scholarly journals The intraspecific structure of the Yellow-spotted ringlet Erebia manto (Denis & Schiffermüller, [1775]), with special reference to the bubastis group: an integration of morphology, allozyme and mtDNA data (Lepidoptera, Nymphalidae, Satyrinae)

2020 ◽  
Vol 43 ◽  
pp. 43-60
Author(s):  
Frans Cupedo ◽  
Camiel Doorenweerd
Keyword(s):  
Genetic Relationships ◽  
Mitochondrial Gene ◽  
Level Structure ◽  
Haplotype Network ◽  
Western Alps ◽  
Intraspecific Diversity ◽  
Genetic Lineage ◽  
Genetic Lineages ◽  
Spatial And Temporal Scales ◽  
Intraspecific Structure

Abstract. Present-day intraspecific diversity has largely been shaped by previous climatic events, but the spatial and temporal scales of differentiation processes in most species remain to be clarified. In Europe, the Pleistocene glacial cycles have generated population structures that remain especially evident in montane taxa. The intraspecific variation of the European subalpine Yellow-spotted Ringlet, Erebia manto (Denis & Schiffermüller, [1775]), shows a hierarchical, two-level structure that allows us to study intermediate stages of speciation. Morphologically, three subspecies clusters have been described in this butterfly: the manto, bubastis and vogesiaca type. An allozyme study previously revealed two genetic lineages within the manto type, and two within the vogesiaca type, but lacked bubastis representatives. To further our knowledge of the intraspecific structure of E. manto, we sampled all known and presumed intraspecific groups and sequenced 1,496 base pairs of the mitochondrial gene COI for 152 specimens from 15 localities. A median joining haplotype network, based on 40 parsimony informative sites, confirmed the four allozyme based lineages. The bubastis type was acknowledged as a fifth genetic lineage, replacing the manto type populations in the southern part of the western Alps, and separated from it by a well-known zoogeographic borderline. We discuss how the present-day distributions, genetic relationships and timing of the differentiations align.

scholarly journals Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 302
Author(s):  
Malik Sallam ◽  
Azmi Mahafzah
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Rapid Evolution ◽  
Molecular Signature ◽  
Special Focus ◽  
Genetic Lineage ◽  
Synonymous Mutation ◽  
Spike Gene ◽  
Genetic Lineages ◽  
The Uk

The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is manifested by the emergence of an ever-growing pool of genetic lineages. The aim of this study was to analyze the genetic variability of SARS-CoV-2 in Jordan, with a special focus on the UK variant of concern. A total of 579 SARS-CoV-2 sequences collected in Jordan were subjected to maximum likelihood and Bayesian phylogenetic analysis. Genetic lineage assignment was undertaken using the Pango system. Amino acid substitutions were investigated using the Protein Variation Effect Analyzer (PROVEAN) tool. A total of 19 different SARS-CoV-2 genetic lineages were detected, with the most frequent being the first Jordan lineage (B.1.1.312), first detected in August 2020 (n = 424, 73.2%). This was followed by the second Jordan lineage (B.1.36.10), first detected in September 2020 (n = 62, 10.7%), and the UK variant of concern (B.1.1.7; n = 36, 6.2%). In the spike gene region, the molecular signature for B.1.1.312 was the non-synonymous mutation A24432T resulting in a deleterious amino acid substitution (Q957L), while the molecular signature for B.1.36.10 was the synonymous mutation C22444T. Bayesian analysis revealed that the UK variant of concern (B.1.1.7) was introduced into Jordan in late November 2020 (mean estimate); four weeks earlier than its official reporting in the country. In Jordan, an exponential increase in COVID-19 cases due to B.1.1.7 lineage coincided with the new year 2021. The highest proportion of phylogenetic clustering was detected for the B.1.1.7 lineage. The amino acid substitution D614G in the spike glycoprotein was exclusively present in the country from July 2020 onwards. Two Jordanian lineages dominated infections in the country, with continuous introduction/emergence of new lineages. In Jordan, the rapid spread of the UK variant of concern should be monitored closely. The spread of SARS-CoV-2 mutants appeared to be related to the founder effect; nevertheless, the biological impact of certain mutations should be further investigated.

scholarly journals Phylogeographic Investigation of an Endangered Longhorn Beetle, Callipogon relictus (Coleoptera: Cerambycidae), in Northeast Asia: Implications for Future Restoration in Korea

