Polymorphism of MHC class IIB in an acheilognathid species, Rhodeus sinensis shaped by historical selection and recombination

Abstract Background Rhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Here, we analyzed the diversity of the MHC class IIB (DAB) genes from this species, which may offer meaningful insights into evolutionary processes in this species as well as other bitterlings. Results Using cDNA and gDNA samples from 50 individuals, we discovered classical 140 allelic sequences that could be allocated into either DAB1 (Rhsi-DAB1) or DAB3 (Rhsi-DAB3). DAB sequences completely lacking the intron, but identical or similar to Rhsi-DAB1, were also discovered from our gDNA samples, and this intron loss likely originated from the retrotransposition events of processed mDNA. The β1 domain was the most polymorphic in both Rhsi-DAB1 and -DAB3. Putative peptide biding residues (PBRs) in Rhsi-DAB1, but not in Rhsi-DAB3, exhibited a significant dN/dS, presumably indicating that different selection pressures have acted on those two DABs. Recombination between different alleles seemed to have contributed to the increase of diversity in Rhsi-DABs. Upon phylogenetic analysis, Rhsi-DAB1 and -DAB3 formed independent clusters. Several alleles from other species of Cypriniformes were embedded in the clade of Rhsi-DAB1, whereas Rhsi-DAB3 clustered with alleles from the wider range of taxa (Cyprinodontiformes), indicating that these two Rhsi-DABs have taken different historical paths. Conclusions A great deal of MHC class IIB allelic diversity was found in R. sinensis, and gene duplication, selection and recombination may have contributed to this diversity. Based on our data, it is presumed that such historical processes have commonly or differently acted on the polymorphism of Rhsi-DAB1 and -DAB3.

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MHC genes and oxidative stress in sticklebacks: an immuno-ecological approach

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2005.3450 ◽

2006 ◽

Vol 273 (1592) ◽

pp. 1407-1414 ◽

Cited By ~ 55

Author(s):

Joachim Kurtz ◽

K. Mathias Wegner ◽

Martin Kalbe ◽

Thorsten B.H Reusch ◽

Helmut Schaschl ◽

...

Keyword(s):

Oxidative Stress ◽

Susceptibility To Infection ◽

Mhc Genes ◽

Histocompatibility Complex ◽

Individual Host ◽

Experimental Approaches ◽

Mhc Class Iib ◽

Class Iib ◽

First Time ◽

And Oxidative Stress

Individual variation in the susceptibility to infection may result from the varying ability of hosts to specifically recognize different parasite strains. Alternatively, there could be individual host differences in fitness costs of immune defence. Although, these two explanations are not mutually exclusive, they have so far been treated in separate experimental approaches. To analyse potential relationships, we studied body condition and oxidative stress, which may reflect costs of immunity, in three-spined sticklebacks that had been experimentally exposed to three species of naturally occurring parasite. These sticklebacks differed in a trait, which is crucial to specific parasite defence, i.e. individual genetic diversity at major histocompatibility complex (MHC) class IIB loci. Oxidative stress was quantified as tissue acrolein, a technique that has been applied to questions of immuno-ecology for the first time. We measured gene expression at the MHC and other estimates of immune activation. We found that fish with high levels of MHC expression had poor condition and elevated oxidative stress. These results indicate that MHC-based specific immunity is connected with oxidative stress. They could, thus, also be relevant in the broader context of the evolution of sexually selected signals that are based on carotenoids and are, thus supposed to reflect oxidative stress resistance.

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Phylogenetic Analysis and Selection Pressures of 5-HT Receptors in Human and Non-human Primates: Receptor of an Ancient Neurotransmitter

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2010.10508573 ◽

2010 ◽

Vol 27 (5) ◽

pp. 581-598 ◽

Cited By ~ 17

Author(s):

Padmanabhan Anbazhagan ◽

Meera Purushottam ◽

H. B. Kiran Kumar ◽

Odity Mukherjee ◽

Sanjeev Jain ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Selection Pressures

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Phylogenetic analysis reveals an ancient gene duplication as the origin of the MdtABC efflux pump

PLoS ONE ◽

10.1371/journal.pone.0228877 ◽

2020 ◽

Vol 15 (2) ◽

pp. e0228877 ◽

Cited By ~ 2

Author(s):

Kamil Górecki ◽

Megan M. McEvoy

Keyword(s):

Phylogenetic Analysis ◽

Gene Duplication ◽

Efflux Pump ◽

Ancient Gene ◽

Ancient Gene Duplication

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The Development of Thanatology in Japan and its Position in East Asia, with a Focus on Thanatology’s Relationship to Religion

Numen ◽

10.1163/15685276-12341535 ◽

2019 ◽

Vol 66 (2-3) ◽

pp. 114-138

Author(s):

