Mismatch Between Phylogenetic and Taxonomic Diversity Hotspots in Freshwater Fish Reveals Critical Conservation Gaps

Aim

Phylogenetic diversity (PD) and phylogenetic endemism (PE) offer biogeographical and conservation insights beyond taxonomic approaches, yet their environmental associations in freshwater ecosystems remain unclear. Using freshwater fish, we mapped PD and PE patterns, identified their environmental correlates, and compared them with taxonomic metrics (species richness [SR], weighted endemism [WE]), while assessing conservation gaps.

Location: Qinghai‐Tibetan Plateau (QTP) and surrounding regions.

Time period: Mid‐Pliocene to present.

Major taxa studied: Schizothoracine fishes.

Methods

We compiled species distribution and reconstructed a molecular‐based phylogeny. PD, PE, SR, and WE were quantified at the subdrainage scale. Phylogenetic hotspots were categorised as ‘cradles’ (neo‐endemism) or ‘museums’ (paleo‐endemism). Linear mixed‐effects models evaluated environmental correlates (climate, hydrology, topography, and geology). Hotspot overlap with protected areas was assessed.

Results

Subdrainages exhibiting high values for both phylogenetic and taxonomic metrics were predominantly distributed along the southern margin of the QTP, particularly in the Hindu Kush–Himalaya–Hengduan mountains, yet showed substantial spatial incongruence between metrics (SR vs. PD: r  = 0.67, p  < 0.001; WE vs. PE: r  = 0.29, p  < 0.001). Both hotspot types were concentrated in these high‐value subdrainages, covering 13.36% (phylogenetic) and 11.96% (taxonomic) of the study area, with limited spatial overlap (Jaccard index = 0.18). Notably, 65.89% of ‘cradles’ and ‘museums’ exhibited co‐occurrence. Although most environmental factors, dominated by temperatures (annual mean and seasonality), showed generally consistent associations with both phylogenetic and taxonomic metrics, their contributions varied considerably. Conservation coverage remained inadequate for both hotspots (phylogenetic: 27.43%; taxonomic: 31.89%).

Main Conclusions

We highlight substantial incongruence between phylogenetic and taxonomic diversity patterns and their environmental correlates in freshwater fishes. Our drainage‐scale framework provides a template for analyzing freshwater phylogenetic diversity metrics, complementing taxonomic diversity in conservation planning, as protecting both is essential for maintaining ecosystem adaptive capacity under anthropogenic pressures.