scholarly journals PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

2018 ◽  
Author(s):  
Sean P. Gordon ◽  
Joshua J. Levy ◽  
John P. Vogel
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Related Species ◽  
Software Package ◽  
Gc Content ◽  
Individual Species ◽  
Closely Related Species ◽  
As Species ◽  
Pooled Dna ◽  
Species Specific

AbstractExisting methods for assigning sequences to individual species from pooled DNA samples rely on differences in genome properties like GC content or sequences from related species. These approaches do not work for closely related species where gross features are indistinguishable and related genomes are lacking. We describe a method and associated software package that uses rapidly evolving repetitive DNA to circumvent these limitations. By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes without any prior knowledge. This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

scholarly journals Repeated evolution of asymmetric genitalia and right-sided mating behavior in theDrosophila nannopteraspecies group

2019 ◽  
Author(s):  
Andrea Acurio ◽  
Flor T. Rhebergen ◽  
Sarah Paulus ◽  
Virginie Courtier-Orgogozo ◽  
Michael Lang
Keyword(s):  
Related Species ◽  
Current Data ◽  
The Other ◽  
Genital Morphology ◽  
Closely Related Species ◽  
Outgroup Species ◽  
Repeated Evolution ◽  
Drosophila Pachea ◽  
Species Specific ◽  
Group Species

AbstractBackgroundMale genitals have repeatedly evolved left-right asymmetries, and the causes of such evolution remain unclear. TheDrosophila nannopteragroup contains four species, among which three exhibit left-right asymmetries of distinct genital organs. In the most studied species,Drosophila pachea, males display asymmetric genital lobes and they mate right-sided on top of the female. Copulation position of the other species is unknown.ResultsTo assess whether the evolution of genital asymmetry could be linked to the evolution of one-sided mating, we examined phallus morphology and copulation position inD. pacheaand closely related species. The phallus was found to be symmetric in all investigated species exceptD. pachea, which display an asymmetric phallus with a right-sided gonopore, andD. acanthoptera, which harbor an asymmetrically bent phallus. In all examined species, males were found to position themselves symmetrically on top of the female, except inD. pacheaandD. nannoptera, where males mated right-sided, in distinctive, species-specific positions. In addition, the copulation duration was found to be increased innannopteragroup species compared to closely related outgroup species.ConclusionOur study shows that gains, and possibly losses, of asymmetry in genital morphology and mating position have evolved repeatedly in thenannopteragroup. Current data does not allow us to conclude whether genital asymmetry has evolved in response to changes in mating position, or vice versa.

Are polymorphic species of Uropodina (Acari: Mesostigmata) more successful evolutionarily?—A case study of closely related species from the genus Oodinychus Berlese, 1917 based on DNA sequences

2019 ◽  
Vol 24 (5) ◽  
pp. 866
Author(s):  
Jerzy Błoszyk ◽  
Katarzyna Buczkowska ◽  
Anna Maria Bobowicz ◽  
Alina Bączkiewicz ◽  
Zbigniew Adamski ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Habitat Preferences ◽  
Abundant Species ◽  
Systematic Position ◽  
Genetic Differences ◽  
Similar Species ◽  
Closely Related Species ◽  
Wide Range

The study presented in this research paper is the first taxonomic investigation focusing on Uropodina (Acari: Mesostigmata) mites with a brief discussion of the genetic differences of two very closely related species from the genus Oodinychus Berlese, 1917, i.e. O. ovalis (C.L. Koch, 1839) and O. karawaiewi (Berlese, 1903). These two morphologically similar species are quite common and they have a wide range of occurrence in Europe. They also live in almost the same types of habitat. However, O. ovalis usually exhibits higher abundance and frequency of occurrence. The major aim of the study was to carry out a comparative analysis of the systematic position, morphological and biological differences, as well as habitat preferences and distribution of O. ovalis and O. karawaiewi. The next aim was to ascertain whether the differences in number and frequency of these species may stem from the genetic differences at the molecular level (16S rDNA and COI). The study shows that O. ovalis, which is a more abundant species than O. karawaiewi, turned out to be genetically more polymorphic.

