distribution of D-loop or the allele size in microsatellite loci of EI19 or HWB05, it could be distinguished perfectly among E. ilishaeformis, E. dabryi and E. mongolicus. Some historical and environmental elements might result in the high genetic divergence and promote the speciation of E. ilishaeformis, E. dabryi and E. mongolicus. These results would be of avail in the conservation and sustainable utilization of these three species.

Elicitation of T-cell-derived IFN-γ-dependent immunity by highly conserved Plasmodium ovale curtisi Duffy binding protein domain region II (PocDBP-RII)

BackgroundInfections with Plasmodium ovale are widely distributed but rarely investigated, and the resulting burden of disease has been underestimated. Plasmodium ovale curtisi Duffy binding protein domain region II (PocDBP-RII) is an essential ligand for reticulocyte recognition and host cell invasion by P. ovale curtisi. However, the genomic variation, antigenicity and immunogenicity of PocDBP-RII remain major knowledge gaps.MethodsA total of 93 P. ovale curtisi samples were collected from migrant workers who returned to China from 17 countries in Africa between 2012 and 2016. The genetic polymorphism, natural selection and copy number variation (CNV) were investigated by sequencing and real-time PCR. The antigenicity and immunogenicity of the recombinant PocDBP-RII (rPocDBP-RII) protein were further examined, and the humoral and cellular responses of immunized mice were assessed using protein microarrays and flow cytometry.ResultsEfficiently expressed and purified rPocDBP-RII (39 kDa) was successfully used as an antigen for immunization in mice. The haplotype diversity (Hd) of PocDBP-RII gene was 0.105, and the nucleotide diversity index (π) was 0.00011. No increased copy number was found among the collected isolates of P. ovale curtisi. Furthermore, rPocDBP-RII induced persistent antigen-specific antibody production with a serum IgG antibody titer of 1: 16,000. IFN-γ-producing T cells, rather than IL-10-producing cells, were activated in response to the stimulation of rPocDBP-RII. Compared to PBS-immunized mice (negative control), there was a higher percentage of CD4+CD44highCD62L− T cells (effector memory T cells) and CD8+CD44highCD62L+ T cells (central memory T cells) in rPocDBP-RII‑immunized mice.ConclusionsPocDBP-RII sequences were highly conserved in clinical isolates of P. ovale curtisi. rPocDBP-RII protein could mediate protective blood-stage immunity through IFN-γ-producing CD4+ and CD8+ T cells and memory T cells, in addition to inducing specific antibodies. Our results suggested that rPocDBP-RII protein has potential as a vaccine candidate to provide assessment and guidance for malaria control and elimination activities.Graphical

Insights into chloroplast genome structure and phylogenetic relationships within the Sesamum species complex (Pedaliaceae).

Background: In the Sesamum species complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships. Results: In the present study, we generated complete chloroplast genomes of six wild relatives (Sesamum alatum, Sesamum angolense, Sesamum pedaloides, Ceratotheca sesamoides (syn. Sesamum sesamoides), Ceratotheca triloba (syn. Sesamum trilobum), and Sesamum radiatum) and a Korean cultivar, Sesamum indicum cv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863-153, 338bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, including ndhA, ndhE, ndhF, ycf1, and psaC-ndhD. Concordant tree topologies suggest ndhF as a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate that S. radiatum (2n = 64) occurred concomitantly with the sister species C. sesamoides (2n = 32) approximately 0.05million years ago (Mya). In addition, S. alatum was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others. Conclusion: Altogether, we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum, respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in the Sesamum species complex.

Comparison genetic diversity and population structure of four Pseudaspius leptocephalus populations in Heilongjiang River Basin based on mitochondrial COI gene

The Pseudaspius leptocephalus is a unique fish in the Heilongjiang River Basin and has important economic and ecological value. In the present study, the complete mitochondrial genome of P. leptocephalus were determined, and COI partial sequences of 85 individuals from Erguna river (EH), Mohe (MH), Fuyuan (FY), Hulan (HL) were used to evaluated the genetic diversity of four populations of P. leptocephalus in Heilongjiang River Basin. The mitogenome is 16,607 bp in length and contained one D-loop, 2 rRNA, 13 PCG, and 22 tRNA. 4 variable sites and 5 haplotypes were detected in 705 bp COI, and 705 bp COI exhibited a lower content of C + G (45.95%) than A + T (54.05%). The nucleotide diversity (π) and haplotype diversity (h) indices ranged from 0.00027 (HL) to 0.00065 (EH and FY) and from 0.192 (HL) to 0.462 (EH), respectively. The genetic distance within the population and between populations ranged from 0.0006554 to 0.0002728 and from 0.0003541 to 0.0006974, respectively. Pairwise values of FST and Nm showed that there was moderate genetic differentiation between EH population and other populations and individuals between EH population and other populations can mate randomly (0.15 > FST > 0.05, Nm > 4). Significant negative values of neutrality tests (P < 0.05) indicated that MH and FY populations may had experienced population expansion, but mismatch distribution analysis suggested that all populations have remained basically stable. These results provide strong basis for the protection and utilization of P. leptocephalus germplasm resources, and provide valuable information for the population structure and genetic diversity of P. leptocephalus.

