scholarly journals Patterns of Nucleotide Diversity of theldpACircadian Gene in Closely Related Species of Cyanobacteria from Extreme Cold Deserts

2012 ◽  
Vol 79 (5) ◽  
pp. 1516-1522 ◽  
Author(s):  
Ka Wai Ng ◽  
Stephen B. Pointing ◽  
Volodymyr Dvornyk
Keyword(s):  
Related Species ◽  
Nucleotide Diversity ◽  
Population Expansion ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Closely Related Species ◽  
Content Type ◽  
Population Sizes ◽  
Extreme Cold ◽  
Small Effective Population Size

ABSTRACTIn the circadian system of cyanobacteria, theldpAgene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted asSynechococcusspecies S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (FST= 0.2242) compared to those of species S1 (FSTbetween 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (P< 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.

scholarly journals Evolution and Genetic Diversity of the k13 Gene Associated with Artemisinin Delayed Parasite Clearance in Plasmodium falciparum

2019 ◽  
Vol 63 (8) ◽  
Author(s):  
M. Andreína Pacheco ◽  
Esha R. Kadakia ◽  
Zainab Chaudhary ◽  
Douglas J. Perkins ◽  
Julia Kelley ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Related Species ◽  
Population Expansion ◽  
Population Level ◽  
Parasite Clearance ◽  
Recent Common Ancestor ◽  
Closely Related Species ◽  
Content Type ◽  
Time Of Divergence ◽  
Generation Sequencing

ABSTRACT Mutations in the Plasmodium falciparum k13 (Pfk13) gene are linked to delayed parasite clearance in response to artemisinin-based combination therapies (ACTs) in Southeast Asia. To explore the evolutionary rate and constraints acting on this gene, k13 orthologs from species sharing a recent common ancestor with P. falciparum and Plasmodium vivax were analyzed. These comparative studies were followed by genetic polymorphism analyses within P. falciparum using 982 complete Pfk13 sequences from public databases and new data obtained by next-generation sequencing from African and Haitian isolates. Although k13 orthologs evolve at heterogeneous rates, the gene was conserved across the genus, with only synonymous substitutions being found at residues where mutations linked to the delayed parasite clearance phenotype have been reported. This suggests that those residues were under constraint from undergoing nonsynonymous changes during evolution of the genus. No fixed nonsynonymous differences were found between Pfk13 and its orthologs in closely related species found in African apes. This indicates that all nonsynonymous substitutions currently found in Pfk13 are younger than the time of divergence between P. falciparum and its closely related species. At the population level, no mutations linked to delayed parasite clearance were found in our samples from Africa and Haiti. However, there is a high number of single Pfk13 mutations segregating in P. falciparum populations, and two predominant alleles are distributed worldwide. This pattern is discussed in terms of how changes in the efficacy of natural selection, affected by population expansion, may have allowed for the emergence of mutations tolerant to ACTs.

scholarly journals Why panmictic bacteria are rare

2018 ◽  
Author(s):  
Chao Yang ◽  
Yujun Cui ◽  
Xavier Didelot ◽  
Ruifu Yang ◽  
Daniel Falush
Keyword(s):  
Nucleotide Diversity ◽  
Bacterial Species ◽  
Structured Populations ◽  
Effective Population ◽  
Recombination Rates ◽  
Continuous Increase ◽  
Population Structures ◽  
Population Sizes ◽  
Current Value ◽  
Neutral Models

AbstractBackgroundBacteria typically have more structured populations than higher eukaryotes, but this difference is surprising given high recombination rates, enormous population sizes and effective geographical dispersal in many bacterial species.ResultsWe estimated the recombination scaled effective population size Ner in 21 bacterial species and find that it does not correlate with synonymous nucleotide diversity as would be expected under neutral models of evolution. Only two species have estimates substantially over 100, consistent with approximate panmixia, namely Helicobacter pylori and Vibrio parahaemolyticus. Both species are far from demographic equilibrium, with diversity predicted to increase more than 30 fold in V. parahaemolyticus if the current value of Ner were maintained, to values much higher than found in any species. We propose that panmixia is unstable in bacteria, and that persistent environmental species are likely to evolve barriers to genetic exchange, which act to prevent a continuous increase in diversity by enhancing genetic drift.ConclusionsOur results highlight the dynamic nature of bacterial population structures and imply that overall diversity levels found within a species are poor indicators of its size.

