Morphological characterisation and molecular phylogeny of several species of Criconematina (Nematoda: Tylenchida) associated with turfgrass in Korea, as inferred from ribosomal and mitochondrial DNA

Summary Six species belonging to the Criconematina, including a morphologically cryptic population within the Mesocriconema curvatum-group, are characterised based on integrative taxonomy based on morphological and molecular phylogenetic inferences from analyses of the 28S-rRNA, ITS-rRNA and COI gene sequences. Mesocriconema sp. 1 is morphologically similar to M. nebraskense and M. curvatum, differing from M. curvatum by the occasional presence of 1-2 anastomoses and a relatively higher R value, and from M. nebraskense by only a narrowed first lip annulus. However, based on COI gene sequence analysis, significant differences among the three species are evident. The sequence information in the COI gene among Mesocriconema spp. continues to reveal the existence of cryptic species within well-established species designations, and the concept of Molecular Operational Taxonomic Units might be helpful in grouping the different lineages according to sequence identities. Mesocriconema nebraskense is detailed herein for the first time outside the USA. DNA sequences of Hemicycliophora labiata were similar to those in GenBank while the existence in Korea of M. curvatum, Hemicriconemoides brachyurus and Paratylenchus nanus is molecularly confirmed.

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Molecular phylogeny of several species of Hoplolaimina (Nematoda: Tylenchida) associated with turfgrass in Korea, with comments on their morphology

Nematology ◽

10.1163/15685411-bja10061 ◽

2020 ◽

pp. 1-18

Author(s):

Abraham Okki Mwamula ◽

Gayeong Lee ◽

Yeong Ho Kim ◽

Young Ho Kim ◽

Kwang-Soo Lee ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Integrative Taxonomy ◽

Rrna Genes ◽

28S Rrna ◽

Gene Sequences ◽

Meloidogyne Graminicola ◽

Molecular Phylogenetic ◽

Its Rrna ◽

First Time ◽

Pratylenchus Zeae

Summary Seven species belonging to Suborder Hoplolaimina are characterised using integrative taxonomy, considering both morphological and molecular phylogenetic analyses of the 28S-rRNA, ITS-rRNA and COI gene sequences. It is evident that, as more populations of Pratylenchus zeae are continuously characterised, the species continues to display an ever-increasing intraspecific genetic variation within the 28S-rRNA and ITS-rRNA genes. However, the COI gene sequences exhibit minimum intraspecific variation and thus might be the most powerful DNA barcoding marker for the precise identification of P. zeae and should therefore be recommended as a complementary technique in the identification process of the species. Pratylenchus zeae, Meloidogyne graminicola and Heterodera pratensis are characterised herein for the first time in Korea, while the presence in Korea of P. penetrans, P. scribneri, H. avenae, and M. marylandi, is molecularly confirmed.

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Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes

Plants ◽

10.3390/plants10020408 ◽

2021 ◽

Vol 10 (2) ◽

pp. 408

Author(s):

Phougeishangbam Rolish Singh ◽

Gerrit Karssen ◽

Marjolein Couvreur ◽

Sergei A. Subbotin ◽

Wim Bert

Keyword(s):

18S Rrna ◽

Parasitic Nematode ◽

Integrative Taxonomy ◽

Coi Gene ◽

Integrated Analysis ◽

Gene Sequences ◽

Unknown Species ◽

New Gene ◽

First Time ◽

Plant Parasitic

Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.

