International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 74-82 http://ecoevopublisher.com/index.php/ijmec 75 pressures on survival- and reproduction-based traits. Molecular ecology combines genetic data with environmental and spatial data to expose evolutionary pressures at genome and landscape scales. The aim of this study is to examine differential genetic structure and adaptive traits of domesticated and wild duck populations in various climatic zones, employing the presently available molecular tools including genome-wide SNP analysis, ecological niche modeling, and phylogeographic reconstruction. These results can be utilized to guide conservation programs, inform breeding schemes, and refine the understanding of bird response to environmental change. 2 Phylogeny and Lineage Evolution of Domestic and Wild Ducks 2.1 Taxonomic history and phylogenetic controversies of ducks The classification of ducks, especially in the genus Anas, has been confusing regarding which immediate wild relatives of domesticated ducks. The mallard (Anas platyrhynchos) and Chinese spot-billed duck (A. zonorhyncha) were historically proposed as primary ancestors. However, new genomic studies report broad introgression and deduces the real wild ancestor of the domestic duck to be potentially an as-yet-undefined or unsampled population, rather than was believed previously and despite present phylogenetic divergence (Guo et al., 2020; Feng et al., 2020; Zhang et al., 2023). 2.2 Phylogenetic relationships revealed by molecular data Molecular investigations, including whole-genome resequencing and mitochondrial DNA sequencing, have clarified domestic-wild duck relationships. Chinese domestic duck breeds are mostly discovered to carry mallard and spot-billed duck haplotypes, indicating both species' contributions to domestic lineages (Zhang et al., 2023). Phylogenetic network analysis and networks never reveal a deep divergence between wild ducks and domestic ducks with signatures of hybridization events and gene flow, particularly among Chinese spot-billed ducks and domestic ducks (Feng et al., 2020; Guo et al., 2020; Feng et al., 2021; Pal et al., 2022; Zhang et al., 2023) (Figure 1). 2.3 Methods for phylogenetic tree construction and lineage divergence time estimation Researchers employ a suite of molecular and computational methods of duck phylogeny reconstruction. Maximum-likelihood (ML) phylogenies and median-joining (MJ) networks are the preferred mitochondrial DNA data (Zhang et al., 2023). Population and demographic inferences may be achieved by resequencing the complete genome, including divergence time estimation using coalescent-based and molecular clock methods. These methods have shown that domestic ducks descended from mallards and spot-billed ducks hundreds of thousands of years ago, prior to the supposed period of domestication (Guo et al., 2020; Feng et al., 2020; Liu et al., 2020; Pal et al., 2022). 2.4 Evolutionary trends in wild duck lineages and domestication events of domestic ducks Genetic research indicates that wild duck lineages split relatively extensively during the most recent glacial cycle and that mallards and spot-billed ducks speciated around 70 000 years ago (Liu et al., 2020). Domestic ducks are also believed to have diverged from their closest wild ancestors even earlier, with domestication then having had sophisticated selection trends for aspects such as egg and meat production, feather pigmentation, and domesticatability (Zhang et al., 2018; Feng et al., 2020; Liu et al., 2020; Zhu et al., 2021). Hybridization and introgression between wild and domestic animals have also contributed to the genetic landscape, resulting in phenotypic diversity among modern domestic ducks (Feng et al., 2020; Guo et al., 2020; Liu et al., 2020; Zhu et al., 2021). 3 Geographic Origin and Dispersal History of Ducks 3.1 Hypotheses on the origin of ducks and their biogeographical background Anas genus and related groups of ducks are believed to have originated in Eurasia, with fossil and molecular evidence proposing widespread Eurasian distribution during the Miocene, followed by dispersal across other continents (Zelenkov et al., 2018). Phylogeographic study indicates that huge duck lineages, such as mallard-like ducks, spread across Oceania, broader Indonesia, and the Philippines over the last 1~2 million years, developing unique genetic lineages in island regions (Kaminski et al., 2024) (Figure 2). High dispersal capacity of ducks enabled them to have broad biogeographical distribution and complex evolutionary history (Zelenkov et al., 2018).
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