DOI: 10.5061/dryad.bzkh189r2
title: Female reed warblers in social pairs with low MHC dissimilarity achieve higher MHC dissimilarity through random extra-pair mating

description: Major Histocompatibility Complex (MHC) polymorphism is maintained by
 balancing selection through host-pathogen interactions and mate choice.
 MHC-based mate choice has been investigated across a wide range of
 vertebrates, and an established concept is that females should choose a
 mate with an MHC genotype that is dissimilar to her own to ensure high MHC
 divergence in her offspring. Here we present evidence from a population of
 reed warblers, Acrocephalus scirpaceus, that social pairs with extra-pair
 young in their nest have significantly lower MHC dissimilarity than
 expected by random MHC-based mate choice. Moreover, social pairs with
 extra-pair young in their nest have lower MHC dissimilarity than the
 potential pairs females could form with other males surrounding the social
 nest. Therefore, females in pairs with low MHC dissimilarity could improve
 the MHC divergence of their offspring through extra-pair mating. We
 propose that when the MHC dissimilarity in the social pair is low, any
 alternative male represents a better genetic prospect for the female in
 terms of MHC dissimilarity. This scenario generates a pattern of
 MHC-disassortative extra-pair mating without requiring active MHC-based
 mate choice.
description: # Female reed warblers in social pairs with low MHC dissimilarity achieve
 higher MHC dissimilarity through random extra-pair mating Dataset DOI:
 [10.5061/dryad.bzkh189r2](https://doi.org/10.5061/dryad.bzkh189r2) ##
 Description of the data and file structure Data to accompany the
 manuscript "Female reed warblers in social pairs with low MHC
 dissimilarity achieve higher MHC dissimilarity through random extra-pair
 mating." ### Files and variables #### Supplementary_file_1.fasta
 **Description of Supplementary_file_1.fasta** Fasta file containing
 nucleotide sequences of the 281 MHC-I sequences found in the study. This
 can be opened using a standard text editor or any programs capable of
 reading fasta files. These sequences are publicly available in the NCBI
 database ([https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/))
 using the accession numbers KU169387, KU169375, KU169386, KU169388,
 KU169376, KU169393 and OR053210 to OR053484). #### Supplementary_file_2.R
 **Description of Supplementary_file_2.R** Annotated R script for all
 analyses used in the study. Input files required to run all analyses can
 be found as supplementary tables (Tables S1, S3, S7-10). #### Table_S1.csv
 **Description of Table_S1.csv** Table of all MHC-I genotyped individuals
 in the study and the MHC-I sequences identified in each.
 "Seq_id" = sequence name allocated in the study;
 "Sequence" = nucleotide sequence. Columns C to IW contain bird
 identification numbers. Female IDs start with “F”. Male IDs start with
 “M”. #### Table_S2.csv **Description of Table_S2.csv** Table of data used
 for statistical analyses containing MHC-I dissimilarity data for all
 pairs. “Category” = pair type (1 = SP-EPY [where EGP male is known]; 2 =
 EGP; 3 = SP-WPY; 4 = SP-EPY [where EGP male is not known]); “year” = year
 pair were observed; “nest_ID” = ID of nest; “lay_date” = date of first egg
 recorded; “female” = female ID; “F_allelic_n” = number of MHC-I alleles of
 female; “male” = male ID; “M_allelic_n” = number of MHC-I alleles of male;
 “Pair”= combination of female and male ID; “mhc_dist” = MHC-I
 dissimilarity; “F_allelic_n” = number of MHC-I alleles in female;
 “M_allelic_n” = number of MHC-I alleles in male. #### Table_S3.csv
 **Description of Table_S3.csv** Key to sequence names used in study and
 the corresponding sequence names on GenBank. "Sequence" =
 sequence name allocated in the study; "Accession" = GenBank
 accession number; "NCBI_name" = name used on GenBank. ####
 Table_S5.csv **Description of Table_S5.csv** Table containing details of
 the amino acid sequence of the PBR for each sequence and which sequences
 were found in which individuals in the study. “PBR_name” = sequence name;
 “PBR_sequence” = amino acid sequence; Columns C to IW contain bird
 identification numbers. Female IDs start with “F”. Male IDs start with
 “M”. #### Table_S6.csv **Description of Table_S6.csv** Matrix of MHC-I
 dissimilarity scores (functional distances) between all MHC-I genotyped
 males and females. #### Table_S7.csv **Description of Table_S7.csv** Table
 of data used for statistical analyses on the putatively available males
 surrounding each nest. “OBS” = running number for each social pair;
 “Female” = female ID; “year” = year; “s_M” = social male ID; “EPP_M” = EGP
 male ID; “putative.M” = ID of putatively available male; “dist.put.M..m” =
 physical distance of male from female's nest in meters; “Combo” =
 combination of female & social male ID; “put_pair” = combination of
 female & putative male ID; “extra_pair” = combination of female &
 EGP male ID; “sp_mhc_dist” = MHC-I dissimilarity between social pair
 (SP-EPY); “pp_mhc_dist” = MHC-I dissimilarity between female and
 putatively available male; “ep_mhc_dist” = MHC-I dissimilarity between
 genetic pair (EGP). #### Table_S8.csv **Description Table_S8.csv** Table
 containing microsatellite genotypes for all 214 individuals in the social
 pairs (35 SP-EPY & 98 SP-WPY) analysed in this study.
