scholarly journals Short Communication: Lack of differentiation within the bigeye tuna population of Indonesia

2017 ◽  
Vol 18 (4) ◽  
pp. 1406-1413
Author(s):  
NI PUTU DIAN PERTIWI ◽  
BUDI NUGRAHA ◽  
RIRIK KARTIKA SULISTYANINGSIH ◽  
IRWAN JATMIKO ◽  
ANDRIANUS SEMBIRING ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Short Communication ◽  
Haplotype Diversity ◽  
Genetic Data ◽  
Bigeye Tuna ◽  
High Haplotype Diversity ◽  
Loop Control ◽  
Thunnus Obesus ◽  
Sampling Locations ◽  
D Loop

Pertiwi NPD, Nugraha B, Kartika R, Sulistyaningsih RK, Jatmiko I, Sembiring A, Mahardini A, Cahyani NKD, Anggoro AW, Madduppa HH, Ambariyanto A, Barber PH, Mahardika GN. 2017. Short Communication: Lack of differentiation within the bigeye tuna population of Indonesia. Biodiversitas 18: 1406-1413. All highly migratory tuna and tuna-like species have vast feeding grounds and spawning grounds. Indonesia’s tuna catch is the largest in the world. However, genetic diversity in the population structure within particular tuna species in Indonesia is very limited. Here we provide genetic data for bigeye tuna (Thunnus obesus) covering fishing grounds and local fish markets throughout Indonesia. A fragment of mitochondrial DNA in the D-loop control region was amplified from samples collected across Indonesia in the biennium 2012-2013. The results showed high haplotype diversity and low nucleotide diversity in our samples. Little differentiation occured between the eleven diverse sampling locations, nor was any separation detected between general regions of Indonesia, nor between samples from fishing grounds and samples from fish markets.

Genetic analysis of populations of brown trout (Salmo trutta L.) from the Romanian Carpathians

2019 ◽  
Vol 32 ◽  
pp. 23
Author(s):  
Gina-Oana Popa ◽  
Andreea Dudu ◽  
Doru Bănăduc ◽  
Angela Curtean-Bănăduc ◽  
Alexandru Burcea ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Brown Trout ◽  
Salmo Trutta ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Genetic Analysis ◽  
High Haplotype Diversity ◽  
Brown Trout Salmo Trutta ◽  
D Loop ◽  
Romanian Carpathians

The Carpathian Mountains are one of the most complex orogenetic areas of Europe, with unique fauna, including the brown trout (Salmo trutta). In this study we performed population genetic analysis of 12 different S. trutta populations using two types of molecular markers: nine microsatellites and mitochondrial D-loop sequences. The following working hypothesis was considered: the Romanian Carpathians and their surrounding lowlands can be key relief units based on which the S. trutta genetic diversity, spread, distribution, connectivity, relative isolation and genetic divergence can be at least partially explained. The phylogenetic analysis revealed that the majority of sequences were grouped in the Danubian clade. The high haplotype diversity of the 12 analyzed brown trout populations can be explained by the high nucleotide diversity. The microsatellite analysis revealed an inbreeding event for all the loci and for the populations analyzed. The Romanian Carpathians' shape and geographic orientation play a zoogeographical key role driving force in respect to the S. trutta populations.

scholarly journals Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

2021 ◽  
Vol 17 (2) ◽  
pp. 105-114
Author(s):  
Anik Budhi Dharmayanthi ◽  
Achmad Muchsinin ◽  
Afriana Pulungan ◽  
Moch Syamsul Arifin Zein
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Bird Populations ◽  
Low Genetic Diversity ◽  
In Captivity ◽  
D Loop ◽  
Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

scholarly journals Spread beyond the border: Small Scale genetic structure of the introduced Banggai cardinalfish (Pterapogon kauderni) population in the Bali Strait

2021 ◽  
Vol 26 (3) ◽  
pp. 165-172
Author(s):  
I Nyoman Giri Putra ◽  
Ni Luh Putu Ria Puspitha ◽  
Endang Wulandari Suryaningtyas ◽  
Endang Wulandari Suryaningtyas
Keyword(s):  
Genetic Structure ◽  
Native Species ◽  
Population Genetic ◽  
Nucleotide Diversity ◽  
Dna Marker ◽  
Haplotype Diversity ◽  
Small Scale ◽  
Aquarium Trade ◽  
High Haplotype Diversity ◽  
Multiple Introduction

