haplotype network
Recently Published Documents


TOTAL DOCUMENTS

186
(FIVE YEARS 136)

H-INDEX

14
(FIVE YEARS 4)

2022 ◽  
Vol 10 (1) ◽  
pp. 186
Author(s):  
Alejandro Flores-Alanis ◽  
Lilia González-Cerón ◽  
Frida Santillán-Valenzuela ◽  
Cecilia Ximenez ◽  
Marco A. Sandoval-Bautista ◽  
...  

For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax-infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp142 fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R2 index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance.


2022 ◽  
Author(s):  
Jin-Yong Kim ◽  
Soo Hyung Eo ◽  
Seung-Gu Kang ◽  
Jung Eun Hwang ◽  
Yonggu Yeo ◽  
...  

Abstract Background Hill pigeons (Columba rupestris) are close to local extinction (ca. less than 100 individuals) in South Korea where a variety of conservation management procedures are urgently required. Objective This study was aimed at determining the conservation direction of captive propagation and reintroduction of hill pigeons using genetic information based on mitochondrial DNA. We also evaluated the extent of hybridization between hill pigeons and cohabiting domestic pigeons. Methods We used 51 blood samples of hill pigeons from Goheung (GH), Gurye (GR), and Uiryeong (UR), and domestic pigeons cohabiting with hill pigeon populations. Genetic diversity, pairwise Fst, analysis of molecular variance, and haplotype network analysis were used to examine the genetic structure of hill pigeons. Results Hill pigeons that inhabited South Korea were not genetically distinct from Mongolian and Russian populations and showed relatively low genetic diversity compared with other endangered species in Columbidae. The GR population that exhibited the largest population size showed lower genetic diversity, compared to the other populations, although the pairwise Fst values of the three populations indicated low genetic differentiation. The GH and GR populations were confirmed to lack hybridization, relatively, whereas the UR population was found to exhibit some degrees of hybridization. Conclusion To conserve hill pigeons with low genetic diversity and differentiation in South Korea, the conservation process of captive propagation and reintroduction may require artificial gene flows among genetically verified populations in captivity and wildness. The introduction of foreign individuals from surrounding countries is also considered an alternative strategy for maintaining genetic diversity.


2022 ◽  
Author(s):  
Amanda de Faria Santos ◽  
Eliana Marques Cancello ◽  
Adriana Coletto Morales

Abstract The neotropical region ranks third in the number of termites with five different families. Of these, Termitidae is the most diverse and includes the species Nasutitermes ephratae and is common in the neotropics. To date, only one study has been published about phylogeographic issues in neotropical termites (N. corniger). Here, we aimed to investigate and analyze the population genetic patterns of N. ephratae and then evaluated the phylogeographical processes involved in the evolutionary history of the species. We used the mitochondrial genes 16S rRNA and COII as molecular markers: These were sequenced for 128 samples of N. ephratae. We estimated the genetic diversity and divergence time as well as the demographic and genetic structure analyses. We also produced ancestral area reconstruction and a haplotype network. The results showed high genetic variability, recent demographic expansion, and strong genetic structure. We also inferred a dispersal route for the species that occurred in both directions between South and Central America. The results emphasize a temporary separation between the South and Central America population that affected the origin of the current Central America populations. These were formed form different phylogeographic histories.


2022 ◽  
Vol 43 (1) ◽  
pp. 59-65
Author(s):  
K.G. Padwal ◽  
◽  
S. Chakravarty ◽  
C.P. Srivastava ◽  
◽  
...  

Aim: The present study was undertaken to provide valuable insights regarding population genetic structure of Leucinodes orbonalis from diverse agro-ecologies of India. Methodology: Molecular characterization of L. orbonalis populations collected from five major agro-climatic zones of India was carried out using mitochondrial cytochrome oxidase I (COI) gene. Collected specimens were subjected to DNA extractions, partial PCR amplification and sequencing of the target gene, and multiple sequence alignments. Results: The results showed very less diversity in the nucleotide positions of the COI sequences of 79 studied specimens, with a low number of segregating sites (30), nucleotide diversity (0.00438) and overall mean genetic distance (0.004 ± 0.001). The significant negative values of neutrality tests and unimodal mismatch distribution supported the demographic expansion theory in Indian L. orbonalis. Analysis of the molecular variance revealed that 93.13% of the genetic variation was within populations, and the variation among populations was only 6.87%. The pairwise genetic differentiation was also found to be low to moderate between most of the populations. Multiple haplotypes were recorded from all the populations, and both neighbour-joining tree as well as the haplotype network showed that clustering of the haplotypes was independent of the geographical location. Interpretation: Thus, it can be inferred that Indian populations of L. orbonalis have very low genetic variation levels concerning the COI gene. There is a possible occurrence of stable inherited gene flow among populations, thereby reducing genetic variation in India.