Genetic diversity and haplotype analysis of Leishmania tropica identified in sand fly vectors of the genera Phlebotomus and Sergentomyia using next-generation sequencing technology.

Next-generation sequencing (NGS) was used to investigate the genetic diversity of Leishmania tropica in the sand fly vector, targeting the internal transcribed spacer 1 (ITS1) of the genus Leishmania. Bioinformatics analyses were conducted using Galaxy, MEGA version X, DnaSP ver. 6.12.03, and PopART 1.7 software for NGS analysis, phylogenetic tree, genetic diversity, and haplotype networking, respectively. A total of 307 engorged sand flies were trapped, with an overall Leishmania infection rate of 9.4 (29/307) and 6.8% by NGS and ITS1-PCR, respectively. Two Leishmania-infectedsand fly genera were identified: Phlebotomus (10.2%, 26/254) and Sergentomyia (5.7% (3/53). The phylogenetic tree showed two clusters, cluster I included the four study sequences along with 25 GenBank-retrieved DNA sequences. Cluster II consisted of three sequences from Iran and Pakistan. The genetic diversity analysis for the 29 L. tropica sequences showed high haplotype (gene) diversity index (Hd) (0.62 ± 0.07) but low nucleotide diversity index (π) (0.04 ± 0.01). Tajima's D, a neutrality test, is more negative in cluster I (D = - 2.0) than in total population (D = - 1.83), but both are equally significant (P < 0.001), indicating that observed variation in cluster I and whole population is less frequent than expected. The median-joining haplotype network produced a total of 11 active haplotypes. In conclusion, L. tropica from sand flies in Palestine is monophyletic that assembled in one main phylogroup and one haplotype.

Genetic diversity of mitochondrial DNA D-loop in wild and domestic pigs (Sus scrofa) in East Asia

Chinese domestic pig breeds have abundant genetic resources, but definite information about the geographic specificity and genetic structure is lacking. In this study, we analysed 359 mitochondrial D-loop sequences, including 86 sequences from Chinese domestic pigs and the rest downloaded from GenBank. The haplotype and nucleotide diversity indices ranged from 0.467 ±0.132 (Duroc) to 1.000 ±0.500 (Thailand, North Korea and Cambodia) and 0.00067 ±0.00019 (Duroc) to 0.02000 ±0.01000 (Thailand), respectively. The neighbour-joining tree revealed two clads in the individual pigs, with a Chinese domestic breed distributed discontinuously among several breeds. The network data indicated that the gene pools of Chinese domestic pigs are likely related to Chinese, Japanese and some other Southeast Asian wild boars.

Genetic Diversity and Phylogenetic Position of Traditional Rice (Oryza sativa L.) Landraces: A Case Study of South Kalimantan in Indonesia

Traditional rice (Oryza sativa L.) landraces provide many essential genes for improving yield, disease resistance, abiotic stress tolerance, and other parameters for future rice breeding. This study aimed to analyze the genetic diversity and determine the phylogenetic position of the traditional rice landraces from the tidal swamp areas of South Kalimantan, Indonesia, compared to other rice germplasm, including wild relatives, obtained from the GenBank database, using a cpDNA-rbcL marker. In this case, six traditional rice landraces from this region were collected and analyzed molecularly using the rbcL marker and compared with 16 similar others and 25 wild relatives from the GenBank database. The genetic diversity of this germplasm was determined using the nucleotide diversity index (π), whereas the phylogenetic analysis by maximum likelihood with bootstrap for 1 000 replicates. The principal component analysis (PCA) was employed to confirm this grouping. Based on this marker, the traditional rice landraces have a genetic diversity of 0.38, lower than intra-species and inter-species levels, i.e., 0.44 and 0.83, respectively. The phylogenetic analysis shows that this germplasm has separated from most O. sativa rice cultivars and their wild relatives, except for the ‘GBVN’ and ‘NARC’ (comparison cultivars obtained from GenBank). This information has substantial implications for future rice breeding and conservation efforts, locally and globally.

