scholarly journals DIAGRAM FILOGENIK HASIL SEKUENS BASA DNA MENGGUNAKAN PROGRAM MEGA-7 (MOLECULAR EVOLUTIONARY GENETICS ANALYSIS)

2017 ◽  
Vol 1 (2) ◽  
Author(s):  
Harumi Yuniarti ◽  
Bambang Cholis S ◽  
Astri Rinanti
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Genetic Basis ◽  
Sequence Data ◽  
Evolutionary Genetics ◽  
Image Data ◽  
Dna Sequence Data ◽  
Tree Diagram ◽  
Analysis Application ◽  
Relationship Of

Sequencing techniques Deoxyribonucleic Acid (DNA) at this time is a method to identify the genetic basis of living <br />beings, including to determine the accurate genetic relationship of several DNA sequence data. Kinship clearly and <br />easily can be expressed in the form of a phylogenetic tree diagram (Phylogenetic Tree). This diagram represents <br />kinship obtained from the elektroferogram process of electrophoresis sequencing of DNA bases. From some sequences <br />experimental results using sequence analysis application program gradually, starting from installing, editing, and <br />alignment so as to obtain the analysis and phylogenetic branching diagram view. This study uses a sequence analysis <br />program Mega-7 (Molecular Evolutionary Genetics Analysis) to obtain a phylogenetic diagram for high accuracy <br />and relatively easy to operate. This program can translate image data into nucleotide bases that shows the kinship of <br />the distance the nearest branch with a standard sequence. The major advantage of this program is that it can do some <br />analysis in a single program.

Generic Delimitations and Relationships of the Cape Genera Capnophyllum, Dasispermum, and Sonderina, the North African Genera Krubera and Stoibrax, and a New Monotypic Genus of the Subfamily Apioideae (Apiaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 580-594 ◽  
Author(s):  
Anthony R. Magee ◽  
Ben-Erik van Wyk ◽  
Patricia M. Tilney ◽  
Stephen R. Downie
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Monotypic Genus ◽  
North African ◽  
African Species ◽  
Dna Sequence Data ◽  
The North ◽  
Relationship Of

Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum, Dasispermum, Sonderina, and the only southern African species of Stoibrax (S. capense) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera. The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina. This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum, occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense. New combinations are formalized for Dasispermum capense, D. hispidum, D. humile, and D. tenue. An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum–Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii. This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum, analyses of DNA sequence data place Scaraboides closer to the Dasispermum–Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.

scholarly journals Helminthosporium velutinum and H. aquaticum sp. nov. from aquatic habitats in Yunnan Province, China

Phytotaxa ◽  
2016 ◽  
Vol 253 (3) ◽  
pp. 179 ◽  
Author(s):  
DAN ZHU ◽  
ZONG-LONG LUO ◽  
DARBHE JAYARAMA BAHT ◽  
ERIC.H.C. MCKENZIE ◽  
ALI H. BAHKALI ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Yunnan Province ◽  
Sequence Data ◽  
Its Sequence ◽  
Aquatic Habitats ◽  
Submerged Wood ◽  
Dna Sequence Data ◽  
A New Species

Helminthosporium species from submerged wood in streams in Yunnan Province, China were studied based on morphology and DNA sequence data. Descriptions and illustrations of Helminthosporium velutinum and a new species H. aquaticum are provided. A combined phylogenetic tree, based on SSU, ITS and LSU sequence data, place the species in Massarinaceae, Pleosporales. The polyphyletic nature of Helminthosporium species within Massarinaceae is shown based on ITS sequence data available in GenBank.

Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data

2014 ◽  
Vol 62 (3) ◽  
pp. 235 ◽  
Author(s):  
S. Safaei Chaei Kar ◽  
F. Ghanavati ◽  
M. R. Naghavi ◽  
H. Amirabadi-zade ◽  
R. Rabiee
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Group I ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Cultivated Species ◽  
Relationship Of

Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

Molecular data allow to elucidate the taxonomic placement of some Umbelliferae from Middle Asia and Afghanistan (Pinacantha, Ladyginia, Peucedanum mogoltavicum)

Phytotaxa ◽  
2018 ◽  
Vol 350 (1) ◽  
pp. 42 ◽  
Author(s):  
GALINA V. DEGTJAREVA ◽  
MICHAEL G. PIMENOV ◽  
TAHIR H. SAMIGULLIN
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Sequence Data ◽  
Molecular Data ◽  
Systematic Position ◽  
New Combination ◽  
Dna Sequence Data ◽  
Middle Asia ◽  
Molecular Phylogenetic Tree ◽  
Molecular Phylogenetic

