Bayesian inference phylogenetic tree based on Hsp90 protein sequences from Chordata.

<p>Species in which multiple <i>hsp90</i> genes have been detected are in dark blue. Filled diamonds denote putative species-specific duplication events, predicted by this study. Filled square denotes the duplication event resulting in the cognate and inducible isoforms of vertebrates. Numbers at nodes represent Posterior Probability (PP) values. Scale bar: substitutions/site.</p

Bayesian inference phylogenetic tree based on Hsp90 protein sequences from Mollusca.

<p>Species in which multiple <i>hsp90</i> genes have been detected are in dark blue. Filled diamonds denote putative species-specific duplication events, predicted by this study. Numbers at nodes represent Posterior Probability (PP) values. Scale bar: substitutions/site.</p

Bayesian inference phylogenetic tree based on Hsp90 protein sequences from Arthropoda.

<p>Species in which multiple <i>hsp90</i> genes have been detected are in dark blue. Filled diamonds denote putative species-specific duplication events predicted by this study. Filled squares denote duplication events in the common ancestor of a wide taxonomic group (e.g. Pleocyemata), predicted by this study. Filled circle shows the gain of type 2 isoform in Hymenoptera; empty-strikethrough circle shows loss of type 1 isoform in Formicidae. Numbers at nodes represent Posterior Probability (PP) values. Scale bar: substitutions/site.</p

Bayesian inference phylogenetic tree based on Hsp90 protein sequences from Fungi.

<p>Species in which multiple <i>hsp90</i> genes have been detected are in dark blue. Filled diamonds denote putative species-specific duplication events, predicted by this study. Stars represent whole-genome duplications reported by previous studies. Numbers at nodes represent Posterior Probability (PP) values. Scale bar: substitutions/site.</p

Assessment and Reconstruction of Novel HSP90 Genes: Duplications, Gains and Losses in Fungal and Animal Lineages

<div><p>Hsp90s, members of the Heat Shock Protein class, protect the structure and function of proteins and play a significant task in cellular homeostasis and signal transduction. In order to determine the number of <i>hsp90</i> gene copies and encoded proteins in fungal and animal lineages and through that key duplication events that this family has undergone, we collected and evaluated Hsp90 protein sequences and corresponding Expressed Sequence Tags and analyzed available genomes from various taxa. We provide evidence for duplication events affecting either single species or wider taxonomic groups. With regard to Fungi, duplicated genes have been detected in several lineages. In invertebrates, we demonstrate key duplication events in certain clades of Arthropoda and Mollusca, and a possible gene loss event in a hymenopteran family. Finally, we infer that the duplication event responsible for the two (a and b) isoforms in vertebrates occurred probably shortly after the split of Hyperoartia and Gnathostomata.</p></div

List of siluriform and outgroup species used in this study.

<p>List of siluriform and outgroup species used in this study.</p

A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes)

<div><p>A very significant part of the world’s freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of “Big Asia” and “Big Africa” are also recovered, albeit nodal support for the latter is poor. Within “Big Asia”, Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the “Out-of-South America” hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America’s freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.</p></div

Chronogram derived from the Bayesian relaxed-clock analysis using the 12–3–R—T partitioned dataset and calibrated with six fossil-based constraints following exponential distributions (see text for details).

<p>Horizontal timescale is in million years before present (Ma). Blue horizontal bars at nodes are 95% age credibility intervals. Boxed numbers 1–6 indicate the respective nodes calibrated using fossil constraints. Numbers at selected nodes indicate node ages in Ma.</p