scholarly journals Dna barcoding, population genetics, and phylogenetics of the illegally hunted Philippine Duck Anas luzonica (Aves: Anseriformes: Anatidae)

2017 ◽  
Vol 9 (5) ◽  
pp. 10141
Author(s):  
Ardea Mingoa Licuanan ◽  
Mariano RoyMartin Duya ◽  
Perry Sim Ong ◽  
Ian Kendrich Carandang Fontanilla
Keyword(s):  
Dna Barcoding ◽  
Sampling Site ◽  
Haplotype Diversity ◽  
The Philippines ◽  
Habitat Destruction ◽  
High Genetic Diversity ◽  
Tissue Samples ◽  
Duck Species ◽  
Dabbling Duck ◽  
Coi Sequences

DNA barcoding is extensively used as a species identification and delineation tool.  The aim of this study was to generate a barcode profile for mitochondrial cytochrome c oxidase subunit 1 (COI) in the Philippine Duck Anas luzonica, a dabbling duck species endemic to the Philippines that is classified as ‘Vulnerable’ by the International Union for Conservation of Nature (BirdLife International 2016).  COI barcodes were successfully obtained using muscle tissue samples from 46 A. luzonica individuals confiscated from illegal hunters in Pantabangan, Nueva Ecija.  Analysis of TrN+Γ+I distances among the Anas luzonica COI sequences and those of 25 other Anas species revealed that COI barcodes cannot generally delineate hybridizing species.  While Anas luzonica was differentiated from other species it is known to hybridize with and formed a monophyletic group in the neighbor-joining tree generated, sampling from areas of sympatry is needed since individuals were obtained from only one sampling site.  The population structure of the Anas luzonica population was also examined using mitochondrial DNA control region and COI sequences.  The population had high haplotype diversity and low nucleotide diversity, an indication that a bottleneck event had occurred, which is likely due to extreme hunting pressures and habitat destruction.  The population under study exhibited high genetic diversity.  Given that the samples for this study came from a single locality, sampling from other localities is required to determine whether other populations are facing the risk of reduced fitness (inbreeding depression).

DNA barcoding in Nautilus pompilius (Mollusca : Cephalopoda): evolutionary divergence of an ancient species in modern times

2012 ◽  
Vol 26 (6) ◽  
pp. 548 ◽  
Author(s):  
Rachel C. Williams ◽  
Stephen J. Newman ◽  
William Sinclair
Keyword(s):  
Dna Barcoding ◽  
Evolutionary Biology ◽  
Minimum Spanning Tree ◽  
Phylogenetic Analyses ◽  
Geographic Origin ◽  
American Samoa ◽  
The Philippines ◽  
Evolutionary Divergence ◽  
Nautilus Pompilius ◽  
Coi Sequences

DNA barcoding studies to elucidate the evolutionary and dispersal history of the current populations of Nautilus pompilius allow us to develop a greater understanding of their biology, their movement and the systematic relationships between different groups. Phylogenetic analyses were conducted on Australian N. pompilius, and COI sequences were generated for 98 discrete accessions. Sequences from samples collected across the distribution were sourced from GenBank and included in the analyses. Maximum likelihood revealed three distinct clades for N. pompilius: (1) populations sourced from west Australia, Indonesia and the Philippines; (2) populations collected from east Australia and Papua New Guinea; (3) western Pacific accessions from Vanuatu, American Samoa and Fiji, supporting previous findings on the evolutionary divergence of N. pompilius. A minimum spanning tree revealed 49 discrete haplotypes for the 128 accessions, from a total of 16 discrete sampling locations. Population similarity reflects oceanic topographic features, with divergence between populations across the N. pompilius range mirroring geographical separation. This illustrates the success of DNA barcoding as a tool to identify geographic origin, and looks to the future role of such technology in population genetics and evolutionary biology.

scholarly journals Keragaman genetik ikan tuna sirip kuning (Thunnus albacares) dari dua populasi di Laut Maluku, Indonesia

DEPIK ◽  
2014 ◽  
Vol 3 (1) ◽  
Author(s):  
Nebuchadnezzar Akbar ◽  
Neviaty P Zamani ◽  
Hawis H Madduppa
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Yellowfin Tuna ◽  
Conservation Strategy ◽  
High Genetic Diversity ◽  
Tissue Samples ◽  
Chain Reactions ◽  
Polymerase Chain ◽  
Two Populations