The systematic position of three Apiaceae-Apioideae taxa, Pinacantha porandica, Ladyginia bucharica and Peucedanum mogoltavicum, from Middle Asia and Afghanistan, is clarified based on nrITS DNA sequence data. In the molecular phylogenetic tree, the monotypic Pinacantha is placed in unresolved position within the Ferulinae. Although there is no morphological information on essential characters, we propose a new position of Pinacantha porandica within the genus Ferula. As a result a new combination Ferula porandica is proposed, with a new section Pinacantha to accommodate it. The attribution of Peucedanum mogoltavicum to Ferula has been confirmed, its correct name being Ferula lithophila. The genus Ladyginia should not be included in Ferula, its closest relatives being Mozaffariania and Glaucosciadium from the Glaucosciadium Clade.

Preliminary use of DNA sequences for Dohrniphora (Diptera: Phoridae) phylogeny and taxonomy JOHN M. HASH, BRIAN V. BROWN & PAUL T. SMITH (USA)

Zootaxa ◽  
2011 ◽  
Vol 2991 (1) ◽  
pp. 13
Author(s):  
JOHN M. HASH ◽  
BRIAN V. BROWN ◽  
PAUL T. SMITH
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Male And Female ◽  
Dna Sequence Data ◽  
16S Gene ◽  
Monophyletic Lineage ◽  
Relationship Of

Phylogenetic analysis of DNA sequence data from the nuclear CAD (rudimentary) and mitochondrial NDI, COI, and 16S gene regions (2817 bp total) recovered exemplars of the genus Dohrniphora as a monophyletic lineage. The data also supported the sister-group relationship of Dohrniphora + Diplonevra and were used to associate a morphologically dissimilar male and female of the species D. ecitophila. Further, we discuss the implications of this designation and provide support for the synonymy of D. ecitophila and D. geminata as proposed by Borgmeier (1968).

Dwarf minke whales from the South Pacific share a matrilineal lineage distinct from Balaenoptera acutorostrata acutorostrata and B. a. scammoni

2019 ◽  
Vol 41 (2) ◽  
pp. 231
Author(s):  
Omar Ramirez-Flores ◽  
Alastair Birtles ◽  
Diana Pazmino ◽  
Kyall R. Zenger ◽  
Lynne Van-Herwerden
Keyword(s):  
Sequence Data ◽  
South Pacific ◽  
Nuclear Data ◽  
Minke Whale ◽  
Balaenoptera Acutorostrata ◽  
Conservation Action ◽  
Dna Sequence Data ◽  
Minke Whales ◽  
Satellite Tagging ◽  
Relationship Of

Dwarf minke whales are regarded as an undescribed subspecies of common minke whales (Balaenoptera acutorostrata), but appropriate conservation action requires taxonomic confirmation. The relationship of the Australian Great Barrier Reef (GBR) dwarf minke whale aggregation to other minke whales is unknown. This study aims to clarify the phylogenetic relationship of GBR dwarf minke whales, using partial mitochondrial DNA sequence data from 23 GBR dwarf minke whales, compared with other available minke whale sequences. GBR dwarf minke whales share haplotypes with other West South Pacific (WSP) dwarf minke whales. Satellite tagging studies corroborate these findings, indicating that GBR dwarf minke whales migrate south along the east Australian coast towards the Southern Ocean. Despite nuclear data not being available, GBR and WSP dwarf minke whales share a distinctive mitochondrial lineage compared with other common minke whales and should be managed independently of North Pacific and Atlantic Ocean common minke whale populations.

scholarly journals Darwin and Genetics

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 757-766 ◽  
Author(s):  
Brian Charlesworth ◽  
Deborah Charlesworth
Keyword(s):  
Natural Selection ◽  
Dna Sequence ◽  
Sequence Data ◽  
Evolutionary Genetics ◽  
Adequate Account ◽  
Dna Sequence Data ◽  
Recent Advances ◽  
Answering Questions

Darwin's theory of natural selection lacked an adequate account of inheritance, making it logically incomplete. We review the interaction between evolution and genetics, showing how, unlike Mendel, Darwin's lack of a model of the mechanism of inheritance left him unable to interpret his own data that showed Mendelian ratios, even though he shared with Mendel a more mathematical and probabilistic outlook than most biologists of his time. Darwin's own “pangenesis” model provided a mechanism for generating ample variability on which selection could act. It involved, however, the inheritance of characters acquired during an organism's life, which Darwin himself knew could not explain some evolutionary situations. Once the particulate basis of genetics was understood, it was seen to allow variation to be passed intact to new generations, and evolution could then be understood as a process of changes in the frequencies of stable variants. Evolutionary genetics subsequently developed as a central part of biology. Darwinian principles now play a greater role in biology than ever before, which we illustrate with some examples of studies of natural selection that use DNA sequence data and with some recent advances in answering questions first asked by Darwin.

