DOI: 10.5061/dryad.nvx0k6f3n
title: Genetic confirmation of an “Uncommon Mourningthroat” (Geothlypis philadelphia x G. trichas): a rare but persistent hybrid warbler

description: For much of the history of American ornithology, hybrid birds discovered
 outside of known hybrid zones have presented an identification
 challenge—given the likely parental species are typically identified based
 on inferences from plumage patterns—but also a source of insight into
 evolutionary processes. With the advance of modern genetics, the tools are
 now available to definitively identify hybrids for which genetic samples
 are available and, in many cases, determine the identity and the sex of
 each parent species as well as F1 versus backcross status. Typically,
 these kinds of hybrids are rare; however, one apparently common hybrid
 wood-warbler (family Parulidae) are putative crosses between Mourning
 Warblers (Geothlypis philadelphia) and Common Yellowthroats (G. trichas),
 which have been reported at least thirteen times between 1955 and 2024,
 though never confirmed genetically. Here we describe the results of
 genetic and plumage analysis to identify a putative G. philadelphia x G.
 trichas hybrid captured in July, 2017 in New York, USA. We used genotype
 likelihoods derived from whole-genome sequencing data of the putative
 hybrid and several species in Geothlypis and Oporornis (the most likely
 genera of the parents) to confirm bird’s identity as an F1 hybrid between
 G. philadelphia and G. trichas. We sequenced one mitochondrial gene and
 used publicly available sequences of several related species to identify
 the maternal parent as G. philadelphia. The data and code presented here
 and in GenBank are intended to permit reproduction of the analyses that
 made up the study, including processing reads, making trees, and running
 PCA and admixture.
description: # Genetic confirmation of an “Uncommon Mourningthroat” (Geothlypis
 philadelphia x G. trichas): a rare but persistent hybrid warbler Dataset
 DOI: [10.5061/dryad.nvx0k6f3n](10.5061/dryad.nvx0k6f3n) ## Description of
 the data and file structure ### Data * bam.list - Example input to to
 PCAngsd, sample order is unchanged. * bam.2.list - Example input to
 NGSAdmix, sample order is unchanged. Both bamlist sample names follow
 those found in NCBI BioProject PRJNA630247. * moye.gl1.cov - The
 covariance matrix, output of PCAngsd. The eigenvectors can be calculated
 using the eigen() command in R. The order of individuals is the same as
 bam.list. * moye_maf0.2_k2_gl1.txt - Admixture proportions of each
 individual. The order is the same as bam.2.list. * sanger1.ab1 - The
 forward Sanger trace. * sanger2.ab1 - The reverse Sanger trace. *
 geothlypis_coi_unaligned.fasta - The COI sequences from the hybrid and
 each Geothlypis/Oporornis species as downloaded from GenBank. *
 geothlypis_coi_aligned.fasta - The aligned fasta of the above after
 trimming to the maximum common length across all samples. ### Code (All
 code is run on the command line, just change the directories to your own)
 * trim-align-sort-mark-index.sh - Code that takes demultiplexed raw reads
 and a reference genome, then trims adapters, aligns to the reference,
 marks duplicates, and indexes the resulting bam file. * gls-pca-admix.sh -
 Code to calculate genotype likelihoods from bam files, then run the PCA
 and admixture analyses. * iqtree_geothlypis_coi.sh - Code that makes a COI
 tree from the alignment geothlypis_coi_aligned.fasta.