scholarly journals Keragaman Genetik Kukang Jawa (Nycticebus javanicus) Menggunakan Control Region (D-loop) DNA Mitokondria (mtDNA) (GENETIC DIVERSITY ON JAVAN SLOW LORIS (NYCTICEBUS JAVANICUS) USING OF CONTROL REGION (D-LOOP) mtDNA)

2019 ◽  
Vol 20 (3) ◽  
pp. 360
Author(s):  
Wirdateti Wirdateti ◽  
Hayati Aziza ◽  
Handayani Handayani
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Control Region ◽  
West Java ◽  
Slow Loris ◽  
Genetic Population ◽  
Central Java ◽  
Low Genetic Diversity ◽  
The Status ◽  
D Loop

Javan slow loris (Nycticebus javanicus)  one of the species of the genus Nycticebus is endemic in Java.  Their distribution region  is in West Java and Banten, and also reported to be found in Central Java and East Java, although very rarely.  Status of the species is Critically Endangered due to high levels of poaching, habitat loss and habitat fragmentation, so that the necessary conservation in order to increase the population. For conservation management it is necessary to know the status of genetic resources that play of  role in breeding, then this research is to explore the genetic population of the Javan slow loris  from some locations in West Java. The research objective was to assess the diversity of their current population of Java loris through the control region (D-loop) of mitochondrial DNA (mtDNA). A total of 23 individuals samples from Gunung Halimun Park, Tasikmalaya, Garut, Ciamis, Jember and confiscated at the Rehabilitation Center IAR Bogor were used in this stydy. Specific primers of D-loop are used for loris with a length of 296 bp sequence. The result showed there are only five different sites and formed six haplotypes, each haplotypes only 1-3 nucleotides different. Low genetic diversity is shown as much as 42.96% of individuals show the same sequence or genetic distance (d) = 0 that indicate was monomorf population from different population. The genetic distance of the entire population was 0.003 ± 0:01 (0.3%).

scholarly journals Low Genetic Diversity of the Endangered Franciscana (Pontoporia blainvillei) in Its Northernmost, Isolated Population (FMAIa, Espírito Santo, Brazil)

2020 ◽  
Vol 7 ◽  
Author(s):  
Vanessa K. M. de Oliveira ◽  
Drienne M. Faria ◽  
Haydée A. Cunha ◽  
Teresa E. C. dos Santos ◽  
Adriana C. Colosio ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Microsatellite Loci ◽  
Distribution Analysis ◽  
Sample Number ◽  
Espírito Santo ◽  
Low Genetic Diversity ◽  
Southwestern Atlantic Ocean ◽  
Espirito Santo ◽  
Pontoporia Blainvillei

The franciscana, Pontoporia blainvillei, is the most endangered small cetacean in the Southwestern Atlantic Ocean, occurring from Itaúnas, Espírito Santo, Brazil to Chubut province, Argentina. This area is divided into four Franciscana Management Areas (FMA). The northern portion of this species distribution is not continuous and a previous genetic study using mitochondrial DNA (mtDNA) separated it into FMAIa (Espírito Santo state) and FMAIb (North of Rio de Janeiro state). In order to increase the information about this population we expanded the sample number and evaluated mitochondrial and nuclear DNA diversity. Samples of 68 franciscanas found stranded on beaches from 2005 to 2020 were analyzed. Analyses included 350 bp of the mtDNA control region (D-loop) and 12 microsatellite loci. We identified three control region haplotypes in FMAIa, two of them not previously observed in this population, one being a new haplotype. Haplotype and nucleotide diversities were 0.0408 and 0.00012 respectively, the lowest reported for all FMAs analyzed until now. The Neutrality tests were not significant and Mismatch Distribution analysis did not reject the hypothesis of population expansion. One of the microsatellite loci was monomorphic, and for the other loci, two to nine alleles were identified, with expected heterozygosities ranging from 0.306 to 0.801. No substructure was revealed and effective population size (Ne) was estimated in 117.9 individuals. Even with an increased sample size, the high mitochondrial genetic homogeneity suggested for the population in a previous study was confirmed. Among six loci previously analyzed in other franciscana populations, five showed the lowest observed heterozygosities for the Espírito Santo population. The novel microsatellite data also showed low genetic diversity and could not reject the hypothesis of a single, panmitic population along the coast of Espírito Santo. This species has been intensively impacted in the last years by incidental capture during fishing activities and habitat degradation, caused by pollution, coastal development and environmental disasters in FMAIa. Considering that this population is small, isolated, and with low levels of genetic diversity, we reinforce the necessity of different conservation actions, focusing mainly on the reduction of bycatch of this species in the region.

