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1.
Sci Total Environ ; 751: 141729, 2021 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-32889465

RESUMO

In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.


Assuntos
Código de Barras de DNA Taxonômico , Ecossistema , Biodiversidade , DNA , DNA Ambiental
2.
Sci Total Environ ; 750: 141969, 2021 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-33182191

RESUMO

Worldwide, multiple stressors affect stream ecosystems and frequently lead to complex and non-linear biological responses. These combined stressor effects on ecologically diverse and functionally important macroinvertebrate communities are often difficult to assess, in particular species-specific responses across many species and effects of different stressors and stressor levels in concert. A central limitation in many studies is the taxonomic resolution applied for specimen identification. DNA metabarcoding can resolve taxonomy and provide greater insights into multiple stressor effects. This was detailed by results of a recent multiple stressor mesocosm experiment, where only for the dipteran family Chironomidae 183 Operational Taxonomic Units (OTUs) could be distinguished. Numerous OTUs showed very different response patterns to multiple stressors. In this study, we applied DNA metabarcoding to assess multiple stressor effects on all non-chironomid invertebrates from the same experiment. In the experiment, we applied three stressors (increased salinity, deposited fine sediment, reduced flow velocity) in a full-factorial design. We compared stressor responses inferred through DNA metabarcoding of the mitochondrial COI gene to responses based on morphotaxonomic taxa lists. We identified 435 OTUs, of which 122 OTUs were assigned to EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa. The most common 35 OTUs alone showed 15 different response patterns to the experimental manipulation, ranging from insensitivity to any applied stressor to sensitivity to single and multiple stressors. These response patterns even comprised differences within one family. The species-specific taxonomic resolution and the inferred response patterns to stressors highlights the potential of DNA metabarcoding in the context of multiple stressor research, even for well-known taxa such as EPT species.


Assuntos
Rios , Salinidade , Animais , Código de Barras de DNA Taxonômico , Ecossistema , Monitoramento Ambiental , Invertebrados/genética
3.
BMC Bioinformatics ; 21(1): 492, 2020 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-33129268

RESUMO

BACKGROUND: The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool. RESULTS: BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups. CONCLUSIONS: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.


Assuntos
Archaea/genética , Bactérias/genética , Biodiversidade , Biologia Computacional/métodos , Código de Barras de DNA Taxonômico , Fungos/genética , Genes de RNAr , Software , Análise por Conglomerados , Simulação por Computador , Bases de Dados Genéticas , Microbiota/genética , RNA Ribossômico 16S/genética , RNA Ribossômico 23S/genética , Microbiologia do Solo
4.
Zootaxa ; 4790(1): zootaxa.4790.1.5, 2020 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-33055856

RESUMO

Chironomids of the tribe Boreoheptagyiini from the mountains of Iran, China and East Kazakhstan are revised using both morphological characters and partial DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene. Using adult males, Palatovia lorestanica gen. nov. sp. nov., as well as Boreoheptagyia iranica sp. nov. both from Iran (Lorestan Province, Zagros Mountains), B. joeli sp. nov. from China (Tien Shan Mountains), and B. sarymsactyensis sp. nov. from Eastern Kazakhstan (Kazakh Mountain Altai), are described and figured. A brief redescription of the rare species B. brevitarsis (Tokunaga) from Iran (Mazandaran Province), previously known only from Japan, is also given. The DNA barcoding analysis shows well-supported genetic divergence between all studied taxa (four species of the genus Boreoheptagyia and one of Palatovia). Combining DNA barcodes obtained in this study with available sequences in GenBank, the phylogenetic relationships of the tribe Boreoheptagyiini are reconstructed. In the resulting Bayesian and maximum likelihood (ML) tree the polyphyly of the genus Boreoheptagyia is recognized. B. iranica is placed as a sister species to P. lorestanica, despite the lack of confirmation of their morphological similarity.


