From taxonomic deflation to newly detected cryptic species: Hidden diversity in a widespread African squeaker catfish

Abstract Cryptic genetic diversity and erroneous morphological species determination represent frequent problems in biodiversity research. Here, examination of 138 specimens of Synodontis (Mochokidae, Siluriformes) from the Nile River and Lake Turkana revealed the presence of both S. schall-like and S. frontosus-like morphotypes, with a phenotypic gradient between them. We concluded phylogenetic and population genetic analyses based on two mitochondrial and one nuclear marker including 131 coxI (565 bp), 96 cytb (973 bp) and 19 RAG2 (896 bp) sequences from the Nile-Turkana population, plus additional GenBank data of Synodontis spp. Whilst nuclear data were inconclusive, mitochondrial sequences suggested that both morphotypes and intermediate forms are conspecific. The results imply probable synonymy of S. frontosus with S. schall. Conversely, a strong biogeographical signal was revealed among widely distributed and supposedly conspecific S. schall-like catfish of the Nilo-Sudanian ichthyological province. Synodontis schall sensu stricto (=Eastern clade), as defined by type locality in the Nile, is apparently restricted to the eastern part of the Nilo-Sudanian ichthyological province (e.g. Nile, Turkana, Chad). Synodontis schall Western clade (Senegambia, Niger, Chad) most probably represents a cryptic taxon, unrecognized thus far due to the absence of distinctive morphological differences.

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Mitochondrial phylogeny and taxonomic revision of Italian and Slovenian fluvio-lacustrine barbels, Barbus sp. (Cypriniformes, Cyprinidae)

BMC Zoology ◽

10.1186/s40850-021-00073-x ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Giovanni Rossi ◽

Federico Plazzi ◽

Gianluca Zuffi ◽

Andrea Marchi ◽

Salvatore De Bonis ◽

...

Keyword(s):

Taxonomic Revision ◽

Nuclear Data ◽

Distinct Species ◽

Sensu Stricto ◽

Zoological Nomenclature ◽

Conservation Policies ◽

D Loop ◽

Cyprinid Fishes ◽

Northern Croatia ◽

And Control

Abstract Background Barbels are ray finned cyprinid fishes of the Old-World with partially unresolved, intricate taxonomy. Within the Barbus sensu lato paraphyletic assemblage, Barbus sensu stricto is a monophyletic tetraploid lineage of Europe, northern Africa and Middle East, including two monophyletic sibling genera: Barbus and Luciobarbus. Italy, Slovenia and northern Croatia are natively inhabited by several entities of the genus Barbus, whose relationships and taxonomic ranks are still unclear. Aim of the present work is to focus on phylogeography of Italian and Slovenian barbels, with an appraisal of their current taxonomy. Results One hundred fifty specimens were collected in 78 sampling sites from 33 main watersheds, widely distributed along Italian and Slovenian ichthyogeographic districts. We amplified two mitochondrial markers, cytochrome b (cytb) and control region (D-loop), to infer a robust phylogeny for our sample and investigate on species delimitation. Our results strongly indicate all Italian and Adriatic Slovenian fluvio-lacustrine barbels to be comprised into at least three distinct species. We provide a proposal of taxonomic revision and a list of synonymies for two of them and a new description under the International Code of Zoological Nomenclature rules for the third one. Conclusions If nuclear data will confirm our findings, at least three specific entities should be acknowledged across our sampling area. Namely, the three species are (i) Barbus plebejus, in the Padano-Venetian district; (ii) Barbus tyberinus, in the Tuscany-Latium district; (iii) Barbus oscensis Rossi & Plazzi sp. nov., in the Tyrrhenian and southernmost-Adriatic parts of Apulia-Campania district. Finally, we briefly discuss the implications of such a taxonomic scenario on conservation policies.

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The Olduvai buffaloPelorovisand the origin ofBos

Quaternary Research ◽

10.1016/j.yqres.2007.06.002 ◽

2007 ◽

Vol 68 (2) ◽

pp. 220-226 ◽

Cited By ~ 53

Author(s):

Bienvenido Martínez-Navarro ◽

Juan Antonio Pérez-Claros ◽

Maria Rita Palombo ◽

Lorenzo Rook ◽

Paul Palmqvist

Keyword(s):

Western Europe ◽

Sensu Stricto ◽

Early Pleistocene ◽

Middle Pleistocene ◽

Morphometric Study ◽

Large Size ◽

Morphological Differences ◽

Mammal Assemblages ◽

Tool Technology ◽

Different Origin

AbstractThe origin of the genusBosis a debated issue. From ∼ 0.5 Ma until historic times, the genus is well known in the Eurasian large mammal assemblages, where it is represented byBos primigenius. This species has a highly derived cranial anatomy that shows important morphological differences from other Plio-Pleistocene Eurasian genera of the tribe Bovini such asLeptobos,Bison,Proamphibos-Hemibos, andBubalus. The oldest clear evidence ofBosis the skull fragment ASB-198-1 from the middle Pleistocene (∼ 0.6–0.8 Ma) site of Asbole (Lower Awash Valley, Ethiopia). The first appearance ofBosin Europe is at the site of Venosa-Notarchirico, Italy (∼ 0.5–0.6 Ma). Although the origin ofBoshas traditionally been connected withLeptobosandBison, after a detailed anatomical and morphometric study we propose here a different origin, connecting the middle Pleistocene Eurasian forms ofB. primigeniuswith the African Late Pliocene and early Pleistocene large size member of the tribe BoviniPelorovis sensu stricto. The dispersal of theBoslineage in Western Europe during middle Pleistocene times seems to coincide with the arrival of the Acheulean tool technology in this continent.

