scholarly journals Molecular barcoding of marine ornamental fish from the southern coast of West Java validates conventional identification

2021 ◽  
Vol 322 ◽  
pp. 01004
Author(s):  
Agus Nuryanto ◽  
Kusbiyanto Kusbiyanto ◽  
Dian Bhagawati
Keyword(s):  
Taxonomic Status ◽  
Genetic Distances ◽  
Ornamental Fish ◽  
Coi Gene ◽  
Southern Coast ◽  
Color Patterns ◽  
West Java ◽  
Molecular Barcoding ◽  
Different Color ◽  
Monophyletic Branch

Conventional identification of marine ornamental fish has faced difficulties due to similar color patterns of closed related species, or juvenile individuals have different color patterns from adult individuals. Molecular barcoding using the cytochrome c oxidase I (COI) gene provides a reliable tool for unmasking such difficulties. This study aimed to barcode marine ornamental fish from the southern coast of West Java. Fragment of the COI gene was sequenced from 54 morphotypes. In this study, we determined the taxonomic status of the samples based on a 5% genetic divergence, with the parameter including sequence percent identity, genetic distance, and length of monophyletic branch in a phylogenetic tree. The result showed that most samples had a high percentage of sequence identities, low genetic distances, and short chapters in monophyletic clades, but the remaining were not. Those data indicated that most samples could be identified at species-level without doubt and support conventional identification. Barcoding success is also depending on the availability of conspecific sequences in the databases. This study concluded that molecular barcoding could strengthen and validate traditional identification.

scholarly journals Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene

2021 ◽  
Vol 22 (3) ◽  
Author(s):  
Sri Riani ◽  
ROMANUS EDY PRABOWO ◽  
Agus Nuryanto
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Field Trips ◽  
Coi Gene ◽  
Molecular Characteristics ◽  
Severe Problem ◽  
Molecular Barcoding ◽  
Level Identification

Abstract. Riani S, Prabowo RE, Nuryanto A. 2021. Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene. Biodiversitas 22: 1456-1466. Amphibalanus variegatus and A. reticulatus have similar external morphology. Morphological similarities can be a severe problem for direct species-level identification. The problem can be overcome through anatomy-based identification and validated through molecular barcoding. Molecular characterization using the cytochrome c oxidase 1 (COI) gene provides a useful tool for precise species identification. This study attempted to assess the molecular characteristics of morphologically similar barnacle (Amphibalanus) specimens collected at five localities in Indonesia to validate their taxonomic status. Forty-five barnacle specimens were collected during the field trips in Lampung, Jakarta, Semarang, Bali, and Lombok. The COI gene was amplified using LCO1490 and HCO2198 primers. The gene was sequenced using bidirectional sequencing at 1st base Asia. The specimens' taxonomic status was determined based on sequence identity, genetic distance, monophyly, nucleotide compositions, and nucleotides in a particular position. Shell shapes-based identification placed barnacle specimens into A. reticulatus. However, anatomical-based identification placed barnacle samples into two different anatomic groups, which was further validated by molecular data that two anatomic groups of Amphibalanus samples have significant differences in their COI gene. Based on the molecular characteristics, 43 samples were identified as A. reticulatus, while the two remaining samples were identified as A. variegatus.

scholarly journals Phylogenetic analysis of ornamental Pomacentridae from the southern coast of West Java

DEPIK ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 32-43
Author(s):  
Munatul Khayah Almusyarofah ◽  
Romanus Edy Prabowo ◽  
Agus Nuryanto
Keyword(s):  
Phylogenetic Analysis ◽  
Species Richness ◽  
Maximum Parsimony ◽  
Sampling Technique ◽  
Wide Distribution ◽  
Ornamental Fish ◽  
Survey Method ◽  
Southern Coast ◽  
West Java ◽  
Basal Group

