scholarly journals Detection of cross-contamination and strong mitonuclear discordance in two species groups of sawfly genus Empria (Hymenoptera, Tenthredinidae)

2019 ◽  
Author(s):  
Marko Prous ◽  
Kyung Min Lee ◽  
Marko Mutanen
Keyword(s):  
Sanger Sequencing ◽  
Nuclear Gene ◽  
Nuclear Data ◽  
Nuclear Genes ◽  
High Rate ◽  
Coi Gene ◽  
Contamination Rate ◽  
Cross Contamination ◽  
Mitochondrial Coi ◽  
Species Groups

AbstractIn several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggesting different relationships. As previous studies were based on only few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtain genomic-scale ddRAD data together with Sanger sequencing of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups within the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on previous and new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in E. immersa group are not recovered as monophyletic also based on nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10–20% of recovered loci) cross-contaminated. A reason could be due to specimen identification tag jumps during sequencing library preparation of pooled specimens that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting identical sequences between immersa and longicornis groups that are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using unique combination of limited number of tags (less than the number of specimens).

First report of incidence of eriophyid mite Aceria sp. on Amaranthus

ENTOMON ◽  
2020 ◽  
Vol 44 (4) ◽  
pp. 309-310
Author(s):  
K. M. Sreekumar ◽  
N. Srinivasa ◽  
R. Sivamoorthy
Keyword(s):  
Foliar Application ◽  
Nuclear Gene ◽  
Coi Gene ◽  
Species Delineation ◽  
Amaranthus Tricolor ◽  
Eriophyid Mite ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
First Time ◽  
Damage Symptoms

Eriophyid mite Aceria sp. damaging Amaranthus (Amaranthus tricolor) is reported from India for the first time. The mite cause severe malformation of the shoot, making it fibrous and reducing the yield. Foliar application of spiromesifen or fenpyroximate reduced the damage symptoms. DNA data for the mitochondrial COI gene and nuclear gene (ITS 2 region) are being generated for accurate species delineation.

Allopatric separation represents an overlooked cryptic species in theAnania hortulataspecies complex (Lepidoptera: Crambidae: Pyraustinae): congruence between genetic and morphological evidence

2019 ◽  
Vol 151 (2) ◽  
pp. 163-186 ◽  
Author(s):  
Zhaofu Yang ◽  
Jean-François Landry
Keyword(s):  
North America ◽  
Nuclear Gene ◽  
Single Species ◽  
Coi Gene ◽  
Morphological Evidence ◽  
Widespread Species ◽  
Mitochondrial Coi ◽  
Network Analyses ◽  
Geographical Regions ◽  
Morphological Differences

AbstractAnania hortulata(Linnaeus, 1758) (Lepidoptera: Crambidae: Pyraustinae) is a strikingly coloured, common, and widespread species that has long been recognised as a single species widely distributed in Asia, Europe, and North America. Using a combination of molecular and morphometric data, this study resolved thatA. hortulatais actually a species complex of two superficially indistinguishable species. Phylogenetic and network analyses based on the mitochondrial COI gene discriminated lineages from all major geographical regions of China as distinct,A. sinensisYang and Landrynew species, whereasA. hortulataoccurs in Central Asia, Europe, and North America. Nuclear gene (CAD) and morphological differences in the genital characters provided further evidence for the separation ofA. hortulataandA. sinensis.

scholarly journals Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

2017 ◽  
Author(s):  
Étienne Léveillé-Bourret ◽  
Julian R. Starr ◽  
Bruce A. Ford ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon
Keyword(s):  
Estimation Error ◽  
Gene Tree ◽  
Nuclear Gene ◽  
Nuclear Data ◽  
Pcr Primers ◽  
Nuclear Genes ◽  
Flowering Plant ◽  
Nuclear Ribosomal Dna ◽  
Anchored Phylogenomics ◽  
Rapid Radiations

