Explore the vast range of titles available.

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. Sample distribution of American black ducks (ABDU), mallards (MALL), and putative hybrids (MBDH). Visualization of population structure based on PCA scatter plots of PC1 (x‐axis) and PC2 (y‐axis) plotted for 3,037 Autosomal and 163 Z‐chromosome ddRAD‐seq loci. Additionally, we present ADMIXTURE based maximum likelihood estimation of individual assignment probabilities for K population values of 2 and 3 based on autosomal or Z‐linked markers, respectively.

Evidence from a variety of organisms points to convergent evolution on the mitochondria associated with a physiological response to oxygen deprivation or temperature stress, including mechanisms for high-altitude adaptation. Here, we examine whether demography and/or selection explains standing mitogenome nucleotide diversity in high-altitude adapted populations of three Andean waterfowl species: yellow-billed pintail ( Anas georgica ), speckled teal ( Anas flavirostris ), and cinnamon teal ( Spatula cyanoptera ). We compared a total of 60 mitogenomes from each of these three duck species ( n = 20 per species) across low and high altitudes and tested whether part(s) or all of the mitogenome exhibited expected signatures of purifying selection within the high-altitude populations of these species. Historical effective population sizes ( N e ) were inferred to be similar between high- and low-altitude populations of each species, suggesting that selection rather than genetic drift best explains the reduced genetic variation found in mitochondrial genes of high-altitude populations compared to low-altitude populations of the same species. Specifically, we provide evidence that establishment of these three Andean waterfowl species in the high-altitude environment, coincided at least in part with a persistent pattern of negative purifying selection acting on oxidative phosphorylation (OXPHOS) function of the mitochondria. Our results further reveal that the extent of gene-specific purifying selection has been greatest in the speckled teal, the species with the longest history of high-altitude occupancy.

Identifying contemporary population structure and genetic connectivity among seabird populations is essential for developing conservation plans for threatened species, especially as factors like philopatry, non-breeding behavior, and oceanographic features might limit gene flow between isolated populations and influence changes in genetic diversity over time. Here, we characterize the population structure of three closely related crested penguin species in New Zealand: Tawaki ( Eudyptes pachyrhynchus ; Fiordland penguins), erect-crested penguins/tawaki nana hī ( Eudyptes sclateri ), and eastern rockhopper penguins/tawaki piki toka ( Eudyptes filholi ). Whereas tawaki populations appear to be stable, the erect-crested and eastern rockhopper penguin populations have seen dramatic declines in the recent historical record. To understand the genetic implications of these differences in population trajectories, we assessed genetic connectivity among multiple colonies using thousands of nuclear autosomal loci. Our results indicate that tawaki are a single, genetically diverse population without colony-based structure, which is consistent with the currently observed stable or increasing population of tawaki. However, conservation efforts should continue to prioritize protecting marine habitats to safeguard this species. In contrast, we identified two genetically distinct populations of erect-crested penguins corresponding to the Antipodes Islands and the Bounty Islands groups. The Antipodes Islands eastern rockhopper population exhibited high levels of coancestry and low genetic diversity, consistent with population decline and limited immigration. The lack of gene flow and genetic diversity in both erect-crested and eastern rockhopper penguins on the Antipodes Islands raises concerns and highlights the need for continued research to identify the causes of declines to inform conservation efforts of these penguins.

The genetic composition of mallards in eastern North America has been changed by release of domestically-raised, game-farm mallards to supplement wild populations for hunting. We sampled 296 hatch-year mallards harvested in northwestern Ohio, October–December 2019. The aim was to determine their genetic ancestry and geographic origin to understand the geographic extent of game-farm mallard introgression into wild populations in more westward regions of North America. We used molecular analysis to detect that 35% of samples were pure wild mallard, 12% were early generation hybrids between wild and game-farm mallards (i.e., F1–F3), and the remaining 53% of samples were assigned as part of a hybrid swarm. Percentage of individuals in our study with some form of hybridization with game-farm mallard (65%) was greater than previously detected farther south in the mid-continent (~4%), but less than the Atlantic coast of North America (~ 92%). Stable isotope analysis using δ 2 H f suggested that pure wild mallards originated from areas farther north and west than hybrid mallards. More specifically, 17% of all Ohio samples had δ 2 H f consistent with more western origins in the prairies, parkland, or boreal regions of the mid-continent of North America, with 55%, 35%, and 10% of these being genetically wild, hybrid swarm, and F3, respectively. We conclude that continued game-farm introgression into wild mallards is not isolated to the eastern population of mallards in North America, and may be increasing and more widespread than previously detected. Mallards in our study had greater incidence of game-farm hybridization than other locales in the mid-continent but less than eastern North American regions suggesting further need to understand game-farm mallard genetic variation and movement across the continent.

Nest parasitism is a common reproductive strategy used by many species of cavity nesting birds. Among these, the wood duck ( Aix sponsa ) is known to have evolved very specific strategies of when and whom to parasitize that is often based on population and/or environmental queues. Here, we investigated the genetic relationship of two female wood ducks competing over an artificial nesting box in Delaware, including the continued incubation of one female despite the death and body remains of the other female throughout the incubation process. We test whether such an extreme case of nest parasitism can be explained by relatedness, egg lineage composition, or a combination of other factors. To do so, we extracted genomic DNA from blood and tissue of the females, as well as chorioallantoic membranes of all viable and inviable eggs. Subsequently, we assessed relatedness among females and eggs based on hundreds of nuclear loci and the mitochondrial control region. We concluded that (1) the two incubating females were entirely unrelated, (2) the single clutch is in fact represented by a minimum of four unrelated females, and (3) a single female can lay eggs sired by different males. The latter finding is the first direct evidence for successful extra-pair copulation in wood ducks. With decreasing costs and increasing effectiveness, genomic methods have the potential to provide important insights into more complex ecological and evolutionary tactics of such populations.

