Mating Strategy in the Arab Horse Population Over 30 Years in Algeria

Background: Uncaria gambir is one Uncaria species that exclusively grows in Indonesia. The phytochemical constituents of this species have been widely explored and its extracts are used as traditional medicine. However, the relationship between Uncaria gambir and other Uncaria species is still unknown. DNA barcoding was used in this study to reveal this relationship. Methods: Genomic DNA was isolated from four main cultivated variants of Uncaria gambir species in Indonesia. ITS primer was used to amplify the specific gene region. Genetic distance analysis was carried out on Uncaria gambir and 12 other Uncaria species. A phylogenetic tree was created to determine the relationship among Uncaria species using the maximum likelihood method. Results: The ITS primer successfully amplified the ITS region in Uncaria gambir. Genetic distance and phylogenetic tree analyses showed that Uncaria gambir has a close relationship with Uncaria scandens, Uncaria yunnanensis, and Uncaria macrophylla which is also indicated by Interspecific distance analysis. Conclusions: Although the DNA barcoding gap is absent in genetic distance analysis, the phylogenetic tree analysis from the ITS region can differentiate Uncaria gambir from other Uncaria species.

The toxic dinoflagellate Gymnodinium catenatum Graham has formed recurrent toxic blooms in southeastern Tasmanian waters since its discovery in the area in 1986. Current evidence suggests that this species might have been introduced to Tasmania prior to 1973, possibly in cargo vessel ballast water carried from populations in Japan or Spain, followed by recent dispersal to mainland Australia. To examine this hypothesis, cultured strains from G. catenatum populations in Australia, Spain, Portugal, and Japan were examined using allozymes and randomly amplified polymorphic DNA (RAPD). Allozyme screening detected very limited polymorphism and was not useful for population comparisons; however, Australian, Spanish, Portuguese, and Japanese strains showed considerable RAPD diversity, and all strains examined represented unique genotypes. Multidimensional scaling analysis (MDS) of RAPD genetic distances between strains showed clear separation of strains into three nonoverlapping regional clusters: Australia, Japan, and Spain/Portugal. Analysis of genetic distances between strains from the three regional populations indicated that Australian strains were almost equally related to both the Spanish/Portuguese population and the Japanese population. Analysis of molecular variance (AMOVA) found that genetic variation was partitioned mainly within populations (87%) compared to the variation between the regions (8%) and between populations within regions (5%). The potential source population for Tasmania’s introduced G. catenatum remains equivocal; however, strains from the recently discovered mainland Australian population (Port Lincoln, South Australia, 1996) clustered with Tasmanian strains, supporting the notion of a secondary relocation of Tasmanian G. catenatum populations to the mainland via a shipping vector. Geographic and temporal clustering of strains was evident among the Tasmanian strains, indicating that genetic exchange between neighboring estuaries is limited and that Tasmanian G. catenatum blooms are composed of localized, estuary‐bound subpopulations.

To analyze the genetic characteristics of HIV-1 CRF01_AE strains prevailing in the four provinces of southern China. Plasma samples were collected from the newly diagnosed HIV-1 individuals reported in 2006 in Guangdong, Guangxi, Jiangxi and Hunan province. The gag and env gene fragments were amplified from RNA template extracted from plasma using RT and nested PCR methods. CRF01_AE sequences were analyzed by phylogenetic methods and characterized by calculating the genetic distance and Entropy analysis. Two main epidemic clusters were found to exist in the CRF01_AE strains from 210 HIV-1 CRF01_ AE infected individuals collected in the 4 provinces, southern China. It was found that no international reference strain was closely correlated with cluster I, which including 123 samples. The strains in cluster II, consisting 57 cases of samples, were closely related with the strains identified in Vietnam. Genetic distance analysis of gag and env genes showed that the diversity of cluster I was obviously less than that of cluster II. Data on nucleotide polymorphism showed that nucleotides compositions of 42 sites in gag and 40 sites in env were significantly different between the two clusters. When compared with cluster II, the polymorphism decreased at 61 nucleotide sites but increased at 21 sites in cluster I. This was the first report describing that two main epidemic clusters were existed in CRF01_AE strains prevailing in the 4 provinces, Southern China. The virus in cluster I was the dominant strain in this region, with shorter period of circulation and higher proportion seen in the HIV-infected population, which might belong to CRF01_AE strain with certain features facilitating the spread of the virus. The virus in cluster II was highly homology with the CRF01_AE strains from Vietnam, and seemed to have had several events of epidemics in populations in border regions of China and Vietnam.

