Native fish assemblages in natural lakes across Japan: Endemism deterioration lasting centuries

This study aimed to illustrate the changing diversity patterns of native freshwater fish in the past two centuries and to identify priority locations for native fish conservation to counter future degradation.


| INTRODUC TI ON
The global biodiversity crisis, an alarming decline in the variety of life on Earth, has put nearly one million species at risk of extinction (Díaz et al., 2019;Sills et al., 2018;Singh, 2002).With its roots in anthropogenic activities, the crisis had accelerated since the mid-20th century (Steffen et al., 2015), when pollution, habitat destruction and fragmentation, invasive species, overexploitation and climate change became more pronounced (Dirzo et al., 2014;Foley et al., 2005;Haddad et al., 2015;Noyes et al., 2009;Pecl et al., 2017).
Freshwater ecosystems undergo a significant rate of biodiversity loss, nearly four times higher than that of terrestrial ecosystems (Albert et al., 2021;Turak et al., 2017).Freshwater fishes rank as the second most endangered group of vertebrates, surpassed only by amphibians in terms of threat levels (Arthington et al., 2016;Darwall & Freyhof, 2015).The list of extinct fish continues to grow with new extinction records worldwide (Reid et al., 2019).Nonetheless, this silent crisis, concealed below water, has not received adequate public, political or scientific attention (Cooke et al., 2016).Hence, it is urgent to propose appropriate conservation strategies for freshwater fish assemblages towards the post-2020 goals and targets negotiated at the 15th meeting of the Conference of the Parties to the United Nations Convention on Biological Diversity (COP15).
Amidst the global biodiversity crisis, native fishes, especially those endemic to specific regions, are considered the most affected group within aquatic systems, accounting for a significant proportion of the overall loss of freshwater species (Dudgeon et al., 2006).Endemic fish species developed morphological, physiological, reproductive, feeding and behavioural adaptations during long-term evolutionary processes, enabling them to thrive under specific ecological conditions of their local habitat context (Braaten & Guy, 2002;Chapman et al., 2011;Schulte, 2001;Wainwright & Richard, 1995;Werner & Hall, 1988).In addition, some endemic fish species with narrow distributional ranges could be attributed to historical geographic events, such as tectonic movements and volcanic activity (Crandall et al., 2010;Salzburger et al., 2014).However, disturbance or destruction to ecosystems often poses a challenge for endemic species, making it difficult for them to adapt to the altered environment and leading to declines in their populations and, in some instances, extinction.The loss of endemic fish species can disrupt local ecosystems, leading to nutrient cycling and food web imbalances while impacting local economies and cultural practices that depend on these species (Ding et al., 2023;Reis et al., 2015).
Protecting endemic fish populations through diverse conservation measures has become one of the utmost priorities at the present moment.
Re-establishing essential ecological processes is a practical approach to fish conservation, necessitating an integrated and efficient framework for understanding assembling processes of fish assemblages (Jiang et al., 2020;Radinger et al., 2023).A growing consensus among ecologists has come to acknowledge that, alongside traditional taxonomic diversity, phylogenetic relatedness and functional composition offer valuable insights into the community assembling mechanisms.Phylogenetic distances among species reflect their evolutionary histories and can reveal ecological differences (Webb et al., 2002).Native species extinctions are not random occurrences within hierarchical phylogenetic trees; instead, they expose the life history responses of these species to environmental changes (Fréville et al., 2007;Winter et al., 2009).Extinctions disproportionally impact native or endemic fish species, often originating from families with lower species richness and representing unique components of their biotas (Gaston, 1998;Vamosi & Wilson, 2008).
Functional diversity assessments consider the functional traits of fish species, enabling direct inferences about ecological responses to environmental alterations.For example, by examining morphoanatomical traits related to food acquisition, researchers can assess the effects of fish on other aquatic organisms through trophic interactions (Villéger et al., 2017).Although the importance of phylogenetic and functional diversity indicators for conservation is widely acknowledged, prioritizing one over the other remains a debated issue (Mazel et al., 2018;Owen et al., 2019).Concurrently, numerous phylogenetic and functional diversity indices and computational approaches have emerged in the past decades, proposing various perspectives on ecosystem functions and services.However, these metrics' intricacy presents challenges to researchers and policymakers involved in native fish conservation (Tuomisto, 2010).Pursuing a concise and comprehensive index that integrates taxonomic, phylogenetic and functional information is thus a pressing concern in practical conservation biology.
Native conservation necessitates understanding biodiversity organization from local to regional spatial scales, thereby aiding conservation planning (Gardner et al., 2013;Socolar et al., 2016).Alpha and beta diversity of community serve as vital tools for analysing species assembling within local sites and among distinct locations, respectively (Veech et al., 2002).Measuring the multifaceted alpha diversity can identify local biodiversity hotspots and guide the establishment of protected areas (Jiang et al., 2020).Meanwhile, assessing the multifaceted beta diversity, including its turnover and nestedness components, can guide decisions on the numbers and locations of conservation sites from a broader scale (Gering et al., 2003;Simberloff & Abele, 1976).Spatial turnover quantifies the extent to which species are exchanged between communities, while nestedness reflects unidirectional concentration of species among communities (Baselga, 2010).If the turnover pattern is the primary driver of beta diversity, conservation measures should prioritize protecting several locations with unique species; while if the nestedness pattern is more important, the conservation approach targeting areas that exhibit high alpha diversity would be adequate (Jiang et al., 2019;Tscharntke et al., 2002;Tuomisto et al., 2003).
Furthermore, the recently widely utilized index known as the Local Contribution to Beta Diversity (LCBD) holds significant value in conservation studies (Legendre & De Cáceres, 2013).It measures the uniqueness of a community at each study site within a larger region.
High LCBD values, which represent unique species composition, help prioritize specific locations for conservation efforts and assess the effectiveness of these strategies over time (Dai et al., 2023).
Hence, by employing concurrent measurements of alpha and beta diversity, as well as related metrics, conservation-related insights can be gained comprehensively, supporting efforts to prevent additional loss of biodiversity at both local and regional scales (Jiang et al., 2020;Montaño-Centellas et al., 2020).
The Japanese archipelago, stretching about 2000 km in a northeast-southwest direction, is an ideal natural laboratory to study spatial patterns of freshwater fishes.During the Plio-Pleistocene (about 5 million years ago), the archipelago was frequently connected and disconnected from continental Asia, thereby leading to a unique freshwater fish fauna (Lindberg, 1972;Watanabe et al., 2017).
Stemmed from continental Asia, freshwater fishes established themselves in the Japanese archipelago through two main pathways: the Siberian route and the Chinese route (Aoyagi, 1957).The Siberian route involved predominantly cold-water fishes spreading from the Heilongjiang River (aka Amur River) to the waters in Hokkaido, the northernmost island of present-day Japan (Kai, 2022).The Chinese route witnessed a fish fauna primarily composed of temperate species originating from the ancient Yellow River basin, relocating to Kyushu, the southernmost main island of Japan (Tabata, 2022).
Subsequently, fishes from Hokkaido and Kyushu made their way to Honshu, Japan's largest island in the middle (see Figure 1 for island locations), yielding a unique spatial pattern of freshwater compositions across the Japanese archipelago.According to previous research, native freshwater fishes in the Japanese archipelago experienced alterations due to escalating environmental and artificial pressures, as evidenced by a decline in species richness and significant shifts in functional group composition from roughly two centuries ago (Matsuzaki et al., 2013(Matsuzaki et al., , 2016)).However, these studies did not consider phylogenetic information and regional beta diversity patterns of native fishes across the nation.Phylogenetic information reflects the historical and ecological uniqueness of fish species and also suggests the foundation for adapting to environmental changes.
Failure to measure phylogenetic diversity could result in gaps within comprehensive fish conservation initiatives.Additionally, without depicting regional fish dissimilarity patterns among the studied lakes using beta diversity they did not provide direct evidence for identifying specific areas for practical conservation measures.What's more, previous studies have only examined alterations in fish diversity spanning from the historical to the current period, yet without conducting quantitative analyses to anticipate potential future trends.Considering that the fish species lost during this transition are primarily threatened species identified as at risk of extinction by the Japanese Red List, simulating future native extinctions based on the fish species in the current period and their categories in the Red List is deemed a viable approach to address this gap.
In this context, the present study emphasizes regional fish beta diversity and spatial distribution patterns, supplemented with phylogenetic information of native freshwater fishes in Japanese lakes.
Specifically, this study analyses and compares the changes over time in the multifaceted alpha and beta diversity of native fishes in Japanese lakes from the past to the present and anticipates future trends.We also introduced a framework designed to measure the cumulative diversity of fish assemblages that combine the three aspects of taxonomic, phylogenetic and functional diversity together.
Based on the cumulative alpha and beta diversity, as well as the cumulative contribution of each lake to beta diversity, this study aimed to unravel the mechanisms behind the spatiotemporal shifts in the diversity of native fishes in Japanese lakes since about two centuries ago.Additionally, by investigating the association between cumulative fish diversity and the geographical location of the studied lakes, we attempt to pinpoint locations that should be prioritized in native conservation.Ultimately, we believe this study will provide direct theoretical support for restoring and conserving freshwater ecosystems in Japan amidst the ongoing biodiversity crisis.