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Jumping through the hoops: the challenges of daffodil (Narcissus) classification

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz032 ◽

2019 ◽

Vol 190 (4) ◽

pp. 389-404 ◽

Cited By ~ 2

Author(s):

Kálmán Könyves ◽

John David ◽

Alastair Culham

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Plastid Dna ◽

Microsatellite Data ◽

Population Sampling ◽

Molecular Phylogenetic ◽

History Of ◽

Nuclear Microsatellite ◽

Congruent Group ◽

First Time

Abstract Hoop-petticoat daffodils are a morphologically congruent group comprised of two distinct lineages in molecular phylogenetic trees of Narcissus. It is possible that the morphological similarity is a product of both historic and current low-level gene flow between these lineages. For the first time, we report population sampling from across the entire range of distribution covering the Iberian Peninsula and Morocco. In total, 455 samples were collected from 59 populations. Plastid DNA sequences of matK and ndhF were generated alongside 11 microsatellite loci to permit comparison between plastid and nuclear lineage histories. The plastid DNA phylogenetic tree was highly congruent with previous molecular studies and supported the recognition of these two lineages of hoop-petticoat daffodils as separate sections. Assignment of samples to sections sometimes differed between plastid DNA and (nuclear) microsatellite data. In these cases, the taxa had previously been the focus of dissent in taxonomic placement based on morphology. These discrepancies could be explained by hybridization and introgression among the two lineages during the evolution of hoop-petticoat daffodils, and shows that placement of species in sections is dependent on the source of data used. This study underlines the complex evolutionary history of Narcissus and highlights the discrepancies between floral morphology and phylogeny, which provides a continuing challenge for the systematics of Narcissus.

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Homology difference analysis of invasive mealybug speciesPhenacoccus solenopsisTinsley in Southern China with COI gene sequence variability

Bulletin of Entomological Research ◽

10.1017/s0007485314000674 ◽

2014 ◽

Vol 105 (1) ◽

pp. 32-39 ◽

Cited By ~ 7

Author(s):

F.Z. Wu ◽

J. Ma ◽

X.N. Hu ◽

L. Zeng

Keyword(s):

Dna Sequences ◽

Gene Sequence ◽

Southern China ◽

Geographic Origin ◽

Mitochondrial Genes ◽

Coi Gene ◽

Sequence Variability ◽

Phenacoccus Solenopsis ◽

The Usa ◽

Coi Sequences

AbstractThe mealybug speciesPhenacoccus solenopsis(P. solenopsis) has caused much agricultural damage since its recent invasion in China. However, the source of this invasion remains unclear. This study uses molecular methods to clarify the relationships among different population ofP. solenopsisfrom China, USA, Pakistan, India, and Vietnam to determine the geographic origin of the introduction of this species into China.P. solenopsissamples were collected from 25 different locations in three provinces of Southern China. Samples from the USA, Pakistan, and Vietnam were also obtained. Parts of the mitochondrial genes for cytochrome oxidase I (COI) were sequenced for each sample. Homologous DNA sequences of the samples from the USA and India were downloaded from Gen Bank. Two haplotypes were found in China. The first was from most samples from the Guangdong, Guangxi, and Hainan populations in the China and Pakistan groups, and the second from a few samples from the Guangdong, Guangxi, Hainan populations in the China, Pakistan, India, and Vietnam groups. As shown in the maximum likelihood of trees constructed using the COI sequences, these samples belonged to two clades. Phylogenetic analysis suggested that mostP. solenopsismealybugs in Southern China are probably closely related to populations in Pakistan. The variation, relationship, expansion, and probable geographic origin ofP. solenopsismealybugs in Southern China are also discussed.

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Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽

10.12688/f1000research.23635.2 ◽

2020 ◽

Vol 9 ◽

pp. 339 ◽

Cited By ~ 1

Author(s):

Tshifhiwa G. Matumba ◽

Jody Oliver ◽

Nigel P. Barker ◽

Christopher D. McQuaid ◽

Peter R. Teske

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Sequence Data ◽

Mitochondrial Gene ◽

Population Expansion ◽

Species Level ◽

Molecular Dating ◽

Coi Gene ◽

28S Rrna ◽

Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

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Hide-and-seek with hoverflies: Merodon aureus – a species, a complex or a subgroup?

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa016 ◽

2020 ◽

Vol 190 (3) ◽

pp. 974-1001

Author(s):

Ante Vujić ◽

Ljiljana Šašić Zorić ◽

Jelena Ačanski ◽

Laura Likov ◽

Snežana Radenković ◽

...

