Phylogenetic Relationship and Molecular Divergence Dating Using SRY Gene Polymorphism about Four Ladoum Sheep Lineages in Senegal

Animal genetic resources are playing a vital role in livestock production and are essential to food security. The present study aims to contribute to a better understanding genetic local sheep breeds and to elucidate the phylogenetic relationships through the evolution of the SRY gene in four different lineages of Ladoum sheep raised in Senegal. After a brief analysis of genetic diversity, the phylogenetic relationships and molecular dating were inferred through haplotype networks and four phylogenetic reconstruction methods. The different haplotype networks are constructed with NETWORK ver. 5.0.0.0 using the Median-Joining method. Phylogenetic trees were reconstructed using neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference. The robustness of the nodes in phylogenetic trees of the three first methods was assessed by 1000 bootstraps. For Bayesian inference, the posterior probability distribution of the trees was estimated by 4 MCMC chains. 5,000,000 generations were performed for each of the chains by sampling the different parameters every 1000 generations. Results show a low polymorphism. Haplotypic diversity is much higher than the average nucleotide divergence between all pairs of haplotypes. The majority and central haplotype indicates a close relationship between “Batling” and “Tyson” individuals. “Birahim” lineage is very distinct from the rest. Phylogenetic trees confirm two genetically separate clades between “Birahim” and the other lineages. The period of divergence between “Birahim” lineage versus the common ancestor of the other three lineages was 2504 years ago. The polyphyly revealed in “Birahim” lindicates that this lineage does not contain the common ancestor of all individuals who compose it. It could therefore be derived from two or more sheep breeds with a common ancestor, Ovis aries. The monophyletic clade appears to be a group including a common ancestor and all of its genetic descendants. This group, bringing together the other three lineages, is in the process of being structured into sub-lineages. This study is the first to show that there are only two genetic lines within ladoum sheep in Senegal.

Studies on Phylogenetic Relationship of Sheep Population in East and South of Central Asia

This paper was based on the Hu sheep in China, after collecting the same data about 9 Asia sheep populations and 5 European sheep (breeds in Japan) populations. It clustered 15 populations in terms of the gene frequency of 10 loci and 33 allele in blood enzyme and other protein variations. The result of Hierarchy Clustering showed that the sheep populations in the East and South of Central Asia could be classified into three genetic groups: Mongolia sheep, South Asia sheep and European sheep, and the Hu sheep belonged to Mongolia sheep.

High gene flows promote close genetic relationship among finewool sheep populations(Ovis aries) in China

The aim of our present study was to construct genetic structure and relationships among Chinese fine-wool sheep breeds. 46 individuals from 25 breeds or strains were genotyped based on the Illumina Ovine 50K SNP array. Meanwhile, genetic variations among 482 individuals from 9 populations were genotyped with 10 microsatellites. In this study, we found high genetic polymorphisms for the microsatellites, while 7 loci in the Chinese superfine Merino strain （Xinjiang types） （CMS） and 5 loci in Gansu alpine superfine-wool sheep strain （GSS） groups were found deviated from Hardy-Weinberg equilibrium （HWE）. Genetic drift FsT=0.019 （P〈0.001） and high gene flows were detected in all the 7 fine-wool sheep populations. Phylogenetic analysis showed fine-wool sheep populations were clustered in a group independent from the Chinese indigenous breeds such that the 7 fine-wool sheep clustered distinct from Liangshan semifine-wool sheep （LS） and Hu sheep （HY） reflected by different population differentiation analyses. Overall, our findings suggested that all fine-wool sheep populations have close genetic relationship, which is consistent with their breeding progress. These populations, therefore, can be regarded as open-breeding populations with high levels of gene flows. Furthermore, the two superfine-wool strains, viz., CMS and GSS, might be formed by strong artificial selection and with frequent introduction of Australian Merino. Our results can assist in breeding of superfine-wool sheep and provide guidance for the cultivation of new fine-wool sheep breeds with different breeding objectives.