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Morphological and molecular systematic investigation of Laurencia karachiana sp. nov. (Ceramiales, Rhodophyta) from Karachi, Pakistan

Phytotaxa ◽

10.11646/phytotaxa.404.1.3 ◽

2019 ◽

Vol 404 (1) ◽

pp. 23 ◽

Cited By ~ 1

Author(s):

RABIA BIBI ◽

VALÉRIA CASSANO ◽

ROSÂNGELA DA SILVA MEDEIROS ◽

SHAHNAZ RASHID ◽

MUNAWWER RASHEED

Keyword(s):

Sri Lanka ◽

Genetic Divergence ◽

Novel Species ◽

Systematic Investigation ◽

Sensu Stricto ◽

Molecular Systematic ◽

Interspecific Divergence ◽

Morphological Differences ◽

Open Question ◽

Rbcl Phylogeny

Laurencia karachiana sp. nov. is described from the Karachi coast of Pakistan, based on rbcL and COI-5P genes sequences. The molecular analyses for both markers positioned L. karachiana within Laurencia sensu stricto and it possesses all vegetative and reproductive structures typical of the genus. Laurencia karachiana grouped with Laurencia sp. from Sri Lanka for both markers. The genetic divergence between these taxa for rbcL was only 0.27%, whereas for COI-5P was much higher, 2.7%. The latter is within ranges of interspecific divergence for Laurencia s.s. The discrepancy of divergence between these markers and the lack of description and illustrations of Laurencia sp. from Sri Lanka for comparison leave the identity of Laurencia sp. as an open question. The rbcL phylogeny resolved L. karachiana and Laurencia sp. as sister to a subclade formed by sequences of Laurencia pumila and L. pumila var. dehoopiensis from South Africa, diverging by 1.7–1.8%. This genetic divergence and also morphological differences observed support the recognition of L. karachiana as a novel species. Our finding shows that this complex from Pakistan requires major revision, because its diversity is likely underestimated.

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Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences

10.22541/au.161516405.50876931/v2 ◽

2021 ◽

Author(s):

Lynne Christianson ◽

Shannon Johnson ◽

Darrin Schultz ◽

Steven Haddock

Keyword(s):

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Environmental Dna ◽

Mitochondrial Coi ◽

Rdna Sequences ◽

Coi Barcoding ◽

18S Rdna Sequences ◽

Mitochondrial Sequences ◽

Coi Sequences ◽

Morphological Differences

[Definitive version of this article may be found here] The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI ‘barcoding’ primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata. The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar lobates (Lampocteis sp. ‘V’ stratified by depth, and ‘A’ differentiated by color). The newly described primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyze environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.

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Ptyctimous mites (Acari, Oribatida) of the Azores

Systematic and Applied Acarology ◽

10.11158/saa.25.12.3 ◽

2020 ◽

Vol 25 (12) ◽

pp. 2172-2189

Author(s):

Wojciech Niedbała ◽

Katarzyna Buczkowska

Keyword(s):

New Species ◽

Molecular Data ◽

Sensu Stricto ◽

Soil Samples ◽

Key To Species ◽

Morphological Differences ◽

Morphological And Molecular Data ◽

First Time ◽

One New Species ◽

Species Variability

Seven soil samples have been collected on four islands of the Azores, in which 14 species of ptyctimous mites (Acari, Oribatida) were found. One new species Phthiracarus andreasi Niedbała sp. nov. from Faial Island is described. Four species have been recorded for the first time from the Azores. Molecular analysis showed that the differences in the sculpture patterns in Euphthiracarus excultus Pérez-Iñigo, 1987 represent within-species variability. However, the length of body setae can separate two different species: Phthiracarus atlanticus Pérez-Iñigo, 1987 sensu stricto and Phthiracarus falciformis Morell & Subías, 1991, despite the absence of any other morphological differences. On the basis of our morphological and molecular data, a key to species from the Azores is provided.

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Achnanthes Bory Sensu Stricto (Bacillariophyta) from Terrestrial Habitats of Rio de Janeiro (Brazil), with Description of Achnanthes pseudoinflata sp. nov.

Diversity ◽

10.3390/d12100375 ◽

2020 ◽

Vol 12 (10) ◽

pp. 375

Author(s):

Mateusz Rybak ◽

Łukasz Peszek ◽

Łukasz Skoczylas ◽

Teresa Noga ◽

Luc Ector ◽

...

