scholarly journals Population Structure of Leishmania using POPSICLE reveals extensive dichotomy in zygosity and discloses the role of sex in diversity of the parasite

2018 ◽  
Author(s):  
Jahangheer S. Shaik
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Neurological Disorders ◽  
Mating Preference ◽  
F1 Hybrids ◽  
Driving Mechanisms ◽  
Multiple Cycles ◽  
Mosaic Aneuploidy

AbstractMosaic aneuploidy prevalent in organisms such as Leishmania and Fungi and in genomes of some neurological disorders and cancers manifest as non-integer haplotypes due to heterogeneity in somy across a population of cells. Thus, the tools designed for strictly haploid or diploid genomes are insufficient to study them. We addressed this issue by upgrading our population genetics tool POPSICLE for aneuploid genomes and studied the population structure of 50 strains of Leishmania to understand genetic diversity and the sexual strategies that predispose to that diversity. Leishmania showed enormous diversity but a dichotomic nature of extreme zygosities. To understand this dichotomy, we specifically studied two species, L. tropica that contained strains with both hetero and homozygosities and L. major that were mainly homozygous. The homozygosity in L. tropica was a consequence of extreme inbreeding while heterozygosity was due to recent hybridizations involving two different genotypes. In contrast, L. major also contained two different genotypes and products of extreme inbreeding but no recent hybridizations. The heterozygous strains of L. tropica that were geographically isolated from the homozygous strains were F1 hybrids that appeared sterile to each other while those in proximity to the homozygous strains were outcrosses involving multiple cycles of hybridization indicating their mating preference with homozygous strains. Development of POPSICLE for aneuploid genomes offers a unique tool for determining the shared ancestries and in reinforcing sex as one of the driving mechanisms for speciation as demonstrated for Leishmania. POPSICLE is a Java based utility available for free download at https://popsicle-admixture.sourceforge.io/

scholarly journals POPULATION STRUCTURE OFDIPODOMYS INGENS(HETEROMYIDAE): THE ROLE OF SPATIAL HETEROGENEITY IN MAINTAINING GENETIC DIVERSITY

Evolution ◽  
1997 ◽  
Vol 51 (4) ◽  
pp. 1296-1310 ◽  
Author(s):  
Sara V. Good ◽  
Daniel F. Williams ◽  
Katherine Ralls ◽  
Robert C. Fleischer
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Spatial Heterogeneity

scholarly journals Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2326 ◽  
Author(s):  
Vaishali P. Waman ◽  
Pandurang Kolekar ◽  
Mukund R. Ramtirthkar ◽  
Mohan M. Kale ◽  
Urmila Kulkarni-Kale
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Dengue Virus ◽  
Positive Selection ◽  
Asian American ◽  
Complete Genome ◽  
Severe Dengue ◽  
Structural Genes ◽  
Genotype Diversity

BackgroundDengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genusFlavivirus,familyFlaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages.MethodsComplete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches.ResultsDENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach.DiscussionComplete genome-based analysis revealed that the worldwide population of DENV-2 strains is subdivided into fifteen lineages. The population structure of DENV-2 is spatiotemporal and is shaped by episodic positive selection and recombination. Intra-genotype diversity was observed in four genotypes (Asian/American, Asian I, cosmopolitan and sylvatic). Episodic positive selection on envelope and non-structural genes translates into antigenic diversity and appears to be responsible for emergence of strains/lineages in DENV-2 genotypes. Understanding of the genotype diversity and emerging lineages will be useful to design strategies for epidemiological surveillance and vaccine design.

scholarly journals Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Cristhian Danilo Joya ◽  
Ricardo Marcel Landínez-García ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Anthropogenic Activities ◽  
Lower Section ◽  
Habitat Disturbances ◽  
Genetic Groups ◽  
Lack Of Information ◽  
Species Specific

ABSTRACT Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.

scholarly journals Interspecific Hybridization and Introgression Influence Biodiversity—Based on Genetic Diversity of Central European Viola epipsila-V. palustris Complex

Diversity ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 321
Author(s):  
Justyna Żabicka ◽  
Grzegorz Migdałek ◽  
Aneta Słomka ◽  
Elwira Sliwinska ◽  
Leszek Mackiewicz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
F1 Hybrids ◽  
Hybrid Index ◽  
Parent Species ◽  
Simple Sequence ◽  
Stable Feature

The Viola epipsila-V. palustris complex is a highly taxonomically complicated group of species in its entire circumboreal range of distribution. Habitat loss, forest flooding, and hybridization could lead to the extinction of V. epipsila. A hybrid index and principal component analysis (PCA) were used to select qualitative and quantitative morphological features to distinguish parent species and hybrids, inter simple sequence repeat (ISSR) markers to determine the genetic diversity of the populations, flow cytometry to estimate the genome size (GS), and non-coding chloroplast DNA (cpDNA) regions to indicate the directions of crosses. All taxa are very morphologically variable, and their features can change within a season. The most stable feature is the distance of the bracts on the pedicel from the rhizome. The genetic diversity of all taxa populations is low and highly influenced by selfing and vegetative propagation. The population structure is differentiated: populations of V. epipsila or V. palustris, mixed populations with both parent species, F1 hybrids and populations with introgressive forms occur in different regions. The interspecific GS variation corresponds to the ploidy level (4x = 2.52 pg, 8x = 4.26 pg, 6x = 3.42 pg). Viola epipsila is the mother plant of the hybrids. Research has shown the risk of V. epipsila extinction in Central Europe and the importance of local populations in studying the role of hybridization in reducing/maintaining/increasing biodiversity.

