Mitochondrial phylogeography reveals high haplotype diversity and unique genetic lineage in Indian dugongs ( Dugong dugon )

2020 ◽  
Author(s):  
Yellapu Srinivas ◽  
Anant Pande ◽  
Swapnali Gole ◽  
P.V.R. Prem Jothi ◽  
K. Madhu Magesh ◽  
...  
Keyword(s):  
Haplotype Diversity ◽  
Genetic Lineage ◽  
High Haplotype Diversity

scholarly journals Phylogeography of Bulinus truncatus (Audouin, 1827) (Gastropoda: Planorbidae) in Selected African Countries

2018 ◽  
Vol 3 (4) ◽  
pp. 127 ◽  
Author(s):  
Eniola Abe ◽  
Yun-Hai Guo ◽  
Haimo Shen ◽  
Masceline Mutsaka-Makuvaza ◽  
Mohamed Habib ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Haplotype Diversity ◽  
Snail Host ◽  
Snail Species ◽  
African Countries ◽  
Urinary Schistosomiasis ◽  
Bulinus Truncatus ◽  
High Haplotype Diversity ◽  
Gene Coi ◽  
Mitochondrial Cytochrome Oxidase

The transmission of some schistosome parasites is dependent on the planorbid snail hosts. Bulinus truncatus is important in urinary schistosomiasis epidemiology in Africa. Hence, there is a need to define the snails’ phylogeography. This study assessed the population genetic structure of B. truncatus from Giza and Sharkia (Egypt), Barakat (Sudan) and Madziwa, Shamva District (Zimbabwe) using mitochondrial cytochrome oxidase subunit 1 gene (COI) and internal transcribed spacer 1 (ITS 1) markers. COI was sequenced from 94 B. truncatus samples including 38 (Egypt), 36 (Sudan) and 20 (Zimbabwe). However, only 51 ITS 1 sequences were identified from Egypt (28) and Sudan (23) (because of failure in either amplification or sequencing). The unique COI haplotypes of B. truncatus sequences observed were 6, 11, and 6 for Egypt, Sudan, and Zimbabwe, respectively. Also, 3 and 2 unique ITS 1 haplotypes were observed in sequences from Egypt and Sudan respectively. Mitochondrial DNA sequences from Sudan and Zimbabwe indicated high haplotype diversity with 0.768 and 0.784, respectively, while relatively low haplotype diversity was also observed for sequences from Egypt (0.334). The location of populations from Egypt and Sudan on the B. truncatus clade agrees with the location of both countries geographically. The clustering of the Zimbabwe sequences on different locations on the clade can be attributed to individuals with different genotypes within the population. No significant variation was observed within B. truncatus populations from Egypt and Sudan as indicated by the ITS 1 tree. This study investigated the genetic diversity of B. truncatus from Giza and Sharkia (Egypt), Barakat area (Sudan), and Madziwa (Zimbabwe), which is necessary for snail host surveillance in the study areas and also provided genomic data of this important snail species from the sampled countries.

Cross-fertilization as a reproductive strategy in a tissue flukesDidymosulcus katsuwonicola(Platyhelmintes: Didymozoidae) inferred by genetic analysis

Parasitology ◽  
2015 ◽  
Vol 142 (11) ◽  
pp. 1422-1429
Author(s):  
IVONA MLADINEO ◽  
MARINA TOMAŠ ◽  
RINO STANIĆ
Keyword(s):  
Life Cycle ◽  
Haplotype Diversity ◽  
Common Mechanism ◽  
High Haplotype Diversity ◽  
Atlantic Bluefin Tuna ◽  
Food Borne ◽  
Self Fertilization ◽  
Successful Fulfillment ◽  
Cross Fertilization ◽  
Host Tissues

SUMMARYMitochondrial DNA locus cytochrome oxidase I was used to asses intraspecific genetic diversity of a didymozoid speciesDidymosulcus katsuwonicola.Adult forms of this species live encapsulated in pairs in the gills of the reared Atlantic bluefin tuna (Thunnus thynnus). The life cycle of this food-borne parasites and its migration in the host tissues after releasing from the digestive tract to the definitive site in the gills are unknown. Our goal was to assess whether two encysted didymozoids share the same haplotype, indicative of a common maternal origin, as well as the extent of cross- in respect to self-fertilization strategy. Intraspecific comparison showed high haplotype diversity, while the presence of two matching haplotypes within a single cyst encompassed only 17% of sampled individuals. This infers that cross-fertilization between paired individuals within the cyst is more common mechanism than self-fertilization. Such hermaphroditic parasite's trait suggests the existence of intricate infection and reproduction mechanisms, presumably as an adaptation for successful fulfillment of their indirect life cycle through dissemination of genetically more diverse and consequently more fit offspring.

