High haplotype diversity in a microendemic Malagasy gecko species, Lygodactylus mirabilis (Pasteur, 1962)

Zootaxa ◽  
2009 ◽  
Vol 2269 (1) ◽  
pp. 43-52
Author(s):  
YLENIA CHIARI ◽  
DAVID R. VIEITES ◽  
JERRY GUO ◽  
PARFAIT BORA ◽  
MIGUEL VENCES
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Distribution Area ◽  
Low Frequencies ◽  
High Haplotype Diversity ◽  
Mitochondrial Data ◽  
Distribution Ranges ◽  
Report Data ◽  
Past Population

Among Malagasy montane reptiles, the diurnal gecko Lygodactylus mirabilis has one of the most restricted distribution ranges, occurring only on the Tsiafajavona mountain on the Ankaratra massif. Here we report data on the current distribution of this species and its genetic diversity. Mitochondrial data based on samples collected in the only previously known distribution area (the Tsiafajavona peak) showed numerous haplotypes at low frequencies, suggesting a past population expansion and a relatively high within-species genetic diversity in an extremely small distribution area. Our field survey also revealed that the range of the species is larger than previously thought, but still is extremely small and restricted to the Ankaratra massif.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

scholarly journals VARIASI GENETIK TIGA POPULASI IKAN NILA ( Oreochromis niloticus ) BERDASARKAN POLIMORFISME mt-DNA

2016 ◽  
Vol 2 (1) ◽  
pp. 67
Author(s):  
Otong Zenal Arifin ◽  
Titin Kurniasih
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Oreochromis Niloticus ◽  
Selective Breeding ◽  
Haplotype Diversity ◽  
Mt Dna ◽  
High Haplotype Diversity ◽  
Freshwater Aquaculture ◽  
Preliminary Information ◽  
Nile Tilapia Oreochromis Niloticus

Penelitian untuk mengevaluasi keragaman genetik tiga populasi ikan nila telah dilakukan di Balai Riset Perikanan Budidaya Air Tawar, Bogor. Penelitian ini bertujuan untuk mendapatkan informasi variasi genetik ikan nila populasi GET, GIFT, dan nila Danau Tempe sebagai informasi dasar bagi program seleksi karakter kuantitatif. Hasil menunjukkan bahwa ikan nila GET, GIFT, dan nila Danau Tempe memiliki keragaman genetik yang tinggi dengan nilai haplotype diversity berturut-turut sebesar 0,7579; 0,5895; dan 0,5333. Jarak genetik terdekat terdapat antara ikan nila GIFT dan nila Danau Tempe, sedangkan jarak genetik terjauh terdapat pada ikan nila GET dengan populasi Danau Tempe.Research on evaluating genetic diversity between three populations of nile tilapia ( Oreochromis niloticus ) was conducted at Research Institute for Freshwater Aquaculture, Bogor. This research aimed to obtain preliminary information related with the genetic diversity of GET, GIFT, and Tempe Lake tilapia, which will be used as basic information for the future selective breeding program. Result showed that GET, GIFT, and Tempe Lake tilapia have high haplotype diversity of 0.7579, 0.5895, and 0.5333 respectively. The closest genetic distance was found between GIFT and Tempe Lake tilapia, while the farthest genetic distance was observed between GET and the Tempe Lake population.

scholarly journals Short Communication: Genetic diversity of scalloped hammerhead sharks (Sphyrna lewini) landed in Muncar Fishing Port, Banyuwangi

2019 ◽  
Vol 20 (4) ◽  
pp. 1154-1159 ◽  
Author(s):  
FAQIH AKBAR ALGHOZALI ◽  
DIAH PERMATA WIJAYANTI ◽  
AGUS SABDONO
Keyword(s):  
Genetic Diversity ◽  
Short Communication ◽  
Polymerase Chain Reaction Amplification ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Fishing Ground ◽  
Sphyrna Lewini ◽  
Scalloped Hammerhead ◽  
Hammerhead Sharks ◽  
Longline Fisheries

