An investigation on the chloroplast and nuclear genomes of taxa belong to the subgenus Dracunculus (Bess.) Rydb. of Artemisia L. (Asteraceae) in Turkey

Abstract Artemisia is one of the biggest genera in the family Asteraceae, with around 500-600 taxa at specific and sub-specific levels and organised in 5 subgenera. Due to the high number of taxa, a lot taxonomists are trying to solve the problem of its classification and phylogeny but its natural classification still hasn’t been achieved. In this research, 60 individuals belonging to 4 taxa of the subgenus Dracunculus of Artemisia L. in Turkey were examined. For all the examined individuals from both the same and different populations belonging to the taxa of the subgenus Dracunculus, the sequences of the regions both psbA-trnH of chloroplast DNA and ITS of nuclear DNA were determined. Also, the gene regions obtained were recorded in the NCBI GenBank database and an accession number was taken. It was found that there was no gene flow and hybridization between the four studied taxa of the subgenus Dracunculus, and these 4 taxa also completed their speciation. According to the results of this molecular study, A. campestris var. campestris, A. campestris var. marschalliana and A. campestris var. araratica were proposed to be raised from the variety level to the species level. This research is important as it is the first molecular based study relating with the subgenus Dracunculus growing in Turkey.

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GENETIC DRIFT AND GENE FLOW IN POPULATIONS OF THE GREAT GERBILS

Acta biomedica scientifica ◽

10.29413/abs.2018-3.4.22 ◽

2018 ◽

Vol 3 (4) ◽

pp. 147-151

Author(s):

V. V. Sutyagin

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Genetic Drift ◽

Small Groups ◽

Stochastic Matrix ◽

Large Population ◽

Random Fluctuation ◽

Gene Frequencies ◽

The Family ◽

Different Populations

The article describes the additional evolutionary factors, apart from natural selection, which can influence the genetic structure of the populations of the main carriers of the plague microbe – the great gerbil. The influence of genetic drift on random fluctuation of alleles is considered. With the help of a stochastic matrix, on the example of the family group of gerbils consisting of four individuals, the probabilities of the transition of allele frequencies from parents to offspring are calculated. Based on the previously calculated size of the neighborhood in gerbils, it is concluded that any large population of great gerbils can be considered as small in terms of deviation of gene frequencies. In such small groups – parcels – the drift of genes will be of great importance. In addition, the effect of the gene flow on the genetic structure of the gerbil population on the example of the simplest population model “continent-island” is considered. The dynamics of changes in allelic frequencies for 100 generations has been calculated. It is shown that the allele frequency during the 20-30 generations changes at the maximum rate, and then slows as the equilibrium is approached. It is concluded that different populations of gerbils should be considered as separate historically formed structures, with different sequence of influence of external environmental factors on them.

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Morphological, Karyological and Phylogenetic Analyses of three Artemisia species that Around the Van Lake in Turkey

Caryologia ◽

10.36253/caryologia-1139 ◽

2021 ◽

Author(s):

Pelin Yilmaz Sancar ◽

Semsettin CIVELEK ◽

Murat KURSAT

Keyword(s):

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Genetic Isolation ◽

Natural Classification ◽

Morphological Studies ◽

Phylogenetic Studies ◽

The Family ◽

Close Proximity ◽

Artemisia Species ◽

Different Populations

Artemisia is one of the biggest genera in the family Asteraceae, with around 500-600 taxa at specific and sub-specific levels and organised in five subgenera. Due to the high number of taxa, a lot taxonomists are trying to solve the problem of its classification and phylogeny but its natural classification still has not been achieved.The aim of this study is to try to solve the problematic systematic relationship between three different Artemisia species growing in close proximity to each other in the light of morphological, karyological and molecular data.The roots, stems, leaves, flowers structures of the plant samples collected from different populations belong to these species were investigated within the framework of morphological studies. Additionally, the chromosome counts and karyotype analysises of these species were made and idiograms were drawn in the karyological studies. In the context of phylogenetic studies, ITS and trn regions of 22 individuals belonging to 3 taxa were studied. It has been found that there is complete speciation genetic isolation mechanism between the species A. spicigera, A. taurica and A. fragrans that inhibit gene flow. A. fragrans and A. spicigera species are very similar to each other in terms of morphological characteristics. However, since populations of the species a fragrans are otopolyploid, the dimensional values of their morphological squares are larger than those of the species A. spicigera.This study is important as it is the first molecular based study relating with some species of Artemisia growing naturally in Turkey.

