Haplotype Diversity Values Research Articles

Genetic diversity of Indonesian protected eclectus parrot (Eclectus roratus) based on mitochondrial gene sequences

Electus Parrot (Eclectus roratus) Bird is included in the group of parrots, the Psittacidae family, consists of nine subspecies. The body size is 35-42 cm, and its weight is 355–615 g. Eclectus bird has nine subspecies. Their distribution is in the Solomon Islands, Sumba, New Guinea, and its nearby islands, northeastern Australia, and the Maluku Islands (Moluccas). Seven of these subspecies are in the territory of Indonesia. The wild population is in decline. The species has been included in CITES appendix II. Like other parrot birds, this bird has high economic value, so its existence needs to be conserved for use sustainably. Information about its genetic diversity might be useful for its conservation program. Therefore, this study aimed to assess the genetic diversity of these birds revealed based on 720 bp of DNA sequences of the mitochondrial cytB gene. This information might be needed for their conservation efforts. Blood samples of 0.1 mL were taken from 103 birds in the zoo and two captivities. The total genomic DNA was extracted from each blood sample. DNA fragments of mitochondrial cytB gene were amplified through a PCR process and then the nucleotide was sequenced. The DNA sequence data of the cytB gene were analyzed using ProSeq, DnaSP, and Mega7specific software to obtain information about variations, genetic diversity, and grouping of individual birds. The cyt B sequences observed had no stop codons. Of the 720 cytB base pairs had no stop condons observed. There were eight variable sites starting at 212 to 616 position. Genetic distance among individual birdsranged from 0,000 to 0.012. The sequences had three haplotypes. Based on the comparison to E. roratus from Genbank data as well as NJ tree, it was suggested that the studied birds consisted of three subspecies. Haplotype diversity (Hd) value was 0.500 ± 0.136 and nucleotide diversity (Pi) value was 0.004431 ± 0.00140. Hence, the genetic diversity among the birds in this study was relatively low.

Genetic Structure Analysis of Y Chromosome STR and SNP in Population of Changshu.

Objective To provide a theoretical basis for building a Y chromosome database in specific regions by analyzing the pedigree specific core haplogroup and region specific genetic structure in Changshu. Methods One thousand seven hundred and two samples from unrelated Han male individuals in Changshu were collected. Then 27 Y-STR were genotyped through YfilerTM Plus PCR Amplification Kit, Y-SNP haplogroup of each sample was speculated using Y-Predictor software and some samples were verified by amplification refractory mutation system-polymerase chain reaction （ARMS-PCR）. Results A total of 1 556 haplotypes were found on the 27 Y-STR genetic markers of the 1 702 samples. The haplotype diversity （HD） value was 0.999 827. DYS385 （0.933） had the highest gene diversity （GD） value while DYS438 （0.409） had the lowest. By the Y-Predictor software, all samples were confirmed to be from 162 sub-haplogroups of C, D, N, O, Q and R. Samples were randomly selected to verify the prediction results by the software and the prediction accuracy of Y-Predictor software was as high as 95.74%. Conclusion This study found that 27 Y-STR genetic markers have relatively high polymorphisms in the Changshu population, and have good forensic individual identification and paternity testing ability.

Forensic Genetic Analysis of 11 Rapidly Mutating Y-STRs (RM-YSTRs) in Sindhi Population of Pakistan

Forensic Science is robustly associated with DNA that has a complex genetic blue print information intended to resolve the queries related to civil cases, judiciary, investigatory purposes and crime scenes. The study was carried out to contribute the data set of RMYSTRs (Rapidly Mutating YSTRs) globally. The study focused on the significance of using RM-YSTRs as compared to the set of 9-17 YSTRs (mutation rate 1 × 10-2), as the later one is not being able to attain a high magnitude of male relatives differentiation. In the present work, 100 Sindh DNA male samples were collected, by genotyping the amplified samples, using RM-YSTRs, having a mutation rate of 1 × 10-3. Forensic efficiency parameters such as, PIC (Polymorphism Information Content) was observed in the range of 0.7745 at locus DYS576 to 0.9313 at locus DYF399S1b, maximum gene diversity (0.9350) was found at locus DYF399S1b, minimum gene diversity (0.7978) was seen at locus DYS576. Highest value of allele frequency was found as 0.350 with the allele no 18 at locus DYS576. The results had shown that haplotype frequency and haplotype diversity value were 0.010 and 0.99297, as no haplotype was repeated, which highlighted on the fact that nearly complete male individualization can be obtainedusing RM YSTRs, thus helpful in avoiding the adventitious matches or exclusion or inclusion of male relatives in forensics cases work. It might be an initiative towards establishing RM YSTR database of Pakistani Sindhi population.