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 555
Author(s):  
Ji-Hyoun Kang ◽  
Dae-Am Yi ◽  
Alexander V. Kuprin ◽  
Chang-Do Han ◽  
Yeon-Jae Bae
Keyword(s):  
South Korea ◽  
Mitochondrial Gene ◽  
Northeast Asia ◽  
Haplotype Network ◽  
Conservation Strategies ◽  
Genetic Characteristics ◽  
Linear Pattern ◽  
Wide Range ◽  
Longhorn Beetle ◽  
High Level

The longhorn beetle, Callipogon (Eoxenus) relictus Semenov, is the only remnant species found in the Palearctic region, while all other Callipogon species are distributed mainly in Central America and partly in South America. This species has been placed in the first category (as ‘critically endangered’) of the Red Data Book in Russia and designated as one of the top-priority target species among all endangered invertebrate species for restoration in South Korea since 2006. Although its restricted distribution in Northeast Asia with a high conservational value has been highlighted, genetic features of C. relictus from different geographic regions remain unexplored. We first investigated the level of genetic diversity and phylogeographic patterns of C. relictus to evaluate the current conservational status and the feasibility of the implementation of a restoration program. The average genetic divergence of mitochondrial gene COI based on Kimura-2-parameter distance among the four regions in Russia, China, North Korea, and South Korea was 2.2%, which lies within the range of intraspecific levels. However, two separate clades with 3.8% divergence were identified, despite no geographical clustering of haplotypes. The linear pattern of the haplotype network with a high level of haplotype and nucleotide diversities suggests that the wide range of currently fragmented populations might be the remnant of genetically diverse populations in the past. This study will provide crucial information on the genetic characteristics and phylogeographic history of C. relictus, which will help to establish conservation strategies for this cherished insect species in Northeast Asia.

scholarly journals Comparative Genetic Analysis of Magnaporthe oryzae Isolates Causing Gray Leaf Spot of Perennial Ryegrass Turf in the United States and Japan

Plant Disease ◽  
2007 ◽  
Vol 91 (5) ◽  
pp. 517-524 ◽  
Author(s):  
Y. Tosa ◽  
W. Uddin ◽  
G. Viji ◽  
S. Kang ◽  
S. Mayama
Keyword(s):  
United States ◽  
Perennial Ryegrass ◽  
Magnaporthe Oryzae ◽  
Leaf Spot ◽  
Genetic Relationships ◽  
The United States ◽  
Gray Leaf Spot ◽  
Genetic Lineage ◽  
Type I ◽  
Type Ii

Gray leaf spot caused by Magnaporthe oryzae is a serious disease of perennial ryegrass (Lolium perenne) turf in golf course fairways in the United States and Japan. Genetic relationships among M. oryzae isolates from perennial ryegrass (prg) isolates within and between the two countries were examined using the repetitive DNA elements MGR586, Pot2, and MAGGY as DNA fingerprinting probes. In all, 82 isolates of M. oryzae, including 57 prg isolates from the United States collected from 1995 to 2001, 1 annual ryegrass (Lolium multiflorum) isolate from the United States collected in 1972, and 24 prg isolates from Japan collected from 1996 to 1999 were analyzed in this study. Hybridization with the MGR586 probe resulted in approximately 30 DNA fragments in 75 isolates (designated major MGR586 group) and less than 15 fragments in the remaining 7 isolates (designated minor MGR586 group). Both groups were represented among the 24 isolates from Japan. All isolates from the United States, with the exception of one isolate from Maryland, belonged to the major MGR586 group. Some isolates from Japan exhibited MGR586 fingerprints that were identical to several isolates collected in Pennsylvania. Similarly, fingerprinting analysis with the Pot2 probe also indicated the presence of two distinct groups: isolates in the major MGR586 group showed fingerprinting profiles comprising 20 to 25 bands, whereas the isolates in the minor MGR586 group had less than 10 fragments. When MAGGY was used as a probe, two distinct fingerprint types, one exhibiting more than 30 hybridizing bands (type I) and the other with only 2 to 4 bands (type II), were identified. Although isolates of both types were present in the major MGR586 group, only the type II isolates were identified in the minor MGR586 group. The parsimony tree obtained from combined MGR586 and Pot2 data showed that 71 of the 82 isolates belonged to a single lineage, 5 isolates formed four different lineages, and the remaining 6 (from Japan) formed a separate lineage. This study indicates that the predominant groups of M. oryzae associated with the recent outbreaks of gray leaf spot in Japan and the United States belong to the same genetic lineage.

