Editorial

6 pages, 262 KiB

Open AccessEditorial

Recent Advances in the Integrative Taxonomy of Plants

by Yevhen Maltsev and Andrey Erst

Plants 2023, 12(24), 4097; https://doi.org/10.3390/plants12244097 - 07 Dec 2023

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Biodiversity conservation and management call for rapid and accurate global assessments at the species level [...] Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

Research

Jump to: Editorial, Review

26 pages, 22092 KiB

Open AccessArticle

New and Interesting Taxa from the Diatom Genus Gomphonema Ehrenberg in Shallow, Nearshore Sites on the Eastern Coast of Lake Baikal

by Maxim S. Kulikovskiy, John Patrick Kociolek, Cüneyt Nadir Solak, Irina V. Kuznetsova and Anton M. Glushchenko

Plants 2023, 12(9), 1835; https://doi.org/10.3390/plants12091835 - 29 Apr 2023

Cited by 1 | Viewed by 1461

Abstract

During this investigation, sixteen species from the genus Gomphonema were found in a shallow bay (near Oimur, Kabansky District) located on the eastern shore of Lake Baikal. Eleven of these taxa have been described previously. Five species are described as new to science. [...] Read more.

During this investigation, sixteen species from the genus Gomphonema were found in a shallow bay (near Oimur, Kabansky District) located on the eastern shore of Lake Baikal. Eleven of these taxa have been described previously. Five species are described as new to science. We provide ecological information about these Gomphonema species, including their distribution within and outside Lake Baikal, and compare and contrast the new taxa with morphologically similar congeners. The diversity of morphologies present in Lake Baikal among the Gomphonema species suggests there has been both in-lake speciation as well as the introduction of various groups of species. The idea that Lake Baikal may support a high number of endemics by their partitioning niches based on depth is supported by the different groups of gomphonemoid diatoms present. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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21 pages, 6495 KiB

Open AccessArticle

Untargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging

by Kristian Peters, Kaitlyn L. Blatt-Janmaat, Natalia Tkach, Nicole M. van Dam and Steffen Neumann

Plants 2023, 12(4), 881; https://doi.org/10.3390/plants12040881 - 15 Feb 2023

Cited by 2 | Viewed by 2154

Abstract

Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca, R. sorocarpa [...] Read more.

Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca, R. sorocarpa, and R. warnstorfii (order Marchantiales, Ricciaceae) with Lunularia cruciata (order Marchantiales, Lunulariacea) as an outgroup. Liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) were integrated with DNA marker-based sequencing of the trnL-trnF region and high-resolution bioimaging. Our untargeted chemotaxonomy methodology enables us to distinguish taxa based on chemophenetic markers at different levels of complexity: (1) molecules, (2) compound classes, (3) compound superclasses, and (4) molecular descriptors. For the investigated Riccia species, we identified 71 chemophenetic markers at the molecular level, a characteristic composition in 21 compound classes, and 21 molecular descriptors largely indicating electron state, presence of chemical motifs, and hydrogen bonds. Our untargeted approach revealed many chemophenetic markers at different complexity levels that can provide more mechanistic insight into phylogenetic delimitation of species within a clade than genetic-based methods coupled with traditional morphology-based information. However, analytical and bioinformatics analysis methods still need to be better integrated to link the chemophenetic information at multiple scales. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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21 pages, 16228 KiB

Open AccessArticle

Integrative Taxonomy of Nitraria (Nitrariaceae), Description of the New Enigmatic Species and Key to All Currently Known Species

by Evgeny V. Banaev, Maria A. Tomoshevich, Sofia A. Khozyaykina, Anna A. Erst and Andrey S. Erst

Plants 2023, 12(3), 593; https://doi.org/10.3390/plants12030593 - 29 Jan 2023

Cited by 3 | Viewed by 1803

Abstract

A new species, Nitraria iliensis sp. nov., is described from the Ili basin, Almaty region, Kazakhstan. It belongs to section Nitraria ser. Sibiricae and is morphologically similar to N. sibirica Pall. An integrative taxonomic approach based on molecular, biochemical and morphological analyses, along [...] Read more.