2022 ◽  
Vol 10 (1) ◽  
pp. 99
Author(s):  
Haruka Abe ◽  
Yuri Ushijima ◽  
Murasaki Amano ◽  
Yasuteru Sakurai ◽  
Rokusuke Yoshikawa ◽  
...  

In the initial phase of the novel coronavirus disease (COVID-19) pandemic, a large-scale cluster on the cruise ship Diamond Princess (DP) emerged in Japan. Genetic analysis of the DP strains has provided important information for elucidating the possible transmission process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on a cruise ship. However, genome-based analyses of SARS-CoV-2 detected in large-scale cruise ship clusters other than the DP cluster have rarely been reported. In the present study, whole-genome sequences of 94 SARS-CoV-2 strains detected in the second large cruise ship cluster, which emerged on the Costa Atlantica (CA) in Japan, were characterized to understand the evolution of the virus in a crowded and confined place. Phylogenetic and haplotype network analysis indicated that the CA strains were derived from a common ancestral strain introduced on the CA cruise ship and spread in a superspreading event-like manner, resulting in several mutations that might have affected viral characteristics, including the P681H substitution in the spike protein. Moreover, there were significant genetic distances between CA strains and other strains isolated in different environments, such as cities under lockdown. These results provide new insights into the unique evolution patterns of SARS-CoV-2 in the CA cruise ship cluster.


2021 ◽  
Vol 8 ◽  
Author(s):  
Sebastián Kraft ◽  
MJosé Pérez-Alvarez ◽  
Carlos Olavarría ◽  
Rodrigo Moraga ◽  
C. Scott Baker ◽  
...  

Commerson’s dolphins (Cephalorhynchus commersonii) are separated into the subspecies C. c. commersonii, found along southern South America (SA) and the Falkland Islands/Islas Malvinas (FI/IM), and C. c. kerguelenensis, restricted to the subantarctic Kerguelen Islands (KI). Following the dispersal model proposed for the genus, the latter is thought to have originated from SA after a long-distance dispersal event. To evaluate this biogeographic scenario, a distribution-wide, balanced sampling of mitochondrial DNA (mtDNA) control region sequences was designed. New tissue samples from southern Chile, Argentina, FI/IM, and KI were added to published sequences from SA and KI, for a total of 256 samples. Genetic diversity indices, genetic and phylogeographic structure, and migration rates were calculated. One haplotype was shared between subspecies, with which all haplotypes of C. c. kerguelenensis formed a distinct group in the haplotype network. A new haplotype for C. c. kerguelenensis is reported. Differentiation in haplotype frequencies was found among localities within the distribution of C. c. commersonii, yet the phylogeographic signal was only statistically significant between subspecies. Coalescent-based historical gene flow estimations indicated migration between the northern and southern portions of the species’ range in SA as well as between SA and the FI/IM, but not between these and the KI. The net nucleotide divergence between dolphins from SA and the FI/IM was lower than the recommended threshold value suggested for delimiting subspecies, unlike that found between C. c. commersonii and C. c. kerguelenensis. The results are consistent with the model of post-glacial colonization of KI by South American C. commersonii, followed by an ongoing divergence process and subspecies status. Thus, C. c. kerguelenensis may represent the most recent diversification step of Cephalorhynchus, where isolation from their source population is driving a process of incipient speciation.


Author(s):  
Muhamad Darmawan ◽  
Neviaty Putri Zamani ◽  
Hari Eko Irianto ◽  
Hawis H Madduppa

The green seaweed Caulerpa racemosa is  a seaweed  of  high prospect that is being given emphasis by the Indonesian government. However, C. racemosa in Indonesia may include multiple species level-entity exhibiting morphological overlap and require molecular analysis for species identification. Molecular documentation of species richness of indigenous populations of C. racemosa is essential to underpin cultivar development and conservation of the species to avoid overharvesting. The present study aimed to determine the genetic diversity of C. racemosa and document the haplotype network of the specimens from four different locations (Bintan Island, Jepara, Takalar and Osi Island) using the chloroplast tufA gene. Twenty individuals from four areas were collected and amplified with the chloroplast-encoded gene tufA for species identification against publicly available data. The identification of C. racemosa based on the tufA gene showed that the species found in four locations were C. cylindracea (previously C. racemosa var. cylindracea), C. macra (previously C. racemosa var. macra), C. racemosa, and C. oligophylla (previously C. racemosa var. lamourouxii). This study records the existence of C. cylindracea in Takalar and Jepara, Indonesia for the first time. The most diverse C. racemosa species was in Osi Island, where the exploitation of this seaweed is very low. In contrast, the lowest number of C. racemosa varieties were found in Takalar, where exploitation is very high. There were only minor light variations of Caulerpa species in the tufA gene in four different sites with only four haplotypes found, and each haplotype corresponded to another species. 


