High-Resolution, Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-modular Coupling

The provenance of the aminoacyl-tRNA synthetases (aaRS) poses challenging questions because of their role in the emergence and evolution of genetic coding. We investigate evidence about their ancestry from curated structure-based multiple sequence alignments of a structurally invariant “scaffold” shared by all 10 canonical Class I aaRS. Three uncorrelated phylogenetic metrics—residue-by-residue conservation, its variance, and row-by-row cladistic congruence—imply that the Class I scaffold is a mosaic assembled from distinct, successive genetic sources. These data are especially significant in light of: (i) experimental fragmentations of the Class I scaffold into three partitions that retain catalytic activities in proportion to their length; and (ii) evidence that two of these partitions arose from an ancestral Class I aaRS gene encoding a Class II ancestor in frame on the opposite strand. Phylogenetic metrics of different modules vary in accordance with their presumed functionality. A 46-residue Class I “protozyme” roots the Class I molecular tree prior to the adaptive radiation of the Rossmann dinucleotide binding fold that refined substrate discrimination. Such rooting is consistent with near simultaneous emergence of genetic coding and the origin of the proteome, resolving a conundrum posed by previous inferences that Class I aaRS evolved long after the genetic code had been implemented in an RNA world. Further, pinpointing discontinuous enhancements of aaRS fidelity establishes a timeline for the growth of coding from a binary amino acid alphabet.

Amphidinium stirisquamtum sp. nov. (Dinophyceae), a new marine sand-dwelling dinoflagellate with a novel type of body scale

Amphidinium species are amongst the most abundant benthic dinoflagellates in marine intertidal sandy ecosystems. Some of them produce a variety of bioactive compounds that have both harmful effects and pharmaceutical potential. In this study, Amphidinium cells were isolated from intertidal sand collected from the East China Sea. The two strains established were subjected to detailed examination by light, and scanning and transmission electron microscopy. The vegetative cells had a minute, irregular, and triangular-shaped epicone deflected to the left, thus fitting the description of Amphidinium sensu stricto. These strains are distinguished from other Amphidinium species by combination characteristics: (1) longitudinal flagellum inserted in the lower third of the cell; (2) icicle-shaped scales, 276 ± 17 nm in length, on the cell body surface; (3) asymmetrical hypocone with the left side longer than the right; and (4) presence of immotile cells. Therefore, they are described here as Amphidinium stirisquamtum sp. nov. The molecular tree inferred from small subunit rRNA, large subunit rRNA, and internal transcribed spacer-5.8S sequences revealed that A. stirisquamtum is grouped together with the type species of Amphidinium, A. operculatum, in a fully supported clade, but is distantly related to other Amphidinium species bearing body scale. Live A. stirisquamtum cells greatly affected the survival of rotifers and brine shrimp, their primary grazers, making them more susceptible to predation by the higher tropic level consumers in the food web. This will increase the risk of introducing toxicity, and consequently, the bioaccumulation of toxins through marine food webs.

On the Inverse Problem for Some Topological Indices

The study of the inverse problem (IP) based on the topological indices (TIs) deals with the numerical relations to TIs. Mathematically, the IP can be expressed as follows: given a graph parameter/TI that assigns a non-negative integer value g to every graph within a given family G of graphs, find some G ∈ G for which TI G = g . It was initiated by the Zefirov group in Moscow and later Gutman et al. proposed it. In this paper, we have established the IP only for the Y -index, Gourava indices, second hyper-Zagreb index, reformulated first Zagreb index, and reformulated F -index since they are closely related to each other. We have also studied the same which is true for the molecular, tree, unicyclic, and bicyclic graphs.

Evolution and phylogeny of the deep-sea isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 (Isopoda: Asellota)

In the deep sea, the phylogeny and biogeography of only a few taxa have been well studied. Although more than 200 species in 32 genera have been described for the asellote isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 from all ocean basins, their phylogenetic relationships are not completely understood. There is little doubt about the close relationship of these families, but the taxonomic position of a number of genera is so far unknown. Based on a combined morphological phylogeny using the Hennigian method with a dataset of 107 described species and a molecular phylogeny based on three markers (COI, 16S, and 18S) with 75 species (most new to science), we could separate Desmosomatidae and Nannoniscidae as separate families. However, we could not support the concept of the subfamilies Eugerdellatinae Hessler, 1970 and Desmosomatinae Hessler, 1970. Most genera of both families were well supported, but several genera appear as para- or even polyphyletic. Within both families, convergent evolution and analogies caused difficulty in defining apomorphies for phylogenetic reconstructions and this is reflected in the results of the concatenated molecular tree. There is no biogeographic pattern in the distribution as the genera occur over the entire Atlantic and Pacific Ocean, showing no specific phylogeographical pattern. Poor resolution at deep desmosomatid nodes may reflect the long evolutionary history of the family and rapid evolutionary radiations.

Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy

Contemporary delimitation of species and populations in the microbial domain relies on an integrative approach combining molecular and morphological techniques. In case of the dinophyte Peridinium volzii, a considerable number of infraspecific taxonomic entities have been reported, but it is unclear at present whether the corresponding traits are stable within reproductively isolated units or refer to intraspecific variability. We established 26 monoclonal strains from Central Europe with a morphology that is consistent for P. volzii and characterised them by sequences gained from the rRNA operon. Ten of such strains, representative for the entire diversity observed, were investigated in detail morphologically using light and electron microscopy. In the molecular tree, P. volzii was monophyletic, sister group of Peridinium willei, and three ITS ribotypes could be distinguished. Some traits corresponding to previously described varieties and forms were found in individual cells across the strains under investigation, but not as stable characters correlating to certain ribotypes. We also observed new morphological variability (e.g., unusual shape of plate 4″). Cell size and displacement of the cingulum were significantly different between certain ribotypes but in turn, such diagnostic traits are impossible to assign to already described taxa due to their ambiguity. Based on the small first apical plate as diagnostic trait and putative apomorphy, P. volzii is a characteristic species but the present data given, we are reserved to accept more than a single reproductive unit. Thus, more research is necessary, including a focus on species delimitation to putative close relatives such as Peridinium maeandricum.

Habrosia (Caryophyllaceae) a monotypic genus endemic to Western Asia

Habrosia (Sagineae, Caryophyllaceae) is a genus that includes only H. spinuliflora, a species occurring in Iran, Iraq, Syria, Lebanon, and Turkey (Irano-Turanian floristic chorological element). Based on the available molecular data published in 2011, Habrosia appears to be nested in a Minuartia-clade, which includes taxa currently recognized under the genus Sabulina. Consequently, Habrosia should be treated as a genus to be included in Sabulina. However, the molecular tree published in 2011 considered only 9 Sabulina members whereas, according to the current concept, Sabulina is a genus comprising about 65 species. Unfortunately, the molecular phylogeny including a larger Sabulina sample published in 2014 did not include H. spinuliflora and the taxonomic position of Habrosia remains, therefore, uncertain. With the aim of verifying the correct position of Habrosia in the tribe Sagineae with respect to its relationship to Sabulina, a comprehensive molecular investigation based on ITS sequences, linked to detailed morphological data, is presented. The results obtained revealed that Habrosia is not part of Sabulina. A detailed description of H. spinuliflora, its ecological preference, and a distribution map are provided. Eventually, the name Arenaria spinulifolia (basionym of H. spinuliflora) is lectotypified on a specimen preserved at G (barcode G00212963).

Behaviour of cranes (family Gruidae) mirrors their phylogenetic relationships

Background The behavioural repertoire of every species evolved over time and its evolution can be traced through the phylogenetic relationships in distinct groups. Cranes (family Gruidae) represent a small, old, monophyletic group with well-corroborated phylogenetic relationships on the species level, and at the same time they exhibit a complex and well-described behavioural repertoire. Methods We therefore investigated the evolution of behavioural traits of cranes in a phylogenetic context using several phylogenetic approaches and two types of trait scoring. The cranes exhibit more than a hundred behavioural displays, almost one third of which may be phylogenetically informative. Results More than half of the analysed traits carry a significant phylogenetic signal. The ancestor of cranes already exhibited a quite complex behavioural repertoire, which remained unchanged in Balearicinae but altered greatly in Gruinae, specifically by the shedding of traits rather than their creation. Trait scoring has an influence on results within the Gruinae, primarily in genera Bugeranus and Anthropoides. Conclusions Albeit the behavioural traits alone cannot be used for resolving species-level relationships within the Gruidae, when optimized on molecular tree, they can help us to detect interesting evolutionary transformations of behaviour repertoire within Gruiformes. The Limpkin (Aramus guarauna) seems to be the most enigmatic species and should be studied in detail for its behavioural repertoire, which may include some precursors of crane behavioural traits.