 "full_id" = individual ID; "sex" = sex (male or
 female) of individual; "Ase18a" = length of Ase18a allele in
 individual; "Ase18b" = length of Ase18b allele in individual;
 "Ase25a" = length of Ase25a allele in individual;
 "Ase25b" = length of Ase25b allele in individual;
 "Ase37a" = length of Ase37a allele in individual;
 "Ase37b" = length of Ase37b allele in individual;
 "Ase48a" = length of Ase48a allele in individual;
 "Ase48b" = length of Ase48b allele in individual;
 "Ppi2a" = length of Ppi2a allele in individual;
 "Ppi2b" = length of Ppi2b allele in individual;
 "Ase58a" = length of Ase58a allele in individual;
 "Ase58b" = length of Ase58b allele in individual. ####
 Table_S9.tsv **Description of Table_S9.tsv** Table of data used for
 statistical analyses containing the MHC-I dissimilarity scores for all
 possible combinations of 128 females and 127 males genotyped in the
 population (16256 theoretical pairs). "Bird_nr" = female ID;
 "Male" = male ID; "value" = MHC-I dissimilarity score;
 "Pair" = combination of female and male IDs. #### Table_S10.tsv
 **Description of Table_S10.tsv** Table of data used for statistical
 analyses containing the number of MHC-I alleles in each of the 127
 genotyped males. "ID" = male ID; "Nr_Alleles" = number
 of MHC-I alleles found. #### Table_S11.csv **Description of
 Table_S11.csv** Table of data on the number of hatched and unhatched eggs
 observed at nests. “Category” = pair type (1 = SP-EPY [where EGP male is
 known]; 2 = EGP; 3 = SP-WPY; 4 = SP-EPY [where EGP male is not known]);
 “year” = year pair were observed; “nest_ID” = ID of nest; "Original
 clutch" = total number of eggs laid in nest; "unhatched
 eggs" = number of eggs not hatched; "all eggs at hatching"
 = number of eggs at day of first egg hatching; “lay_date” = date of first
 egg recorded; “female” = female ID; “male” = male ID; “Pair”= combination
 of female and male ID; "missing_eggs_0_1" = number of eggs that
 disappeared from nest; "notes" = notable observations. Note that
 Tables S4 and S12 to S16 (referred to in the manuscript) can be found in
 the main Supplementary Information document that accompany the manuscript
 ## Code/software The following is a list of file types contained within
 this repository, with brief descriptions of how to work with them: R
 script that can be viewed, edited and run using the statistical software R
 ([https://www.r-project.org/](https://www.r-project.org/)). R will run on
 Windows, MacOS, and a wide variety of UNIX platforms. The R packages
 loaded by the script are forcats_1.0.1,  cowplot_1.2.0,  ggplot2_4.0.0, 
 Hmisc_5.2-3, lme4_1.1-37, Matrix_1.7-4, reshape2_1.4.4, plyr_1.8.9,
 tidyr_1.3.1 and dplyr_1.1.4. The script was run in R version 4.4.0. .csv:
 Plain text files that use symbol delimiter (in this case semicolons) to
 separate values and new lines to separate newlines. These files can be
 viewed and edited with any plain text editor (e.g., Linux less command,
 Nano, Vim, Text Editor). They can also be opened in Excel by specifying
 the delimiter symbol (in this case semicolons). .tsv: Tab-separated values
 files, which are plain text files with tab-delimited data fields. These
 files can be viewed/manipulated with any plain text editor or read with
 the R software using the `read.table` command with the
 `sep="\t"` argument.They can also be opened in Excel by
 specifying tab as the delimiter symbol. .fasta: Plain text DNA sequence
 information in FASTA format. These files can be viewed and edited in any
 of the many free sequence editing programs (e.g., BioEdit, AliView,
 Jalview) but also any plain text editor (e.g., Linux less command, Nano,
 Vim, Text Editor). ## Access information Other publicly accessible
 locations of the data: * The sequences in Supplementary_file_1.fasta are
 publicly available in the NCBI database
 ([https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/)) using
 the accession numbers KU169387, KU169375, KU169386, KU169388, KU169376,
 KU169393 and OR053210 to OR053484).