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1. Population genetics and geographic origins of mallards harvested in northwestern Ohio

   https://doi.org/10.1371/journal.pone.0282874  

   Schummer, Michael L. ; Simpson, John ; Shirkey, Brendan ; Kucia, Samuel R. ; Lavretsky, Philip ; Tozer, Douglas C. ( March 2023 , PLOS ONE)

   Chiang, Tzen-Yuh (Ed.)

   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. 

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2. The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards

   https://doi.org/10.1038/s42003-023-05170-w  

   Lavretsky, Philip ; Mohl, Jonathon E. ; Söderquist, Pär ; Kraus, Robert H. S. ; Schummer, Michael L. ; Brown, Joshua I. ( August 2023 , Communications Biology)

   The translocation of individuals around the world is leading to rising incidences of anthropogenic hybridization, particularly between domestic and wild congeners. We apply a landscape genomics approach for thousands of mallard (Anas platyrhynchos) samples across continental and island populations to determine the result of over a century of supplementation practices. We establish that a single domestic game-farm mallard breed is the source for contemporary release programs in Eurasia and North America, as well as for established feral populations in New Zealand and Hawaii. In particular, we identify central Europe and eastern North America as epicenters of ongoing anthropogenic hybridization, and conclude that the release of game-farm mallards continues to affect the genetic integrity of wild mallards. Conversely, self-sustaining feral populations in New Zealand and Hawaii not only show strong differentiation from their original stock, but also signatures of local adaptation occurring in less than a half-century since game-farm mallard releases have ceased. We conclude that ‘wild’ is not singular, and that even feral populations are capable of responding to natural processes. Although considered paradoxical to biological conservation, understanding the capacity for wildness among feral and feral admixed populations in human landscapes is critical as such interactions increase in the Anthropocene.

    

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3. Chromosomal-level reference genome of a wild North American mallard ( Anas platyrhynchos )

   https://doi.org/10.1093/g3journal/jkad171  

   Lavretsky, Philip ; Hernández, Flor ; Swale, Thomas ; Mohl, Jonathon E ( July 2023 , G3: Genes, Genomes, Genetics)

   Campbell, P (Ed.)

   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, proximity ligation Chicago, and Dovetail Hi-C libraries. The final assembly is ∼1.04 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome-level 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 3 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.

    

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4. A hierarchical model for jointly assessing ecological and anthropogenic impacts on animal demography

   https://doi.org/10.1111/1365-2656.13747  

   Riecke, Thomas V ; Sedinger, Benjamin S ; Arnold, Todd W ; Gibson, Dan ; Koons, David N ; Lohman, Madeleine G ; Schaub, Michael ; Williams, Perry J ; Sedinger, James S ( August 2022 , Journal of Animal Ecology)

   The management of sustainable harvest of animal populations is of great ecological and conservation importance. Development of formal quantitative tools to estimate and mitigate the impacts of harvest on animal populations has positively impacted conservation efforts.

   The vast majority of existing harvest models, however, do not simultaneously estimate ecological and harvest impacts on demographic parameters and population trends. Given that the impacts of ecological drivers are often equal to or greater than the effects of harvest, and can covary with harvest, this disconnect has the potential to lead to flawed inference.

   In this study, we used Bayesian hierarchical models and a 43‐year capture–mark–recovery dataset from 404,241 female mallardsAnas platyrhynchosreleased in the North American midcontinent to estimate mallard demographic parameters. Furthermore, we model the dynamics of waterfowl hunters and habitat, and the direct and indirect effects of anthropogenic and ecological processes on mallard demographic parameters.

   We demonstrate that density dependence, habitat conditions and harvest can simultaneously impact demographic parameters of female mallards, and discuss implications for existing and future harvest management models.

   Our results demonstrate the importance of controlling for multicollinearity among demographic drivers in harvest management models, and provide evidence for multiple mechanisms that lead to partial compensation of mallard harvest. We provide a novel model structure to assess these relationships that may allow for improved inference and prediction in future iterations of harvest management models across taxa.

    

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5. Admixture in Africanized honey bees ( Apis mellifera ) from Panamá to San Diego, California (U.S.A.)

   https://doi.org/10.1002/ece3.8580  

   Zárate, Daniela ; Lima, Thiago G. ; Poole, Jude D. ; Calfee, Erin ; Burton, Ronald S. ; Kohn, Joshua R. ( February 2022 , Ecology and Evolution)

   The Africanized honey bee (AHB) is a New World amalgamation of several subspecies of the western honey bee (Apis mellifera), a diverse taxon historically grouped into four major biogeographic lineages: A (African), M (Western European), C (Eastern European), and O (Middle Eastern). In 1956, accidental release of experimentally bred “Africanized” hybrids from a research apiary in Sao Paulo, Brazil initiated a hybrid species expansion that now extends from northern Argentina to northern California (U.S.A.). Here, we assess nuclear admixture and mitochondrial ancestry in 60 bees from four countries (Panamá; Costa Rica, Mexico; U.S.A) across this expansive range to assess ancestry of AHB several decades following initial introduction and test the prediction that African ancestry decreases with increasing latitude. We find that AHB nuclear genomes from Central America and Mexico have predominately African genomes (76%–89%) with smaller contributions from Western and Eastern European lineages. Similarly, nearly all honey bees from Central America and Mexico possess mitochondrial ancestry from the African lineage with few individuals having European mitochondria. In contrast, AHB from San Diego (CA) shows markedly lower African ancestry (38%) with substantial genomic contributions from all four major honey bee lineages and mitochondrial ancestry from all four clades as well. Genetic diversity measures from all New World populations equal or exceed those of ancestral populations. Interestingly, the feral honey bee population of San Diego emerges as a reservoir of diverse admixture and high genetic diversity, making it a potentially rich source of genetic material for honey bee breeding.

    

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