Intraspecific Taxa Research Articles

Reinterpretation of Potamogeton ×nerviger

Hybrids form an important component of Potamogeton diversity but their exact taxonomic identities and distributions are often insufficiently known. Potamogeton nerviger was described from Lithuania in 1827 as a proper species. Based on morphological and anatomical characters, its interpretation has since varied, ranging from synonymization with other species to identification as different hybrids and intraspecific taxa. Currently, it is universally recognized as the hybrid P. alpinus × P. lucens. Using a combined molecular, morphological and anatomical investigation we re-examined the identity of P. ×nerviger, based on both original and recent plant material. We report a successful amplification and sequencing of nuclear ribosomal ITS1 region from a 188-year-old type collection. This was shown to be genetically identical to the morphologically matching plants recently collected at the type locality. Comparison with molecular characters of the possible parental species shows that P. ×nerviger is not P. alpinus × P. lucens, as currently believed, but another hybrid, P. nodosus × P. perfoliatus, which is currently called P. ×assidens. This molecular identification is also supported by anatomical evidence. In contrast, the actual existence of the hybrid P. alpinus × P. lucens is doubtful. Consequences for nomenclature and identities of records reported from other sites are discussed.

NMR-based metabolomics study of Amphoricarpos species from Montenegro

The genus Amphoricarpos Vis. is endemic of westpart of Balkan peninsula. In order to get more insight into the ambiguous taxonomy of the genus, the metabolomic study of the Amphoricarpos samples, has been undertaken. The1H NMR spectroscopy combined with multivariate data analysis has been applied. OPLS-DA has been shown to be the best method for clear discrimination of these samples based on the metabolites present in the extracts. The main difference between A. autariatus and A. neumayeri has been found to be the presence of characteristic sesquiterpene lactones of guaianolide type named amphoricarpolides. While the main sesquiterpene lactone in A. neumayeri was oxidized in position 2, those present in both subspecies of A. autariatus samples were oxidized in position 9.The use of sesquiterpene lactones as taxonomic characters for differentiating species of the Asteraceae family was reviewed elsewhere. For the differentiation of two subspecies, A. autariatus ssp. autariatus, and A. autariatus ssp. bertisceus, chlorogenic and malic acid have been found to be decisive, but these compounds do not have chemotaxonomic significance. Our results were in accordance with above mentioned classification of Blečić and Mayer but they differentiate from those of the recent genomic study of the genus indicating a single, genetically, morphologically and ecologically variable species, without intraspecific taxa.

The genera Conocybe and Pholiotina (Bolbitiaceae, Agaricales) in the Sverdlovsk Region

A critical revision of the genera Conocybe and Pholiotina from the Sverdlovsk Region based on materials from Museum of the Institute of Plant and Animal Ecology (SVER), Mycological Herbarium of the Komarov Botanical Institute (LE) and recent collections made in 2013–2016 is presented. A checklist of these taxa is provided. The previously published information on the species of Conocybe and Pholiotina from the Sverdlovsk Region is corrected. In all, 34 species and intraspecific taxa of Conocybe and Pholiotina (24 and 10, respectively) were found, 33 of them are confirmed by samples. Twenty five taxa are new to the Sverdlovsk Region.

Are There Two Varieties in Hylomecon japonica (Papaveraceae)? Morphological and Molecular Evidence

Hylomecon japonica (Papaveraceae) is the sole species of its genus. Two varieties, H. japonica var. dissecta and H. japonica var. subincisa, have been recognized, but the presence of numerous morphological intermediates renders the intraspecific taxa controversial. Based on observations of natural populations and molecular sequences of nDNA (NADPH) and cpDNA (rpoB-trnC and trnG intron regions), our results show that the samples identified as distinct varieties are scattered and nested within the subclades of plants identified as H. japonica var. japonica. As a whole, all samples of H. japonica are monophyletic; this is further supported by the continuous variation in leaf morphology. As a result, the two infraspecific names are synonymized with H. japonica. Our study emphasizes the importance of evaluating the full range of morphological variation and molecular data when describing infraspecific taxa within a morphologically variable species.