Keyword(s):

New Species ◽

Cryptic Species ◽

Species Complex ◽

Immature Stage ◽

Rrna Genes ◽

Coi Gene ◽

28S Rrna ◽

Data Types ◽

Gene Sequence Analysis ◽

Taxonomic Approach

Abstract In order to disentangle the currently confused interpretations and nomenclature of Merodon aureus and M. aeneus, we have reviewed all existing type material and species names known to us as assigned synonyms of these taxa. We resolve M. aeneus as being a junior synonym of M. aureus. We designate a lectotype for M. aureus and a neotype for M. aeneus. Additionally, we provide evidence that M. aureus, together with two newly discovered taxa (M. calidus sp. nov. and M. ortus sp. nov.), represent a complex of cryptic species named the M. aureus species complex. This complex, together with the M. unicolor species complex and the species M. pumilus, is part of the M. aureus subgroup. The M. unicolor species complex comprises two cryptic species: M. unicolor and M. albidus sp. nov. The new species are described by applying an integrative taxonomic approach using several data types (COI and 28S rRNA genes, geometric morphometry of the wings, ecological and distributional data). Based on the COI gene sequence analysis and distributional data, the pupa previously described as an immature stage of the species M. aureus is redefined as an immature stage of the new species M. calidus. Speciation within the M. aureus subgroup is discussed in the context of the phylogeographic history in the studied region.

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Disentangling the evolutionary and biogeographical history of the freshwater fish trematode genus Creptotrema (Digenea: Allocreadiidae) using an integrative taxonomy approach: the case of Creptotrema agonostomi in Middle American mountain mullets

Journal of Helminthology ◽

10.1017/s0022149x2000053x ◽

2020 ◽

Vol 94 ◽

Author(s):

G. Pérez-Ponce de León ◽

A.L. Sereno-Uribe ◽

M. García-Varela ◽

B. Mendoza-Garfias ◽

D.I. Hernández-Mena ◽

...

Keyword(s):

New York ◽

Dna Sequences ◽

Phylogenetic Analyses ◽

New York State ◽

Integrative Taxonomy ◽

Similar Species ◽

The North ◽

Middle America ◽

Molecular Phylogenetic ◽

Three New Species

Abstract Species of the allocreadiid genus Creptotrema are parasites of freshwater fishes in the Americas. Species in the genus possess one pair of muscular oral lobes on the oral sucker. Currently, the genus contains eight species, six distributed in South America, one in Middle America and one in North America. Genetic data are only available for the North American species, Creptotrema funduli, a parasite of fundulids originally described from Oneida Lake, New York State. In this study, we obtained 28S ribosomal DNA sequences of trematodes morphologically similar to Creptotrema agonostomi from the mountain mullet, Dajaus monticola, across a wide geographical range in Middle America. Our molecular phylogenetic analyses showed that (1) the genus Creptotrema, as currently conceived, is not monophyletic; (2) the allocreadiids in mountain mullets should be re-allocated in the genus Pseudoparacreptotrema; and (3) the allocreadiid trematodes from D. monticola across Middle America represent four morphologically similar species, three of which can be distinguished genetically. These three new species are described herein using an integrative taxonomy approach. We contend that accurate estimates of species diversity and phylogenetic relationships among allocreadiids, and most likely other species of trematodes, necessarily require an integrative taxonomy approach that should consider at least DNA sequences and scanning electron microscopy.

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Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology

Applied and Environmental Microbiology ◽

10.1128/aem.00298-09 ◽

2009 ◽

Vol 75 (18) ◽

pp. 5797-5808 ◽

Cited By ~ 139

Author(s):

David A. Caron ◽

Peter D. Countway ◽

Pratik Savai ◽

Rebecca J. Gast ◽

Astrid Schnetzer ◽

...

Keyword(s):

Dna Sequences ◽

18S Rrna ◽

Species Level ◽

Rrna Gene ◽

Sequence Information ◽

Ecological Studies ◽

Gene Sequences ◽

Operational Taxonomic Units ◽

Microbial Eukaryotes ◽

Protistan Species

ABSTRACT DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.