Genetic polymorphism of 24 Y-STR loci in Altay Hui and Kazakh populations from northwest China.

24 Y-STR loci were analyzed in 223 Altay Hui individuals and 209 Altay Kazakh individuals. Haplotype diversity (HD) and discrimination capacity (DC) values were calculated. Population pairwise genetic distances (Rst) were evaluated in AMOVA analysis and compared between two studied populations and other populations. The relationships between populations were visualized through multidimensional scaling (MDS) and neighbor-joining (NJ) tree. The results indicated higher discrimination power in the Altay Kazakh and Hui populations. The Altay Kazakh was the most distantly related to Xishuangbanna Dai, while Altay Kazakh was the most closely related to Gansu Kazakh. The results may provide useful information for paternal lineages and increase our understanding of genetic relationships between two studied populations and other populations.

Population genetic structure of the short-beaked common dolphin from the Black Sea and the Turkish Straits System

Our study aims to assess the population connectivity, evolutionary history, and conservation status of the short-beaked common dolphin in the Black Sea and Turkish Straits System (TSS). We also include DNA sequences from the Atlantic Ocean and the Mediterranean Sea to provide a regional perspective to our localized study. Analysis of 366 base pairs of mitochondrial DNA D-loop fragments from 37 samples collected from short-beaked common dolphins in the Black Sea, TSS, and Aegean Sea revealed 13 haplotypes, eight of which have not been previously reported. While analysis of samples archived on GenBank revealed 89 different haplotypes across the region. The haplotype network contains two main peripheral groups that include individuals from all locations. Haplotypes from the Atlantic Ocean are scattered across the network and no obvious population separation was detected. Some shared haplotypes potentially indicate multi-directional colonization events of the Mediterranean Sea from the eastern Atlantic Ocean. Moreover, some less widely distributed haplotypes suggest some level of more recent genetic connectivity through the Strait of Gibraltar and the TSS and point out the importance of these straits in the dispersal of short-beaked common dolphins. The haplotype and nucleotide diversity values were lower in the Black Sea, TSS, and western Mediterranean Sea when compared to the Atlantic Ocean, supporting the expansion of Atlantic populations into the Mediterranean and the Black Seas. Differentiation was observed between the Atlantic Ocean, and the Mediterranean Sea, TSS and the Black Sea based on Фst but not between Mediterranean and the Black Seas. For common dolphins, which have high dispersal potential, the protection of open seas and narrow seaways to enhance connectivity may be crucial.

Genetic polymorphism of both 29 Y-STRs and 213 Y-SNPs in Han populations from Shandong Province, China.

Genetic markers on the Y chromosome, including short tandem repeats (Y-STRs) and single nucleotide polymorphisms (Y-SNPs), are used widely in forensic genetics. Both Y-STR-based haplotypes and Y-SNP-based haplogroups provide information on a population's genetic structure, which is useful for the identification of individuals. However, there are few studies on these two types of genetic markers in the various Chinese populations. In this study, 284 Han individuals from four prefecture-level cities in Shandong Province (Binzhou, Dezhou, Heze, and Weihai) were genotyped by 29 Y-STRs (from our previous study) and 213 Y-SNPs (self-designed for the Haplogroup O2 Y-SNP panel). Haplogroup O was the most predominant among the four cities. The highest haplogroup diversity (0.9745) was observed in the Heze population, with a discrimination capacity (DC) value of 0.5625. The haplotype diversity and DC values of the Binzhou and Heze populations were 1.0000. Furthermore, genetic differences were observed between the coastal and inland cities; the results of their statistical analysis are presented herein.