Mapping the Molecular Tree of Life using Assembly Spaces

<p><b>The mapping of chemical space by the enumeration of graphs generates an infinite number of molecules, yet the experimental exploration of known chemical space shows that it appears to become sparser as the molecular weight of the compounds increases. What is needed is a way to explore chemical space that exploits the information encoded in known molecules to give access to unknown chemical space by building on the common conserved structures found in related families of molecules. Molecular assembly theory provides an approach to explore and compare the intrinsic complexity of molecules by the minimum number of steps needed to build up the target graphs, and here we show this can be applied to networks of molecules to explore the assembly properties of common motifs, rather than just focusing on molecules in isolation. This means molecular assembly theory can be used to define a tree of assembly spaces, allowing us to explore the accessible molecules connected to the tree, rather than the entire space of possible molecules. This approach provides a way to map the relationship between the molecules and their common fragments and thus measures the distribution of structural information collectively embedded in the molecules. We apply this approach to prebiotic chemistry, specifically the construction of RNA, and a family of opiates and plasticizers, as well as to gene sequences. This analysis allows us to quantify the amount of external information needed to assemble the tree and identify and predict new components in this family of molecules, based on the contingent information in the assembly spaces.</b></p>

Mapping the Molecular Tree of Life using Assembly Spaces

<p><b>The mapping of chemical space by the enumeration of graphs generates an infinite number of molecules, yet the experimental exploration of known chemical space shows that it appears to become sparser as the molecular weight of the compounds increases. What is needed is a way to explore chemical space that exploits the information encoded in known molecules to give access to unknown chemical space by building on the common conserved structures found in related families of molecules. Molecular assembly theory provides an approach to explore and compare the intrinsic complexity of molecules by the minimum number of steps needed to build up the target graphs, and here we show this can be applied to networks of molecules to explore the assembly properties of common motifs, rather than just focusing on molecules in isolation. This means molecular assembly theory can be used to define a tree of assembly spaces, allowing us to explore the accessible molecules connected to the tree, rather than the entire space of possible molecules. This approach provides a way to map the relationship between the molecules and their common fragments and thus measures the distribution of structural information collectively embedded in the molecules. We apply this approach to prebiotic chemistry, specifically the construction of RNA, and a family of opiates and plasticizers, as well as to gene sequences. This analysis allows us to quantify the amount of external information needed to assemble the tree and identify and predict new components in this family of molecules, based on the contingent information in the assembly spaces.</b></p>

Phylogeny of Libellulidae (Odonata: Anisoptera): comparison of molecular and morphology-based phylogenies based on wing morphology and migration

Background Establishing the species limits and resolving phylogenetic relationships are primary goals of taxonomists and evolutionary biologists. At present, a controversial question is about interspecific phylogenetic information in morphological features. Are the interspecific relationships established based on genetic information consistent with the traditional classification system? To address these problems, this study analyzed the wing shape structure of 10 species of Libellulidae, explored the relationship between wing shape and dragonfly behavior and living habits, and established an interspecific morphological relationship tree based on wing shape data. By analyzing the sequences of mitochondrial COI gene and the nuclear genes 18S, 28S rRNA and ITS in 10 species of dragonflies, the interspecific relationship was established. Method The wing shape information of the male forewings and hindwings was obtained by the geometric morphometrics method. The inter-species wing shape relationship was obtained by principal component analysis (PCA) in MorphoJ1.06 software. The inter-species wing shape relationship tree was obtained by cluster analysis (UPGMA) using Mesquite 3.2 software. The COI, 18S, ITS and 28S genes of 10 species dragonfly were blasted and processed by BioEdit v6 software. The Maximum Likelihood(ML) tree was established by raxmlGUI1.5b2 software. The Bayes inference (BI) tree was established by MrBayes 3.2.6 in Geneious software. Results The main difference in forewings among the 10 species of dragonfly was the apical, radial and discoidal regions dominated by the wing nodus. In contrast, the main difference among the hindwings was the apical and anal regions dominated by the wing nodus. The change in wing shape was closely related to the ability of dragonfly to migrate. The interspecific relationship based on molecular data showed that the species of Orthetrum genus branched independently of the other species. Compared to the molecular tree of 10 species, the wing shape clustering showed some phylogenetic information on the forewing shape (with large differences on the forewing shape tree vs. molecular tree), and there was no interspecific phylogenetic information of the hindwing shape tree vs. molecular tree. Conclusion The dragonfly wing shape characteristics are closely related to its migration ability. Species with strong ability to migrate have the forewing shape that is longer and narrower, and have larger anal region, whereas the species that prefer short-distance hovering or standing still for a long time have forewing that are wider and shorter, and the anal region is smaller. Integrating morphological and molecular data to evaluate the relationship among dragonfly species shows there is some interspecific phylogenetic information in the forewing shape and none in the hindwing shape. The forewing and hindwing of dragonflies exhibit an inconsistent pattern of morphological changes in different species.