Recessive Z-linked lethals and the retention of haplotype diversity in a captive butterfly population

Abstract Background Red blood cell invasion by the Plasmodium vivax merozoite requires interaction between the Duffy antigen receptor for chemokines (DARC) and the P. vivax Duffy-binding protein II (PvDBPII). Given that the disruption of this interaction prevents P. vivax blood-stage infection, a PvDBP-based vaccine development has been well recognized. However, the polymorphic nature of PvDBPII prevents a strain transcending immune response and complicates attempts to design a vaccine. Methods Twenty-three P. vivax clinical isolates collected from three areas of Ethiopia were sequenced at the pvdbpII locus. A total of 392 global pvdbpII sequences from seven P. vivax endemic countries were also retrieved from the NCBI archive for comparative analysis of genetic diversity, departure from neutrality, linkage disequilibrium, genetic differentiation, PvDBP polymorphisms, recombination and population structure of the parasite population. To establish a haplotype relationship a network was constructed using the median joining algorithm. Results A total of 110 variable sites were found, of which 44 were parsimony informative. For Ethiopian isolates there were 12 variable sites of which 10 were parsimony informative. These parsimony informative variants resulted in 10 nonsynonymous mutations. The overall haplotype diversity for global isolates was 0.9596; however, the haplotype diversity was 0.874 for Ethiopia. Fst values for genetic revealed Ethiopian isolates were closest to Indian isolates as well as to Sri Lankan and Sudanese isolates but further away from Mexican, Papua New Guinean and South Korean isolates. There was a total of 136 haplotypes from the 415 global isolates included for this study. Haplotype prevalence ranged from 36.76% to 0.7%, from this 74.2% were represented by single parasite isolates. None of the Ethiopian isolates grouped with the Sal I reference haplotype. From the total observed nonsynonymous mutations 13 mapped to experimentally verified epitope sequences. Including 10 non-synonymous mutations from Ethiopia. However, all the polymorphic regions in Ethiopian isolates were located away from DARC, responsible for junction formation. Conclusion The results of this study are concurrent with the multivalent vaccine approach to design an effective treatment. However, the presence of novel haplotypes in Ethiopian isolates that were not shared by other global sequences warrant further investigation.

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Haplotype diversity in the mitochondrial genome of the Egyptian river buffalo (Bubalus bubalis)

Mitochondrial DNA Part B ◽

10.1080/23802359.2020.1852622 ◽

2021 ◽

Vol 6 (1) ◽

pp. 145-147

Author(s):

Nouran Adel Youssef ◽

Manon Curaudeau ◽

Soheir Mohamed El Nahas ◽

Amal Ahmed Mohamed Hassan ◽

Alexandre Hassanin

Keyword(s):

Mitochondrial Genome ◽

Haplotype Diversity ◽

Bubalus Bubalis ◽

River Buffalo

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Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽

10.3390/d13020040 ◽

2021 ◽

Vol 13 (2) ◽

pp. 40

Author(s):

Evgeny Genelt-Yanovskiy ◽

Yixuan Li ◽

Ekaterina Stratanenko ◽

Natalia Zhuravleva ◽

Natalia Strelkova ◽

...

Keyword(s):

Genetic Diversity ◽

Barents Sea ◽

Haplotype Diversity ◽

Brittle Star ◽

The Arctic ◽

Coi Gene ◽

High Genetic Diversity ◽

Svalbard Archipelago ◽

Mitochondrial Coi ◽

The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

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Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution

Animals ◽

10.3390/ani11051429 ◽

2021 ◽

Vol 11 (5) ◽

pp. 1429

Author(s):

Yang Teng ◽

Jing Yang ◽

Guofen Zhu ◽

Fuli Gao ◽

Yingying Han ◽

...

Keyword(s):

Genetic Structure ◽

Structure Analysis ◽

Phylogenetic Trees ◽

Molecular Genetic ◽

Genetic Research ◽

Haplotype Diversity ◽

Botanical Garden ◽

Source Population ◽

Independent Evolution ◽

Loop Region

Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.