Abstract. Yellowfin tuna (Thunnus albacores) is a large, pelagic, and migratory species of tuna that inhabits Moluccas Sea in Indonesia, and most sea environment worldwide. However, high fishing activities tend to happen in the Indonesia region and catch product appear to be decreasing. A better understanding of yellowfin tuna genetic diversity is required to plan better conservation strategy of tuna. The study was conducted to infer the genetic diversity of yellowfin tuna (T. albacores) in the Moluccas Sea. A total of 41 tissue samples of yellowfin tuna were collected from two regions in the Moluccas Sea (North Moluccas and Ambon) during an expedition in February 2013. The results showed that genetic diversity and nucleotide diversity of yellowfin tuna from North Moluccas population was 0.984 and 0.021, respectively; while in Ambon population, the genetic and nucleotide diversities were 1.00 and 0.018, respectively. The high genetic diversity (0.990) and nucleotide diversity (0.020) between two populations were observed. Based on phylogenetic analysis, no genetic differentiation between the two populations in Moluccas Sea was revealed .Keywords :  Population genetics; Haplotype diversity; Coral Triangle; Phylogenetics; Polymerase Chain Reactions (PCRs) Abstrak. Tuna sirip kuning (Thunnus albacores) adalah ikan komersial penting dan ditemukan di Laut Maluku, Indonesia. Tetapi, aktivitas penangkapan ikan tuna sirip kuning dapat menurunkan kualitas dan kuantitas stok ikan, sehingga perlu adanya pengkajian keragaman genetik ikan tuna sirip kuning. Pemahaman yang baik tentang keragaman genetika dibutuhkan untuk merencanakan strategi konservasi tuna yang lebih baik. Penelitian ini bertujuan untuk mengetahui keragaman genetik  ikan tuna sirip kuning dari dua populasi di Laut Maluku. Sebanyak 41 sampel jaringan dari tuna sirip kuning dikumpulkan dari dua populasi di Laut Maluku (Maluku Utara dan Ambon) selama ekspedisi pada bulan Februari 2013. Hasil penelitian menunjukkan bahwa keragaman genetik populasi tuna sirip kuning pada perairan Maluku Utara dan Ambon masing-masing sebesar 0,984 dan 1,00 sedangkan nilai keragaman nukleotida masing-masing bernilai 0,021 dan 0,018. Nilai keragaman genetik dan keragaman nukloetida yang tinggi didaptkan antar kedua populasi masing-masing sebesar 0,990 dan 0,020. Berdasarkan analisis filogenetik, dua populasi di Laut Maluku ini memiliki kedekatan secara genetik.Kata kunci : Genetika populasi; Keragaman haplotipe; Segitiga Terumbu Karang; Filogenetika; Polymerase Chain Reaction (PCR)

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 40
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
The Arctic ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

scholarly journals DNA barcoding in recognition of Gammarusflock diversity and distribution in the ancient Lake Ohrid

2021 ◽  
Vol 4 ◽  
Author(s):  
Anna Wysocka ◽  
Michal Grabowski ◽  
Lidia Sworobowicz ◽  
Sasho Trajanovski ◽  
Tomasz Mamos
Keyword(s):  
Dna Barcoding ◽  
Haplotype Diversity ◽  
Morphological Diversity ◽  
Balkan Peninsula ◽  
Species Flock ◽  
Depth Range ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
Haplotypic Diversity ◽  
Main Driver

