scholarly journals Mineralocorticoid Receptors: Evolutionary and Pathophysiological Considerations

Endocrinology ◽  
2011 ◽  
Vol 152 (5) ◽  
pp. 1883-1890 ◽  
Author(s):  
Karin S. Kassahn ◽  
Mark A. Ragan ◽  
John W. Funder
Keyword(s):  
Maximum Likelihood ◽  
Glucocorticoid Receptors ◽  
Retinoic Acid Receptor ◽  
Phylogenetic Analyses ◽  
Progesterone Receptors ◽  
Ancestral State ◽  
Mineralocorticoid Receptors ◽  
Ancestral Gene ◽  
Retinoic Acid Receptor Α ◽  
Nuclear Receptor Family

Mineralocorticoid receptors (MR), glucocorticoid receptors (GR), progesterone receptors (PR), and androgen receptors (AR) comprise a closely related subfamily within the human 49-member nuclear receptor family. These receptors and their cognate ligands play major roles in homeostasis, reproduction, growth, and development, despite which their evolution and diversification remains incompletely understood. Several conflicting models have been advanced for the evolution of this subfamily. We have thus undertaken Bayesian and maximum likelihood phylogenetic analyses of this subfamily. The Bayesian consensus and maximum likelihood trees support a basal position for MR, with the PR and AR forming a sister clade. We next performed analyses using topological constraints to directly contrast the likelihood of seven phylogenetic models. In these analyses, three models have similar support: one proposes two sister clades (MR and GR, PR and AR); the other two propose a different subfamily member (MR or GR) to be the first to have diverged. Ancestral state reconstructions at sites critical for physiological function show that the S810L mutation in the MR, which results in the MR being similar to estrogen receptors and the more distantly related retinoic acid receptor-α is likely to reflect the ancestral receptor sequence before the divergence of this subfamily and provides further support for MR having been the first of the subfamily to diverge. Finally, we drew on pathophysiological comparisons to help to distinguish the different models. On the basis of our phylogenetic analyses and pathophysiological considerations, we propose that the MR was the first to diverge from the ancestral gene lineage from which this subfamily derived.

scholarly journals Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Vol 285 (1893) ◽  
pp. 20181632 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Fossil Record ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record—specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus—may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

scholarly journals The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

2009 ◽  
Vol 58 (1) ◽  
pp. 130-145 ◽  
Author(s):  
Alan R. Lemmon ◽  
Jeremy M. Brown ◽  
Kathrin Stanger-Hall ◽  
Emily Moriarty Lemmon
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Time Estimation ◽  
Rate Variation ◽  
Clear Understanding ◽  
Ancestral State ◽  
Divergence Time Estimation ◽  
Branch Lengths ◽  
Ambiguous Data

Abstract Although an increasing number of phylogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes confounding factors, we provide the first clear understanding of 1 mechanism by which ambiguous data can mislead phylogenetic analyses. We find that in both ML and Bayesian frameworks, among-site rate variation can interact with ambiguous data to produce misleading estimates of topology and branch lengths. Furthermore, within a Bayesian framework, priors on branch lengths and rate heterogeneity parameters can exacerbate the effects of ambiguous data, resulting in strongly misleading bipartition posterior probabilities. The magnitude and direction of the ambiguous data bias are a function of the number and taxonomic distribution of ambiguous characters, the strength of topological support, and whether or not the model is correctly specified. The results of this study have major implications for all analyses that rely on accurate estimates of topology or branch lengths, including divergence time estimation, ancestral state reconstruction, tree-dependent comparative methods, rate variation analysis, phylogenetic hypothesis testing, and phylogeographic analysis.

scholarly journals Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Ancestral State ◽  
Trait Evolution ◽  
Natural Classification ◽  
Multiple Loci ◽  
The Family ◽  
Phylogenetic Perspective ◽  
Taxonomic Framework ◽  
First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

scholarly journals Respiratory syncytial virus B sequence analysis reveals a novel early genotype

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Juan C. Muñoz-Escalante ◽  
Andreu Comas-García ◽  
Sofía Bernal-Silva ◽  
Daniel E. Noyola
Keyword(s):  
Molecular Markers ◽  
Respiratory Syncytial Virus ◽  
Maximum Likelihood ◽  
Respiratory Infections ◽  
Phylogenetic Analyses ◽  
Detection Methods ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Individual Gene ◽  
Syncytial Virus

AbstractRespiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

Retinoic Acid Inhibits Nitric Oxide Synthase-2 Expression through the Retinoic Acid Receptor-α