Typification for reliable application of subspecific names within Peridinium cinctum (Peridiniales, Dinophyceae)

Phytotaxa ◽  
2019 ◽  
Vol 424 (3) ◽  
pp. 147-157 ◽  
Author(s):  
CORINNA ROMEIKAT ◽  
ALEJANDRO IZQUIERDO LÓPEZ ◽  
CHRISTINE TIETZE ◽  
JULIANE KRETSCHMANN ◽  
MARC GOTTSCHLING
Keyword(s):  
Morphological Variation ◽  
Dna Sequences ◽  
Related Species ◽  
Original Material ◽  
Full Spectrum ◽  
Closely Related Species ◽  
Geographic Locations ◽  
Future Studies ◽  
Unicellular Organisms ◽  
Peridinium Cinctum

The application of scientific names is determined by means of nomenclatural types, and every name has to be typified properly. The concept has limitations for unicellular organisms, because original material frequently consists of drawings and/or inadequately preserved physical material. Peridinium cinctum is an abundant freshwater microalga and variable in both morphology and genotype. Morphological variation is mainly expressed in its epithecal conformation: shape deviations of plates, plate rearrangements, plate fusion and plate additions. Different epithecal conformations were traditionally described as either varieties of P. cinctum or were established as closely related species. Despite this, relations between varieties, ribotypes and geographic locations were oversighted, and the full spectrum of plate variation in P. cinctum is still not well represented. For this reason, we sampled localities in Germany and Poland, from which varieties of P. cinctum were described a century ago. We cultivated monoclonal strains, exhibiting two distinct ITS ribotypes, and assessed their epithecal variation of morphology. Based on ca 2,500 observations of individual cells we report a plethora of both plate and suture deviations from the archetypical epithecal conformation of P. cinctum. Morphologies corresponding to previously described varieties were rare, even at their type localities. Nevertheless, we found morphologies consistent with protologues in four cases and use this material for epitypification. These varieties are now linked to specific DNA sequences, allowing reliable application of scientific names for future studies.

scholarly journals Comparing Medicinal Uses of Cochlospermaceae throughout Its Geographic Range with Insights from Molecular Phylogenetics

Diversity ◽  
2018 ◽  
Vol 10 (4) ◽  
pp. 123 ◽  
Author(s):  
Susannah Johnson-Fulton ◽  
Linda Watson
Keyword(s):  
Bioactive Compounds ◽  
Dna Sequences ◽  
Related Species ◽  
Molecular Phylogenetics ◽  
Closely Related Species ◽  
Active Compounds ◽  
Medicinal Uses ◽  
Continental Scale ◽  
Chloroplast Markers ◽  
Geographic Regions

Species of the Cochlospermaceae, a small mostly pantropical plant family, were evaluated at a continental scale for medicinal uses in traditional medicine. This ethnobotanical information was placed in a phylogenetic framework to make informed predictions in the search for new medicines and bioactive compounds. Medicinal plant-use data were mapped onto a molecular phylogeny based on DNA sequences of nuclear and chloroplast markers. Associations of medicinal uses among closely related species occurring in different geographic regions and among diverse cultures were evaluated. The most common medicinal uses for these species are those used to treat skin ailments, gastro-intestinal problems, malaria, and liver issues. The plant species with the most numerous uses is Cochlospermum tinctorium, which occurs primarily in West Africa. Closely related species being used by cultural groups in different geographic regions to treat the same illnesses suggests the presence of bioactive compounds with potential biomedical value, since they may represent independent discoveries of similar medicinally-active compounds. This leads to the speculation that those closely related species not currently being used to treat these ailments may also contain identical or similar medicinally-active compounds and are worthy of laboratory investigations.

