scholarly journals Variation and Diagnostic Power of the Internal Transcribed Spacer 2 in Mediterranean and Atlantic Eolid Nudibranchs (Mollusca, Gastropoda)

2021 ◽  
Vol 8 ◽  
Author(s):  
Matteo Garzia ◽  
Paolo Mariottini ◽  
Daniele Salvi ◽  
Giulia Furfaro
Keyword(s):  
Species Delimitation ◽  
Internal Transcribed Spacer ◽  
Morphological Characters ◽  
Marine Biodiversity ◽  
Cryptic Diversity ◽  
Nuclear Marker ◽  
Nuclear Markers ◽  
Closely Related Species ◽  
Internal Transcribed Spacer 2 ◽  
Mitochondrial Markers

Mediterranean marine biodiversity is still underestimated especially for groups such as nudibranchs. The identification of nudibranchs taxa is challenging because few morphological characters are available and among them chromatic patterns often do not align with species delimitation. Molecular assessments helped unveiling cryptic diversity within nudibranchs and have been mostly based on mitochondrial markers. Fast evolving nuclear markers are much needed to complement phylogenetic and systematic assessments at the species and genus levels. Here, we assess the utility of the nuclear Internal Transcribed Spacer 2 (ITS2) to delimit species in the eolid nudibranchs using both primary and secondary structures. Comparisons between the variation observed at the ITS2 and at the two commonly used mitochondrial markers (COI and 16S) on 14 eolid taxa from 10 genera demonstrate the ability of ITS2 to detect congeneric, closely related, species. While ITS2 has been fruitfully used in several other mollusc taxa, this study represents the first application of this nuclear marker in nudibranchs.

Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea

Zootaxa ◽  
2017 ◽  
Vol 4320 (3) ◽  
pp. 505 ◽  
Author(s):  
ROMANA KALOUSOVA ◽  
LADISLAV BOCAK
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Related Species ◽  
Species Delimitation ◽  
Morphological Differentiation ◽  
Morphological Characters ◽  
Molecular Data ◽  
Closely Related Species ◽  
Dna Fragment ◽  
Colour Patterns

Cladophorus Guérin-Méneville, 1830 are endemic Papuan net-winged beetles which take part in highly diverse Müllerian mimicry rings. Available specimens were sequenced for cox1–tRNA-Leu–cox2 mitochondrial DNA fragment and the species delimitations were based on the genetic distance, phylogenetic analysis, and morphology. Three earlier described species were identified in the recently collected material and further 10 species are described: C. pallescens sp. nov., C. bicolor sp. nov., C. craterensis sp. nov., C. motykai sp. nov., C. mindikensis sp. nov., C. kailakiensis sp. nov., C. manokwarensis sp. nov., C. haiaensis sp. nov., C. humeralis sp. nov., and C. boceki sp. nov. DNA-based identifications provided some ambiguous results and closely related species could not be robustly delimited using solely molecular data. Additionally, the species limits were based on clearly defined morphological characters and the morphological differentiation was found unlinked from the genetic divergence. Colour patterns cannot be used for identification because all species available in more specimens were polymorphic and followed various local co-mimics. The Papuan fauna of Cladophorus is very diverse and the closely related species regularly occur in limited regions. Differentiation within restricted ranges is therefore considered as the main speciation mode. 

scholarly journals Challenging species delimitation in Collembola: cryptic diversity among common springtails unveiled by DNA barcoding

2012 ◽  
Vol 26 (6) ◽  
pp. 470 ◽  
Author(s):  
D. Porco ◽  
A. Bedos ◽  
Penelope Greenslade ◽  
C. Janion ◽  
D. Skarżyński ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Functional Groups ◽  
Species Delimitation ◽  
Sequence Divergence ◽  
Cryptic Diversity ◽  
Congeneric Species ◽  
Nuclear Marker ◽  
Accurate Identification ◽  
Intraspecific Divergence