| Data collection and collation
We utilized the native freshwater fish assemblage data in 39 Japanese lakes (Figure 1) from our previous research (Matsuzaki et al., 2013(Matsuzaki et al., , 2016)).These lakes, situated between 30° and 45° north latitude, broadly scatter across the majority of eco-regions for freshwater fish fauna in Japan (Watanabe, 2012), with areas ranging from less than 1 km 2 to approximately 670 km 2 , and their average depths vary by over 51 m.Additionally, lakes with various trophic statuses are encompassed, including oligotrophic, mesotrophic and eutrophic lakes.Covering such a wide range of latitude, eco-region, area, depth and trophic status, the studied lakes are considered representative of Japanese lakes in general.The native fish dataset was compiled by reviewing over 300 references and over 1000 museum specimens, as described by Matsuzaki et al. (2016).Although the sampling methods of fish collection in the referenced literature varied among lakes, fish records from all studied lakes were cross-corroborated by at least three different sources to ensure the validity of the fish species records in the lakes.In addition, only fish incidence (presence-absence) rather than abundance data was used in this study, further excluding biased results that may have been caused by different sampling intensities (Dai et al., 2023).We specifically targeted strict freshwater fish species that inhabit lakes and those that migrate between lakes and surrounding drainage basins.As previously described by Matsuzaki et al. (2016), distributional records of the strict freshwater fish in both 'historical' and 'current' periods were obtained after careful literature review and dataset collation.The historical period refers to the native fish fauna of the past, specifically before massive anthropogenic extirpation, and roughly corresponds to the pre-Meiji Era , a period characterized by rapid industrialization and modernization in Japan.Thus, the historical period fish dataset contains the greatest number of native freshwater fish species.
The current period dataset, a subset of historical dataset, witnessing some species becoming locally extinct, mainly reflecting the distributional pattern of native fish species after the 21st century.
Considering that 90% of the unrecorded fish species from past to present were designated as threatened (either critically endangered (CR), endangered (EN) or vulnerable (VU), Table S1) according to the Japanese Red List (Ministry of the Environment, 2020), we emulated two extinction scenarios based on the current-period fish datasets following Pimiento et al. (2020).The first scenario, dubbed 'future I', involved categorizing species as extinct or extant according to the associated extinction probability of their respective red list category (Davis et al., 2018).For instance, species categorized as vulnerable (VU) were assigned a minimum extinction probability of 0.1 over the next century (Kindvall & Gärdenfors, 2003;Mooers et al., 2008;Redding & Mooers, 2006).Specifically, during one round of simulation, we simultaneously and randomly excluded 99.90%, 67.23% and 10.00% of fish species from each of the CR, EN and VU categories, F I G U R E 1 Map showing the location of studied lakes across the Japanese archipelago.Derived from Takemura (2015).
respectively.This process resulted in a new fish distribution table, which served as a subset of the fish distribution dataset for the current period.We then calculated diversity indices based on the pruned fish distribution table.After completing both the species removal and diversity calculations, we reintroduced the excluded species for a new round of simulations and calculations.This entire sequence of steps was repeated 1000 times to ensure statistical robustness.
The average of the 1000-time diversity index calculations was subsequently recorded as the measure of diversity among native fishes in lakes across Japan for the 'future I' period.Besides, the second scenario, termed 'future II', assumes the extinction of all currently threatened fish species (Barnosky et al., 2011;Smiley et al., 2020).
This scenario aimed to illustrate the potentially dire consequences of threatened native fish loss if no conservation measures are implemented and emphasize the collective contribution of these species to fish biodiversity assemblages (Toussaint et al., 2016).