scholarly journals 1235. Transmission of Genetically Related, Multidrug Resistant, and Invasive Vancomycin-Resistant Enterococci (VRE) Between Patients and Rooms on the Stem Cell Transplant (SCT) and Leukemia (LKM) Units

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S375-S375
Author(s):  
Lynn El Haddad ◽  
Blake Hanson ◽  
Cesar Arias ◽  
Glen Otero ◽  
Cynthia Harb ◽  
...  
Keyword(s):  
Stem Cell ◽  
Stem Cell Transplant ◽  
Phylogenetic Analyses ◽  
Hospital Setting ◽  
Multidrug Resistant ◽  
Genetic Lineage ◽  
Cell Transplant ◽  
Research Support ◽  
Genetic Lineages ◽  
Sequence Types

Abstract Background VRE are a major cause of morbidity and mortality in immunocompromised patients. Tracking the dissemination of VRE strains is crucial to understand the dynamics of infections, emergence, and spread of VRE in the hospital setting. Methods Whole-genome sequencing (WGS) and phylogenetic analyses were performed to identify dominant VRE strains and potential transmission networks between patients and their rooms on the leukemia (LKM) and the stem cell transplant (SCT) units, located on two consecutive floors. We included 35 VRE-positive rectal swabs from SCT and LKM patients, and 55 environmental swabs from the patients’ main rooms and bathrooms. Sequence types, drug resistance genes, virulence genes, and patients’ outcomes were also determined. Results We identified VRE strains with newly described sequence types (ST) such as ST736, ST494, and ST772 which were isolated from both floors. One VRE genetic lineage belonged to ST494 (only previously isolated in Peru and was the only VanB-type strain). All other strains harbored the vanA gene. We observed highly genetically related strains transmitted between distinct rooms, floors, and time periods within the hospital in a period of 1 month (figure). Of five VRE bacteremia events, three strains were lacking the pili operon fms14-17-13 (ST203) and the remaining two were resistant to daptomycin (ST736, ST664) (figure). Of 10 patients harboring daptomycin-resistant strains, only 3 (30%) were exposed to daptomycin within 18 months before strain recovery. Conclusion Our findings confirmed horizontal transfer of highly related genetic lineages of multidrug resistant and invasive VRE strains between SCT and LKM patients and their room environment. New STs were identified and some correlated with bacteremia events. The use of a routine real-time WGS can characterize VRE strains and identify potential reservoirs of transmission in the healthcare setting in order to design interventions to prevent and control the spread of opportunistic and highly resistant organisms. Disclosures C. Arias, Merck & Co., Inc.: Grant Investigator, Research support. MeMed: Grant Investigator, Research support. Allergan: Grant Investigator, Research support. M. Stibich, Xenex Services: Employee, Salary. R. F. Chemaly, Xenex Services: Consultant and Grant Investigator, Research grant.

Re-examination of the taxonomy of the Macrobrachium australiense Holthuis (Decapoda : Palaemonidae) species-complex: molecular evidence for a single species

2004 ◽  
Vol 18 (2) ◽  
pp. 227 ◽  
Author(s):  
Nicholas P. Murphy ◽  
John W. Short ◽  
Christopher M. Austin
Keyword(s):  
Genetic Relationships ◽  
Mitochondrial Gene ◽  
Taxonomic Status ◽  
Single Species ◽  
Gene Region ◽  
Molecular Evidence ◽  
Morphological Divergence ◽  
Separate Species ◽  
North West ◽  
North East

The freshwater shrimp Macrobrachium australiense is distributed throughout the majority of inland, north-west, north-east and eastern drainages. Owing to the large amount of morphological divergence, both between and within catchments, this species has proven to be taxonomically difficult and, until recently, consisted of three separate species, each with subsequent subspecies. This study uses nucleotide sequences from the 16S rRNA mitochondrial gene region to investigate the genetic relationships between populations and confirm the taxonomic status of M. australiense. The results from sequencing an approximately 450-bp fragment from this gene region from M. australiense sampled from 12 locations across inland, eastern and northern Australia identified very little variation. The variation found between 16S M. australiense haplotypes is much less than that found between Macrobrachium species, indicating that it is in fact a single species. The results are concordant with a recent morphological revision of Australian species in which nominal taxa of the M. australiense complex were synonymised.

