scholarly journals Phylogeny of the genus Percus (Coleoptera: Carabidae) – nuclear genes and the basal splits

2006 ◽  
Vol 17 (3) ◽  
Author(s):  
Martina Brückner ◽  
Dietrich Mossakowski
Keyword(s):  
Iberian Peninsula ◽  
Dna Sequences ◽  
Maximum Likelihood Method ◽  
Western Mediterranean ◽  
Balearic Islands ◽  
Likelihood Method ◽  
Rrna Gene ◽  
28S Rrna ◽  
Messinian Salinity Crisis ◽  
The Third

The phylogeny of the western Mediterranean genus Percus s.l. (Coleoptera, Carabidae) was analysed using partial DNA sequences of the nuclear 28S rRNA gene (865 bp). All 18 species of Percus s.l. with exception of P. espagnoli from the Balearic Islands were included. Phylogenetic analysis using the Maximum likelihood method reveals that the genus splits into three groups. The French Percus villai stands on its own. The Tyrrhenian species of Corsica, Sardinia, Sicily and the Italian mainland form the second group. Within this group, the phylogenetic relationships are not resolved. The third group includes Percus plicatus from Mallorca and the species of the subgenus Pseudopercus from the Iberian Peninsula. These results indicate that the subgenus Percus s.str. is paraphyletic. The split of Pseudopercus and P. plicatus probably occurred with the separation of the Balearic islands from the Iberian peninsula (20million years ago) or by the flooding of the Mediterranean after the Messinian salinity crisis (5.3 million years ago). Based on these assumptions, the divergence rate of the 28S gene can be estimated as being at 0.22–0.27% or at 0.99–1.01% per million years.

Genetic diversity in the gecko Tarentola mauritanica within the Iberian Peninsula

2008 ◽  
Vol 29 (4) ◽  
pp. 583-588 ◽  
Author(s):  
David James Harris ◽  
Ana Perera
Keyword(s):  
Iberian Peninsula ◽  
Dna Sequences ◽  
Western Mediterranean ◽  
Eastern Coast ◽  
Additional Species ◽  
Melting Pot ◽  
The Third ◽  
Western Mediterranean Basin ◽  
Central Regions ◽  
Mediterranean Gecko

AbstractThe Mediterranean gecko Tarentola mauritanica is one of the most abundant reptile species in the western Mediterranean Basin. We use mitochondrial DNA sequences, 12sRNA and 16sRNA, to analyse the patterns of distribution in the Iberian Peninsula. The results show three well defined lineages. The first one, already known to be widespread throughout Europe, is distributed along the eastern coast and southern areas of the Iberian Peninsula. The second one, endemic to the Iberian Peninsula, is widely found in central regions; and the third lineage, found so far only in two southern localities is unrelated to the other Iberian lineages, but rather to a Northern Moroccan clade. The genetic variability found within the Iberian haplogroup and the existence of a single haplotype within the European lineage suggests a complex pattern of rapid radiations and anthropogenic introductions. The third clade seems to be the result of a natural colonization from North Africa. All the data indicate that T. mauritanica is a species complex. The Iberian Peninsula, due to its geological complex history, appears to be both a hotspot and a melting pot of biodiversity, with several studies of diverse herpetofauna indicating that cryptic species occur there. More studies of additional species will be needed to develop a comparative phylogeographic framework for the region.

Morphological and molecular characterisation of Paralongidorus francolambertii sp. n. (Nematoda: Longidoridae) from Serbia

Nematology ◽  
2017 ◽  
Vol 19 (6) ◽  
pp. 681-695 ◽  
Author(s):  
László Barsi ◽  
Francesca De Luca
Keyword(s):  
Phylogenetic Analyses ◽  
The Body ◽  
Likelihood Method ◽  
Rrna Gene ◽  
28S Rrna ◽  
Sister Relationship ◽  
Large Size ◽  
Tilia Tomentosa ◽  
Amphidial Fovea ◽  
Cuticular Layer

