scholarly journals Detection of 16S mitochondrial sequence polymorphism and haplotype network of Ophiocara porocephala (Valenciennes, 1837) from Tekolok Estuary (NTB, Indonesia) using DnaSP and NETWORK

2020 ◽  
Vol 28 ◽  
pp. 01002
Author(s):  
Tuty Arisuryanti ◽  
Yenita Rumahorbo ◽  
Febrina Amaliya Rha’ifa ◽  
Lukman Hakim
Keyword(s):  
Genetic Variation ◽  
Genetic Relationship ◽  
Sequence Data ◽  
Haplotype Network ◽  
Neighbor Joining ◽  
Likelihood Methods ◽  
Maximum Likelihood Methods ◽  
Pcr Method ◽  
Gene Data ◽  
Close Genetic Relationship

The two genetic software, DnaSP and NETWORK, is commonly used to analyse gene polymorphism and haplotype network which is useful for the understanding pattern of genetic variation and genetic relationship. In this study, the two software were applied to detect polymorphism of 16S sequence gene of Ophiocara paracephala from Tekolok Estuary (NTB, Indonesia) which has not been investigated. This study used a PCR method with 16Sar and 16Sbr primers. The results revealed two haplotypes and two variable sites with one parsimony informative within O.paracephala from Tekolok Estuary population. Next, if the 16S sequence data of O.paracephala from Tekolok Estuary was combined with the 16S gene data of O.paracephala from GenBank, three haplotypes were detected with five variables sites and one parsimony informative. This finding showed intra-population and intraspecific genetic variation of O.paracephala. In addition, haplotype network using NETWORK and a phylogenetic tree using Neighbor Joining and Maximum Likelihood methods exhibited that O.paracephala from Tekolok Estuary has a close genetic relationship with O.paracephala from Japan.

scholarly journals Genetic Classification of “Rickettsia heilongjiangii” and “Rickettsia hulinii,” Two Chinese Spotted Fever Group Rickettsiae

2000 ◽  
Vol 38 (9) ◽  
pp. 3498-3501 ◽  
Author(s):  
J. Z. Zhang ◽  
M. Y. Fan ◽  
Y. M. Wu ◽  
P. E. Fournier ◽  
V. Roux ◽  
...  
Keyword(s):  
Spotted Fever ◽  
Phylogenetic Position ◽  
Spotted Fever Group ◽  
Neighbor Joining ◽  
Likelihood Methods ◽  
Genetic Classification ◽  
Repeat Units ◽  
Statistical Bootstrap ◽  
Maximum Likelihood Methods

To determine the phylogenetic position of two new rickettsial strains isolated from ticks in China, 16S ribosomal DNA,gltA, and ompA (apart from the tandem repeat units) genes were amplified by PCR and sequenced. The phylogenetic relationships between these strains and other rickettsiae were inferred from the comparison of sequences of the three genes by the parsimony, neighbor-joining, and maximum-likelihood methods. The results demonstrated that the 054 strain, a rickettsia pathogenic in humans, and the HL-93 strain were related and clustered together withRickettsia japonica. Significant statistical bootstrap values (100 and 92%) supported the nodes in this cluster. Based on previous genotypic and antigenic data and the phylogenetic analysis presented here, the 054 and HL-93 strains should be considered as new species, and we formally propose that they be named “Rickettsia heilongjiangii” and “Rickettsia hulinii,” respectively.

scholarly journals Genome size and endopolyploidy evolution across the moss phylogeny

2019 ◽  
Vol 125 (4) ◽  
pp. 543-555 ◽  
Author(s):  
Jillian D Bainard ◽  
Steven G Newmaster ◽  
Jessica M Budke
Keyword(s):  
Genome Size ◽  
Dna Content ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Likelihood Methods ◽  
Moss Species ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Maximum Likelihood Methods ◽  
Ancestral Character States

Abstract Background and Aims Compared with other plant lineages, bryophytes have very small genomes with little variation across species, and high levels of endopolyploid nuclei. This study is the first analysis of moss genome evolution over a broad taxonomic sampling using phylogenetic comparative methods. We aim to determine whether genome size evolution is unidirectional as well as examine whether genome size and endopolyploidy are correlated in mosses. Methods Genome size and endoreduplication index (EI) estimates were newly generated using flow cytometry from moss samples collected in Canada. Phylogenetic relationships between moss species were reconstructed using GenBank sequence data and maximum likelihood methods. Additional 1C-values were compiled from the literature and genome size and EI were mapped onto the phylogeny to reconstruct ancestral character states, test for phylogenetic signal and perform phylogenetic independent contrasts. Key Results Genome size and EI were obtained for over 50 moss taxa. New genome size estimates are reported for 33 moss species and new EIs are reported for 20 species. In combination with data from the literature, genome sizes were mapped onto a phylogeny for 173 moss species with this analysis, indicating that genome size evolution in mosses does not appear to be unidirectional. Significant phylogenetic signal was detected for genome size when evaluated across the phylogeny, whereas phylogenetic signal was not detected for EI. Genome size and EI were not found to be significantly correlated when using phylogenetically corrected values. Conclusions Significant phylogenetic signal indicates closely related mosses have more similar genome sizes and EI values. This study supports that DNA content in mosses is defined by small genomes that are highly endopolyploid, suggesting strong selective pressure to maintain these features. Further research is needed to understand the functional significance of DNA content evolution in mosses.

