phylogeny
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The phylogenetic relationships of the beetle superfamily Tenebrionoidea are investigated using the most comprehensive genetic data set compiled to date. With ∼34,000 described species in approximately 1250 genera and 28 families, Tenebrionoidea represent one of the most diverse and species-rich superfamilies of beetles. The interfamilial relationships of the Tenebrionoidea are poorly known; previous morphological and molecular phylogenies recovered few well-supported and often conflicting relationships between families. Here we present a molecular phylogeny of Tenebrionoidea based on genes commonly used to resolve family and superfamily-level phylogenies of beetles (18S, 28S, 16S, 12S, tRNA Val and COI). The alignment spanned over 6.5KB of DNA sequence and over 300 tenebrionoid genera from 24 of the 28 families were sampled. Maximum Likelihood and Bayesian analysis could not resolve deeper level divergences within the superfamily and very few relationships between families were supported. Increasing gene coverage in the alignment by removing taxa with missing data did not improve clade support but when rogue taxa were removed increased resolution was recovered. Investigation of signal strength suggested conflicting phylogenetic signal was present in the standard genes used for beetle phylogenetics, even when rogue taxa were removed. Our study of Tenebrionoidea highlights that even with relatively comprehensive taxon sampling within a lineage, this standard set of genes is unable to resolve relationships within this superfamily.
- MeSH
- Bayesova věta MeSH
- brouci klasifikace genetika MeSH
- fylogeneze * MeSH
- hmyzí geny MeSH
- pravděpodobnostní funkce MeSH
- sekvenční analýza DNA MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Elateriformia consists of Dascilloidea, Buprestoidea (jewel beetles), Byrrhoidea and Elateroidea (click beetles, fireflies and relatives). Numerous elateroid lineages contain taxa with modified metamorphosis resulting in sexual maturity while retaining larval characters. Additionally, they evolved unique defensive strategies including clicking mechanism, aposematic coloration and bioluminescence. To investigate the phylogenetic position of Elateroidea within Coleoptera, we merged 1048 newly produced 18S rRNA, 28S rRNA, rrnL mtDNA, and cox1 mtDNA sequences for ∼300 elateriform taxa with data from GenBank. The 975-taxa dataset aligned in BlastAlign was analyzed under maximum likelihood criterion. The results agreed in most aspects with the current morphology-based classification and results of molecular studies. Elateriformia were monophyletic and Elateroidea were sister to Byrrhoidea. Further, we analyzed all-data (513 elateriform taxa) and pruned matrix (417 elateriform taxa, all fragments present) using parsimony and maximum likelihood methods to reveal the phylogenetic relationships among elateroid lineages and examine the evolution of soft-bodiedness, neoteny and bioluminescence. We confirmed the monophyly of Elateroidea sensu lato and most of the families, with Telegeusidae inferred in most trees within paraphyletic Omethidae. The clade Artematopodidae+Telegeusidae+Omethidae was a sister to remaining elateroids. All topologies reject the relationships of hard-bodied Elateridae, Eucnemidae, Throscidae and Cerophytidae, formerly supposed to be a monophylum. Eucnemidae and Throscidae formed independent lineages and the position of Cerophytidae was variable - either a sister to Throscidae, or an independent lineage. The Lampyridae+Cantharidae clade was in most trees sister to Phengodidae+Rhagophthalmidae+Omalisidae+Elateridae. Molecular phylogeny of Elateroidea confirmed the multiple origins of soft-bodied, neotenic and light emiting lineages. On the basis of our molecular phylogeny, we place former Telegeusidae as a subfamily in Omethidae.
- MeSH
- brouci anatomie a histologie klasifikace genetika MeSH
- fylogeneze * MeSH
- geny rRNA genetika MeSH
- luminiscence MeSH
- mitochondriální DNA genetika MeSH
- nejistota MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The evolution of phenotypes is highly understudied in protists, due to the dearth of morphological characters, missing fossil record, and/or unresolved phylogeny in the majority of taxa. The chrysophyte genus Mallomonas (Stramenopiles) forms species-specific silica scales with extraordinary diversity of their ornamentation. In this paper, we molecularly characterized three additional species to provide an updated phylogeny of 43 species, and combined this with evaluations of 24 morphological traits. Using phylogenetic comparative methods, we evaluated phylogenetic signal in traits, reconstructed the trait evolution, and compared the overall phylogenetic and morphological diversity. The majority of traits showed strong phylogenetic signal and mostly dynamic evolution. Phylogenetic relatedness was often reflected by the phenotypic similarity. Both V-rib and dome are very conservative structures that are presumably involved in precise scale overlap and bristle attachment, respectively. Based on modern species, it seems the dome firstly appeared on apical and/or caudal scales, and only later emerged on body scales. Bristle was presumably present in the common ancestor and gradually elongated ever since. However, most other morphological traits readily changed during the evolution of Mallomonas.