Abstract. Pomacentridae has a wide distribution in Indonesia waters. Research on species richness of Pomacentridae has been carried out in some areas in Indonesia. However, there are no data about the relationships of Pomacentridae on the southern coast of West Java. This research aims to know the evolutionary kinship of Pomacentridae ornamental fish in Ujung Genteng and Taman Manalusu Beach, West Java. This research used a survey method with a judgment sampling technique. The parameters measured were the consistency index (CI) and character evolution of the resulting phylogenetic tree. Cladogram reconstructed based on maximum parsimony algorithm with 1000 bootstrap replicates in PAUP software. The result showed that the tree had a CI value of 0.6000 which indicated low homoplasy. Pomacentridae formed a monophyletic group when they compared with Chaetodon collare as outgroup. The Pomacentridae clade divided into two subclades. The first subclade consisted of Abudefduf indicus as a basal species, then Neoglypydodon bonang and Plectroglyphidodon lacrymatus have a closed kinship and diverged after Dascyllus trimaculatus, and then Abudefduf notatus and Abudefduf sexfaciatus have a close kinship and diverged after Abudefduf vaigiensis. The second subclade referred to as a basal group, and within this subclade, Chrysiptera brownriggii has a closely related to Chrysiptera unimaculata and diverged after Chromis opercularis.Keywords: Cladistics, damselfish, meristic, morphometric, Pomacentridae

Molecular barcoding for central-eastern European Crioceris leaf-beetles (Coleoptera: Chrysomelidae)

2012 ◽  
Vol 7 (1) ◽  
pp. 69-76 ◽  
Author(s):  
Daniel Kubisz ◽  
Łukasz Kajtoch ◽  
Miłosz Mazur ◽  
Volodymyr Rizun
Keyword(s):  
Invasive Plant ◽  
Elongation Factor ◽  
Genetic Distances ◽  
Coi Gene ◽  
Conservation Units ◽  
Widespread Species ◽  
Molecular Barcoding ◽  
Leaf Beetles ◽  
Pcr Products ◽  
High Level

AbstractAmong Crioceris leaf-beetles, the two most widespread species (Crioceris asparagi and C. duodecimpunctata) are serious invasive plant pests, while another two (C. quatuordecimpunctata and C. quinquepunctata) are rare species restricted to steppe-like habitats in Eurasia. The aim of the research was to check the genetic distinctiveness of these four species and develop barcodes for their molecular identification using the mitochondrial Cytochrome Oxidase I (COI) gene and two nuclear markers: Elongation Factor 1-α (EF1-α) and Internal Transcribed Spacer 1 (ITS1). The identification of each species was possible and reliable with the use of COI and ITS1 markers. EF1-α was omitted in analyses due to its high level of heterozygosity (presence of multiple PCR products). C. duodecimpunctata and C. quatuordecimpunctata were shown to be sister taxa, but the similar genetic distances between all of the species indicate that these species originated almost simultaneously from a common ancestor. Identification of two separate clades in populations of C. quatuordecimpunctata suggested that the clades are isolated and can be considered as separate conservation units.

scholarly journals Molecular Barcoding Reveal the Existence of Mole Crabs Emerita emeritus in North Coast of Central Java

2020 ◽  
Vol 12 (1) ◽  
pp. 104-110
Author(s):  
Dian Bhagawati ◽  
Elly Tuti Winarni ◽  
Agus Nuryanto
Keyword(s):  
Sustainable Use ◽  
Taxonomic Status ◽  
Single Species ◽  
First Record ◽  
Genetic Distances ◽  
North Coast ◽  
Local Alignment ◽  
Northern Coast ◽  
Molecular Barcoding ◽  
Central Java

The existence of mole crabs had been reported from the southern coast of Central Java. However, no mole crab data was available from the northern coast Central Java.  This study aimed to figure out the existence of mole crabs in the northern coast of Central Java as revealed from the cytochrome c oxidase 1 (COI) barcoding. Mole crabs samples collected in Sendang Sikucing Beach Kendal. Taxonomic status of the samples was inferred from sequences similarity test using basic local alignment search tool to conspecific sequence deposited in GenBank. Pairwise genetic distances were calculated based on the Kimura 2-parameter model. A phylogenetic tree had reconstructed in molecular evolution genetic analysis (MEGA) software based on neighbor-joining algorithm. Branching reliability was obtained from 1000 bootstraps replication while branching polarity was obtained from the out-group comparison. The mole crab samples from the northern coast of Central Java had unambiguously identified as Emerita emeritus based on high sequences similarities (98.27%-99.70%), low genetic distances (0.002-0.005), and their monophyly with Emerita emeritus (KR047035) in GenBank. Pairwise analysis among each possibility pair of samples had genetic distances ranged between 0.000 and 0.005, indicated that all sample belong to single species. The data provide the first record of the existence of Emerita emeritus in the northern coast of Central Java. Our data on the existence of E. emeritus in the northern coast of Central Java is among essentials information as a scientific basis in creating policy for the management of sustainable use of the mole crabs in the areas.

