Mitochondrial cytochrome b sequence data are not an improvement for species identification in Scleractinian corals

Species Delineation ◽

Mitochondrial Cytochrome B

There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of all available Scleractinian CYB sequence data indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.

Mitochondrial cytochrome b sequence data are not an improvement for species identification in Scleractinian corals

10.7287/peerj.preprints.429 ◽

2014 ◽

Author(s):

John Wares

Keyword(s):

Population Genetics ◽

Population Genetic ◽

Sequence Data ◽

Mitochondrial Gene ◽

Gene Region ◽

Mitochondrial Genomes ◽

Species Delineation ◽

Mitochondrial Cytochrome B

There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of all available Scleractinian CYB sequence data indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.

Population structure in the Neisseria , and the biological significance of fuzzy species

Journal of The Royal Society Interface ◽

10.1098/rsif.2011.0601 ◽

2011 ◽

Vol 9 (71) ◽

pp. 1208-1215 ◽

Cited By ~ 26

Author(s):

Jukka Corander ◽

Thomas R. Connor ◽

Clíona A. O'Dwyer ◽

J. Simon Kroll ◽

William P. Hanage

Keyword(s):

Population Structure ◽

Genetic Analysis ◽

Population Genetic ◽

Vaccine Development ◽

Sequence Data ◽

Genetic Material ◽

Biological Significance ◽

Uniform Manner ◽

Complex Forms

Phenotypic and genetic variation in bacteria can take bewilderingly complex forms even within a single genus. One of the most intriguing examples of this is the genus Neisseria , which comprises both pathogens and commensals colonizing a variety of body sites and host species, and causing a range of disease. Complex relatedness among both named species and previously identified lineages of Neisseria makes it challenging to study their evolution. Using the largest publicly available collection of bacterial sequence data in combination with a population genetic analysis and experiment, we probe the contribution of inter-species recombination to neisserial population structure, and specifically whether it is more common in some strains than others. We identify hybrid groups of strains containing sequences typical of more than one species. These groups of strains, typical of a fuzzy species, appear to have experienced elevated rates of inter-species recombination estimated by population genetic analysis and further supported by transformation experiments. In particular, strains of the pathogen Neisseria meningitidis in the fuzzy species boundary appear to follow a different lifestyle, which may have considerable biological implications concerning distribution of novel resistance elements and meningococcal vaccine development. Despite the strong evidence for negligible geographical barriers to gene flow within the population, exchange of genetic material still shows directionality among named species in a non-uniform manner.

Best Practices for Population Genetic Analyses

Phytopathology ◽

10.1094/phyto-12-16-0425-rvw ◽

2017 ◽

Vol 107 (9) ◽

pp. 1000-1010 ◽

Cited By ~ 33

Author(s):

N. J. Grünwald ◽

S. E. Everhart ◽

B. J. Knaus ◽

Z. N. Kamvar

Keyword(s):

Population Genetics ◽

Population Genetic ◽

Sampling Strategy ◽

Population Data ◽

Practical Experience ◽

Genetic Structure Of Populations ◽

Web Of Data ◽

R Programming ◽

Pathogen Populations

Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.

A new species of Gonyosoma Wagler, 1828 (Serpentes, Colubridae), previously confused with G. prasinum (Blyth, 1854)

Evolutionary Systematics ◽

10.3897/evolsyst.5.66574 ◽

2021 ◽

Vol 5 (1) ◽

pp. 129-139

Author(s):

Shuo Liu ◽

Mian Hou ◽

Ye Htet Lwin ◽

Qiaoyan Wang ◽

Dingqi Rao

Keyword(s):

New Species ◽

Bayesian Inference ◽

Cytochrome B ◽

Yunnan Province ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Pairwise Distance ◽

Mitochondrial Cytochrome B ◽

A New Species

A new species of the genus Gonyosoma Wagler is described from Yunnan Province, China. The new species closely resembles G. prasinum (Blyth), but it is differentiated from the latter species by the following characters: precloacal plate divided, iris blue and inside of mouth greyish-white in life. Based on phylogenetic analyses of mitochondrial cytochrome b sequence data, the new species is recovered as the sister species to G. prasinum by Bayesian Inference and Maximum Likelihood analyses. The uncorrected pairwise distance between the new species and other species of the genus Gonyosoma ranged from 11.78% to 17.07% calculated using the mitochondrial cytochrome b sequence. This discovery increases the number of Gonyosoma species to seven.

