Genetic divergence and microbiome differentiation between bisexual and parthenogenetic populations of Haemaphysalis longicornis in Shandong, China

<title>Abstract</title> <p> Background The longhorned tick, <italic>Haemaphysalis longicornis</italic> , is an important vector of severe fever with thrombocytopenia syndrome virus (SFTSV) and other zoonotic pathogens. This tick exhibits a unique dual reproductive strategy—bisexual reproduction and obligate parthenogenesis—which may influence its population dynamics, genetic structure, and microbiome composition. However, the spatial distribution, genetic differentiation, and microbial community variation between these two reproductive types remain poorly understood, particularly in Shandong Province, a high-endemic region for both the tick and SFTS. Methods We collected 525 <italic>H. longicornis</italic> specimens from 14 prefecture-level cities across Shandong Province. Mitochondrial COX1 gene sequencing was used to assess genetic diversity, haplotype distribution, population differentiation ( <italic>Fst</italic> ), and demographic history. Additionally, 16S rRNA gene sequencing was performed to characterize bacterial community composition, diversity, co-occurrence networks, and functional potentials (PICRUSt2, FAPROTAX) in bisexual versus parthenogenetic populations. Results Thirty-three haplotypes were identified, forming two deeply divergent clades: Clade A (bisexual) predominantly in inland mountainous areas, and Clade B (parthenogenetic) largely confined to coastal regions. Bisexual populations exhibited higher genetic diversity and gene flow, whereas parthenogenetic populations showed reduced diversity and pronounced isolation. Microbiome analysis revealed that parthenogenetic ticks were dominated by <italic>Coxiella</italic> (∼80% relative abundance) and possessed a simplified, highly mutualistic co-occurrence network (no negative edges, modularity = 0.59). In contrast, bisexual ticks harboured a more diverse microbiota with a complex, modular network (modularity = 0.74) including competitive interactions. Functional predictions indicated that parthenogenetic populations were enriched for pathogenicity-related pathways, while bisexual populations were enriched for environmental sensing and nutrient cycling functions. Conclusions Reproductive mode is a major driver of both genetic differentiation and microbiome divergence in <italic>H. longicornis</italic> . Parthenogenetic populations rely on a specialised <italic>Coxiella</italic> -dominated symbiosis and exhibit reduced genetic diversity, whereas bisexual populations maintain a flexible, resilient host-microbe system. These findings provide a novel framework for understanding the ecological adaptation and pathogen transmission potential of this important tick, and highlight the need for reproductive-type-specific surveillance and control strategies. </p>