Early Miocene freshwater diatom flora from the Yamato Rise, the Sea of Japan

Fossil freshwater diatoms from tuffaceous–terrigenous deposits of the Yamato Rise, the Sea of Japan are described. The diatom flora includes 133 species and intraspecific taxa belonging to 44 genera. Species of Aulacoseira (19 taxa) and Tetracyclus (17 taxa) are highly diversified, and species of Aulacoseira and Actinocyclus occur very abundantly. Aulacoseira is mainly represented by extinct taxa, including those with elliptic valves that are characteristic of the Early Miocene (23–16 Ma). Such findings of numerous fossil freshwater diatoms in the Yamato Rise deposits strongly suggest that, during the Early Miocene, the Yamato Rise contained a lake basin within a terrestrial environment. Fifty-seven diatom taxa are illustrated.

Algae in sphagnum epiphyton from the mires of the Subpolar Urals

Abstract Species diversity of algal communities of sphagnum epiphyton was studied in six mountain and plain mires of the Subpolar Urals (Russia). A total of 154 species and intraspecific taxa from six divisions were identified. The highest species richness was recorded for Bacillariophyta (96 taxa) and Charophyta (33) divisions. Species Kobayasiella parasubtilissima, Tabellaria flocculosa and Eunotia lunaris had high abundance. Dominant communities were often formed by Eunotia lunaris, E. mucophila, Kobayasiella parasubtilissima and Pinnularia subcapitata. CCA analysis showed that conductivity and altitude above the sea level are the main factors affecting the development of algae in the studied mires.

CHARACTERISTICS OF THE PROTECTIVE ANTIGEN COMPLEX OBTAINED FROM FRANCISELLA TULARENSIS SSP. NOVICIDA

F. tularensis ssp. novicida, considered earlier as a representative of a separate species, has been recently classed among F. tularensis variety, based on the results of comparative analysis of 16S-ribosomal RNA. Subspecies novicida can cause disease only in immunocompromised humans and is low virulent for rabbits. Despite this, high rate of homology of the nucleotide sequence of F. tularensis intraspecific taxon is established. Objective of the study is to obtain protective surface antigen complex from F. tularensis ssp. novicida Utah 112 (ATTC 15 482) cells and investigate its properties. Materials and methods. Protein, carbohydrate, and lipid content of the antigen preparation was measured using conventional colorimetric methods, SDS-PAGE was conducted according to U.Laemmli, and immunoblotting – to H.Towbin. For purification and molecular mass determination column chromatography was applied. Immune-chromatographic activity was analyzed by immune-enzyme assay. Immunogenicity of the produced preparation was tested on scrub white mice, with LD50 and ED50 calculated according to Karber’s method. Results and conclusions. Carried out has been comparative analysis of physical-chemical, antigenic and bio-chemical peculiarities of the protective antigen complex obtained from F. tularensis Utah 112 cells and equivalent antigen complex obtained from the vaccine strain – F. tularensis 15 NIIEG. Protectivity of the preparation has been tested through inoculation of the immunized white mice with virulent F. tularensis 503/840 strain. Demonstrated have been distinctive features of the new preparation, by structure and composition, as compared to similar antigen from the vaccine producer strain, as well as the slowdown of its immunochemical and protective activities.

Freshwater testate amoebae in the Belaya River basin (Northwestern Caucasus)

Fifty-two species and intraspecific taxa of testate amoebae have been detected in 24 different habitats in the Belaya River basin (Northwestern Caucasus). Four types of communities are distinguished which differ in the composition of the complex of dominating species: freshwater species from bottom sediments in water bodies and water courses, soil-dwelling species from inundated parts of floodplains, a mixture of soildwelling and freshwater species in different littoral biotopes, and eurybiontic species in moss hummocks along the banks.