Phylogeography of a Darevskia (caucasica) complex (Lacertidae: Sauria) based on the cytochrome b mitochondrial gene analysis

Proceedings of the Zoological Institute RAS ◽

10.31610/trudyzin/2021.325.1.49 ◽

2021 ◽

Vol 325 (1) ◽

pp. 49-66

Author(s):

I.V. Doronin ◽

P.A. Dzhelali ◽

K.Yu. Lotiev ◽

L.F. Mazanaeva ◽

G.A. Mustafaeva ◽

...

Keyword(s):

Cytochrome B ◽

Mitochondrial Gene ◽

Mitochondrial Marker ◽

South Ossetia ◽

Independent Form ◽

Mitochondrial Cytochrome B ◽

Short Period ◽

Single Clade ◽

Mitochondrial Cytochrome B Gene

The range of superspecific complex of rock lizards Darevskia (caucasica) (D. alpina, D. c. caucasica, D. c. vedenica, D. daghestanica) includes the Main Caucasian ridge and its spurs on the southern and northern macroslopes within heights from 500 m to 3200 m above sea level. A fragment of the mitochondrial cytochrome b gene (1096 bp) was analyzed in 48 specimens of these lizards. Specimens were collected in 23 localities. We have found 39 unique haplotypes. The minimum genetic diversity was found in D. c. vedenica, maximum in D. c. caucasica. All taxa of the complex, except for D. c. vedenica, demonstrate genetic heterogeneity. Four clades can be distinguished on the dendrogram of phylogenetic relationships. They correspond to D. alpina, D. c. caucasica, D. c. vedenica, D. daghestanica. D. c. caucasica forms two distinct haplogroups. On the phylogenetic tree, the sample of D. c. vedenica formed an independent clade close to D. c. caucasica. The Darevskia (caucasica) complex is polyphyletic according to the analysis of the mitochondrial marker. Nucleotide sequences of D. alpina formed a single clade with Darevskia (saxicola) complex representatives and combined with the sequences of D. brauneri into subclade. On the example of the population of D. daghestanica, found in a forest biotope without rocky outcrops and genetically not differing from individuals from the adjacent territory, the ability of rocky lizards to master biotopes unusual for them in a short period of time was demonstrated. This example demonstrates the ability of rock lizards to adapt to unusual biotopes in a short period of time. Genetic distance between D. c. vedenica and D. c. caucasica is comparable to the distance between D. c. caucasica and D. daghestanica. We assume the existence of an independent form of D. caucasica ssp. inhabiting South Ossetia and adjacent territories.

Population Genetic Analysis ofLobelia rhynchopetalumHemsl. (Campanulaceae) Using DNA Sequences fromITSand Eight Chloroplast DNA Regions

The Scientific World JOURNAL ◽

10.1100/2012/276451 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Mulatu Geleta ◽

Tomas Bryngelsson

Keyword(s):

Chloroplast Dna ◽

Dna Sequences ◽

Population Genetic ◽

Sequence Data ◽

Gene Diversity ◽

Nuclear Ribosomal Dna ◽

Bootstrap Support ◽

Mountain Systems ◽

Chloroplast Dna Regions

DNA sequence data from the internal transcribed spacer of nuclear ribosomal DNA and eight chloroplast DNA regions were used to investigate haplotypic variation and population genetic structure of the Afroalpine giant lobelia,Lobelia rhynchopetalum.The study was based on eight populations sampled from two mountain systems in Ethiopia. A total of 20 variable sites were obtained, which resulted in 13 unique haplotypes and an overall nucleotide diversity (ND) of 0.281 ± 0.15 and gene diversity (GD) of 0.85 ± 0.04. Analysis of molecular variance (AMOVA) revealed a highly significant variation (P<0.001) among populations (FST), and phylogenetic analysis revealed that populations from the two mountain systems formed their own distinct clade with >90% bootstrap support. Each population should be regarded as a significant unit for conservation of this species. The primers designed for this study can be applied to anyLobeliaand other closely related species for population genetics and phylogenetic studies.