Dataset to: Reier S., Trontelj P., Kruckenhauser L., Kapun M., Wanka, A., Palandačić A. (2025) "Factors beyond karstification have shaped the population structure of a surface-dwelling minnow (Phoxinus lumaireul) able to disperse underground"

The Dinaric Karst, a biodiversity hotspot,
features complex surface and subterranean hydrological networks that influence
aquatic species distribution. This study investigates how karst hydrology
shapes the genetic structure of the surface-dwelling minnow <i>Phoxinus lumaireul</i>,
examining both large-scale and fine-scale population patterns. Using mitochondrial
DNA (mtDNA) and genome-wide single nucleotide polymorphism (SNP) data of 827
specimens of <i>P. lumaireul</i>, three hypotheses were tested: (1) karst underground
water connections facilitate genetic connectivity within and across river
systems, whereas non-karst rivers exhibit genetic connectivity mostly within
the same system; (2) historical and occasional hydrological connections have
shaped present-day population structure, leaving genetic signatures of
relatedness where no contemporary hydrological links exist; and (3) genomic
approaches provide additional insights into biologically relevant connections
that may not be captured by classical tracing tests. The large-scale analyses
confirmed three main genetic groups (1a–c), whose structure was likely shaped
by Pleistocene glaciations and associated microrefugia rather than by karst
hydrology. Fine-scale structure analyses revealed that while karst hydrology
facilitated gene flow within specific areas, connectivity was uneven and
influenced by local hydrological dynamics and historical admixture events.
Furthermore, some underground pathways identified by classical tracing tests
lacked evidence of genetic connectivity, underscoring the limitations of
traditional methods and the added value of genomic data in indirectly detecting
biologically relevant hydrological connections. These findings highlight the
influence of both historical processes and contemporary karst hydrology on <i>P.
lumaireul</i> populations, emphasizing their vulnerability to karst ecosystems and
the need for targeted conservation efforts.

迪纳里克喀斯特（Dinaric Karst）作为生物多样性热点区域，拥有复杂的地表与地下水文网络，其对水生物种的分布具有显著影响。本研究旨在探究喀斯特水文如何塑造地表栖息的鱥<i>Phoxinus lumaireul</i>的遗传结构，同时考察其大尺度与微尺度种群格局。研究团队基于827尾<i>P. lumaireul</i>样本的线粒体DNA（mtDNA）与全基因组单核苷酸多态性（SNP）数据，验证了三项假说：（1）喀斯特地下水连接可促进河流系统内部及跨系统的遗传连通性，而非喀斯特河流的遗传连通性则主要局限于同一水系内部；（2）历史时期与偶发的水文连接塑造了当前的种群结构，在当代无水文关联的区域仍留存有亲缘相关的遗传信号；（3）基因组学方法可额外揭示传统示踪测试无法捕捉到的、具有生物学意义的水文关联。大尺度分析结果确认了三个主要遗传类群（1a–c），其结构更可能受更新世冰期及相关微避难所影响，而非喀斯特水文作用。微尺度种群结构分析显示，尽管喀斯特水文促进了特定区域内的基因交流，但连通性并不均衡，且受局地水文动态与历史遗传混合事件的调控。此外，部分经传统示踪测试确认的地下通道并未检测到遗传连通性信号，这凸显了传统方法的局限性，以及基因组数据在间接探测具有生物学意义的水文关联方面的附加价值。本研究结果揭示了历史演化过程与当代喀斯特水文共同对<i>P. lumaireul</i>种群的影响，强调了该物种对喀斯特生态系统的脆弱性，以及开展针对性保护工作的必要性。