A new species, Nitraria iliensis sp. nov., is described from the Ili basin, Almaty region, Kazakhstan. It belongs to section Nitraria ser. Sibiricae and is morphologically similar to N. sibirica Pall. An integrative taxonomic approach based on molecular, biochemical and morphological analyses, along with palynological data, was used to delimit this new species. The studied species of the genus are illustrated, and photographs of authentic specimens of the new species, as well as a distribution map of the new species and segregate taxa, are provided. Morphological characters were investigated, more important traits for identification were found, and a new key to distinguish between all species of the genus was prepared. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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7 pages, 1257 KiB

Open AccessCommunication

Primula luquanensis sp. nov. (Primulaceae), a New Species from Southwestern China, Reveals a Novel Floral Form in the Heterostyly-Prevailing Genus

by Zhi-Kun Wu, Yong-Jie Guo, Ting Zhang, Kevin S. Burgess and Wei Zhou

Plants 2023, 12(3), 534; https://doi.org/10.3390/plants12030534 - 24 Jan 2023

Cited by 6 | Viewed by 1722

Abstract

A new species, Primula luquanensis Z.K.Wu and Wei Zhou sp. nov. (Primulaceae) is described and illustrated from Yunnan Province, China. It is morphologically assigned to P. sect Aleuritia based on its dwarf and hairless habit and coverage by farina on both sides of [...] Read more.

A new species, Primula luquanensis Z.K.Wu and Wei Zhou sp. nov. (Primulaceae) is described and illustrated from Yunnan Province, China. It is morphologically assigned to P. sect Aleuritia based on its dwarf and hairless habit and coverage by farina on both sides of the leaf blade and scape. This new species is similar to P. nutantiflora and P. yunnanensis, but it is easily distinguished by its stolons, solitary bract, bell-shaped corolla and monomorphic floral form. The new species also has a substantially reduced corolla tube, presenting a unique floral form in a genus where heterostyly typically prevails. Full article

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16 pages, 3597 KiB

Open AccessArticle

Characterization of the Slovene Autochthonous Rose Hybrid Rosa pendulina × spinosissima (Rosa reversa Waldst. and Kit) Using Biochemical Patterns of the Plant Blossoms

by Nina Kunc, Metka Hudina, Jože Bavcon, Branko Vreš, Zlata Luthar, Kristina Gostinčar, Maja Mikulič-Petkovšek, Gregor Osterc and Blanka Ravnjak

Plants 2023, 12(3), 505; https://doi.org/10.3390/plants12030505 - 22 Jan 2023

Cited by 5 | Viewed by 1437

Abstract

The Rosa genus is characterized by great variability and, consequently, they easily hybridize. The petals of R. pendulina, R. spinosissima and their hybrid Rosa pendulina × spinosissima, collected in western Slovenia, were included in the research. We performed morphometric analysis using [...] Read more.

The Rosa genus is characterized by great variability and, consequently, they easily hybridize. The petals of R. pendulina, R. spinosissima and their hybrid Rosa pendulina × spinosissima, collected in western Slovenia, were included in the research. We performed morphometric analysis using keys to determine roses and genetic analysis to determine the genome size. The phenolic compound content in petals of all rose flowers was measured by liquid chromatography and mass spectrometry (HPLC-MS). Using flow cytometry, we could confirm the native hybridization process due to the amount of 2C DNA. The value of R. pendulina was 1.71 pg, of R. spinosissima 1.60 pg and of the hybrid 1.62 pg. The value for the hybrid was close to values measured for parent plants and, at the same time, those values of parent plants significantly differed from each other. Our results showed that the content of phenolic compounds in petals decreased after crossing. We found that the highest total phenolic content (178.9 g/kg FW) was measured in R. spinossisima, the lowest content was analyzed for the hybrid (84.36 g/kg FW) and the content for R. pendulina was between these two values (110.58 g/kg FW). The content of flavanols and flavonols was lowest in the hybrid petals, whereas the content of anthocyanins was highest in the hybrid petals. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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13 pages, 1900 KiB

Open AccessArticle

A New Cryptic Species of the Genus Mychonastes (Chlorophyceae, Sphaeropleales)

by Nikita Martynenko, Evgeniy Gusev, Dmitry Kapustin and Maxim Kulikovskiy

Plants 2022, 11(23), 3363; https://doi.org/10.3390/plants11233363 - 03 Dec 2022

Cited by 1 | Viewed by 1683

Abstract

A new species of green coccoid algae, Mychonastes hindakii sp. nov., was isolated from the River Moscow (Russia, Moscow). The taxon is described using morphological and molecular methods. Mychonastes hindakii sp. nov. belongs to the group of species of the genus Mychonastes with spherical single [...] Read more.