БИОИНФОРМАЦИОННЫЙ АНАЛИЗ НУКЛЕОТИДНЫХ ПОСЛЕДОВАТЕЛЬНОСТЕЙ ФРАГМЕНТА ГЕНА ЦИТОХРОМОКСИДАЗА МТДНК ПАЛТУСОВ (PLEURONECTIDAE)

Comparative bioinformation analysis of nucleotide composition of subunit 1 cytochrome oxydase gene (Co-1) mtDNA subunit of north-okhotomore population with representatives of other halibut genera was carried out. Statistical analysis of nucleotide sequences of a fragment of the gene cytochrome oxidase mtDNA of pacific halibut Hippoglossus stenolepis: haplotype diversity 0.852 ± 0.0059, nucleotide 0.00430 ± 0.009465. About 1% of the total value of nucleotide diversity in individuals from eastern and western regions is determined. Analysis of nucleotide sequences of the same gene in pacific greenland halibut Reinhardtius hippoglossoides matsuurae: haplotype diversity was 0.806 ± 0.0399, nucleotide diversity - 0.00185 ± 0.000149. About 6% of the relative value of nucleotide diversity is determined by interpopulation differences. The minimum value of haplotype diversity was determined in the northern halibut flounder Hippoglossus robustus, while in the second species of this genus Hipploglossus platessoides, the haplotype diversity is similar to the representatives of two genera Cleisthenes and Hippoglossus. The maximum value of haplotypic diversity was found in the Cleisthenes herzensteini, representatives of the Atherestes and Reinchardtius genera have intermediate values. The species Atherestes stomias is sharply separated from species of other genera, which is associated with a high degree of genetic differences between representatives of this genus and those from other genera.

PSVII-23 Phylogenetic analysis of mitochondrial DNA D-loop region for excavated horse bones at the Asian archaeological sites

Abstract Horses have played a significant role in the development of human society. As an important domestic animal, horses have been used for transport, labor, food and recreation. It is widely accepted that the horse was probably first domesticated on the Eurasian steppes from Ukraine to Turkestan between the fifth and fourth millennium BC, and the earliest domesticated horses subsequently spread out from their original range. However, we currently have little genetic evidence to demonstrate whether Korean domestic horse breeds originated in Korea or if it came into the area via an ancient migration route. In the present study, to obtain more knowledge of the origin and genetic diversity of Korean domestic horses, we analyzed seventeen 247-bp mitochondrial DNA (mtDNA) D-loop sequences of ancient horse bones excavated from seven archaeological sites located in the southern Korean Peninsula and Mongolia, aged between the fifth century B.C and nineteenth century A.D. The seventeen ancient horses revealed 9 variable positions when compared with the reference sequence (GenBank X79547). All the substitutions were transitions, and defined a total of 11 unique haplotypes with the haplotype diversity value of 0.9118±0.056. Among the 11 haplotypes, 3 haplotypes were detected more than once and were thus shared by individuals from the same or close archaeological sites. The largest haplotype consisted of 5 individuals, with another two haplotypes containing 2 individuals respectively, and eight haplotypes were singletons. The data indicate an abundant genetic diversity of the Korean ancient horses, and also suggest that the origin of Korean domestic horses is complex, and several maternal lines were introduced into the gene pool of Korean horses after their initial domestication.

Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin.

Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as "blue crab" and "Product of the USA" may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as "Product of the USA" and "Product of Venezuela." In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise F st values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.

Fasciola hepatica in Brazil: genetic diversity provides insights into its origin and geographic dispersion.

Fasciola hepatica is a trematode parasite that affects mammals, including humans. In Brazil, fascioliasis, a disease caused by the parasite, is of great importance. The disorder affects the welfare of the Brazilian population through impairing the agricultural production of cattle, where the disease causes weight loss as a result of liver damage. This study aimed to evaluate the genetic diversity of F. hepatica throughout Southern Brazil to determine its geographic origin and estimate the colonization route of the parasite. To accomplish these aims, flukes were collected from slaughterhouses in three endemic areas of Rio Grande do Sul and Paraná states. DNA was isolated using the phenol-chloroform protocol from single flukes and two mitochondrial genes, cytochrome oxidase subunit I (COI) and nicotinamide dehydrogenase subunit 1 (Nad1), were amplified and sequenced. Ten haplotypes of COI were found from 75 isolated parasites and the total haplotype and nucleotide diversity observed were 0.475 and 0.002, respectively. Using the Nad1 gene, we found 24 haplotypes from 79 samples, resulting in haplotype and nucleotide diversity values of 0.756 and 0.004, respectively. An analysis of molecular variance showed that 57.4% and 77.5% of variation was within populations (FST), while 9.0 and 36.8% of variation was among groups (FCT) when considering COI and Nad1 genes, respectively. For COI, the fixation index values of 0.425 and 0.368 were obtained for FST and FCT, respectively, while analysis of Nad1 0.225 and 0.089 index values were obtained for FST and FCT, respectively. We have determined that F. hepatica found in the two distinct areas originated from several geographical regions, since we found haplotypes that were shared with at least three different continents. These data are in accordance with the recent colonization of Brazil, and the recent import of cattle from South American, European and, possibly, some African countries. The observed FST and FCT values for COI and Nad1 genes of F. hepatica may be a result of limited movement of animals within states and support the lack of geographical structure of the parasite in Brazil, which are in agreement with the observed cattle production systems in this region.

