Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales.
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ABSTRACT:
SUBMITTER: da Silva SG
PROVIDER: S-EPMC4736946 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Indo-European is the largest and best-documented language family in the world, yet the reconstruction of the Indo-European tree, first proposed in 1863, has remained controversial. Complications may include ascertainment bias when choosing the linguistic data, and disregard for the wave model of 1872 when attempting to reconstruct the tree. Essentially analogous problems were solved in evolutionary genetics by DNA sequencing and phylogenetic network methods, respectively. We now adapt these tools to linguistics, and analyze Indo-European language data, focusing on Celtic and in particular on the ancient Celtic language of Gaul (modern France), by using bilingual Gaulish-Latin inscriptions. Our phylogenetic network reveals an early split of Celtic within Indo-European. Interestingly, the next branching event separates Gaulish (Continental Celtic) from the British (Insular Celtic) languages, with Insular Celtic subsequently splitting into Brythonic (Welsh, Breton) and Goidelic (Irish and Scottish Gaelic). Taken together, the network thus suggests that the Celtic language arrived in the British Isles as a single wave (and then differentiated locally), rather than in the traditional two-wave scenario ("P-Celtic" to Britain and "Q-Celtic" to Ireland). The phylogenetic network furthermore permits the estimation of time in analogy to genetics, and we obtain tentative dates for Indo-European at 8100 BC +/- 1,900 years, and for the arrival of Celtic in Britain at 3200 BC +/- 1,500 years. The phylogenetic method is easily executed by hand and promises to be an informative approach for many problems in historical linguistics.
| S-EPMC166441 | biostudies-literature
Project description:BackgroundLoaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated.ResultsIn this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus.ConclusionsThe current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.
| S-EPMC7809818 | biostudies-literature
Project description:Transferrin is a protein super-family involved in iron transport, a central process in cellular homeostasis. Throughout the evolution of vertebrates, transferrin members have diversified into distinct subfamilies including serotransferrin, ovotransferrin, lactoferrin, melanotransferrin, the inhibitor of carbonic anhydrase, pacifastin, and the major yolk protein in sea urchin. Previous phylogenetic analyses have established the branching order of the diverse transferrin subfamilies but were mostly focused on the transferrin repertoire present in mammals. Here, we conduct a comprehensive phylogenetic analysis of transferrin protein sequences in sequenced vertebrates, placing a special focus on the less-studied nonmammalian vertebrates. Our analyses uncover a novel transferrin clade present across fish, sauropsid, and amphibian genomes but strikingly absent from mammals. Our reconstructed scenario implies that this novel class emerged through a duplication event at the vertebrate ancestor, and that it was subsequently lost in the lineage leading to mammals. We detect footprints of accelerated evolution following the duplication event, which suggest positive selection and early functional divergence of this novel clade. Interestingly, the loss of this novel class of transferrin in mammals coincided with the divergence by duplication of lactoferrin and serotransferrin in this lineage. Altogether, our results provide novel insights on the evolution of iron-binding proteins in the various vertebrate groups.
| S-EPMC3603312 | biostudies-literature
Project description:The genus Cheiromycina is one of the few genera of lichenized hyphomycetes for which no sexual reproductive stages have been observed. The genus includes species from boreal to temperate regions of the Northern Hemisphere where it is found growing on bark or wood. Congeners in Cheiromycina are characterized by a noncorticate thallus, nearly immersed in the substrate and presenting powdery unpigmented sporodochia, and containing chlorococcoid photobionts. The relationships of members of Cheiromycina with other fungi are not known. Here we inferred the phylogenetic placement of Cheiromycina using three loci (nuSSU, nuLSU, and mtSSU) representing C. flabelliformis, the type species for the genus, C. petri, and C. reimeri. Our results revealed that the genus Cheiromycina is found within the family Malmideaceae (Lecanorales) where members formed a monophyletic clade sister to the genera Savoronala and Malmidea. This phylogenetic placement and the relationships of Cheiromycina with other lichenized hyphomycetous taxa are here discussed.
