Data from: Repeated successful nest sharing and cooperation between Western Kingbirds (Tyrannus verticalis) and a female western kingbird X scissor-tailed flycatcher (T. forficatus) hybrid
Data files
Jan 30, 2025 version files 2.35 GB
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5_ind_kingbird_fasta_13_mtDNA_trimmed_named.fas
56.41 KB
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8.joint.dp.maxdp.mp2.qual.pass.missdata.maf.m2.relatedness2
4.99 KB
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8.joint.dp.maxdp.mp2.qual.pass.missdata.maf.m2.vcf
2.34 GB
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Code_for_genomic_data_and_relatedness_analyses.txt
5.93 KB
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Code_for_neighbor_joining_tree_in_R.txt
799 B
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Consensus_H1517_Hybrid_female_mtDNA.unpadded.fasta
17.58 KB
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Consensus_H3020_Fledgling_A_mtDNA.unpadded.fasta
17.56 KB
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consensus_SOK009_Scissor_tailed_outgroup_mtDNA.unpadded.fasta
17.54 KB
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Consensus_W1524_Pure_female_mtDNA.unpadded.fasta
17.58 KB
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Consensus_W3017_Fledgling_B_mtDNA.unpadded.fasta
17.51 KB
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FledglingA_FledglingB_comparison.jpg
2.26 MB
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Fledglings_in_shared_nest.JPG
3.55 MB
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H1517_Hybrid_Female_MITOS.gff
2.13 KB
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H3020_Fledgling_A_MITOS.gff
2.12 KB
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HybirdFemale_PureFemale_coincubating.JPG
3.71 MB
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neighbor_joining_phylogney_of_5_individuals_using_13_mtDNA_genes.png
114.01 KB
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neighbor_joining_phylogney_of_5_individuals_using_13_mtDNA_genes.tre
3.56 KB
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README.md
3.77 KB
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SOK009_Scissor_tailed_outgroup_MITOS.gff
2.16 KB
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W1524_pure_female_MITOS.gff
2.12 KB
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W3017_Fledgling_B_MITOS.gff
2.13 KB
Abstract
Nest sharing by birds, or the phenomenon where multiple individuals of different species contribute genetically and parentally to a single nest, is a rare form of cooperative breeding that has only occasionally been reported in socially monogamous birds. Here we describe, both behaviorally and genetically, the unique case of two female birds, a western kingbird (Tyrannus verticalis) and a western kingbird x scissor-tailed flycatcher (T. forficatus) hybrid simultaneously occupying (and likely co-incubating) a brood in a single nest. Both females provisioned nestlings, and they did this in two consecutive years (producing four fledglings each year). Genomic data from the females revealed that they were unrelated and parentage analyses revealed that both females contributed genetically to at least one of the offspring, and at least two fathers were involved. In total, this is the first reported case of nest sharing involving a hybrid individual and the first case within the family Tyrannidae.
README: Repeated Successful Nest Sharing and Cooperation between Western Kingbirds (Tyrannus verticalis) and a Female Western Kingbird x Scissor-tailed Flycatcher (T. forficatus) Hybrid
https://doi.org/10.5061/dryad.w6m905qz0
Description of the data and file structure
To determine the relatedness of offspring from a shared nest that involved two western kingbirds and a female western kingbird x scissor-tailed flycatcher hybrid in Arkansas.
Files and variables
File: 5_ind_kingbird_fasta_13_mtDNA_trimmed_named.fas
Description: Aligned and trimmed FASTA file of 13 mtDNA genes used to build a neighbor-joining tree of 5 individual kingbirds
File: Consensus_H1517_Hybrid_female_mtDNA.unpadded.fasta
Description: Output file of MITObim used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: Consensus_H3020_Fledgling_A_mtDNA.unpadded.fasta
Description: Output file of MITObim used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: Consensus_W1524_Pure_female_mtDNA.unpadded.fasta
Description: Output file of MITObim used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: Consensus_W3017_Fledgling_B_mtDNA.unpadded.fasta
Description: Output file of MITObim used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: consensus_SOK009_Scissor_tailed_outgroup_mtDNA.unpadded.fasta
Description: Output file of MITObim used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: H1517_Hybrid_Female_MITOS.gff
Description: Output file of MITOS used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: H3020_Fledgling_A_MITOS.gff
Description: Output file of MITOS used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: SOK009_Scissor_tailed_outgroup_MITOS.gff
Description: Output file of MITOS used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: W1524_pure_female_MITOS.gff
Description: Output file of MITOS used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: W3017_Fledgling_B_MITOS.gff
Description: Output file of MITOS used to extract 13 mtDNA protein-coding genes for 5 kingbirds
File: neighbor_joining_phylogney_of_5_individuals_using_13_mtDNA_genes.tre
Description: Neighbor-joining tree built in R with package ape using K80 nuclear subsitution model
File: neighbor_joining_phylogney_of_5_individuals_using_13_mtDNA_genes.png
Description: Neighbor-joining tree of 5 individual kingbirds
File: 8.joint.dp.maxdp.mp2.qual.pass.missdata.maf.m2.relatedness2
Description: Generated output matrix from Relatedness2 to assess relatedness of 8 individuals
File: 8.joint.dp.maxdp.mp2.qual.pass.missdata.maf.m2.vcf
Description: Filtered VCF file used as input in Relatedness2 analysis generated to assess relatedness of 8 individuals
File: HybirdFemale_PureFemale_coincubating.JPG
Description: Photo of both adults co-incubating shared nest
File: FledglingA_FledglingB_comparison.jpg
Description: Photo comparison of Fledgling A and Fledgling B in the hand
File: Fledglings_in_shared_nest.JPG
Description: Photo of 4 nestlings in shared nest
Code/Software
File: Code_for_genomic_data_and_relatedness_analyses.txt
Description: Bash code used to quality check and trim raw reads, generate genome assemblies, call and filter SNPs, perform Relatedness2, and extract mtDNA genes
File: Code_for_neighbor_joining_tree_in_R.txt
Description: Code used to construct neighbor-joining distance tree in R