AquaBOL.SK - how far have we come with the Slovak reference barcode database since DNAqua-Net was launched?

ARPHA Conference Abstracts ◽

10.3897/aca.4.e64939 ◽

2021 ◽

Vol 4 ◽

Author(s):

Zuzana Čiamporová-Zaťovičová ◽

Patrik Macko ◽

Michaela Šamulková ◽

Ondrej Vargovčík ◽

Jana Bozáňová ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Common Species ◽

Reference Database ◽

Aquatic Biota ◽

Nondestructive Monitoring ◽

Widespread Species ◽

Eastern Carpathians ◽

Local Reference ◽

Taxonomic Groups

Essential for implementation of molecular tools in bioassessments are comprehensive databases with high-quality reference DNA sequence data. A recent survey arising from the DNAqua-Net EU COST Action WG1 has revealed significant gaps in the barcode reference data of aquatic biota both on a taxonomic and a geographical level (Weigand 2019). Although reference barcode libraries of all main freshwater groups are continuously improved through a number of national DNA-barcoding campaigns, still little data is available from Central and Eastern Europe. In Slovakia, the barcode coverage of the aquatic biota was very low when DNAqua-Net started. At the end of 2016 only 165 public records (60 OTUs) were available in BOLD (< 3 % of aquatic macroinvertebrates reported from Slovakia), and most of them were mined from GenBank. This led us to launch the campaign “Barcoding aquatic biota of Slovakia” (www.AquaBOL.SK), aiming to improve this unpleasant state. Since many common species in Slovakia are covered by barcodes from other countries, initially we focused on least explored habitat types within Europe - alpine glacial lakes in Tatra Mts and karstic springs. Both are located in Western and Slovak part of Eastern Carpathians, which are considered one of the most valuable biodiversity centers in Europe. More than 2700 sequences of COI-5P (337 BINs), originating in Slovakia, are currently in our dataset. Mostly they represent aquatic insects (86 %) and crustaceans (12 %), followed by minor taxonomic groups. From insects, the best covered orders are Coleoptera (43 % of sequences, 21% of species), followed by Trichoptera (22 % of sequences, 24 % of species) and Ephemeroptera (18 % of sequences, 33 % of species). And even if other groups (Hemiptera, Plecoptera) represent only around 5 % of all sequences each, their species coverage is already 21 % or 28 %, respectively. Relatively high number of unique BINs (35 out of 337) from our area, and separate intraspecific lineages within BINs of many widespread species, supports the premise that the Western Carpathians belong to the most important biodiversity hotspots. Our local reference database, continuously updated, is useful for the analysis and interpretation of metabarcoding data - a prerequisite for effective and nondestructive monitoring of aquatic biotopes including vulnerable, threatened, and protected habitats. It is also beneficial for a number of other purposes such as taxonomic revisions and phylogenetic analyses. This contribution was partially supported by VEGA2/0030/17, VEGA2/0084/2021 and COST CA15219.

Intra- and interspecific genetic diversity of New Zealand hairworms (Nematomorpha)

Parasitology ◽

10.1017/s0031182017000233 ◽

2017 ◽

Vol 144 (8) ◽

pp. 1026-1040 ◽

Cited By ~ 4

Author(s):

ZACHARY J. C. TOBIAS ◽

ARUN K. YADAV ◽

ANDREAS SCHMIDT-RHAESA ◽

ROBERT POULIN

Keyword(s):

Genetic Diversity ◽

New Zealand ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Population Level ◽

