The interplay of evolutionary, ecological, and anthropogenic processes is critical in shaping species distributions and biodiversity patterns. Recent studies highlight the importance of examining functional and phylogenetic traits to gain a more comprehensive understanding of these patterns. However, significant knowledge gaps remain regarding functional and phylogenetic diversity patterns among freshwater fish, particularly in the context of large-scale hydrological alterations such as the South-to-North Water Diversion Project (SNWDP). In this study, we investigated the spatial patterns of fish taxonomic, functional, and phylogenetic diversities and community assemblage, alongside their environmental drivers, within five impounded lakes of SNWDP. Our analysis sought to identify relationships between different aspects of diversity, assessing patterns of mismatch or congruence, and evaluating the efficacy of using one aspect as a proxy for another. Our results revealed that: 1) fish diversity and community assembly showed no longitudinal gradient, with spatial mismatches across diversity dimensions; 2) functional diversity was negatively correlated with both taxonomic and phylogenetic diversities, while the latter two showed no correlation; and 3) the SNWDP primarily affected taxonomic and functional diversities by altering water depth, nutrient status and promoting non-native species invasion, while phylogenetic diversity was mainly influenced by changes in water temperature and dissolved oxygen. These findings underscore the distinct contributions of various diversity measures and emphasize that no single measure can reliably predict another, highlighting the necessity of selecting diversity measures tailored to specific questions (e.g., for conservation or fisheries management).

Field surveys of the five impounded lakes were conducted in January and April 2017 to collect fish and environmental data. Within each lake, eight sampling sites were selected based on the morphological, hydrological, and geographical conditions of the lake, as well as the habitat heterogeneity provided by the fisheries management committee for each lake. Altogether, forty sites were sampled across the five impounded lakes.

At each sampling site, a pelagic multi-mesh gillnet, a benthic multi-mesh gillnet, and a ground trap net were deployed together. The multi-mesh gillnet, adapted from standard Swedish methods, featured 12 panels of varying mesh sizes from 5 to 55 mm (specifically, 5, 6.25, 8, 10, 12.5, 15.5, 19.5, 24, 30, 35, 43, and 55 mm). Each gillnet was designed to be 2 m in height and 30 m in length, with different mesh panels assembled in a random order, yet maintaining uniformity across all gillnets in terms of the sequence of mesh sizes. The trap net, with a mesh size of 5 mm, was 25 m long and segmented into 20 compartments, featuring two 10 cm openings at both ends to allow fish to enter the trap. Given the shallow nature of the lakes surveyed (average water depth < 3 m), this assortment of fishing gear proved effective for sampling fish populations at various water depths. Fish sampling was conducted from the late afternoon (around 17:00) until the following morning (around 05:00), for approximately 12 hours. This timing was chosen to manage the catch size per net, ensuring a manageable number of fish for accurate sampling.

The fish collected were individually identified to species. For each species, the number of individuals was recorded and their weight was measured to the nearest gram. Ten functional traits for each individual fish, including five continuous and five categorical variables, were recorded. These traits, which are integral to functional diversity studies of fish, relate directly to their strategies for feeding (e.g., relative mouth gape size, dietary preferences), reproduction (e.g., mode of reproduction, frequency of reproduction), and movement (e.g., body shape, relative size of the head). In our analysis, we assumed that intraspecific variability was low compared to interspecific variation.

For each identified fish species, comparative sequences of the cytochrome c oxidase subunit Ⅰ gene were retrieved from the National Center for Biotechnology Information (NCBI) public database accessible at  https://www.ncbi.nlm.nih.gov/. Mega software was used to construct the phylogenetic tree with the neighbor-joining method. At each sampling site, Water temperature (WT), conductivity (Cond), dissolved oxygen (DO), and pH were measured in situ using a portable multiparameter probe (YSI Professional Plus). Water depth (WD) and Secchi depth (SDT), indicating water transparency, were measured using a Secchi disc. Concurrently, a 2-liter water sample was collected, chilled on ice, and transported to the laboratory for further analysis. Total nitrogen (TN), total phosphorus (TP), chemical oxygen demand (COD), chlorophyll a (Chl-a), and ammonia nitrogen (NH₃-N) concentrations were analyzed following the procedures described in E.W. Rice (2017). Altogether, eleven environmental variables were measured for each sampling site. In addition, we calculated the proportion of non-native fishes (Pnn) in each lake as the ratio of non-native fish count to overall fish count.

Taxonomic diversity was assessed through species richness (SR) and the Shannon-Wiener diversity index (Shannon), utilizing the “vegan” packages in R for calculations. To characterize the functional and phylogenetic diversities of each fish assemblage, we employed four distinct metrics: mean functional pairwise distance (FD_MPD), mean functional distance to nearest taxon (FD_MNTD), mean pairwise phylogenetic distance (PD_MPD), and mean phylogenetic distance to nearest taxon (PD_MNTD). These metrics were chosen for their efficacy in capturing the various dimensions of functional and phylogenetic diversities. FD_MPD/PD_MPD represents the mean functional/phylogenetic distance between all pairs of species within a community, capturing phylogenetic diversity at the community level. This distance is calculated as the total branch length of the shortest path between each pair of species. In contrast, FD_MNTD/PD_MNTD focuses on the mean distance between each species and its closest functionally similar or phylogenetic relative, providing a measure of diversity that accounts only for the nearest-relative distances in terms of either functional similarity or phylogenetic relatedness. Higher values of FD_MPD/PD_MPD indicate that coexisting species in an assemblage possess highly divergent functional traits or are widely distributed across clades, whereas similarity in functional traits or lower values reflects phylogenetical clustering. Higher values of FD_MNTD/PD_MNTD indicate a scarcity of functionally similar or closely related species within the community, while lower values suggest a prevalence of such relationships. FD_MPD/PD_MPD and FD_MNTD/PD_MNTD were respectively calculated using the ‘‘mpd’’ and ‘‘mntd’’ functions from the “picante’’ package in R. Characteristic trait distances between species were measured using Gower distance and calculated using the ‘‘gowdis’’ function from the ‘‘FD’’ package in R.

We examined community assembly in the phylogenetic dimension using the net phylogenetic relatedness index (PD_NRI), which is calculated as the inverse of the standardized effect size of the mean phylogenetic distance (PD_MPD) between all pairs of taxa in the phylogeny of the assemblage. Similarly, the nearest phylogenetic taxon index (PD_NTI) measures the standardized average phylogenetic distance between each sample and its most closely related taxon (PD_MNTD). To obtain the PD_NRI and PD_NTI, the PD_MPD and PD_MNTD values for each community assemblage were compared with the values of 999 sets of random community assemblages. These random assemblages were created by shuffling the taxa labels within the phylogenetic distance matrix, using the “picante” package in R, in line with. A positive PD_NRI/PD_NTI value signifies phylogenetic clustering, indicating that species are more closely related than expected by chance. Conversely, a negative PD_NRI/PD_NTI value indicates phylogenetic overdispersion, where species are less closely related than expected. A PD_NRI/PD_NTI value close to 0 points to a random phylogenetic structure within the community (Webb et al., 2002). In parallel to the phylogenetic indices PD_NRI and PD_NTI, we calculated the net functional relatedness index (FD_NRI) and the nearest functional taxon index (FD_NTI) as functional analogues. These indices standardize FD_MPD and FD_MNTD against expectations from a null model, following the same standardization approach as PD_MPD to PD_NRI and PD_MNTD to PD_NTI.