scholarly journals Allelic Lineages of the Ficolin Genes (FCNs) Are Passed from Ancestral to Descendant Primates

PLoS ONE ◽  
2011 ◽  
Vol 6 (12) ◽  
pp. e28187 ◽  
Author(s):  
Tina Hummelshøj ◽  
Janna Nissen ◽  
Lea Munthe-Fog ◽  
Claus Koch ◽  
Mads Frost Bertelsen ◽  
...  
Keyword(s):  
Allelic Lineages

scholarly journals The protected phosphoglucomutase polymorphism of the Pompeii worm Alvinella pompejana and its variant adaptability is only governed by two QE mutations at linked sites

2019 ◽  
Author(s):  
Bioy Alexis ◽  
Le Port Anne-Sophie ◽  
Sabourin Emeline ◽  
Verheye Marie ◽  
Piccino Patrice ◽  
...  
Keyword(s):  
Amino Acid ◽  
Hydrothermal Vents ◽  
Allozyme Variation ◽  
Biochemical Properties ◽  
Enzyme Polymorphism ◽  
Thermal Habitat ◽  
Balanced Polymorphism ◽  
Allelic Lineages ◽  
Alvinella Pompejana

AbstractThe polychaete Alvinella pompejana lives exclusively on the walls of deep-sea hydrothermal vents along the East Pacific Rise. This environment is considered as extreme and highly variable and the worm displays specific adaptations to withstand high temperature and hypoxia. Previous studies revealed the existence of a balanced polymorphism on the enzyme phosphoglucomutase associated with differences in the thermal habitat of the worm. Allozymes 90 and 100 exhibited different optimal enzyme activities and thermostabilities. The exploration of the mutational landscape for allozyme variation of the phosphoglucomutase1 revealed the maintenance of four highly divergent allelic lineages that encode the three most frequent electromorphs, these alleles occurring at different frequencies in populations over the worm’s geographic range. Enzyme polymorphism is only governed by two linked amino-acid replacements located in exon 3 (E155Q and E190Q). Unlike other studies dealing with the non-synonymous variations of the Pgm genes, these substitutions are not linked to other cryptic amino-acid polymorphisms. Overdominance under specific environmental ‘hot’ conditions should represent the most likely way for the long-term persistence of these isoforms. Using directed mutagenesis, overexpression of the three recombinant variants allowed us to test the additive effect of these two mutations on the biochemical properties of this enzyme. Results are coherent with those previously obtained from native proteins and reveal a thermodynamic trade-off between the protein thermostability and catalysis, which is likely to explain the long-term selection of these functional phenotypes before their geographic separation across the Equator with the emergence of a barrier to dispersal, about 1.2 Mya.

scholarly journals Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci.

Genetics ◽  
1993 ◽  
Vol 133 (3) ◽  
pp. 669-680 ◽  
Author(s):  
A L Hughes ◽  
M K Hughes ◽  
D I Watkins
Keyword(s):  
Dna Sequences ◽  
Balancing Selection ◽  
Amino Acid Level ◽  
Allelic Diversity ◽  
Class I ◽  
Striking Difference ◽  
Small Scale ◽  
Class I Mhc ◽  
B Locus ◽  
Allelic Lineages

Abstract A statistical study of DNA sequences of alleles at the highly polymorphic class I MHC loci of humans, HLA-A and HLA-B, showed evidence of both large-scale recombination events (involving recombination of exons 1-2 of one allele with exons 3-8 of another) and small-scale recombination events (involving apparent exchange of short DNA segments). The latter events occurred disproportionately in the region of the gene encoding the antigen recognition site (ARS) of the class I molecule. Furthermore, they involved the ARS codons which are under the strongest selection favoring allelic diversity at the amino acid level. Thus, the frequency of recombinant alleles appears to have been increased by some form of balancing selection (such as overdominant selection) favoring heterozygosity in the ARS. These analyses also revealed a striking difference between the A and B loci. Recombination events appear to have occurred about twice as frequently at the B locus, and recombinants at the B locus were significantly more likely to affect polymorphic sites in the ARS. At the A locus, there are well-defined allelic lineages that have persisted since prior to the human-chimpanzee divergence; but at the B locus, there is no evidence for such long-lasting allelic lineages. Thus, relatively frequent interallelic recombination has apparently been a feature of the long-term evolution of the B locus but not of the A locus.