A new species of green coccoid algae, Mychonastes hindakii sp. nov., was isolated from the River Moscow (Russia, Moscow). The taxon is described using morphological and molecular methods. Mychonastes hindakii sp. nov. belongs to the group of species of the genus Mychonastes with spherical single cells joined with mucilaginous, irregularly shaped stalks. A comparison of ITS2 rDNA sequences and its secondary structures combined with the compensatory base changes approach confirms the separation between Mychonastes hindakii and other species of the genus. Mychonastes hindakii sp. nov. represents a cryptic species that can only be reliably identified using molecular data. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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23 pages, 7780 KiB

Open AccessArticle

Production of Fluorescent Dissolved Organic Matter by Microalgae Strains from the Ob and Yenisei Gulfs (Siberia)

by Nikolay V. Lobus, Anton M. Glushchenko, Alexander A. Osadchiev, Yevhen I. Maltsev, Dmitry A. Kapustin, Olga P. Konovalova, Maxim S. Kulikovskiy, Ivan N. Krylov and Anastasia N. Drozdova

Plants 2022, 11(23), 3361; https://doi.org/10.3390/plants11233361 - 03 Dec 2022

Cited by 5 | Viewed by 1643

Abstract

Dissolved organic matter (DOM) is an important component of aquatic environments; it plays a key role in the biogeochemical cycles of many chemical elements. Using excitation–emission matrix fluorescence spectroscopy, we examined the fluorescent fraction of DOM (FDOM) produced at the stationary phase of [...] Read more.

Dissolved organic matter (DOM) is an important component of aquatic environments; it plays a key role in the biogeochemical cycles of many chemical elements. Using excitation–emission matrix fluorescence spectroscopy, we examined the fluorescent fraction of DOM (FDOM) produced at the stationary phase of growth of five strains of microalgae sampled and isolated from the Ob and Yenisei gulfs. Based on the morphological and molecular descriptions, the strains were identified as diatoms (Asterionella formosa, Fragilaria cf. crotonensis, and Stephanodiscus hantzschii), green microalgae (Desmodesmus armatus), and yellow-green microalgae (Tribonema cf. minus). Three fluorescent components were validated in parallel factor analysis (PARAFAC): one of them was characterized by protein-like fluorescence (similar to peak T), two others, by humic-like fluorescence (peaks A and C). The portion of fluorescence intensity of humic compounds (peak A) to the total fluorescence intensity was the lowest (27 ± 5%) and showed little variation between species. Protein-like fluorescence was most intense (45 ± 16%), but along with humic-like fluorescence with emission maximum at 470 nm (28 ± 14%), varied considerably for different algae strains. The direct optical investigation of FDOM produced during the cultivation of the studied algae strains confirms the possibility of autochthonous production of humic-like FDOM in the Arctic shelf regions. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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9 pages, 2403 KiB

Open AccessArticle

Chrysosphaerella septentrionalis sp. nov. (Chrysophyceae, Chromulinales), a New Species from the Arctic Including the Description of Chrysosphaerellaceae, fam. nov.

by Dmitry Kapustin and Maxim Kulikovskiy

Plants 2022, 11(22), 3166; https://doi.org/10.3390/plants11223166 - 18 Nov 2022

Cited by 3 | Viewed by 1265

Abstract

A new species, Chrysosphaerella septentrionalis, is described from a peat bog located on the bank of the Paz River (Pasvik Nature Reserve, Murmansk Region, Russia). Scale ultrastructure was studied using a scanning electron microscope. Morphologically, C. septentrionalis seems to closely resemble C. longispina [...] Read more.

A new species, Chrysosphaerella septentrionalis, is described from a peat bog located on the bank of the Paz River (Pasvik Nature Reserve, Murmansk Region, Russia). Scale ultrastructure was studied using a scanning electron microscope. Morphologically, C. septentrionalis seems to closely resemble C. longispina. However, C. septentrionalis possesses subcircular scales in addition to the oval scales, and they are much smaller than in C. longispina. We suppose that C. septentrionalis is the first pseudocryptic species within the C. longispina complex. Additionally, we proposed an infrageneric classification of Chrysosphaerella based on the scale structure and divided the genus into three sections: Chrysosphaerella, Brevispinae sect. nov. and Septispinae sect. nov. The formal description of a new family Chrysosphaerellaceae fam. nov. is also provided. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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15 pages, 1535 KiB