scholarly journals Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra

MycoKeys ◽  
2018 ◽  
Vol 43 ◽  
pp. 91-113 ◽  
Author(s):  
Felix Grewe ◽  
Elisa Lagostina ◽  
Huini Wu ◽  
Christian Printzen ◽  
H. Thorsten Lumbsch
Keyword(s):  
Sequence Data ◽  
Reproductive Mode ◽  
Fungal Species ◽  
Antarctic Species ◽  
Dna Sequence Data ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Scale Population ◽  
Relationship Of ◽  
Different Levels

Neuropogonoid species in the lichen-forming fungal genus Usnea exhibit great morphological variation that can be misleading for delimitation of species. We specifically focused on the species delimitation of two closely-related, predominantly Antarctic species differing in the reproductive mode and representing a so-called species pair: the asexual U.antarctica and the sexual U.aurantiacoatra. Previous studies have revealed contradicting results. While multi-locus studies based on DNA sequence data provided evidence that these two taxa might be conspecific, microsatellite data suggested they represent distinct lineages. By using RADseq, we generated thousands of homologous markers to build a robust phylogeny of the two species. Furthermore, we successfully implemented these data in fine-scale population genomic analyses such as DAPC and fineRADstructure. Both Usnea species are readily delimited in phylogenetic inferences and, therefore, the hypothesis that both species are conspecific was rejected. Population genomic analyses also strongly confirmed separated genomes and, additionally, showed different levels of co-ancestry and substructure within each species. Lower co-ancestry in the asexual U.antarctica than in the sexual U.aurantiacoatra may be derived from a wider distributional range of the former species. Our results demonstrate the utility of this RADseq method in tracing population dynamics of lichens in future analyses.

Nerve cells of Xenoturbella bocki (phylum uncertain) and Harrimania kupfferi (Enteropneusta) are positively immunoreactive to antibodies raised against echinoderm neuropeptides

2005 ◽  
Vol 85 (6) ◽  
pp. 1519-1524 ◽  
Author(s):  
Thomas Stach ◽  
Samuel Dupont ◽  
Olle Israelson ◽  
Geraldine Fauville ◽  
Hiroaki Nakano ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Dna Sequence ◽  
Sequence Data ◽  
Nerve Cells ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Close Phylogenetic Relationship ◽  
Positive Immunoreactivity ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

The phylogenetic position of Xenoturbella spp. has been uncertain since their discovery in 1949. It has been recently suggested that they could be related to Ambulacraria within Deuterostomia. Ambulacraria is a taxon that has been suggested to consist of Hemichordata and Echinodermata. The hypothesis that X. bocki was related to Ambulacraria as well as the hypothesis of a monophyletic Ambulacraria is primarily based on the analysis of DNA sequence data. We tested both phylogenetic hypotheses using antibodies raised against SALMFamide 1 and 2 (S1, S2), neuropeptides isolated from echinoderms, on X. bocki and the enteropneust Harrimania kupfferi. Both species showed distinct positive immunoreactivity against S1 and S2. This finding supports the Ambulacraria-hypothesis and suggests a close phylogenetic relationship of X. bocki to Ambulacraria. In particular, the presence of immunoreactivity against S2 can be interpreted as a synapomorphy of Enteropneusta, Echinodermata, and Xenoturbella spp.

Inferring evolutionary processes from DNA sequence data

2019 ◽  
pp. 145-172
Author(s):  
Glenn-Peter Sætre ◽  
Mark Ravinet
Keyword(s):  
Molecular Evolution ◽  
Dna Sequence ◽  
Genetic Markers ◽  
Dna Sequences ◽  
Sequence Data ◽  
Neutral Theory ◽  
Evolutionary Genetics ◽  
Haplotype Structure ◽  
Dna Sequence Data ◽  
Neutrality Tests

The allelic evolutionary genetic models explored so far are applicable to genetic markers. However, DNA sequences harbor a lot of information about the evolutionary past that would be missed if different sequences were simply treated as different alleles. This chapter introduces some important methods and concepts applicable to the analysis of DNA-sequence data. The null models for analyzing sequence data are derived from the neutral theory of molecular evolution. Historically, however, the neutral theory has made a large impact on evolutionary genetics. Therefore, this chapter starts by reviewing its important contribution. Then, important parameters and statistics for analyzing sequence variation are introduced, including a plethora of neutrality tests. The chapter ends with a cautious focus on the powerful tool of genome scan analysis and its utility for identifying regions of the genomes potentially under selection. This includes a section on more recently derived statistics which incorporate information on haplotype structure.

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