The living marine aquarium trade has been known to mediate various aquatic invaders to spread and established a new population outside of their natural home range. In most cases, the introduce species cause a cascaded effect which harm the native species and their ecosystem. The successful of the invasion event often related to the genetic properties of the introduced species. Therefore, using a molecular approach based on a mitochondrial DNA marker, the present work aimed to evaluate the population genetic structure of the introduced P. kauderni population in Bali Strait. Samples were collected from four sites in Gilimanuk Bay, Bali Strait. Our results showed  a high haplotype diversity and low nucleotide diversity that might be a signal of a bottleneck. Overall, we found five haplotypes comprising two unique haplotypes and three shared haplotypes. Genetic structure was detected in some localities, which indicates Pterapogon kauderni might originated from various genetically distinct populations. However, we could not conclusively determine the observed patterns of the genetic structure within each site. These patterns are likely related to the multiple introduction event of P. kauderni in Bali Strait. Additional samples from both side (introduced and native habitat) combined with more rapidly evolving markers may describe the structure more clearly.

scholarly journals Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7007
Author(s):  
Bingjie Jiang ◽  
Jianjun Fu ◽  
Zaijie Dong ◽  
Min Fang ◽  
Wenbin Zhu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Important Food ◽  
Red Tilapia ◽  
The Gift ◽  
D Loop ◽  
Food Fish ◽  
Genetic Structures ◽  
Relationship Of

Background Many tilapia species or varieties have been widely introduced and have become an economically important food fish in China. Information on the genetic backgrounds of these populations is deficient and requires more research, especially for red tilapia strains. Methods In the present study, displacement loop (D-loop) sequences were used to evaluate the genetic relationship and diversity of seven tilapia populations that are widely cultured in China; this was done specifically to speculate on the maternal ancestry of red tilapia strains. Three red tilapia varieties of Oreochromis ssp., Taiwan (TW), Israel (IL), and Malaysia (MY) strains and other populations, including O. aureus (AR), O. niloticus (NL), O. mossambicus (MS), and the GIFT strain of O. niloticus, were collected and analyzed in this study. Results A total of 146 polymorphic sites and 32 haplotypes of D-loop sequences were detected among 332 fish and four major haplotypes were shared among the populations. The TW and NL populations had a greater number of haplotypes (20 and 8, respectively). The haplotype diversity (Hd) and nucleotide diversity (π) of each population ranged from 0.234 to 0.826, and 0 to 0.060, respectively. The significant positive Tajima’s D value of neutral test were detected in the NL, IL, and MY populations (P < 0.05), which indicated these populations might have not experienced historical expansion. According to the pairwise F-statistics, highly significant genetic differentiations were detected among populations (P < 0.01), with the exception of the IL and MY populations (P > 0.05). The nearest K2P genetic distance (D = 0.014) was detected between the MS and TW populations, whereas, the farthest (D = 0.101) was found between the GIFT and AR populations. The results from the molecular variance analysis (AMOVA) showed that there was an extremely significant genetic variation observed among the populations (P < 0.01), which contained 63.57% of the total variation. In view of the genetic relationship of red tilapia strains with other populations, TW and IL were detected with more similar genetic structures related to MS, and MY was more genetically similar to GIFT (or NL), which could provide more genetic evidence for the red tilapia strains maternal ancestry.

Polymorphism and Genetic Diversity among Cassava Cultivars based on ITS1-5.8S-ITS2 Sequences of rDNA

2017 ◽  
Vol 6 (6) ◽  
pp. 220-227
Author(s):  
Djirabaye Nadjiam ◽  
Aliou Guisse ◽  
Mbacké Sembéne ◽  
Fatimata Mbaye
Keyword(s):  
Genetic Diversity ◽  
Bayesian Approach ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Nucleotide Sequences ◽  
Its2 Region ◽  
Neighbor Joining ◽  
High Haplotype Diversity ◽  
The Bayesian Approach

Cassava is an important crop in the southern area of the Chad and it is char- acterized by many cultivars. But these cultivars have never been evaluated at the molecular level. Therefore, the objective of this study was to analyze their genetic diversity and their phylogenetic relationships. After DNA extraction, amplification and sequencing, the nucleotide sequences of the ITS1- 5.8S-ITS2 region of the ribosomal DNA of 12 selected cultivars have been analyzed. The Neighbor-Joining method, Maximum Parsimony, Maximum Likelihood and the Bayesian approach allowed studying the ancestral links. The identified nucleotide sequences have 542 bp. The targeted genes showed 468 conserved sites and 59 polymorphic sites. The nucleotide frequency was 18.64% for Adenine, 14.01% for Thymine, 34.46% for Cytosine and 32.89% for Guanine. The (G + C) content was 67.35% compared to 32.65% for the (A+T). The substitution rate was in favor of the transversions (67.46%) against the transitions (32.54%). The analysis revealed high haplotype diversity (Hd=0.954) and low nucleotide diversity (π=0.026) with an average number of pairwise nucleo de di erences (k=14.045). On the all popula on, 9 haplotypes, including 6 individual and 3 double, were identified. Gene c di eren a on is medium (FST=0.314) with a low number of migrants (Nm=0.55) and a medium genetic distance (0.028). Phylogenetic analysis based on the Bayesian approach revealed three groups of cul vars with the existence of two strongly supported clades. The cultivars studied are characterized by demographic stability or moderate population growth.They will be incorporated in the breeding program in order to limit their genetic erosion and to select the interesting characters. 

