scholarly journals The screening and identification of DNA barcode sequences for Rehmannia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hongying Duan ◽  
Wanshen Wang ◽  
Yunpeng Zeng ◽  
Mengmeng Guo ◽  
Yanqing Zhou
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Tree ◽  
Species Identification ◽  
Intraspecific Variation ◽  
Systematic Study ◽  
Dna Barcode ◽  
Barcoding Gap ◽  
Screening And Identification ◽  
Interspecific And Intraspecific Variation ◽  
Interspecific Diversity

AbstractIn this study, ITS, ITS2, matK, rbcL and psbA-trnH in Rehmannia were successfully amplified and sequenced, but some ITS sequences need to be proofread according to ITS2 sequences. Compared with rbcL, matK and psbA-trnH, ITS and ITS2 had higher mutation rate and more information sites, and ITS2 had higher interspecific diversity and lower intraspecific variation in Rehmannia, but the interspecific genetic variation of rbcL and matK was lower. Furthermore, the obvious barcoding gap was found in psbA-trnH or ITS2 + psbA-trnH, and the overlap between interspecific and intraspecific variation of ITS, ITS2 or matK was less. In addition, the phylogenetic tree based on ITS or ITS2 indicated that R. glutinosa, R. chingii or R. henryi with obvious monophyly could be successfully identified, but R. piasezkii and R. elata were clustered into one branch, R. solanifolia could not be distinguished from R. glutinosa, and R. chingii was closer to R. henryi. In phylogenetic tree based on psbA-trnH or ITS2 + psbA-trnH, cultivars and wild varieties of R. glutinosa could be distinguished, were clearly separated from other Rehmannia species, and cultivars or wild varieties of R. glutinosa could be also distinguished by matK. Taken together, ITS2 has great potential in systematic study and species identification of Rehmannia, the combination of ITS2 and psbA-trnH might be the most suitable DNA barcode for Rehmannia species.

scholarly journals A review of the taxonomy of spiny-backed orb-weaving spiders of the subfamily Gasteracanthinae (Araneae, Araneidae) in Thailand

ZooKeys ◽  
2021 ◽  
Vol 1032 ◽  
pp. 17-62
Author(s):  
Kongkit Macharoenboon ◽  
Warut Siriwut ◽  
Ekgachai Jeratthitikul
Keyword(s):  
Phylogenetic Tree ◽  
Cryptic Species ◽  
Species Identification ◽  
Intraspecific Variation ◽  
Molecular Species ◽  
Species Delimitation ◽  
Coi Gene ◽  
Nominal Species ◽  
Model Species ◽  
And Behavior

Spiny-backed orb-weaving spiders of the subfamily Gasteracanthinae are broadly distributed in the Old World. Despite their use as a model species in biology, evolution, and behavior because of their extraordinary characteristics, the systematics of this group of spiders are still poorly understood. This study elucidates the systematics of Gasteracanthinae in Thailand based on morphological and molecular-based analyses. In total, seven species from three genera, namely Gasteracantha, Macracantha, and Thelacantha, were recorded in Thailand. Shape of abdominal spines, pattern of sigilla, and female genitalia are significant characters for species identification. In contrast, coloration shows highly intraspecific variation in most species within Gasteracanthinae. A phylogenetic tree based on partial sequences of COI, 16S, and H3 genes recovered Gasteracanthinae as a monophyletic group and supports the existence of three clades. Gasteracantha hasselti is placed as a sister taxon to Macracantha arcuata. Hence, we propose to transfer G. hasselti to Macracantha. Moreover, molecular species delimitation analyses (ABGD, bPTP, and GMYC) using 675 bp of COI gene support all nominal species, with evidence of possible additional cryptic species.

scholarly journals DNA barcoding British Euphrasia reveals deeply divergent polyploids but lack of species-level resolution

2017 ◽  
Author(s):  
Xumei Wang ◽  
Galina Gussarova ◽  
Markus Ruhsam ◽  
Natasha de Vere ◽  
Chris Metherell ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Species Level ◽  
Ecological Processes ◽  
Evolutionary Patterns ◽  
Ploidy Levels ◽  
Self Fertilization ◽  
Phylogenetic Framework

