Data from: Genomic data reveal unexpected relatedness between a brown female Eastern bluebird and her brood
Data files
Dec 28, 2023 version files 9.54 KB
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nad2_alignment.fasta
7.31 KB
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nad2_alignment.tre
167 B
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README.md
2.06 KB
Abstract
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.
README: Data from: Genomic data reveal unexpected relatedness between a brown female Eastern Bluebird and her brood
https://doi.org/10.5061/dryad.ht76hdrnn
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.
Methods
These data are a result of low-coverage whole genome sequencing from individual Eastern bluebirds (Sialia sialis). 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 nad2 from the filtered genomic data. We used the nad2 sequences to assess maternal lineages among our samples.