| Phylogenetic and functional dendrogram construction
The Linnaeus taxonomy classifications have been commonly employed as a proxy for the phylogeny dendrogram in assessing phylogenetic diversity, especially for endemic and extinct species those are challenging to obtain accurate genetic information for Heino and Tolonen (2017), Jiang et al. (2020), Wang et al. (2021), Zhang et al. (2018).The Linnaean classifications of all recorded Japanese native fishes were arranged for constructing phylogenetic dendrogram across seven levels: subclass, subphylum, superorder, order, family, genus and species.The classification information was subjected to a double comparison between Fishes of the World (Nelson et al., 2016) and Eschmeyer's Catalog of Fishes (Fricke et al., 2023).If there were any conflicting classifications, the latest version was adopted.Villéger et al. (2017) proposed that measuring fish functional diversity should encompass five essential ecological functions: food acquisition, mobility, nutrient budget, reproduction and defence against predation.
Subsequently, we opted to employ 16 functional traits (maximum total body length, body shape, trophic guild, dietary components, diet breadth, foraging period, vertical position, temperature preference, flow preference, substrate preference, age at maturation, parental protection, egg diameter, longevity, fecundity and spawning substrate) that reflecting these crucial ecological functions to construct a functional dendrogram (Table S2).Trait information was obtained by reviewing multiple published monograph and online databases.For further specifics, please refer to Matsuzaki et al. (2013).Utilizing an approach akin to that described by Swenson (2014) and Xu et al. (2022), we estimated phylogenetic and functional distances for all recorded fish species based on their taxonomy classifications and functional traits, respectively.Subsequently, dendrograms were generated in R (R Core Team, 2023) using a combination of functions from various packages, including the taxa2dist and as.phylo functions from the 'vegan' (Oksanen et al., 2022) and the 'ape' package (Paradis & Schliep, 2019), among others.Furthermore, we conducted a Mantel test, performed in R with the 'vegan' package, to evaluate the correlation between the two dendrograms, with the aim of determining whether there were significant overlaps between the two trees (Figure S1).The Mantel test produced a relatively low coefficient value, which suggests that only a limited amount of functional information was found to overlap with phylogenetic signals (Xu et al., 2022).Consequently, in the subsequent assessments of native fish diversity, we separately considered the phylogenetic and functional dendrograms.