RAPD technique was applied to study intraspecific genetic polymorphism and differentiation of Suaeda acuminata populations in oasis-desert transitional zone in Fukang, Xinjiang. By analysis of RAPD data, higher genetic variability was found in the populations of S. acuminata, with a percentage of polymorphic loci of 98.9%. Both estimations by Shannon diversity index and by Nei's gene diversity index from RAPD data, it was found identically that about 72% of molecular variation existed within the subpopulations, while about 28% of which existed among subpopulations. Analysis of genetic identity, genetic distance and cluster analysis showed that genetic differentiation has taken place in the populations of Suaeda acuminata in oasis-desert transitional zone in Fukang, Xinjiang, China. The correlation analytical result between the soil factures and the genetic diversity indicted that there was a significant positive relation between genetic diversity and concentrations of Mg++, conductivity (CO) and absorbed water(W) in soil, while there was no significant relation between genetic distance among subpopulations and geographical distance. Analysis of genetic identity, genetic distance and cluster analysis between the five subpopulations showed that genetic differentiation has taken place in the population of Suaeda acuminata in oasis-desert transitional zone in Fukang, Xinjiang. No correlation existed between genetic distance among subpopulations and their locations in oasis-desert transitional zone. Adaptation to its habitats and restricted gene flow among subpopulations may be a cause of genetic differentiation of Suaeda acuminata population in oasis-desert transitional zone in Fukang, Xinjiang.

Musculoskeletal injuries (MSI) are common in racehorses and have been of increasing concern in horses travelling internationally to compete. Understanding the differences in bone turnover between local horses and international horses following long-distance air transportation may inform MSI prevention strategies. To understand the differences in bone turnover markers and risk of MSI between local horses and international horses following long-distance air transportation. Prospective cohort. The concentrations of bone turnover markers (OCN and CTXI), markers of stress (cortisol), inflammation (serum amyloid A) and circadian rhythm (melatonin), and bisphosphonates were determined in blood samples collected twice (14-17 days apart), from horses following international travel (n = 69), and from local horses (n = 79). The associations between markers, long-distance travel and MSI were determined using multivariable generalised linear regression models. Within 3-5 days post-transport, concentrations of cortisol in international horses were higher than those of local horses (main effect, Coef. 0.39; 95% CI 0.24, 0.54; p < 0.001) but they decreased and were not different to those of local horses at the second timepoint (interaction effect, Coef. -0.27; 95% CI -0.46, -0.07; p = 0.007). After adjusting for age and sex, OCN and CTXI were not significantly different between international and local horses; however, OCN was lower in international horses at timepoint 2 (interaction effect, Coef. -0.16; 95% CI -0.31, -0.01; p = 0.043). The prevalence of MSI was higher in the international (26%; 95% CI 16, 38%) compared with local horses (8%; 95% CI 3, 16%; p < 0.001), with all severe MSI sustained by the international horses. At the second timepoint compared with the first timepoint post-transport, cortisol remained high or increased (interaction effect, Coef. 0.43; 95% CI 0.24, 0.61; p < 0.001) and OCN increased (interaction effect, Coef. 0.26; 95% CI 0.08, 0.44; p = 0.006) in the horses that sustained severe MSI. Horse population and racing career parameters differed between groups. Bone turnover markers have low sensitivity to detect local bone changes. Most horses showed minimal effects of long-distance air transport within 2 weeks relative to local horses as assessed by stress and bone turnover markers. Screening for persistent high cortisol and evidence of net bone formation after long-distance air transportation may help to identify racehorses at high risk of catastrophic MSI.