Morphological Classification ◽

Widespread Species ◽

Sampling Locations ◽

Host Parasite ◽

Eggs And Larvae

SUMMARYHairworms (Nematomorpha) are a little-known group of parasites, and despite having been represented in the taxonomic literature for over a century, the implementation of molecular genetics in studies of hairworm ecology and evolution lags behind that of other parasitic taxa. In this study, we characterize the genetic diversity of the New Zealand nematomorph fauna and test for genetic structure within the most widespread species found. We provide new mitochondrial and nuclear ribosomal sequence data for three previously described species from New Zealand:Gordius paranensis, Parachordodes diblastusandEuchordodes nigromaculatus. We also present genetic data on a previously reported but undescribedGordiussp., as well as data from specimens of a newGordionussp., a genus new for New Zealand. Phylogenetic analyses of CO1 and nuclear rDNA regions correspond with morphological classification based on scanning electron microscopy, and demonstrate paraphyly of the genusGordionusand the potential for cryptic species withinG. paranensis. Population-level analyses ofE. nigromaculatusshowed no genetic differentiation among sampling locations across the study area, in contrast to previously observed patterns in known and likely definitive hosts. Taken together, this raises the possibility that factors such as definitive host specificity, intermediate host movement, and passive dispersal of eggs and larvae may influence host–parasite population co-structure in hairworms.

Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

PeerJ ◽

10.7717/peerj.8999 ◽

2020 ◽

Vol 8 ◽

pp. e8999

Author(s):

Sigrid Liede-Schumann ◽

Guido W. Grimm ◽

Nicolai M. Nürk ◽

Alastair J. Potts ◽

Ulrich Meve ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Cape Floristic Region ◽

Rapid Radiation ◽

Widespread Species ◽

Dna Sequence Data ◽

Phylogenetic Affinities ◽

African Genus

Background Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum, together with the highly succulent and species-rich tribe Ruschieae, constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. Methods Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence dataset comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. Results Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.

MtDNA lineage diversity of a potamonautid freshwater crab in KwaZulu-Natal, South Africa

Koedoe ◽

10.4102/koedoe.v57i1.1324 ◽

2015 ◽

Vol 57 (1) ◽

Cited By ~ 7

Author(s):

Gavin Gouws ◽

Nasreen Peer ◽

Renzo Perissinotto

Keyword(s):

South Africa ◽

Sequence Data ◽

Novel Species ◽

Phylogenetic Analyses ◽

Intraspecific Diversity ◽

Freshwater Crab ◽

Widespread Species ◽

Mitochondrial Sequence ◽

Kwazulu Natal ◽

Lineage Diversity

Five species of freshwater crab (genus Potamonautes) are known from KwaZulu-Natal, South Africa, whilst a sixth (Potamonautes isimangaliso) was recently described from the iSimangaliso Wetland Park. Earlier molecular studies of crab diversity in the province were largely limited in geographic scope or employed genetic markers, ill-suited for identifying intraspecific diversity. Possible species-level diversity or cryptic taxa may have thus remained undetected. In this study, lineage diversity was examined in a widespread species, Potamonautes sidneyi, using mitochondrial sequence data, to determine whether this species harbours cryptic diversity that could be of conservation importance in the province, particularly with respect to the iSimangaliso Wetland Park. The taxonomic status of P. isimangaliso was also assessed. Mitochondrial sequence data were generated and analysed to identify unique lineages and to examine their distributions. Phylogenetic analyses were used to determine whether these lineages represented known or potentially novel species, using comparative data from southern African Potamonautes species. Seven independent networks were identified within P. sidneyi and substantial structure was observed amongst sampling localities. Phylogenetic analyses revealed two distinct, divergent lineages in P. sidneyi. One was positively assigned to P. sidneyi, whereas the placement of the other suggested a novel species. These results suggested possible species diversity within P. sidneyi, with one lineage occurring in the north-east of the province, around the iSimangaliso Wetland Park. Potamonautes isimangaliso was clearly allied to Potamonautes lividus, but genetic divergences suggested that P. isimangaliso is a distinct taxon and that P. lividus may represent a species complex.Conservation implications: This study confirmed unique freshwater crab diversity, both within KwaZulu-Natal and associated with the iSimangaliso Wetland Park.

Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

10.1101/824623 ◽

2019 ◽

Author(s):

Sigrid Liede-Schumann ◽

Guido W. Grimm ◽

Nicolai M. Nürk ◽

Alastair J. Potts ◽

Ulrich Meve ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Cape Floristic Region ◽

Rapid Radiation ◽

Data Set ◽

Widespread Species ◽

Dna Sequence Data ◽

Phylogenetic Affinities

AbstractBackgroundDrosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions of Drosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades within Drosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.