Genetic variation among the geographic population of Cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae) in Indonesia inferred from mitochondrial COI gene sequence

Abstract. Nopriawansyah N, Rauf A, Kusumah YM, Nurmansyah A, Koesmaryono Y. 2019. Genetic variation among the geographic population of Cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae) in Indonesia inferred from mitochondrial COI gene sequence. Biodiversitas 20: 2685-2692. Cassava mealybug, Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae) is an invasive pest native to South America. Research was conducted with the objective to study genetic variation of cassava mealybug from different geographic areas in Indonesia. Thirty-six samples of cassava mealybugs were collected from eight different population locations. Genomic DNA was extracted from individual specimens of P. manihoti using gSYNC DNA Extraction Kit from Geneaid Lot No. FB221707. PCR amplification using primary CO1 gene showed the target position as long as 518 bp. Analysis of homology from eight populations revealed eight haplotypes in Indonesia with different variable sites. Genetic distance analysis was done by calculating base pair differences in each population. The percentage of genetic distance between populations was 0.0000% -0.00409%. The results of the analyst using the Kimura-2 parameter showed that the population was divided into 2 clusters. The highest haplotype (Hd) diversity value was 0.8333, while the lowest was zero (Hd = 0). The highest nucleotide diversity (π) was 0.00225 and the lowest was 0.000000. The genetic distance and nucleotide diversity were low because P. manihoti was thelytoky parthenogenesis.

Genetic Diversity and Population Structure Analysis of Three Deep-Sea Amphipod Species from Geographically Isolated Hadal Trenches in the Pacific Ocean.

Amphipods of the superfamily Lysianassoidea that inhabit the hadal zone ( > 6000m) have large bathymetric ranges and play a key role in deep ocean ecosystems. The endemism of these amphipod species makes them a good model for investigating potent natural selection and restricted dispersal in deep ocean trenches. Here, we describe genetic diversity and intraspecific population differentiation among three amphipod species from four Pacific trenches based on a mtDNA concatenated dataset (CO Ι and 16S rRNA genes) from 150 amphipod individuals. All amphipod populations had low genetic diversity, as indicated by haplotype and nucleotide diversity values. Population geographic relationship analysis of two Alicella gigantea populations revealed no genetic differentiation between these two localities (pairwise genetic differentiation coefficient = 0.00032, gene flow = 784.58), and the major variation (99.97%) was derived from variation within the populations. Historical demographic events were investigated using Tajima's D and Fu's F neutrality tests and analysis of mismatch distribution. Consistent results provided strong evidence to support the premise that demographic expansion occurred only for the Mariana population of Hirondellea gigas, possibly within the last 2.1-3.4 million years. These findings suggest that the formation of amphipod population structure might be the result of multiple factors including high hydrostatic pressure, food distribution, trench topographic forcing and potential ecological interactions.

Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis.

Kashmiris phylogenetic depictions through uniparental and biparental genetic markers.

In this study, the Kashmiri population was genetically screened for fifteen autosomal STRs, seventeen Y-chromosomal STRs and mitochondrial DNA control region SNPs. Autosomal STRs exhibited that D2S1338 was the most discriminatory locus with value of 0.963 whereas combine power of discrimination was 0.999999999999999. On the other hand, analysis of Y-chromosomal STRs generated 59 distinct haplotypes of which 52 were unique with haplotype diversity value of 0.99752. Mitochondrial D-loop analysis resulted that haplogroups M and U were found most prevalent with 25% each. Haplotypic data of Y-STRs was submitted to YHRD under accession number YA004153 whereas mitochondrial DNA control region (CR) sequences were submitted to EMPOP with accession number EMP00683.

Haplotype characterization of Ceraeochrysa cubana (Hagen) and Ceraeochrysa valida (Banks) (Neuroptera: Chrysopidae) from the state of Colima, Mexico.