Paralongidorus francolambertii sp. n., a bisexual species found in the rhizosphere of silver lime (Tilia tomentosa) and common juniper (Juniperus communis), is described. The species is characterised by its medium to large size (L = 5.86-8.29 mm) and slender body (a = 143-197), a lip region flattened with rounded profile, clearly offset from the body by a deep constriction, a narrow neck between the head and body, a shoulder-like body posterior to the neck, a stirrup-shaped amphidial fovea, with conspicuous slit-like aperture, lying on the lateral cuticular collar, a moderately long odontostyle ca 140 μm long, a guide ring located at ca 28 μm from anterior end, a tail terminus with thickened outer cuticular layer in both sexes, and males with spicules ca 52 μm long. The D2-D3 expansion domains of the 28S rRNA gene and the ITS-containing region of P. francolambertii sp. n. were amplified and sequenced. Phylogenetic analyses by using the Maximum Likelihood method showed that P. francolambertii sp. n. had a sister relationship with P. rex and that all Paralongidorus species formed a well-supported group.

scholarly journals Genetic similarities and phylogenetic analysis of Muntjac (Muntiacus spp.) by comparing the nucleotide sequence of 16S rRNA and cytochrome B genome

2023 ◽  
Vol 83 ◽  
Author(s):  
B. M. Khan ◽  
M. Sabir ◽  
M. N. Alyemeni ◽  
P. Kaushik ◽  
M. Saeed ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Cytochrome B ◽  
Maximum Likelihood Method ◽  
Nucleotide Sequences ◽  
Likelihood Method ◽  
Rrna Gene ◽  
B Genome ◽  
The One

Abstract This study aimed to identify the phylogenetic similarities among the muntjac (Muntiacus spp.). The phylogenetic similarities among seven major muntjac species were studied by comparing the nucleotide sequence of 16s rRNA and cytochrome b genome. Nucleotide sequences, retrieved from NCBI databases were aligned by using DNASTAR software. A phylogenetic tree was created for the selected species of muntjac by using the maximum likelihood method on MEGA7 software. The results of nucleotide sequences (16s rRNA) showed phylogenetic similarities between, the M. truongsonensis and M. rooseveltorum had the highest (99.2%) while the lowest similarities (96.8%) found between M. crinifrons and M. putaoensi. While the results of nucleotide sequences (Cty b) showed the highest similarity (100%) between M. muntjak and M. truongsonensis and the lowest s (91.5%) among M. putaoensis and M. crinifrons. The phylogenetic tree of muntjac species (16s rRNA gene) shows the main two clusters, the one including M. putaoensis, M. truongsonensis, M. rooseveltorum, and M. muntjak, and the second one including M. crinifrons and M. vuquangensis. The M. reevesi exists separately in the phylogenetic tree. The phylogenetic tree of muntjac species using cytochrome b genes shows that the M. muntjak and M. truongsonensis are clustered in the same group.

Multilocus phylogeny, species delimitation and biogeography of Iberian valvatiform springsnails (Caenogastropoda: Hydrobiidae), with the description of a new genus

2019 ◽  
Vol 186 (4) ◽  
pp. 892-914 ◽  
Author(s):  
Diana Delicado ◽  
Beatriz Arconada ◽  
Amanda Aguado ◽  
Marian A Ramos
Keyword(s):  
Iberian Peninsula ◽  
Species Delimitation ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Physical Geography ◽  
Rrna Gene ◽  
Nominal Species ◽  
28S Rrna

Abstract Valvatiform gastropods of the family Hydrobiidae are frequently found in European spring-fed systems. Their simplified and sometimes convergent morphological structures and restricted geographical ranges make the description and identification of valvatiform species challenging. In the Iberian Peninsula, to date, 20 valvatiform species have been described morphologically. To test morphological species delimitations and to evaluate the role of physical geography on their evolutionary history, we analysed two mitochondrial (COI and 16S rRNA) and two nuclear (28S rRNA and 18S rRNA) gene fragments of 16 valvatiform species from the Iberian Peninsula. Molecular species delimitation methods consistently inferred 11 of the nominal species. Our phylogenetic analyses recovered the species Islamia azarum as an independent lineage, distantly related to other genera, which we place in the new genus Deganta. Furthermore, Iberian valvatiform hydrobiids do not form a monophyletic subunit, but they are included in two distinct clades of Hydrobiidae. Divergence times indicate that speciation in these clades is likely to have coincided with the formation of major Iberian mountain ranges and river basins. Similarities of geographical subdivision and divergent times between this assemblage and the non-valvatiform genus Corrosella provide strong evidence for the role of the Iberian geographical barriers in shaping the biogeography of these springsnails.

scholarly journals Detection of a putative novel genotype of Ehrlichia sp. from opossums (Didelphis aurita) from Brazil