Abstract. Alghozali FA, Wijayanti DP, Sabdono A. 2019. Short Communication: Genetic diversity of scalloped hammerhead sharks (Sphyrna lewini) landed in Muncar Fishing Port, Banyuwangi. Biodiversitas 20: 1154-1159. The majority of sharks caught in Indonesian fisheries were bycatch products from the tuna longline fisheries, but some regions in Indonesia fish the sharks as their main target. One of these regions is located in Muncar, Banyuwangi, which fishes the endangered Scalloped Hammerhead sharks (Sphyrna lewini) as target species. This research aimed to study the genetic diversity of the endangered Scalloped Hammerhead sharks landed in Muncar Fishing Port, Banyuwangi. Genetic analysis was done through PCR (Polymerase Chain Reaction) amplification and sequencing of the mitochondrial DNA COI (Cytochrome Oxidase subunit I) gene. Out of the 37 samples collected, 30 were successfully amplified and sequenced.The results showed moderate haplotype diversity (Hd: 0,582 ± 0,079) and low nucleotide diversity (π: 0,00392± 0,0024) with five haplotypes (h) and 26 polymorphic sites (S). Tajima’s D neutrality model values indicated a population expansion event. Two different clades were determined through phylogenetic analysis and by GenBank sequences comparison. These results provided basic information and present status of the Scalloped Hammerhead sharks population genetically within the fishing ground (Makassar Strait-Kangean Islands).

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 Novel Insights Into the Genetic Population Connectivity of Transient Whale Sharks (Rhincodon typus) in Pacific Panama Provide Crucial Data for Conservation Efforts

2021 ◽  
Vol 8 ◽  
Author(s):  
Héctor M. Guzmán ◽  
Caitlin E. Beaver ◽  
Edgardo Díaz-Ferguson
Keyword(s):  
Genetic Diversity ◽  
Gulf Of California ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Population Connectivity ◽  
Region Gene ◽  
Genetic Population ◽  
Regional Patterns ◽  
Rhincodon Typus ◽  
Whale Sharks

The whale shark (Rhincodon typus) is an endangered and highly migratory species, of which solitary individuals or aggregations are observed in oceans worldwide and for which conservation efforts are hindered by a lack of comprehensive data on genetic population connectivity. Tissue samples were collected from wandering whale sharks in Pacific Panama to determine genetic diversity, phylogeographic origin, and possible global and local connectivity patterns using a 700–800 bp fragment of the mitochondrial control region gene. Genetic diversity among samples was high, with five new haplotypes and nine polymorphic sites identified among the 15 sequences. Haplotype diversity (Hd = 0.83) and nucleotide diversity (π = 0.00516) were similar to those reported in other studies. Our sequences, in particular haplotypes PTY1 and PTY2, were similar to those previously reported in the Arabian Gulf and the Western Indian Ocean populations (a novel occurrence in the latter case). Haplotypes PTY3, PTY4, and PTY5 were similar to populations in Mexico and the Gulf of California. In contrast, the only populations to which our Panamanian sequences were genetically dissimilar were those from the Atlantic Ocean. The absence of reference sequences in GenBank from southern sites in the Eastern Tropical Pacific, such as Galapagos (Ecuador), Gorgona and Malpelo Islands (Colombia), and Coco Island (Costa Rica), reduced our capacity to genetically define regional patterns. Genetic differentiation and connectivity were also assessed using an analysis of molecular variance (AMOVA), which showed a similar population structure (five groups) to the neighbor-joining tree. Other population features based on neutrality tests, such as Tajima’s D and Fu’s Fs statistics, showed positive values for Panama of 0.79 and 1.61, respectively. Positive values of these statistics indicate a lack of evidence for population expansion among the sampled individuals. Our results agree with previous reports suggesting that whale sharks can travel over long distances and that transboundary conservation measures may be effective for species protection.

scholarly journals Post-Disturbance Genetic Changes: The Impact of the 2010 Mega-Earthquake and Tsunami on Chilean Sandy Beach Fauna

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Antonio Brante ◽  
Garen Guzmán-Rendón ◽  
Erwin M. Barría ◽  
Marie-Laure Guillemin ◽  
Iván Vera-Escalona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Adult Survival ◽  
Genetic Changes ◽  
Species Response ◽  
Emerita Analoga ◽  
Mtdna Sequence ◽  
The Impact