Parmarion martensi Simroth, 1893 is a snail a reduction of shell and often known as semislug. The species is distributed from Southeast Asia to the Hawaian Archipelago. There are two species of Parmarion in Java which can be distinguished only from the genitalia. This study was conducted to reveal the phylogenetic and genetic distance of P. martensi in Java based on the COX1 gene with K2P genetic pairwise distance, mrbayes, and IQtree analysis. The analysed specimens were the scientific collections of the Museum Zoologicum Bogoriense. We used two specimens from the GenBank for comparison, and three specimens as outgroup . The phylogenetic analysis resulted three clades i.e., clade A as consist of Microparmarion from Borneo as semi-slug outgroup, clade B consist of P. martensi from Java, and clade C consist of P. martensi from Taiwan. P. martensi has a polytomy relationship between P. martensi Java and Taiwan. Beside that, P. martensi Java also has a polytomy relationship between West Java and East Java species with statistical support (PP = 93; BS = 51). Then, genetic distance between P. martensi Java have genetic distance around 0 – 4,64 %, whereas genetic distance between P. martensi Java and Taiwan have a high genetic distance around 5.89 – 10.18%. In this case, P. martensi has a high threshold on the COX1 gene around 0 – 10.18% as the same species.

Genetic diversity and relatedness in Pyrenophora tritici-repentis, the causal agent of tan spot disease of wheat, were examined in a geographically diverse collection of 80 isolates representing the eight races of the pathogen. Thirty-one simple sequence repeat markers were designed from the P. tritici-repentis genome which amplified 31 different loci in the isolates tested. Data were examined using: (i) Nei's analysis of genetic diversity and genetic distance, (ii) analysis of molecular variance (AMOVA), and (iii) clustering by the unweighted pair group method using arithmetic averages (UPGMA). A significant genetic differentiation (ΦPT = 0.153, P ≤ 0.001) was detected among populations, with isolates from different origins having similar levels of genetic diversity. Nei's analysis of genetic distance revealed that isolates of P. tritici-repentis can be grouped into four distinct populations based on their region of origin. The AMOVA showed that Canadian isolates have less than 9% genetic dissimilarity with isolates from the Caucasus region, while they have up to 32% genetic dissimilarity with isolates from the Fertile Crescent. Isolates were also compared by race, genetic distance and cluster analysis based on pooled allele frequency. Ptr ToxA non-producing isolates clustered together but were distantly related to Ptr ToxA-producing isolates, suggesting that the host-specificity imposed by the different Ptr toxins could lead to differentiation among isolates of P. tritici-repentis.

Racospermaauriculiforme (Cunn. ex Benth.) Pedley and Racospermamangium (Willd.) Pedley are two fast-growing multipurpose leguminous species that have great potential for reforestation in the subhumid and humid tropics. The level and distribution of genetic variability were evaluated among and within 13 populations of each species at 18 loci encoding 10 enzymes, using starch gel electrophoresis. At the population level, the mean number of alleles per locus, the mean percentage of polymorphic loci, and mean expected heterozygosity were, respectively, 1.9, 52.1%, and 0.122 for R. auriculiforme, and 1.5, 24.3%, and 0.064 for R. mangium. Therefore, R. mangium appeared genetically depauperate compared with R. auriculiforme. The proportion of the total genetic diversity that resided among populations in R. auriculiforme (18%) was twice that in R. mangium (9%). No linear relationships were detected between genetic and geographic distances among populations. Cluster analysis of Nei's genetic distances and discriminant analysis did not show any significant geographic pattern of population differentiation for R. mangium. These same analyses revealed two distinct clusters of populations for R. auriculiforme, one in Queensland, Australia, and Papua New Guinea, and the other in the Northern Territory of Australia and Indonesia. For both taxa, seed of unknown origin of some introduced populations in Zaire and Congo could be identified. The genetic distance between the two species (D = 0.097) was, as expected, much larger than the average intraspecific genetic distance derived from comparisons of conspecific populations (D = 0.034 for R. auriculiforme and D = 0.007 for R. mangium). However, the amplitude of the interspecific genetic distance calculated is representative of divergence levels usually observed among subspecific taxa. Based on this, and the lower levels of genetic diversity found in R. mangium, it is suggested that R. mangium derived recently from R. auriculiforme.