scholarly journals Origin, Genetic Diversity, and Population Structure of Rabbits (Oryctolagus cuniculus) in Kenya

2019 ◽  
Vol 2019 ◽  
pp. 1-6 ◽  
Author(s):  
Sharon Auma Owuor ◽  
Edward George Mamati ◽  
Remmy Wekesa Kasili
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Western Region ◽  
Eastern Region ◽  
Low Genetic Diversity ◽  
Loop Region ◽  
Agriculture Industry ◽  
D Loop ◽  
Breeding Programmes ◽  
Geographic Regions

To evaluate the origin, genetic diversity, and population structure of domesticated rabbits in Kenya, a 263-base pair region of mtDNA D-loop region of 111 rabbits sampled from Kakamega, Vihiga, and Bungoma counties in the western region, Laikipia and Nyandarua counties in the central region, and Kitui, Machakos, and Makueni in the eastern region of the country were analyzed. The average haplotype (0.40702) and nucleotide (0.01494) diversities observed were low, indicating low genetic diversity of domesticated rabbits in Kenya. This study resolved 5 unique haplotypes in the mtDNA D-loop region. A population genetic structure distinguishing Europe grouping and domesticated rabbits in Kenya was obtained on incorporating 32 known haplotypes. Domesticated rabbits in Kenya clustered together with rabbits from other geographic regions, suggesting common origin. The results suggested that the Kenyan domesticated rabbits may have originated from Europe. Integration of exotic breeds into breeding programmes could have contributed to the low genetic diversity. These results provide useful information for breeding and conservation decisions by the relevant stakeholders in the agriculture industry in Kenya.

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 Low Genetic Diversity in Turkish Populations of Wels Catfish Silurus glanis L., 1758 (Siluridae, Pisces) Revealed by Mitochondrial Control Region Sequences

2020 ◽  
Vol 20 (10) ◽  
pp. 767-776
Author(s):  
Yusuf Bektas ◽  
Ismail Aksu ◽  
Gokhan Kalayci ◽  
Davut Turan
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Mismatch Distribution ◽  
Phylogenetic Trees ◽  
Goodness Of Fit ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Silurus Glanis ◽  
Low Genetic Diversity

This study aimed to investigate the genetic diversity and population structure of Wels catfish Silurus glanis L. 1758 in Turkey using squences of the mitochondrial DNA control region The 887-bp fragment of D-loop was aligned for 112 S. glanis individuals from ten wild populations in Turkey, defined by 29 polymorphic sites comprising 16 haplotypes. The low haplotype diversity and nucleotide diversity within each population ranged from 0.000 to 0.378 and from 0.0000 to 0.0045, respectively. Analysis of molecular variance showed significant genetic differentiation among ten populations (FST =0.940; P<0.01). AMOVA revealed that the most of genetic variation was found between Thrace and Anatolia clades (74,07 %). The phylogenetic trees and haplotype network topologies were consistent with the results of AMOVA analysis. The non-significant negative Tajima's D (-0.875 P<0.05) and Fu's Fs (-0.381, P<0.02) values and mismatch distribution for S. glanis populations indicated no evidence for changes in population size. Furthermore, goodness-of-fit of the observed versus the theoretical mismatch distribution tested the sum of squared deviation (SSD; 0.00308, P>0.05), Harpending’s raggedness index (Hri; 0,300, P>0.05) and Ramos-Onsins & Rozas (R2; 0,0771, P>0.05), supporting population neutrality.

