Decrypting species in the Nacobbus aberrans (Nematoda: Pratylenchidae) complex using integrative taxonomy

Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.

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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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Looking at the Nudibranch Family Myrrhinidae (Gastropoda, Heterobranchia) from a Mitochondrial ‘2D Folding Structure’ Point of View

Life ◽

10.3390/life11060583 ◽

2021 ◽

Vol 11 (6) ◽

pp. 583

Author(s):

Giulia Furfaro ◽

Paolo Mariottini

Keyword(s):

16S Rrna ◽

Phylogenetic Analyses ◽

Integrative Taxonomy ◽

Point Of View ◽

Past Study ◽

Mitochondrial Coi ◽

The Past ◽

Combining Data ◽

Folding Structure ◽

Comparison Of The Results

Integrative taxonomy is an evolving field of multidisciplinary studies often utilised to elucidate phylogenetic reconstructions that were poorly understood in the past. The systematics of many taxa have been resolved by combining data from different research approaches, i.e., molecular, ecological, behavioural, morphological and chemical. Regarding molecular analysis, there is currently a search for new genetic markers that could be diagnostic at different taxonomic levels and that can be added to the canonical ones. In marine Heterobranchia, the most widely used mitochondrial markers, COI and 16S, are usually analysed by comparing the primary sequence. The 16S rRNA molecule can be folded into a 2D secondary structure that has been poorly exploited in the past study of heterobranchs, despite 2D molecular analyses being sources of possible diagnostic characters. Comparison of the results from the phylogenetic analyses of a concatenated (the nuclear H3 and the mitochondrial COI and 16S markers) dataset (including 30 species belonging to eight accepted genera) and from the 2D folding structure analyses of the 16S rRNA from the type species of the genera investigated demonstrated the diagnostic power of this RNA molecule to reveal the systematics of four genera belonging to the family Myrrhinidae (Gastropoda, Heterobranchia). The “molecular morphological” approach to the 16S rRNA revealed to be a powerful tool to delimit at both species and genus taxonomic levels and to be a useful way of recovering information that is usually lost in phylogenetic analyses. While the validity of the genera Godiva, Hermissenda and Phyllodesmium are confirmed, a new genus is necessary and introduced for Dondice banyulensis, Nemesis gen. nov. and the monospecific genus Nanuca is here synonymised with Dondice, with Nanuca sebastiani transferred into Dondice as Dondice sebastiani comb. nov.

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Integrative taxonomy uncovers a new Culicoides (Diptera: Ceratopogonidae) biting midge species from Thailand

Acta Tropica ◽

10.1016/j.actatropica.2021.105941 ◽

2021 ◽

pp. 105941

Author(s):

Pairot Pramual ◽

Panya Jomkumsing ◽

Kanyakorn Piraonapicha ◽

Waraporn Jumpato

Keyword(s):

Integrative Taxonomy ◽

Biting Midge

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Integrative taxonomy of herbaceous plants with narrow fragmented distributions: a case study on Primula merrilliana species complex

Journal of Systematics and Evolution ◽

10.1111/jse.12726 ◽

2021 ◽

Author(s):

Xiao He ◽

Jing‐Jing Cao ◽

Wei Zhang ◽

Yong‐Quan Li ◽

Chao Zhang ◽

...

Keyword(s):

Species Complex ◽

Integrative Taxonomy ◽

Herbaceous Plants

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Integrative Taxonomy Reveals That the Marine Brachyuran Crab Pyromaia tuberculata (Lockington, 1877) Reached Eastern Atlantic

Diversity ◽

10.3390/d13060225 ◽

2021 ◽

Vol 13 (6) ◽

pp. 225

Author(s):

Jorge Lobo-Arteaga ◽

Miriam Tuaty-Guerra ◽

Maria José Gaudêncio

Keyword(s):