Relationships of scincid lizards (Mabuya spp.) from the islands of the Gulf of Guinea based on mtDNA sequence data

2005 ◽  
Vol 26 (4) ◽  
pp. 467-473 ◽  
Author(s):  
José Jesus ◽  
D. James Harris ◽  
António Brehm
Keyword(s):  
16S Rrna ◽  
Species Complex ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
12S Rrna ◽  
Gulf Of Guinea ◽  
Recent Proposal ◽  
Genetic Lineages ◽  
Sao Tome And Principe ◽  
Mtdna Sequence

AbstractRelationships of Mabuya lizards from the islands of the Gulf of Guinea where estimated using partial 12S rRNA, 16S rRNA and cytochrome b mitochondrial gene sequences. Mabuya maculilabris from São Tomé and Principe are discreet monophyletic units, highly divergent from each other and from mainland populations, indicating M. maculilabris may be a species complex. Mabuya affinis from Principe is similarly distinct from mainland populations of this species. The relationships of Mabuya ozorii from Annobon are unclear, but the three species in the Gulf of Guinea islands are not closely related, indicating multiple independent colonization events. The recent proposal to partition Mabuya into four genera is premature, since at least five distinct genetic lineages can be identified.

scholarly journals Integrative taxonomy reveals a cryptic species of the nudibranch genus Polycera (Polyceridae) in European waters

2020 ◽  
Vol 100 (5) ◽  
pp. 733-752
Author(s):  
Cecilie Gotaas Sørensen ◽  
Cessa Rauch ◽  
Marta Pola ◽  
Manuel António E. Malaquias
Keyword(s):  
Species Delimitation ◽  
Molecular Phylogenetics ◽  
Mitochondrial Gene ◽  
Haplotype Network ◽  
Integrative Taxonomy ◽  
Geographic Range ◽  
Yellow Orange ◽  
Anatomical Characters ◽  
Taxonomic Approach ◽  
Barcode Gap

AbstractThis work aimed to test whether the colour variability featured by the European nudibranch Polycera quadrilineata is consistent with the concept of a single polychromatic species or may hide multiple lineages. Samples from across the geographic range of P. quadrilineata together with representatives from worldwide species with a focus on Atlantic diversity, were gathered and studied using an integrative taxonomic approach. Morpho-anatomical characters were investigated by light and scanning electron microscopy. Bayesian molecular phylogenetics using MrBayes, the Automatic Barcode Gap Discovery species delimitation method, and haplotype network analysis using the PopArt software were employed to help delimit species using the mitochondrial gene cytochrome c oxidase subunit I (COI). The results supported the existence of a second species, here described and named Polycera norvegica sp. nov., only known from Norway where it is sympatric with P. quadrilineata. The COI uncorrected p-genetic distance between the two species was estimated at 9.6–12.4%. Polycera norvegica sp. nov. differs by exhibiting a black dotted or patchy dotted pattern occasionally with more or less defined orange/brown patches, but never black continuous or dashed stripes as in P. quadrilineata. The two species share a common colouration with a whitish base and yellow/orange tubercles. Anatomically, P. norvegica sp. nov. has a weaker labial cuticle, a smaller radula with fewer rows, and only four marginal teeth, a reproductive system with a single lobed bursa copulatrix, shorter reproductive ducts, and a penis armed with two kinds of spines: needle-like and hook-shaped penile spines.

Determination of evolutionary units in European representatives of the crab genus Pilumnus

2014 ◽  
Vol 9 (1) ◽  
pp. 104-113 ◽  
Author(s):  
Christoph Schubart ◽  
Bianca Aichinger
Keyword(s):  
Sequence Data ◽  
Mitochondrial Gene ◽  
Haplotype Network ◽  
Mtdna Sequences ◽  
Dna Sequence Data ◽  
Coastal Marine ◽  
Eastern Atlantic Ocean ◽  
Genetic Clusters ◽  
Evolutionary Units