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High Intraspecific Genetic Diversity ofNocardia brasiliensis, a Pathogen Responsible for Cutaneous Nocardiosis Found in France: Phylogenetic Relationships by Usingsodandhsp65Genes

BioMed Research International ◽

10.1155/2018/7314054 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10

Author(s):

D. Kosova-Maali ◽

E. Bergeron ◽

Y. Maali ◽

T. Durand ◽

J. Gonzalez ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Genetic Characterization ◽

Haplotype Diversity ◽

Species Level ◽

Genotype 1 ◽

Tropical Regions ◽

High Bootstrap ◽

Almost All ◽

A New Species ◽

Immunocompetent Patients

This study aims at genetic characterization and phylogenetic relationships ofNocardia brasiliensisfocusing by using housekeepingrrs,hsp65,andsodAgenes.N. brasiliensisis the species responsible for 80% of cases of actinomycetoma, one form of cutaneous nocardiosis which occurs mainly in tropical regions reaching immunocompetent patients in which the disease can lead to amputation. We analyze 36 indigenous cases ofN. brasiliensisthat happened in France. Phylogenetic analysis targetingrrsgene showed no robustness at phylogenetic nodes level. However, the use of a concatenation ofhsp65andsodAgenes showed that the tested strains surprisingly ranked in 3 well-defined genotypes. Genotypes 2 and 3 were phylogenetically closer to each other and both diverged from genotype 1 sustained by a high bootstrap of 81%. This last genotype hosts all the cases of pulmonary forms (3), the sole cerebral form, and almost all the cases of immunocompromised patients (3 out of 4). Moreover, excepting one of them, all the strains belonging to this group present a susceptibility to imipenem which is not the case in the other genotypes that rarely count among them strains being susceptible to this drug. The haplotype diversity (Hd) ofhsp65(0.927) andsodA(0.885) genes was higher than that ofrrs(0.824). For this gene, we obtained 16 polymorphic sites whereas, forhsp65andsodAgenes, up to 27 and 29 were identified, respectively. This study reveals that these two genes have an important genetic discriminatory power for the evaluation of the intraspecies genetic variability ofN. brasiliensisand they may be useful for identification purposes at species level. This study also reveals the possible existence of a new species harbored by genotype 1.

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Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

Bulletin of Entomological Research ◽

10.1017/s0007485311000678 ◽

2011 ◽

Vol 102 (3) ◽

pp. 333-343 ◽

Cited By ~ 16

Author(s):

K.C. Albernaz ◽

K.L. Silva-Brandão ◽

P. Fresia ◽

F.L. Cônsoli ◽

C. Omoto

Keyword(s):

Genetic Structure ◽

Genetic Variability ◽

Heliothis Virescens ◽

Demographic History ◽

Haplotype Diversity ◽

Low Frequency ◽

Haplotype Network ◽

Demographic Expansion ◽

Significant Genetic Structure ◽

History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

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Chloroplast DNA polymorphism reveals geographic structure and introgression in the Quercus crassifolia × Quercus crassipes hybrid complex in Mexico

Botany ◽

10.1139/b07-128 ◽

2008 ◽

Vol 86 (3) ◽

pp. 228-239 ◽

Cited By ~ 17

Author(s):

E. Tovar-Sánchez ◽

P. Mussali-Galante ◽

R. Esteban-Jiménez ◽

D. Piñero ◽

D. M. Arias ◽

...

Keyword(s):

Parental Species ◽

Diversity Index ◽

Hot Spot ◽

Haplotype Diversity ◽

Hybrid Zones ◽

Chloroplast Microsatellite ◽

Colonization Routes ◽

Allopatric Populations ◽

Genetic Structure Of Populations ◽

Hybrid Complex

Quercus crassifolia H. & B. and Quercus crassipes H. & B. are two common temperate forest species in Mexico that form hybrids when they occur in mixed (sympatric) areas. In this study, we used chloroplast microsatellite haplotypes to infer phylogeographic patterns onto the genetic structure of populations of both parental species, thus defining probable colonization routes throughout Mexico. Haplotype diversity in seven hybrid zones and four allopatric sites with nonmixed (allopatric) populations of both putative parental species was analyzed. To determine the expansion and colonization routes for the two species, we carried out a nested clade phylogeographic analysis that would allow us to infer the haplotype correspondence to a phylogeographical approach. In spite of sharing many common populations, we determined that there is a different genetic historical colonization for Q. crassipes and for Q. crassifolia. Hybrid populations had the highest levels of genetic variation (Gv), Shannon diversity index (H), and haplotype number (nh) in comparison with nonmixed/allopatric populations of their putative parentals. Furthermore, populations of hybrid zones showed the highest values of genetic differentiation FST, RST . Moreover, both species share four distinctive cpDNA haplotypes, which were most likely acquired by introgression through hybrids located in several populations throughout the Eje Neovolcánico area. This last region was confirmed to be a “hot spot” for oak diversity, a place in which different maternal lineages merged.

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