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Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

Journal of Fungi ◽

10.3390/jof7060478 ◽

2021 ◽

Vol 7 (6) ◽

pp. 478

Author(s):

Xue-Wei Wang ◽

Tom W. May ◽

Shi-Liang Liu ◽

Li-Wei Zhou

Keyword(s):

Phylogenetic Analyses ◽

Taxonomic Status ◽

Ancestral State ◽

Trait Evolution ◽

Natural Classification ◽

Multiple Loci ◽

The Family ◽

Phylogenetic Perspective ◽

Taxonomic Framework ◽

First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

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Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

Genetics ◽

10.1093/genetics/147.4.1843 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1843-1854 ◽

Cited By ~ 8

Author(s):

Nancy N FitzSimmons ◽

Craig Moritz ◽

Colin J Limpus ◽

Lisa Pope ◽

Robert Prince

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Green Turtle ◽

Nuclear Dna ◽

Nuclear Gene ◽

Chelonia Mydas ◽

Single Copy ◽

Microsatellite Data ◽

Ecological Data ◽

Infinite Allele Model

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

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Phylogeny accurately predicts behaviour in Indian Ocean Clitaetra spiders (Araneae:Nephilidae)

Invertebrate Systematics ◽

10.1071/is09002 ◽

2009 ◽

Vol 23 (3) ◽

pp. 193 ◽

Cited By ~ 18

Author(s):

Matjaž Kuntner ◽

Ingi Agnarsson

Keyword(s):

South Africa ◽

Phylogenetic Analysis ◽

Indian Ocean ◽

Species Level ◽

Web Architecture ◽

Evolutionarily Conserved ◽

The Family ◽

Behavioural Biology

Phylogenies are underutilised, powerful predictors of traits in unstudied species. We tested phylogenetic predictions of web-related behaviour in Clitaetra Simon, 1889, an Afro-Indian spider genus of the family Nephilidae. Clitaetra is phylogenetically sister to all other nephilids and thus important for understanding ancestral traits. Behavioural information on Clitaetra has been limited to only C. irenae Kuntner, 2006 from South Africa which constructs ladder webs. A resolved species-level phylogeny unambiguously optimised Clitaetra behavioural biology and predicted web traits in five unstudied species and a uniform intrageneric nephilid web biology. We tested these predictions by studying the ecology and web biology of C. perroti Simon, 1894 on Madagascar and C. episinoides Simon, 1889 on Mayotte. We confirm predicted arboricolous web architecture in these species. The expected ontogenetic allometric transition from orbs in juveniles to elongate ladder webs in adults was statistically significant in C. perroti, whereas marginally not significant in C. episinoides. We demonstrate the persistence of the temporary spiral in finished Clitaetra webs. A morphological and behavioural phylogenetic analysis resulted in unchanged topology and persisting unambiguous behavioural synapomorphies. Our results support the homology of Clitaetra hub reinforcement with the nephilid hub-cup. In Clitaetra, behaviour was highly predictable and remained consistent with new observations. Our results confirm that nephilid web biology is evolutionarily conserved within genera.

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Identification of medicinal plant Schisandra chinensis using a potential DNA barcode ITS2

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2013.032 ◽

2013 ◽

Vol 82 (4) ◽

pp. 283-288 ◽

Cited By ~ 8

Author(s):

Xian-kuan Li ◽

Bing Wang ◽

Rong-chun Han ◽

Yan-chao Zheng ◽

Hai-bo Yin Yin ◽

...

Keyword(s):