Abstract Earthquake/tsunamis can have profound impacts on species and their genetic patterns. It is expected that the magnitude of this impact might depend on the species and the time since the disturbance occurs, nevertheless these assumptions remain mostly unexplored. Here we studied the genetic responses of the crustacean species Emerita analoga, Excirolana hirsuticauda, and Orchestoidea tuberculata to the 27F mega-earthquake/tsunami that occurred in Chile in February 2010. mtDNA sequence analyses revealed a lower haplotype diversity for E. analoga and E. hirsuticauda in impacted areas one month after the 27F, and the opposite for O. tuberculata. Three years after the 27F we observed a recovery in the genetic diversity of E. analoga and E. hirsuticauda and decrease in the genetic diversity in O. tuberculata in 2/3 of sampled areas. Emerita analoga displayed decrease of genetic differentiation and increase in gene flow explained by long-range population expansion. The other two species revealed slight increase in the number of genetic groups, little change in gene flow and no signal of population expansion associated to adult survival, rapid colonization, and capacity to burrow in the sand. Our results reveal that species response to a same disturbance event could be extremely diverse and depending on life-history traits and the magnitude of the effect.

scholarly journals Indo-Pacific Phylogeography of the Lemon Sponge Leucetta chagosensis

Diversity ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 466
Author(s):  
Olivier Pasnin ◽  
Oliver Voigt ◽  
Gert Wörheide ◽  
Andrea P. Murillo Rincón ◽  
Sophie von der Heyden
Keyword(s):  
Genetic Diversity ◽  
Spatial Variation ◽  
Haplotype Diversity ◽  
Wide Distribution ◽  
Evolutionary Patterns ◽  
High Haplotype Diversity ◽  
Sponge Diversity ◽  
The Indian Ocean ◽  
Biogeographic Regions ◽  
First Time

The sponge Leucetta chagosensis Dendy (1913) has a wide distribution throughout the Indo-Pacific (IP) region, with previous studies focussing primarily on the western Pacific Ocean. To increase our knowledge of the spatial variation of genetic diversity throughout the IP, we constructed a phylogeny for L. chagosensis for the IP to assess the evolutionary patterns for this species. We generated 188 sequences of L. chagosensis and constructed maximum likelihood and Bayesian inference trees, using concatenated mitochondrial cytochrome oxidase subunit 3 gene (cox3) and nuclear ribosomal RNA gene (28S) markers for the first time. The spatial variation of genetic diversity of L. chagosensis was assessed using a phylogeographic approach. Leucetta chagosensis is composed of five cryptic lineages confined to different biogeographic regions with the specimens found in the Indian Ocean differing significantly from those found in the rest of the IP region. Genetic divergence was particularly high for the cox3 marker, with a low nucleotide diversity but high haplotype diversity for most lineages. This study highlights the need for a sustained effort in studying sponge diversity, boosted by the ongoing discovery of hidden biodiversity among this ecologically important taxon.

scholarly journals Genetic Diversity and Distribution ofBlastocystisSubtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Liliana Rojas-Velázquez ◽  
Patricia Morán ◽  
Angélica Serrano-Vázquez ◽  
Leonardo D. Fernández ◽  
Horacio Pérez-Juárez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Human Population ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Human Populations ◽  
High Haplotype Diversity ◽  
Genetic Diversity And Structure ◽  
High Prevalence ◽  
The World ◽  
Parasitic Protist

Blastocystissubtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity ofBlastocystisST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations ofBlastocystisST3 from other regions of the planet. Our analyses reveled that diversity ofBlastocystisST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity ofBlastocystisST3 worldwide.

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 Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nur Ilham Syahadah Mohd Yusoff ◽  
Tun Nurul Aimi Mat Jaafar ◽  
Veera Vilasri ◽  
Siti Azizah Mohd Nor ◽  
Ying Giat Seah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Resource Management ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Dna Recombination ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Management Program ◽  
Sampling Station

AbstractBenthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490–0.900, nucleotide diversity, π = 0.0010–0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118–0.216; π = 0.0004–0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.

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