Quasispecies Fitness Partition to Characterize the Molecular Status of a Viral Population. Negative Effect of Early Ribavirin Discontinuation in a Chronically Infected HEV Patient.

The changes occurring in viral quasispecies populations during infection have been monitored using diversity indices, nucleotide diversity, and several other indices to summarize the quasispecies structure in a single value. In this study, we present a method to partition quasispecies haplotypes into four fractions according to their fitness: the master haplotype, rare haplotypes at two levels (those present at <0.1%, and those at 0.1−1%), and a fourth fraction that we term emerging haplotypes, present at frequencies >1%, but less than that of the master haplotype. We propose that by determining the changes occurring in the volume of the four quasispecies fitness fractions together with those of the Hill number profile we will be able to visualize and analyze the molecular changes in the composition of a quasispecies with time. To develop this concept, we used three data sets: a technical clone of the complete SARS-CoV-2 spike gene, a subset of data previously used in a study of rare haplotypes, and data from a clinical follow-up study of a patient chronically infected with HEV and treated with ribavirin. The viral response to ribavirin mutagenic treatment was selection of a rich set of synonymous haplotypes. The mutation spectrum was very complex at the nucleotide level, but at the protein (phenotypic/functional) level the pattern differed, showing a highly prevalent master phenotype. We discuss the putative implications of this observation in relation to mutagenic antiviral treatment.

Polymorphism of mtDNA gene Cyt b of the Chukchi Sea polar cod, Boreogadus saida (Gadidae, Gadiformes)

Polar cod (Boreogadus saida) is a species with an extensive pan-Arctic distribution. Although it is not an important target of commercial fisheries, due to its extremely high abundance and as a keystone species linking zooplankton with higher trophic levels of mammals and birds, polar cod are considered a critical component of the Arctic Ocean pelagic ecosystem. For the Chukchi and Beaufort Seas, either a complete absence of a population structure or very weak differences between this part of its range and others is shown. The purpose of this work is to identify the intraspecific organization of the polar cod based on mtDNA from most areas of the Chukchi Sea and the adjacent part of the Beaufort Sea. This is the first presentation of results from analysis of the Cytb gene polymorphism of mitochondrial DNA in samples of polar cod from the western Chukchi Sea. Results indicated that there is no genetic differentiation of polar cod in the surveyed area. The exception are several samples from the Kotzebue Sound, central Chukchi Sea and western Beaufort Sea, which may be due to the transport of polar cod eggs, larvae or early juveniles by currents from the spawning grounds of Kotzebue Sound first to the central Chukchi Sea, and then to the western Beaufort Sea. The Kotzebue Sound population differs in nucleotide diversity index, as well as in pairwise values of the FST genetic differentiation index, which may be due to the isolation of this site from main currents in the area.

Allele Diversity of the Major Histocompatibility Complex in the Common Hamster (Cricetus cricetus) in Urban and Rural Populations

Based on the results of targeted sequencing on the Illumina platform we compared the allelic diversity of exon 2 of the DRB gene in urban (city of Simferopol) and rural populations of the common hamster. The urban population significantly differs from the rural one in terms of the composition and diversity of gene alleles. For individuals living in the city, a larger number of alleles, higher values of haplotype and nucleotide diversity indices, and a smaller proportion of individuals with a homozygous genotype were noted. Both populations are characterized by a significant excess of non-synonymous substitutions over synonymous ones and almost every allele of a gene corresponds to a different amino acid sequence. However, the influence of positive selection on the diversity of variants of antigen-binding sites in the alleles of the DRB gene in urban conditions is much more pronounced. The data suggest that resistance of common hamsters living in specific and varied conditions of the urban environment to various kinds of pathogenic load is higher than in rural populations.

Molecular Phylogeny of Selected Kenyan Eucalyptus Species Inferred from MatK, rbcL and TrnL-F Genes and Their Suitability for Power Transmission Poles