scholarly journals Maternal Origins and Haplotype Diversity of Seven Russian Goat Populations Based on the D-loop Sequence Variability

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1603
Author(s):  
Tatiana Deniskova ◽  
Nekruz Bakoev ◽  
Arsen Dotsev ◽  
Marina Selionova ◽  
Natalia Zinovieva
Keyword(s):  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Maternal Origin ◽  
Migration Routes ◽  
Altai Mountain ◽  
Loop Sequence ◽  
Genetic Pattern ◽  
D Loop ◽  
Diverse Groups ◽  
Official Recognition

The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai Mountain (n = 9), Dagestan Downy (n = 18), Dagestan Local (n = 12), Dagestan Milk (n = 15), Karachaev (n = 21), Orenburg (n = 10), and Soviet Mohair (n = 7) breeds, based on 715 bp D-loop mitochondrial DNA (mtDNA) sequences. Saanen goats (n = 5) were used for comparison. Our findings reveal a high haplotype (HD = 0.843–1.000) and nucleotide diversity (π = 0.0112–0.0261). A total of 59 haplotypes were determined in the Russian goat breeds, in which all differed from the haplotypes of the Saanen goats. The haplotypes identified in Altai Mountain, Orenburg, Soviet Mohair, and Saanen goats were breed specific. Most haplotypes (56 of 59) were clustered together with samples belonging to haplogroup A, which was in accordance with the global genetic pattern of maternal origin seen in most goats worldwide. The haplotypes that were grouped together with rare haplogroups D and G were found in the Altai Mountain breed and haplogroup C was detected in the Soviet Mohair breed. Thus, our findings revealed that local goats might have been brought to Russia via various migration routes. In addition, haplotype sharing was found in aboriginal goat populations from overlapping regions, which might be useful information for their official recognition status.

scholarly journals Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1970
Author(s):  
Emel Özkan Ünal ◽  
Fulya Özdil ◽  
Selçuk Kaplan ◽  
Eser Kemal Gürcan ◽  
Serdar Genç ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Loop Region ◽  
Geographical Regions ◽  
D Loop ◽  
Significant Comparison ◽  
Loop Regions ◽  
Frequent Haplotype

In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.

scholarly journals The very low genetic variability on Aceh Tamiang’s (Indonesia) population of Painted Terrapin (Batagur borneoensis) inferred by cytochrome oxidase I (CO I) and D-loop (control region)

2020 ◽  
Vol 21 (6) ◽  
Author(s):  
JOKO GUNTORO ◽  
WIRDATETI ◽  
AWAL RIYANTO
Keyword(s):  
Genetic Variability ◽  
Cytochrome Oxidase ◽  
Control Region ◽  
Haplotype Diversity ◽  
Cytochrome Oxidase I ◽  
Conservation Strategy ◽  
Wild Populations ◽  
Loop Control ◽  
Loop Region ◽  
D Loop

Abstract. Guntoro J, Wirdateti, Riyanto A. 2020. The very low genetic variability on Aceh Tamiang’s (Indonesia) population of Painted Terrapin (Batagur borneoensis) inferred by cytochrome oxidase I (CO I) and D-loop (control region). Biodiversitas 21: 2514-2520. Populations of Batagur borneoensis have been rapidly decreasing due to the harvesting of adults and eggs for food and the construction of beachfront property causing the loss of nesting areas. By the new Indonesian regulation, since 2018 this turtle listed in the protected animal. Meanwhile, IUCN placed as critically endangered which indicating a high risk of extinction in the wild in the near future (www.iucnredlist.org). We used cytochrome oxidase I (COI) and control region D-loop region to investigate intraspecific variations on Aceh Tamiang’s population of painted terrapin, Batagur borneoensis. DNA material was gathered from saliva collected from 90 juveniles in the reaching facility of Sukacita Lestari Indonesia Foundation which hatched from eggs collected from December 2015 to April 2016 from 30 nests on beach area at Aceh Tamiang. The population showed very low genetic variability (haplotype diversity, Hd = 0.457 based on COI and 0.405 based on D-loop; nucleotide diversity, π = 0.00089 based on COI and 0.00076 based on D-loop). So, we suggested that further study such as more exploration to find new wild populations and genetic study across wild populations should be done to reveal genetic variability and genetic structure which important to decide the conservation strategy. At the time for Aceh Tamiang's population, the ranching conservation program should be maintained at least to keep the successful hatchling from hunters and natural predators both during eggs laying and hatching.