Morphological and phylogenetic analyses of Toniniopsis subincompta s. lat. (Ramalinaceae, Lecanorales) in Eurasia

The Lichenologist ◽

10.1017/s0024282921000013 ◽

2021 ◽

Vol 53 (2) ◽

pp. 171-183

Author(s):

Julia V. Gerasimova ◽

Irina N. Urbanavichene ◽

Gennady P. Urbanavichus ◽

Andreas Beck

Keyword(s):

Rna Polymerase Ii ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Species Level ◽

New Combination ◽

Lateral Part ◽

Widespread Species ◽

Brown Colour

AbstractIn recent years, several species that have long been considered to belong in Bacidia s. lat. have been transferred to other genera such as Bellicidia, Bibbya, Scutula, and also to Toniniopsis, accommodating species previously placed in Bacidia and Toninia. One of its widespread species, Toniniopsis subincompta, can be recognized by its thinly granular thallus, dark brown to black apothecia, green epithecium, red-brown hypothecium, and bacilliform ascospores. However, it shows considerable variation in thallus structure, and coloration of apothecia, hypothecium and exciple. We sequenced 20 specimens of T. subincompta to investigate whether there is phylogenetic support for the delimitation of species in accordance with the variability of the observed characters. For phylogenetic analyses, we used newly generated sequence data from the nuclear internal transcribed spacer (nrITS), mitochondrial small subunit (mtSSU) and DNA-directed RNA polymerase II subunit (RPB2). Maximum likelihood and Bayesian inference analyses, as well as three species delimitation programs, provided consistent evidence that T. subincompta forms two separate lineages, to be recognized at the species level. The complex nomenclature of T. subincompta (basionym Lecidea subincompta) shows it to be a synonym of Bellicidia incompta. For the most common taxon previously called Bacidia (Toniniopsis) subincompta, the new combination T. separabilis is made, rather than proposing a conserved type for Lecidea subincompta. Toniniopsis dissimilis is newly described to accommodate the less common taxon. Toniniopsis dissimilis is characterized by a predominantly wrinkled to warted to subsquamulose thallus; generally grey-brown to dark brown apothecia, often with a lighter margin; a dark brown hypothecium, frequently gradually merging into the coloration of the exciple below and the lateral part of the exciple attached to the hymenium; a mostly colourless rim and lateral part of the exciple. The closely related T. separabilis is characterized by a thallus of mostly single or contiguous ±loose granules, often forming short, coralloid, isidium-like bulges; darker apothecia, with a margin mostly of the same colour or darker than the disc; a comparatively thinner hypothecium easily separated from the exciple below. The rim and lateral part of the exciple often contain either a blue, brown or mixed blue-brown colour in the upper part or along the whole margin. Lectotypes of Bacidia vegeta, Lecidea bacillifera f. melanotica and Secoliga atrosanguinea var. affinis (the synonyms of T. separabilis) are selected. Cyanotrophy and the occurrence of albino morphs in T. separabilis are discussed.

Salix transect of Europe: records of willow-associated weevils (Coleoptera: Curculionoidea) from Greece to Arctic Norway, with insights from DNA barcoding

Biodiversity Data Journal ◽

10.3897/bdj.8.e52881 ◽

2020 ◽

Vol 8 ◽

Author(s):