Open AccessArticle

Color Variation and Secondary Metabolites’ Footprint in a Taxonomic Complex of Phyteuma sp. (Campanulaceae)

by Mariana Cecilia Grohar, Aljaz Medic, Tea Ivancic, Robert Veberic and Jernej Jogan

Plants 2022, 11(21), 2894; https://doi.org/10.3390/plants11212894 - 28 Oct 2022

Cited by 1 | Viewed by 1195

Abstract

In the genus Phyteuma, the taxonomic delimitation of some species is difficult since a high variability of morphological traits, such as flower color, is present, probably due to high levels of hybridization. Historic descriptions and the morphological traits used in the taxonomic [...] Read more.

In the genus Phyteuma, the taxonomic delimitation of some species is difficult since a high variability of morphological traits, such as flower color, is present, probably due to high levels of hybridization. Historic descriptions and the morphological traits used in the taxonomic keys are sometimes unclear and lead to misinterpretations. Here, a detailed analysis of flower color variability in different populations of sympatric P. spicatum, P. ovatum, and P. persicifolium constitutes a new approach to clarifying the taxonomic statuses. The numeric analysis of color, providing colorimetric variables, together with the detailed description of the metabolic profiles of populations with different flower colors, constitute a unique chemical fingerprint that identifies species and subspecies with clear markers. This study is the most complete metabolic research on genus Phyteuma, since we identified and quantified 44 phenolic compounds using HPLC-MS, comprising 14 phenolic acids, 23 flavonols and flavones, and, for the first time in the genus, 7 anthocyanins involved in flower color variability. This approach contributes to clarifying the differences between species, which is particularly relevant in taxonomic complexes such as the present, where morphology fails to clearly differentiate taxa at specific and intraspecific levels. Full article

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22 pages, 3251 KiB

Open AccessArticle

Biogeography and Systematics of the Genus Axyris (Amaranthaceae s.l.)

by Alexander P. Sukhorukov, Valeriia D. Shiposha, Maria Kushunina and Maxim A. Zaika

Plants 2022, 11(21), 2873; https://doi.org/10.3390/plants11212873 - 27 Oct 2022

Cited by 1 | Viewed by 1481

Abstract

Axyris is a small genus of six species with a disjunct geographic range. Five species are present in Siberia, Central Asia, the Himalayas, and Tibet, whereas Axyris caucasica has been registered in the Central Caucasus only. Axyris species diversity is the highest in [...] Read more.

Axyris is a small genus of six species with a disjunct geographic range. Five species are present in Siberia, Central Asia, the Himalayas, and Tibet, whereas Axyris caucasica has been registered in the Central Caucasus only. Axyris species diversity is the highest in the Altai Mountains (four spp.), followed by the Tian Shan and Pamir Mountains (three spp.), and the Himalayas and Tibet (two spp.). Axyris sphaerosperma, sometimes considered endemic to Southern Siberia, in fact has a disjunct range: it is present in the lowlands of Eastern Siberia and in the Altai, Tian Shan, and Pamir Mountains. It has also been found in Mongolia and China for the first time. An updated detailed distribution of Axyris in Siberia is presented on the basis of thorough herbarium revisions. One nuclear and three plastid markers were selected for phylogenetic analysis. Divergence times were estimated using a time-calibrated Bayesian approach. Axyris shows two major clades: an Axyris amaranthoides clade and a clade including the remaining species. The latter clade consists of two subclades (A. sphaerosperma/A. caucasica and A. mira/A. prostrata + A. hybrida). The crown age for Axyris dates back to the Early Pliocene (~5.11 mya, the Zanclean). The ancestral range of Axyris covers Southern Siberia, Mongolia, NW China, and the Tian Shan/Pamir Mountains, with extensions toward Eastern Siberia, the Himalayas/Tibet, and the Caucasus. Fruit and seed characteristics of Axyris are discussed with reference to the present phylogenetic results. Closely related A. sphaerosperma and A. caucasica have the thickest seed coat among all Chenopodiaceae, and these traits have probably evolved as adaptations to extremely low winter temperatures. This reproductive peculiarity may explain the disjunct range of A. sphaerosperma, which is restricted to harsh climatic conditions. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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16 pages, 4397 KiB

Open AccessArticle

Molecular and Morphological Investigations of Two Giant Diatom Cymbella Species from the Transbaikal Area (Russia, Siberia) with Comments on Their Distributions

by Anton M. Glushchenko, Yevhen I. Maltsev, John Patrick Kociolek, Irina V. Kuznetsova and Maxim S. Kulikovskiy

Plants 2022, 11(18), 2445; https://doi.org/10.3390/plants11182445 - 19 Sep 2022

Cited by 7 | Viewed by 1563

Abstract

For the first time, a giant diatom species of the genus Cymbella from Lake Baikal was studied using molecular methods. Molecular and morphological investigations allowed to us to described one new species, Cymbella baicalaspera Glushchenko, Kulikovskiy and Kociolek sp. nov. This species is [...] Read more.

