Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America

Abstract

Resolving evolutionary relationships and establishing population structure depends on molecular diagnosability that is often limited for closely related taxa. Here, we use 3,200 ddRAD‐seq loci across 290 mallards, American black ducks, and putative hybrids to establish population structure and estimate hybridization rates. We test between traditional assignment probability and accumulated recombination events based analyses to assign hybrids to generational classes. For hybrid identification, we report the distribution of recombination events complements ADMIXTURE simulation by extending resolution past F4 hybrid status; however, caution against hybrid assignment based on accumulated recombination events due to an inability to resolve F1 hybrids. Nevertheless, both analyses suggest that there are relatively few backcrossed stages before a lineage's hybrid ancestry is lost and the offspring are effectively parental again. We conclude that despite high rates of observed interspecific hybridization between mallards and black ducks in the middle part of the 20th century, our results do not support the predicted hybrid swarm. Conversely, we report that mallard samples genetically assigned to western and non‐western clusters. We indicate that these non‐western mallards likely originated from game‐farm stock, suggesting landscape level gene flow between domestic and wild conspecifics.

Assessing changes in genomic divergence following a century of human‐mediated secondary contact among wild and captive‐bred ducks

“…Raw Illumina reads have been deposited in NCBI's Sequence Read Archive (SRA; http://www.ncbi.nlm.nih.gov/sra; SRA data PRJNA591912). We included sequenced mallard samples from Lavretsky, Janzen, et al () that were genetically characterized as either “Pure Western Mallard,” “Pure Non‐Western Mallard” or hybrids of the two ( N = 104; NCBI's SRA data PRJNA516035: see Table for BioSample Accession Numbers). These latter samples were from birds harvested by hunters in the wild.…”

“…Processing of raw Illumina reads followed the computational pipeline described by DaCosta and Sorenson (; Python scripts available at http://github.com/BU-RAD-seq/ddRAD-seq-Pipeline) and following the steps outlined in Lavretsky, Janzen, et al (). Final output files (e.g., FASTA, ADMIXTURE, fineRADstructure ) were generated with custom python scripts (Lavretsky et al, ), in which alleles were scored as missing if they had less than 5× coverage.…”

“…The chromosome position of each sequence capture was known because the ddRAD‐seq loci used to build the capture array were previously assigned chromosomal positions by blasting to a chromosome‐aligned mallard genome (Hou et al, unpublished; SRA BioProject PRJNA554956 & BioSample SAMN12287667). This made it possible to align and quantify differentiation across chromosomes, and compare results with previously aligned mallard and black duck genomes (Lavretsky, Janzen, et al, ). We also tested for the presence of mitochondrial DNA (mtDNA) by‐catch in our data sets.…”

“…This expansion was likely due to (a) direct augmentation by game managers, sportsmen and others, who have released ~500,000 captive‐bred mallards per year along the eastern seaboard since the 1920s (Hepp, Novak, Scribner, & Stangel, ; Heusmann, ; Soutiere, ) and have continued to release ~210,000 birds annually in recent years (Osborne et al, ; USFWS, ), and (b) conversion of boreal forests into open, prairie‐like habitat, allowing mallards to naturally expand eastward in the 1950s (e.g., southern Ontario; Hanson, Rogers, & Rogers, ). Using genomewide markers, Lavretsky, Janzen, and McCracken () recently identified two mallard genetic clusters in North America, a “Western” mallard genetic cluster to which all mallards west of the Mississippi River were assigned and a “Non‐Western” mallard cluster that was largely recovered in mallards from eastern North America. Their results suggest that historical releases and habitat changes have fostered gene flow between game‐farm and wild populations of mallards, and even with their eastern North American sister species, the American black duck ( Anas rubripes ; “black duck”).…”

Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands

“…All sequences have been submitted to GenBank (accession numbers ‐ and –). In addition to new sequences, 40 previously published sequences were also used (accession numbers –, Fowler et al, ; & , Lavretsky et al ; & , Peters et al ; –, Lavretsky, Engilis, Eadie, & Peters ; and –, Lavretsky, Janzen, & McKracken ; –, –, Lavretsky, Engilis, Eadie, & Peters, ). Sequences were cut to the 303 bp present in all samples, which included the hypervariable region.…”