Number of ancestral human species: a molecular perspective

Genetic distance analysis among quality protein maize (QPM) inbred lines and the correlation of genetic distance with heterosis would help to design breeding strategy and predict hybrid performance. This study was carried out to determine the amount of genetic diversity among QPM inbred lines using SSR markers and morphological distances; to classify the inbred lines according to their relationships; and to estimate the correlations of SSR markers and morphological distances with hybrid performance, heterosis and specific combining ability (SCA). One-hundred and five hybrids generated by diallel crossing of 15 QPM inbred lines were evaluated with the 15 parents for 17 morphological traits at Harare, Zimbabwe and Bako, Ethiopia and also examined for DNA polymorphism using 40 SSR markers. SSR markers and morphological methods of genetic distance estimates showed moderately high genetic distance among the inbred lines studied. Cluster analysis based on the two distance measures grouped the 15 parental lines differently. The SSR marker-based genetic distance was positively and highly significantly correlated with grain yield (r = 0.37), and negatively and highly significantly with days to anthesis (r = −0.40) and days to silking (r = −0.42). These relationships suggest that high grain yield and earliness of QPM hybrids can be predicted from SSR marker determined distances of the parents, although the correlation values were not very high. The correlations of SSR marker distance with heterosis were too low to be of predictive value except for the case of plant height. Morphological distances were of less importance in predicting hybrid performance and SCA effects of hybrids.

Information about genetic distances among populations (geographics) of local swamp buffalo is less published. Genetic distance analysis was done among seven local swamp buffalo populations trhough a morphological analysis. Female and male buffaloes were observed for a total number of 905 hds, originating from the Provices of NAD (100 hds), North Sumatera (51 hds), Banten (180 hds), Central Java (203 hds), South Kalimantan (121 hds), NTB (200 hds), dan South Sulawesi (50 hds). Â Genetic variation among buffalo populations was calculated by discriminant function of Mahalonobis distance. Genetic distance was estimated by MEGA program. Morphometric measurements of female buffalo in North Sumatera were larger (P 0,01) than those of buffaloes in Banten, South Kalimantan, NAD and South Sulawesi. Morphometric measurements of male buffalo in South Sulawesi were larger than those of buffaloes in Central Java, Banten, and NAD. Chest width was the highest different morphometric factor (0.969). Buffalo from NTB had the highest similarity (95.0%), followed by buffaloes from North Sumatera (74.51%) and South Sulawesi (74.19%); while the lowest one was from South Sulawesi (38.02%) and Banten (49.44%). Morphological distribution map indicated existence of three local swamp buffalo groups. Grup 1 was presented by buffalo from NTB, distributed in the II and III quadrants. Group 2 was presented by buffaloes from five locations (North Sumatera, Central Java, South Kalimantan, South Sulawesi, and Banten), distrributed in I and II quadrants, and a smaller part distributed in III and IV quadrants. Group 3 was presented by buffaloes from NAD and a smaller part from South Kalimantan and Banten, distributed in IV quadrant. The lowest genetic distance was identified between buffaloes in NAD and South Kalimantan (0.348), while the highest one was between buffloes in Banten and South Kalimantan (1.883). Based on phenogram tree structure, the observed local swamp buffaloes could be classified into 3 cluster, namely: Cluster 1 from South Kalimantan, NAD and Banten; Cluster 2 from South Sulawesi, Central Java and North Sumatera, and Cluster 3 from NTB. Key Words: Swamp Buffalo, Morphology, Discriminant Analysis, Genetic Distance

The six species of the genus Bubalus include the lowland and mountain anoa, Asian wild buffalo, tamaraw, swamp buffalo, and riverine buffalo. Few studies were conducted on the matrilineal phylogeny and genetic diversity of Bubalus species. In addition, there is controversy regarding the identity of the two domesticated water buffaloes in the Philippines – the introduced riverine and the native swamp buffalo. Thus, this study aimed to determine the genetic distance and phylogenetic relationship of Bubalus species using the mitochondrial cytochrome b (cytb) variation and to re-evaluate the taxonomic species designation of Bubalus bubalis. A total of499 Philippine cytb sequences from this study (n = 179), as well as other Asian countries (n = 319)and Syncerus caffer (n = 1), from NCBI were included in the analysis. The highest interspecies genetic distance (d) (0.040) was between the tamaraw and lowland anoa, whereas the lowest genetic distance (0.020) was between mountain and lowland anoa. Moreover, the phylogenetic tree indicated 52 haplotypes that delineated three groups, including lowland anoa, mountain anoa, and tamaraw with two domesticated buffaloes. The latter group further separated into three species – tamaraw, riverine, and swamp buffaloes. The analyses of genetic distance,phylogeny, and median-joining network structure based on cytb confirmed that the swamp buffaloes from Occidental Mindoro and South Cotabato, Philippines belong to maternal lineage B. Karyotype analysis consistently confirms that riverine buffaloes possess 50 chromosomes, whereas swamp buffaloes have 48 chromosomes, aligning with previous findings. Moreover, the swamp and riverine buffaloes appear to be distinct species, with the swamp buffalo having a closer affinity to the tamaraw than to the riverine buffalo. We, therefore, propose to revive the species assignment of the Bubalus kerabau Fitzinger, 1860 as a distinct species to the swamp buffalo. Furthermore, a common maternal ancestry was confirmed between the tamaraw and two domesticated buffaloes – the swamp and riverine. Research findings provided valuable information on understanding and monitoring the matrilineal genetic diversity of the genus Bubalus toward conservation and management.