Dna Barcode ◽

Population Level ◽

Species Level ◽

Its2 Region ◽

Schisandra Chinensis ◽

Success Rates ◽

Wild Populations ◽

Efficient Tool ◽

Different Populations ◽

Cultivated Populations

To test whether the internal transcribed spacer 2 (ITS2) region is an effective marker for using in authenticating of the Schisandra chinensis at the species and population levels, separately. And the results showed that the wild populations had higher percentage of individuals that had substitution of C→A at site 86-bp than the cultivated populations. At sites 10-bp, 37-bp, 42-bp and 235-bp, these bases of the Schisandra sphenanthera samples differed from that of S. chinensis. Two species showed higher levels of inter-specific divergence than intra-specific divergence within ITS2 sequences. However, 24 populations did not demonstrate much difference as inter-specific and intra-specific divergences were concerned. Both S. chinensis and S. sphenanthera showed monophyly at species level, yet the samples of different populations shown polyphyly at population level. ITS2 performed well when using BLAST1 method. ITS2 obtained 100% identification success rates at the species level for S. chinensis, with no ambiguous identification at the genus level for ITS2 alone. The ITS2 region could be used to identify S. chinensis and S. sphenanthera in the “Chinese Pharmacopoeia”. And it could also correctly distinguish 100% of species and 100% of genera from the 193 sequences of S. chinensis. Hence, the ITS2 is a powerful and efficient tool for species identification of S. chinensis.

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A comparative study of the British species of Nucula and Nuculana

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s002531540000847x ◽

1954 ◽

Vol 33 (2) ◽

pp. 457-472 ◽

Cited By ~ 23

Author(s):

J. A. Allen

Keyword(s):

Comparative Study ◽

Species Level ◽

Present Survey ◽

Faecal Pellets ◽

The Family ◽

Marine Station ◽

Clyde Sea ◽

Sea Area

The survey of the sublittoral fauna of the Clyde Sea Area from 1949 onwards has shown that five species of the Protobranchiata are abundant throughout this region on a variety of substrata. Pelseneer (1891, 1899, 1911), Heath (1937), and Yonge (1939) have contributed much to the knowledge of the group as a whole, but little comparative work has been done at species level. Verrill & Bush (1897, 1898) studied the shell characters of the American Atlantic species. Moore (1931 a, b) worked on the faecal pellets of the British Nuculidae and attempted to distinguish the species by this means, while Winckworth (1930,1931), mainly in the light of the latter work, attempted to clarify the nomenclature of these species. Winckworth (1932) lists six British species of the family Nuculidae: Nucula sulcata Bronn, N. nucleus (Linné), N. hanleyi Winckworth, N. turgida Leckenby & Marshall, N. moorei Winckworth and N. tenuis (Montagu); and four species of the family Nuculanidae: Nuculana minuta (Müller), Yoldiella lucida (Loven), Y. tomlini Winckworth and Phaseolus pusillus (Jeffreys). All species of Nucula, except N. hanleyi, were taken from the Clyde Sea Area, although the latter species is included in the Clyde fauna list (Scott Elliot, Laurie & Murdoch, 1901). Only Nuculana minuta of the Nuculanidae has been taken on the present survey. Yoldiella tomlini is included in the 1901 list but is noted as being ‘insufficiently attested’. Nucula hanleyi was obtained from the Marine Station, Port Erin, but Yoldiella and Phaseolus were unobtainable.

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Leafhoppers and cixiids in phytoplasma-infected carrot fields: Species composition and potential phytoplasma vectors

Pesticidi i fitomedicina ◽

10.2298/pif1004311d ◽

2010 ◽

Vol 25 (4) ◽

pp. 311-318 ◽

Cited By ~ 7

Author(s):

Tanja Drobnjakovic ◽

Pantelija Peric ◽

Dejan Marcic ◽

Luca Picciau ◽

Alberto Alma ◽

...

Keyword(s):