Assuntos
Chironomidae , Animais , Teorema de Bayes , DNA , Código de Barras de DNA Taxonômico , Masculino , Oriente Médio , Filogenia
5.
Zootaxa ; 4808(2): zootaxa.4808.2.9, 2020 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-33055982

RESUMO

A new species of the orphnine scarab beetle genus Madecorphnus Paulian, 1992, Madecorphnus grebennikovi Frolov, Akhmetova Vishnevskaya, new species, is described from the Marojejy National Park, Sava Region, northeastern Madagascar. The new species can be distinguished from the congeners by the parameres narrowly rounded in lateral view and having a small but distinct lateral teeth, and by the endophallic armature consisting of 1) a long straight sclerite with attached to its end a 2/3 shorted, somewhat curved sclerite, 2) separate smaller, elongate sclerite, and 3) a rather large area of microspinules. The 811 bp long fragment of the mitochondrial gene COI (DNA barcode) is provided as a part of the diagnosis of the new species. An updated key to the Madecorphnus species is given.


Assuntos
Besouros , Animais , Código de Barras de DNA Taxonômico
6.
Zootaxa ; 4802(3): zootaxa.4802.3.13, 2020 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-33056053

RESUMO

Chironomids of the Diamesinae subfamily from the Russian Arctic were studied using both morphological characters and molecular data. Adult males of Diamesa urvantsevi sp. nov., D. amplexivirilia Hansen, Arctodiamesa appendiculata (Lundström) from Severnaya Zemlya Archipelago and D. arctica (Boheman), Pseudokiefferiella sp. from Vaigach Island were described, redescribed, annotated and figured. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. For D. arctica (Boheman) and Pseudokiefferiella sp. close DNA barcodes from Norway were performed, which allowed to relate these specimens to the described species. Comparisons with corresponding regions of COI between each described species and close related congeneric species produced K2P genetic distances of 0.11-0.16, values well associated with interspecific variation. Phylogenetic relationships for genera Arctodiamesa Makarchenko and Pseudokiefferiella Zavrel were reconstructed for the first time.


Assuntos
Chironomidae , Animais , Código de Barras de DNA Taxonômico , Ilhas , Masculino , Filogenia , Federação Russa
7.
Zootaxa ; 4821(1): zootaxa.4821.1.11, 2020 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-33056339

RESUMO

We diagnose a new butterfly species from the Belmira paramo in the central cordillera of the Colombian Andes. We infer from the barcoding analysis, wing pattern, morphology and distribution that this entity is not a geographical variation or subspecies of any named lycaenid, and it is described herein as Rhamma eleonorae sp. nov. Adult specimens and female genitalia are illustrated and compared with R. arria (Hewitson, 1870) and R. oxida (Hewitson, 1870), the most closely related taxa based on similarities of wing pattern and COI sequences.


Assuntos
Borboletas , Animais , Código de Barras de DNA Taxonômico , Feminino , Asas de Animais
8.
Zootaxa ; 4853(3): zootaxa.4853.3.3, 2020 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-33056366

RESUMO

The Nearctic species of Gimnomera Rondani are revised and includes eight species, of which three are new to science (G. aquilonia sp. nov., G. cerea (Coquillett), G. cuneiventris (Zetterstedt), G. incisurata Malloch, G. subvittata (Malloch), G. terrywheeleri sp. nov., G. tibialis (Malloch), G. vockerothi sp. nov.). Gimnomera cuneiventris is newly recognized as Holarctic in distribution. Gimnomera fasciventris Malloch is removed and transferred to the genus Acerocnema, comb. nov. An additional Nearctic species is recognized but not described due to lack of male specimens. Species descriptions, diagnoses and distribution maps are presented, including images of the male terminalia as well as additional diagnostic characters. A key to the Nearctic species is also provided. A morphological cladistic analysis of 12 species reveals that the Nearctic and Palearctic species do not form separate monophyletic groups. COI mitochondrial DNA barcode sequences were obtained for eight Nearctic species of Gimnomera.


Assuntos
Dípteros , Animais , Código de Barras de DNA Taxonômico , DNA Mitocondrial , Masculino , Filogenia
9.
Zootaxa ; 4845(4): zootaxa.4845.4.1, 2020 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-33056752

