Species divergence, selection and polymorphism in the MHC of crows

, , , ,
1 Department of Evolutionary Studies of Biosystems, Graduate University for Advanced Studies (SOKENDAI), Hayama, Japan
2 Department of Biology, Hamilton College, Clinton, New York, USA
3 Department of Zoology, University of Oxford, Oxford, UK
4 Department of Zoology, National Museum of Nature and Science, Tsukuba, Japan
DOI
10.7287/peerj.preprints.621v1
Published
Accepted
Subject Areas
Evolutionary Studies, Genetics, Molecular Biology, Zoology, Immunology
Keywords
crow, MHC, pathogen-mediated selection, trans-species polymorphism, species divergence
Copyright
© 2014 Eimes et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Eimes JA, Townsend AK, Sepil I, Nishiumi I, Satta Y. 2014. Species divergence, selection and polymorphism in the MHC of crows. PeerJ PrePrints 2:e621v1

Abstract

The relatively high level of polymorphism usually found in the major histocompatibility complex (MHC) is usually attributed to pathogen mediated selection; however, the timescale of selection is often unclear. Here we describe the MHC class II (IIB) in three passerine bird species in the genus Corvus: American, carrion and jungle crows. Carrion and American crows are recently diverged, but allopatric, sister species, whereas carrion and jungle crows are more distantly related but sympatric, likely sharing pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to examine evidence for ancient versus recent selection, trans-species polymorphism, and convergent evolution of the MHC in closely related species. Among the three species, the MHC IIB genes were highly duplicated (7-20 variants per individual) and polymorphic (an average of 79 variants per species; N = 18/species). Phylogenetic reconstructions of MHC IIB revealed patterns that were inconsistent with the evolutionary histories of the species. Several well supported interspecific clusters were observed, indicating trans-species polymorphism within this genus. Clustering of positively selected amino acids by supertyping revealed a single supertype shared by only jungle and carrion crows, whereas all other supertypes were shared among the three species, a pattern consistent with convergent evolution.

Author Comment

This is part of a long term study of the evolution of the MHC in the Passeriformes. This paper will be submitted to PeerJ for review.

Supplemental Information

Fig. S1. Map of Collection Sites for Jungle and Carrion Crows

Map of collection sites with number of samples in Japan for carrion (circles) and jungle (triangles) crows. Okinawa (inset) resides 663 km southwest of the southernmost tip of the main archipelago (Kagoshima).

DOI: 10.7287/peerj.preprints.621v1/supp-1

Fig. S2. Amino acid alignment of MHC IIB exon 2 in Crows

DOI: 10.7287/peerj.preprints.621v1/supp-2

Fig. S3. Neutral Marker NJ Tree and Divergence Estimates of Crows

DOI: 10.7287/peerj.preprints.621v1/supp-3

Fig. S4. NJ Tree of Synonymous Substitutions for MHC IIB Exon 2

DOI: 10.7287/peerj.preprints.621v1/supp-4

Fig. S5. NJ Tree of Non-synonymous Substitutions of MHC IIB exon 2 Wu-Kabot Varaible Sites

DOI: 10.7287/peerj.preprints.621v1/supp-5

Fig. S6. NJ Tree of Non-synonymous substitutuions of MHC IIB Peptide BInding Codons in Crows

DOI: 10.7287/peerj.preprints.621v1/supp-6