scholarly journals Extensive, Recent Intron Gains in Daphnia Populations

Science ◽  
2009 ◽  
Vol 326 (5957) ◽  
pp. 1260-1262 ◽  
Author(s):  
Wenli Li ◽  
Abraham E. Tucker ◽  
Way Sung ◽  
W. Kelley Thomas ◽  
Michael Lynch
Keyword(s):  
Daphnia Pulex ◽  
Double Strand Breaks ◽  
Intron Gain ◽  
Strand Breaks ◽  
Strong Force ◽  
Allelic Lineages ◽  
Allele Frequency Spectrum ◽  
Population Genomic ◽  
Genomic Approach ◽  
Conserved Genes

Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a population-genomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.

Evolution of a triplet repeat in a conifer

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 417-426 ◽  
Author(s):  
Kerry A Sokol ◽  
Claire G Williams
Keyword(s):  
North American ◽  
New World ◽  
Repeat Expansion ◽  
Triplet Repeat ◽  
Seed Plant ◽  
Allelic Lineages ◽  
Repeat Units ◽  
Microsatellite Evolution ◽  
Vicariance Event ◽  
Shared Alleles

The opportunity to trace the evolution of a triplet repeat is rare, especially for seed-plant lineages with a well-defined fossil record. Microsatellite PtTX2133 sequences from 18 species in 2 conifer genera were used to calibrate the birth of a CAGn repeat, from its protomicrosatellite origins to its repeat expansion. Birth occurred in the hard-pine genome ~ 136 million years ago, or 14 million generations ago, then expanded as a polymorphic triplet repeat 136-100 million years before a major North American vicariance event. Calibration of the triplet-repeat birth and expansion is supported by the shared allelic lineages among Old and New World hard pines and the shared alleles solely among North American diploxylon or hard pines. Five CAGn repeat units appeared to be the expansion threshold for Old and New World diploxylon pines. Haploxylon pine species worldwide did not undergo birth and repeat expansion, remaining monomorphic, with a single imperfect 198-bp allele. A sister genus, Picea, had only a region of cryptic simplicity, preceding a proto-microsatellite region. The polymorphic triplet repeat in hard pines is older than some long-lived microsatellites reported for reptiles, yet younger than those reported for insects. Some cautionary points are raised about phylogenetic applications for this long-lived microsatellite.Key words: gymnosperms, microsatellite evolution, cladogenesis, phylogenetic analysis.

MHC polymorphism and parasites

1994 ◽  
Vol 346 (1317) ◽  
pp. 351-358 ◽  
Keyword(s):  
Human Leucocyte Antigen ◽  
Genetic Distances ◽  
Major Influence ◽  
Entire Body ◽  
Sequence Motifs ◽  
Short Sequence ◽  
Allelic Lineages ◽  
Body Of Knowledge ◽  
Histocompatibility Complex ◽  
Mhc Polymorphism

The major histocompatibility complex (MHC) polymorphism is marked by the existence of allelic lineages that are extremely old, having been passed from one species to another in an evolutionary line of descent. Each species has several of these lineages and many of their more recent derivatives, the actual alleles. The lineages are separated by large genetic distances and are characterized by the presence of short sequence motifs which, at the protein level, have remained virtually unaltered for over 40 million years. Several explanations for the mhc polymorphism have been proposed. We argue that the only one consistent with the entire body of knowledge about the MHC is an explanation based on the immune response to parasites. Furthermore, we propose that parasites coevolving with their hosts have had a major influence on MHC polymorphism, whereas parasites that switched hosts recently and became very virulent have had little effect. The latter category includes micro- and macroparasites responsible for the major human infectious diseases. This hypothesis explains why no convincing association between human leucocyte antigen ( HLA ) alleles and resistance to infectious disease can thus far be documented, and indicates the direction in which the search for such associations should be taken.