scholarly journals Draft Genome Sequences of Basidiomycetous Epiphytic Phylloplane Yeast Type Strains Dioszegia crocea JCM 2961 and Dioszegia aurantiaca JCM 2956

2019 ◽  
Vol 8 (26) ◽  
Author(s):  
Masako Takashima ◽  
Ri-ichiroh Manabe ◽  
Moriya Ohkuma
Keyword(s):  
Related Species ◽  
Draft Genome ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Phylloplane Yeasts ◽  
Type Strains ◽  
Plant Microbiome

We report the draft genome sequences of type strains for Dioszegia crocea and its closely related species Dioszegia aurantiaca, which should improve our understanding of the epiphytic phylloplane yeasts. These data will also have implications for the plant microbiome, since Dioszegia is considered a microbial “hub” taxon.

scholarly journals Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 424-431 ◽  
Author(s):  
Víctor Gonzalo Arnau ◽  
Leandro Arturo Sánchez ◽  
Osvaldo Daniel Delgado
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Psychrotolerant Bacterium ◽  
Type Strains

A psychrotolerant strain, 8H1T, was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4–35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1T to the ‘Pseudomonas fluorescens group’, displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1T could be discriminated from closely related species of the genus Pseudomonas and placed in the ‘Pseudomonas gessardii subgroup’, including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA–DNA hybridization analysis between 8H1T and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1T ( = DSM 26522T = CCUG 63249T = LMG 27247T).

scholarly journals Bacillus invictae sp. nov., isolated from a health product

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3867-3876 ◽  
Author(s):  
Raquel Branquinho ◽  
Clara Sousa ◽  
Hugo Osório ◽  
Luís Meirinhos-Soares ◽  
João Lopes ◽  
...  
Keyword(s):  
Related Species ◽  
Acid Production ◽  
Type Species ◽  
Rrna Gene ◽  
Spectroscopic Techniques ◽  
Health Product ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-positive, rod-shaped, endospore-forming Bacillus isolate, Bi.FFUP1 T, recovered in Portugal from a health product was subjected to a polyphasic study and compared with the type strains of Bacillus pumilus , Bacillus safensis , Bacillus altitudinis and Bacillus xiamenensis , the phenotypically and genotypically most closely related species. Acid production from cellobiose, d-glucose and d-mannose and absence of acid production from d-arabinose, erythritol, inositol, maltose, mannitol, raffinose, rhamnose, sorbitol, starch and l-tryptophan discriminated this new isolate from the type strains of the most closely related species. Additionally, a significant different protein and carbohydrate signature was evidenced by spectroscopic techniques, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and Fourier transform IR spectroscopy with attenuated total reflectance. Using a chemometric approach, the score plot generated by principal component analysis clearly delineated the isolate as a separate cluster. The quinone system for strain Bi.FFUP1 T comprised predominantly menaquinone MK-7 and major polar lipids were diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. Strain Bi.FFUP1 T showed ≥99 % 16S rRNA gene sequence similarity to B. safensis FO-036bT, B. pumilus (7061T and SAFR-032), B. altitudinis 41KF2bT and B. xiamenensis HYC-10T. Differences in strain Bi.FFUP1 T gyrB and rpoB sequences in comparison with the most closely related species and DNA–DNA hybridization experiments with Bi.FFUP1 T and B. pumilus ATCC 7061T, B. safensis FO-036bT, B. altitudinis 41KF2bT and B. xiamenensis HYC-10T gave relatedness values of 39.6 % (reciprocal 38.0 %), 49.9 % (reciprocal 42.9 %), 61.9 % (reciprocal 52.2 %) and 61.7 % (reciprocal 49.2 %), respectively, supported the delineation of strain Bi.FFUP1 T as a representative of a novel species of the genus Bacillus , for which the name Bacillus invictae sp. nov. is proposed, with strain Bi.FFUP1 T ( = DSM 26896T = CCUG 64113T) as the type strain.

scholarly journals Assessing genetic diversity and connectivity in a tule elk (Cervus canadensis nannodes) metapopulation in Northern California

2021 ◽  
Author(s):  
Thomas J. Batter ◽  
Joshua P. Bush ◽  
Benjamin N. Sacks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Expansion ◽  
Active Management ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Sex Marker ◽  
Cervus Canadensis ◽  
Population Sizes ◽  
Tule Elk