Collembola is one of the major functional groups in soil as well as a model taxon in numerous disciplines. Therefore the accurate identification of specimens is critical, but could be jeopardised by cases of cryptic diversity. Several populations of six well characterised species of springtails were sequenced using the COI barcode fragment as a contribution to the global Collembola barcoding campaign. Each species showed high intraspecific divergence, comparable to interspecific sequence divergence values observed in previous studies and in 10 congeneric species barcoded here as a reference. The nuclear marker, 28S, confirmed all the intraspecific lineages found with COI, supporting the potential specific status of these entities. The implications of this finding for taxonomy and for disciplines relying on species names, such as evolution and ecology, are discussed.

scholarly journals Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Svante Martinsson ◽  
Mårten Klinth ◽  
Christer Erséus
Keyword(s):  
Species Delimitation ◽  
Single Species ◽  
The Other ◽  
Cryptic Speciation ◽  
Incipient Speciation ◽  
Nuclear Markers ◽  
Separate Species ◽  
Mitochondrial Markers ◽  
Morphological Differences ◽  
Barcode Gap

Abstract 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.

Lactarius cucurbitoides (Russulales, Basidiomycota), a new species from South Korea supported by molecular and morphological data

Phytotaxa ◽  
2015 ◽  
Vol 205 (3) ◽  
pp. 168 ◽  
Author(s):  
Hyun Lee ◽  
Myung Soo Park ◽  
Paul Eunil Jung ◽  
Jonathan J. Fong ◽  
Seung-Yoon Oh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Closely Related Species ◽  
The Status ◽  
A New Species

A new species belonging to Lactarius subg. Plinthogalus was discovered during a long-term project on the diversity of Korean Lactarius. This species is proposed here as Lactarius cucurbitoides. The status of L. cucurbitoides as a new species is supported by molecular data and morphological features. Phylogenetic analysis based on internal transcribed spacer (ITS) sequences shows that L. cucurbitoides is closely related to L. subplinthogalus, L. friabilis, and L. oomsisiensis, with pairwise distances of 2.8–4.3%. Morphological characters of L. cucurbitoides that distinguish it from these closely related species are a pale yellow to pale orange colored pileus and non-discoloration of white latex. The new species is described and illustrated in the present paper.

scholarly journals Species delimitation and inter-specific gene flow in Tamarix L. (Tamaricaceae)

Hacquetia ◽  
2019 ◽  
Vol 18 (2) ◽  
pp. 313-322
Author(s):  
Masoud Sheidai ◽  
Tahmineh Shagholi ◽  
Maryam Keshavarzi ◽  
Fahimeh Koohdar ◽  
Habibollah Ijbari
Keyword(s):  
Gene Flow ◽  
Molecular Phylogeny ◽  
Species Delimitation ◽  
Morphological Characters ◽  
Morphological Data ◽  
Specific Gene ◽  
Closely Related Species ◽  
Specific Hybridization ◽  
Wide Range ◽  
Semnan Province

Abstract Tamarix L. play important role in preventing deforestation in Iran. Tamarix species exhibit wide range of morphological variation therefore, the species delimitation become difficult. This is further complicated due to similarity of morphological characters in closely related species and the occurrence of inter-specific hybridization. The present study was performed to identify Tamarix species and their potential hybrids in Semnan Province of Iran. We used ITS and ISSR and 42 morphological characters for our investigation. Molecular phylogeny of the studied species and their relationship was not in agreement with the species tree of morphological characters and with taxonomic treatment of the genus. HGT tree of ITS and morphological data obtained revealed the occurrence of inter-specific hybridization or introgression between Tamarix species.

scholarly journals Ten genes and two topologies: an exploration of higher relationships in skipper butterflies (Hesperiidae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2653 ◽  
Author(s):  
Ranjit Kumar Sahoo ◽  
Andrew D. Warren ◽  
Niklas Wahlberg ◽  
Andrew V. Z. Brower ◽  
Vladimir A. Lukhtanov ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Gene Markers ◽  
Mitochondrial Markers ◽  
Molecular Dataset