AbstractDespite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur. In another contribution on anchored phylogenomics in angiosperms, we presented flowering plant-specific anchored enrichment probes for hundreds of conserved nuclear genes and demonstrated their use at the level of all angiosperms. In this contribution, we focus on a common problem in phylogenetic reconstructions below the family level: weak or unresolved backbone due to rapid radiations (≤ 10 million years) followed by long divergence, using the Cariceae-Dulichieae-Scirpeae clade (CDS, Cyperaceae) as a test case. By comparing our nuclear matrix of 461 genes to a typical Sanger-sequence dataset consisting of a few plastid genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our nuclear data is fully compatible with the Sanger dataset and resolves short backbone internodes with high support in both concatenated and coalescence-based analyses. In addition, we show that nuclear gene tree incongruence is inversely proportional to phylogenetic information content, indicating that incongruence is mostly due to gene tree estimation error. This suggests that large numbers of conserved nuclear loci could produce more accurate trees than sampling rapidly evolving regions prone to saturation and long-branch attraction. The robust phylogenetic estimates obtained here, and high congruence with previous morphological and molecular analyses, are strong evidence for a complete tribal revision of CDS. The anchored hybrid enrichment probes used in this study should be similarly effective in other flowering plant groups. [Carex, coalescent based species tree, flowering plants, low-copy nuclear genes, low-level phylogenetics, universal hybrid enrichment probes]

Combining Nuclear and Mitochondrial Loci Provides Phylogenetic Information in the Philopterus Complex of Lice (Psocodea: Ischnocera: Philopteridae)

2020 ◽  
Author(s):  
Tomas Najer ◽  
Ivo Papousek ◽  
Oldrich Sychra ◽  
Andrew D Sweet ◽  
Kevin P Johnson
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Nuclear Genes ◽  
Morphological Data ◽  
Coi Gene ◽  
Phylogenetic Information ◽  
Mitochondrial Coi ◽  
Putative Species ◽  
Mitochondrial Loci

Abstract The Philopterus Complex includes several lineages of lice that occur on birds. The complex includes the genera Philopterus (Nitzsch, 1818; Psocodea: Philopteridae), Philopteroides (Mey, 2004; Psocodea: Philopteridae), and many other lineages that have sometimes been regarded as separate genera. Only a few studies have investigated the phylogeny of this complex, all of which are based on morphological data. Here we evaluate the utility of nuclear and mitochondrial loci for recovering the phylogeny within this group. We obtained phylogenetic trees from 39 samples of the Philopterus Complex (Psocodea: Philopteridae), using sequences of two nuclear (hyp and TMEDE6) and one mitochondrial (COI) marker. We evaluated trees derived from these genes individually as well as from concatenated sequences. All trees show 20 clearly demarcated taxa (i.e., putative species) divided into five well-supported clades. Percent sequence divergence between putative species (~5–30%) for the COI gene tended to be much higher than those for the nuclear genes (~1–15%), as expected. In cases where species are described, the lineages identified based on molecular divergence correspond to morphologically defined species. In some cases, species that are host generalists exhibit additional underlying genetic variation and such cases need to be explored by further future taxonomic revisions of the Philopterus Complex.

Characterizing population structure of coral-associated fauna from mesophotic and shallow habitats in the Caribbean

2018 ◽  
Vol 99 (3) ◽  
pp. 619-629 ◽  
Author(s):  
Alex J. Veglia ◽  
Nicholas M. Hammerman ◽  
Carlos R. Rivera Rosaly ◽  
Matthew Q. Lucas ◽  
Alexandra Galindo Estronza ◽  
...  
Keyword(s):  
Population Structure ◽  
Puerto Rico ◽  
Marine Invertebrates ◽  
Geographic Distance ◽  
Harpacticoid Copepod ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Symbiotic Relationships ◽  
Harpacticoid Copepods ◽  
Obligate Symbiont

Symbiotic relationships are a common phenomenon among marine invertebrates, forming both obligatory and facultative dependencies with their host. Here, we investigate and compare the population structure of two crustacean species associated with both shallow and mesophotic ecosystems: an obligate symbiont barnacle (Ceratoconcha domingensis), of the coral Agaricia lamarcki and a meiobenthic, free-living harpacticoid copepod (Laophontella armata). Molecular analyses of the Cytochrome Oxidase Subunit I (COI) gene revealed no population structure between mesophotic and shallow barnacle populations within south-west Puerto Rico (ΦST = 0.0079, P = 0.33). The absence of population structure was expected due to the pelagic naupliar larvae of the barnacles and the connectivity patterns exhibited by the coral itself within the same region. Laophontella armata exhibited significant structure based on the mitochondrial COI gene between the mesophotic reef ecosystem of El Seco, Puerto Rico and mangrove sediments of Curaçao (ΦST = 0.2804, P = 0.0). The El Seco and Curaçao copepods shared three COI haplotypes despite the obligatory benthic development of harpacticoid copepods and the geographic distance between the two locations. Three other COI haplotypes from El Seco exhibited higher than expected (up to 7%) intra-species variability, potentially representing three new cryptic species of harpacticoid copepods or rare, deeply divergent lineages of L. armata. This result is evidence for the urgent need of a deeper investigation into the meiofauna diversity associated with mesophotic coral ecosystems (MCEs), arguably the most diverse metazoan component of MCEs.