scholarly journals A PRELIMINARY COMPARISON OF MITOCHONDRIAL D-LOOP REGION OF FUNAAB ALPHA AND NIGERIAN INDIGENOUS CHICKENS

2021 ◽  
Vol 20 (1) ◽  
pp. 1-11
Author(s):  
S.O. DUROSARO ◽  
B.T. OSHINOWO ◽  
A.C. AKPOJO ◽  
L.T. OLUYOMBO ◽  
I.C. NWOSU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Nucleotide Polymorphisms ◽  
Indigenous Chickens ◽  
Loop Region ◽  
D Loop ◽  
Selective Forces ◽  
Loss Of Diversity

Nigerian indigenous chickens possess immunity from endemic diseases and have a better survival rate than commercial hybrid strains under local production conditions. FUNAAB Alpha chicken was developed by improving Nigerian indigenous chickens through crossbreeding and selection. This study compared the mitochondrial d-loop of FUNAAB Alpha and Nigerian indigenous chickens to check likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Blood samples were collected from Nigerian indigenous (n=23) and FUNAAB Alpha (n=20) chickens sampled from farms and houses in Ogun state, Nigeria. The Hypervariable 1 (HV1) of the mitochondrial d-loop region was amplified and sequenced. Single nucleotide polymorphisms present in HV1 of chickens were identified using Clustal W. Genetic diversity of the region was determined using DnaSp v5 while selective forces acting on the chickens were predicted using HyPhy software implemented inside MEGA 6 software. Phylogenetic relationship among FUNAAB Alpha, Nigerian indigenous and other chicken breeds was determined using MEGA 6 software. Five polymorphisms were identified in FUNAAB Alpha chickens while twelve were identified in Nigerian indigenous chickens. All the polymorphisms identified in FUNAAB Alpha chickens were also observed in Nigerian indigenous chickens while seven polymorphisms were unique to Nigerian indigenous chickens. Higher diversity indices were observed in Nigerian indigenous chickens (number of haplotype: 4; haplotype diversity: 0.743±0.012; nucleotide diversity: 0.014±0.0013 and average number of nucleotide differences: 4.332) compared with FUNAAB Alpha chickens (number of haplotype: 2; haplotype diversity: 0.485±0.001; nucleotide diversity: 0.008±0.0001 and average number of nucleotide differences: 2.424). Positive selective forces were acting on FUNAAB Alpha chickens while negative selective forces were acting on Nigerian indigenous chickens. Phylogenetic analysis revealed that FUNAAB Alpha chickens clustered with Nigerian indigenous and South American chickens. It can be concluded that there was likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Breeding programmes aimed at improvement of genetic diversity and reduction of genetic erosion should be applied in subsequent improvement of FUNAAB Alpha chickens.

scholarly journals Genetic Diversity and Population Structure of Endangered Indian Catfish, Clarias magur as Revealed by mtDNA D-loop Marker

2020 ◽  
Vol 21 (01) ◽  
pp. 9-18
Author(s):  
Lakshman Sahoo ◽  
Ashoktaru Barat ◽  
Sangram Ketan Sahoo ◽  
Bismay Sahoo ◽  
Gargee Das ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Habitat Degradation ◽  
Haplotype Diversity ◽  
Improvement Program ◽  
Loop Control ◽  
Population Genetic Differentiation ◽  
Geographical Regions ◽  
D Loop

Clarias magur, popularly known as magur, is one of the economically important catfish species having high aquaculture potential in India due to its efficient food conversion, taste, and nutritional benefits. Due to habitat degradation, over exploitation, lack of resources, indiscriminate use of agricultural pesticides and introduction of competitor exotic species, the wild populations are dwindling day by day. According to IUCN, it is listed as endangered species. In the present study, the population genetic structure of 206 magur samples collected from seven different geographical regions was examined using partial mitochondrial D-loop (control region) sequence variation. In total of 17 haplotypes were observed with high number of private alleles, number of haplotypes ranged from 2 to 6 and maximum number of haplotypes was observed in UP population. Haplotype diversity and nucleotide diversity ranged from 0.06897 to 0.76322 and 0.00019 to 0.00208, respectively. Pairwise FST values ranged from 0.01383 to 0.62069 and highest genetic differentiation was observed between AP and AS population. Low genetic diversity and significant population genetic differentiation was observed in the present study. The information generated in the present investigation would facilitate formulating appropriate strategy for management, conservation, and genetic improvement program of this commercially important aquaculture species.

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