Although most birds are considered to be at least partially monogamous, molecular evidence continues to uncover that many species can have multiple sexual mates. Many species of Waterfowl (Order Anseriformes) consistently deploy alternative breeding strategies, and although cavity nesting species have been well studied, few attempts to understand rates of alternative breeding strategies exist in the Anatini tribe. Here, we assay mitochondrial DNA and thousands of nuclear markers across 20 broods of American black ducks ( Anas rubripes ; “black duck”) that included 19 females and 172 offspring to study population structure as well as types and rates of secondary breeding strategies in coastal North Carolina. First, we report high levels of relatedness among nesting black ducks and offspring and while 17 (of 19) females were of pure black duck descent, three were found to be black duck x mallard ( A . platyrhynchos ) hybrids. Next, we evaluated for mismatched mitochondrial DNA and paternity identities across each female’s clutch to determine types and frequency of alternative or secondary breeding strategies. Although we report that nest parasitism occurred in two nests, 37% (7 of 19) of the sampled nests were multi-paternal as a result of extra-pair copulation. In addition to being part of a mix of strategies used to increase fecundity by successfully breeding females, we posit nest densities providing easier alternative mate access for males also explains high rates of extra-pair copulation among our sampled black ducks. Ultimately, however, while some proportion of females of many species engage in forms of secondary breeding strategies, we conclude that the decision to do so appears to be seasonally flexible for each individual.

Causes for genomic and morphological similarities among recently radiated species are often multifaceted and are further convoluted among species that readily interbreed. Here, we couple genomic and morphological trait comparisons to test the extent that ancestry and gene flow explain the retention of mallard-like traits within a sister species, the Mexican duck. First, we confirm that these taxa remain genetically structured, and that Mexican ducks exhibit an isolation-by-distance pattern. Despite the assumption of wide-spread hybridization, we found only a few late-stage hybrids, all from the southwestern USA. Next, assessing 23 morphological traits, we developed a genetically-vetted morphological key that is > 97% accurate in distinguishing across sex-age cohorts of Mexican ducks, mallards, and hybrids. During key development, we determined that 25% of genetically pure, immature male Mexican ducks of the northern population naturally displayed mallard-like traits in their formative plumage. In fact, applying this key to 55 museum specimens, we identified that only four of the 14 specimens originally classified as phenotypic hybrids were truly hybrids. We discuss how genomic and morphological comparisons shed light into the mechanism(s) underlying the evolution of complex phenotypic traits in recent radiations, and how misunderstanding the true morphological diversity within Mexican ducks resulted in taxonomic revisions that hindered conservation efforts.

Prevailing theory suggests that sex ratios of offspring at birth should not differ from parity if costs of producing offspring of both sexes are similar. However, offspring sex ratios may deviate from parity when there is sex specific variation in fitness returns. We assessed offspring sex ratios of eastern wild turkeys (Meleagris gallopavo silvestris) across the southeastern United States by molecular determination of sex from eggshell membranes of hatched clutches. Our objective was to evaluate whether offspring sex ratios differed from parity and to examine potential drivers of variation in offspring sex ratios across and within our study sites. We sexed 724 offspring from 83 nests using molecular markers and identified 278 males and 446 females, with a sex ratio of 38% male. We found that offspring sex ratios were biased towards females on three hunted study sites but did not differ from parity at our remaining non‐hunted site. Specifically, on sites with spring hunting, where male mortality was increased due to harvest, the probability of producing male offspring was 47% lower than on our non‐hunted site. Our findings suggest that female wild turkeys may adaptively adjust the sex ratio of their offspring based on predictable, sex specific mortality, favoring the sex with higher survival, thereby enhancing their lifetime fitness. Our results provide insights into reproductive strategies of wild turkeys and the influence of hunting on sex ratios in Galliform offspring.

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.

Anthropogenically mediated hybridization can lead to several outcomes, with the most severe being hybrid swarms and the genetic extirpation of local populations. With the frequency of introductions by humans increasing, understanding the genetic consequences is critical for future conservation actions. Here, we investigate the consequences of domestic Mallard (Anas platyrhynchos) introductions in New Zealand (NZ) on the genetic integrity of native NZ Gray Ducks (Anas superciliosa superciliosa; known locally as Pārera). Although presumed to be genetically extinct, pockets of pure Gray Ducks persist (around 9% of samples), with the western portion of the South Island as the core of their range. In contrast, introduced Mallards have experienced widespread introgression from Gray Ducks that has likely facilitated their rapid establishment and expansion throughout NZ. Moreover, levels of gene flow and divergent selective pressures have resulted in NZ Mallards no longer genetically resembling their original stock and instead have resulted in a hybrid swarm. Estimates of genomic vulnerability for NZ Mallards suggest higher resiliency to future ecological changes as compared to local NZ Gray Ducks. While conservation of NZ's uniquely adapted Gray Duck should remain the priority, we discuss the evolutionary implications of naturalization resulting from anthropogenic hybridization for a now self‐sustaining Mallard population. Anthropogenic hybridization resulting from the introduction of domestic mallards in New Zealand has led to widespread introgression of native Gray Ducks, resulting in a hybrid swarm. While pure Gray Ducks continue to persist in isolated areas of more undisturbed habitat, mallards have become genetically unique and are likely more resilient to ecological change than the native NZ Gray Ducks.