scholarly journals Molecular identification of Rosa x damascena growing in Taif region (Saudi Arabia)

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Sayed Amer ◽  
Salih A. Basaid ◽  
Esmat Ali
Keyword(s):  
Saudi Arabia ◽  
Maximum Likelihood ◽  
Genetic Distance ◽  
Molecular Identification ◽  
Maximum Parsimony ◽  
Rooted Tree ◽  
Tree Topology ◽  
Neighbor Joining ◽  
Likelihood Methods ◽  
Maximum Likelihood Methods

A fragment of 772 bp of the chloroplast maturase K gene was amplified and sequenced for <em>Rosa x damascena trigintipetala</em> variety growing in Taif region of Saudi Arabia. The data were aligned with their counterparts of other varieties already found in the Genbank database and were analyzed by maximum-parsimony, neighbor-joining and maximum-likelihood methods and a single rooted tree was executed. <em>R. x damascena trigintipetala</em> was paraphyletic where one sample [A] clustered with all varieties while the second [B] was basal. <em>R. x damascena</em> was sister to <em>R. x chinensis semperflorens</em> with the later being basal. <em>R. x damascena gori</em> was basal for all taxa studied. <em>R. moschata</em> was inside the clade of <em>R. x damascena</em>. Hybridization could be possible among <em>R. damascena, R. chinensis</em> and <em>R. moschata</em>. The genetic distance and tree topology indicated that [A] variety could be originated from <em>R. moshata</em> while [B] could be originated from gori or <em>R. chinensis semperflorens</em>. We, therefore, may consider that <em>R. x damascena gori</em> or <em>R. chinensis</em> could be the origin of all nowadays <em>R. x damascena</em> varieties.

Molecular review of the genus Panaspis sensu lato (Reptilia: Scincidae) in Cameroon, with special reference to the status of the proposed subgenera

Zootaxa ◽  
2005 ◽  
Vol 863 (1) ◽  
pp. 1 ◽  
Author(s):  
ANDREAS SCHMITZ ◽  
IVAN INEICH ◽  
LAURENT CHIRIO
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Inference ◽  
12S Rrna ◽  
Rrna Gene ◽  
Likelihood Methods ◽  
Morphological Studies ◽  
The Status ◽  
Maximum Likelihood Methods ◽  
Taxonomic Changes ◽  
Mitochondrial 12S Rrna

The scincid taxa connected to the genus Panaspis sensu lato have undergone various taxonomic changes based mainly on morphological studies in the last century, but their true relationships are still far from clear. In the present study we applied Bayesian, maximum parsimony, and maximum likelihood methods of phylogenetic inference to mitochondrial 12S rRNA and 16S rRNA gene fragments to examine the degree of genetic variation within the genus. We found considerable genetic differentiation between the different proposed subgenera. Similarly, we could show that two species considered to be part of the former subgenus Leptosiaphos are in reality genuine members of the genus Lacertaspis. Based on our results we propose the recognition of the four former subgenera as full genera, and we identify several additional, possibly subgeneric, lineages within the different newly recognized full genera.

scholarly journals DNA Barcode of Barred Mudskipper (Periophthalmus argentilineatus Valenciennes, 1837) from Tekolok Estuary (West Nusa Tenggara, Indonesia) and Their Phylogenetic Relationship with Other Indonesian Barred Mudskippers

2021 ◽  
Vol 6 (2) ◽  
pp. 59702
Author(s):  
Febrina Amaliya Rha'ifa ◽  
Deiandra Jasmine Audrea ◽  
Lukman Hakim ◽  
Tuty Arisuryanti
Keyword(s):  
Genetic Relationship ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Single Species ◽  
Universal Primers ◽  
Human Consumption ◽  
Accurate Identification ◽  
Mangrove Ecosystems ◽  
Pcr Method ◽  
Close Genetic Relationship