AbstractBristle crabs of the genus Pilumnus (Brachyura: Heterotremata: Pilumnidae) are common inhabitants of European waters. They are easily identifiable as a genus, but with the exception of P. inermis, intrageneric classification turns out to be quite complex. There is no general agreement on the number and distinction of species. Therefore, this genus is well-suited for comparative molecular studies. Specimens of the Pilumnus hirtellus complex, here defined as including Pilumnus hirtellus, P. villosissimus, P. spinifer, P. aestuarii, and an undescribed species, were gathered from throughout the Mediterranean Sea and the eastern Atlantic Ocean. DNA sequence data were obtained from the barcoding region of the cytochrome oxidase 1 mitochondrial gene and used for reconstruction of a phylogenetic tree and a haplotype network. The morphology of the gastric ossicles was compared in the search of separating characters. Our results give evidence for five genetic clusters within the P. hirtellus complex. There is negligible geographic variation within these clusters. Unambiguous mtDNA sequences within morphologically variable local populations argue against possible hybridization. The here encountered evolutionary units are relatively young and possibly allow to study ongoing processes of morphological, genetic, and ecological differentiation, leading to speciation and radiations in the coastal marine environment.

scholarly journals Genetic identification of populations of Bactrocera dorsalis (Diptera Tephritidae) in the Niayes and Lower Casamance areas in Senegal

2021 ◽  
Vol 158 ◽  
pp. 16351-16362
Author(s):  
Mariama FAYE ◽  
Awa NDIAYE ◽  
Ibrahima DIALLO ◽  
Pape Mbacké SEMBENE
Keyword(s):  
Genetic Structure ◽  
Cytochrome B ◽  
Mitochondrial Gene ◽  
Food Preferences ◽  
Haplotype Network ◽  
Bactrocera Dorsalis ◽  
Genetic Identification ◽  
Genetic Structure Of Populations ◽  
Identity Card ◽  
High Level

Objectives: the study examines the effect of the host plant and of the agro-ecological area on the genetic structure of populations of Bactrocera dorsalis in order to apprehend an appropriate period to fight this pest. Methodology and results: this study was conducted in two large areas mango productions Senegal (area Niayes and the forest area South) on 41 individuals of Bactrocera dorsalis with mitochondrial gene sequencing (cytochrome B). Several haplotypes (28) of which 27 individual have been identified with a high level of genetic diversity (Hd 0.972 and Pi 0.1563). The genetic demo tests suggested a population in equilibrium, a moderate expansion and a grouping according to the areas thus revealing a genetic structure linked to the localities. In addition, the haplotype network showed a majority haplotype comprising all areas, 24 individual haplotypes and a typical haplotype to Notto. Conclusion and application of findings : this exploratory study was in addition to having provided information on the genetic characterization of the species Bactrocera dorsalis , describes its structure and its genetic differentiation based on two areas - ecological where mango is practically cultivated in Senegal . It helped to understand the genetic identity card of the species Bactrocera dorsalis, whose purpose will be to know its weakest link and food preferences to provide alternative struggles. Keywords: Bactrocera dorsalis, Niayes, lower Casamance, mangoes, citrus, PCR, sequencing, cytochrome B

scholarly journals Two partial mitochondrial gene sequences (COI and 12S-rRNA) suggested that Ceramaster japonicus (Sladen, 1889) and Ceramaster patagonicus (Sladen, 1889) (Asteroidea: Goniasteridae) from the Japanese waters are probably of the same species

Zoosymposia ◽  
2019 ◽  
Vol 15 (1) ◽  
pp. 129-140
Author(s):  
DAVIN H.E. SETIAMARGA ◽  
RENA SHIBA ◽  
YUKI KAMITO ◽  
MASAKI YAMAMOTO ◽  
NAZIFA NAZIHA BT. RAZALI ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Mitochondrial Gene ◽  
Haplotype Network ◽  
12S Rrna ◽  
National Museum ◽  
Network Analyses ◽  
Morphological Studies ◽  
The Pacific ◽  
Japanese Waters

Our recent morphological studies on the echinoderm collection of the National Museum of Nature and Science, Tokyo (NMST), indicated that the goniasterid starfishes Ceramaster japonicus (Sladen, 1889) and Ceramaster patagonicus (Sladen, 1889) are distributed in the Pacific Oceanside of Japan. In this study, we studied the NMST samples of C. japonicus and C. patagonicus from Japan, by using two mitochondrial DNA genes, the COI and 12S-rRNA, as markers to test relationships between these species in Japan. C. patagonicus sequences from GenBank were mined and included in the analyses. Results of phylogenetic and haplotype network analyses of both genes (final sequence lengths: COI = 317 bp, 12S = 477 bp) suggested that "Ceramaster patagonicus" and "Ceramaster japonicus" from Japanese waters are almost certainly synonymous without any population structure inside Japan.

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