scholarly journals Individual copy number variation and extensive diversity between major MHC-DAB1 allelic lineages in the European bitterling

2022 ◽  
Author(s):  
Lorenzo Talarico ◽  
Anna Bryjová ◽  
Dagmar Čížková ◽  
Karel Douda ◽  
Martin Reichard
Keyword(s):  
Balancing Selection ◽  
Amplicon Sequencing ◽  
Synonymous Mutations ◽  
Allelic Lineages ◽  
Histocompatibility Complex ◽  
Number Variation ◽  
Long Time ◽  
Host Parasite ◽  
First Time

AbstractPolymorphism of the major histocompatibility complex (MHC), DAB1 gene was characterized for the first time in the European bitterling (Rhodeus amarus), a freshwater fish employed in studies of host-parasite coevolution and mate choice, taking advantage of newly designed primers coupled with high-throughput amplicon sequencing. Across 221 genotyped individuals, we detected 1–4 variants per fish, with 28% individuals possessing 3–4 variants. We identified 36 DAB1 variants, and they showed high sequence diversity mostly located within predicted antigen-binding sites, and both global and codon-specific excess of non-synonymous mutations. Despite deep divergence between two major allelic lineages, functional diversity was surprisingly low (3 supertypes). Overall, these findings suggest the role of positive and balancing selection in promotion and long-time maintenance of DAB1 polymorphism. Further investigations will clarify the role of pathogen-mediated selection to drive the evolution of DAB1 variation.

scholarly journals Two highly divergent ancient allelic lineages of the transporter associated with antigen processing(TAP) gene inXenopus: further evidence for co-evolution among MHC class I region genes

2003 ◽  
Vol 33 (11) ◽  
pp. 3017-3027 ◽  
Author(s):  
Yuko Ohta ◽  
Simon J. Powis ◽  
Rebecca L. Lohr ◽  
Masaru Nonaka ◽  
Louis Du Pasquier ◽  
...  
Keyword(s):  
Mhc Class I ◽  
Antigen Processing ◽  
Class I ◽  
Allelic Lineages ◽  
Class I Region

scholarly journals Persistence of Mhc Heterozygosity in Homozygous Clonal Killifish, Rivulus marmoratus: Implications for the Origin of Hermaphroditism

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1791-1803
Author(s):  
Akie Sato ◽  
Yoko Satta ◽  
Felipe Figueroa ◽  
Werner E Mayer ◽  
Zofia Zaleska-Rutczynska ◽  
...  
Keyword(s):  
Genetic Distances ◽  
Gene Duplications ◽  
Neotropical Fish ◽  
The Bahamas ◽  
Rivulus Marmoratus ◽  
Allelic Lineages ◽  
Histocompatibility Complex ◽  
Different Populations ◽  
Shed Light ◽  
Mhc Alleles

Abstract The mangrove killifish Rivulus marmoratus, a neotropical fish in the order Cyprinodontiformes, is the only known obligatorily selfing, synchronous hermaphroditic vertebrate. To shed light on its population structure and the origin of hermaphroditism, major histocompatibility complex (Mhc) class I genes of the killifish from seven different localities in Florida, Belize, and the Bahamas were cloned and sequenced. Thirteen loci and their alleles were identified and classified into eight groups. The loci apparently arose ∼20 million years ago (MYA) by gene duplications from a single common progenitor in the ancestors of R. marmoratus and its closest relatives. Distinct loci were found to be restricted to different populations and different individuals in the same population. Up to 44% of the fish were heterozygotes at Mhc loci, as compared to near homozygosity at non-Mhc loci. Large genetic distances between some of the Mhc alleles revealed the presence of ancestral allelic lineages. Computer simulation designed to explain these findings indicated that selfing is incomplete in R. marmoratus populations, that Mhc allelic lineages must have diverged before the onset of selfing, and that the hermaphroditism arose in a population containing multiple ancestral Mhc lineages. A model is proposed in which hermaphroditism arose stage-wise by mutations, each of which spread through the entire population and was fixed independently in the emerging clones.

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