For the first time, a giant diatom species of the genus Cymbella from Lake Baikal was studied using molecular methods. Molecular and morphological investigations allowed to us to described one new species, Cymbella baicalaspera Glushchenko, Kulikovskiy and Kociolek sp. nov. This species is both morphologically similar and phylogenetically close to a second giant Cymbella species that we investigated here, identified by us as Cymbella himalaspera Jüttner and Van de Vijver in Jüttner et al. 2010. This species was first described from Nepal on the basis of a morphological investigation. Small morphological differences exist between the type population and specimens from Lake Baikal, but otherwise the two are identical. These very interesting results show that some Baikalian diatoms can be distributed more widely and are not only endemic to this ancient lake. Similarity between Cymbella baicalaspera sp. nov. and Cymbella himalaspera on the basis of both morphological features and their close phylogenetic relationships suggested by molecular data indicate they are sister species and an example of sympatric speciation. These results also suggest an early development of a species flock. This species group warrants additional research in terms of. their diversification and biogeography. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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9 pages, 1769 KiB

Open AccessArticle

Planoplatessa gen. nov.—A New, Neglected Monoraphid Diatom Genus with a Cavum

by Maxim S. Kulikovskiy, Anton M. Glushchenko, Irina V. Kuznetsova and John Patrick Kociolek

Plants 2022, 11(17), 2314; https://doi.org/10.3390/plants11172314 - 03 Sep 2022

Cited by 4 | Viewed by 1380

Abstract

A new monoraphid diatom genus, Planoplatessa gen. nov., is described on the basis of a detailed morphological investigation using light and scanning electron microscopy. We transferred Achnanthes joursacensis Héribaud, a species described from fossil deposits in France, to our new genus. We investigated [...] Read more.

A new monoraphid diatom genus, Planoplatessa gen. nov., is described on the basis of a detailed morphological investigation using light and scanning electron microscopy. We transferred Achnanthes joursacensis Héribaud, a species described from fossil deposits in France, to our new genus. We investigated material from Mongolia from Recent populations. This taxon is known from fossils to Recent across the Holarctic. Achnanthes joursacensis was previously transferred to the genera Planothidium and Platessa, but the morphology of A. joursacensis does not share all morphological features with these two genera. We discuss important morphological features for the delimitation of monoraphid genera based on careful morphological and molecular investigations we presented previously. Planoplatessa gen. nov. as a genus is characterized by having uniseriate striae on both the raphe and the rapheless valves, a cavum in rapheless valves only, and straight distal raphe ends on the valve face. Full article

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22 pages, 5863 KiB

Open AccessArticle

Description of the Soil Diatom Sellaphora terrestris sp. nov. (Bacillariophyceae, Sellaphoraceae) from Vietnam, with Remarks on the Phylogeny and Taxonomy of Sellaphora and Systematic Position of Microcostatus

by Anton Glushchenko, Elena Kezlya, Yevhen Maltsev, Sergei Genkal, John Patrick Kociolek and Maxim Kulikovskiy

Plants 2022, 11(16), 2148; https://doi.org/10.3390/plants11162148 - 18 Aug 2022

Cited by 4 | Viewed by 1573

Abstract

In material isolated from soils of Cát Tiên National Park, we isolated four strains that were assigned to the genus Sellaphora. Identification was carried out on the basis of morphological and molecular studies. We proposed a new species named Sellaphora terrestris sp. [...] Read more.