Keyword(s):

Rio De Janeiro ◽

Morphological Characteristics ◽

Sensu Stricto ◽

Sem Analysis ◽

Similar Species ◽

Original Material ◽

Botanic Garden ◽

Concrete Wall ◽

Terrestrial Habitats ◽

Morphological Differences

The aim of the present work was to present the ecological and morphological characteristics of species from the genus Achnanthes Bory sensu stricto, which develops in terrestrial mosses near the Rio de Janeiro Botanic Garden, Brazil. A literature comparison was made with other similar species, including the LM and SEM analysis of original material bearing Achnanthes inflata (Kützing) Grunow housed at the Grunow Collection in Vienna, and data from the available literature. Samples were collected from clumps of moss growing on tree trunks, and from a concrete wall within the botanic garden. Four taxa from the genus Achnanthes were recorded: A. coarctata, A. inflata var. gibba, A. mauiensis and Achnanthes pseudoinflata sp. nov. The main morphological differences between these taxa were cell dimensions (length and width), striae and areolae density. The most common diatom species found in these samples were Humidophila sp. (90%), Humidophila contenta (74.8%), Luticola moreirae (17.9%), and Achnanthes pseudoinflata sp. nov. (7.4%).

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Resurrection of genus Nidirana (Anura: Ranidae) and synonymizing N. caldwelli with N. adenopleura, with description of a new species from China

Amphibia-Reptilia ◽

10.1163/15685381-00003130 ◽

2017 ◽

Vol 38 (4) ◽

pp. 483-502 ◽

Cited By ~ 4

Author(s):

Zhi-Tong Lyu ◽

Zhao-Chi Zeng ◽

Jian Wang ◽

Chao-Yu Lin ◽

Zu-Yao Liu ◽

...

Keyword(s):

New Species ◽

Morphological Characters ◽

Sensu Stricto ◽

Advertisement Call ◽

Morphological Comparison ◽

The Past ◽

The Family ◽

Significant Divergence ◽

Morphological Differences ◽

A New Species

The taxonomy of Babina sensu lato was controversial in the past decades. In this study, the phylogeny of genus Babina sensu lato was re-constructed based on genetic analysis, morphological comparison and advertisement call analysis. We found that Babina sensu stricto and previous subgenus Nidirana should be two distinct genera in the family Ranidae. N. caldwelli is confirmed to be a synonym of N. adenopleura because of the small genetic divergence and the lack of distinct morphological differences. A new species, Nidirana nankunensis sp. nov. is described based on a series of specimens collected from Mt. Nankun, Guangdong Province, China, which can be distinguished from other known congeners by having a behavior of nest construction, distinctive advertisement calls, significant divergence in the mitochondrial genes, and a combination of morphological characters. Currently, the genus Babina contains two species and the genus Nidirana contains eight species.

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Study of the type material of Navicula egregia Hustedt and descriptions of two new aerial Microcostatus (Bacillariophyta) species from Central Europe

Phytotaxa ◽

10.11646/phytotaxa.280.2.6 ◽

2016 ◽

Vol 280 (2) ◽

pp. 163 ◽

Cited By ~ 1

Author(s):

JADWIGA STANEK-TARKOWSKA ◽

CARLOS E. WETZEL ◽

TERESA NOGA ◽

LUC ECTOR

Keyword(s):

New Species ◽

Light Microscopy ◽

New Genus ◽

Original Material ◽

Species Determination ◽

The Family ◽

German Original ◽

Two New Species ◽

Morphological Differences ◽

First Time

The genus Microcostatus was described for the first time by Johansen & Sray in 1998. They established a new genus in the family Naviculaceae for Navicula krasskei. Subsequently, Lange-Bertalot proposed the transfer of further species from the genus Navicula to the Microcostatus. Species determination is very difficult using light microscopy since species are small and very similar to each other, and only ultrastructural features allow their placement in the genus. The aim of this paper was to describe morphologically and ecologically two new species of the genus Microcostatus from aerial habitats in Germany and Poland and compare their morphologies with the original gathering of Navicula egregia. Polish material was collected once a month from April to November 2013 at two sampling sites located in cultivated fields. For comparison, German original material from the Hustedt Collection was also observed. During this study, Microcostatus aerophilus sp. nov. and M. edaphicus sp. nov. were described, and M. egregius was also illustrated and discussed in detail. The species mentioned are very similar to each other under light microscopy. They differ slightly in dimension and number of striae. Only SEM observations showed morphological differences, such as the presence of conopeum or pseudoconopeum.

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

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.2159 ◽

2018 ◽

Vol 285 (1871) ◽

pp. 20172159 ◽

Cited By ~ 29

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 .

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Mitochondrial DNA Sequence Phylogeny of Daucus

Systematic Botany ◽

10.1600/036364420x15862837791311 ◽

2020 ◽

Vol 45 (2) ◽

pp. 403-408 ◽

Cited By ~ 1

Author(s):

David M. Spooner ◽

Holly Ruess ◽

Philipp Simon ◽

Douglas Senalik

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Phylogenetic Trees ◽

Plastid Dna ◽

Nuclear Data ◽

Bootstrap Support ◽

Illumina Hiseq ◽

Data Set ◽

Closely Related Species ◽

Mitochondrial Sequences

Abstract—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.

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