Insects ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1094
Author(s):  
Andrea L. Joyce ◽  
Hannah Parolini ◽  
Harry Brailovsky

The leaffooted plant bug, Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) is polyphagous and widely distributed in the Western Hemisphere. Although it has been recorded in California since around 1900, it has become a more common pest in almonds in the last decade. Other studies have shown that an established insect can become a pest when a new genotype is introduced. This study investigated the distribution of two lineages (strains) of L. zonatus in the Western Hemisphere. Specimens from the Leptoglossus collection in the national insect collection in Mexico were used to extract DNA and sequence the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene, for use in population genetic and phylogenetic analyses. New sequences from Mexico, Central and South America were combined with those available in GenBank, from California and Brazil. Two lineages (strains) of L. zonatus were uncovered. One lineage occurs in California, Mexico and Ecuador. The second lineage is more widespread and found in California, Mexico, Guatemala, Nicaragua, Bolivia and Brazil. The haplotype number and diversity, and nucleotide diversity, were found for samples from California, Mexico, and Brazil, for the two lineages, and for all 118 sequences combined. All sequences combined produced five haplotypes, and a haplotype diversity of 0.54. California and Brazil had 3 haplotypes each, with one haplotype shared (5 total). Haplotype diversity in California and in Brazil were 0.526 and 0.505, respectively. A haplotype network found that one haplotype was most abundant and widespread. The small number of haplotypes, a range expansion, and economic pest status of L. zonatus in California, all contribute to this insect being a potentially invasive insect pest.


Author(s):  
JULIA WANGUI ◽  
David Nokes ◽  
Victor Mobegi ◽  
James Otieno ◽  
Charles Agoti ◽  
...  

Background: Human respiratory syncytial virus (HRSV) is a major cause of severe viral acute respiratory illness and contributes significantly to severe pneumonia cases in Africa. Little is known about its spatial-temporal distribution as defined by its genetic diversity. Methods: A retrospective study conducted utilizing archived nasopharyngeal specimens from patients attending outpatient clinics in hospitals located in five demographically and climatically distinct regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The viral total RNA was extracted and tested using multiplex real time RT-PCR (reverse transcriptase polymerase chain reaction). A segment of the G-gene was amplified using one-step RT-PCR and sequenced by Sanger di-deoxy method. Bayesian analysis of phylogeny was utilized and subsequently median joining methods for haplotype network reconstruction. Results: Three genotypes of HRSVA were detected; GA5 (14.0%), GA2 (33.1%) and NA1 (52.9%). HRSVA prevalence varied by location from 33% to 13.2% in the Highlands and the Eastern regions respectively. The mean nucleotide diversity (Pi(π)) varied by genotype: highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58 haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes were introduced into the population locally by single haplotypes and additional subsidiary seeds amongst the GA2 and the NA1 haplotypes. Conclusions: HRSVA was found across all the regions throughout the study period and comprised three genotypes; GA5, GA2 and NA1 genotypes. The genotypes were disproportionately distributed across the regions with GA5 gradually increasing towards the Western zones and decreasing towards the Eastern zones of the country.


Author(s):  
Zhao Cai

The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of limestone Karst Islands and features the Wumeng Mountains (Mts), which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aims to assess the effects of past geographic and environmental isolation and climate fluctuation on the flora distribution in the YGP. To this effect, we analyzed the phylogeographical pattern and genetic structure for Myrica nana, a vulnerable species endemic to the YGP, based on chloroplast and nuclear ribosomal DNA sequence. The results suggest that the genetic and haplotype network structures are divided into at least two groups—cpDNA haplotype H2 (or nrDNA haplotypes h1, h2, and the native haplotype) mainly distributed to the east of the Wumeng Mts, and cpDNA haplotype H1 and haplotypes H3–H10 (or nrDNA haplotype h3) distributed to the west of the Wumeng Mts. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. The east–west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mts, which divides the YGP into the Yunnan and Guizhou Plateaus. Therefore, there existed at least two glacial refugia during the Quaternary glacial period, along with a genetic diversity center, and at least two large geographic protection units for the vulnerable species of M. nana, distributed throughout the eastern and western sides of the Wumeng Mts. This study not only clarifies that the phylogeographical pattern and genetic structure for M. nana can be attributed to geographic and environmental isolation and climate fluctuation, but it also proposes an effective strategy to protect vulnerable species and the important wild flora of the YGP.


Sign in / Sign up

Export Citation Format

Share Document