Human activities, including domestication and biological introductions, profoundly affect species' genomic architecture and diversity. While the effects of these processes are increasingly documented, genome-wide analyses comparing independent domestication and introduction events within a single species have been limited. *Undaria pinnatifida*, a Pacific kelp, presents a unique opportunity for such a study. It has been cultivated for centuries in its native range in Northeast Asia and introduced to four other continents within the last 50 years. This study investigates the genomic consequences of both cultivation and introduction in *U. pinnatifida*, aiming to understand human-driven evolutionary changes. Domestication involves co-evolution between humans and a species they cultivate, influencing reproductive traits and creating 'domestication phenotypes' through conscious or unconscious selection. Globalization has led to widespread biological introductions, mixing populations that evolved in isolation and creating new selective pressures in the introduced ranges. Few studies have examined the simultaneous effects of domestication and introduction. *U. pinnatifida*, with its independent cultivation history and widespread introduction, offers a valuable model to address this gap. This study will use whole-genome sequencing to compare genomic architecture across natural, cultivated, and introduced populations, disentangling the influences of demography and selection.

Existing literature highlights the significant impacts of human activities on the evolution of various species. Studies on domesticated plants and animals reveal the genomic signatures of selection during domestication (e.g., Fan et al., 2019; Wang et al., 2014; Stein et al., 2018). Similarly, research on invasive species demonstrates the genomic changes associated with introduction and adaptation to new environments (e.g., Lee et al., 2019; Puzey & Vallejo-Marín, 2014). However, few studies have integrated the effects of both domestication and introduction within the same species. The impacts of globalization and the increasing concern over non-indigenous species necessitate further understanding of the evolutionary processes involved in human-mediated range expansions (Pyšek & Richardson, 2010; Pimentel et al., 2001; Rius & Darling, 2014). Understanding *U. pinnatifida*'s genomic response to both cultivation and introduction can provide valuable insights into the interplay of domestication and invasion.

This study involved genome sequencing and population genomic analysis of *Undaria pinnatifida*. First, a high-quality reference genome was generated from a Korean cultivar (Kr2015) using PacBio long reads and Illumina paired-end reads. The assembly was polished, anchored to a genetic map, and annotated using transcriptome and homology-based methods. This resulted in a 634 Mb assembly with 20,716 predicted protein-coding genes. The genome's size and composition were compared to other brown algal genomes, revealing differences in repeated element insertion and gene density. Synteny analysis compared Kr2015 to another *U. pinnatifida* genome (from China) and *E. siliculosus*, revealing conserved gene order despite significant evolutionary distance. Next, 41 individuals from diverse populations (natural, cultivated, and introduced in France and New Zealand) were resequenced. Approximately 7 million high-quality SNPs and indels were identified using GATK, and used to analyze genetic diversity, population structure, linkage disequilibrium (LD), and runs of homozygosity (ROH). Population structure was investigated using PCA, phylogenetic tree reconstruction, and admixture analysis. Measures of genetic diversity (heterozygosity), LD, and ROH were compared across population types. Finally, to detect signatures of selection, a decorrelated composite of multiple signals (DCMS) method was applied using reduction of diversity, delta Tajima’s D, and FST. Genes located in regions under putative selection were functionally annotated and enriched biological pathways were identified. The study used several statistical tests including the Wilcoxon rank sum test to compare gene density between *U. pinnatifida* and *E. siliculosus* and parametric bootstrap replications for phylogenetic support.

The study generated a high-quality genome assembly for *Undaria pinnatifida*, allowing for detailed population genomic analysis. Population structure analyses clearly distinguished individuals based on geographic origin (native, cultivated, introduced to France, and introduced to New Zealand), reflecting independent introduction events. Introduced populations showed expected patterns of reduced genetic diversity, low recombination rates (high LD), and high homozygosity (high ROH). Surprisingly, cultivated populations in Korea exhibited high genetic diversity, high recombination rates, and low homozygosity, unlike the predictions for bottlenecked populations. This was attributed to large-scale cultivation practices involving mixing of individuals from various sources. Comparison between French and New Zealand introduced populations highlighted differences in their introduction histories, with France exhibiting more pronounced founder effects than New Zealand. Analysis for signals of selection revealed significant genomic regions under selection in cultivated populations, enriched for genes involved in carbohydrate biosynthesis, potentially reflecting selection for increased yield. Conversely, no significant enrichment in biological functions was found in comparisons across generations in the Wellington Harbour population, likely due to insufficient time for selection to act and the comparable environments between New Zealand and Korea. Cultivated populations in Korea, due to their high genetic variation, could serve as valuable reservoirs of evolutionary potential.

The findings demonstrate the impact of human activity on the genome evolution of *Undaria pinnatifida*. The distinct genomic landscapes observed in introduced populations strongly support the previously proposed introduction scenarios, showing how introduction history shapes genome architecture. Unexpectedly, large-scale cultivation in Korea maintained high genetic diversity, contradicting typical domestication bottleneck effects. This highlights the importance of considering cultivation practices in shaping genomic diversity. The absence of strong selection signatures in New Zealand contrasts with the findings in cultivated populations, possibly due to the ecological plasticity of *U. pinnatifida*. Future research should integrate phenotypic data with genomic information to fully understand the interplay of selection, adaptation, and domestication. This includes quantitative trait locus mapping and genome-wide association studies. The study's findings have implications for conservation and management of *U. pinnatifida* and other seaweed species.

This study provides a comprehensive genome-wide analysis of the impact of human activities on *Undaria pinnatifida*. The results reveal distinct genomic signatures reflecting independent introductions and unexpected effects of large-scale cultivation. The high genetic diversity maintained in Korean cultivated populations suggests their potential as reservoirs of evolutionary potential. Future research integrating phenotypic and genomic data, particularly through quantitative trait locus mapping, can provide a more detailed understanding of the domestication and adaptation processes.

The study's relatively small sample size, particularly for some populations, could limit the power of the analyses. The study focused primarily on genetic diversity and did not directly assess phenotypic traits. Future studies should incorporate more detailed phenotypic characterization to further understand the link between genotype and phenotype. The study relies on existing hypotheses regarding introduction pathways and mechanisms; more detailed investigations into these would strengthen the conclusions.