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Purifying selection can reduce intraspecific mitochondrial gene variation to that of nuclear rRNA

10.1101/2020.03.31.017764 ◽

2020 ◽

Author(s):

Tshifhiwa G. Matumba ◽

Jody Oliver ◽

Nigel P. Barker ◽

Christopher D. McQuaid ◽

Peter R. Teske

Keyword(s):

Mitochondrial Dna ◽

Dna Barcoding ◽

Dna Sequences ◽

Mitochondrial Gene ◽

Population Expansion ◽

Purifying Selection ◽

Species Level ◽

Molecular Dating ◽

Coi Gene ◽

28S Rrna

AbstractMitochondrial DNA (mtDNA) has long been used to date the divergence between species, and to explore the time when species’ effective population sizes changed. The idea that mitochondrial DNA is useful for molecular dating rests on the premise that its evolution is neutral. This premise was questionable to begin with, and even though it has long been challenged, the evidence against clock-like evolution of mtDNA is usually ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related and widely distributed rocky shore snails whose geographical ranges are defined by different thermal preferences. To our knowledge, this is the first study to use nuclear rRNA sequence for studying species-level genealogies instead of phylogenetics, presumably because this marker is considered to be uninformative at this taxonomic level. Even though the COI gene evolves at least an order of magnitude faster, which was reflected in high inter-specific divergence, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions were completely different for the two markers. Assuming that 28S evolves effectively clock-like, these findings likely illustrate variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by divergent selection between the two species. Although these two selective forces together make mtDNA suitable as a DNA barcoding marker because they create a ‘barcoding gap’, estimates of demographic change can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA beyond DNA barcoding is limited.

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Recharacterisation of three Parasitodiplogaster species based on morphological and molecular profiles

Nematology ◽

10.1163/15685411-00002967 ◽

2016 ◽

Vol 18 (4) ◽

pp. 417-437 ◽

Cited By ~ 6

Author(s):

Natsumi Kanzaki ◽

Robin M. Giblin-Davis ◽

Weimin Ye ◽

Edward Allen Herre ◽

Barbara J. Center

Keyword(s):

Dna Sequences ◽

Large Subunit ◽

Small Subunit ◽

Barro Colorado Island ◽

Research Station ◽

Stomatal Morphology ◽

Molecular Phylogenetic ◽

First Time ◽

Rna Genes ◽

Isolated Species

Three previously described Parasitodiplogaster spp., P. nymphanema, P. obtusinema and P. trigonema were re-isolated from their type locality, Barro Colorado Island Research Station, Smithsonian Tropical Research Institute, in Panama. The re-isolated materials were morphologically observed to compare with the original descriptions and molecularly characterised by DNA sequences of the near-full-length small subunit and D2-D3 expansion segments of the large subunit of the ribosomal RNA genes. Although the male tail characters, i.e., arrangement of genital papillae and spicule and gubernaculum morphologies, were close to the original descriptions, a compressed stoma with two (right subventral and dorsal) teeth was observed for the first time and confirmed in the newly re-isolated materials. The molecular phylogenetic analysis revealed that the three re-isolated species are close to P. laevigata, P. citrinema and P. popenema, forming the P. laevigata group in the genus, and this group was separated into three subgroups, P. citrinema + P. popenema (subgroup 1), P. nymphanema + P. obtusinema (subgroup 2) and P. laevigata + P. trigonema and three undescribed species (subgroup 3). The P. laevigata group is characterised by a relatively compressed stoma with two (right subventral and dorsal) teeth, arrangement of genital papillae (three or four precloacal and four postcloacal pairs), but distinguishable from each other by stomatal morphology, i.e., the shortest and most compressed being in subgroup 3, widest in subgroup 1, and intermediate in subgroup 2. Furthermore, a large and long spicule and gubernaculum were observed in subgroup 2 as its hypothesised apomorphy.

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