| Calculation of alpha diversity
The alpha diversity of native fish assemblages in 39 lakes was evaluated independently for four periods (historical, current, future I and future II).Taxonomic, phylogenetic and functional diversity was parallelly calculated.The species richness of native fishes was counted as the indicators for taxonomic alpha diversity.Phylogenetic alpha diversity was measured via two indices: the mean phylogenetic distance (MPD) and the mean nearest phylogenetic distance (MNPD).Based on the generated phylogenetic dendrogram, the MPD metric calculates the MPD between pairs of species randomly selected from a given fish assemblage.
Instead, the MNPD metric performs a similar calculation, but the distance between individuals is measured only to their closest non-conspecific relative (Pinto-Ledezma et al., 2020;Vamosi et al., 2009;Zu et al., 2019).We also computed the mean functional distance (MFD) and the mean nearest functional distance (MNFD) for each fish assemblage based on the functional dendrogram, using an analogous methodology (Xu et al., 2022).The calculations of MPD, MNPD, MFD and MNFD were performed in R using the 'picante' package (Kembel et al., 2010).

| Calculation of beta diversity
Similar to alpha diversity, the beta diversity assessment of native fish assemblages was also respectively conducted for four periods (historical, current, future I and future II) from three perspectives (taxonomic, phylogenetic and functional diversity components).
To calculate the taxonomic beta diversity (tβ) of native fish assemblages in each lake, we took the average value of pairwise comparisons in species dissimilarity between that lake and the other 38 lakes.The overall tβ was then divided into two additive components, species turnover (tβ turn ) and nestedness (tβ nest ), based on the species patterns triggering overall dissimilarity (Baselga, 2010).Turnover quantifies the extent to which certain species are replaced by others when transitioning from one habitat to another, suggesting that different environments or locations may host different species.In contrast, nestedness measures how much the species composition of one habitat (particularly a less diverse one) is a subset of a more diverse habitat, indicating that species-poor sites tend to have species also present in species-rich sites but not vice versa.Elevated turnover values underscore substantial ecological differences between habitats, whereas increased nestedness could indicate a trend of species loss (Baselga, 2010).To differentiate the relative strengths of the two components in driving overall dissimilarity, we computed the proportion of species turnover to overall dissimilarity.A value over 0.5 indicates the predominance of species turnover, while a value under 0.5 suggests nestedness is the main component (Si et al., 2016).Employing a similar approach, we incorporated phylogenetic and functional dendrograms into calculations to determine the phylogenetic (pβ) and functional (fβ) beta diversity of native fish assemblages in each lake.Analogously, phylogenetic turnover (pβ turn ) and nestedness (pβ nest ), as well as functional turnover (fβ turn ) and nestedness (fβ nest ), were also assessed.Meanwhile, we also computed the respective proportions of turnover components accounting for phylogenetic and functional dissimilarity.
Given that the fish dataset utilized in our study is binary incidence data across a relatively broader spatial scale, we chose to use the Sørensen dissimilarity index and its derived indexes to evaluate the multifaceted beta diversity (Dai et al., 2020;Jost et al., 2011).

| Calculation of ecological uniqueness
The ecological uniqueness of fish assemblages in each lake was evaluated for each of the four periods using the LCBD index (Legendre & De Cáceres, 2013).The LCBD evaluations were conducted concurrently from three perspectives to obtain the taxonomic (tLCBD), phylogenetic (pLCBD) and functional (fLCBD) contributions to the corresponding nationwide native fish dissimilarity patterns.We first Hellinger-transformed the species × lake matrix for native fishes and subsequently calculated the total variance (SS total ) of the generated matrix.Then the tLCBD values were computed following tLCBD i = SS i /SS total .The SS i values are defined as the squared distance between a given lake i and the average lake in the multivariate ordination distance space (Legendre & De Cáceres, 2013).Furthermore, applying an expanded algorithm to this methodology enables the quantification of both the phylogenetic (pLCBD) and functional (fLCBD) uniqueness of fish assemblages in the studied lakes, akin to the tLCBD (Nakamura et al., 2020).Despite the growing number of literature utilizing the tLCBD index as a guidance indicator for biodiversity conservation (da Silva et al., 2018;Xia et al., 2022), a considerable proportion of such studies lack the inclusion of phylogenetic and functional information (Hill et al., 2021;Li et al., 2023;Santos et al., 2021).
Our study design thus presents a promising chance to enhance the understanding of the ecological uniqueness of native fish assemblages from a more comprehensive and integrated perspective.
The computations for tLCBD were conducted utilizing the beta.divfunction, while those for pLCBD and fLCBD were executed using the Beta.div_adaptfunction (Nakamura et al., 2020) in R.

