scholarly journals Phylogenetics and population genetics ofPlotosus canius(Siluriformes: Plotosidae) from Malaysian coastal waters

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1930 ◽  
Author(s):  
Nima Khalili Samani ◽  
Yuzine Esa ◽  
S.M. Nurul Amin ◽  
Natrah Fatin Mohd Ikhsan
Keyword(s):  
Genetic Structure ◽  
Small Sample Size ◽  
Genomic Structure ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Peninsular Malaysia ◽  
Small Sample ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Significant Finding

Plotosus canius(Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics ofP. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure ofP. caniusfor the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification ofTandanus tandanusmicrosatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho) value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho= 0.79). This alongside the highFisvalues estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotypeKR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure inP. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.

scholarly journals Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters

2016 ◽  
Author(s):  
Nima Khalili Samani ◽  
Yuzine Esa ◽  
S.M Nurul Amin ◽  
Natrah Fatin Mohd Ikhsan
Keyword(s):  
Genetic Structure ◽  
Small Sample Size ◽  
Genomic Structure ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Peninsular Malaysia ◽  
Small Sample ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Significant Finding

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.

scholarly journals Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters

2016 ◽  
Author(s):  
Nima Khalili Samani ◽  
Yuzine Esa ◽  
S.M Nurul Amin ◽  
Natrah Fatin Mohd Ikhsan
Keyword(s):  
Genetic Structure ◽  
Small Sample Size ◽  
Genomic Structure ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Peninsular Malaysia ◽  
Small Sample ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Significant Finding

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.

scholarly journals Phylogenetics and population genetics of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters

2016 ◽  
Author(s):  
Nima Khalili Samani ◽  
Yuzine Esa ◽  
Natrah Fatin Mohd Ikhsan ◽  
S.M Nurul Amin
Keyword(s):  
Genetic Structure ◽  
Small Sample Size ◽  
Genomic Structure ◽  
Haplotype Diversity ◽  
Marine Species ◽  
Peninsular Malaysia ◽  
Small Sample ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Significant Finding

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of more COI genes and nuclear hypervariable markers.

scholarly journals Phylogenetic analysis and population genetic study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters

2016 ◽  
Author(s):  
Nima Khalili Samani ◽  
Yuzine Esa ◽  
Natrah Fatin Mohd Ikhsan ◽  
Nurul Amin
Keyword(s):  
Genetic Structure ◽  
Population Genetic ◽  
Small Sample Size ◽  
Genomic Structure ◽  
Haplotype Diversity ◽  
Small Sample ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Significant Finding ◽  
Population Genetic Study

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively, which pointed out the unlikelihood of mutation effects on gene flow. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of more COI genes and nuclear hypervariable markers.

Genetic diversity and population structure of Synthesium pontoporiae (Digenea, Brachycladiidae) linked to its definitive host stocks, the endangered Franciscana dolphin, Pontoporia blainvillei (Pontoporiidae) off the coast of Brazil and Argentina

2013 ◽  
Vol 89 (1) ◽  
pp. 19-27 ◽  
Author(s):  
J. Marigo ◽  
H.A. Cunha ◽  
C.P. Bertozzi ◽  
S.P. Souza ◽  
F.C.W. Rosas ◽  
...  
Keyword(s):  
Population Structure ◽  
Small Sample Size ◽  
High Mobility ◽  
Biological Marker ◽  
Population Expansion ◽  
Intraspecific Variability ◽  
Small Sample ◽  
Coi Gene ◽  
Pontoporia Blainvillei

AbstractPontoporia blainvillei (Gervais and d'Orbigny, 1844) is an endangered small cetacean endemic to South America with four Franciscana Management Areas (FMA) recognized as different population stocks. The role of the intestinal parasite Synthesium pontoporiae (Digenea: Brachycladiidae) as a possible biological marker to differentiate P. blainvillei stocks was evaluated using nuclear and mitochondrial DNA markers. Internal transcribed sequence 1 and 2 (ITS1 and ITS2) regions of S. pontoporiae did not show intraspecific variability. The mitochondrial NADH dehydrogenase subunit 3 (ND3) and cytochrome oxidase subunit I (COI) gene sequences suggested lack of population structure in S. pontoporiae and population expansion. The apparent panmixia of S. pontoporiae may be due to the high mobility of one or more of its intermediary hosts. Alternatively, it may be due to the small sample size. This result is incongruent with the previously proposed FMA.

Effectiveness of the Weighted Blanket With Psychiatric Patients in the Emergency Department: A Pilot Study

2021 ◽  
pp. 107839032110267
Author(s):  
Debra A. Dickson ◽  
Laura Gantt ◽  
Melvin Swanson
Keyword(s):  
Emergency Department ◽  
Pilot Study ◽  
Small Sample Size ◽  
Psychiatric Patients ◽  
Small Sample ◽  
Control Group ◽  
Significant Finding ◽  
Control Group Design ◽  
Research With Children ◽  
Quasi Experimental