Pacific Ocean ◽

Sampling Period ◽

Integrative Taxonomy ◽

Tagus Estuary ◽

Native Range ◽

Accurate Identification ◽

Southwest Atlantic ◽

Brachyuran Crab ◽

The North ◽

Mainland Portugal

Pyromaia tuberculata is native to the north-eastern Pacific Ocean and currently established in distant regions in the Pacific Ocean and southwest Atlantic. Outside its native range, this species has become established in organically polluted enclosed waters, such as bays. The Tagus estuary, with a broad shallow bay, is one of the largest estuaries in the west coast of Europe, located in western mainland Portugal, bordering the city of Lisbon. In this study, sediment samples were collected in the estuary between 2016 and 2017. Several adult specimens of P. tuberculata, including one ovigerous female, were morphologically and genetically identified, resulting in accurate identification of the species. The constant presence of adults over a 16-month sampling period suggests that the species has become established in the Tagus estuary. Moreover, their short life cycle, which allows for the production of at least two generations per year, with females reaching maturity within six months after settlement, favours population establishment. Despite being referred to as invasive, there are no records of adverse effects of P. tuberculata to the environment and socio-economy in regions outside its native range. However, due to its expanding ability, its inclusion in European monitoring programmes would indeed be desirable.

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From wood to vent: first cocculinid limpet associated with hydrothermal activity discovered in the Weddell Sea

Antarctic Science ◽

10.1017/s095410202000022x ◽

2020 ◽

Vol 32 (5) ◽

pp. 354-366

Author(s):

Chong Chen ◽

Katrin Linse

Keyword(s):

Hydrothermal Vents ◽

Deep Ocean ◽

First Record ◽

Hydrothermal Activity ◽

Integrative Taxonomy ◽

Weddell Sea ◽

Anatomical Reconstruction ◽

Cold Seeps ◽

Evolutionary Trajectory ◽

Genetic Sequencing

AbstractLush ‘oases’ of life seen in chemosynthetic ecosystems such as hot vents and cold seeps represent rare, localized exceptions to the generally oligotrophic deep ocean floor. Organic falls, best known from sunken wood and whale carcasses, are additional sources of such oases. Kemp Caldera (59°42'S, 28°20'W) in the Weddell Sea exhibits active hydrothermal vents and a natural whale fall in close proximity, where an undescribed cocculinid limpet was found living in both types of chemosynthetic habitats. This represents the first member of the gastropod order Cocculinida discovered from hot vents, and also the first record from the Southern Ocean. Here, we applied an integrative taxonomy framework incorporating traditional dissection, electron microscopy, genetic sequencing and 3D anatomical reconstruction through synchrotron computed tomography in order to characterize this species. Together, our data revealed an unusual member of the genus Cocculina with a highly modified radula for feeding on bacterial film, described herein as Cocculina enigmadonta n. sp. Its phylogenetically derived position within the largely wood-inhabiting Cocculina indicates that it probably evolved from an ancestor adapted to living on sunken wood, providing a compelling case of the ‘stepping stone’ evolutionary trajectory from organic falls to seeps and vents.

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Integrative taxonomy of giant crested Eusirus in the Southern Ocean, including the description of a new species (Crustacea: Amphipoda: Eusiridae)

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa141 ◽

2020 ◽

Author(s):

Marie L Verheye ◽

Cédric D’Udekem D’Acoz

Keyword(s):

New Species ◽

Species Diversity ◽

Morphological Analysis ◽

Integrative Taxonomy ◽

Putative Species ◽

Species Complexes ◽

Statistical Parsimony ◽

Bayesian Implementation ◽

A New Species ◽

Giant Species

Abstract Among Antarctic amphipods of the genus Eusirus, a highly distinctive clade of giant species is characterized by a dorsal, blade-shaped tooth on pereionites 5–7 and pleonites 1–3. This lineage, herein named ‘crested Eusirus’, includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, in addition to the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks (COI, CytB and ITS2) of crested Eusirus are herein reconstructed. This study aims to formally revise species diversity within crested Eusirus by applying several species delimitation methods (Bayesian implementation of the Poisson tree processes model, general mixed Yule coalescent, multi-rate Poisson tree processes and automatic barcode gap discovery) on the resulting phylogenies. In addition, results from the DNA-based methods are benchmarked against a detailed morphological analysis of all available specimens of the E. perdentatus complex. Our results indicate that species diversity of crested Eusirus is underestimated. Overall, DNA-based methods suggest that the E. perdentatus complex is composed of three putative species and that the E. giganteus complex includes four or five putative species. The morphological analysis of available specimens from the E. perdentatus complex corroborates molecular results by identifying two differentiable species, the genuine E. perdentatus and a new species, herein described as Eusirus pontomedon sp. nov.

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