The larvae of Ceraeochrysa cubana and Ceraeochrysa valida, green lacewing species widely spread in Mexico, have been described as natural enemies of Diaphorina citri (Hemiptera: Liviidae), vector of the bacteria Candidatus Liberibacter spp. causing Huanglongbing disease. To develop an effective biological control program, the establishment of the genetic structure of the biocontrol agent species is mandatory. Consequently, the goal of this work was to obtain reliable DNA barcoding regions of the two species, and then by sequence analysis of the mitochondrial gene cytochrome c oxidase subunit I, evaluate the genetic structure of Mexican lime populations of C. cubana and C. valida from the state of Colima. This research produced the first barcode region of C. cubana and C. valida with morphological and molecular confirmation. The genetic parameters revealed the presence of 15 and 10 haplotypes, and haplotype diversity values of 0.889 and 0.838 for C. cubana and C. valida, respectively. The populations showed high diversity and gene flow, and AMOVA analysis demonstrated no genetic structure in the two populations. Consequently, these single populations of C. cubana and C. valida could be used as unique genetic source for mass production and release in the Mexican lime-producing state of Colima to control D. citri.

Genetic diversity and metapopulation structures of two intertidal species along the coast of Zhejiang, China: implications for conservation

To priority areas for conservation in the coast of Zhejiang, this study attempts to map the spatial patterns of the intra-specific genetic diversity of two intertidal species, Septifer virgatus and Tetraclita japonica, using the sequences of mitochondrial DNA cytochrome oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA) genes. In total, 129 and 112 specimens were collected from 12 and 11 populations for S. virgatus and T. japonica, respectively. These two species revealed congruent population historical signals, including (1) high levels of haplotype diversity and low values of nucleotide diversity, (2) post-LGM expansion, (3) the lack of population genetic structure, sharing haplotypes over all sampling populations, (4) gene flow connections, and (5) migration directions. Largely, all results supported that all sampling populations could be divided into two main metapopulations, exhibiting a northern and southern distribution. The north metapopulation could be considered as a marine protected area. The genetic patterns of the two species should be considered in the management and conservation in the islands along the Zhejiang, China.

Study on the Genetic Differentiation of Geographic Populations of Calliptamus italicus (Orthoptera: Acrididae) in Sino-Kazakh Border Areas Based on Mitochondrial COI and COII Genes.

Calliptamus italicus L. is an important pest on the desert and semidesert steppes along the Sino-Kazakh border. To elucidate the molecular mechanism of its continuous outbreaks, we studied 11 different geographic populations of C. italicus to determine: 1) the complete sequences of the entire mitochondrial cytochrome oxidase subunit I (COI) and mitochondrial cytochrome oxidase subunit II (COII) genes, and 2) performed genetic diversity, differentiation, gene flow, and molecular variation analyses. Of the 11 populations, the Yining County (YNX) population had the highest haplotype diversity and Pi values. There are significant differences in Tajima’s D and Fu’s Fs (P < 0.05). The fixation index Fst values of the total C. italicus population were 0.03352, and its gene flow Nm values of the total C. italicus population were 15.32. Taken together, there were five main findings: 1) the current genetic differentiation of C. italicus arose within populations; 2) genetic exchange levels were high between geographical populations; 3) genetic variation level was low; 4) C. italicus populations likely expanded in recently, and 5) there was no significant correlation between genetic distance and geographic distance for any geographic population. Findings from this study indicate that frequent gene exchange between populations may enhance the adaptability of C. italicus along the Sino-Kazakh border, leading to frequent outbreaks.

Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences

Abstract. Hapsari L, Trimanto, Wahyudi D. 2019. Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences. Biodiversitas 20: 1266-1283. Heliconia L. is a single genus in the family Heliconiaceae, with approximate consists of 200 species. It has wide morphological variations among and within species which led to problems in species identification. Species diversity and phylogenetic analysis using morphology and rbcL marker subjected to 17 Heliconia spp. living collections of Purwodadi Botanic Garden (PBG) have been conducted. The rbcL gene located in chloroplast genome is one of appropriate proposed marker for plant barcoding assessment. This study aimed to study morphology and genetic variability of the PBG Heliconiaceae collections, to confirms the species name for a more accurate identity record and to reveal the diversity and phylogenetics of the species. Morphological characterization showed high variability among Heliconia species, which included 3 subgenera (Heliconia, Stenochlamys, and Griggsia) and 1 hybrid. Each species possessed unique morphological characteristics. The common morphological characters which distinguished among and within Heliconia species includes leaf form, inflorescence type, and bract characteristics. Key to the Heliconia species examined is presented in this paper. However, molecular confirmation using rbcL sequences showed high conservation level (0.932) and low genetic variability. About 656 nucleotides were monomorphic and 33 positions were polymorphic which comprised 18 singleton variable sites and 15 parsimony informative sites. Twelve haplotypes were produced with haplotype diversity value 0.8952. Pairwise distance analysis shows that they were shared high similarity of rbcL sequences with very low genetic distance (0.022 to 0.000). The topology of phylogenetic tree resulted by Neighbour-Joining algorithm has the best grouping and be able to explain the relationship among species of Heliconia, although supported by low bootstrap (65). It was separated into two clades following its subgen. classification. Clade 1 consists of subgen. Heliconia and Griggsia; while clade 2 consists of subgen. Heliconia and Stenochlamys; also hybrid species. Further, separation of deeper branchings (section) was inconsistent and unclear. Upon this study, rbcL marker was considered too conserved thus less valuable for phylogenetic analysis at lower taxa among and within Heliconia spp. However, rbcL was suggested to distinguish at higher level taxa between closely related genus and above.