| Calculation of cumulative diversity
Ultimately, we devised a novel composite index referred to as the cumulative diversity that integrates multiple independent diversity indices, incorporating taxonomic, phylogenetic and functional information.The cumulative diversity index is calculated by taking the arithmetic mean of logarithmically transformed values of the taxonomic, phylogenetic and functional indices of the same type.
The equation for cumulative diversity calculation of assemblage j can be expressed succinctly as:

| Statistical analysis
First, we conducted a comparative analysis of the discrepancies in the values of each measured alpha and beta diversity index and related metrics across the four temporal periods to discern the temporal trends in the diversity of native fish assemblages within the Japanese lakes.This was accomplished by utilizing the one-way permutational multivariate analysis of variance with 9999 permutations to assess the differences among four data sets, which comprised the diversity indices of fish fauna in all studied lakes during the historical, current, future I and future II periods, respectively.The p-values were corrected by the Bonferroni method during the pairwise comparisons between periods.Then, we constructed a three-dimensional spatial coordinate system, utilizing the taxonomic, phylogenetic and functional LCBD indices as the three respective axes.Lakes exhibiting relatively greater ecological uniqueness were identified according to the positions within this three-dimensional space.In this context, lakes with greater relative importance (ecological uniqueness of species composition) refer to those with LCBD index values surpassing the mean values of the corresponding indices (Duarte et al., 2022;Sor et al., 2018).Finally, besides the temporal change in cumulative diversity of each lake, we employed regression analysis to associate the latitude of each lake with its cAlpha, cBeta and cLCBD values for the four periods, respectively, with the aim of delineating the spatial distribution patterns as well as their temporal alterations in the integrated cumulative diversity of native fishes throughout Japan over hundreds of years.

| Temporal changes in multifaceted alpha diversity
In the studied lakes across Japan, an enumeration of 55 freshwater fish species, categorized into 29 genera and 13 families, was recorded in the historical period, of which 30 species were designated as threatened.In the current period, after the 21st century, a total of 45 native freshwater fish species were recorded, of which nine out of the 10 extirpated species were classified as threatened.In the two scenarios of extinction simulations, 35 species were preserved for future I and 23 for future II period.The PERMANOVA results demonstrate that native fish richness is significantly lower compared with the historical period, irrespective of whether it is in the current (F = 5.252, p = .019),future I (F = 8.747, p = .003)or future II (F = 17.990, p < .001)period (Figure 2a; Table S3).However, we discovered that phylogenetic and functional alpha diversity exhibited divergent trends.We observed a substantial decline in the MPD index from the historical period to future (F = 8.833, p < .001),while simultaneously, the alterations in MNPD values remained insignificant across all periods (p = .678).Contrarily, for functional indices, little changes were observed in MFD values throughout the time (p > .407),but MNFD values consistently and significantly rose across four periods (F = 3.098, p = .027).

| Temporal changes in multifaceted beta diversity
Unlike the monotonic alterations in alpha diversity across all periods, the changes in beta diversity over time exhibited significant hump-shaped trends (p < .019, Figure 3; Table S4).During the historical periods, the average tβ, pβ and fβ values were 0.059 ± 0.096, 0.398 ± 0.092 and 0.402 ± 0.087 (mean ± SD), respectively.These beta diversity indices then experienced an increase till the current periods to 0.525 ± 0.081, 0.443 ± 0.065 and 0.430 ± 0.068.However, as for the simulated results, in the future I period, there was a decrease in these beta diversity values, which continued to fall in the future II period to 0.465 ± 0.086, 0.390 ± 0.067 and 0.377 ± 0.069, respectively.
Meanwhile, a steady decline was noted in the proportion of turnover patterns.While taxonomic turnover was the primary factor influencing species beta diversity in the historical period (contributing to 57.8% of overall dissimilarity, Figure 3a), its dominance began to equalize with the nestedness pattern during both the current and future I period (accounting for 50.5%, Figure 3b,c).This dominance eventually lessened in the future II period, with its proportion falling below 50% (Figure 3d).
However, the influence of phylogenetic and functional turnovers consistently remained lower than that of nestedness and also continued diminishing over time (Figure 3; Table S4).

| Lakes with unique fish assemblages
By positioning the studied lakes in a three-dimensional coordinate space based on their tLCBD, pLCBD and fLCBD values, we were able to pinpoint the lakes whose indices exceeded the corresponding mean in all three dimensions, as labelled in Figure 4.These and southernmost (Kyushu) islands.In the current period, only one lake was determined to have greater uniqueness.However, in the simulated future I and II, the number of unique lakes increased to six and seven, respectively, and the majority of them were located in Honshu rather than Hokkaido or Kyushu (Figure 4).