Phylogenetic Relationships in Genus Arachis Based on SSR and AFLP Markers

Fourteen wild species of different sections in the genus Arachis and 24 accessions of the AABB allotetraploid A. hypogaea （cultivated peanut） from several countries which belong to different botanical varieties, were analyzed by SSR and AFLP marker systems. The assay-units per system needed to distinguish among all the tested accessions were at least five for SSR or two for AFLP. The genetic distance detected by the SSR markers ranged from 0.09 to 0.95, and the mean was 0.73; and the genetic distance detected by the AFLP markers ranged from 0.01 to 0.79 with an average of 0.42. All the tested peanut SSR primer pairs were multilocus ones, and the amplified fragments per SSR marker in each peanut genome ranged from 2 to 15 with the mean of 4.77. The peanut cultivars were closely related to each other, and shared a large numbers of SSR and AFLP fragments. In contrast, the species in the genus Arachis shared few fragments. The results indicated that the cultivated peanut （A. hypogaea L.） varieties could be partitioned into two main groups and four subgroups at the molecular level, and that A. duranensis is one of the wild ancestors of A. hypogaea. The lowest genetic variation was detected between A. cardenasii and A. batizocoi, and the highest was detected between A. pintoi and the species in the section Arachis. The relationships among the botanical varieties in the cultivated peanut （A. hypogaea L.） and among wild species accessions in section Arachis and those in other sections in the genus Arachis were discussed.

A preliminary analysis of phylogenetic relationships of Arundinaria and related genera based on nucleotide sequences of nrDNA （ITS region） and cpDNA （trnL-F intergenic spacer）

Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS) and the cpDNA trnL-F intergenic spacer (IGS). Comparison with trnL-F IGS sequence, the ITS region provided the higher number of parsimony informative characters, and the interspecific variation of the ITS sequence was higher than that of the trnL-F IGS sequence.The tree obtained by combining both sets of data showed that the species sampled in Arundinaria and the related genera were monophyletic and divided into two clades. The relationships and positioning of all the taxa surveryed (including A. oleosa, A. hsienchuensis, A. chino, A. amara, A. yixingensis, A. amabilis, A. fortunei, A. pygmaea, A. gramineus, A. fargesii, A. faberi, A. hupehense, Pseudosasa japonica cv. Tsutsumiana, P. japonica and Brachystachyum densiflorum) were also discussed. The results from the sequences were broadly consistent with morphological characters, appearing all these taxa sampled belong to the genus of Arundinaria. The topologies of the trees generated from individual data and the combined data were similar.

Phylogenetic Relationships of Sorghum and Related Species Inferred from Sequence Analysis of the nrDNA ITS Region

Analysis of phylogenetic and evolution in six species of Sorghum was based on internal transcribed spacer （ITS） sequences in nuclear ribosomal DNA. Results showed that the length of the ITS regions among the six species ranged from 588 to 589 bp and the contents of G＋C in ITS （ITS1 ＋5.8S＋ITS2） regions ranged from 60.27 to 61.05%; the length of ITS1 ranged from 207 to 208 bp and the contents of G ＋ C in the ITS 1 regions ranged from 53.91 to 61.54%. The length of the 5.8S rDNA and ITS2 regions in the six species was 164 and 217 bp respectively, and the contents of G ＋ C ranged from 56.10 to 58.54% in the 5.8S rDNA region and 66.36 to 67,28% in the ITS2 region. Among regions of ITS, ITS1, ITS2, and 5.8S, the best sequence for genetic relationship analysis in the six species was the ITS region. On the basis of the Jaccard coefficient and phylogentic tree, S. sp. was more related to S, propinguum than to other species. This was consistent with the fact that S. sp. is derived from S. propinguum. From the phylogenetic tree based on ITS1, S. halepense, silk sorghum and S. sudanense, are identical in the ITS 1 sequence, whereas the phylogenetic tree based one shows that S. sudanense has a closer genetic association with S. almum rather than with S. halepense and silk sorghum.

Phylogenetic relationships among five species of Armeniaca Scop. (Rosaceae) using microsatellites (SSRs) and capillary electrophoresis

The genus Armeniaca Scop. is well known for its popular cultivated edible fruit trees such as Armeniaca vul- garis Lam. and ornamental flowers such as A. mume Sieb. Another species, A. cathayana Fu et al., one of six important dry fruits （kernel-using apricot）, is cultivated for its edible seeds in North China. In the present study, DNA from 70 individuals of A rmeniaca, including 38 of A. cathayana, 18 ofA. vulgaris, 12 ofA. sibirica, 1 ofA. dasycarpa and 1 of A. mume, was extracted and analyzed using microsatellites and capillary electrophoresis. For 20 polymorphic loci selected, 339 alleles and 140.7 effective alleles were detected. The number of alleles per locus ranged from 8 to 28, with an average of 16.95 alleles per locus. The observed heterozygosity （Ho） and the expected heterozygosity （He） ranged from 0.427 to 0.971 and from 0.737 to 0.912, respectively. The polymorphism information content varied from 0.708 to0.905, with an average of 0.827. Based on the genetic similarity among 70 individuals, a UPGMA was used to establish the phylogenetic relationships. The taxonomic positions among five species were clearly revealed, and A. cathayana was more closely related to A. vulgaris than to A. sibirica. The results will provide a scientific basis for research on the taxonomy, germplasm resources and breeding ofArmeniaca, especially for A. cathayana.