Control Strategies ◽

Species Level ◽

Effective Control ◽

Correct Identification ◽

Vegetable Crops ◽

Vegetative Period ◽

Aster Yellows ◽

Scaphoideus Titanus ◽

The Family ◽

Pcr Rflp

The first molecular analysis of samples collected in southern Backa (Serbia) confirmed the presence of aster yellows (16SrI) and stolbur phytoplasmas (16SrXII) in insects belonging to the family Cicadellidae, as well as in carrot plants where the insects were collected. A correct identification of the phytoplasmas and their vectors is essential to arrange effective control strategies to prevent diseases associated with phytoplasmas from spreading to carrots and other vegetable crops. In order to enhance knowledge about insect vectors of aster yellows and stolbur phytoplasmas in Serbia, Cicadellidae and Cixiidae (Homoptera Auchenorrhyncha), the most common vectors of these phytoplasmas, were monitored in southern Backa during 2008. Adults leaf- and planthoppers were collected and identified at species level using standard entomological methods, and tested for phytoplasma presence by means of PCR/RFLP. A total of 13 insect species of Cicadellidae were identified, as follows: a) three species of the subfamily Agallinae: Anaceratagallia ribauti (Ossiannilsson), Anaceratagallia venosa (Fourcroy), and Anaceratagallia laevis (Ribaut); b) seven species of the subfamily Deltocephalinae: Psammotettix confinis (Dahlbom), Psammotettix striatus (Linnaues) Psammottettix alienus (Dahlbom), Macrosteles sexnotatus (Fall?n), Ophiola decumana (Kontkanen), Errastunus ocellaris Fall?n, and Scaphoideus titanus Ball; c) three species of the subfamily Typhlocibinae: Eupteryx atropunctata (Goeze), Eupteryx mellissae Curtis, Zyginidia pullula (Boheman). Female specimens of the genus Euscelis (Deltocephalinae) were also collected, as well as one species of Reptalus quinquecostatus (Dufour) of the family Cixiidae. Stolbur phytoplasmas were detected in A. laevis, A. ribauti, A. venosa, P. striatus, P. confinis and P. alienus. The species: A. laevis, O. decumana, and P. confinis were AY-infected (subgroup 16SrI-A), while subgroup 16SrI-C was found only in one specimen of P. confinis. Since some aster yellows- and stolbur-infected species of the genera Psammotettix and Anaceratagallia (especially P. confinis and A. laevis) were regularly and commonly found in the infected carrot fields during the whole vegetative period, they could play a significant role in transmitting and spreading these pathogens in natural environment.

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The millipede family Diplomaragnidae Attems, 1907 in the Asian part of Russia, with the descriptions of two new genera and seven new species (Diplopoda, Chordeumatida)

Zootaxa ◽

10.11646/zootaxa.5060.1.1 ◽

2021 ◽

Vol 5060 (1) ◽

pp. 1-44

Author(s):

ELENA V. MIKHALJOVA

Keyword(s):

New Species ◽

Type Species ◽

Russian Far East ◽

Far East ◽

Species Level ◽

New Genera ◽

Primorsky Krai ◽

The Family ◽

First Time ◽

The Russian Far East

The family Diplomaragnidae Attems, 1907 of the Asian part of Russia is reviewed and shown to comprise 11 genera and 60 species + 1 dubious species. Two genera and seven species are described here as new to science: Alineuma gen. nov., with type species A. rodionovi sp. nov. and Litovkia gen. nov., with the type species L. anisimovka sp. nov., Diplomaragna budilovi sp. nov., Diplomaragna dentifer sp. nov., Pacifiosoma shabalini sp. nov., Pacifiosoma acutum sp. nov., Pacifiosoma triangulatum sp. nov. Pacifiosoma asperum Mikhaljova, 2016 is recorded from the Primorsky Krai for the first time. Five genera are endemic to the Asian part of Russia. At the species level, the rate of endemism amounts to 91.7%. A key is given to all species of Diplomaragnidae presently known from Siberia and the Russian Far East. The distributions of the region’s diplomaragnids are discussed. Taxonomic remarks are provided for many species.

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DNA polymorphism of dogs (Canis familiaris L.). I. Origin, distribution of dogs in the light of molecular biological data about their mitochondrial and nuclear genomes

Biomics ◽

10.31301/2221-6197.bmcs.2021-21 ◽

2021 ◽

Vol 13 (3) ◽

pp. 298-308

Author(s):

D.A. Chemeris ◽

Yu.R. Giniyatov ◽

R.R. Garafutdinov ◽

A.V. Chemeris

Keyword(s):

Western Europe ◽

Dna Polymorphism ◽

Nuclear Dna ◽

Canis Familiaris ◽

Biological Data ◽

Migration Routes ◽

Points Of View ◽

Nuclear Genomes ◽

Biological Methods ◽

Mtdna Polymorphism

Information is given on the size and organization of the mitochondrial and nuclear genomes of dogs, including information on polymorphisms of some loci used to clarify the phylogenetic relationships of wolves and the first dogs, including hypotheses about the places of domestication of ancient now extinct wolves and the dates of these events. It is noted that the introduction of molecular biological methods in archaeology has allowed to obtain the principally new data on ancient wolves and dogs. Based on mtDNA polymorphism and nuclear DNA polymorphism, migration routes of already domesticated dogs together with humans have been tracked. The previously existing points of view about the origin of the first dogs in Western Europe, as well as in East Asia, have been supplemented in recent years by assumptions about the appearance of the first proto-dogs in Siberia.

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