scholarly journals Living in isolation for almost 40 years: molecular divergence of the 28S rDNA and COI sequences between French and Polish populations of the cave beetle Speonomus normandi hydrophilus (Jeannel, 1907)

2021 ◽  
Vol 37 ◽  
pp. 75-88
Author(s):  
Joanna Kocot-Zalewska ◽  
Paweł J. Domagała ◽  
Barbara Lis
Keyword(s):  
Genetic Variations ◽  
28S Rdna ◽  
French Population ◽  
Rdna Genes ◽  
Cave System ◽  
Native Populations ◽  
Molecular Divergence ◽  
Coi Sequences ◽  
Cave Beetle ◽  
Central Pyrenees

The paper gives the results of the first studies on the molecular divergence between native and non-native populations of Speonomus normandi hydrophilus (Jeannel, 1907). This species is endemic to Massif Arize in the Central Pyrenees (France), and represents highly specialised organisms that live underground. In 1982, one hundred specimens of S. normandi hydrophilus had been experimentally introduced into the Dzwonnica Cave (Poland). Since then, a numerous population has developed in the Towarna-Dzwonnica cave system, and the neighbouring Cabanowa Cave. After almost 40 years of isolation between native and non-native populations, the genetic variations were examined using the COI and 28S rDNA genes. Analyses of the haplotypes of 28S showed one common haplogroup, which confirms the origin of the Polish group. The differentiation of haplotypes for the COI marker was high for both the French and Polish populations. Altogether 18 haplotypes of this marker have been detected, 12 in the French population and 9 in the Polish. However, only a portion of the haplotypes is shared between the native and introduced population.

Preferential loss of 5S and 28S rDNA genes in human adipose tissue during ageing

2005 ◽  
Vol 37 (2) ◽  
pp. 409-415 ◽  
Author(s):  
A. Zafiropoulos ◽  
E. Tsentelierou ◽  
M. Linardakis ◽  
A. Kafatos ◽  
D.A. Spandidos
Keyword(s):  
Adipose Tissue ◽  
Human Adipose Tissue ◽  
28S Rdna ◽  
Rdna Genes ◽  
Preferential Loss

scholarly journals Polyclad phylogeny persists to be problematic

2019 ◽  
Vol 19 (4) ◽  
pp. 585-608 ◽  
Author(s):  
Isabel L. Dittmann ◽  
Daniel Cuadrado ◽  
Maria Teresa Aguado ◽  
Carolina Noreña ◽  
Bernhard Egger
Keyword(s):  
Phylogenetic Trees ◽  
Marker Gene ◽  
Molecular Data ◽  
28S Rdna ◽  
Alignment Method ◽  
Consensus Tree ◽  
Rdna Genes ◽  
Weak Support ◽  
Maximum Likelihood Tree ◽  
Good Support

Abstract Two conflicting morphological approaches to polyclad systematics highlight the relevance of molecular data for resolving the interrelationships of Polycladida. In the present study, phylogenetic trees were reconstructed based on a short alignment of the 28S rDNA marker gene with 118 polyclad terminals (24 new) including 100 different polyclad species from 44 genera and 22 families, as well as on a combined dataset using 18S and 28S rDNA genes with 27 polyclad terminals (19 new) covering 26 different polyclad species. In both approaches, Theamatidae and Cestoplanidae were included, two families that have previously been shown to switch from Acotylea to Cotylea. Three different alignment methods were used, both with and without alignment curation by Gblocks, and all alignments were subjected to Bayesian inference and maximum likelihood tree calculations. Over all trees of the combined dataset, an extended majority-rule consensus tree had weak support for Theamatidae and Cestoplanidae as acotyleans, and also the cotylean genera Boninia, Chromyella and Pericelis appeared as acotyleans. With the most inclusive short 28S dataset, on the other hand, there is good support for the aforementioned taxa as cotyleans. Especially with the short 28S matrix, taxon sampling, outgroup selection, alignment method and curation, as well as model choice were all decisive for tree topology. Well-supported parts of the phylogeny over all trees include Pseudocerotoidea, Prosthiostomoidea, Stylochoidea, Leptoplanoidea and Cryptoceloidea, the latter three with new definitions. Unstable positions in the tree were found not only for Theamatidae, Cestoplanidae, Boninia, Chromyella and Pericelis, but also for Anonymus, Chromoplana and Cycloporus.

