MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion

Shandiya Balasubramaniam, Raoul A. Mulder, Paul Sunnucks, Alexandra Pavlova, Jane Melville

Research output: Contribution to journalArticleResearchpeer-review

Abstract

The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influenced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signatures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes.

Original languageEnglish
Pages (from-to)101-111
Number of pages11
JournalImmunogenetics
Volume69
Issue number2
DOIs
Publication statusPublished - 2017

Keywords

  • Balancing selection
  • Gene conversion
  • Major histocompatibility complex
  • Pardalotus
  • Passerine
  • Recombination

Cite this

@article{c05dbf064d024595979c2ca9bf67d942,
title = "MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion",
abstract = "The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influenced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signatures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes.",
keywords = "Balancing selection, Gene conversion, Major histocompatibility complex, Pardalotus, Passerine, Recombination",
author = "Shandiya Balasubramaniam and Mulder, {Raoul A.} and Paul Sunnucks and Alexandra Pavlova and Jane Melville",
year = "2017",
doi = "10.1007/s00251-016-0953-7",
language = "English",
volume = "69",
pages = "101--111",
journal = "Immunogenetics",
issn = "0093-7711",
publisher = "Springer",
number = "2",

}

MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion. / Balasubramaniam, Shandiya; Mulder, Raoul A.; Sunnucks, Paul; Pavlova, Alexandra; Melville, Jane.

In: Immunogenetics, Vol. 69, No. 2, 2017, p. 101-111.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion

AU - Balasubramaniam, Shandiya

AU - Mulder, Raoul A.

AU - Sunnucks, Paul

AU - Pavlova, Alexandra

AU - Melville, Jane

PY - 2017

Y1 - 2017

N2 - The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influenced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signatures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes.

AB - The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influenced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signatures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes.

KW - Balancing selection

KW - Gene conversion

KW - Major histocompatibility complex

KW - Pardalotus

KW - Passerine

KW - Recombination

UR - http://www.scopus.com/inward/record.url?scp=84990890002&partnerID=8YFLogxK

U2 - 10.1007/s00251-016-0953-7

DO - 10.1007/s00251-016-0953-7

M3 - Article

VL - 69

SP - 101

EP - 111

JO - Immunogenetics

JF - Immunogenetics

SN - 0093-7711

IS - 2

ER -