Investigation of Phylogenetic Relationship among Three Species of Channa Based on ITS Sequence Analysis

[ Objective ] This study aimed to analyze genetic variation of ribosomal ITS region sequences in Channa argus, C moculata and C. asiatica, and to in- vestigate the phylogenetic relationship among Charma species based on ITS sequences. [ Method] ITS sequences of three Channa species were amplified by PCR, cloned and assembled to obtain the full length of ITS sequences. [ Result] The full length of ITS sequences of C. argus, C. maculata and C. asiatica was 902, 927, and 902/903 bp, respectively. ITS sequences of C. argus, C. maculata and C. asiatica exhibited higher G ＋ C （72%） than A ＋ T. Interspecific nucleotide differences were significantly greater than intraspecific differences of these three Channa species. Thus, these remarkably differential ITS fragments could be used to identify C. argus, C. maculata and C. asiatica. Phylogenetic tree constructed by Neighbor-joining and Maximum Likehood methods showed that C. argus shared the lowest genetic distance with C. maculata and the highest genetic distance with C. asiatica. [ Conclusion] This study provided reference for classification, i- dentification, phylogenetic analysis and interspecific hybridization of Channa species.

Evaluation of the effect of genetic diversity and phylogenetic relationships on different strains of Staphylococcus aureus in clinical specimens

Introduction:Staphylococcus aureus is one of the main pathogens in humans.Also,this bacterium can be colonized in the nose.The spa gene is present in all strains of Staphylococcus aureus(S.aureus)and can be used to identify species and toxins such as Panton-Valentine Leukocidin(PVL)that can affect a wide range of skin,soft tissue,and necrotizing pneumonia.Arthritis and life-threatening infections.This study aimed to investigate the effect of genetic diversity and phylogenetic relationships on different strains of Staphylococcus aureus in clinical specimens.Methods:This review study was conducted in 2021 by searching for keywords such as genetic diversity,phylogenetics,and Staphylococcus aureus in reputable databases such as pub med and google scholar.Finally,30 articles were found,of which 30 articles were used out of 26 articles.Results:In general,23%and 18%of health care workers and patients were carriers,respectively.The incidence of methicillin-resistant Staphylococcus aureus(MRSA)is higher in the relevant population.The molecular types of MRSA isolates indicate that the most common virulence gene is Hla,and the most common type of SCCmec is SCCmec type III.Conclusion:Sites with high risk of Staphylococcus aureus should be highly protected,and relevant personnel should be paid attention and health management.

Phylogenetic Relationships in the Genus <i>Spiraea</i>(Rosaceae) Inferred from the Chloroplast DNA Region, <i>trn</i>L-<i>trn</i>F

The 26 taxa of genus Spiraea (Rosaceae) in 14 Korean taxa and four taxa of them doubled in the world itself were collected and investigated phylogenetic relationships within these taxa using the chloroplast trnL-trnF region. Sequence variation within the genus Spiraea was mostly due to insertion/deletion. Total alignment sequence of trnL-trnF region in genus Spiraea was 1004 positions, of which 126 were parsimony-informative, 149 variable, 23 singleton, and 847 constant characters. The base furtherance did not show a significant difference among total taxa. Although many taxa of genus Spiraea were well separated each other, many branches were not congruent with the taxon positions with botanical names. In addition, sequences of the chloroplast trnL-trnF region for same species are different from each other according to authors. The taxonomic identification of genus Spiraea are in need of revision.

Phylogenetic Relationships of <i>Termitomyces aurantiacus</i>Inferred from Internal Transcribed Spacers DNA Sequences

Fungus-growing termites cultivate species of the mutualistic basidiomycete genus Termitomyces on a substrate called the fungal comb. Identification of fungal species based on morphological features is complicated, tedious, and prone to errors. As an alternative, nuclear ribosomal DNA sequences consisting of the internal transcribed spacers (ITS1 and ITS2) and 5.8S rDNA were used to identify Malaysian isolates of Termitomyces sp. The morphological characteristics and molecular data indicate that Malaysian Termitomyces isolated is clearly monophyletic and belongs to the Tricholomataceae family. The Malaysian isolates analyzed in this study represent the termite fungus species called T. aurantiacus.