Masaru Ikezawa

Keyword(s):

East Asia ◽

Religious Beliefs ◽

Religious Orientation ◽

Essential Element ◽

Religious Studies ◽

Academic Field ◽

Religious Traditions ◽

Japanese Case ◽

Historical Processes ◽

Private Beliefs

AbstractThis article deals with the religiosity of thanatology in Japan, which was introduced under the name shiseigaku (death and life studies) in the 1980s. Although many religious believers and scholars of religious studies have been connected with this field in Japan, religions are not necessarily highlighted by studies of Japanese thanatology. The Japanese pioneers of thanatology did not have clear ideas on the positioning of religion in this field, but they unconsciously merged their own faith into their discipline. Later, other scholars tried to re-construct this field by weakening its religious orientation. The Japanese case is in contrast to Taiwanese thanatology, in which the pioneers tried to position religious beliefs as the essential element of the field. Indeed, this difference was partially influenced by the religious traditions of both societies, but other factors such as the historical processes of this academic field and the private beliefs of researchers were important causes of that difference.

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SSCP analysis of Mhc class IIB genes in the threespine stickleback

Journal of Fish Biology ◽

10.1111/j.1095-8649.2001.tb00540.x ◽

2001 ◽

Vol 58 (3) ◽

pp. 887-890 ◽

Cited By ~ 5

Author(s):

T. Binz ◽

T. B. H. Reusch ◽

C. Wedekind ◽

M. Milinski

Keyword(s):

Threespine Stickleback ◽

Sscp Analysis ◽

Mhc Class Iib ◽

Class Iib

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Ancient Genome Duplications Did Not Structure the Human Hox-Bearing Chromosomes

Genome Research ◽

10.1101/gr.160001 ◽

2001 ◽

Vol 11 (5) ◽

pp. 771-780 ◽

Cited By ~ 2

Author(s):

Austin L. Hughes ◽

Jack da Silva ◽

Robert Friedman

Keyword(s):

Phylogenetic Analysis ◽

Gene Duplication ◽

Genome Duplication ◽

Gene Families ◽

Gene Duplications ◽

Human Chromosomes ◽

Time Period ◽

Genome Duplications

The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the fourHox-bearing chromosomes (the chromosomes bearing theHox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the humanHox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hoxclusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.

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A new Indo-Malayan family of Grassatores (Arachnida : Opiliones : Laniatores)

Invertebrate Systematics ◽

10.1071/is19035 ◽

2019 ◽

Vol 33 (6) ◽

pp. 892

Author(s):

Adriano B. Kury ◽

Abel Pérez-González ◽

Daniel N. Proud

Keyword(s):

Phylogenetic Analysis ◽

East Asia ◽

Male Genitalia ◽

Broad Context ◽

External Morphology ◽

Molecular Phylogenetic Analysis ◽

South East Asia ◽

New Family ◽

The Family ◽

Molecular Phylogenetic

The laniatorean family Phalangodidae has been largely reduced to a core of Holarctic species; however, many taxa were never formally transferred to other families. We examined a group of harvestmen related to Beloniscus Thorell, 1891, from South-east Asia and determined the nature of the relationships of the ‘Beloniscus-like harvestmen’, herein described as the new family Beloniscidae, fam. nov., in the broad context of Laniatores. Based on a molecular phylogenetic analysis of a broad representative laniatorean Sanger-sequences dataset we found support for our taxonomic hypotheses that (1) inclusion of Beloniscidae, fam. nov. in Phalangodidae would render the family non-monophyletic, and (2) Beloniscidae, fam. nov. represents a lineage that is morphologically and genetically distinct from all other known laniatorean families. The new family Beloniscidae is endemic to South-east Asia and comprises 37 species in two new subfamilies: Beloniscinae, subfam. nov. and Buparinae, subfam. nov. Beloniscinae includes the genera Beloniscellus Roewer, 1931, Beloniscops Roewer, 1949, Belonisculus Roewer, 1923, Beloniscus (type genus) and Kendengus Roewer, 1949. Buparinae includes the genera Buparellus Roewer, 1949, Bupares Thorell, 1889 (type genus) and Buparomma Roewer, 1949. Members of Beloniscidae are relatively homogeneous in their external morphology, but are recognised by well marked genitalic features. Male genitalia are described for exemplar species, and the morphology is compared with that of Epedanidae. Names are given to two new genitalic structures: sella curulis and pseudocalyx. http://zoobank.org/urn:lsid:zoobank.org:act:540BCE49-6F2E-4372-BFD4-D3C6068F045D http://zoobank.org/urn:lsid:zoobank.org:act:FE8B011B-AA6D-4E6C-A321-123542A0563F http://zoobank.org/urn:lsid:zoobank.org:act:E4A559CD-170A-40F2-924A-541C22974344

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