The major histocompatibility antigen (HLA) complex is among the most polymorphic genetic systems in humans. The distribution of HLA alleles and haplotypes differs within ethnic groups and geographical regions. Russian populations evolving in different regions of Russia may have distinct immunogenetic characteristics due to the influence of internal and external factors (vast territories, multinational population, interethnic contacts). The aim of this study was to evaluate the genetic distances between Russians from different regions of Russia, and other populations. The results of this study show that the Russians living in St. Petersburg, Nizhny Novgorod and Rostov-on-Don had a similar distribution of HLA allele groups. The pan-European HLA haplotypes A*01-B*08-C*07-DRB1*03-DQB1*02 and A*03-B*07-C*07-DRB1*15-DQB1*06 were most common in Russians from all regions. When comparing 10 most common HLA haplotypes, nine of them were similar for the residents of St. Petersburg and Nizhny Novgorod. In addition, we have registered the following haplotypes: A*02-B*13-C*06-DRB1*07-DQB1*02, A*03-B*35-C*04-DRB1*01-DQB1*05, A*02-B*07-C*07DRB1*15-DQB1*06, A*02-B*18-C*07-DRB1*11-DQB1*03, A*25-B*18-C*12-DRB1*15-DQB1*06, A*02B*41-C*17-DRB1*13-DQB1*03, A*30-B*13-C*06-DRB1*07-DQB1*02. The A*02-B*15-C*03-DRB1*04DQB1*03 haplotype was one of the most common among Russians of St. Petersburg, but its frequency was less in Russians from Nizhny Novgorod (0.0119 vs. 0.0034, p = 0.03) and it was not found among Russians of Rostov-on-Don. The residents of Rostov-on-Don had the more significant differences of HLA haplotype profile. In particular, the following HLA haplotypes were among the most common in Russians living in Rostov-on-Don: A*23-B*44-C*04-DRB1*07-DQB1*02, A*02-B*57-C*06-DRB1*07-DQB1*03, A*24-B*35C*04-DRB1*11-DQB1*03, A*01-B*52-C*12-DRB1*15-DQB1*06, A*11-B*35-C*04-DRB1*01-DQB1*05, A*02-B*27-C*02-DRB1*01-DQB1*05, A*02-B*44-C*02-DRB1*16-DQB1*05. Two of these haplotypes (A*24B*35-C*04-DRB1*11-DQB1*03 and A*02-B*44-C*02-DRB1*16-DQB1*05) were not detected in Russians of Nizhny Novgorod, the frequency of other haplotypes was &lt; 0.01. Frequency of these haplotypes in Russians of St. Petersburg was also less than 0.01. The haplotype A*23-B*44-C*04-DRB1*07-DQB1*02 was less common in Russians of St. Petersburg (0.0246 vs. 0.0062, p = 0.01). An analysis of genetic distances between populations showed that Russians of Nizhny Novgorod, as well as Russian residents of Moscow and Belarus were the closest to Russians living in St. Petersburg. The genetic distance between Russians living in St. Petersburg and the residents of Rostov-on-Don and Chelyabinsk Region is a bit greater. Comparison of genetic distances between the various Slavic populations showed that the Eastern (Belarusians, Russians) and Western (Poles, Slovaks, Czechs) Slavs are closest to each other. The Southern Slavic folks (Serbs, Croats, Macedonians) are more genetically remote. The results of present research can be used to study the processes of ethnogenesis, searching for associations between HLA and diseases, and also being applied in practical activities of hematopoietic stem cell donor registries.