| Spatiotemporal patterns of cumulative diversity
The proposed cumulative diversity allows us to visualize changes in the diversity and distribution patterns of native fish assemblages in Japanese lakes (Figure 5).The cumulative alpha diversity (cAlpha), revealing hump-shaped associations with the latitude (p < .001; Figure 5b; Table S5), suggested that the richness of native fishes was comparatively low on Hokkaido (the northernmost) and Kyushu (the southernmost).Instead, lakes in the Honshu demonstrated high levels of species richness.This spatial distribution pattern of cAlpha was consistently observed across all temporal periods, despite a continuous decline in the average index values (F = 6.521, p = .001,Figure 5a; Table S6).Conversely, we observed higher cumulative beta diversity (cBeta) values in the lakes of Hokkaido and Kyushu, resulting in a U-shaped curve along the latitudinal gradient (p < .001, Figure 5d; Table S5).These spatial patterns were similarly observed across all three temporal periods, but with an increase in cBeta values from 0.156 in the historical period to 0.165 in the current period, followed by a decrease to 0.149 in the simulative future II period (F = 3.879, p = .012,Figure 5c; Table S6).
Finally, our study identified a significant spatiotemporal pattern shift in cumulative LCBD values throughout the Japan archipelago.During the historical period, the lakes located in the northernmost and southernmost islands exhibited the most outstanding contribution to nationwide fish beta diversity (highest cLCBD values), resulting in significant U-shaped curves along the latitude (R 2 = .647,p < .001,Table S6).However, in the following periods, this curve was flattened, indicating the homogeneous Points on the map of Japan denote each lake's cumulative diversity, with point size reflecting the diversity index value.Squares symbolize cumulative alpha diversity (cAlpha, a), diamonds represent cumulative beta diversity (cBeta, c), and circles indicate each lake's cumulative location contribution to beta diversity (cLCBD, e).Average values with a standard deviation of cumulative diversity are presented in the corresponding panels.On the right side, three scatter plots display the spatial correlation between each lake's cAlpha (b), cBeta (d), cLCBD (f) and its latitude, respectively.Colour codes distinguish between the four periods: blue for the historical period, yellow for the current period, and orange and red for the future I and II periods, respectively.
relative contribution of individual lakes (Figure 5f).Upon the removal of all threatened species in the future simulations, lakes located in southern Honshu, such as Lake Biwa, experienced a significant increase in cLCBD values, establishing them as the lakes with the more important contribution to nationwide native fish dissimilarity patterns (Figure 5e).