Intraspecific Relationship of Sheep Based on Mitochondrial Cytochrome b Gene

[ Objective] To preliminarily explore the intraspecific relationship of sheep based on cytochrome b （ Cyt b） gene of mitochondrial DNA （mtDNA）. [Method] The Cyt b gene sequences in 112 sheep individuals of two local sheep breeds were amplified by PCR. Then the amplified products were digested with EcoR I and analyzed by restriction fragment length polymorphism （RFLP）. [ Result] As many as 56 samples from Tan sheep and 56 samples from Wadi sheep were detected. The results showed that the amplified Cyt b gene in 51 individuals of Tan sheep had one EcoR I restriction site and no EcoR I restriction site in other five individuals, thus the Cyt b gene in Tan sheep showed two restriction morphs; the Cyt b gene in all 56 individuals of Wadi sheep had one EcoR I restriction site and showed one restriction morph. [ Conclusion] The polymorphism of mitochondrial Cyt b gene in Tan sheep and Wadi sheep is poor, and the Cyt b gene in sheep breeds is very conservative. Therefore, using Cyt b gene as gene marker to study the intraspecific relationship of sheep has some limitations.

Sequence Divergence of Mitochondrial 12S rRNA Gene and Phylogenetic Relationship Between Rattus rattus Sladeni and Rattus rattus Hainanicus

The appearance and hair color between these two subspecies Rattus rattus Sladeni and R.r. Hainanicus are similar to each other. Their most major distinctive characteristic is the length ratio of tail to body. However, this characteristic was unstable in some measuring records. In Guangdong, R.r. Hainanicus is restrictedly distributed in the west region, and R.r. Sladeni is widely distributed in the other regions of this province. In this study, we detected the sequences of mitochondrial 12S rRNA gene fragments of 9 samples from R.r. Hainanicus and R.r. Sladeni (Longmen and Hong Kong populations). These 385 nucleotide positions of 12S rRNA gene fragment include 26 variable sites and 14 parsimony-informative sites. 3 insertion/deletion sites are observed. The phylogenetic relationships among these samples were constructed by Neighbor-joining and Maximum parsimony methods. The analysis shows that R.r. Hainanicus is more closely relative to the Longmen population of R.r. Sladeni than to the Hong Kong population of R.r. Sladeni. The sequencing analysis of 12S rRNA gene fragments is not agreement on the classification of subspecies R. r. Hainanicus inferred from the morphology and geographical distribution. The morphological variation of R.r. Hainanicus should result from the natural selection, which causes local adaptation and geographic isolation.

Phylogenetic relationships among small <i>barbus</i>,<i>barbus</i>(actinopterygii: Cyprinidae) from malagarasi and Pangani river basins, Tanzania

The phylogenetic relationships among “Barbus” species (Barbus jacksonii, B. paludinosus and B. trimaculatus) from Malagarasi and Pangani River systems were examined by partial mitochondrial cytochrome b (cyt.b) gene. Sequences of the same samples from elsewhere in Africa obtained from the South African Institute of Aquatic Biodiversity (SAIAB’s) collection were also included in the analysis. Molecular technique was necessary due to phenotypic plasticity and extensive overlap of morphological features among the “Barbus species”. The findings of this study revealed that B. paludinosus from hale and Pangani populations occurred in two distinct genetic lineages though separated by a distance of approximately 10 km apart. Similar results were also noted amongst the population of B. paludinosus in Songati and Muumbara located on Lake Sagara in Malagarasi River basin. B. trimaculatus and B. jacksonii were indistinguishable such that it is envisaged that the two species are one and the same. The Barbus spp. from Africa included in the current study showed genetic affinity to neither European Barbus spp. nor South African redfins of the Pseudobarbus to conclude that the studied species of barbs are taxonomically quite different that needs further investigation to warrant renaming.

Phylogenetic analysis of 48 gene families revealing relationships between Hagfishes, Lampreys, and Gnathostomata

It has become clear that the extant vertebrates are divided into three major groups, that is, hagfishes, lampreys, and jawed vertebrates. Morphological and molecular studies, however, have resulted in conflicting views with regard to their interrelationships. To clarify the phylogenetic relationships between them, 48 orthologous protein-coding gene families were analyzed. Even as the analysis of 34 nuclear gene families supported the monophyly of cyclostomes, the analysis of 14 mitochondrial gene families suggested a closer relationship between lampreys and gnathostomes compared to hagfishes. Lampreys were sister group of gnathostomes. The results of this study supported the cyclostomes. Choice of outgroup, tree-making methods, and software may affect the phylogenetic prediction, which may have caused much debate over the subject. Development of new methods for tackling such problems is still necessary.