scholarly journals Review of the potter wasps (Hymenoptera: Vespidae, Eumeninae) with a petiolate metasoma from Indonesian Archipelago

2020 ◽  
Vol 19 ◽  
pp. 00005
Author(s):  
Hari Nugroho ◽  
Pungki Lupiyaningdyah ◽  
Jun-ichi Kojima
Keyword(s):  
Literature Review ◽  
Taxonomic Status ◽  
Peripheral Populations ◽  
Color Patterns ◽  
Australian Species ◽  
Indonesian Archipelago ◽  
Wide Range ◽  
Different Color ◽  
Specific Species ◽  
Range Of Variation

The taxonomy and biogeography of potter wasps with a petiolate metasoma occurring in the Indonesian Archipelago are reviewed. Literature review and specimens examination were carried out for the present study. Within the Eumeninae, the wasps with a petiolate metasoma distributed in the region have been more or less well studied compared with those with a non-petiolate metasoma, but their generic affinities and the concepts of some species yet remain unestablished. A total of 80 species belonging to 16 genera of the “petiolate metasoma” are known to occur from the region. Sumatra, Java, Bali and Borneo have mainly Oriental eumenine fauna, including several area- specific species of the Oriental genera. New Guinean fauna is comprised of Papua-Australian species of the widely distributed genera, together with widely distributed species and species endemic to New Guinea. The Wallacean fauna is constituted mainly with the area-specific species in the rather widely distributed genera; in the western part of Wallacea, they are represented mainly by widely distributed genera, together with Oriental genera; in the eastern part of Wallacea, they are constituted mainly by area endemic species of widely distributed Oriental genera. Widely distributed species generally show a wide range of variation in the marking patterns, and occurs sympatrically in some areas, even the peripheral populations usually characterized by the island(s)-specific marking patterns. Sympatric occurrences of forms with quite different color patterns in widely distributed species need further study to establish their taxonomic status, namely whether they are variations within a given area or different species.

scholarly journals Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae)

2020 ◽  
Vol 96 (2) ◽  
pp. 609-635
Author(s):  
Vassily A. Spiridonov ◽  
Ulyana V. Simakova ◽  
Sergey E. Anosov ◽  
Anna K. Zalota ◽  
Vitaly A. Timofeev
Keyword(s):  
Black Sea ◽  
Genetic Distances ◽  
Morphological Data ◽  
Coi Gene ◽  
The Black Sea ◽  
Gene Marker ◽  
Mediterranean Species ◽  
Crimean Peninsula ◽  
Molecular Barcoding ◽  
Coi Sequences

Macropodia czernjawskii (Brandt, 1880), described from the Black Sea, was ignored in the regional faunal accounts for more than a century, although it was recognised in the Mediterranean. Instead, M. longirostris (Fabricius, 1775) and M. rostrata (Linnaeus, 1761) were frequently listed for the Black Sea. We selected a lectotype and redescribed the species on the basis of the type series from the Crimean Peninsula and the new material collected in the Black Sea. Historical and new collections, as well as the analysis of publications, indicate that M. czernjawskii is the only Macropodia species occurring in the Black Sea. Molecular barcode (COI gene marker) data show that M. czernjawskii is a species well-diverged from other studied species of the group. Furthermore, M. parva van Noort & Adema, 1985 has very low genetic distances from M. rostrata and M. longipes A. Milne-Edwards & Bouvier, 1899 is indistinguishable from M. tenuirostris (Leach, 1814), using COI sequences. The respective synonimisations, supported by morphological data, are proposed. M. czernjawskii is a Black Sea – Mediterranean endemic occurring also in the neighbouring Atlantic coastal zone of the Iberian Peninsula and occupying shallower depth, compared to other Mediterranean species of Macropodia. As an upper subtidal inshore species, it is particularly specialised in self-decoration and stimulates abundant epibiosis, providing masking and protection. The bulk of epibiosis consists of algae and cyanobacteria. Amongst the 25 autotrophic eukaryote taxa, identified to the lowest possible level, green chlorophytes Cladophora sp. and calcareous rhodophytes Corallinales gen. sp. were most commonly recorded. Non-indigenous red alga Bonnemaisonia hamifera Hariot, first officially recorded at the Caucasian coast of the Black Sea in 2015, was present in the epibiosis of M. czernjawskii in Crimea as early as 2011.