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 40
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
The Arctic ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

A review of the genus Forficuloecus Conci (Phthiraptera: Philopteridae) from parrots (Psittaciformes: Psittacidae), with descriptions of four new species

Zootaxa ◽  
2008 ◽  
Vol 1859 (1) ◽  
pp. 49 ◽  
Author(s):  
ROGER D. PRICE ◽  
KEVIN P. JOHNSON ◽  
RICARDO L. PALMA
Keyword(s):  
New Species ◽  
Coi Gene ◽  
Chewing Louse ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Genetic Distinctiveness

Ten species, including four new species, of the chewing louse genus Forficuloecus Conci, 1941, are recognized from Australasian parrots, and a key is given for their identification. The new species and their type hosts are: F. cameroni ex the Red-winged Parrot, Aprosmictus erythropterus (J.F. Gmelin, 1788); F. banksi ex the Mulga Parrot, Psephotus varius Clark, 1910; F. wilsoni ex the Northern Rosella, Platycercus venustus (Kuhl, 1820); and F. josephi ex the Bourke's Parrot, Neopsephotus bourkii (Gould, 1841). Partial sequences of the mitochondrial COI gene support the genetic distinctiveness of these new species.

Are Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara (Acari: Tetranychidae) one species? Morphological and molecular evidences for synonymy between these two spider mite species and a note on invasiveness of T. macfarlanei on okra and eggplant in India

2017 ◽  
Vol 22 (4) ◽  
pp. 467
Author(s):  
Mahran Zeity ◽  
Nagappa Srinivas ◽  
Chinnamade Channegowde Gowda
Keyword(s):  
Spider Mite ◽  
Morphological Characters ◽  
Molecular Data ◽  
Mite Species ◽  
Coi Gene ◽  
High Similarity ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
High Degree ◽  
Degree Of Similarity

Study of morphological characters of Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara revealed high similarity by comparing all the important characters in addition to the characters pointed out by Ehara to separate those two species. Molecular phylogeny of seven Indian populations of T. macfarlanei and one population of T. malaysiensis from Philippines along with few distantly related species of Tetranychus was attempted. High degree of similarity between these two species at mitochondrial COI gene (96%) as well as ITS2 (rDNA) (96–99%) region was evident. Based on both morphological features and molecular data, T. malaysiensis is proposed as a junior synonym of T. macfarlanei based on ICZN’s law of priority. Also more female characters are prompted in this study to distinctly discriminate T. macfarlanei from its most resembling species, Tetranychus ludeni Zacher. Tetranychus macfarlanei has emerged as a pest of several cultivated crop plants in India. 

Quantification and Variability Analysis of Bacterial Cross-Contamination Rates in Common Food Service Tasks

2001 ◽  
Vol 64 (1) ◽  
pp. 72-80 ◽  
Author(s):  
YUHUAN CHEN ◽  
KRISTIN M. JACKSON ◽  
FABIOLA P. CHEA ◽  
DONALD W. SCHAFFNER
Keyword(s):  
Food Service ◽  
Enterobacter Aerogenes ◽  
Scientific Basis ◽  
Food Preparation ◽  
Contamination Rate ◽  
Cross Contamination ◽  
Transfer Rates ◽  
Washing Efficiency ◽  
The Cross ◽  
Contamination Events

This study investigated bacterial transfer rates between hands and other common surfaces involved in food preparation in the kitchen. Nalidixic acid–resistant Enterobacter aerogenes B199A was used as a surrogate microorganism to follow the cross-contamination events. Samples from at least 30 different participants were collected to determine the statistical distribution of each cross-contamination rate and to quantify the natural variability associated with that rate. The transfer rates among hands, foods, and kitchen surfaces were highly variable, being as low as 0.0005% and as high as 100%. A normal distribution was used to describe the variability in the logarithm of the transfer rates. The mean ± SD of the normal distributions were, in log percent transfer rate, chicken to hand (0.94 ± 0.68), cutting board to lettuce (0.90 ± 0.59), spigot to hand (0.36 ± 0.90), hand to lettuce (−0.12 ± 1.07), prewashed hand to postwashed hand (i.e., hand washing efficiency) (−0.20 ± 1.42), and hand to spigot (−0.80 ± 1.09). Quantifying the cross-contamination risk associated with various steps in the food preparation process can provide a scientific basis for risk management efforts in both home and food service kitchens.

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