Population Structure of Dipodomys ingens (Heteromyidae): The Role of Spatial Heterogeneity in Maintaining Genetic Diversity

Evolution ◽  
1997 ◽  
Vol 51 (4) ◽  
pp. 1296 ◽  
Author(s):  
Sara V. Good ◽  
Daniel F. Williams ◽  
Katherine Ralls ◽  
Robert C. Fleischer
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Spatial Heterogeneity ◽  
Dipodomys Ingens

scholarly journals Population genetics ofMycobacterium tuberculosiscomplex in Scotland analysed by pulsed-field gel electrophoresis

1995 ◽  
Vol 114 (1) ◽  
pp. 153-160 ◽  
Author(s):  
E. S. Olson ◽  
K. J. Forbes ◽  
B. Watt ◽  
T. H. Pennington
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Mycobacterium Tuberculosis ◽  
Population Structure ◽  
Gel Electrophoresis ◽  
Distinct Species ◽  
Pulsed Field Gel Electrophoresis ◽  
Pulsed Field ◽  
Limited Genetic Diversity

SUMMARYThe results of typing of 121 strains in theMycobacterium tuberculosiscomplex by PFGE are presented. Every isolate from patients in Scotland over a 3-month period forM. tuberculosisand for 1 year forM. boviswere included along with several laboratory strains including those of BCG. The PFGE results suggest that the population structure of all the strains in this complex is distinctly simple with limited genetic diversity and also suggest thatM. bovisis not a distinct species.

scholarly journals Genetic diversity and population structure of Corollospora maritima sensu lato: new insights from population genetics

2016 ◽  
Vol 59 (5) ◽  
Author(s):  
Patricia Velez ◽  
Jaime Gasca-Pineda ◽  
Akira Nakagiri ◽  
Richard T. Hanlin ◽  
María C. González
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Genetic Variation

AbstractThe study of genetic variation in fungi has been poor since the development of the theoretical underpinnings of population genetics, specifically in marine taxa.

scholarly journals Population Genetics of New Zealand Scampi (Metanephrops challengeri)

2021 ◽  
Author(s):  
◽  
Alexander Verry
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Demographic History ◽  
Eastern Coast ◽  
Genetic Structuring ◽  
The North ◽  
Dispersal Potential

<p>A fundamental goal of fisheries management is sustainable harvesting and the preservation of properly functioning populations. Therefore, an important aspect of management is the identification of demographically independent populations (stocks), which is achieved by estimating the movement of individuals between areas. A range of methods have been developed to determine the level of connectivity among populations; some measure this directly (e.g. mark-recapture) while others use indirect measures (e.g. population genetics). Each species presents a different set of challenges for methods that estimate levels of connectivity. Metanephrops challengeri is a species of nephropid lobster that supports a commercial fishery and inhabits the continental shelf and slope of New Zealand. Very little research on population structure has been reported for this species and it presents a unique set of challenges compared to finfish species. M. challengeri have a short pelagic larval duration lasting up to five days which limits the dispersal potential of larvae, potentially leading to low levels of connectivity among populations. The aim of this study was to examine the genetic population structure of the New Zealand M. challengeri fishery.  DNA was extracted from M. challengeri samples collected from the eastern coast of the North Island (from the Bay of Plenty to the Wairarapa), the Chatham Rise, and near the Auckland Islands. DNA from the mitochondrial CO1 gene and nuclear ITS-1 region was amplified and sequenced. The aligned dataset of DNA sequences was then used to estimate levels of both genetic diversity and differentiation, and examine demographic history. Analyses of population structure indicate that M. challengeri from the Auckland Islands region are genetically distinct from M. challengeri inhabiting the Chatham Rise, and those collected from waters off the eastern coast of the North Island. There appears to be gene flow among the sampling sites off the eastern coast of the North Island and on the Chatham Rise, but some isolation by distance was detected. These results indicate that some of these populations may be demographically uncoupled. Genetic diversity estimates combined with Bayesian skyline plots and demographic history parameters suggest that M. challengeri populations have recently undergone a size expansion.  The genetic structuring between the Auckland Islands site and all others may be due to a putative habitat disjunction off the Otago shelf. In contrast, a largely continuously distributed population along the eastern coast of the North Island and the Chatham Rise most likely promotes gene flow as larvae can be transported limited distances by oceanic currents. Historical changes in climate may have influenced the patterns of present-day structure and genetic diversity of M. challengeri, by altering habitat availability and other characteristics of their environment. This study provides evidence that species which appear to have limited dispersal potential can still maintain connected populations, but there are situations where large breaks in suitable habitat appear to limit gene flow. The results of this study will help inform stock structure of the M. challengeri fishery, which will enable stock assessments to be more precisely aligned to natural population boundaries.</p>

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