Lake Ohrid, located on the Balkan Peninsula at the Albanian-Macedonian border, is the oldest European lake (1.3-1.9 My old) and one of the world’s smallest ancient lakes. Taking into account the size of the lake and its biodiversity, it harbors the highest level of endemism, especially within amphipod crustaceans (ca. 90%) with the endemic Gammarus species flock. Our previous studies upon this flock have shown a substantial decoupling between molecular and morphological diversity, existence of cryptic species and puzzling speciation history. In order to explore sources of observed diversity, in the current study we are investigating ecological preferences of the species within the flock, based on their distribution in depth gradient, in relation to molecular diversity based on DNA barcoding. In the study over 200 barcodes were generated and combined with 173 previously published. The specimens were collected from all depth ranges of Lake Ohrid as well as from springs located on or near the banks of the lake. Within the species flock, 13 BIN’s were identified, 12 previously known and one newly recognized, representing separate lineage and putatively a new species. Two of the flock species were found only in the springs: G. sketi and G. cryptosalemaai. G. sketi, previously found only in springs on the southern banks of Lake Ohrid, has now also been discovered in springs in its north-eastern part. Both species show low haplotypic diversity. All remaining species were recorded from the depth between 20 and 60 meters, that is characterized by the highest ecological diversity with different types of substrates: stones, macrophytes, abundant Dreissena shells as well as sand and silt. Among them G. sywulai, G. macedonicus, G. cryptoparechiniformis, G. lychnidensis, G. ochridensis, G. parechinifromis were found exclusively within this depth range. The three latter species represent single BIN and share haplotypes, at the same time this BIN has the highest number of haplotypes in comparison to others. The remaining species found on this depth represent separate BINs with different levels of haplotype diversity. Only G. lychnidensis, G. stankokaramani and G. solidus were found below the depth of 60 meters, in a quite homogenous environment dominated by silt. In the deepest parts of the lake, between 260 and 290 meters, only G. solidus was found. This species is represented only by three haplotypes while G. stankokaramani is characterized by multiple haplotypes partially shared with G. lychnidensis. The shared haplotype represents the only G. lychnidensis occurrences on the depths below 60 meters. Summarizing, the highest abundance of BINs, species and haplotypes was recovered from the most ecologically diversified depth range of the lake (20 to 60 meters). This suggests that ecological heterogeneity could be the main driver of Gammarus species flock diversification in the ancient Lake Ohrid. Due to the complex pattern of morphological diversity, DNA barcoding proved to be the best if not the only method in identification of the species flock diversity.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav K Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

Genealogical relationship inference to identify areas of intensive poaching of the Orange-fronted Parakeet (Eupsittula canicularis)

BMC Zoology ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Gabriela Padilla-Jacobo ◽  
Tiberio C. Monterrubio-Rico ◽  
Horacio Cano-Camacho ◽  
María Guadalupe Zavala-Páramo
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Coastal Region ◽  
Central American ◽  
Illegal Trade ◽  
Wild Populations ◽  
High Genetic Diversity ◽  
Genealogical Relationship ◽  
Genetic Pool

Abstract Background The Orange-fronted Parakeet (Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets. Results Poached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico. Conclusions Poached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.

scholarly journals Gcd Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment

2018 ◽  
Vol 16 (1) ◽  
pp. 1 ◽  
Author(s):  
Yong Li ◽  
Jianqiang Zhang ◽  
Zhiliang Gong ◽  
Wenlai Xu ◽  
Zishen Mou
Keyword(s):  
Correlation Analysis ◽  
High Throughput Sequencing ◽  
Gene Diversity ◽  
Pearson Correlation ◽  
Glucose Dehydrogenase ◽  
Sampling Site ◽  
Soluble Phosphate ◽  
High Genetic Diversity ◽  
Alpha And Beta Diversity ◽  
Insoluble Phosphate

Quinoprotein glucose dehydrogenase (GDH) is the most important enzyme of inorganic phosphorus-dissolving metabolism, catalyzing the oxidation of glucose to gluconic acid. The insoluble phosphate in the sediment is converted into soluble phosphate, facilitating mass reproduction of algae. Therefore, studying the diversity of gcd genes which encode GDH is beneficial to reveal the microbial group that has a significant influence on the eutrophication of water. Taking the eutrophic Sancha Lake sediments as the research object, we acquired samples from six sites in the spring and autumn. A total of 219,778 high-quality sequences were obtained by DNA extraction of microbial groups in sediments, PCR amplification of the gcd gene, and high-throughput sequencing. Six phyla, nine classes, 15 orders, 29 families, 46 genera, and 610 operational taxonomic units (OTUs) were determined, suggesting the high genetic diversity of gcd. Gcd genes came mainly from the genera of Rhizobium (1.63–77.99%), Ensifer (0.13–56.95%), Shinella (0.32–25.49%), and Sinorhizobium (0.16–11.88%) in the phylum of Proteobacteria (25.10–98.85%). The abundance of these dominant gcd-harboring bacteria was higher in the spring than in autumn, suggesting that they have an important effect on the eutrophication of the Sancha Lake. The alpha and beta diversity of gcd genes presented spatial and temporal differences due to different sampling site types and sampling seasons. Pearson correlation analysis and canonical correlation analysis (CCA) showed that the diversity and abundance of gcd genes were significantly correlated with environmental factors such as dissolved oxygen (DO), phosphorus hydrochloride (HCl–P), and dissolved total phosphorus (DTP). OTU composition was significantly correlated with DO, total organic carbon (TOC), and DTP. GDH encoded by gcd genes transformed insoluble phosphate into dissolved phosphate, resulting in the eutrophication of Sancha Lake. The results suggest that gcd genes encoding GDH may play an important role in lake eutrophication.