Genus Eucalyptus belongs to the family Myrtaceae and consists of more than 900 species, various hybrids and varieties. The major species that are grown in Kenya are Eucalyptus grandis, E. globulus, E. saligna and E. camaldulensis. Most Eucalyptus species are highly dependent on rainfall and this is challenged by climatic changes owing to global warming making it difficult to effectively match the availability of mature trees and the market demand especially for use as power transmission poles. With the widespread availability of other naturally occurring Eucalyptus species such as E. camaldulensis and E. globulus, it becomes important to determine the genetic diversity and to analyze the phenotypic traits of these species for suitability as power transmission poles in order to counter the overdependence on E. grandis. Phenotypic traits investigated included measuring total tree height and diameter at breast height (DBH), while molecular data were obtained from sequencing MatK, rbcL and TrnL-F genes from selected species and evolutionary analyses such as nucleotide substitution rates, base composition disparity indices, evolutionary divergence, nucleotide diversity indices and phylogeny construction were conducted in MEGA 11. Significant differences in DBH and height among Eucalyptus species were observed when the phenotypic data were subjected to ANOVA. In this study, E. robusta, E. paniculata, E. maculata, E. dunnii, E. camaldulensis and E. citriodora are fit to be used as power transmission poles but they are limited by their short height. However, E. tereticornis and E. glaucina have the desired DBH and height and hence can be used as substitutes for E.grandis. Generally, the molecular phylogeny study has shown that the studied Eucalyptus species are closely related and form various monophyletic clades which can be attributed to the short genetic distances, low substitution rates, low nucleotide bias disparity indices and low diversity scores. Further phylogenetic and gene expression studies involving more Eucalyptus species are needed to better understand Eucalyptus phylogeny, and diversity and identify species with similar genetic make-up to that of E. grandis which has been used extensively for the provision of electricity transmission poles.

Complete human mtDNA genome sequences revealed haplotype features of the Hmong-Mien language family in Vietnam

Vietnam is the homeland of 54 different ethnicities that belong to 5 major language families of the world, including Austroasiatic, Tai-Kadai, Hmong-Mien, Sino-Tibetan and Austronesian. Hmong-Mien, an ethnolinguistic family, presumably stemmed from Southern China and later spread to the Southeast Asia region. In this study, we analyzed the mitochondrial DNA sequences taken from 120 males belonging Hmong-Mien (HM) language family in Vietnam: Dao, Hmong, and Pathen, revealing 352 unique variants. Dao has the most number of polymorphisms (230 unique SNPs occurring 1469 times), followed by Hmong (181 unique SNPs occurring 1367 times) and Pathen (159 SNPs occurring 1243 times). Genetic variations within each population and among Hmong-Mien speakers were further measured by computations of haplotype diversity (H), nucleotide diversity (π) and fixation index (FST). There are nine major haplogroups (A, B, C, D, F, G, M, N9, and R) detected, with F and B making up over half of each population (Hmong: 56.09% (23/41), Pathen: 58.33% (21/36), Dao: 62.79% (27/43)). Haplotype classification was further divided into 30 haplogroups, of which 80% of them were specific to a single minority. Dao remained the most genetically diverse (H=0.957), while Pathen was the most homogeneous population (H=0.900). In terms of genetic distance, Dao and Hmong were more distinguished from each other, while Hmong and Pathen were more related. Complete mtDNA sequences of Viet HM speakers increased the mtDNA depository, improving the understanding of the genetic structure underlying this language family.

Genetic Diversity of Elephant Foot Yam (&lt;i&gt;Amorphophallus paeoniifolius&lt;/i&gt;) and Two Other Relatives from the Meratus Mountains of South Kalimantan, Indonesia

Elephant foot yam (Amorphophallus paeoniifolius) is a tuber crop with high economic value, so it is very prospective to be developed. This study aimed to characterize and determine the genetic diversity and relationship of A. paeoniifolius and two other relatives from the Meratus Mountains of South Kalimantan, Indonesia, using the rbcL marker. Eight samples of A. paeoniifolius and three other ones (outgroups), two of A. muelleri and one of A. borneensis, were used in the study. The genetic diversity was determined using the nucleotide diversity index (π), whereas the phylogenetic relationships were reconstructed using the Maximum Likelihood (ML) and Neighbor-Joining (NJ) methods. The results show that this germplasm has a high diversity at an inter-species level of 0.95% and a low at intra-species (0.33%). The phylogenetic analyses revealed that Amorphophallus from this region separated into different clades, three for NJ and one for ML. In this case, A. paeoniifolius var. sylvestris from Bati-Bati, Tanah Laut is closely related to A. paeoniifolius var. hortensis from Marajai, Balangan. In conclusion, although Amorphophallus from the Meratus Mountains of South Kalimantan, Indonesia, shows a high diversity at an inter-species level, the phylogenetic analyses revealed a unique relationship. This finding is expected to be a reference in supporting efforts to conserve, cultivate, and utilize sustainable Amorphophallus, globally and locally, particularly for the Dayak Meratus community of the South Kalimantan, Indonesia.