Mitochondrial genome announcements need to consider existing short sequences from closely related species to prevent taxonomic errors

Conservation Genetics Resources ◽

10.1007/s12686-021-01214-7 ◽

2021 ◽

Author(s):

Peter R. Teske

Keyword(s):

South African ◽

Dna Sequences ◽

Related Species ◽

Closely Related Species ◽

Single Marker ◽

Taxonomic Confusion ◽

Species Taxonomy ◽

Pacific Species ◽

Complete Mitochondrial Genomes ◽

Study Species

AbstractThe reconstruction of complete mitochondrial genomes (mitogenomes) has considerable potential to clarify species relationships in cases where morphological analysis and DNA sequencing of individual genes are inconclusive. However, the trend to use only mitogenomes for the phylogenies presented in mitogenome announcements carries the inherent risk that the study species’ taxonomy is incorrect because no mitogenomes have yet been reconstructed for its sister species. Here, I illustrate this problem using the mitogenomes of two seahorses, Hippocampus capensis and H. queenslandicus. Both specimens used for mitogenome reconstruction originated from traditional Chinese medicine markets rather than native habitats. Although mitogenome phylogenies placed these specimens correctly among the seahorses from which mitogenomes were available at the time, incorporating single-marker sequence from closely related species into the phylogenies revealed that both mitogenomes are problematic. The mitogenome of the endemic South African H. capensis did not cluster among single-marker DNA sequences of seahorses from the species’ native habitat, but among sequences submitted under the names H. casscsio, H. fuscus and H. kuda that originated from all over the Indo-Pacific, including China. Phylogenetic placement of the mitogenome of H. queenslandicus within a cluster of seahorses that also included H. spinosissimus confirms an earlier finding that H. queenslandicus is a synonym of H. spinosissimus, a widespread Indo-Pacific species that also occurs in China. It is recommended that mitogenome announcements incorporate available single-marker sequences of closely related species, not only mitogenomes. The reconstruction of mitogenomes can exacerbate taxonomic confusion if existing information is ignored.

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Are polymorphic species of Uropodina (Acari: Mesostigmata) more successful evolutionarily?—A case study of closely related species from the genus Oodinychus Berlese, 1917 based on DNA sequences

Systematic and Applied Acarology ◽

10.11158/saa.24.5.10 ◽

2019 ◽

Vol 24 (5) ◽

pp. 866

Author(s):

Jerzy Błoszyk ◽

Katarzyna Buczkowska ◽

Anna Maria Bobowicz ◽

Alina Bączkiewicz ◽

Zbigniew Adamski ◽

...

Keyword(s):

Dna Sequences ◽

Related Species ◽

Habitat Preferences ◽

Abundant Species ◽

Systematic Position ◽

Genetic Differences ◽

Similar Species ◽

Closely Related Species ◽

Wide Range

The study presented in this research paper is the first taxonomic investigation focusing on Uropodina (Acari: Mesostigmata) mites with a brief discussion of the genetic differences of two very closely related species from the genus Oodinychus Berlese, 1917, i.e. O. ovalis (C.L. Koch, 1839) and O. karawaiewi (Berlese, 1903). These two morphologically similar species are quite common and they have a wide range of occurrence in Europe. They also live in almost the same types of habitat. However, O. ovalis usually exhibits higher abundance and frequency of occurrence. The major aim of the study was to carry out a comparative analysis of the systematic position, morphological and biological differences, as well as habitat preferences and distribution of O. ovalis and O. karawaiewi. The next aim was to ascertain whether the differences in number and frequency of these species may stem from the genetic differences at the molecular level (16S rDNA and COI). The study shows that O. ovalis, which is a more abundant species than O. karawaiewi, turned out to be genetically more polymorphic.

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Typification for reliable application of subspecific names within Peridinium cinctum (Peridiniales, Dinophyceae)

Phytotaxa ◽

10.11646/phytotaxa.424.3.2 ◽

2019 ◽

Vol 424 (3) ◽

pp. 147-157 ◽

Cited By ~ 2

Author(s):

CORINNA ROMEIKAT ◽

ALEJANDRO IZQUIERDO LÓPEZ ◽

CHRISTINE TIETZE ◽

JULIANE KRETSCHMANN ◽

MARC GOTTSCHLING

Keyword(s):

Morphological Variation ◽

Dna Sequences ◽

Related Species ◽

Original Material ◽

Full Spectrum ◽

Closely Related Species ◽

Geographic Locations ◽

Future Studies ◽

Unicellular Organisms ◽

Peridinium Cinctum

The application of scientific names is determined by means of nomenclatural types, and every name has to be typified properly. The concept has limitations for unicellular organisms, because original material frequently consists of drawings and/or inadequately preserved physical material. Peridinium cinctum is an abundant freshwater microalga and variable in both morphology and genotype. Morphological variation is mainly expressed in its epithecal conformation: shape deviations of plates, plate rearrangements, plate fusion and plate additions. Different epithecal conformations were traditionally described as either varieties of P. cinctum or were established as closely related species. Despite this, relations between varieties, ribotypes and geographic locations were oversighted, and the full spectrum of plate variation in P. cinctum is still not well represented. For this reason, we sampled localities in Germany and Poland, from which varieties of P. cinctum were described a century ago. We cultivated monoclonal strains, exhibiting two distinct ITS ribotypes, and assessed their epithecal variation of morphology. Based on ca 2,500 observations of individual cells we report a plethora of both plate and suture deviations from the archetypical epithecal conformation of P. cinctum. Morphologies corresponding to previously described varieties were rare, even at their type localities. Nevertheless, we found morphologies consistent with protologues in four cases and use this material for epitypification. These varieties are now linked to specific DNA sequences, allowing reliable application of scientific names for future studies.