| S-EPMC5769673 | biostudies-literature
Project description:High-throughput analyses have frequently been used to characterize herbivory-induced reconfigurations in plant primary and secondary metabolism in above- and below-ground tissues, but the conclusions drawn from these analyses are often limited by the univariate methods used to analyze the data. Here we use our previously described multivariate time-series data analysis to evaluate leaf herbivory-elicited transcriptional and metabolic dynamics in the roots of Nicotiana attenuata. We observed large, but transient, systemic responses in the roots that contrasted with the pattern of co-linearity observed in the up- and downregulation of genes and metabolites across the entire time series in treated and systemic leaves. Using this newly developed approach for the analysis of whole-plant molecular responses in a time-course multivariate data set, we simultaneously analyzed stress responses in leaves and roots in response to the elicitation of a leaf. We found that transient systemic responses in roots resolved into two principal trends characterized by: (i) an inversion of root-specific semi-diurnal (12 h) transcript oscillations and (ii) transcriptional changes with major amplitude effects that translated into a distinct suite of root-specific secondary metabolites (e.g. alkaloids synthesized in the roots of N. attenuata). These findings underscore the importance of understanding tissue-specific stress responses in the correct day-night phase context and provide a holistic framework for the important role played by roots in above-ground stress responses.
| S-EPMC4190575 | biostudies-literature
Project description:BackgroundPinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.Methods and resultsWe sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68-111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.ConclusionsThe cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.
| S-EPMC9304046 | biostudies-literature
Project description:Pentatomoidea is the largest superfamily of Pentatomomorpha; however, the phylogenetic relationships among pentatomoid families have been debated for a long time. In the present study, we gathered the mitogenomes of 55 species from eight common families (Acanthosomatidae, Cydnidae, Dinidoridae, Scutelleridae, Tessaratomidae, Plataspidae, Urostylididae and Pentatomidae), including 20 newly sequenced mitogenomes, and conducted comparative mitogenomic studies with an emphasis on the structures of non-coding regions. Heterogeneity in the base composition, and contrasting evolutionary rates were encountered among the mitogenomes in Pentatomoidea, especially in Urostylididae, which may lead to unstable phylogenetic topologies. When the family Urostylididae is excluded in taxa sampling or the third codon positions of protein coding genes are removed, phylogenetic analyses under site-homogenous models could provide more stable tree topologies. However, the relationships between families remained the same in all PhyloBayes analyses under the site-heterogeneous mixture model CAT + GTR with different datasets and were recovered as (Cydnidae + (((Tessaratomidae + Dinidoridae) + (Plataspidae + Scutelleridae)) + ((Acanthosomatidae + Urostylididae) + Pentatomidae)))). Our study showed that data optimizing strategies after heterogeneity assessments based on denser sampling and the use of site-heterogeneous mixture models are essential for further analysis of the phylogenetic relationships of Pentatomoidea.
| S-EPMC8471585 | biostudies-literature
Project description:Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75?000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.
| S-EPMC3329107 | biostudies-other
Project description:BackgroundThere exist differences in morphological traits and phytochemical compositions between field- and mountain-cultivated Panax ginseng (FCG and MCG), which might be attributed to variations of terpenoids metabolism adapting to different growth conditions. The present work aims to uncover these variations.ResultsAmong 26,648 differentially expressed genes, 496 genes distributed in seven dominant terpenoids pathways were identified. Diterpenoids and triterpenoids biosynthesis genes were significantly higher-expressed in FCG root. Conversely, biosynthesis of carotenoids was significantly more active in MCG root. Additionally, terpenoids backbones, monoterpenoids, sesquiterpenoids, and terpenoid-quinones biosyntheses were neither obviously inclined. Our determination also revealed that there were more gibberellins and steroids accumulated in FCG root which might be responsible for its quick vegetative growth, and enriched abscisic acid and germacrenes as well as protopanaxatriol-type ginsenosides might be major causes of enhanced stress-resistance in MCG root.ConclusionsThe study firstly provided an overview of terpenoids metabolism in roots of FCG and MCG in elucidating the underlying mechanisms for their different morphological appearances and phytochemical compositions.
| S-EPMC6381674 | biostudies-literature
Project description:CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation.Here we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of the BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells.We discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells.
| S-EPMC4562119 | biostudies-literature