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New data from basal Australian songbird lineages show that complex structure of MHC class II ? genes has early evolutionary origins within passerines.

ABSTRACT: The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune system and has been extensively studied across vertebrate taxa. Although the function of MHC genes appears to be conserved across taxa, there is great variation in the number and organisation of these genes. Among avian species, for instance, there are notable differences in MHC structure between passerine and non-passerine lineages: passerines typically have a high number of highly polymorphic MHC paralogs whereas non-passerines have fewer loci and lower levels of polymorphism. Although the occurrence of highly polymorphic MHC paralogs in passerines is well documented, their evolutionary origins are relatively unexplored. The majority of studies have focussed on the more derived passerine lineages and there is very little empirical information on the diversity of the MHC in basal passerine lineages. We undertook a study of MHC diversity and evolutionary relationships across seven species from four families (Climacteridae, Maluridae, Pardalotidae, Meliphagidae) that comprise a prominent component of the basal passerine lineages. We aimed to determine if highly polymorphic MHC paralogs have an early evolutionary origin within passerines or are a more derived feature of the infraorder Passerida.We identified 177 alleles of the MHC class II ? exon 2 in seven basal passerine species, with variation in numbers of alleles across individuals and species. Overall, we found evidence of multiple gene loci, pseudoalleles, trans-species polymorphism and high allelic diversity in these basal lineages. Phylogenetic reconstruction of avian lineages based on MHC class II ? exon 2 sequences strongly supported the monophyletic grouping of basal and derived passerine species.Our study provides evidence of a large number of highly polymorphic MHC paralogs in seven basal passerine species, with strong similarities to the MHC described in more derived passerine lineages rather than the simpler MHC in non-passerine lineages. These findings indicate an early evolutionary origin of highly polymorphic MHC paralogs in passerines and shed light on the evolutionary forces shaping the avian MHC.

SUBMITTER: Balasubramaniam S

PROVIDER: S-EPMC4875725 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines.

Balasubramaniam Shandiya S Bray Rebecca D RD Mulder Raoul A RA Sunnucks Paul P Pavlova Alexandra A Melville Jane J

BMC evolutionary biology 20160521 1

<h4>Background</h4>The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune system and has been extensively studied across vertebrate taxa. Although the function of MHC genes appears to be conserved across taxa, there is great variation in the number and organisation of these genes. Among avian species, for instance, there are notable differences in MHC structure between passerine and non-passerine lineages: passerines typically have a high number of highly polymorp ...[more]

PMID: 27206579

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Project description:Song in oscine birds (as in human speech and song) relies upon the rare capacity of vocal learning. Transmission can be vertical, horizontal, or oblique. As a rule, memorization and production by a naïve bird are not simultaneous: the long-term storage of song phrases precedes their first vocal rehearsal by months. While a wealth of detail regarding songbird enculturation has been uncovered by focusing on the apprentice, whether observational learning can fully account for the ontogeny of birdsong, or whether there could also be an element of active teaching involved, has remained an open question. Given the paucity of knowledge on animal cultures, I argue for the utility of an inclusive definition of teaching that encourages data be collected across a wide range of taxa. Borrowing insights from musicology, I introduce the Australian pied butcherbird (Cracticus nigrogularis) into the debate surrounding mechanisms of cultural transmission. I probe the relevance and utility of mentalistic, culture-based, and functionalist approaches to teaching in this species. Sonographic analysis of birdsong recordings and observational data (including photographs) of pied butcherbird behavior at one field site provide evidence that I assess based on criteria laid down by Caro and Hauser, along with later refinements to their functionalist definition. The candidate case of teaching reviewed here adds to a limited but growing body of reports supporting the notion that teaching may be more widespread than is currently realized. Nonetheless, I describe the challenges of confirming that learning has occurred in songbird pupils, given the delay between vocal instruction and production, as well as the low status accorded to anecdote and other observational evidence commonly mustered in instances of purported teaching. As a corrective, I press for an emphasis on biodiversity that will guide the study of teaching beyond human accounts and intractable discipline-specific burdens of proof.

Project description:BackgroundPeptides binding to Major Histocompatibility Complex (MHC) class II molecules are crucial for initiation and regulation of immune responses. Predicting peptides that bind to a specific MHC molecule plays an important role in determining potential candidates for vaccines. The binding groove in class II MHC is open at both ends, allowing peptides longer than 9-mer to bind. Finding the consensus motif facilitating the binding of peptides to a MHC class II molecule is difficult because of different lengths of binding peptides and varying location of 9-mer binding core. The level of difficulty increases when the molecule is promiscuous and binds to a large number of low affinity peptides. In this paper, we propose two approaches using multi-objective evolutionary algorithms (MOEA) for predicting peptides binding to MHC class II molecules. One uses the information from both binders and non-binders for self-discovery of motifs. The other, in addition, uses information from experimentally determined motifs for guided-discovery of motifs.ResultsThe proposed methods are intended for finding peptides binding to MHC class II I-Ag7 molecule - a promiscuous binder to a large number of low affinity peptides. Cross-validation results across experiments on two motifs derived for I-Ag7 datasets demonstrate better generalization abilities and accuracies of the present method over earlier approaches. Further, the proposed method was validated and compared on two publicly available benchmark datasets: (1) an ensemble of qualitative HLA-DRB1*0401 peptide data obtained from five different sources, and (2) quantitative peptide data obtained for sixteen different alleles comprising of three mouse alleles and thirteen HLA alleles. The proposed method outperformed earlier methods on most datasets, indicating that it is well suited for finding peptides binding to MHC class II molecules.ConclusionWe present two MOEA-based algorithms for finding motifs, one for self-discovery and the other for guided-discovery by experimentally determined motifs, and thereby predicting binding peptides to I-Ag7 molecule. Our experiments show that the proposed MOEA-based algorithms are better than earlier methods in predicting binding sites not only on I-Ag7 but also on most alleles of class II MHC benchmark datasets. This shows that our methods could be applicable to find binding motifs in a wide range of alleles.

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New data from basal Australian songbird lineages show that complex structure of MHC class II ? genes has early evolutionary origins within passerines.

Publications

New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines.

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