scholarly journals Genetic diversity of Sragen Black Cattle based on D-Loop gene sequencing analysis

2020 ◽  
Vol 18 (2) ◽  
pp. 124
Author(s):  
Rahayu Kusumaningrum ◽  
Sutopo Sutopo ◽  
Edy Kurnianto
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Evolutionary Genetics ◽  
Sequencing Analysis ◽  
Dna Sequence Polymorphism ◽  
D Loop

<p class="MDPI17abstract"><strong>Objective: </strong>The objective of this study was to investigate the genetic diversity of Sragen Black Cattle based on D-loop sequences analysis.</p><p class="MDPI17abstract"><strong>Methods: </strong>A total of 25 blood samples belonged to Sragen Black Cattle that had no genetic relationship within sample. The DNA genome was extracted based on the manufacturer’s standard protocol using gSYNC DNA Mini Kit (Geneaid Biotech Ltd.). D-loop gene was amplified using specific primer forward: 5’- TAGTGCTAATACCAACGGCC-3’ and reverse: 5’- AGGCATTTTGAGTGCCTTGC-3’ and then was sequenced. The sequencing result was aligned and analyzed by Molecular Evolutionary Genetics Analysis (MEGA) version 6.0 to reveal genetic distance and phylogenetic tree. Genetic diversity and haplotype were analysed by DNA Sequence Polymorphism (DnaSp) v6.12.03.<strong></strong></p><p class="MDPI17abstract"><strong>Results: </strong>The results revealed that there were 11 haplotypes with Pi = 0.00675±0.00201 and Hd = 0.767±0.086. Sragen Black Cattle was divided by two cluster in phylogenetic tree with average of genetic distance was 0.0032.<strong></strong></p><p class="MDPI17abstract"><strong>Conclusions: </strong>In conclusion, all of Sragen Black Cattle are on the same cluster and have closer genetic relationship to Bos indicus rather than Bos taurus with similarity level 85.76 % based on BLAST program.</p>

scholarly journals Low genetic diversity in the Endangered Crested Ibis Nipponia nippon and implications for conservation

2004 ◽  
Vol 14 (3) ◽  
pp. 183-190 ◽  
Author(s):  
BEI ZHANG ◽  
SHENG-GUO FANG ◽  
YONG-MEI XI
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Haplotype Diversity ◽  
Mtdna Control Region ◽  
Significant Information ◽  
Nipponia Nippon ◽  
Low Genetic Diversity ◽  
Captive Populations ◽  
Crested Ibis ◽  
Wide Range

Crested Ibis Nipponia nippon is an Endangered species that has experienced a severe but short-lived population bottleneck in recent years. Only one wild population and two captive populations exist in China today, all of which were probably initiated from two breeding pairs rediscovered in 1981. This paper represents the first study of the genetic diversity of Crested Ibis by analysing sequence variation of a fragment spanning domains II and III of the mitochondrial DNA (mtDNA) control region of both wild and captive populations. Two haplotypes were identified in both wild and captive populations, and the captive population had a bias towards haplotype 1. The species as a whole demonstrated an extremely low level of genetic diversity, with a haplotype diversity and nucleotide diversity of 0.386 ± 0.074 and 0.069% ± 0.013%, respectively. Despite the rapid increase in numbers of birds under intensive management, the paucity of genetic diversity remains a real threat to the species. The mtDNA control region variations detected in the present study could provide significant information additional to the studbook data of Crested Ibis; therefore we suggest that special attention be paid to individuals with haplotype 2 when considering captive breeding management. Overall, great care should be taken in the selection of reintroduction sites for this rare bird, as species with low genetic diversity are thought to be more limited in their ability to tolerate a wide range of environmental extremes and diseases.

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