ABSTRACTBackground and aimsDNA barcoding is emerging as a useful tool not only for species identification but for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode datasets can provide insights into the mechanisms underlying the generation of species diversity. Here, we use DNA barcoding to study evolutionary processes in taxonomically complex British Euphrasia, a group with multiple ploidy levels, frequent self- fertilization, young species divergence and widespread hybridisation.MethodsWe sequenced the core plant barcoding loci, supplemented with additional nuclear and plastid loci, in representatives of all 19 British Euphrasia species. We analyse these data in a population genetic and phylogenetic framework. We then date the divergence of haplotypes in a global Euphrasia dataset using a time-calibrated Bayesian approach implemented in BEAST.Key resultsNo Euphrasia species has a consistent diagnostic haplotype. Instead, haplotypes are either widespread across species, or are population specific. Nuclear genetic variation is strongly partitioned by ploidy levels, with diploid and tetraploid British Euphrasia possessing deeply divergent ITS haplotypes (DXY = 5.1%), with haplotype divergence corresponding to the late Miocene. In contrast, plastid data show no clear division by ploidy, and instead reveal weakly supported geographic patterns.ConclusionsUsing standard DNA barcoding loci for species identification in Euphrasia will be unsuccessful. However, these loci provide key insights into the maintenance of genetic variation, with divergence of diploids and tetraploids suggesting that ploidy differences act as a barrier to gene exchange in British Euphrasia, with rampant hybridisation within ploidy levels. The scarcity of shared diploid-tetraploid ITS haplotypes supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, DNA barcoding can reveal insightful evolutionary patterns in taxonomically complex genera.

scholarly journals Modeling Mito-nuclear Compatibility and Its Role in Species Identification

2020 ◽  
Vol 70 (1) ◽  
pp. 133-144 ◽  
Author(s):  
Débora Princepe ◽  
Marcus A M De Aguiar
Keyword(s):  
Spatial Distribution ◽  
Phylogenetic Tree ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Genetic Material ◽  
Dna Barcode ◽  
Model Parameters ◽  
Uniparental Inheritance ◽  
Speciation Process ◽  
Nuclear Interactions

Abstract Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation—as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here, we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA’s. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (Tigriopus californicus). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.[Mito-nuclear coevolution; mtDNA barcode; parapatry; phylogeny.]

scholarly journals Berlian, SOJ A3 and Jawa Local Rice Varieties Phylogenetically Distinct From Oryza sativa Indica and Oryza sativa Japonica

el–Hayah ◽  
2019 ◽  
Vol 6 (4) ◽  
pp. 112-125
Author(s):  
Yudrik Lathif ◽  
Riri Wiyanti Retnaningtyas ◽  
Dwi Listyorini ◽  
Suharti Suharti
Keyword(s):  
Oryza Sativa ◽  
Phylogenetic Tree ◽  
Dna Barcode ◽  
Rbcl Gene ◽  
Tree Reconstruction ◽  
Rice Varieties ◽  
Local Varieties ◽  
Precise Position ◽  
Total Dna ◽  
Taxonomical Position

The genetic resources identification of Indonesian local rice varieties is a crucial work should be done to conserve our native germplasm. This research aimed to know the taxonomical position of East Java local rice varieties including Jawa (JW), Berlian (BR), and SOJ A3 (SJ) using DNA barcode based on rbcL gene. Total DNA of each sample was isolated from leaves. A pair of forward 5'-ATG TCA CCA CAA ACA SJA AC-3' and reverse 5'-TCG GTA CCT GCA GTA GC-3' primers were used to amplify fragments of rbcL gene resulting in 751bp, 755bp, and 754bp fragments from BR, SJ, and JW varieties, respectively. Phylogenetic tree reconstruction revealed that our three local varieties were forming a cluster separated from the widely cultivated subspecies Oryza sativa Indica and Oryza sativa Japonica. However, further studies are necessary to reveal a more precise position of the local varieties in a phylogenetic tree on the species level.

scholarly journals DNA barcode approaches to reveal interspecies genetic variation of Indian ungulates

2020 ◽  
Vol 5 (1) ◽  
pp. 938-944 ◽  
Author(s):  
Ranjana Bhaskar ◽  
Praveen Kanaparthi ◽  
Rengasamy Sakthivel
Keyword(s):  
Genetic Variation ◽  
Dna Barcode

scholarly journals Using DNA barcodes to assess identity and diversity of Dendropsophus minutus: Failure?

Zootaxa ◽  
2008 ◽  
Vol 1691 (1) ◽  
pp. 67 ◽  
Author(s):  
M. ALEX SMITH
Keyword(s):  
Cytochrome C ◽  
Small Group ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Gene Region ◽  
Dna Barcodes ◽  
Taxonomic Groups

The 5' end (Folmer or Barcode region) of cytochrome c oxidase 1 (CO1) has been proposed as the gene region of choice for a standardized animal DNA barcode (Hebert et al. 2003). Concerns have been raised regarding the decision to utilize this particular mitochondrial gene region as a barcode. Nevertheless, widely divergent taxonomic groups have reported success using CO1 for both species identification and discovery. The utility of CO1 for barcoding amphibians was raised early on (Vences, et al. 2005) and concerns for this group were reported widely (Waugh 2007)—although some considered that the reporting of the concerns outstripped the data that had been analyzed at that point (Smith et al. 2008). Indeed, our analysis of CO1 for a small group of Holarctic amphibians was neither more difficult to generate nor to analyze than for other groups where we have utilized the technique.