BACKGROUND Restraint and seclusion continue to be used with patients demonstrating aggressive and violent behaviors while in the emergency department and as inpatients in behavioral health (BH) units. The use of sensory interventions such as the weighted blanket (WB) is garnering interest as alternatives to aid in managing anxiety, anger, and aggressive behaviors. Reports of the effectiveness of the WB have primarily been anecdotal, and results of research with children have been mixed. Only one study has been conducted with the WB with adults on an inpatient psychiatric unit. OBJECTIVES The aim of this pilot study was to assess the effectiveness of the WB by determining whether it decreases anxiety and/or anger in adult emergency department patients with preexisting psychiatric diagnoses. METHODS The study used a quasi-experimental, nonequivalent control group design with pre- and posttests for anxiety and anger. The intervention was a 15-pound WB. Participants ( N = 15) were in one of three groups, which included no weighted blanket (NWB), WB for 15 minutes, or WB for 30 minutes. RESULTS All three groups showed a decrease in anxiety and anger scores. However, participants in the WB groups had a greater decrease in anxiety and anger posttest scores. CONCLUSIONS The small sample size in this study did not allow for the determination of any differences between groups on anxiety or anger scores that could be viewed as a significant finding.

scholarly journals Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand

2021 ◽  
Vol 32 (1) ◽  
pp. 61-80
Author(s):  
Verakiat Supmee ◽  
◽  
Apirak Songrak ◽  
Juthamas Suppapan ◽  
Pradit Sangthong ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Genetic Information ◽  
Population Genetic ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Andaman Sea ◽  
Gulf Of Thailand ◽  
The Gulf Of Thailand

Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The Analysis of molecular variance (AMOVA) analysis, pairwise FST, and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.

scholarly journals Population genetic structure of the malaria vector Anopheles minimus in Thailand based on mitochondrial DNA markers

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Kamonchanok Bunmee ◽  
Urusa Thaenkham ◽  
Naowarat Saralamba ◽  
Alongkot Ponlawat ◽  
Daibin Zhong ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Malaria Vector ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Anopheles Minimus ◽  
The Past ◽  
Oxidase Subunit

Abstract Background The malaria vector Anopheles minimus has been influenced by external stresses affecting the survival rate and vectorial capacity of the population. Since An. minimus habitats have continuously undergone ecological changes, this study aimed to determine the population genetic structure and the potential gene flow among the An. minimus populations in Thailand. Methods Anopheles minimus was collected from five malaria transmission areas in Thailand using Centers for Disease Control and Prevention (CDC) light traps. Seventy-nine females from those populations were used as representative samples. The partial mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (Cytb) gene sequences were amplified and analyzed to identify species and determine the current population genetic structure. For the past population, we determined the population genetic structure from the 60 deposited COII sequences in GenBank of An. minimus collected from Thailand 20 years ago. Results The current populations of An. minimus were genetically divided into two lineages, A and B. Lineage A has high haplotype diversity under gene flow similar to the population in the past. Neutrality tests suggested population expansion of An. minimus, with the detection of abundant rare mutations in all populations, which tend to arise from negative selection. Conclusions This study revealed that the population genetic structure of An. minimus lineage A was similar between the past and present populations, indicating high adaptability of the species. There was substantial gene flow between the eastern and western An. minimus populations without detection of significant gene flow barriers. Graphical abstract

scholarly journals Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines

2021 ◽  
Author(s):  
Jay-Vee S. Mendoza ◽  
Fe M. Dela Cueva ◽  
Cris Q. Cortaga ◽  
Anand Noel C. Manohar ◽  
Roanne R. Gardoce ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Phylogenetic Analyses ◽  
Infected Plant ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
The Philippines ◽  
Recent Population Expansion ◽  
Banana Bunchy Top Virus ◽  
Reference Sequences ◽  
Genetic Structure And Diversity

Banana bunchy top virus (BBTV) is an important disease of banana in the Philippines and in other banana-producing countries. This study was conducted to investigate the genetic structure and diversity of Philippine BBTV isolates which remain unexplored in the country. BBTV-infected plant tissues were sampled from banana-growing provinces (i.e., Cagayan, Isabela, Quirino, Batangas, Laguna, Rizal, Quezon, Palawan, Cebu, Leyte, and Davao del Sur) and the partial DNA-R gene of BBTV was sequenced. Analysis of all local BBTV isolates showed a nucleotide diversity (π) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fu′s Fs and Tajima′s D showed significant and highly negative values which suggest an excess number of rare alleles due to recent population expansion or from genetic hitchhiking. Haplotype network and phylogenetic analyses revealed that the local BBTV isolates were closely related to Southeast Asian (SEA) group and exhibited a monophyletic clade with distinct haplotype grouping from other SEA sequences. However, some Indonesian and Indian reference sequences were also clustered within the Philippine BBTV group suggesting sequence homology. Results also showed that the local BBTV isolates may be categorized into three major haplotype groups (HA, HB, and HC) but only the HC group remained distinct upon comparison with other Philippine and SEA reference sequences. BBTV isolates from Quezon were the most diverse while isolates from Palawan displayed low genetic diversity indices and belonged only in the HC group. The assessment of the degree of variability among Philippine BBTV isolates will provide a reference towards the development of high-throughput BBTV detection systems as well as enable to devise plant breeding strategies to manage the current BBTV spread and variations.

scholarly journals Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India

2020 ◽  
Vol 43 ◽  
pp. 199-207
Author(s):  
A Jha ◽  
K Vasudevan
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Genetic Connectivity ◽  
Founder Population ◽  
Effective Population ◽  
Genetic Structuring

The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’s D and Fu’s Fs and small positive value of Ramos-Onsins and Rozas’ R2 suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.

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