Despite multiple attempts to infer the higher-level phylogenetic relationships of skipper butterflies (Family Hesperiidae), uncertainties in the deep clade relationships persist. The most recent phylogenetic analysis included fewer than 30% of known genera and data from three gene markers. Here we reconstruct the higher-level relationships with a rich sampling of ten nuclear and mitochondrial markers (7,726 bp) from 270 genera and find two distinct but equally plausible topologies among subfamilies at the base of the tree. In one set of analyses, the nuclear markers suggest two contrasting topologies, one of which is supported by the mitochondrial dataset. However, another set of analyses suggests mito-nuclear conflict as the reason for topological incongruence. Neither topology is strongly supported, and we conclude that there is insufficient phylogenetic evidence in the molecular dataset to resolve these relationships. Nevertheless, taking morphological characters into consideration, we suggest that one of the topologies is more likely.

scholarly journals Overview of the Genetic Diversity of African Macrotermes (Termitidae: Macrotermitinae) and Implications for Taxonomy, Ecology and Food Science

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 518
Author(s):  
Bronwyn Egan ◽  
Zwannda Nethavhani ◽  
Barbara van Asch
Keyword(s):  
Negative Impact ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Food Science ◽  
Cryptic Diversity ◽  
African Species ◽  
Genetic Groups ◽  
Wide Range ◽  
Coi Sequences ◽  
High Level

Macrotermes termites play important ecological roles and are consumed by many communities as a delicacy and dietary complement throughout Africa. However, lack of reliable morphological characters has hampered studies of Macrotermes diversity in a wide range of scientific fields including ecology, phylogenetics and food science. In order to place our preliminary assessment of the diversity of Macrotermes in South Africa in context, we analysed a comprehensive dataset of COI sequences for African species including new and publicly available data. Phylogenetic reconstruction and estimates of genetic divergence showed a high level of incongruity between species names and genetic groups, as well as several instances of cryptic diversity. We identified three main clades and 17 genetic groups in the dataset. We propose that this structure be used as a background for future surveys of Macrotermes diversity in Africa, thus mitigating the negative impact of the present taxonomic uncertainties in the genus. The new specimens collected in Limpopo fell into four distinct genetic groups, suggesting that the region harbours remarkable Macrotermes diversity relative to other African regions surveyed in previous studies. This work shows that African Macrotermes have been understudied across the continent, and that the genus contains cryptic diversity undetectable by classic taxonomy. Furthermore, these results may inform future taxonomic revisions in Macrotermes, thus contributing to advances in termitology.

scholarly journals Combination of nuclear and mitochondrial markers as a useful tool to identify Ctenophthalmus species and subspecies (Siphonaptera: Ctenophthalmidae)

2021 ◽  
Author(s):  
Antonio Zurita ◽  
Cristina Cutillas
Keyword(s):  
Taxonomic Status ◽  
Molecular Study ◽  
Molecular Data ◽  
Point Of View ◽  
Morphological Data ◽  
Molecular Approach ◽  
Nuclear Marker ◽  
Mitochondrial Markers ◽  
Morphological Criteria ◽  
Mtdna Markers

AbstractCtenophthalmus is considered the largest genus within the Order Siphonaptera. From a morphological point of view, only males of this genus can be identified at species and subspecies levels using morphological keys, whereas there are no morphological criteria in order to classify females at these taxonomical levels. Furthermore, the amount of available molecular and phylogenetic data for this genus is quite scarce so far. The main objective of this work was to assess the utility of the combination of nuclear and mitochondrial markers with respect to their ability to differentiate among different subspecies within the Ctenophthalmus genus. With this purpose, we carried out a comparative morphological and molecular study of three different subspecies (Ctenophthalmus baeticus arvernus, Ctenophthalmus nobilis dobyi, and Ctenophthalmus andorrensis catalaniensis) in order to clarify and discuss its taxonomic status. In addition, our study complemented the molecular data previously provided for Ctenophthalmus baeticus boisseauorum and Ctenophthalmus apertus allani subspecies. We sequenced five different molecular markers: EF1-α, ITS1, ITS2, cox1, and cytb. Our results confirmed that morphological data by themselves are not able to discriminate among Ctenophthalmus female taxa; however, the combination of the nuclear marker EF1-α together with mtDNA markers cytb and cox1 constituted a useful taxonomical and phylogenetic tool to solve this issue. Based on these results, we consider that the use of this molecular approach should be gradually used within Ctenophthalmus genus in order to complement its classical taxonomy and clarifying the complex taxonomy of other congeneric species of fleas.

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