Notes on the molecular taxonomy of the Proclossiana eunomia complex (Lepidoptera, Nymphalidae: Argynnini): analysis of DNA barcodes

2018 ◽  
Vol 8 (1) ◽  
pp. 222-232 ◽  
Author(s):  
R. V. Yakovlev ◽  
N. A. Shapoval ◽  
G. N. Kuftina ◽  
A. V. Kulak ◽  
S. V. Kovalev
Keyword(s):  
Body Size ◽  
Molecular Taxonomy ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Coi Gene ◽  
Wing Pattern ◽  
Molecular Approach ◽  
Dna Barcodes ◽  
Morphological Differences ◽  
Proclossiana Eunomia

The Proclossiana eunomia (Esper, 1799) complex is currently composed of the several subspecies distributed throughout Palaearсtic region and North America. Despite the fact that some of the taxa have differences in wing pattern and body size, previous assumptions on taxonomy not supported by molecular data. Therefore, the identity of certain populations of this complex has remained unclear and the taxonomic status of several recently described taxa is debated. Here, we provide insights into systematics of some Palaearctic members of this group using molecular approach, based on the analysis of the barcoding fragment of the COI gene taking into account known morphological differences.

Estimating the copy number of the agouti signaling protein (ASIP) gene in goat breeds with different color patterns

2021 ◽  
Vol 246 ◽  
pp. 104440
Author(s):  
Dailu Guan ◽  
Anna Castelló ◽  
María Gracia Luigi-Sierra ◽  
Vincenzo Landi ◽  
Juan Vicente Delgado ◽  
...  
Keyword(s):  
Copy Number ◽  
Color Patterns ◽  
Signaling Protein ◽  
Different Color

Biochemical Systematics, Biogeography and Evolutionary Rates in Species of the Mediterranean Genus Tyrrhenoleuctra (Plecoptera, Leuctridae)

2004 ◽  
Vol 35 (3) ◽  
pp. 299-306 ◽  
Author(s):  
◽  
J. M. Tierno de Figueroa ◽  
◽  
◽  
Keyword(s):  
North Africa ◽  
Evolutionary Rate ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Genetic Distances ◽  
Western Mediterranean ◽  
Similar Distribution ◽  
Undescribed Species ◽  
Vicariance Event ◽  
Definition Of

AbstractThe western Mediterranean stonefly genus Tyrrhenoleuctra traditionally includes 3 species: T. minuta (Spain, North Africa, Balearic Islands), T. tangerina (Spain, North Africa), T. zavattarii (Corsica and Sardinia). Since the traditional morphological characters display great and overlapping variation, allozyme electrophoresis was used to clarify taxonomic and phylogenetic relationships within the genus and to discuss biogeographical implications. The results clearly discriminate at least four entities: the Corso-Sardinian unit, for which the name T. zavattarii can be used; the Balearic population, representing an undescribed species; at least two Iberian peninsular species. However, more data on topotypic populations are needed to define the taxonomic status of the Iberian species (including definition of the currently used names T. minuta and T. tangerina). The presence of Tyrrhenoleuctra in Sardinia and Corsica is likely due to an old vicariance event following separation of the Sardinia-Corsica microplate from the Iberian Peninsula. Calibration of the molecular clock (genetic distances vs. Corso-Sardinian plate split from Iberia) resulted in a very low evolutionary rate (0.008 D/my), lower than those found in taxonomically distant groups (including stoneflies) with similar distribution.

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