RESUMO

This study represents a detailed taxonomic account of 31 species of Plusiinae (Lepidoptera: Noctuidae) from India. The survey and collection of 39 localities from different regions of India between 2015 and 2018. The tribe Argyrogrammatini Eichlin Cunningham, 1978 with Ctenoplusia Dufey, 1970 was the most species rich genera with seven species, followed by Thysanoplusia Ichinose, 1973 and Chrysodeixis Hubner, 1821 with four and three species respectively. Among 31 species, 15 species are commonly found in Himalayan regions and while other species were distributed from subtropical to tropical region. Five species, T. orichalcea (Fabricius, 1775), Chrysodeixis eriosoma (Doubleday, 1843), C. acuta (Walker, 1858), C. chalcites (Esper, 1789), Trichoplusia ni (Hubner, 1803) are widespread throughout India and reported as serious crop pests. Present study also revealed range expansion of four species viz., Dactyloplusia impulsa (Walker, 1865), Ctenoplusia mutans (Walker, 1865), Ctenoplusia tarassota (Hampson, 1913) and Zonoplusia ochreata (Walker, 1865). Systematic accounts of all 31 species are discussed here with adult images, species diagnostic characters, collection localities, detailed distributions and reported larval host plants. In addition to morphological studies, for the first time, a preliminary barcode library for 25 species of Indian Plusiinae with average intra-specific distance (%), maximum intra-specific distance (%) and distance to nearest neighbor (%) for individual species is provided. Among 25 species, four species barcode data (Ctenoplusia mutans, C. kosemponesis, Plusiopalpa adrasta, Sclerogenia jessica) are novel to world and 18 species barcode sequences were novel to India.


Assuntos
Código de Barras de DNA Taxonômico , Mariposas , Animais , DNA , Índia , Larva
10.
Zootaxa ; 4822(3): zootaxa.4822.3.5, 2020 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-33056279

RESUMO

Based on a study of the type material, Genaxiphia hirashimai Okutani, 1965, a southern Japanese xiphydriid showing remarkable sexual dimorphism, is newly combined with the genus Hyperxiphia Maa, 1949. The previously unknown female is described, and the male is redescribed with additional material. The sexes are associated by examination of specimens of both sexes that apparently emerged from the same piece of branch and by a molecular analysis using mitochondrial COI sequences. Hyperxiphia hirashimai, originally described from Amami-oshima Island, is newly recorded from Miyake-jima Island, southwestern Shikoku, southern Kyushu, Yakushima, Kuroshima and Okinawa-jima Islands.


Assuntos
Himenópteros , Animais , Código de Barras de DNA Taxonômico , Feminino , Japão , Masculino , Filogenia , Caracteres Sexuais
11.
Zootaxa ; 4768(2): zootaxa.4768.2.9, 2020 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-33056529

RESUMO

Morphology and DNA barcodes confirm a new chironomid species within the Rheocricotopus (Psilocricotopus) orientalis group (Diptera: Chironomidae). Rheocricotopus (Psilocricotopus) kongi Lin et Wang sp. n. is described and illustrated based on adult male from Hainan, China. Key to adult males of the R. orientalis group is given.


Assuntos
Chironomidae , Animais , Código de Barras de DNA Taxonômico , Masculino
12.
J Plant Res ; 133(6): 841-853, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33099700

RESUMO

Mixotrophic plants obtain carbon by their own photosynthetic activity and from their root-associated mycorrhizal fungi. Mixotrophy is deemed a pre-adaptation for evolution of mycoheterotrophic nutrition, where plants fully depend on fungi and lose their photosynthetic activity. The aim of this study was to clarify mycorrhizal dependency and heterotrophy level in various phenotypes of mixotrophic Pyrola japonica (Ericaceae), encompassing green individuals, rare achlorophyllous variants (albinos) and a form with minute leaves, P. japonica f. subaphylla. These three phenotypes were collected in two Japanese forests. Phylogenetic analysis of both plants and mycorrhizal fungi was conducted based on DNA barcoding. Enrichment in 13C among organs (leaves, stems and roots) of the phenotypes with reference plants and fungal fruitbodies were compared by measuring stable carbon isotopic ratio. All plants were placed in the same clade, with f. subaphylla as a separate subclade. Leaf 13C abundances of albinos were congruent with a fully mycoheterotrophic nutrition, suggesting that green P. japonica leaves are 36.8% heterotrophic, while rhizomes are 74.0% heterotrophic. There were no significant differences in δ13C values among organs in both albino P. japonica and P. japonica f. subaphylla, suggesting full and high mycoheterotrophic nutrition, respectively. Among 55 molecular operational taxonomic units (OTUs) detected as symbionts, the genus Russula was the most abundant in each phenotype and its dominance was significantly higher in albino P. japonica and P. japonica f. subaphylla. Russula spp. detected in P. japonica f. subaphylla showed higher dissimilarity with other phenotypes. These results suggest that P. japonica sensu lato is prone to evolve mycoheterotrophic variants, in a process that changes its mycorrhizal preferences, especially towards the genus Russula for which this species has a marked preference.


