Genetic confirmation of a hybrid between two highly divergent cardinalid species: A rose-breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea)

Abstract

Using low-coverage whole-genome sequencing, analysis of vocalizations, and inferences from natural history, we document a first-generation hybrid between a rose-breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). These two species occur sympatrically throughout much of eastern North America, although were not previously known to interbreed. Following the field identification of a putative hybrid, we use genetic and bioacoustic data to show that a rose-breasted grosbeak was the maternal parent and a scarlet tanager was the paternal parent of the hybrid, whose song was similar to the latter species. These two species diverged >10 million years ago, and thus it is surprising to find a hybrid formed under natural conditions in the wild. Notably, the hybrid has an exceptionally heterozygous genome, with a conservative estimate of a heterozygous base every 100 bp. The observation that this hybrid of such highly divergent parental taxa has survived until adulthood serves as another example of the capacity for hybrid birds to survive with an exceptionally divergent genomic composition.

Keywords: birds; genomics; hybridization; reproductive isolation.

FIGURE 1

Photographs of the hybrid from the front (a), while singing (b), and in the hand (c). The putative parental species: A rose‐breasted grosbeak (d) and a scarlet tanager (e). Photos A–C by Steve grosser, D by John Harrison (cc‐by‐2.0), and E by Andy Reago & Chrissy McClarren (cc‐by‐2.0).

FIGURE 2

Spectrograms of (a) hybrid Scarlet Tanager x Rose‐Breasted Grosbeak song, (b) scarlet tanager song (Jim Berry, XC317656) and (c) rose‐breasted grosbeak song (Jim Berry, XC372244).

FIGURE 3

Sequence variation showing heterozygosity and intermediate genotypes of the hybrid Scarlet Tanager × Rose‐breasted Grosbeak compared to parental genera, including a western tanager (MSB:Bird:47847) as the Piranga representative. (a) Illustrates a small (50 bp) region of the LNPEP gene with multiple heterozygous sites (represented by ambiguous nucleotides). (b) The same LNPEP gene, but condensed to those 137 sites where the parental genera differed in non‐ambiguous nucleotides, and where there were no completely ambiguous (“N”) nucleotides for any of the three sequences.

FIGURE 4

Genome‐wide heterozygosity estimate for 156 wood warblers (family Parulidae; open circles) from two genera (Setophaga and Vermivora) published previously (Baiz et al., 2021), and the putative Rose‐Breasted Grosbeak × Scarlet Tanager hybrid sequenced here (red filled point).