2019 ◽  
Vol 28 (1) ◽  
pp. 140-144
Author(s):  
Andresa Guimarães ◽  
Juliana Macedo Raimundo ◽  
Aline Tonussi da Silva ◽  
Fernanda Modesto Carpintero ◽  
Jeferson Rocha Pires ◽  
...  
Keyword(s):  
16S Rrna ◽  
Maximum Likelihood Method ◽  
Evolutionary Model ◽  
Geographic Area ◽  
Likelihood Method ◽  
Rrna Gene ◽  
Tick Vectors ◽  
Didelphis Aurita ◽  
Southeastern Region ◽  
The 16S Rrna Gene

Abstract Erlichiosis affects humans and animals worldwide. Its distribution and prevalence depends on the presence of tick vectors and hosts in one geographic area. The aim of the present study was to investigate the occurrence of Ehrlichia spp. and Anaplasma spp. in opossums (Didelphis sp.) from the State of Rio de Janeiro, southeast Brazil. Blood samples from 37 animals were tested for these two pathogens using molecular methods. One animal (2.7%) was positive for Ehrlichia sp. by 16S rRNA-based nested PCR. In a phylogenetic analysis based on the 16S rRNA gene using the maximum likelihood method and the GTRGAMMA+I evolutionary model, we detected a novel Ehrlichia sp. genotype closely related to genotypes of E. canis previously reported in dogs from Brazil. To the authors’ knowledge, this is the first molecular detection of Ehrlichia sp. in opossums from this State in the southeastern region of the country.

Characterisation of amphimictic and parthenogenetic populations of Pratylenchus bolivianus Corbett, 1983 (Nematoda: Pratylenchidae) and their phylogenetic relationships with closely related species

Nematology ◽  
2016 ◽  
Vol 18 (6) ◽  
pp. 651-678 ◽  
Author(s):  
Alberto Troccoli ◽  
Sergei A. Subbotin ◽  
John J. Chitambar ◽  
Toon Janssen ◽  
Lieven Waeyenberge ◽  
...  
Keyword(s):  
Costa Rica ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
28S Rrna ◽  
Rapid Diagnostics ◽  
Lateral Field ◽  
Lesion Nematodes ◽  
Root Lesion Nematodes

Amphimictic populations of root-lesion nematodes with numerous males and females having three lip annuli, a functional spermatheca and non-areolated lateral field occur on sword fern (Nephrolepis exaltata) in Florida. Identified for decades asPratylenchus penetrans, they appeared to be a morphologically separated species on the basis of a longer stylet (17.8-18.3 μm) thanP. penetrans(15-17 μm) and different lip pattern inen faceview (rectangularvsdumb-bell inP. penetrans). Morphologically similar amphimictic root-lesion nematodes have also been detected on flax lily in Costa Rica. Subsequent morphological observations indicated that these amphimictic root-lesion nematodes from fern and flax lily are closely related to the parthenogenetic speciesP. bolivianus, which has areolated lateral fields. In spite of the reproductive and morphological dissimilarities between these populations, their separation into different species was not supported by the results of molecular analyses of their DNA sequences. The populations used in these analyses included those that are amphimictic from Florida and Costa Rica and others that are parthenogenetic from the type locality in Bolivia, and geographically distant localities in Chile, China, Colombia and Europe. Phylogenetic analyses of the ITS and D2-D3 expansion segments of the 28S rRNA gene indicated that they belong to the same species,P. bolivianus, which consists of two morphotypes,P. bolivianus(am) amphimictic andP. bolivianus(pm) parthenogenetic, herein described and illustrated. Contradictory results were obtained by the analyses using a portion of thehsp90gene. The phylogenetic study, which included sequences of other root-lesion nematodes, a topotype and geographical distant populations ofP. zeae, revealed thatP. bolivianusandP. zeaeformed highly supported clades in the majority consensus trees. PCR with species-specific primers for rapid diagnostics ofP. bolivianusandP. zeaewere developed and tested.

scholarly journals From 18S to 28S rRNA Gene: An Improved Targeted Sarcocystidae PCR Amplification, Species Identification with Long DNA Sequences

2021 ◽  
Vol 104 (4) ◽  
pp. 1388-1393
Author(s):  
Florence C. H. Lee ◽  
Vickneshwaran Muthu
Keyword(s):  
Species Identification ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Environmental Samples ◽  
Pcr Amplification ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Index Test ◽  
Identity Matching