POSSIBILITIES OF DE NOVO TRANSCRIPTOME SEQUENCING IN PYLOGENETIC RESEARCH ON AN EXAMPLE OF TARAXACUM OFFICINALE (ASTERACEAE)

<p class="Default"> </p><p>As a result of the research we obtained a cDNA library, sequences and carried out <em>de novo </em>assembly and functional annotation of the transcriptome of systematically complex, almost cosmopolitan <em>Taraxacum officinale</em>. Systematics of the species is complicated because of separation of many microspecies and intraspecific taxa, which may be explained by the presence of ploidy races, the phenomenon of apomixis and significant polymorphism. Attempts of separation of microspecies and closely related species based on sequencing of chloroplast and nuclear DNA fragments, did not give acceptable results. We have made the first attempt to analyze the transcriptome for understanding the genome evolution of agamospermous-sexual complex of the species. A total of 84440 reads were obtained with a total 31,540,710 bp. As a result of the <em>de novo </em>assembly, we obtained 13902 contigs, with an average GC content equal to 38.1% and a maximum length of 5255 bp. In total, we received 3798 annotated genes. According to the functional annotation based on sequence homology, 2687 contigs were attributed to biological processes (19.32%), 3299 – to molecular functions (23.7%), 2157 – to the cellular component (15.51%) and 7497 contigs – with unknown functions. In the first category “single-organism cellular process”, “response to stimulus”, “photosynthesis-light reaction”, “oxidation-reduction” and “translation” have dominated. In the category of molecular function “nucleic acid binding”, “hydrolase activity”, “transferase” and “oxidoreductase” activities have dominated. In the cellular component category “integral component of membrane”, “chloroplast thylakoid membrane”, “photosystems” and “nucleus” have dominated.</p>

On the young age of intraspecific herbaceous taxa.

Dated phylogenies rarely include the divergence times of sister intraspecific taxa, and when they do little is said about this subject. We show that over 90% of the intraspecific plant taxa found in a literature search are estimated to be 5million yr old or younger, with only 4% of taxa estimated to be over 10 million yr old or older. A Bayesian analysis of intraspecific taxon ages indicates that indeed these taxa are expected to be <10million yr old. This result for the young age of intraspecific taxa is consistent with the earlier observation that post-pollination reproductive barriers develop between 5 and 10million yr after lineage splitting, thus leading to species formation. If lineages have not graduated to the species level of divergence by 10million yr or so, they are likely to have gone extinct by that time as a result of narrow geographical distributions, narrow niche breadths, and relatively small numbers across populations.

Materials on the flora of Bacillariophyta in aquatic ecosystems of the Yarayakha River basin (Yamal Peninsula)

The study of phytoplankton in lakes, sors, streams, and rivers of the Yarayakha River basin with the help of scanning electron microscopy has made it possible to broaden the taxonomic spectrum of Bacillariophyta; 236 specific and intraspecific taxa from 63 genera are detected. A total of 16 species and varieties that are new for the flora of Russia were documented; 30 forms from 18 genera are identified only to the species. The maximum species diversity is recorded in a stream in the Yarayakha River mouth (82 species) and in the channel of the Khureikhotarka River (105 species). Species such as Cyclotella meneghiniana, Fragilaria exiguiformis, Navicula hanseatica, Neidium bisulcatum, Stauroneis anceps, Thalassiosira inserta, and Tabellaria flocculosa are the most widespread in the waterbodies.

Структурные основы региональных отличий таксономического разнообразия донных диатомовых (Bacillariophyta) Чёрного моря