| DISCUSS ION
We demonstrated the deterioration process of native fishes across the Japanese lakes.As the decline of native fish species continues, species that are functionally close are particularly vulnerable to the threat of local extinction.These species, often ranked as threatened in the Japanese Red List (Ministry of the Environment, 2020), are the first to vanish from the lakes, leading to a nationwide homogenous distributional pattern.Based on our proposed cumulative diversity assessment, we depicted that the lakes situated in Hokkaido and Kyushu islands have pronouncedly lost their fish endemism.Our findings suggested that the decline of native fish species, along with the fish homogenization and endemism loss, is an ongoing process that will exacerbate without immediate, specific conservation actions, especially for threatened fish species.
Our results of the decline of native fish alpha diversity revealed that the shrinking of phylogenetic and functional dendrograms was not synchronized.The incongruent findings reported in this study are consistent with those of previous research (Devictor et al., 2010;Jiang et al., 2020;Purschke et al., 2013;Xu et al., 2022), suggesting that examining changes in community diversities using either perspective alone might lead to biased conclusions.We observed that the branches lost in the phylogenetic tree tended to be more distant and isolated, while species with closer phylogenetic associations were retained, resulting in decreasing MPD values while the MNPD values remained unchanged.In contrast, the degradation of functional dendrograms showed a preferential loss of species from groups with high functional similarity, while keeping the basic skeleton of functional tree intact, leading to stable MFD values accompanied by increasing MNFD values.The contrasting degradation of phylogenetic and functional alpha diversity can be explained by the complementary nature of phylogenetic and functional information (Galland et al., 2019).Phylogenetic relations generally reflect internal pre-adaptation to novel environments, whereas functional similarity suggests phenotypic characteristics related to interspecific resource competitions (Xu et al., 2022).Phylogenetic diversity reveals species' abilities adapted to local environmental conditions over long periods of evolution, especially physiological traits such as heat tolerance and low oxygen tolerance (Collins et al., 2013;Comte & Olden, 2017;Karabanov et al., 2021).Our result of conserved phylogenetic shrinking lends support to the theory that disturbances tend to select assemblages of phylogenetically close species, as these species are more likely to share similar resistance abilities (Helmus et al., 2010).Given that the majority of the fish species that were the first to be lost in this research were predominantly This finding also highlights the importance of functional redundancy in ecosystem stability, which provides insurance against species loss (Chua et al., 2019;Oliver et al., 2015;Xu et al., 2022).
Homogenization is a significant issue in global freshwater biodiversity (Su et al., 2021).This study also revealed a clear homogenization trend in the Japanese archipelago lakes.Beta diversity is crucial for biodiversity conservation since it reveals the variations in species composition and distribution across different habitats or regions, enabling targeted conservation strategies and the preservation of diverse ecological communities (Socolar et al., 2016).Our findings suggest that the loss of native fish species in Japanese lakes was independent, resulting in an initial increase and a subse- is also believed to contribute to the observed low regional freshwater dissimilarity (Su et al., 2021).In addition to geographical isolation and human footprint, we acknowledge that habitat heterogeneity across islands could further account for this spatial distribution pattern.This is particularly significant given the colder temperatures in Hokkaido lakes result in a limited native fish richness when compared to the temperate southern islands.
The LCBD results pronouncedly highlight the endemism degeneration of fish species in Hokkaido and Kyushu.Within the historical period, eight lakes were identified with high ecological uniqueness.
These lakes encompassed 80% of the investigated lakes on Hokkaido Island and half on Kyushu Island.This observation posits that barring anthropogenic interference, lakes on the northernmost (Hokkaido) and southernmost (Kyushu) islands harbour exceedingly unique fish fauna.Moreover, most native fish species found on these two islands are not shared, underlining the paramount role of these distant lakes in fostering respective endemic species.This historical pattern of distinctiveness resonates with the function of Hokkaido and Kyushu as the northern and southern gateways for the dispersion of freshwater fish from continental Asia to the Japanese archipelago (Aoyagi, 1957;Watanabe et al., 2017) Additionally, the beta diversity decomposition results provide evidence that the primary manifestation of native fish dissimilarity in Japanese lakes would be the nestedness pattern during the future period.In this context, the fish species composition in most lakes will become subsets of that in a few species-rich lakes.The findings derived from the cLCBD underscore the pivotal role of these species-rich lakes, such as Lake Biwa, in shaping native fish diversity and distribution, particularly in scenarios where only species with a low risk of extinction persist.
Our findings on the cumulative diversity of native fish species in lakes within the Japanese archipelago offer valuable insights for the native conservation management.Regarding spatial considerations, it is crucial to prioritize conservation efforts in the northernmost (Hokkaido) and the southernmost island (Kyushu).These areas require immediate attention to safeguard the remaining endemic fish species unique to each region.While conservation priorities on Honshu Island should focus on lakes with a higher number of species, as they can serve as important dispersal centres for native species.Furthermore, our results emphasized that particular attention should be given to threatened species, especially endemic ones, as their unique status and restricted distribution make them particularly vulnerable.Prioritizing actions such as re-establishing native habitats and minimizing both biotic and abiotic negative impacts is crucial for effective native conservation efforts.The former provides environments that closely resemble the preferred habitats of the threatened species, thereby providing them with suitable conditions for survival and reproduction, while the latter creates more favourable conditions for the recovery and population growth of the threatened species.
We are excited about the potential of our proposed new framework assessing cumulative diversity by combining multidimensional information, including taxonomic, phylogenetic and functional components.Our novel cumulative diversity index offers a comprehensive perspective on changes in community diversity patterns.
Without requiring additional data, the cumulative diversity index could be derived directly from existing metrics, making them easy to interpret and highly usable.Generally, greater cumulative diversity values indicate richer diversity information.However, we would like to point out that, as a limitation, our new index cannot directly reflect respective changes in taxonomic, phylogenetic or functional information from numerical differences in the cumulative diversity index.Additionally, in this study, we assigned equal weights to the taxonomic, phylogenetic and functional indices.The rational allocation of these weights remains a topic of ongoing ecological debate.
Thus, we also advocate for further exploration, involving more models or examples in future research, to validate the weighting of these components.We believe this framework assessing cumulative diversity supports macroecological studies and explorations with a focus on conserving biodiversity, especially valuable for forecasting shifts in species diversity, and for the strategic prioritization of regions and species.The cumulative diversity index is especially suitable in cases where the complexity of multiple diversity indices calculated from different perspectives necessitates a concise yet informative diversity measure to depict diversity patterns in the region.Although our study is centred predominantly on freshwater ichthyofauna within the Japanese archipelago, we envisage that this methodological structure could serve as an invaluable resource for future conservation planning efforts concerning various biotas, regions and ecosystems.Instead of primarily focusing on particular facets of diversity (Devictor et al., 2010), we champion safeguarding of ecological integrity in specific regions by conserving a broad scope of biodiversity (Jiang et al., 2020;Meynard et al., 2011).Nonetheless, we acknowledge the imperative of interpreting the outcomes of diverse forms of diversity analysis with circumspection.Furthermore, our results emphasize the significance of considering the biodiversityhabitat relationships specific to each region when devising conservation strategies (de Carvalho & Tejerina-Garro, 2015).Ultimately,

CO N FLI C T O F I NTER E S T S TATEM ENT
The authors declare that they have no conflicts of interest.

