DOI: 10.5061/dryad.ht76hdrnn
title: Data from: Genomic data reveal unexpected relatedness between a brown female Eastern bluebird and her brood

description: Because plumage coloration is frequently involved in sexual selection, for
 both male and female mate choice, birds with aberrant plumage should have
 fewer mating opportunities and thus lower reproductive output. Here we
 report an Eastern Bluebird (Sialia sialis) female with a brown phenotype
 that raised a brood of four chicks to fledging. The brown female and her
 mate were only related to their social offspring to the second degree and
 one of the offspring was a half-sibling. We propose four family tree
 scenarios and discuss their implications (e.g., extra-pair paternity,
 conspecific brood parasitism), but regardless of the tree, the brown
 female was able to find a mate, which may have been facilitated by the
 bottleneck created by the severe snowstorms in February 2021.
description: These data are
 a result of low-coverage whole genome sequencing from individual Eastern
 bluebirds (<em>Sialia sialis</em>). We isolated
 genetic material from blood samples of bluebirds collected in northeast
 Arkansas, USA. We filtered the raw reads and mapped them to an existing
 reference (GenBank accession GCA_009812075.1) to call single nucleotide
 polymorphisms (SNPs). We then used the SNPs in a relatedness analysis to
 assess the familial relationship among samples. We also assembled the
 mitochondrial gene <em>nad2</em> from the filtered
 genomic data. We used the <em>nad2</em> sequences to assess
 maternal lineages among our samples.
description: # Data from: Genomic data reveal unexpected relatedness between a brown
 female Eastern Bluebird and her brood
 These data include files
 related to the phylogenetic and relatedness analysis among seven samples
 of Eastern bluebirds (*Sialia sialis*). Phylogenetic files include an
 alignment of the mitochondrial *nad2* gene and a resulting
 neighbor-joining distance tree generated from the APE package in R. The
 phylogeny shows the relationships among the different samples, most
 notably the maternal lineages present among the juvenile individuals. The
 file involved in the relatedness analysis is a Bash shell script to map
 nuclear genomic data from seven individual bluebirds to a reference and
 call single nucleotide polymorphisms (SNPs). The SNPs were used in an
 analysis to estimate relatedness among the individuals. ## Description of
 the data and file structure .fasta files and .tre files can both be viewed
 in a standard text editor. nad2_alignment.fasta: A FASTA-formatted file
 containing the aligned sequences of the mitochondrial *nad2* gene from
 seven individual Eastern bluebirds. One sequence (AY049510.1) was obtained
 from NCBI GenBank and was used as an outgroup. The other six sequences
 were obtained from adults and juveniles associated with a single nest. The
 adults were at least the social parents of the juveniles, although not
 likely the genetic parents. Adult female is sequence f601a, adult male
 m601a, and four juveniles are c1601a-c4601a. nad2_alignment.tre: NEWICK
 tree file for a neighbor-joining distance phylogeny of seven Eastern
 bluebird individuals. The phylogeny was generated from an alignment of the
 mitochondrial *nad2* gene (nad2_alignment.fasta). bluebird_mapping.sh:
 Bash shell script for mapping filtered paired-end reads from seven
 individual Eastern bluebirds to a reference genome from NCBI
 (GCA_009812075.1) and calling single nucleotide polymorphisms (SNPs). The
 script also details the parameters for filtering and counting SNPs and
 running a relatedness analysis.