Introductions and invasions provide opportunities for interaction and hybridization between colonists and closely related native species. We investigate this phenomenon using the mitochondrial DNA COI and 81,416 base-pairs of overlapping nuclear variation to examine the evolutionary histories and signatures of hybridization among introduced feral Rock Pigeon and Eurasian Collared-Dove and native White-winged and Mourning doves in southwestern North America. First, we report all four species to be highly divergent across loci (overall pair-wise species ΦST range = 0.17–0.70) and provide little evidence for gene flow at evolutionary timescales. Despite this, evidence from multiple population genetics analyses supports the presence of six putative contemporary late-stage hybrids among the 182 sampled individuals. These putative hybrids contain various ancestry combinations, but all involve the most populous species, the Mourning Dove. Next, we use a novel method to reconstruct demographic changes through time using partial genome sequence data. We identify recent, species-specific fluctuations in population size that are likely associated with changing environments since the Miocene and suggest that these fluctuations have influenced the genetic diversity of each dove species in ways that may impact their future persistence. Finally, we discuss the importance of using multiple marker types when attempting to infer complex evolutionary histories and propose important considerations when analyzing populations that were recently established or of domestic origins.

Some birds replace feathers after the formative plumage of the first cycle and after basic plumages in subsequent cycles as a consequence of prealternate molts. The presence of prealternate molts has been suggested to be due to prolonged exposure to sunlight, especially for birds inhabiting exposed and scrubby areas. Although prealternate molts appear to be common in many Nearctic-Neotropic passerines, these can be also present in resident Neotropical species. For example, prealternate molt has been reported in 14 species among nine genera in thraupids. Here, using wild individuals and museum specimens, we describe the presence of a Complex Alternate Strategy in the molt cycle of the Peru's Blueand-yellow Tanager (Pipraeidea bonariensis darwinii). We categorized seven molt cycle-based age groups in 75 wildcaptured birds and thirteen molt cycle-based age categories across 167 museum specimens. Our results confirm the existence of limited to partial prealternate molts in Blue-and-yellow Tanager and demonstrate the importance of investigating the presence of these types of molts in wild bird populations.

We document a unusual variation in the extent of preformative molt across 20 formative-plumaged Blueand-yellow Tanager (Pipraeidea bonariensis darwinii Bonaparte, 1838) museum specimens from Peru. Our finding represents the first evidence of eccentric replacement of primaries and primary coverts during the preformative molt for this species.

The mallard (Anas platyrhynchos) is one of the most common, economically, and socially important birds around the world. Mallards were not only an important food source for early humans, but eventually becoming intimately linked with people as they were domesticated over the last 2,000 years. To date, mallard genomes are largely reconstructed from samples of domestic or unknown genetic heritage. Here, we report the first high-quality genome assembly and annotation of a genetically vetted wild mallard from North America (NAwild_v1.0). The genome was assembled using a combination of shotgun libraries and proximity ligation ChicagoTM and Dovetail Hi-CTM libraries, respectively. The final assembly is ∼1.04 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 79.1 Mb/4 scaffolds. We used a combination of gene prediction and similarity approaches to annotate a total of 23,584 functional genes, of which 19,242 were associated to GO terms. The genome assembly and the set of annotated genes yielded a 95.4% completeness score when compared with the BUSCO aves_odb10 dataset. Next, we aligned three previously published mallard genomes to ours, and demonstrate how runs of homozygosity and nucleotide diversity are substantially higher and lower, respectively, to ours and how these artificially changed genomes resulted in profoundly different and biased demographic histories. Our wild mallard assembly not only provides a valuable resource to shed light onto genome evolution, speciation and other adaptive processes, but also helping with identifying functional genes that have been significantly altered during the domestication process.

No abstract