Larval anatomy of Andean tadpoles of Telmatobius (Anura: Ceratophryidae) from Northwestern Argentina

Zootaxa ◽  
2008 ◽  
Vol 1938 (1) ◽  
pp. 40-60 ◽  
Author(s):  
M. FLORENCIA VERA CANDIOTI
Keyword(s):  
Intraspecific Variation ◽  
Characteristic Pattern ◽  
Species Discrimination ◽  
Shape Variation ◽  
Geometric Morphometric ◽  
Northwestern Argentina ◽  
Preliminary Results ◽  
Internal Morphology ◽  
Morphometric Methods ◽  
Interspecific And Intraspecific Variation

In this paper I study the oral, buccopharyngeal, and musculoskeletal configuration in tadpoles of nine Telmatobius species from Northwestern Argentina (T. atacamensis, T. ceiorum, T. laticeps, T. oxycephalus, T. pinguiculus, T. pisanoi, T. cf. schreiteri, T. scrocchii, and T. stephani; N = 30, Gosner stages 31–36). Specimens were prepared according to standard clearing and staining protocols; additionally, I applied landmark and outline-based geometric morphometric methods in order to quantify shape variation in chondrocrania, hyobranchial skeletons, and suprarostral cartilages. Although preliminary, results show a marked morphological uniformity on the analyzed levels, and overlapping interspecific and intraspecific variation, which renders species discrimination difficult. Some distinctive traits for the genus are bicuspidate buccal spurs, peculiar arrangement of buccal roof and floor papillae, tetrapartite suprarostral, adrostral cartilages, a lateral slip of the m. subarcualis rectus II-IV invading branchial septum IV, and a characteristic pattern of muscles inserted on the diaphragm. The conservative larval internal morphology in this genus could be explained by a recent speciation and a development possibly characterized by the postmetamorphic appearance of specific features.En este trabajo estudio la morfología oral, bucofaríngea y musculoesquelética de larvas de nueve especies de Telmatobius del Noroeste argentino (T. atacamensis, T. ceiorum, T. laticeps, T. oxycephalus, T. pinguiculus, T. pisanoi, T. cf. schreiteri, T. scrocchii y T. stephani; N = 30, estadios de Gosner 31–36). Los especímenes se prepararon siguiendo protocolos clásicos de transparentación y coloración diferencial; adicionalmente, apliqué métodos de morfometría geométrica basada en landmarks y contornos para cuantificar la variación de formas en condrocráneos, esqueletos hiobranquiales y cartílagos suprarostrales. Aunque de carácter preliminar, los resultados muestran una notable uniformidad morfológica en los niveles analizados, y una variación intraespecífica que se superpone con la interespecífica, dificultando la distinción entre especies. Algunos rasgos distintivos del género son un par de espolones bucales bífidos, un arreglo particular de las papilas del techo y piso bucales, suprarostral tetrapartito, adrostrales, un haz del m. subarcualis rectus II-IV invadiendo el septo branquial IV, y un patrón aparentemente característico de los músculos insertos en el diafragma. La morfología larval interna conservadora en el género podría explicarse por una especiación reciente y un desarrollo posiblemente caracterizado por la aparición postmetamórfica de los rasgos específicos.

Quantitative analysis of interspecific and ontogenetic variation in Osteoglossum species (Teleostei: Osteoglossiformes: Osteoglossidae)

Zootaxa ◽  
2006 ◽  
Vol 1239 (1) ◽  
pp. 49 ◽  
Author(s):  
MARIA E.C. LEAL ◽  
VIVIANNE B. DE SANT-ANNA
Keyword(s):  
Principal Component Analysis ◽  
Quantitative Analysis ◽  
Intraspecific Variation ◽  
Principal Component ◽  
Component Analysis ◽  
Growth Trajectories ◽  
Ontogenetic Variation ◽  
Morphometric Characters ◽  
Interspecific And Intraspecific Variation

Patterns of interspecific and intraspecific variation were investigated on samples of postembryos, juveniles, and adults of the two species of the osteoglossid genus Osteoglossum (O. bicirrhosum and O. ferreirai). Twenty-two morphometric characters were analyzed, utilizing principal component analysis (PCA) that discriminate ontogenetic classes and between species. The results showed differences in both categories. Morphometric characters related to dorsal and anal fin lengths proved to be the most important in taxonomic recognition. The comparison of growth trajectories for these characters showed that growth offset for O. bicirrhosum overlaps with growth onset for O. ferreirai, which may be indicative of a peramorphic morphology in the latter species.

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