Patterns of nucleotide diversity for different domains of centromeric histone H3 (CENH3) gene in Secale L.

Rye (Secale) is among staple cereals along with other members of the Triticeae tribe: wheat and barley. The genus Secale includes perennial and annual, cross-pollinating and self-pollinating species, and they can be donors of valuable genes in wheat and rye breeding programs. Studies of the structure of the gene for centromeric histone H3 (CENH3), essential for centromere functions, are relevant to the breeding of agronomically important crops. We have investigated the nucleotide diversity of sequences of two variants of the rye CENH3 gene inside the N-terminal tail (NTT) and the conservative HFD (histone fold domain) domain in the genus Secale. The mean values of nucleotide diversity in the NTT and HFD of wild cross- and self-pollinating taxa are close in αCENH3: πtot = 0.0176–0.0090 and 0.0136–0. 0052, respectively. In the case of βCENH3, the mean values for NTT (πtot = 0.0168–0.0062) are lower than for HFD (πtot = 0.0259–0.084). The estimates of nucleotide and haplotype diversity per site for the CENH3 domains are considerably lower in taxa with narrow geographic ranges: S. cereale subsp. dighoricum and S. strictum subsp. kuprijanovii. Commercial breeding reduces the nucleotide sequence variability in αCENH3 and βCENH3. Cultivated rye varieties have π values within 0.0122–0.0014. The nucleotide and haplotype diversity values in αCENH3 and βCENH3 are close in S. sylvestre, which is believed to be the oldest rye species. The results of this study prove that the frequency of single nucleotide polymorphisms and nucleotide diversity of sequences in genes for CENH3 in Secale species are influenced by numerous factors, including reproduction habits, the geographic isolation of taxa, breeding, and the evolutionary age of species.

A view of the maternal inheritance of Espírito Santo populations: The contrast between the admixed and Pomeranian descent groups

In addition to its valuable utility in forensic investigations, mitochondrial DNA (mtDNA) analysis is a reliable tool to uncover the origins of admixed populations, such as Brazilians. The state of Espírito Santo (ES), similar to other coastal Brazilian states, has a population shaped by 3 main ancestral roots: Amerindian, African and European. Among the latter, the Pomeranian descendants stand out due to the preservation of the traditional aspects of their culture, especially the Pomeranian language. Despite the genetic data already available, there is no mtDNA database that adequately reflects the diversity, the geographic distribution, and the origins of the maternal lineages from ES. To increase the knowledge of maternal ancestry and to investigate the population’s genetic stratification, a total of 291 samples were collected in the 4 macroregions (Metropolitan, South, Central and North) of ES and in the Pomeranian communities. Complete control region data were produced for the general (N=214) and Pomeranian (N=77) groups. Regarding the general population, the high values of haplotype diversity (H=99.9%) and pairwise differences (MNPD=16.9) found are in agreement with those reported for other populations in the southeast region of the country. Regarding maternal inheritance, the ES populations stood out due to the predominance of European haplogroups (49.5%), although the North macroregion had a higher African ancestry (47.1%). Among the Pomeranians, the lowest MNPD value (11.2) and the high percentage of shared haplotypes (15%) were indicative of founder events. The FST analysis showed that the Pomeranians (98.7% of European lineages) are genetically isolated from the other admixed populations in Brazil. This study demonstrated that the ES state contains singularities regarding the intrapopulational and interpopulational diversity of mtDNA. Even after 5 centuries of interethnic admixture, the present-day population of Espírito Santo harbors genetic marks that trace back to the historical aspects of its formation.