Важной задачей сохранения микроводорослей Чёрного моря является оценка разнообразия диатомовой флоры и выявление закономерностей его формирования. Работа сфокусирована на анализе разнообразия бентосных диатомовых в регионах северного шельфа Чёрного моря и причин их различий на разных уровнях таксономической иерархии. На основе литературных и собственных данных проведена ревизия региональных флор Bacillariophyta и осуществлена оценка разнообразия с помощью индексов таксономической отличительности TaxDI. Современное таксономическое богатство диатомовых бентоса Чёрного моря насчитывает 1094 вида и ввт (953 вида, 149 родов, 61 семейство, 32 порядка и 3 класса). У берегов Крыма отмечено 884 вида и ввт (81 % общего числа видов диатомовых Чёрного моря), в СЗЧМ ― 556 (51 %), у побережья Болгарии ― 271 (25 %), Румынии ― 358 (33 %), Кавказа ― 310 (28 %). Прослежено отклонение показателей индексов TaxDI от среднеожидаемого уровня для Чёрного моря в целом, которое зависит от строения филогенетических ветвей в каждом из трех классов. Наибольшее влияние на формирование древа Bacillariophyta оказывают олиго- и моновидовые ветви. Характер отклонения структуры региональных флор диатомовых от среднеожидаемого уровня обусловлен видами, формирующими моно- или олиговидовую ветвь вплоть до уровня порядка. Выделены подобные 33 вида с рангом высокой таксономической исключительности, которые отмечены в нескольких регионах. При их исчезновении из состава региональной флоры элиминируется целая ветвь из иерархического древа диатомовых. Особо выделена группа из 12 регион-специфичных видов с рангом наивысшей исключительности, обнаруженных однократно лишь в одном из регионов. Элиминация такого вида из флоры данного региона приводит к редукции моновидовой ветви (включая род, семейство и порядок) из флоры всего Чёрного моря. Это вызовет снижение таксономического разнообразия и изменения структуры иерархического древа Bacillariophyta как конкретного региона, так и архитектоники древа Bacillariophyta Чёрного моря в целом. Структура регионального древа диатомовых Крымского региона близка к среднеожидаемой структуре флоры Чёрного моря. Минимальное значение индекса TaxDI для Крыма (81,38) указывает на большую долю поливидовых ветвей в структуре древа, его максимальную видовую насыщенность (вид/род = 7) и пониженную вертикальную выровненность. У Румынии значение TaxDI максимально (85,9), что обусловлено значительной долей моно- и олиговидовых ветвей и минимальной насыщенностью видами в структуре древа (вид/род = 4).

Upper Oligocene-Lower Miocene diatom assemblages of the submarine Vityaz Ridge (Island slope of the Kuril-Kamchatka trench)

The diatom assemblages of the Upper Oligocene-Lower Miocene Rocella gelida (28.2-24.0 Ma, Thalassiosira praefraga (24.0-20.3 Ma), and Thalassiosira fraga (20.3-18.4 Ma) zones established in the sed� imentary section of the southern plateau in the submarine Vityaz Ridge of the Northwest Pacific include 123 species and intraspecific taxa belonging to 55 genera. The assemblages are correlated with their coeval analogs from sections of the Northwest Pacific. Taking into consideration the fact that Lower Oligocene dia� tom assemblages were previously documented in the Vityaz Ridge area, it is assumed that the sedimentary section with wellpreserved siliceous microfossils observ able in the southern plateau of the ridge corresponds to the continuous Oligocene-Lower Miocene interval.

A study of Bacillariophyta flora in water bodies and water courses of the Messoyakha River (Gydansky Peninsula)

A total of 236 species and intraspecific taxa of Bacillariophyta diatoms from 55 genera, including 15 new ones for Russian flora, were found in an SEM study of phytoplankton in Lake Glubokoe and large tributaries (Nizhnyaya Messoyakha, Purparod, Erparod, Paravanga, and Nyakhataparod) in the basin of the lower reaches of the Messoyakha River. The maximum species diversity was recorded in the tributaries Nizhnyaya Messoyakha (117), Nyakhataparod (109), and Lake Glubokoe (97). The following species are the most widespread in the studied water bodies: Asterionella formosa, Aulacoseira subarctica, Navicula cryptocephala, Nitzschia gracilis, and Tabellaria flocculosa.

Musa aurantiaca (Musaceae) and its intraspecific taxa in India

Musa aurantiaca Baker (Musaceae) is distributed from northeast India, Tibet to northern Myanmar. In the present study its intraspecific taxa are thoroughly investigated. Two new varieties are described and illustrated based on live plants in the field: M. aurantiaca Baker var. homenborgohainiana Gogoi and M. aurantiaca Baker var. jengingensis Gogoi. A key to the varieties of Musa aurantiaca Baker and closely related taxa is also provided.

Diatoms from surface sediments of Amurskiy Bay, Sea of Japan

The results of a study of diatoms from surface sediments (0–1 cm) of Amurskiy Bay are presented for the first time. The specific composition (221 species and intraspecific taxa) and ecological structure of the diatom flora were determined. The diatom species composition of phytoplankton, periphyton, and surface sediments is compared.

