scholarly journals Analysis of the Opsin Repertoire in the Tardigrade Hypsibius dujardini Provides Insights into the Evolution of Opsin Genes in Panarthropoda

2014 ◽  
Vol 6 (9) ◽  
pp. 2380-2391 ◽  
Author(s):  
Lars Hering ◽  
Georg Mayer
Keyword(s):  
Opsin Genes ◽  
Hypsibius Dujardini

scholarly journals Evolution of regulatory networks associated with traits under selection in cichlids

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tarang K. Mehta ◽  
Christopher Koch ◽  
Will Nash ◽  
Sara A. Knaack ◽  
Padhmanand Sudhakar ◽  
...  
Keyword(s):  
Visual System ◽  
Regulatory Sequence ◽  
Potential Candidate ◽  
East African ◽  
Regulatory Regions ◽  
A Genome ◽  
Opsin Genes ◽  
East African Cichlids ◽  
Gene Regulatory ◽  
African Cichlids

Abstract Background Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. Results To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait—the visual system—for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. Conclusions Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.

An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)

Zootaxa ◽  
2018 ◽  
Vol 4415 (1) ◽  
pp. 45 ◽  
Author(s):  
PIOTR GĄSIOREK ◽  
DANIEL STEC ◽  
WITOLD MOREK ◽  
ŁUKASZ MICHALCZYK
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Model Organism ◽  
Laboratory Strain ◽  
Sensu Stricto ◽  
Nominal Species ◽  
28S Rrna ◽  
The Family ◽  
The 19Th Century ◽  
Hypsibius Dujardini

A laboratory strain identified as “Hypsibius dujardini” is one of the best studied tardigrade strains: it is widely used as a model organism in a variety of research projects, ranging from developmental and evolutionary biology through physiology and anatomy to astrobiology. Hypsibius dujardini, originally described from the Île-de-France by Doyère in the first half of the 19th century, is now the nominal species for the superfamily Hypsibioidea. The species was traditionally considered cosmopolitan despite the fact that insufficient, old and sometimes contradictory descriptions and records prevented adequate delineations of similar Hypsibius species. As a consequence, H. dujardini appeared to occur globally, from Norway to Samoa. In this paper, we provide the first integrated taxonomic redescription of H. dujardini. In addition to classic imaging by light microscopy and a comprehensive morphometric dataset, we present scanning electron photomicrographs, and DNA sequences for three nuclear markers (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial marker (COI) that are characterised by various mutation rates. The results of our study reveal that a commercially available strain that is maintained in many laboratories throughout the world, and assumed to represent H. dujardini sensu stricto, represents, in fact, a new species: H. exemplaris sp. nov. Redescribing the nominal taxon for Hypsibiidae, we also redefine the family and amend the definitions of the subfamily Hypsibiinae and the genus Hypsibius. Moreover, we transfer H. arcticus (Murray, 1907) and Hypsibius conifer Mihelčič, 1938 to the genus Ramazzottius since the species exhibit claws and eggs of the Ramazzottius type. Finally, we designate H. fuhrmanni as subjectively invalid because the extremely poor description precludes identifying neotype material. 

Soil tardigrades from the Antarctic Peninsula with a description of a new species and some remarks on the genusRamajendas(Eutardigrada: Isohypsibiidae)

Polar Record ◽  
2013 ◽  
Vol 50 (2) ◽  
pp. 176-182 ◽  
Author(s):  
Łukasz Kaczmarek ◽  
Karel Janko ◽  
Jerzy Smykla ◽  
Łukasz Michalczyk
Keyword(s):  
New Species ◽  
Antarctic Peninsula ◽  
Morphometric Characters ◽  
Antarctic Continent ◽  
Fourth Species ◽  
The Antarctic ◽  
A New Species ◽  
Mixed Samples ◽  
Hypsibius Dujardini

ABSTRACTIn thirteen (mostly soil) mixed samples, collected from nine localities on the Antarctic continent and some of the neighbouring islands, 788 specimens and 32 eggs of tardigrades were found. In total, five species were identified:Acutuncus antarcticus, Echiniscus jenningsi,Diphascon(D.)victoriae,Hypsibius dujardiniandRamajendas dastychisp. nov.A. antarcticuswas the most abundant (nearly 90% of all specimens) and was the prevailing taxon found in the majority of locations.R. dastychisp. nov. is the fourth species described in the exclusively Antarctic/sub-Antarctic genus. The new species differs from all other congeners by the presence of four gibbosities on the caudo-dorsal cuticle (configuration II:2–2) and also by some morphometric characters. In this paper we also briefly discuss the taxonomy and zoogeography of the genusRamajendas.

scholarly journals Variation in opsin genes correlates with signalling ecology in North American fireflies

2015 ◽  
Vol 24 (18) ◽  
pp. 4679-4696 ◽  
Author(s):  
S. E. Sander ◽  
D. W. Hall
Keyword(s):  
North American ◽  
Opsin Genes

scholarly journals Evidence from opsin genes rejects nocturnality in ancestral primates

2005 ◽  
Vol 102 (41) ◽  
pp. 14712-14716 ◽  
Author(s):  
Y. Tan ◽  
A. D. Yoder ◽  
N. Yamashita ◽  
W.-H. Li
Keyword(s):  
Opsin Genes

scholarly journals Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 168 ◽  
Author(s):  
Brahim Mali ◽  
Markus A Grohme ◽  
Frank Förster ◽  
Thomas Dandekar ◽  
Martina Schnölzer ◽  
...  
Keyword(s):  
Hypsibius Dujardini

scholarly journals Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

2020 ◽  
Author(s):  
Katherine M. Eaton ◽  
Moisés A. Bernal ◽  
Nathan J.C. Backenstose ◽  
Trevor J. Krabbenhoft
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Parallel Evolution ◽  
Amplicon Sequencing ◽  
Species Flock ◽  
Closely Related Species ◽  
Oxford Nanopore ◽  
Opsin Genes ◽  
Potential Case ◽  
Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

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