In material isolated from soils of Cát Tiên National Park, we isolated four strains that were assigned to the genus Sellaphora. Identification was carried out on the basis of morphological and molecular studies. We proposed a new species named Sellaphora terrestris sp. nov. An evolutionary distance matrix, based on the 18S rDNA gene including the V4 domain, showed the new species shared 94.1–97.2% similarities with other Sellaphora sequences. The new species is morphologically similar to species previously identified as representatives of the genus Microcostatus. Full article

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19 pages, 2423 KiB

Open AccessEditor’s ChoiceArticle

The Warps and Wefts of a Polyploidy Complex: Integrative Species Delimitation of the Diploid Leucanthemum (Compositae, Anthemideae) Representatives

by Tankred Ott, Maximilian Schall, Robert Vogt and Christoph Oberprieler

Plants 2022, 11(14), 1878; https://doi.org/10.3390/plants11141878 - 19 Jul 2022

Cited by 7 | Viewed by 2015

Abstract

Species delimitation—owing to the paramount role of the species rank in evolutionary, ecological, and nature conservation studies—is an essential contribution of taxonomy to biodiversity research. In an ‘integrative taxonomy’ approach to species delimitation on the diploid level, we searched for evolutionary significant units [...] Read more.

Species delimitation—owing to the paramount role of the species rank in evolutionary, ecological, and nature conservation studies—is an essential contribution of taxonomy to biodiversity research. In an ‘integrative taxonomy’ approach to species delimitation on the diploid level, we searched for evolutionary significant units (the warps and wefts) that gave rise to the polyploid complex of European ox-eye daisies (Leucanthemum; Compositae-Anthemideae). Species discovery and validation methods based on genetic, ecological, geographical, and morphometric datasets were applied to test the currently accepted diploid morpho-species, i.e., morphologically delimited species, in Leucanthemum. Novel approaches were taken in the analyses of RADseq data (consensus clustering), morphometrics of reconstructed leaf silhouettes from digitized herbarium specimens, and quantification of species-distribution overlaps. We show that 17 of the 20 Leucanthemum morpho-species are supported by genetic evidence. The taxonomic rank of the remaining three morpho-species was resolved by combining genealogic, ecologic, geographic, and morphologic data in the framework of von Wettstein’s morpho-geographical species concept. We herewith provide a methodological pipeline for the species delimitation in an ‘integrative taxonomy’ fashion using sources of evidence from genealogical, morphological, ecological, and geographical data in the philosophy of De Queiroz’s “Unified Species Concept”. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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17 pages, 3870 KiB

Open AccessArticle

Multilocus Data Analysis Reveal the Diversity of Cryptic Species in the Tillandsia ionantha (Bromeliaceae: Tillansiodeae) Complex

by Juan J. Ancona, Juan P. Pinzón-Esquivel, Eduardo Ruiz-Sánchez, Clarisse Palma-Silva, Juan J. Ortiz-Díaz, Juan Tun-Garrido, Germán Carnevali and Néstor E. Raigoza

Plants 2022, 11(13), 1706; https://doi.org/10.3390/plants11131706 - 28 Jun 2022

Cited by 5 | Viewed by 2361

Abstract

Independent evolutionary lineages or species that lack phenotypic variation as an operative criterion for their delimitation are known as cryptic species. However, these have been delimited using other data sources and analysis. The aims of this study are: (1) to evaluate the divergence [...] Read more.

Independent evolutionary lineages or species that lack phenotypic variation as an operative criterion for their delimitation are known as cryptic species. However, these have been delimited using other data sources and analysis. The aims of this study are: (1) to evaluate the divergence of the populations of the T. ionantha complex; and (2) to delimit the species using multilocus data, phylogenetic analysis and the coalescent model. Phylogenetic analyses, genetic diversity and population structure, and isolation by distance analysis were performed. A multispecies coalescent analysis to delimit the species was conducted. Phylogenetic analysis showed that T. ionantha is polyphyletic composed of eight evolutionary lineages. Haplotype distribution and genetic differentiation analysis detected strong population structure and high values of genetic differentiation among populations. The positive correlation between genetic differences with geographic distance indicate that the populations are evolving under the model of isolation by distance. The coalescent multispecies analysis performed with starBEAST supports the recognition of eight lineages as different species. Only three out of the eight species have morphological characters good enough to recognize them as different species, while five of them are cryptic species. Tillandsia scaposa and T. vanhyningii are corroborated as independent lineages, and T. ionantha var. stricta changed status to the species level. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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14 pages, 3204 KiB

Open AccessFeature PaperArticle

Reevaluation of Parasynechococcus-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites

by Jie Tang, Dan Yao, Huizhen Zhou, Lianming Du and Maurycy Daroch

Plants 2022, 11(8), 1060; https://doi.org/10.3390/plants11081060 - 13 Apr 2022

Cited by 5 | Viewed by 1337

Abstract

Morphologically similar to Synechococcus, a large number of Parasynechococcus strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 Synechococcus-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains [...] Read more.