Variability of the taxa of the Bidens L. Genera and the problem of hybridization

The complex of microspecies of the Bidens genus referred earlier to B. × garumnae is characterized. Generation F1 does not inherit the prostrate habit and entire leaves, which are specific to parental plants, but each sample is uniform and has its own set of morphological and biological characteristics. In the studied locality, only one B. radiata × B. frondosa hybrid grows. No proof of the hybrid origin of other microspecies was found. It is proposed to perform the molecular genetic analysis of plant samples referred earlier to Bidens × garumnae and to describe them in the future as independent microspecies or intraspecific taxa.

Use of leaf morphometric parameters for identification of the most common cultivated intraspecific taxa of Tilia platyphyllos

Abstract Evarte-Bundere G., Evarts-Bunders P., 2013: Use of leaf morphometric parameters for identification of the most common cultivated intraspecific taxa of Tilia platyphyllos [Morfometrinių požymių panaudojimas dažniausiems kultūriniams Tilia platyphyllos vidurūšiniams taksonams apibūdinti]. - Bot. Lith., 19(2): 83-90. To determine variation of the most important morphological parameters of Tilia platyphyllos Scop., we studied four most frequently found in Latvia taxa: T. platyphyllos subsp. platyphyllos, T. platyphyllos subsp. cordifolia (Besser) C.K.Schneid., T. platyphyllos ‘Rubra’, T. platyphyllos ‘Obliqua.’ Morphometric measurements (length of petioles, width and length of leaf blades, pubescence and margin of leaves) were performed for 10 different specimens of every selected taxon measuring five typical leaves from each specimen. The cultivated intraspecific taxa of Tilia platyphyllos differed by the following morphometric parameters - the pubescence of leaves, the margin of leaves and the length of leaf blades. No significant differences were ascertained between taxa in such morphometric parameters as the width of leaf blades and the length of petioles.

Biogeography of testate amoebae in the soils of Mexico

We studied testate amoebae (testates) in the soils of coniferous and deciduous forests and in the wetland and aquatic habitats of Mexico. In 141 samples we found 205 taxa identified to the species or intraspecies level and 68 testate amoebae, which could not be identified to the species level. The highest species diversity of testates was found in the soils of the tropical rainforest (126 species and intraspecific taxa, including spp.) and in tropical wetlands (144 species and intraspecific taxa, including spp.). The study documented testate amoebae with a limited geographical distribution (genera Centropyxis, Cornuapyxis, Ellipsopyxis, Hoogenraadia, Planhoogenraadia, Apolimia, Certesella, Apodera, and Alocodera). We found that testate amoebae in the soils of Mexico had a high level of polymorphism and individual variability. We discuss the value of soil testate amoebae for defining biogeographical regions of Mexico.

Crossing barriers in an extremely fragmented system: two case studies in the afro-alpine sky island flora

The flora on the afro-alpine sky islands is renowned for extreme fragmentation, representing a unique natural experiment in biogeography. Here we address the roles of isolation and gene flow, in particular across the narrow Rift Valley (the RV barrier) that cuts through the Ethiopian Highlands (EH), and across the vast low-lying landscape that separates EH from the East African mountains (the EH–EA barrier). We inferred the history of two species with different dispersal mechanisms, but with similar geographic ranges and habitats based on Amplified fragment length polymorphisms (AFLPs). Contrary to our predictions, we found that the populations from opposite sides of the RV barrier were less similar than those from opposite sides of the EH–EA barrier, and that only the supposedly short distance-dispersed species (Trifolium cryptopodium) showed a strong signal of secondary gene flow across the RV barrier. In the wind-dispersed Carduus schimperi, we rather found an evidence for the gene flow between differentiated populations inhabiting different EA mountains. Both species harbored little genetic diversity but considerable genetic rarity in several individual mountains, suggesting long-term isolation and bottlenecks during climatically unfavorable periods. Our genetic data corroborate a division of C. schimperi into three subspecies, but with new delimitation of their ranges, and of T. cryptopodium into two intraspecific taxa. Our findings support the idea that stochasticity may play a major role in shaping extremely fragmented ecosystems such as the afro-alpine. After initial colonization of different mountains, periods of isolation may alternate with unpredictable episodes of intermountain gene flow.