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Abstract AimIntroduced species offer insight on whether and how organisms can shift their ecological niches during translocation. The genusAmazonaoffers a clear test case, where sister species Red‐crowned (A. viridigenalis) and Lilac‐crowned Parrots (A. finschi) have established breeding populations in southern California following introduction via the pet trade from Mexico where they do not coexist. After establishment in the 1980s, introduced population sizes have increased, with mixed species flocks found throughout urban Los Angeles. Here, we investigate the differences between the environmental conditions of the native and introduced ranges of these now co‐occurring species. LocationSouthern California and Mexico. MethodsUsing environmental data on climate and habitat from their native and introduced ranges, we tested whether Red‐crowned and Lilac‐crowned Parrots have divergent realized niches between their native ranges, and whether each species has significantly shifted its realized niche to inhabit urban southern California. We also analysed data from Texas and Florida introductions of Red‐crowned Parrots for comparative analysis. ResultsThere are significant differences in the native‐range niches of both parrot species, but a convergence into a novel, shared environmental niche into urban southern California, characterized by colder temperatures, less tree cover and lower rainfall. Texas and Florida Red‐crowned Parrots also show evidence for niche shifts with varying levels of niche conservatism through the establishment of somewhat different realized niches. Main ConclusionsDespite significant niche shifts, introduced parrots are thriving, suggesting a broad fundamental niche and an ability to exploit urban resources. Unique niche shifts in different U.S. introductions indicate thatAmazonaparrots can adapt to diverse environmental conditions, with cities offering a resource niche and the timing of introduction playing a crucial role. Cities can potentially serve as refugia for threatened parrot species, but the risk of hybridization between species emphasizes the need for ongoing monitoring and genetic investigations. 

Abstract The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction, and new community assemblages, which sparked competition, adaptation, and speciation. Diversification across many bird groups, and the elevational zonation of others, ties back to events triggered by the GABI. But the exact timing of these events is still being revealed, with recent studies suggesting a much earlier time window for faunal exchange, perhaps as early as 20 million years ago (Mya). Using a time‐calibrated phylogenetic tree, we show that the jay genusCyanolycais emblematic of bird dispersal trends, with an early, pre‐land bridge dispersal from Mesoamerica to South America 6.3–7.3 Mya, followed by a back‐colonization ofC. cucullatato Mesoamerica 2.3–4.8 Mya, likely after the land bridge was complete. AsCyanolycaspecies came into contact in Mesoamerica, they avoided competition due to a prior shift to lower elevation in the ancestor ofC. cucullata. This shift allowedC. cucullatato integrate itself into the Mesoamerican highland avifauna, which our time‐calibrated phylogeny suggests was already populated by higher‐elevation, congeneric dwarf‐jays (C. argentigula,C. pumilo,C. mirabilis, andC. nanus). The outcome of these events and fortuitous elevational zonation was thatC. cucullatacould continue colonizing new highland areas farther north during the Pleistocene. Resultingly, fourC. cucullatalineages became isolated in allopatric, highland regions from Panama to Mexico, diverging in genetics, morphology, plumage, and vocalizations. At least two of these lineages are best described as species (C. mitrataandC. cucullata). Continued study will further document the influence of the GABI and help clarify how dispersal and vicariance shaped modern‐day species assemblages in the Americas. 

Abstract Hybrid zones are natural experiments for the study of avian evolution. Hybrid zones can be dynamic, moving as species adjust to new climates and habitats, with unknown implications for species and speciation. There are relatively few studies that have comparable modern and historic sampling to assess change in hybrid zone location and width over time, and those studies have generally found mixed results, with many hybrid zones showing change over time, but others showing stability. The white‐throated magpie‐jay (Calocitta formosa) and black‐throated magpie‐jay (Calocitta colliei) occur along the western coast of Mexico and Central America. The two species differ markedly in throat color and tail length, and prior observation suggests a narrow hybrid zone in southern Jalisco where individuals have mixed throat color. This study aims to assess the existence and temporal stability of this putative hybrid zone by comparing throat color between georeferenced historical museum specimens and modern photos from iNaturalist with precise locality information. Our results confirm the existence of a narrow hybrid zone in Jalisco, with modern throat scores gradually increasing from the parental ends of the cline toward the cline center in a sigmoidal curve characteristic of hybrid zones. Our temporal comparison suggests that the hybrid zone has not shifted its position between historical (pre‐1973) and modern (post‐2005) time periods—a surprising result given the grand scale of habitat change to the western Mexican lowlands during this time. An anomalous pocket of white‐throated individuals in the northern range of the black‐throated magpie‐jay hints at the possibility of prehistorical long‐distance introduction. Future genomic data will help disentangle the evolutionary history of these lineages and better characterize how secondary contact is affecting both the DNA and the phenotype of these species. 

Abstract Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley’s (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (Pipilo maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (FST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. This towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages. 

Abstract Next‐generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol–chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol–chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol–chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol–chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols. 

Seasonal migration is highly labile from an evolutionary perspective and known to rapidly evolve in response to selective pressures. However, long‐distance migratory birds rely partially on innate genetic programs and may be constrained in their ability to alter their migratory behavior. We take advantage of recent advances in our ability to genotype historical DNA samples to examine the temporal stability of migratory connections between breeding and nonbreeding populations (i.e. migratory connectivity) and population‐level nonbreeding distributions in the Wilson's warblerCardellina pusilla, a long‐distance migratory songbird. By assigning historical and contemporary samples collected across the nonbreeding range to genetically distinct breeding clusters, we suggest that broad‐scale population‐level nonbreeding distributions within this species have remained largely consistent within Mexico from the mid‐1900s to the present day. These findings support the idea that the nonbreeding distributions of long‐distance migrants may remain stable over long time scales, even in the face of rapid environmental change. 

Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii) comprises 7 subspecies, ranging from the Rocky Mountains to southern Mexico. We quantified the phenotype of specimens throughout Mexico and found support for significant phenotypic differences between “Sumichrast’s group” in southern Mexico (A. w. sumichrasti and A. w. remota) and the 2 subspecies in northern Mexico, or “Woodhouse’s group” (A. w. grisea and A. w. cyanotis). Despite significant differentiation in body size and mantle color, we found no clear geographic boundary between the groups, suggesting either a geographic cline or hybridization upon secondary contact. We tested for selection against hybridization by fitting models to geographic clines for both body size and back color, and found support for a stable contact zone centered near Mexico City, with selection against intermediate back color. Based on these results, we infer that Sumichrast’s and Woodhouse’s groups diverged during a period of geographic and genetic isolation. The phenotypic introgression between Sumichrast’s and Woodhouse’s groups near Mexico City likely represents a case of recent secondary contact, with selection against hybridization maintaining a geographically stable contact zone.