Altitudinal Variation in, and Morphological Divergence between, Three Related Species of Grasshopper, Praxibulus sp., Kosciuscola cognatus and K. usitatus (Orthoptera:Acrididae)

1980 ◽  
Vol 28 (1) ◽  
pp. 103 ◽  
Author(s):  
NA Campbell ◽  
JM Dearn
Keyword(s):  
Related Species ◽  
Character Displacement ◽  
Altitudinal Variation ◽  
Multivariate Statistical ◽  
Closely Related Species ◽  
Genetic Changes ◽  
Parallel Change ◽  
Variable Character ◽  
Multivariate Statistical Approach ◽  
Species Specific

Morphological variation between and within the closely related species Praxibuius sp.. Kosciuscola cognatus and K. usiratus has been examined along three independent altitudinal transects, by a multivariate statistical approach. The analyses, which were restricted to males. show that there is complete morphological separation between the three species. Moreover. there are species-specific patterns of character correlation which are consistent and relatively invariant within species, and do not exhibit altitudinal variation. The results suggest that there exist both distinct invariant species-specific character patterns and variable character patterns showing intraspecific variation. It is concluded that speciation in these grasshoppers could have involved genetic changes quite distinct from those involved in local intraspecific adaptation. Two further results are: first. evidence has been obtained for character displacement between Kosciuscola cognaius and Praxibulus sp. in an area of extensive sympatry: second. populations of K. cognatus along one transect, with a karyotype intermediate between typical K. cognatus and X usiiatus, show a parallel change in morphology towards that characteristic of K. usiiatus.

scholarly journals Site-specificity of streptococci in the oral microbiome

2021 ◽  
Author(s):  
Anthony R. McLean ◽  
Julian Torres-Morales ◽  
Gary G. Borisy ◽  
Jessica L. Mark Welch
Keyword(s):  
Oral Cavity ◽  
Related Species ◽  
Oral Microbiome ◽  
Individual Species ◽  
Rrna Gene ◽  
Site Specificity ◽  
Oral Streptococci ◽  
Closely Related Species ◽  
Streptococcus Species ◽  
Human Oral Cavity

Patterns of microbial distribution are determined by as-yet poorly understood rules governing where microbes can grow and thrive. Therefore, a detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely-related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here we assess whether individual species within this genus are generalists using publicly available genomic sequence data that provides species-level resolution. We chose a set of high-quality representative genomes for Streptococcus species from the human oral microbiome. Onto these genomes, we mapped short-read metagenomic sequences from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every reliably detectable Streptococcus species in the human oral cavity was a site-specialist and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. These three species also share substantially the same species-specific core genes indicating that neither taxonomy nor gene content are clear predictors of site-specialization. Site-specificity may instead be influenced by subtle characteristics such as nucleotide-level divergences within conserved genes.

Review of the leafhopper genus Anaceratagallia Zachvatkin, 1946 (Homoptera: Auchenorrhyncha: Cicadellidae: Megophthalminae: Agalliini) from Russia, Kazakhstan, and Central Asia

Zootaxa ◽  
2020 ◽  
Vol 4821 (2) ◽  
pp. 250-276
Author(s):  
DMITRI YU. TISHECHKIN
Keyword(s):  
Central Asia ◽  
Related Species ◽  
Male Genitalia ◽  
Comparative Investigation ◽  
Allopatric Speciation ◽  
Closely Related Species ◽  
New Synonyms ◽  
Male Calling ◽  
Species Specific

In Russia, Kazakhstan, and Central Asia the genus Anaceratagallia includes 14 species from two subgenera; all species except one belong to the nominotypical subgenus and can be classified into four groups according to the structure of male genitalia. The illustrated descriptions for all species are given, with male calling signal oscillograms provided for nine species. Ten new synonyms are established. Comparative investigation of morphological and acoustic characters of Anaceratagallia species showed that small differences in the structure of male genitalia and 2nd abdominal apodemes are not species-specific traits. All species studied in nature appeared to be polyphagous feeding on different species of herbaceous dicotyledons. It is assumed that closely related species within each group of the subgenus Anaceratagallia arose as a result of allopatric speciation and became secondarily sympatric due to subsequent range expansions.

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