Genome-wide insights into adaptive divergence, historical demography, and habitat suitability of Ptychobarbus Kaznakovi and P. leptosomus

Our previous study from 2024 indicated that Ptychobarbus leptosomus is a new species found only in the Yalong River (the largest tributary of the Jinsha River). P. leptosomus was historically classified as P. kaznakovi, which lives in the Jinsha River. To date, the evolutionary history and population dynamics of P. leptosomus and P. kaznakovi have not been reported. In our study, both species have similar morphologies, which may reflect gene flow between the two species. Genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single-nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses based on SNPs indicated that P. leptosomus is an independent Picea species. Additionally, P. kaznakov is more closely related to P. chungtienensis, which is consistent with its geographic distribution. The obvious gene flow from P. kaznakovi and P. chungtienensis branches to P. dipogon was detected. Historical population dynamics analysis revealed that tectonic events in the Shaluli Mountains and the Quaternary climate oscillation had important impacts on the current distribution patterns of the two species, which experienced similar population contraction and expansion processes. Local adaptation promoted differentiation between P. leptosomus and P. kaznakov. Genotype and environment association analysis revealed that 35,654 SNPs were related to environmental factors, mainly related to adaptation to precipitation seasonality and temperature seasonality. Selective elimination analysis revealed that the selected genes were enriched mainly in glycan biosynthesis and metabolism and growth hormone synthesis, secretion, and action (genes such as glycine decarboxylase (gldc), cyp51, igf-1, and tnf-α), which can help P. leptosomus and P. kaznakov adapt better to the water environment of the high mountains and valleys in the Shaluli Mountains. This study emphasizes the significant role of geological and environmental changes in shaping the population history and evolutionary processes of P. kaznakovi and P. leptosomus, and deepens our understanding of the species classification of Ptychobarbus and provides a basis for future species protection.