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 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 Inter-island dispersal of flightless Bothrometopus huntleyi (Coleoptera: Curculionidae) from the sub-Antarctic Prince Edward Island archipelago

2011 ◽  
Vol 23 (3) ◽  
pp. 225-234 ◽  
Author(s):  
G.C. Grobler ◽  
A.D.S. Bastos ◽  
C.T. Chimimba ◽  
S.L. Chown
Keyword(s):  
Gene Flow ◽  
Prince Edward Island ◽  
Haplotype Diversity ◽  
Marion Island ◽  
High Haplotype Diversity ◽  
Prince Edward Islands ◽  
Cytochrome Oxidase I Gene ◽  
Low Levels ◽  
Dispersal Events ◽  
I Gene

AbstractBothrometopus huntleyi is a flightless weevil endemic to the volcanically-formed sub-Antarctic Prince Edward Islands archipelago that arose approximately 0.5 million years ago (m.y.a.). Since emergence, a series of volcanic and glaciation events have occurred on Marion Island, whilst Prince Edward Island, the second island constituting the archipelago, has remained largely unaffected by glaciation. Cytochrome oxidase I gene analyses indicate that major historical dispersal events in this species are linked to the geologically discrete histories of these islands and underlie the high haplotype diversity (0.995) recovered for the Prince Edward Islands archipelago. The estimated time to haplotype coalescence of ∼ 0.723 m.y.a. is in keeping with estimated dates of island emergence, and the majority of individuals appear to have descended from a relict, high-altitude population that is still present on Marion Island. The first major inter-island dispersal event occurred ∼ 0.507 m.y.a., coinciding with the oldest dated rocks on Marion Island. Apart from this early inter-island colonization, only one other between-island dispersal event was detected. The genetically discrete B. huntleyi complexes on each of the islands of the Prince Edward Islands archipelago together with the low levels of inter-island gene flow reaffirm the need to control alien invasive mice, which are restricted to Marion Island, and which prey on this weevil species.

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.

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 Haplogroup Distribution of 309 Thais from Admixed Populations across the Country by HVI and HVII Sanger-Type Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 496
Author(s):  
Prapatsorn Areesirisuk ◽  
Kornsorn Srikulnath ◽  
Preyaporn Onsod ◽  
Juthamas Jaroensuk ◽  
Budsaba Rerkamnuaychoke
Keyword(s):  
Population Sample ◽  
Haplotype Diversity ◽  
Thai Population ◽  
High Haplotype Diversity ◽  
Forensic Casework ◽  
Asian Populations ◽  
Hypervariable Regions ◽  
Historical Factors ◽  
Control Region Sequences ◽  
Haplogroup Distribution

The mitochondrial DNA (mtDNA) control region sequences for the hypervariable regions I (HVI) and II (HVII) of 309 Thai citizens were investigated using Sanger-type sequencing to generate an mtDNA reference dataset for forensic casework, and the haplogroup distribution within geographically proximal Asian populations was analyzed. The population sample set contained 264 distinct haplotypes and showed high haplotype diversity, low matching probability, and high powers of discrimination, at 0.9985, 0.4744%, and 0.9953, respectively, compared with previous reports. Subhaplogroup F1a showed the highest frequency in the Thai population, similar to Southeast Asian populations. The haplotype frequencies in the northern, northeastern, and southern populations of Thailand illustrate the relevance of social, religious, and historical factors in the biogeographical origin of the admixed Thai population as a whole. The HVI and HVII reference datasets will be useful for forensic casework applications, with improved genetic information content and discriminatory power compared to currently available techniques.

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. 

Population structure of Cicada barbara Stål (Hemiptera, Cicadoidea) from the Iberian Peninsula and Morocco based on mitochondrial DNA analysis

2007 ◽  
Vol 98 (1) ◽  
pp. 15-25 ◽  
Author(s):  
G.A. Pinto-Juma ◽  
J.A. Quartau ◽  
M.W. Bruford
Keyword(s):  
Population Structure ◽  
Iberian Peninsula ◽  
Dna Analysis ◽  
Haplotype Diversity ◽  
Molecular Data ◽  
Climatic Conditions ◽  
Isolated Populations ◽  
High Haplotype Diversity ◽  
Mitochondrial Dna Analysis ◽  
Northwest Region

AbstractWe assess the genetic history and population structure of Cicada barbara in Morocco and the Iberian Peninsula, based on analysis of the mitochondrial cytochrome b gene. The divergence between Morocco and the Iberian Peninsula populations was strongly corroborated by the molecular data, suggesting genetically isolated populations with a low level of gene flow. The Ceuta population from Spanish North Africa was more similar to the Iberian populations than the surrounding Moroccan populations, suggesting that the Strait of Gibraltar has not been acting as a strict barrier to dispersal while the Rif Mountains have. The Iberian Peninsula specimens showed a signature of demographic expansion before that which occurred in Morocco, but some of the assumptions related to the demographic parameters should be considered with caution due to the small genetic variation found. The high haplotype diversity found in Morocco implies higher demographic stability than in the Iberian Peninsula populations. These results do not, however, suggest a Moroccan origin for Iberian cicadas; but the most northwest region in Africa, such as Ceuta, might have acted as a southern refuge for Iberian cicadas during the most severe climatic conditions, from where they could expand north when climate improved. The separation of two subspecies within C. barbara (C. barbara lusitanica and C. barbara barbara) finds support with these results.

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