Assuntos
Micorrizas , Pyrola/microbiologia , Código de Barras de DNA Taxonômico , Processos Heterotróficos , Japão , Filogenia , Folhas de Planta , Rizoma , Simbiose
13.
PLoS One ; 15(10): e0231127, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33022692

RESUMO

Biodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA Ambiental/análise , Peixes/classificação , Animais , Biodiversidade , Monitoramento Ambiental/métodos , Estuários , Peixes/genética , Atividades Humanas , Japão , Filogenia , Rios
14.
Nat Commun ; 11(1): 5432, 2020 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-33116134

RESUMO

Adeno-associated virus (AAV) forms the basis for several commercial gene therapy products and for countless gene transfer vectors derived from natural or synthetic viral isolates that are under intense preclinical evaluation. Here, we report a versatile pipeline that enables the direct side-by-side comparison of pre-selected AAV capsids in high-throughput and in the same animal, by combining DNA/RNA barcoding with multiplexed next-generation sequencing. For validation, we create three independent libraries comprising 183 different AAV variants including widely used benchmarks and screened them in all major tissues in adult mice. Thereby, we discover a peptide-displaying AAV9 mutant called AAVMYO that exhibits superior efficiency and specificity in the musculature including skeletal muscle, heart and diaphragm following peripheral delivery, and that holds great potential for muscle gene therapy. Our comprehensive methodology is compatible with any capsids, targets and species, and will thus facilitate and accelerate the stratification of optimal AAV vectors for human gene therapy.


Assuntos
Proteínas do Capsídeo/genética , Dependovirus/genética , Vetores Genéticos , Músculos/metabolismo , Músculos/virologia , Animais , Capsídeo , Código de Barras de DNA Taxonômico , Feminino , Biblioteca Gênica , Terapia Genética/métodos , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Mutação , Especificidade de Órgãos
15.
Fa Yi Xue Za Zhi ; 36(4): 559-564, 2020 Aug.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-33047543

RESUMO

Abstract: Traditional species identification has gone through five stages -- morphology, cytology, biochemistry, immunology and molecular biology. At present, the use of DNA technology for species identification has become a research hotspot. In the use of DNA for species identification, the presentation and application of DNA barcode is of epoch-making significance. With the successful application of new technology in species identification, forensic species identification has also made corresponding development, and is expected to play an important role in forensic related fields. This paper briefly describes the general situation and principles of DNA barcode technology as well as its advantages and limitations when applied to biological classification, and discusses the future significance and feasibility of DNA barcode technology in forensic applications, in order to provide new ideas for future forensic identification.


Assuntos
Código de Barras de DNA Taxonômico , Medicina Legal , DNA/genética
16.
Mar Environ Res ; 160: 104946, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32907716

RESUMO

Zooplankton biodiversity assessment is a crucial element in monitoring marine ecosystem processes and community responses to environmental alterations. In order to evaluate the suitability of metabarcoding for zooplankton biodiversity assessment and biomonitoring as a fast and more cost-effective method, seasonal zooplankton sampling was carried out in the Venice Lagoon and the nearby coastal area (Northern Adriatic Sea). The molecular analysis showed higher taxa richness compared to the classical morphological method (224 vs. 88 taxa), discriminating better the meroplanktonic component, morphologically identified only up to order level. Both methods revealed a similar spatio-temporal distribution pattern and the sequence abundances and individual counts were significantly correlated for various taxonomic groups. These results indicate that DNA metabarcoding is an efficient tool for biodiversity assessments in ecosystems with high spatial and temporal variability, where high sampling effort is required as well as fast alert systems for non-native species (NIS).


