DOI: 10.5061/dryad.rr4xgxdhx
title: Spatial mismatch and congruence in the taxonomic, functional, and phylogenetic diversities of fish assemblages in China’s water diversion lakes

description: 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).
description: 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 &lt; 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 (NH<sub>3</sub>-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 “<em>vegan</em>” 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 “<em>picante</em>’’
 package in R. Characteristic trait distances between species were measured
 using Gower distance and calculated using the ‘‘gowdis’’ function from the
 ‘‘<em>FD</em>’’ 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 “<em>picante</em>”
 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.
description: # Spatial mismatch and congruence in the taxonomic, functional, and
 phylogenetic diversities of fish assemblages in China's water
 diversion lakes 1. Author Information A. Principal Investigator Contact
 Information Name: Zhice Liang Institution: Institute of Hydrobiology
 Address: Wuhan, China Email:
 [liangzhice@ihb.ac.cn](mailto:liangzhice@ihb.ac.cn) B. Associate or
 Co-investigator Contact Information Name: Chuanbo Guo Institution:
 Institute of Hydrobiology Address: Wuhan, China Email:
 [guocb@ihb.ac.cn](mailto:guocb@ihb.ac.cn) 2. Date of data collection
 (single date, range, approximate date): January and April 2017 3.
 Geographic location of data collection: Five impounded lakes of
 China's South-to-North Water Diversion Project 4. Information about
 funding sources that supported the collection of the data: National
 Natural Science Foundation of China, Award: 32172980; the earmarked fund
 for China Agriculture Research System: CARS-45 SHARING/ACCESS INFORMATION
 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0)
 Public Domain 2. Links to publications that cite or use the data: Liang,
 Z. C., Gozlan, R. E., et al. (2024). Spatial mismatch and congruence in
 the taxonomic, functional, and phylogenetic diversities of lake fish
 assemblages in Eastern China. Ecological Informatics. 3. Links to other
 publicly accessible locations of the data: None 4. Links/relationships to
 ancillary data sets: None 5. Was data derived from another source? No If
 yes, list source(s): NA 6. Recommended citation for this dataset: Liang,
 Z. C., Gozlan, R. E., et al. (2024). Data from: Spatial mismatch and
 congruence in the taxonomic, functional, and phylogenetic diversities of
 lake fish assemblages in Eastern China. Dryad Digital Repository. DOI:
 10.5061/dryad.rr4xgxdhx DATA & FILE OVERVIEW 1. File List: A) Table
 S1: Fish abundance in the five impounded lakes of the China's
 South-to-North Water Diversion Project B) Table S2: Environment Variables
 in the five impounded lakes of the China's South-to-North Water
 Diversion Project C) Table S3: Taxonomic, functional, and phylogenetic
 α-diversity indices D) Table S4: Standardized effect values for functional
 and phylogenetic α-diversity indices E) Fasta S1: Comparative sequences of
 the mitochondrial COI gene (cytochrome c oxidase subunit Ⅰ) for each
 identified fish species 1. Relationship between files, if important: None
 2. Additional related data collected that was not included in the current
 data package: None 3. Are there multiple versions of the dataset? No A. If
 yes, name of file(s) that was updated: NA i. Why was the file updated? NA
 ii. When was the file updated? NA
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Table S1:Fish abundance in the five
 impounded lakes of the China's South-to-North Water Diversion Project
 1. Number of variables: 42 2. Number of cases/rows: 81 3. Variable List: *
 GYL: Gaoyou Lake * HZL: Hongze Lake * LML: Luoma Lake * NSL: Nansi Lake *
 DPL: Dongping Lake 4. Missing data codes: None 5. Specialized formats or
 other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Table S2: Environment Variables in the five
 impounded lakes of the China's South-to-North Water Diversion Project
 1. Number of variables: 12 2. Number of cases/rows: 81 3. Variable List: *
 GYL: Gaoyou Lake * HZL: Hongze Lake * LML: Luoma Lake * NSL: Nansi Lake *
 DPL: Dongping Lake * WT: Water temperature, ℃ * WD: Water depth, m * SDT:
 Secchi depth, m * Cond: Conductivity, µS/cm * DO: Dissolved oxygen
 concentration, mg/L * pH: Potential of hydrogen * TN: Total nitrogen, mg/L
 * TP: Total phosphorus, mg/L * NH3-N: Ammonia nitrogen, mg/L * COD:
 Chemical oxygen demand, mg/L * Chl-a: Chlorophyll a, µg/L * Pnn:
 Proportion of non-native fishes 4. Missing data codes: None 5. Specialized
 formats or other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Table S3: Taxonomic, functional, and
 phylogenetic α-diversity indices 1. Number of variables: 6 2. Number of
 cases/rows: 81 3. Variable List: * GYL: Gaoyou Lake * HZL: Hongze Lake *
 LML: Luoma Lake * NSL: Nansi Lake * DPL: Dongping Lake * SR: Species
 richness * Shannon: Shannon-Wiener diversity index * FD_MPD: Mean
 functional pairwise distance * FD_MNTD: Mean functional distance to
 nearest taxon * PD_MPD: Mean pairwise phylogenetic distance * PD_MNTD:
 Mean phylogenetic distance to nearest taxon 4. Missing data codes: None 5.
 Specialized formats or other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Table S4: Standardized effect values for
 functional and phylogenetic α-diversity indices 1. Number of variables: 4
 2. Number of cases/rows: 21 3. Variable List: * GYL: Gaoyou Lake * HZL:
 Hongze Lake * LML: Luoma Lake * NSL: Nansi Lake * DPL: Dongping Lake *
 FD_NRI: Net functional relatedness index * FD_NTI: Nearest functional
 taxon index * PD_NRI: Net phylogenetic relatedness index * PD_NTI: Nearest
 phylogenetic taxon index 4. Missing data codes: None 5. Specialized
 formats or other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Fasta S1: Comparative sequences of the
 mitochondrial COI gene (cytochrome c oxidase subunit Ⅰ) for each
 identified fish species. 1. Variable List: * Fish species * Comparative
 sequences of the mitochondrial COI gene * Branch Lengths * Bootstrap
 values 2. Missing data codes: None 3. Specialized formats or other
 abbreviations used: None