Barred mudskipper (Periophthalmus argentilineatus) has a potency to be developed as protein for human consumption and ornamental fish. The fish also has an important role in mangrove ecosystems. Nevertheless, many barred mudskippers have been considered a cryptic species. Therefore, accurate identification is needed to clarify species identification of the barred mudskipper using DNA barcoding.  This research aimed to identify barred mudskippers from Tekolok Estuary (East Lombok, West Nusa Tenggara, Indonesia) using COI mitochondrial gene as a DNA barcode and analyze genetic relationship with other barred mudskippers from several regions of Indonesia recorded in GenBank. This study used a PCR method with universal primers FishF2 and FishR2.  The data was then analysed using DNASTAR, BLAST, Mesquite, MEGA, DnaSP, BEAST, GenAlEx, and NETWORK. The results revealed that barred mudskipper from Tekolok Estuary has been verified as Periophthalmus argentilineatus. The results also exhibited that P. argentilineatus from Tekolok Estuary has a close genetic relationship to P.argentilineatus from Tukad Bilukpoh (Jembrana, Bali).  In addition, phylogenetic analysis showed that P.argentilineatus from Indonesia consisted of two clades with a genetic distance of approximately 6.64%. This analysis revealed evidence of the cryptic diversity of P.argentilineatus from Indonesia. Further detailed studies are needed to clarify whether Indonesian P.argentilineatus should be categorized into more than one species or single species with several subspecies.

scholarly journals KARAKTERISASI GENETIK IKAN LELE DUMBO BERDASARKAN MARKER RAPD FINGERPRINTING

2018 ◽  
Vol 17 (1) ◽  
pp. 85
Author(s):  
Estu Nugroho ◽  
Sabara Putera
Keyword(s):  
Genetic Variation ◽  
Fresh Water ◽  
Genetic Relationship ◽  
Genetic Information ◽  
Rapd Markers ◽  
Development Program ◽  
African Catfish ◽  
Fresh Water Fish ◽  
Water Fish ◽  
Close Genetic Relationship

African catfish, namely lele dumbo, is an economically important fresh water fish in Nusa Tenggara Barat. There are three strains of African catfish that are well distributed among farmers. Genetic information of three strain catfish stocks is needed in order to sustain their development program. Genetic variations of the three strains of catfish, i.e. Sangkuriang, Masamo, Paiton has been evaluated using RAPD markers. DNA genome was extracted using phenol-chloroform methods. DNA was amplified using 20 primers (OPA 1 – 20). The results showed that three of the 20 primers have good amplification products. There was no significant genetic differences among three strains of catfish analyzed (P>0.05). Genetic variation of three African catfish stocks ranges from low to middle value. The highest genetic variation is found in strain Masamo with heterozygosity of 0.273 (with 70% polymorphism loci), followed by Sangkuriang 0.189 (60%) and Paiton 0.147 (40%). Hybrid candidates of Masamo-Sangkuriang have eterozygosity ranges between 0.256 - 0.306 (with 66.6 7 – 73.77% polymorphism loci). Strain Masamo and Paiton has more close genetic relationship than among the both and Sangkuriang.

scholarly journals BIOMETRICAL GENETICS WITH ONE OR TWO LOCI: THE INHERITANCE OF PHYSIOLOGICAL CHARACTERS IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (4) ◽  
pp. 675-693
Author(s):  
John Stewart ◽  
R C Elston
Keyword(s):  
Experimental Data ◽  
Genetic Variation ◽  
Maximum Likelihood ◽  
F1 Hybrids ◽  
Likelihood Methods ◽  
Biometrical Genetics ◽  
Naturally Occurring ◽  
Maximum Likelihood Methods ◽  
The Mean ◽  
Physiological Characters

ABSTRACT Maximum likelihood methods have been used to compare the fit of twenty different genetic models to experimental data on fourteen characters, each measured on two parental strains, F1 hybrids and both backcrosses. Although variation in all characters was continuous, differentiation between the various models was meaningful, the mean likelihood ratio between the best and worst models for each character being greater than 1O4. Models with only one or two loci were adequate to account for the observed genetic variation in eleven of the fourteen characters. These results indicate that even in species without special genetic advantages, it may be possible to identify individually some of the genes responsible for naturally-occurring variation within the range of normality.

A description of eleven new species of Agaricus sections Xanthodermatei and Hondenses collected from Tibet and the surrounding areas

Phytotaxa ◽  
2016 ◽  
Vol 257 (2) ◽  
pp. 99 ◽  
Author(s):  
Jun-Liang Zhou ◽  
Sheng-Yu Su ◽  
Hong-Yan Su ◽  
Bo Wang ◽  
Philippe Callac ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Likelihood ◽  
Sequence Data ◽  
Molecular Phylogenetic Analysis ◽  
Likelihood Methods ◽  
Maximum Likelihood Methods ◽  
Molecular Phylogenetic ◽  
Surrounding Areas ◽  
First Time

Specimens of Agaricus sections Xanthodermatei and Hondenses were collected in Tibet and the surrounding areas. All specimens were morphologically described and subjected to molecular phylogenetic analysis of the ITS and combined ITS, LSU and tef-1α sequence data using Bayesian and Maximum Likelihood methods. Twelve species were identified in this study, eleven of which were new species and one of which was identified in China for the first time. All of the identified species are described and illustrated with photo plates.

Sign in / Sign up

Export Citation Format

Share Document