Oil palm (Elaeis guineensis Jacq.) is a plantation commodity that has an important role in various aspects of life in Indonesia, especially the domestic economy. This is supported by the increasing demand for world palm oil for food needs (edible oil), industrial (oleochemical), and alternative energy sources based on biodiesel. The development of the palm oil industry requires several efforts to achieve increased national productivity, one of which is the utilization of quality seeds supported by the availability of genetic resources (germplasm) that have a high level of genetic diversity. Efforts that can be made for the development of oil palm in Indonesia is through the characterization of oil palm intoduction from abroad. Considering this, further research on genetic distance analysis of palm oil accession introduced from Cameroon is based on morphological characters to produce parent elders that can produce heterosis properties.&#x0D; Research conducted at Seed Garden of Adolina PTPN IV and laboratory analysis of plant material of Palm Oil Research Center located on Jl. Brigjen Katamso No. 5, Medan, North Sumatera, which lasted from December 2017 to February 2018. Single observations were made on 47 accession palm oil from Cameroon planted on December 2010 and ten trees from PPKS 540 variety for compare. Data analysis used was a description of the plant to know the character of plant morphology as well as genetic distance analysis. Analysis of genetic distance using PCA analysis and cluster analysis.&#x0D; The results obtained are based on the results of PCA (Principal Component Analysis) reduce the observed character into six major components that have eigen value &gt; 1 and able to explain the material diversity tested for 73.8%. Based on the cluster analysis obtained the genetic distance of 47 accessions of palm oil from Cameroon by 57%. It can be concluded that, when the genetic distance between accessions is further away, the larger the genetic variability between the observed characters. If the genetic diversity is wider the greater the chance for successful selection in increasing the desired gene frequency.

Fasciola hepatica, F. gigantica and “intermediate” forms of Fasciola species, are responsible for fascioliasis in ruminant animals and humans in many countries. There are two forms: “natural/admixed” and “introgressive” hybridization. Vietnam is a "hot spot" country, where the “hybrid” Fasciola forms have been found nationwide. Determination of phylogenetic relationships and genetic distance of these hybrid forms with those in family Fasciolidae and class Trematoda (Phyllum Platyhelminthes) is necessary to confirm their taxonomic classification. In this study, we sequenced the ITS1 and ITS2 for discrimination of two kinds of hybrid Fasciola mentioned above. The deduced amino acid sequences of the entire mitochondrial genes, cytochrome b (cob), nicotinamide dehydrogenase 1 (nad1) and cytochrome oxidase 1 (cox1), from two hybrid Fasciola spp. including Fsp-DL11-VN (from buffalo, admixed hybrid), Fsp-FH1-VN (from human, introgressive hybrid) and “pure” F. gigantica (Fgig-T4V-VN, from cattle) were obtained and combined (cob+nad1+cox1). These sequences were used as markers for phylogenetic analysis together with 28 representative isolates/species of Fasciolidae and Trematoda. Genetic distances between 13 isolates/species in the family Fasciolidae have also been determined to accurately account for their species-relationships. As results, pairwise genetic distance calculation showed that the distance rate was only 0.4% – 0.7% between Fasciola spp. hybrids of Vietnam and China, slightly higher, 1.3 – 2.0% with “pure” F. gigantica, whilist this rate was quite high compared with F. hepatica (5.7% – 5.9%), with Fasciolopsis buski (20.6% – 21.0%), and two other fasciolids, Fasciola jacksoni and Fascioloides magna (11.0% – 12.6%). The phylogenetic tree of 31 strains/species showed 5 distinct groups, corresponding to 5 families, ie., Fasciolidae, Echinostomatidae, Echinochasmidae, Heterophyidae, Opisthorchiidae and an outgroup, Schistosomatidae. Two "hybrid" Fasciola species of Vietnam (Fsp-FH1-VN and Fsp-DL11-VN) grouped with the reference "hybrid" Fsp-GHL-CN strain of China; and “pure” Fgig-T4V-VN with the two “pure” F. gigantica, Fgig-Bali-ID (Indonesia) and Fgig-GX-CN (China). These results confirmed that “hybrid” Fasciola spp. were of the maternally inherited mitochondrial lineage from F. gigantica.