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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. Low levels of hybridization between domestic and wild Mallards wintering in the lower Mississippi Flyway

   https://doi.org/10.1093/ornithology/ukac034  

   Davis, J_Brian; Outlaw, Diana_C; Ringelman, Kevin_M; Kaminski, Richard_M; Lavretsky, Philip (August 2022, Ornithology)

   Abstract The Mallard (Anas platyrhynchos) duck is a ubiquitous and socio-economically important game bird in North America. Despite their generally abundant midcontinent population, Mallards in eastern North America are declining, which may be partially explained by extensive hybridization with human-released domestically derived game-farm Mallards. We investigated the genetic composition of Mallards in the middle and lower Mississippi flyway, key wintering regions for the species. We found that nearly 30% of wild Mallards carried mitochondrial (mtDNA) haplotypes derived from domestic Mallards present in North America, indicating that the individuals had female game-farm Mallard lineage in their past; however, nuclear results identified only 4% of the same sample set as putative hybrids. Recovering 30% of samples with Old World (OW) A mtDNA haplotypes is concordant with general trends across the Mississippi flyway and this percentage was stable across Mallards we sampled a decade apart. The capture and perpetuation of OW A mtDNA haplotypes are likely due to female breeding structure, whereas reversal of the nuclear signal back to wild ancestry is due to sequential backcrossing and lower and/or declining admixture with game-farm Mallards. Future studies of wild ancestry of Mississippi flyway Mallards will benefit from coupling molecular and spatial technology across flyways, seasons, and years to search for potential transitions of Mallard populations with different genetic ancestry, and whether the genetic ancestry is somehow linked to an individual’s natal and subsequent breeding location. 

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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.)

   Abstract 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)

   Abstract 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. Building a feral future: Open questions in crop ferality

   https://doi.org/10.1002/ppp3.10367  

   Mabry, Makenzie E.; Bagavathiannan, Muthukumar V.; Bullock, James M.; Wang, Hongru; Caicedo, Ana L.; Dabney, Clemon J.; Drummond, Emily B. M.; Frawley, Emma; Gressel, Jonathan; Husband, Brian C.; et al (March 2023, PLANTS, PEOPLE, PLANET)

   Societal Impact StatementGiven the rapidly increasing drought and temperature stresses associated with climate change, innovative approaches for food security are imperative. One understudied opportunity is using feral crops—plants that have escaped and persisted without cultivation—as a source of genetic diversity, which could build resilience in domesticated conspecifics. In some cases, however, feral plants vigorously compete with crops as weeds, challenging food security. By bridging historically siloed ecological, agronomic, and evolutionary lines of inquiry into feral crops, there is the opportunity to improve food security and understand this relatively understudied anthropogenic phenomenon. SummaryThe phenomenon of feral crops, that is, free‐living populations that have established outside cultivation, is understudied. Some researchers focus on the negative consequences of domestication, whereas others assert that feral populations may serve as useful pools of genetic diversity for future crop improvement. Although research on feral crops and the process of feralization has advanced rapidly in the last two decades, generalizable insights have been limited by a lack of comparative research across crop species and other factors. To improve international coordination of research on this topic, we summarize the current state of feralization research and chart a course for future study by consolidating outstanding questions in the field. These questions, which emerged from the colloquium “Darwins' reversals: What we now know about Feralization and Crop Wild Relatives” at the BOTANY 2021 conference, fall into seven categories that span both basic and applied research: (1) definitions and drivers of ferality, (2) genetic architecture and pathway, (3) evolutionary history and biogeography, (4) agronomy and breeding, (5) fundamental and applied ecology, (6) collecting and conservation, and (7) taxonomy and best practices. These questions serve as a basis for ferality researchers to coordinate research in these areas, potentially resulting in major contributions to food security in the face of climate change. 

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