Sample site selection for tracer studies applying a unidirectional circulatory approach

1987 ◽  
Vol 253 (2) ◽  
pp. E173-E178 ◽  
Author(s):  
D. K. Layman ◽  
R. R. Wolfe
Keyword(s):  
Specific Activity ◽  
Sampling Site ◽  
Vena Cava ◽  
Gas Chromatography Mass Spectrometry ◽  
Tracer Studies ◽  
Tissue Samples ◽  
Circulatory Model ◽  
Plasma Leucine ◽  
Relationship Of ◽  
The Relationship

The optimal arterial or venous sites for infusion and sampling during isotopic tracer studies have not been established. This study determined the relationship of plasma and tissue enrichment (E) when isotopes were infused in an artery and sampled from a vein (av mode) or infused in a vein and sampled from an artery (va mode). Adult dogs were given primed constant infusions of [3-13C]lactate, [1-13C]leucine, and 14C-labeled bicarbonate. Simultaneous samples were drawn from the vena cava, aortic arch, and breath. Tissue samples were removed from skeletal muscle, liver, kidney, and gut. Breath samples were analyzed for 14CO2 by liquid scintillation counting and plasma isotopic enrichments of [13C]lactate, [13C]leucine, and alpha-[13C]ketoisocaproate (KIC) were determined by gas chromatography-mass spectrometry. By using the va mode, the plasma E for lactate and leucine were 30-40% above tissue E. The av mode provided an accurate reflection of tissue E for lactate, which equilibrates rapidly with tissues, and a reasonable estimate for leucine, which exchanges more slowly. The isotopic enrichment of plasma KIC more directly reflected tissue leucine E than did plasma leucine E, and KIC enrichment was insensitive to sampling site. We also evaluated theoretically a circulatory model that predicts venous isotopic enrichments when the va mode is used. We conclude that the av mode is optimal but that the problems arising from use of the va mode can be overcome by use of a metabolic product (i.e., KIC) or by calculation of venous specific activity with our circulatory mode.

scholarly journals Authentication of Chinese Crude Drug Gecko by DNA Barcoding

2011 ◽  
Vol 6 (1) ◽  
pp. 1934578X1100600 ◽  
Author(s):  
Hai-Feng Gu ◽  
Yun Xia ◽  
Rui Peng ◽  
Bang-Hui Mo ◽  
Li Li ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Habitat Destruction ◽  
Full Length ◽  
Correct Identification ◽  
Molecular Method ◽  
Specific Sequence ◽  
Gekko Gecko ◽  
Crude Drug

Gekko gecko, an animal used as a valued traditional Chinese medicine, has been widely used for over 2000 years. Due to localized habitat destruction, the amount of G. gecko has dramatically decreased in recent years. As a result, more and more adulterants have been detected in the traditional medicine, which has resulted in a chaotic market. Therefore, a correct identification method is badly needed. In this study, we employed a new molecular method of DNA barcoding for discriminating gecko from its adulterants. Fifty-seven specimens of gecko and its adulterants were collected as test samples. The full-barcode and mini-barcode sequences of these specimens were separately amplified and sequenced separately. Together with other published barcode sequences, we detected that the intra-specific sequence diversity was far lower than the inter-specific diversity in G. gecko and its adulterants (3% compared with 35% in full-length barcode; 4% compared with 33.5% in mini-barcode). These results showed that both the full-length and mini-barcodes were effective for identifying gecko, which suggested that the DNA barcode could be an effective and powerful tool for identifying the Chinese crude drug gecko.

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