scholarly journals Correction to ‘Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes ’

2018 ◽  
Vol 285 (1873) ◽  
pp. 20180266
Author(s):  
Y. Zhao ◽  
Z. Yi ◽  
A. Warren ◽  
W. Song
Keyword(s):  
Species Delimitation ◽  
Molecular Taxonomy ◽  
Microbial Eukaryote

scholarly journals Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora)

2018 ◽  
Vol 285 (1871) ◽  
pp. 20172159 ◽  
Author(s):  
Yan Zhao ◽  
Zhenzhen Yi ◽  
Alan Warren ◽  
Weibo B. Song
Keyword(s):  
Species Delimitation ◽  
High Throughput Sequencing ◽  
Large Subunit ◽  
Molecular Taxonomy ◽  
Integrative Taxonomy ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Gene Markers ◽  
Morphological Differences ◽  
Large Subunit Rdna

Recent advances in high-throughput sequencing and metabarcoding technologies are revolutionizing our understanding of the diversity and ecology of microbial eukaryotes (protists). The interpretation of protist diversity and the elucidation of their ecosystem function are, however, impeded by problems with species delimitation, especially as it applies to molecular taxonomy. Here, using the ciliate Euplotes as an example, we describe approaches for species delimitation based on integrative taxonomy by using evolutionary and ecological perspectives and selecting the most appropriate metabarcoding gene markers as proxies for species units. Our analyses show that: Euplotes ( sensu lato ) comprises six distinct clades, mainly as result of ecological speciation; the validity of the genera Euplotes ( sensu stricto ), Euplotoides , Euplotopsis and Moneuplotes are not supported; the vannus -type group, which includes species without distinct morphological differences, seems to be undergoing incipient speciation and contains cryptic species; the hypervariable V4 region of the small subunit rDNA and D1–D2 region of the large subunit rDNA are the promising candidates for general species delimitation in Euplotes .

scholarly journals Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7531
Author(s):  
Carlos A. Santamaria
Keyword(s):  
Cryptic Species ◽  
Species Delimitation ◽  
Molecular Taxonomy ◽  
Hawaiian Islands ◽  
Nuclear Gene ◽  
Morphological Differentiation ◽  
Taxonomic Revision ◽  
Hawaiian Archipelago ◽  
Genetic Lineages ◽  
Molecular Characters

Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai‘i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.

scholarly journals Range sizes of groundwater amphipods (Crustacea) are not smaller than range sizes of surface amphipods: a case study from Iran

2019 ◽  
Vol 89 (1) ◽  
pp. 1-13
Author(s):  
Somayeh Esmaeili-Rineh ◽  
Mahmoud Mamaghani-Shishvan ◽  
Cene Fišer ◽  
Vahid Akmali ◽  
Nargess Najafi
Keyword(s):  
Surface Waters ◽  
Species Delimitation ◽  
Molecular Taxonomy ◽  
Taxonomic Structure ◽  
Mitochondrial Marker ◽  
Operational Taxonomic Units ◽  
Groundwater Aquifers ◽  
Linear Extent ◽  
Surface And Groundwater

The connectivity of groundwater aquifers is lower compared to surface waters. Consequently, groundwater species are expected to have smaller distributional ranges than their surface relatives. Molecular taxonomy, however, unveiled that many species comprise complexes of morphologically cryptic species, with geographically restricted distributional ranges in subterranean as well as in surface waters. Hence, the range sizes of surface and groundwater species might be more similar in size than hitherto thought. We tested this hypothesis by comparing the range size of surface amphipods of the genus Gammarus and subterranean amphipods of the genus Niphargus in Iran. We re-analyzed the taxonomic structure of both genera using two unilocus species delimitation methods applied to a fragment of the COI mitochondrial marker, to identify molecular operational taxonomic units (MOTUs), and assessed the maximum linear extent (MLE) of the ranges of MOTUs from both genera. Genus Gammarus comprised 44–58 MOTUs while genus Niphargus comprised 20–22 MOTUs. The MLEs of the two genera were not significantly different, regardless the delimitation method applied. The results remained unchanged also after exclusion of single site MOTUs. We tentatively conclude that in this case there is no evidence to consider that groundwater species are geographically more restricted than surface species.

scholarly journals Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252546
Author(s):  
Warut Siriwut ◽  
Ekgachai Jeratthitikul ◽  
Somsak Panha ◽  
Ratmanee Chanabun ◽  
Peng Bun Ngor ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
Species Delimitation ◽  
Gap Analysis ◽  
Molecular Taxonomy ◽  
Dna Barcode ◽  
Freshwater Ecosystems ◽  
Nominal Species ◽  
Morphological Examination ◽  
High Genetic Diversity ◽  
Riverine Systems

The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.

Molecular taxonomy and species delimitation in Andean Schistocerca (Orthoptera: Acrididae)

2009 ◽  
Vol 53 (2) ◽  
pp. 404-411 ◽  
Author(s):  
Amir Yassin ◽  
Christiane Amédégnato ◽  
Corinne Cruaud ◽  
Michel Veuille
Keyword(s):  
Species Delimitation ◽  
Molecular Taxonomy

Notes on the molecular taxonomy of the Proclossiana eunomia complex (Lepidoptera, Nymphalidae: Argynnini): analysis of DNA barcodes

2018 ◽  
Vol 8 (1) ◽  
pp. 222-232 ◽  
Author(s):  
R. V. Yakovlev ◽  
N. A. Shapoval ◽  
G. N. Kuftina ◽  
A. V. Kulak ◽  
S. V. Kovalev
Keyword(s):  
Body Size ◽  
Molecular Taxonomy ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Coi Gene ◽  
Wing Pattern ◽  
Molecular Approach ◽  
Dna Barcodes ◽  
Morphological Differences ◽  
Proclossiana Eunomia

The Proclossiana eunomia (Esper, 1799) complex is currently composed of the several subspecies distributed throughout Palaearсtic region and North America. Despite the fact that some of the taxa have differences in wing pattern and body size, previous assumptions on taxonomy not supported by molecular data. Therefore, the identity of certain populations of this complex has remained unclear and the taxonomic status of several recently described taxa is debated. Here, we provide insights into systematics of some Palaearctic members of this group using molecular approach, based on the analysis of the barcoding fragment of the COI gene taking into account known morphological differences.

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