Molecular identification of two morphologically similar Eulecanium species: E. giganteum and E. kuwanai (Hemiptera: Coccidae)

2015 ◽  
Vol 148 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Jun Deng ◽  
Hai-Bin Li ◽  
Xu-Bo Wang ◽  
Fang Yu ◽  
Yan-Zhou Zhang ◽  
...  
Keyword(s):  
Host Plants ◽  
Ornamental Plants ◽  
Fruit Trees ◽  
28S Rdna ◽  
Similar Species ◽  
Cytochrome C Oxidase I ◽  
Match Analysis ◽  
Accurate Identification ◽  
Close Match ◽  
Coi Sequences

AbstractMost species of the genus Eulecanium Cockerell (Hemiptera: Coccidae) are important economic pests for ornamental plants and fruit trees. Two morphologically similar species, Eulecanium giganteum Shinji and E. kuwanai Kanda, are distributed mainly in China and are quite difficult to identify because of the paucity of distinguishing characteristics, which can only be observed in slide-mounted young, adult females. Furthermore, we demonstrate here that the species occur in sympatry and on many of the same host plants. Mitochondrial cytochrome c oxidase I (COI) and the D2–D3 expansion segments of 28S rDNA were used for accurate identification of these two Eulecanium species from 19 different locations in China. The average K2P distances of COI sequences were 0.47% in E. kuwanai and 0.32% in E. giganteum, and the interspecific divergences varied from 7.23% to 8.34%. Neighbour-joining (NJ) trees of COI and 28S rDNA revealed two distinct non-overlapping clusters, respectively. Meanwhile, “best close match” analysis also showed that 100% of individuals were classified successfully using COI and 28 S sequences. Differentiating between E. giganteum and E. kuwanai is challenging when using ecological and morphological traits. In contrast, identification using DNA diagnostics appears to be very effective, especially when slide-mounted specimens are difficult to obtain.

Some Representative Subterranean Communities

2019 ◽  
pp. 206-225
Author(s):  
David C. Culver ◽  
Tanja Pipan
Keyword(s):  
West Virginia ◽  
Western Australia ◽  
Iron Ore ◽  
Washington Dc ◽  
Edwards Aquifer ◽  
Lava Tubes ◽  
National Monument ◽  
Cave System ◽  
Phreatic Aquifers ◽  
Central Pyrenees

Among shallow subterranean habitats, representative communities of hypotelminorheic (Lower Potomac seeps, Washington, DC), epikarst (Postojna–Planina Cave System, Slovenia), milieu souterrain superficiel (MSS) (central Pyrenees, France), soil (central Pyrenees, France), calcrete aquifers (Pilbara, Western Australia), lava tubes (Tenerife, Spain and Lava Beds National Monument, California), fluvial aquifers (Lobau wetlands, Austria), and iron-ore caves (Brazil) are described. Among non-cave deeper habitats, communities of phreatic aquifers (Edwards Aquifer, Texas), and deep phreatic aquifers (basalt aquifers, Washington) are described. Among cave habitats, representative tropical terrestrial (Gua Salukkan Kallang, Sulawesi, Indonesia), temperate terrestrial (Mammoth Cave, Kentucky), chemoautotrophic (Peştera Movile, Romania), hygropetric (Vjetrenica, Bosnia & Herzegovina), anchialine (Šipun, Croatia), cave streams (West Virginia and U.K.) and springs (Las Hountas, Baget basin, France) communities are discussed.

Testing the reliability of detrital cave sediments as recorders of paleomagnetic secular variations, Seso Cave System (Central Pyrenees, Spain)

CATENA ◽  
2014 ◽  
Vol 119 ◽  
pp. 36-51 ◽  
Author(s):  
Belén Oliva-Urcia ◽  
Miguel Bartolomé ◽  
Ana Moreno ◽  
Graciela Gil-Romera ◽  
Carlos Sancho ◽  
...  
Keyword(s):  
Cave System ◽  
Cave Sediments ◽  
Secular Variations ◽  
Central Pyrenees

scholarly journals Morphometric and genetic variations of species composers of nike fish assemblages in Gorontalo Bay Waters, Indonesia

2020 ◽  
Vol 21 (10) ◽  
Author(s):  
Femy M. Sahami ◽  
Rene Charles Kepel ◽  
Abdul Hafidz Olii ◽  
Silvester Benny Pratasik ◽  
Ridwan Lasabuda ◽  
...  
Keyword(s):  
Life Cycle ◽  
Molecular Analysis ◽  
Morphometric Analysis ◽  
Fish Assemblages ◽  
Genetic Variations ◽  
Morphometric Characters ◽  
Juvenile Stages ◽  
Coi Sequences ◽  
Amphidromous Species ◽  
Molecular Characters

Abstract. Sahami FM, Kepel RC, Olii AH, Pratasik SB, Lasabuda R, Wantasen A, Habibie SA. 2020. Morphometric and genetic variations of species composers of nike fish assemblages in Gorontalo Bay Waters, Indonesia. Biodiversitas 21: 4571-4581.  Nike is Gobioidei fish at the post-larval and juvenile stages whose habitat is still in seawater before they migrate to the freshwater, grow up, and spawn to fulfill their life cycle as an amphidromous species. This study aims to identify the species composers of Nike fish in Gorontalo Bay waters based on their morphometric and molecular characters. 2,523 samples were collected from the catches of fishermen during three periods of their appearance in Gorontalo Bay waters from January to March 2019. The samples were grouped based on their similarity of melanophore patterns, and morphometric characters of 10 units were then measured. This study found 20 different groups of melanophore patterns; 15 of them were new melanophore patterns. DNA samples from each group of new melanophore patterns were then isolated for molecular analysis. The morphometric analysis grouped the 20 melanophore patterns into three separate clusters that were confirmed through molecular analysis. The results of Gen Cytochrome Oxidase I (COI) sequences indicate that the new melanophore patterns of Nike fish assemblages consisting of six species; five species in the Gobiidae family (i.e. Sicyopterus parvei, S. cynocephalus, S. longifilis, S. lagocephalus, and Stiphodon semoni) and a species in the Eleotridae family (Belobranchus belobranchus).