The Echinostomatoidea is a large, cosmopolitan group of digeneans currently including nine families and 105 genera, the vast majority parasitic, as adults, in birds with relatively few taxa parasitising mammals, reptiles and, exceptionally, fish. Despite the complex structure, diverse content and substantial species richness of the group, almost no attempt has been made to elucidate its phylogenetic relationships at the suprageneric level based on molecules due to the lack of data. Herein, we evaluate the consistency of the present morphology-based classification system of the Echinostomatoidea with the phylogenetic relationships of its members based on partial sequences of the nuclear lsrRNA gene for a broad diversity of taxa (80 species, representing eight families and 40 genera), including representatives of five subfamilies of the Echinostomatidae, which currently exhibits the most complex taxonomic structure within the superfamily. This first comprehensive phylogeny for the Echinostomatoidea challenged the current systematic framework based on comparative morphology. A morphology-based evaluation of this new molecular framework resulted in a number of systematic and nomenclatural changes consistent with the phylogenetic estimates of the generic and suprageneric boundaries and a new phylogeny-based classification of the Echinostomatoidea. In the current systematic treatment: (i) the rank of two family level lineages, the former Himasthlinae and Echinochasminae, is elevated to full family status; (ii) Caballerotrema is distinguished at the family level; (iii) the content and diagnosis of the Echinostomatidae (sensu stricto) (s. str.) are revised to reflect its phylogeny, resulting in the abolition of the Nephrostominae and Chaunocephalinae as synonyms of the Echinostomatidae (s. str.); (iv) Artyfechinostomum, Cathaemasia, Rhopalias and Ribeiroia are re-allocated within the Echinostomatidae (s. str.), resulting in the abolition of the Cathaemasiidae, Rhopaliidae and Ribeiroiinae, which become synonyms of the Echinostomatidae (s. str.); and (v) refinements of the generic boundaries within the Echinostomatidae (s. str.), Psilostomidae and Fasciolidae are made.
- MeSH
- Echinostomatidae klasifikace genetika izolace a purifikace MeSH
- fylogeneze * MeSH
- infekce červy třídy Trematoda parazitologie veterinární MeSH
- lidé MeSH
- molekulární evoluce MeSH
- molekulární sekvence - údaje MeSH
- obratlovci klasifikace parazitologie MeSH
- plazi MeSH
- ptáci MeSH
- ryby MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
The molecular phylogeny of Flabellula Schaeffer, 1926 has been updated by analysing 18S rRNA and actin gene sequences of 19 new strains collected and characterised by the authors over the past ten years. The genus Flabellula Schaeffer, 1926 (Amoebozoa: Leptomyxida) is a taxon in which species delineation based on morphological data by themselves is insufficient or even misleading. The description of two novel species, F. schaefferi n. sp. and F. sawyeri n. sp., is justified by the congruence of morphological data with 18S rRNA and actin gene sequence phylogenies, in-silico secondary structure prediction of the V2 region in the 18S rRNA, and by recognition of species-specific sequential motifs within this region.
BACKGROUND: The classification of the Musaceae (banana) family species and their phylogenetic inter-relationships remain controversial, in part due to limited nucleotide information to complement the morphological and physiological characters. In this work the evolutionary relationships within the Musaceae family were studied using 13 species and DNA sequences obtained from a set of 19 unlinked nuclear genes. RESULTS: The 19 gene sequences represented a sample of ~16 kb of genome sequence (~73% intronic). The sequence data were also used to obtain estimates for the divergence times of the Musaceae genera and Musa sections. Nucleotide variation within the sample confirmed the close relationship of Australimusa and Callimusa sections and showed that Eumusa and Rhodochlamys sections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections. Divergence time analysis supported the previous dating of the Musaceae crown age to the Cretaceous/Tertiary boundary (~ 69 Mya), and the evolution of Musa to ~50 Mya. The first estimates for the divergence times of the four Musa sections were also obtained. CONCLUSIONS: The gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae. An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.
- MeSH
- fylogeneze MeSH
- lidé MeSH
- metabolismus fyziologie MeSH
- mikrocirkulace MeSH
- plicní oběh fyziologie patologie růst a vývoj MeSH
- srovnávací fyziologie MeSH
- výměna plynů v plicích fyziologie MeSH
- vývojová biologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- přehledy MeSH
- srovnávací studie MeSH
Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%-30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by-product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans-generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM.
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- Bacteria klasifikace MeSH
- feces mikrobiologie MeSH
- fylogeneze * MeSH
- Passeriformes klasifikace mikrobiologie MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- střevní mikroflóra genetika MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
Arthroderma is the most diverse genus among dermatophytes encompassing species occurring in soil, caves, animal burrows, clinical material and other environments. In this study, we collected ex-type, reference and authentic strains of all currently accepted Arthroderma species and generated sequences of three highly variable loci (ITS rDNA, β-tubulin, and translation elongation factor 1-α). The number of accepted species was expanded to 27. One novel species, A. melbournense (ex-type strain CCF 6162T = CBS 145858T), is described. This species was isolated from toenail dust collected by a podiatrist in Melbourne, during an epidemiological study of four geographical regions of Eastern Australia. Trichophyton terrestre, Chrysosporium magnisporum, and Chrysosporium oceanitis are transferred to Arthroderma. Typification is provided for T. terrestre that is not conspecific with any of the supposed biological species from the former T. terrestre complex, that is, A. insingulare, A. lenticulare and A. quadrifidum. A multi-gene phylogeny and reference sequences provided in this study should serve as a basis for future phylogenetic studies and facilitate species identification in practice.LAY ABSTRACT: The genus Arthroderma encompasses geophilic dermatophyte species that infrequently cause human and animal superficial infections. Reference sequences from three genetic loci were generated for all currently accepted Arthroderma species and phylogeny was constructed. Several taxonomic novelties are introduced. The newly provided data will facilitate species identification and future taxonomic studies.
- MeSH
- Arthrodermataceae klasifikace genetika MeSH
- DNA fungální genetika MeSH
- elongační faktor 1 genetika MeSH
- fylogeneze * MeSH
- geny hub genetika MeSH
- lidé MeSH
- mezerníky ribozomální DNA genetika MeSH
- Microsporum klasifikace genetika MeSH
- Trichophyton klasifikace genetika MeSH
- tubulin genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Austrálie MeSH