Phylogenetic and morphometric relationships between two species of genus Auxis from the South China Sea and Java Sea

This study was aimed at examining the phylogenetic and morphometric relationship of frigate tuna（Auxis thazard） and bullet tuna（Auxis rochei） using mt DNA D-loop（control） region sequences and truss measurements,respectively. Maximum-likelihood（ML） tree and median-joining network showed that haplotypes from Auxis populations grouped separately. Discriminant function analyses and non-metric multidimensional scaling of morphometric data showed that bullet and frigate tuna were differed mainly with respect to truss measurements on the anterior region, suggesting adaptation to different diets available in different environments. Historic demographic analyses of sequence data showed that both bullet and frigate tuna had not undergone a significant sudden population expansion recently. Non-significant value of Tajimas＇ s D and Fu＇s F_S were indicated an effective large and stable population size for longer period of both species in South China Sea and Java Sea species. This study gives first report on the complementary relationship between morphometric and genetic analysis in stock discrimination of genus Auxis.

Molecular phylogenetic relationship of Epinephelus based on sequences of mtDNA Cty b

The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae,Epinephelinae and seven endemic species of groupers—Epinephelus awoara,E.brunneus,E.coioides,E.longispinis,E.sexfasciatus,E.spilotoceps and E.tauvina in China.The seven endemic species and other seven foreign species of groupers—E.aeneus,E.caninus,E.drummondhayi,E.haifensis,E.labriformis,E.marginatus and E.multinotatus from the GenBank were combined and analysed as ingroup,while Variola louti was used as outgroup.We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method(MP)and neighbor-joining method(NJ)respectively.The results were as follows:(1)As to the base composition of mtDNA Cyt b sequence(402 bp)of 14 species of Epinephelus,the content of(A+T)was 53.6%,higher than that of(G+C)(46.4%).The transition/transversion ratio was 4.78 with no mutation saturation.(2)The cluster relationships between E.awoara and E.sexfasciatus,E.coioides and E.tauvina,E.longispinis and E.spilotoceps were consistent with phenotypes in taxonomy.(3)In the phylogenetic tree,the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean,which suggested that the Cyt b sequences of Epinephelus were highly conserved.This may be attributed to the coordinate evolution.(4)In wel1-bred mating or heredity management,mating Epinephelus of the same branch should be avoided.It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species.

The complete mitochondrial genome of Parachiloglanis hodgarti and its phylogenetic position within Sisoridae

The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized,which is the first mitogenome of the genus Parachiloglanis within Sisoridae.The mitogenome is 16511-bp long and included 13 protein-coding genes,22 transfer RNAs,two ribosomal RNAs,and one control region.The genome composition was A+T biased(58.64%)and exhibited a positive AT-skew(0.095)and a negative GC-skew(-0.283).Compared with other Sisoridae fishes,the characteristics of nucleotide skews,codon usage,and amino acid usage of the P.hodgarti mitogenome are more similar to those of non-Glyptosternoid fishes.Furthermore,the phylogenetic trees show that Sisoridae fishes fall into four major clades and P.hodgarti(CladeⅠ)is basal to the Sisoridae family,forming a sister clade to the Glyptosternoids(CladeⅣ).The topological structures constructed in this study raised doubts over the traditional classification system.These results will help better understand the feature s of the P.hodgarti mitogenome and provide a reference for further phylogenetic research on Sisoridae species.

Phylogenetic relationships of Cyprinidae (Teleostei:Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1

The family Cyprinidae is widely distributed in East Asia, and has the important phylogenetic signifi- cance in the fish evolution. In this study, the 5′ end partial sequences (containing exon 1, exon 2 and indel 1) of S6K1 gene were obtained from 30 representative species in Cyprinidae and outgroup using PCR amplification and sequencing. The phylogenetic relationships of Cyprinidae were reconstructed with neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian meth- ods. Myxocyprinus asiaticus (Catostomidae) was assigned to the outgroup taxon. Similar phylogenetic relationships within the family Cyprinidae were achieved with the four analyses. Leuciscini and Barbini were monophyletic lineages respectively with the high nodal supports. Leuciscini comprises Hy- pophthalmichthyinae, Xenocyprinae, Cultrinae, Gobioninae, Acheilognathinae and East Asian species of Leuciscinae and Danioninae. Monophyly of East Asian clade was supported with high nodal support. Barbini comprises Schizothoracinae, Barbinae, Cyprininae and Labeoninae. The monophyletic lineage consisting of Danio rerio, D. myersi, and Rasbora trilineata was basal in the tree. In addition, the large fragment indels in intron 1 were analyzed to improve the understanding of Cyprinidae relationships. The results showed that the large fragment indels were correlated with the relations among species. Some conserved regions in intron 1 were thought to be involved in the functional regulation. However, no correlation was found between sequence variations and species characteristic size.