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Comparing Medicinal Uses of Cochlospermaceae throughout Its Geographic Range with Insights from Molecular Phylogenetics

Diversity ◽

10.3390/d10040123 ◽

2018 ◽

Vol 10 (4) ◽

pp. 123 ◽

Cited By ~ 1

Author(s):

Susannah Johnson-Fulton ◽

Linda Watson

Keyword(s):

Bioactive Compounds ◽

Dna Sequences ◽

Related Species ◽

Molecular Phylogenetics ◽

Closely Related Species ◽

Active Compounds ◽

Medicinal Uses ◽

Continental Scale ◽

Chloroplast Markers ◽

Geographic Regions

Species of the Cochlospermaceae, a small mostly pantropical plant family, were evaluated at a continental scale for medicinal uses in traditional medicine. This ethnobotanical information was placed in a phylogenetic framework to make informed predictions in the search for new medicines and bioactive compounds. Medicinal plant-use data were mapped onto a molecular phylogeny based on DNA sequences of nuclear and chloroplast markers. Associations of medicinal uses among closely related species occurring in different geographic regions and among diverse cultures were evaluated. The most common medicinal uses for these species are those used to treat skin ailments, gastro-intestinal problems, malaria, and liver issues. The plant species with the most numerous uses is Cochlospermum tinctorium, which occurs primarily in West Africa. Closely related species being used by cultural groups in different geographic regions to treat the same illnesses suggests the presence of bioactive compounds with potential biomedical value, since they may represent independent discoveries of similar medicinally-active compounds. This leads to the speculation that those closely related species not currently being used to treat these ailments may also contain identical or similar medicinally-active compounds and are worthy of laboratory investigations.

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Reproductive traits of two closely related species-pairs on adjacent, different soil types in South African Fynbos

Vegetatio ◽

10.1007/bf00040335 ◽

1994 ◽

Vol 111 (2) ◽

pp. 161-171 ◽

Cited By ~ 6

Author(s):

P. J. Mustart ◽

R. M. Cowling ◽

T. T. Dunne

Keyword(s):

South African ◽

Related Species ◽

Reproductive Traits ◽

Soil Types ◽

Closely Related Species ◽

Species Pairs

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Review of Oculogaster Kluge 2016 (Ephemeroptera, Baetidae, Procloeon Bengtsson 1915)

Zootaxa ◽

10.11646/zootaxa.4820.3.1 ◽

2020 ◽

Vol 4820 (3) ◽

pp. 401-437

Author(s):

NIKITA J. KLUGE

Keyword(s):

South Africa ◽

South African ◽

Related Species ◽

New South ◽

Single Specimen ◽

African Species ◽

Closely Related Species ◽

African Group ◽

Species Groups ◽

Single Larva

The subgenus Oculogaster Kluge 2016 is divided into two species groups: the «African group» includes Procloeon (Oculogaster) cylindroculum Kimmins 1956, P. (O.) barnardi sp. n., P. (O.) niger sp. n., unnamed species P. (O.) sp. «Wolfkloof» and presumably P. (O.) silvicola Gillies 1997; the «Asian group» includes P. (O.) album Kluge 2016, P. (O.) regularum Müller-Liebenau & Hubbard 1985, P. (O.) malabarensis sp. n., presumably Procloeon julia (Gillies 1949) comb. n. and unnamed species P. sp. «Thailand-3», P. sp. «Sulawesi» and P. sp. «Philippines». New South African species P. (O.) barnardi sp. n. and P. (O.) niger sp. n. are described from South Africa based on larvae, subimagines and imagines of both sexes associated by rearing; among them, P. (O.) barnardi sp. n. was formerly described by Barnard (1932) under the name «Austrocloeon africanum», being wrongly regarded to be the species originally described as Cloeon africanum Esben-Petersen 1913. Characters of larva and female subimago of another South African species, P. (O.) sp. «Wolfkloof» are described based on a single specimen. Two closely related species, P. (O.) regularum Müller-Liebenau & Hubbard 1985 from Sri Lanka and P. (O.) malabarensis sp. n. from India are described based on larvae, subimagines and imagines of both sexes associated by rearing; these two species have 2 (rarely 1 or 3) cross veins in pterostigma, in contrast to other species of Oculogaster which normally have one vein (rarely two veins). Procloeon julia is presumptively placed in Oculogaster based on the presence of one vein in pterostigma. Unnamed species P. sp. «Thailand-3», P. sp. «Sulawesi» and P. sp. «Philippines» are presumably placed in Oculogaster; each is briefly described based on a single larva.