scholarly journals Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod

2017 ◽  
Author(s):  
Michał Grabowski ◽  
Tomasz Mamos ◽  
Karolina Bącela-Spychalska ◽  
Tomasz Rewicz ◽  
Remi A Wattier
Keyword(s):  
Evolutionary History ◽  
28S Rdna ◽  
Cryptic Diversity ◽  
The Balkans ◽  
Operational Taxonomic Units ◽  
Freshwater Biota ◽  
History Of ◽  
Riverine Habitats ◽  
Coi Sequences ◽  
High Level

Background. The Balkans are a major biodiversity and endemism hotspot, worldwide. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: 1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; 2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; 3) given that G. roeselii thrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; 4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification of G. roeselii. Material and Methods. DNA was extracted from 136 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors' occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes. Results. We revealed that G. roeselii includes at least 13 cryptic species or molecular operational taxonomic units (MOTUs), mostly of Miocene origin. A substantial Pleistocene diversification within-MOTUs was observed in several cases. We evidenced secondary contacts between very divergent MOTUs and introgression of nDNA. The Miocene ancestors could live in either lacustrine or riverine habitats yet their presumed geographic localisations overlapped with those of the Neogene lakes. Several extant riverine populations had Pleistocene lacustrine ancestors. Discussion. Neogene divergence of lineages resulting in substantial cryptic diversity may be a common phenomenon in extant freshwater benthic crustaceans occupying areas that were not glaciated during the Pleistocene. Evolution of G. roeselii could be associated with gradual deterioration of the paleolakes. The within-MOTU diversification might be driven by fragmentation of river systems during the Pleistocene. Extant ancient lakes could serve as local microrefugia during that time.

scholarly journals Thelytokous Reproduction of Onion Thrips, Thrips tabaci Lindeman 1889, Infesting Welsh Onion and Genetic Variation among Their Subpopulations

Insects ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 78
Author(s):  
Falguni Khan ◽  
Miltan Chandra Roy ◽  
Yonggyun Kim
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Genetic Variations ◽  
Thrips Tabaci ◽  
Population Subdivision ◽  
Onion Thrips ◽  
Welsh Onion ◽  
Female Progeny ◽  
Reproduction Mode ◽  
Local Populations ◽  
Coi Sequences

Parthenogenesis is not uncommon in thrips. This asexual reproduction produces males (arrhenotokous) or female (thelytokous). Only females are found in the onion thrips (Thrips tabaci Lindeman 1889) infesting Welsh onion (Allium fistulosum) in several areas of Korea. To determine the reproduction mode of T. tabaci, thrips infesting Welsh onion were collected from different localities in Korea. Cytochrome oxidase I (COI) sequences were then assessed. Results showed that all test local populations had signature motif specific to a thelytokous type. These COI sequences were clustered with other thelytokous populations separated from arrhenotokous T. tabaci populations. In a laboratory test, individual rearing produced female progeny without any males. These results support that Korean onion thrips infesting Welsh onion have the thelytokous type of parthenogenesis. Local thrips populations exhibited significant variations in susceptibility to chemical and biological insecticides. Random amplified polymorphic DNA (RAPD) analysis indicated genetic variations of local populations. However, the genetic distance estimated from RAPD was independent of the actual distance among different local populations. These results suggest that genetic variations of T. tabaci are arisen from population subdivision due to asexual thelytokous reproductive mode.

Two new species and the molecular phylogeny of eight species of Macrostomum (Platyhelminthes: Macrostomorpha) from southern China

Zootaxa ◽  
2017 ◽  
Vol 4337 (3) ◽  
pp. 423 ◽  
Author(s):  
YI-TAO LIN ◽  
WEI-TAO FENG ◽  
FAN XIN ◽  
LV ZHANG ◽  
YU ZHANG ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Phylogeny ◽  
Molecular Phylogenetics ◽  
Southern China ◽  
Morphological Characteristics ◽  
Guangdong Province ◽  
28S Rdna ◽  
Rdna Genes ◽  
Two New Species

Two new species of Macrostomum (Platyhelminthes: Macrostomorpha), M. shiyanensis n. sp. and M. lankouensis n. sp. are described from Shiyan Reservoir and Lankou Town. Morphological characteristics of the penis stylets and sperm, as well as the phylogenetic analysis using concatenated sequences of 18S and 28S rDNA genes support the establishment of these two new species and indicate that they are closely related to M. sinensis and M. heyuanensis described from different regions of Guangdong province. Finally, the progress of molecular phylogenetics of Macrostomum worldwide is also discussed. 

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