Morphologically similar to Synechococcus, a large number of Parasynechococcus strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 Synechococcus-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains as Parasynechococcus-like strains and showing considerably intragenus genetic divergence among the subclades identified. Further, bioinformatics analysis disclosed diversified patterns of distribution, abundance, density, and diversity of microsatellites (SSRs) and compound microsatellites (CSSRs) in genomes of these Parasynechococcus-like strains. Variations of SSRs and CSSRs were observed amongst phylotypes and subclades. Both SSRs and CSSRs were in particular unequally distributed among genomes. Dinucleotide SSRs were the most widespread, while the genomes showed two patterns in the second most abundant repeat type (mononucleotide or trinucleotide SSRs). Both SSRs and CSSRs were predominantly observed in coding regions. These two types of microsatellites showed positive correlation with genome size (p < 0.01) but negative correlation with GC content (p < 0.05). Additionally, the motif (A)_n, (AG)_n and (AGC)_n was a major one in the corresponding category. Meanwhile, distinctive motifs of CSSRs were found in 39 genomes. This study characterizes SSRs and CSSRs in genomes of Parasynechococcus-like strains and will be useful as a prerequisite for future studies regarding their distribution, function, and evolution. Moreover, the identified SSRs may facilitate fast acclimation of Parasynechococcus-like strains to fluctuating environments and contribute to the extensive distribution of Parasynechococcus species in global marine environments. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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Review

Jump to: Editorial, Research

64 pages, 3873 KiB

Open AccessReview

Marine Floral Biodiversity, Threats, and Conservation in Vietnam: An Updated Review

by Manh-Linh Nguyen, Myung-Sook Kim, Nhu-Thuy Nhat Nguyen, Xuan-Thuy Nguyen, Van-Luong Cao, Xuan-Vy Nguyen and Christophe Vieira

Plants 2023, 12(9), 1862; https://doi.org/10.3390/plants12091862 - 30 Apr 2023

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Abstract

Part of the Indo-Chinese peninsula and located on the northwest edge of the Coral Triangle in the South China Sea, the Vietnamese coastal zone is home to a wealthy marine biodiversity associated with the regional geological setting and history, which supports a large [...] Read more.

Part of the Indo-Chinese peninsula and located on the northwest edge of the Coral Triangle in the South China Sea, the Vietnamese coastal zone is home to a wealthy marine biodiversity associated with the regional geological setting and history, which supports a large number of marine ecosystems along a subtropical to tropical gradient. The diversity of coastal benthic marine primary producers is also a key biological factor supporting marine biological diversity. The present review provides: (1) an updated checklist of the Vietnamese marine flora, (2) a review of molecular-assisted alpha taxonomic efforts, (3) an analysis of marine floral biodiversity spatial distribution nationally and regionally (South China Sea), (4) a review of the impact of anthropogenic and environmental stressors on the Vietnamese marine flora, and (5) the efforts developed in the last decade for its conservation. Based on the studies conducted since 2013 and the nomenclatural changes that occurred during this period, an updated checklist of benthic marine algae and seagrasses consisted in a new total of 878 species, including 439 Rhodophyta, 156 Ochrophyta, 196 Chlorophyta, 87 Cyanobacteria, and 15 phanerogam seagrasses. This update contains 54 new records and 5 new species of macroalgae. The fairly poor number of new records and new species identified in the last 10 years in a “mega-diverse” country can be largely attributed to the limited efforts in exploring algal biodiversity and the limited use of genetic tools, with only 25.4% (15 species) of these new records and species made based on molecular-assisted alpha taxonomy. The South Central Coast supports the highest species diversity of marine algae, which coincides with the largest density of coral reefs along the Vietnamese coast. Vietnam holds in the South China Sea one of the richest marine floras, imputable to the country’s geographical, geological, and climatic settings. However, Vietnam marine floral biodiversity is under critical threats examined here, and current efforts are insufficient for its conservation. A methodical molecular-assisted re-examination of Vietnam marine floral biodiversity is urgently needed, complemented with in-depth investigations of the main threats targeting marine flora and vulnerable taxa, and finally, conservation measures should be urgently implemented. Full article

(This article belongs to the Special Issue Integrative Taxonomy of Plants)

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