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Additions to Taiwan fungal flora 2: Ophiosphaerella taiwanica sp. nov.

Phytotaxa ◽

10.11646/phytotaxa.413.1.4 ◽

2019 ◽

Vol 413 (1) ◽

pp. 39-48 ◽

Cited By ~ 1

Author(s):

HIRAN A. ARIYAWANSA ◽

E. B. GARETH JONES

Keyword(s):

Dna Sequences ◽

Related Species ◽

Phylogenetic Reconstruction ◽

New Taxon ◽

The Novel ◽

Fungal Flora ◽

Closely Related Species ◽

Natural Classification

The genus Ophiosphaerella contains 14 formerly illustrated species and is characterized by papillated ascomata bearing fissitunicate cylindrical asci frequently narrower near the base, with a short furcate pedicel and filamentous, pale brown, multi-septate ascospores without swollen cells or separating into part spores. We describe an Ophiosphaerella taxon that is new to science isolated from Yushania niitakayamensis in Cilai Mountain, Taiwan. We conducted polyphasic methods using single and multi-locus (ITS, LSU, SSU, and tef1-α) phylogenetic reconstruction united with morphology to evaluate the natural classification of the novel taxon. The results show that our Ophiosphaerella isolates are different from closely related species O. aquaticus and O. agrostidis based on distinct size differences of the ascomata, asci, ascospores, host and DNA sequences data, thus should be recognised here as a new taxon Ophiosphaerella taiwanica sp. nov.

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Molecular phylogenetics of species of Bulbophyllum sect. Trias (Orchidaceae; Epidendroideae; Malaxidae) based on nrITS and plastid rbcL and matK

Phytotaxa ◽

10.11646/phytotaxa.226.1.1 ◽

2015 ◽

Vol 226 (1) ◽

pp. 1 ◽

Cited By ~ 1

Author(s):

Passorn Wonnapinij ◽

Ajaraporn Sriboonlert

Keyword(s):

Dna Sequences ◽

Related Species ◽

Phylogenetic Relationships ◽

Internal Transcribed Spacer ◽

Molecular Phylogenetics ◽

Nuclear Region ◽

Closely Related Species ◽

Vegetative Characters ◽

Relationship Of ◽

The Relationship

Phylogenetic relationships among species of Bulbophyllum sect. Trias and related taxa in Bulbophyllum has not been previously studied due to scarcity of appropriate samples. In this study, we aimed to assess the relationship of these taxa and investigate interspecific relationships of these orchids using DNA sequences from two plastid genes, rbcL and matK, and one nuclear region, nuclear ribosomal internal transcribed spacer, nrITS. Our results showed that all Bulbophyllum sect. Trias species were embedded among other groups of Bulbophyllum, supporting the already published transfer of Trias to synonymy of Bulbophyllum. All trees revealed that the Indochinese sect. Trias form a monophyletic group that could be divided into three groups coincident with their vegetative characters. This study further shows that nrITS sequences can be sufficient for inferring phylogenetic relationship among Trias species, although this marker and the combination of this plus the plastid genes are not able to distinguish the differences between some closely related species.

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Mitochondrial DNA analysis of Pacific salmonid evolution

Canadian Journal of Zoology ◽

10.1139/z86-158 ◽

1986 ◽

Vol 64 (5) ◽

pp. 1058-1064 ◽

Cited By ~ 64

Author(s):

W. Kelley Thomas ◽

Ruth E. Withler ◽

Andrew T. Beckenbach

Keyword(s):

Mitochondrial Dna ◽

Rainbow Trout ◽

Dna Sequences ◽

Chinook Salmon ◽

Related Species ◽

Life Histories ◽

Chum Salmon ◽

Dna Analysis ◽

Salmo Gairdneri ◽

Closely Related Species

The salmonids of Pacific North America are a group of closely related species with complex life histories and interesting distribution. Previous studies of their evolution and population structure have involved classical morphological and genetic techniques. We have analysed both intra- and inter-specific variation in mitochondrial DNA sequences of the five North American species of the genus Oncorhynchus and the rainbow trout species, Salmo gairdneri. Cleavage sites for 13 different restriction enzymes were sampled, comparing an average of 48 sites per individual, or approximately 1.7% of the genome. No obvious size variation in the 16 500 ± 500 base pair length was observed. Levels of intraspecific variation detected in the chum salmon and rainbow trout were 0.24 ± 0.23 and 0.45 ± 0.26%, respectively. This variation was population specific; no variation was detected within any of the populations sampled, suggesting the existence of population substructuring. Estimates of divergence between species range from 2.46 ± 0.72% in the coho–chinook salmon comparison to 6.88 ± 1.27% between coho and chum salmon. The phylogenetic relationship among these species, based on the levels of sequence divergence, organizes the species into three distinct groups. One group includes the pink and chum salmon while a second group contains the coho and chinook salmon, as well as the rainbow trout. The sockeye salmon are distinct from both groups. Although most of these results are in accordance with classical analyses, the relationship of the rainbow trout to the coho and chinook salmon suggests different interpretations of the evolution of life histories and morphological traits in these closely related species.

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