2000 ◽  
Vol 270 (3) ◽  
pp. 846-851 ◽  
Author(s):  
Allan Sirsjö ◽  
Andreas C Gidlöf ◽  
Anneli Olsson ◽  
Hans Törmä ◽  
Mikko Ares ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Retinoic Acid ◽  
Nitric Oxide Synthase ◽  
Retinoic Acid Receptor ◽  
Acid Receptor ◽  
Retinoic Acid Receptor Α ◽  
Nitric Oxide Synthase 2 ◽  
Oxide Synthase

Progestin receptors in prolactin and growth hormone producing tumours in rats

1982 ◽  
Vol 100 (1) ◽  
pp. 25-30 ◽  
Author(s):  
Oddvar Naess ◽  
Egil Haug ◽  
Arne Attramadal ◽  
Kaare M. Gautvik
Keyword(s):  
Growth Hormone ◽  
Glucocorticoid Receptors ◽  
Progesterone Receptors ◽  
Pituitary Tumour ◽  
Tumour Cells ◽  
Female Rats ◽  
Progestin Receptors ◽  
High Affinity ◽  
Protein Nature ◽  
Specific Receptors

Abstract. Progesterone and corticosterone have a similar effect on the production of growth hormone (GH) and prolactin (Prl) by pituitary tumour cells (GH3 cells) in culture. Previously we have shown that progesterone has a high affinity for the glucocorticoid receptors in these cells. Progesterone may therefore exert its effects through binding to the glucocorticoid receptor. The aim of the present study was to investigate if the GH3 tumour cells and an oestrogen induced pituitary tumour, which also produce GH and Prl, possess specific receptors for progesterone. Both the GH3 tumours and the oestrogen induced pituitary tumour were in fact found to possess cytoplasmatic receptor molecules for progesterone by using the potent progestin R5020 as a marker. Isoelectric focusing revealed one binding component (pH 5.9), which was of protein nature. The binding was of high affinity (Kd 2 × 10−9 mol/l). In the oestrogen induced tumour, the maximal binding was 70 fmol/mg cytosol protein. In female rats with GH3 tumours the binding was 55 fmol/mg cytosol protein. Priming of the animals with 1 mg oestradiol-valerate increased the binding to 116 fmol/mg cytosol protein, whereas very little binding was found in GH3 tumours from rats castrated 7 days before sacrifice. The receptors in the oestrogen induced pituitary tumour and the GH3 tumours exhibited high affinity for R5020 and progesterone, whereas corticosterone had no significant affinity for the receptors. Using exchange assay, it was demonstrated that the cytoplasmic progestin receptors could be translocated to the nucleus after administration of progesterone to the animals. Thus, the presence of specific progesterone receptors, different from the glucocorticoid receptors, strongly indicates that the effects of progesterone on GH and Prl production are mediated through the progesterone receptors.

scholarly journals Evolutionary Analysis of Cystatins of Early-Emerging Metazoans Reveals a Novel Subtype in Parasitic Cnidarians

Biology ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 110
Author(s):  
Pavla Bartošová-Sojková ◽  
Jiří Kyslík ◽  
Gema Alama-Bermejo ◽  
Ashlie Hartigan ◽  
Stephen D. Atkinson ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Organization ◽  
Gene Repertoire ◽  
Evolutionary Analysis ◽  
Ancestral Gene ◽  
Protein Architecture ◽  
Basal Metazoan ◽  
Cystatin Gene ◽  
Evolutionary Aspects

The evolutionary aspects of cystatins are greatly underexplored in early-emerging metazoans. Thus, we surveyed the gene organization, protein architecture, and phylogeny of cystatin homologues mined from 110 genomes and the transcriptomes of 58 basal metazoan species, encompassing free-living and parasite taxa of Porifera, Placozoa, Cnidaria (including Myxozoa), and Ctenophora. We found that the cystatin gene repertoire significantly differs among phyla, with stefins present in most of the investigated lineages but with type 2 cystatins missing in several basal metazoan groups. Similar to liver and intestinal flukes, myxozoan parasites possess atypical stefins with chimeric structure that combine motifs of classical stefins and type 2 cystatins. Other early metazoan taxa regardless of lifestyle have only the classical representation of cystatins and lack multi-domain ones. Our comprehensive phylogenetic analyses revealed that stefins and type 2 cystatins clustered into taxonomically defined clades with multiple independent paralogous groups, which probably arose due to gene duplications. The stefin clade split between the subclades of classical stefins and the atypical stefins of myxozoans and flukes. Atypical stefins represent key evolutionary innovations of the two parasite groups for which their origin might have been linked with ancestral gene chimerization, obligate parasitism, life cycle complexity, genome reduction, and host immunity.

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