AbstractThe tule elk (Cervus canadensis nannodes) is a California endemic subspecies that experienced an extreme bottleneck (potentially two individuals) in the mid-1800s. Through active management, including reintroductions, the subspecies has grown to approximately 6000 individuals spread across 22 recognized populations. The populations tend to be localized and separated by unoccupied intervening habitat, prompting targeted translocations to ensure gene flow. However, little is known about the genetic status or connectivity among adjacent populations in the absence of active translocations. We used 19 microsatellites and a sex marker to obtain baseline data on the genetic effective population sizes and functional genetic connectivity of four of these populations, three of which were established since the 1980s and one of which was established ~ 100 years ago. A Bayesian assignment approach suggested the presence of 5 discrete genetic clusters, which corresponded to the four primary populations and two subpopulations within the oldest of them. Effective population sizes ranged from 15 (95% CI 10–22) to 51 (95% CI 32–88). We detected little or no evidence of gene flow among most populations. Exceptions were a signature of unidirectional gene flow to one population founded by emigrants of the other 30 years earlier, and bidirectional gene flow between subpopulations within the oldest population. We propose that social cohesion more than landscape characteristics explained population structure, which developed over many generations corresponding to population expansion. Whether or which populations can grow and reach sufficient effective population sizes on their own or require translocations to maintain genetic diversity and population growth is unclear. In the future, we recommend pairing genetic with demographic monitoring of these and other reintroduced elk populations, including targeted monitoring following translocations to evaluate their effects and necessity.

scholarly journals Bacillus aciditolerans sp. nov., isolated from paddy soil

2019 ◽  
Vol 69 (4) ◽  
pp. 1155-1161 ◽  
Author(s):  
Meng-Jiao Ding ◽  
Nian-Jie Shang ◽  
Zhi-xin Xiao ◽  
Fei Shao ◽  
Li Liu ◽  
...  
Keyword(s):  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Test Results ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
The Town

A Gram-stain-positive, motile, rod-shaped bacterial strain, YN-1T, was isolated from a rice field in the town of Jietou, Yunnan Province, PR China. Colonies were circular, 1–2 mm in diameter, creamy white, with slightly irregular margins. The isolate grew optimally at 37 °C, pH 7.0 and with 1.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence similarity comparisons, YN-1T clustered together with other species of the genus Bacillus and showed highest similarities with Bacillus onubensis 0911MAR22V3T (98.0 %), Bacillus humi LMG22167T (97.5 %), ' Bacillus timonensis ' 10403023 (97.4 %) and ' Bacillus sinesaloumensis' P3516 (97.1 %). However, the DNA–DNA hybridization values between YN-1T and closely related strains of species of the genus Bacillus were well below 47 %, indicating that they represent different taxa. The average nucleotide identity and the Genome-to-Genome Distance Calculator also revealed low relatedness (below 95 and 70 %, respectively) between YN-1T and type strains of closely related species of the genus Bacillus . The DNA G+C content of the strain was 40 mol%. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, three unidentified aminophospholipids and two other unidentified lipids. Physiological and biochemical test results were also different from those of the most closely related species. On the basis of the phenotypic, genetic and chemotaxonomic data, strain YN-1T is considered to represent a novel species of the genus Bacillus , for which the name Bacillus aciditolerans sp. nov. is proposed, with strain YN-1T (=CCTCC AB 2017280T=JCM 32973T) as the type strain.

scholarly journals Veillonella nakazawae sp. nov., an anaerobic Gram-negative coccus isolated from the oral cavity of Japanese children

2020 ◽  
Author(s):  
Izumi Mashima ◽  
Citra F. Theodorea ◽  
Ariadna A. Djais ◽  
Tadao Kunihiro ◽  
Yoshiaki Kawamura ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
Related Species ◽  
Type Strain ◽  
Type Species ◽  
Japanese Children ◽  
Closely Related Species ◽  
Gram Negative ◽  
Content Type ◽  
Link Type