ABSTRACTSarcocystosis outbreaks in Tioman and Pangkor islands of Malaysia between 2011 and 2014 have raised the need to improve Sarcocystis species detection from environmental samples. In-house works found that published primers amplifying the 18S rRNA gene of Sarcocystis either could not produce the target from environmental samples or produced Sarcocystis DNA sequence that was insufficient for species identification. Using the primer pair of 18S S5 F (published) and 28S R6 R (new), this study improved the PCR amplification of Sarcocystidae to overcome these two difficulties. The PCR product spanned from the 18S to 28S rRNA genes, providing more information for species identification. The long DNA sequence allowed comparison between the “Ident” and “Query Cover” sorting in GenBank identity matching. This revealed the ambiguity in identity matching caused by different lengths of reference DNA sequences, which is seldom discussed in the literature. Using the disparity index test, a measurement of homogeneity in nucleotide substitution pattern, it is shown that the internal transcribed spacer (ITS)1-5.8S-ITS2 and 28S genes are better than the 18S gene in indicating nucleotide variations, implying better potentials for species identification. The example given by the handful of Sarcocystidae long DNA sequences reported herein calls for the need to report DNA sequence from the 18S to the 28S rRNA genes for species identification, especially among emerging pathogens. DNA sequence reporting should include the hypervariable 5.8S and ITS2 regions where applicable, and not be limited to single gene, per the current general trend.

scholarly journals First record of the genus Paranebalia Claus, 1880 (Crustacea: Leptostraca) from the Mediterranean Sea

2017 ◽  
Vol 18 (2) ◽  
pp. 332
Author(s):  
J. MOREIRA ◽  
J. JUNOY
Keyword(s):  
New Species ◽  
Mediterranean Sea ◽  
Type Species ◽  
Taxonomic Status ◽  
First Record ◽  
Western Mediterranean ◽  
Balearic Islands ◽  
The Third ◽  
The Mediterranean ◽  
A New Species

Benthic monitoring of the marine shallow bottoms off Menorca (Balearic Islands, western Mediterranean) has yielded several specimens of the leptostracan genus Paranebalia Claus, 1880. This finding constitutes the first report of the genus from European latitudes and the Mediterranean Sea and therefore the third leptostracan genus known from the Mediterranean. Specimens are described, illustrated and compared to other known species; they might represent a new species but their state of maturity and the lack of an appropriate diagnosis for the type species of the genus, Paranebalia longipes (Willemöes-Suhm, 1875), did not allow to confirm its taxonomic status.

scholarly journals On the Occurrence of Metadiaptomus chevreuxi (Calanoida, Diaptomidae, Paradiaptominae) in the Iberian Peninsula, With Notes on the Ecology and Distribution of its European Populations

Water ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1989
Author(s):  
Federico Marrone ◽  
Fernando Ortega ◽  
Francesc Mesquita-Joanes ◽  
Francisco Guerrero
Keyword(s):  
Iberian Peninsula ◽  
Dna Sequences ◽  
Mediterranean Area ◽  
First Record ◽  
Western Mediterranean ◽  
Temporary Ponds ◽  
Small Water ◽  
The North ◽  
Molecular Phylogenetic ◽  
Migrating Birds

Temporary ponds are one of the most peculiar ecosystems in the world, being characterized by an extraordinarily rich crustacean fauna, with a high degree of endemism. Among them, diaptomid copepods are among the most biogeographically interesting taxa. However, the present knowledge on diaptomid distribution is still far from being exhaustive, even in the relatively well-studied western European countries. In this study, we report the first record of the diaptomid calanoid copepod Metadiaptomus chevreuxi for the Iberian Peninsula, where it was collected in five temporary ponds in Andalusia (Spain). The characteristics of the new sites are described, the literature dealing with the European localities of the species is reviewed, and a molecular phylogenetic tree has been built, based on new and previously available mitochondrial DNA sequences, thus expanding the knowledge on the ecology and phylogeography of this rare species. The species mainly occupies small isolated temporary ponds in (semi-)arid regions, suggesting adaptations to unpredictable aquatic habitats. The existence of two molecular clades separating the Iberian from the Sicilian and Tunisian populations supports the existence of a longitudinal long-term disjunction, whereas the north-south flow is probably facilitated by migrating birds. Further research on the biota of the small water bodies of the western Mediterranean area may help to expand our knowledge on rare aquatic species, such as M. chevreuxi, and to better interpret their natural history.

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