Assuntos
Biodiversidade , Código de Barras de DNA Taxonômico , Ecossistema , Zooplâncton , Animais , DNA
17.
Parasitol Res ; 119(10): 3359-3368, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32893331

RESUMO

Acanthocephalans are multi-host endoparasites, many of which use freshwater amphipods as intermediate hosts for their larval stages (e.g., cystacanths) while adults live in the intestines of vertebrates, including waterfowl. In central Alberta, Canada, several co-occurring species of the acanthocephalan genus Polymorphus use the amphipod Gammarus lacustris Sars, 1863 as an intermediate host. We applied DNA barcoding and morphometric analysis to differentiate cystacanth larvae from G. lacustris sampled from 17 Albertan water bodies. We slide-mounted specimens and measured morphological traits relating to proboscis hooks. We sequenced the standard DNA barcoding region of the mitochondrial cytochrome c oxidase subunit I gene (COI). Morphometric analysis suggested that the acanthocephalans we collected belonged to four morphologically different groups that keyed to Polymorphus contortus (Bremser, 1821) Travassos, 1926; P. marilis Van Cleave, 1939; P. paradoxus Connel et Corner, 1957; and P. strumosoides (Lundström, 1942) Amin, 2013. Our Bayesian tree based on COI sequences generally corroborated the morphological results and supported that the specimens assigned to P. cf. contortus and P. cf. strumosoides belong to two distinct species. In contrast, the Bayesian tree showed that specimens of P. cf. marilis were nested as a cluster within the P. cf. paradoxus clade. Similarly, small pairwise genetic distance (< 2%) between specimens identified as P. cf. contortus and P. cf. strumosoides suggests that they are conspecific. Future studies should use morphology and sequence data from adult acanthocephalans to assess the taxonomic identity of the cystacanth-based Polymorphus taxa. Our study is the first to provide genetic information for the four Polymorphus taxa and emphasizes the importance of applying multiple approaches to differentiate parasite species.


Assuntos
Acantocéfalos/classificação , Acantocéfalos/anatomia & histologia , Acantocéfalos/genética , Alberta , Anfípodes/parasitologia , Animais , Código de Barras de DNA Taxonômico , Água Doce/parasitologia , Genes de Helmintos/genética , Genes Mitocondriais/genética , Larva/anatomia & histologia , Larva/classificação , Larva/genética , Especificidade da Espécie
18.
BMC Evol Biol ; 20(1): 116, 2020 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-32928097

RESUMO

BACKGROUND: Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species. RESULTS: A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species. CONCLUSION: We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.


Assuntos
DNA Mitocondrial/genética , Oligoquetos/classificação , Filogenia , Animais , Teorema de Bayes , Código de Barras de DNA Taxonômico , Especiação Genética , Genética Populacional , Países Escandinavos e Nórdicos
19.
Sci Total Environ ; 738: 140249, 2020 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-32806340

RESUMO

Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies.


Assuntos
Código de Barras de DNA Taxonômico , DNA Ambiental , Fungos/genética , Itália , Estações do Ano
20.
PLoS One ; 15(7): e0235569, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32735584

RESUMO

The palm family (Arecaceae) is of high ecological and economic value, yet identification in the family remains a challenge for both taxonomists and horticulturalists. The family consists of approximately 2600 species across 181 genera and DNA barcoding may be a useful tool for species identification within the group. However, there have been few systematic evaluations of DNA barcodes for the palm family. In the present study, five DNA barcodes (rbcL, matK, trnH-psbA, ITS, ITS2) were evaluated for species identification ability across 669 samples representing 314 species and 100 genera in the Arecaceae, employing four analytical methods. The ITS gene region was found to not be a suitable barcode for the palm family, due in part, to low recovery rates and paralogous gene copies. Among the four analyses used, species resolution for ITS2 was much higher than that achieved with the plastid barcodes alone (rbcL, matK, trnH-psbA), and the barcode combination ITS2 + matK + rbcL gave the highest resolution among all single barcodes and their combinations, followed by ITS2 + matK. Among 669 palm samples analyzed, 110 samples (16.3%) were found to be misidentified. The 2992 DNA barcode sequences generated in this study greatly enriches the existing identification toolbox available to plant taxonomists that are interested in researching genetic relationships among palm taxa as well as for horticulturalists that need to confirm palm collections for botanical garden curation and horticultural applications. Our results indicate that the use of the ITS2 DNA barcode gene region provides a useful and cost-effective tool to confirm the identity of taxa in the Palm family.


Assuntos
Arecaceae/classificação , Arecaceae/genética , Código de Barras de DNA Taxonômico , Jardins
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