Roy Canty ◽

Enrico Ruzzier ◽

Quentin Cronk ◽

Diana Percy

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Sequence Data ◽

Size Variation ◽

Common Species ◽

Widespread Species ◽

Dna Sequence Data ◽

Geographic Clustering ◽

Site Variation ◽

The Mean

Curculionid beetles associated with willow (Salix spp.) were surveyed at 42 sites across Europe, from Greece (lat. 38.8 °N) to arctic Norway (lat. 69.7 °N). DNA sequence data provide additional verification of identifications and geographic clustering. In all, 73 curculionid species were collected from willows, of which seven were particularly abundant. The most widespread species were: Acalyptus carpini Fabricius, 1793 at 15 sites; Tachyerges stigma Germar, 1821 at 13 sites; Phyllobius oblongus (Linnaeus, 1758) at 11 sites; Phyllobius maculicornis Germar, 1824 at 10 sites; and Archarius salicivorus (Paykull, 1792), Melanapion minimum (Herbst, 1797), and Phyllobius cf. pyri (Linnaeus, 1758) all at nine sites. The mean number of curculionid species collected on willow at each site was 5.5 (range 0-14). Compared to chrysomelids, curculionids were richer in species but the species had relatively low average abundance. Widespread curculionid species appear to have scattered and patchy observed distributions with limited geographical structuring in our data. However, deeper sampling (e.g. over multiple seasons and years), would give a better indication of distribution, and may increase apparent geographical structuring. There is some site-to-site variation in colour in a few taxa, but little notable size variation. DNA barcoding, performed on some of the more common species, provides clear species clusters and definitive separation of the taxonomically more challenging species, as well as some interesting geographic insights. Our northernmost sample of Phyllobius oblongus is unique in clustering with Canadian samples of this species. On the other hand, our samples of Acalyptus carpini cluster with European samples and are distinct from a separate Canadian cluster of this species. We provide the first available DNA sequences for Phyllobius thalassinus Gyllenhal, 1834 (Hungary).

Molecular evidence for hybridization in the aquatic plant Limosella on sub-Antarctic Marion Island

Antarctic Science ◽

10.1017/s0954102021000079 ◽

2021 ◽

pp. 1-9

Author(s):

John H. Chau ◽

Michelle Greve ◽

Bettine Jansen van Vuuren

Keyword(s):

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Variability ◽

Molecular Evidence ◽

Marion Island ◽

Specific Sequence ◽

Nuclear Locus ◽

Species Specific ◽

Taxonomic Groups

Abstract DNA sequence data have become a crucial tool in assessing the relationship between morphological variation and genetic and taxonomic groups, including in the Antarctic biota. Morphologically distinct populations of submersed aquatic vascular plants were observed on sub-Antarctic Marion Island, potentially representing the two species of such plants listed in the island's flora, Limosella australis R.Br. (Scrophulariaceae) and Ranunculus moseleyi Hook.f. (Ranunculaceae). To confirm their taxonomic identity, we sequenced a nuclear locus (internal transcribed spacer; ITS) and two plastid loci (trnL-trnF, rps16) from three specimens collected on Marion Island and compared the sequences with those in public sequence databases. For all three loci, sequences from the Marion Island specimens were nearly identical despite morphological dissimilarity, and phylogenetic analyses resolved them to a position in Limosella. In phylogenetic trees and comparisons of species-specific sequence polymorphisms, the Marion Island specimens were closest to a clade comprising Limosella aquatica L., L. curdieana F.Muell. and L. major Diels for ITS and closest to L. australis for the plastid loci. Cytonuclear discordance suggests a history of hybridization or introgression, which may have consequences for morphological variability and ecological adaptation.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

Microorganisms ◽

10.3390/microorganisms9030666 ◽

2021 ◽

Vol 9 (3) ◽

pp. 666

Author(s):

Niccolò Forin ◽

Alfredo Vizzini ◽

Federico Fainelli ◽

Enrico Ercole ◽

Barbara Baldan

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Illumina Miseq ◽

Botanical Garden ◽

Molecular Study ◽

Its2 Sequence ◽

Type Specimens ◽

Its1 Sequence ◽

Dna Sequence Data ◽

Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

Toward a global reference database of COI barcodes for marine zooplankton

Marine Biology ◽

10.1007/s00227-021-03887-y ◽

2021 ◽

Vol 168 (6) ◽

Author(s):

Ann Bucklin ◽

Katja T. C. A. Peijnenburg ◽

Ksenia N. Kosobokova ◽

Todd D. O’Brien ◽

Leocadio Blanco-Bercial ◽

...

Keyword(s):

Species Diversity ◽

Dna Sequences ◽

Reference Sequence ◽

Global Ocean ◽

Reference Database ◽

Data Repositories ◽

Marine Zooplankton ◽

The North ◽

Coi Sequences ◽

Taxonomic Groups

AbstractCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.