Two strains of previously unknown Gram-negative cocci, T1-7T and S6-16, were isolated from the oral cavity of healthy Japanese children. The two strains showed atypical phenotypic characteristics of members of the genus Veillonella , including catalase production. Sequencing of their 16S rRNA genes confirmed that they belong to genus Veillonella . Under anaerobic conditions, the two strains produced acetic acid and propionic acid as metabolic end-products in a trypticase–yeast extract–haemin medium containing 1 % (w/v) glucose, 1 % (w/v) fructose and 1 % (v/v) sodium lactate. Comparative analysis of the 16S rRNA, dnaK, rpoB and gltA gene sequences revealed that the two strains are phylogenetically homogeneous and comprise a distinct, novel lineage within the genus Veillonella . The sequences from the two strains shared the highest similarity, at 99.9, 95.8, 96.9 and 96.7 %, using the partial 16S rRNA, dnaK, rpoB and gltA gene sequences, respectively, with the type strains of the two most closely related species, Veillonella dispar ATCC 17748T and Veillonella infantium JCM 31738T. Furthermore, strain T1-7T shared the highest average nucleotide identity (ANI) value (94.06 %) with type strain of the most closely related species, V. infantium . At the same time, strain T1-7T showed the highest digital DNA–DNA hybridization (dDDH) value (55.5 %) with the type strain of V. infantium . The two strains reported in this study were distinguished from the previously reported species from the genus Veillonella based on catalase production, partial dnaK, rpoB and gltA sequences, average ANI and dDDH values. Based on these observations, the two strains represent a novel species, for which the name Veillonella nakazawae sp. nov. is proposed. The type strain is T1-7T (JCM 33966T=CCUG 74597T).

scholarly journals Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Zeyu Zheng ◽  
Ying Li ◽  
Minjie Li ◽  
Guiting Li ◽  
Xin Du ◽  
...  
Keyword(s):  
Gene Flow ◽  
Related Species ◽  
Biological Diversity ◽  
Population Decline ◽  
Evolutionary Process ◽  
Speciation Analysis ◽  
Central Place ◽  
Future Research ◽  
Effective Population ◽  
Closely Related Species

Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.

scholarly journals Molecular phylogeny of the Anopheles hyrcanus group (Diptera: Culicidae) based on rDNA–ITS2 and mtDNA–COII

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Canglin Zhang ◽  
Rui Yang ◽  
Linbo Wu ◽  
Chunhai Luo ◽  
Xiaofang Guo ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Molecular Identification ◽  
Malaria Vector ◽  
Related Species ◽  
Genetic Divergence ◽  
Morphological Characteristics ◽  
Population Expansion ◽  
Closely Related Species ◽  
Rdna Its2 ◽  
Interspecific Divergence

Abstract Background The Anopheles hyrcanus group, which includes 25 species, is widely distributed in the Oriental and Palaearctic regions. Given the difficulty in identifying cryptic or sibling species based on their morphological characteristics, molecular identification is regarded as an important complementary approach to traditional morphological taxonomy. The aim of this study was to reconstruct the phylogeny of the Hyrcanus group using DNA barcoding markers in order to determine the phylogenetic correlations of closely related taxa and to compare these markers in terms of identification efficiency and genetic divergence among species. Methods Based on data extracted from the GenBank database and data from the present study, we used 399 rDNA–ITS2 sequences of 19 species and 392 mtDNA–COII sequences of 14 species to reconstruct the molecular phylogeny of the Hyrcanus group across its worldwide range. We also compared the performance of rDNA–ITS2 against that of mtDNA–COII to assess the genetic divergence of closely related species within the Hyrcanus group. Results Average interspecific divergence for the rDNA–ITS2 sequence (0.376) was 125-fold higher than the average intraspecies divergence (0.003), and average interspecific divergence for the mtDNA–COII sequence (0.055) was eightfold higher than the average intraspecies divergence (0.007). The barcoding gap ranged from 0.015 to 0.073 for rDNA–ITS2, and from 0.017 to 0.025 for mtDNA–COII. Two sets of closely related species, namely, Anophels lesteri and An. paraliae, and An. sinensis, An. belenrae and An. kleini, were resolved by rDNA–ITS2. In contrast, the relationship of An. sinensis/An. belenrae/An. kleini was poorly defined in the COII tree. The neutrality test and mismatch distribution revealed that An. peditaeniatus, An. hyrcanus, An. sinensis and An. lesteri were likely to undergo hitchhiking or population expansion in accordance with both markers. In addition, the population of an important vivax malaria vector, An. sinensis, has experienced an expansion after a bottleneck in northern and southern Laos. Conclusions The topology of the Hyrcanus group rDNA–ITS2 and mtDNA–COII trees conformed to the morphology-based taxonomy for species classification rather than for that for subgroup division. rDNA–ITS2 is considered to be a more reliable diagnostic tool than mtDNA–COII in terms of investigating the phylogenetic correlation between closely related mosquito species in the Hyrcanus group. Moreover, the population expansion of an important vivax malaria vector, An. sinensis, has underlined a potential risk of malaria transmission in northern and southern Laos. This study contributes to the molecular identification of the Anopheles hyrcanus group in vector surveillance. Graphical abstract

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