PE E R R E V I E W
The peer review history for this article is available at https:// www.webof scien ce.com/ api/ gatew ay/ wos/ peer-review/ 10. 1111/ ddi.
where x is the number of diversity indices integrated into the assessment, and DI ik represents the value of diversity index k of the assemblage i.For instance, within the context of this study, when employing the equation to compute the cumulative LCBD (cLCBD) values, k denotes an element of the set encompassing all the LCBD indices ascertained in previous steps, that is, k ∈ {tLCBD, pLCBD, fLCBD}, subsequently assigning a value of three to x.In a parallel manner, we computed the cumulative alpha (cAlpha) and cumulative beta (cBeta) diversity for each studied native fish assemblage, respectively.
Boxplots showing taxonomic alpha diversity (Richness, a), two phylogenetic alpha diversity: mean phylogenetic distance (MPD, b) and mean nearest phylogenetic distance (MNPD, c), and two functional alpha diversity: mean functional distance (MFD, d) and mean nearest functional distance (MNFD, e) for freshwater fish across historical (blue), current (yellow), future I (orange) and future II (red) periods.
particular lakes were indicated to possess the most unique native fish compositions.During the historical period, we identified eight lakes with the most unique species composition.These lakes displayed tLCBD, pLCBD and fLCBD values exceeding their respective average values simultaneously.Notably, the lakes with the highest LCBD values were concentrated in the northernmost (Hokkaido)

F
Triangular plots depict the beta diversity of freshwater fish populations during the historical (blue, a), current (yellow, b), future I (orange, c) and future II (red, d) periods.The three axes, ranging from zero to one, denote similarity and two aspects of beta diversity (turnover and nestedness).Individual points on the plots represent beta diversity in a specific lake, each from a different measurement: taxonomic (square), phylogenetic (circle) and functional (triangle).Bar charts beneath each triangular plot, from top to bottom, illustrate the proportions of taxonomic, phylogenetic, and functional turnover (coloured) and nestedness (white) to the overall beta diversity, respectively.Proportional values of turnover metrics are accompanied by their mean values in parentheses.Three-dimensional scatter plots demonstrate the Local Contribution to Beta Diversity (LCBD) values for individual lakes during the historical (a), current (b), future I (c) and future II (d) periods.Each axis represents a different aspect of LCBD: taxonomic (tLCBD), phylogenetic (pLCBD) and functional (fLCBD).Lakes with all three LCBD values exceeding their respective means are labelled by their names.DAI et al.
endemic or rare fish with restricted habitats, their early disappearance indicates the limited inherent resilience and heightened susceptibility to environmental shifts of endemic fishes.The vanishing of these imperilled species correlates with a reduction in phylogenetic dendrogram branch (evidenced by decreased MPD values), underscoring the urgent need for heightened conservation efforts and closer scrutiny of these unique and scarce species.Meanwhile, our findings reveal a clear trend of decreased functional redundancy in native fish assemblages, indicating that species with similar traits have similar resource utilization patterns and, thus, high levels of competition, ultimately leading to a greater risk of local extinction.
quent drastic decrease in fish composition dissimilarity.Although high beta diversity can reflect high habitat heterogeneity and ecological resistance in some cases with abundant and stable species pools, our study highlights the need for caution when interpreting beta diversity results, particularly in the context of shrinking species pools.As an empirical demonstration of the conceptual trajectory proposed bySocolar et al. (2016), illustrating the typical patterns of beta diversity change in response to anthropogenic disturbances, our study corroborates the transient increase in beta diversity at the early onset of ongoing biodiversity degradation processes at a long temporal scale.Accordingly, we believe that a comprehensive assessment and detection of species diversity patterns, in combination with within-site richness and among-site dissimilarity, is a prerequisite for effective conservation efforts.Moreover, during the historical period, the high beta diversity pattern of native fishes throughout Japan was dominated by species turnover, indicating the presence of unique endemic fishes in scattered lakes.However, with species loss, especially when species with high extinction risk were excluded, the dominant patterns of overall beta diversity shifted to nestedness patterns.This means that, during fish homogenization, more fish assemblages become subsets of certain species-rich lakes, such as Lake Biwa (Figures4d and 5e).Moreover, the proportions of turnover patterns in taxonomic, phylogenetic and functional aspects are consistently decreasing over time, while there is a rising trend in nestedness across all three perspectives.It is worth highlighting that the rate of decline in taxonomic turnover remains consistently slower compared with that of phylogenetic and functional metrics.Put simply, phylogenetic and functional measures show a more pronounced decrease in turnover over the same time interval when compared to the taxonomic turnover ratio.This slower reduction in taxonomic turnover ratio could be attributed to the increased sensitivity of informative phylogenetic and functional diversity indications.Upon integrating taxonomic, phylogenetic and functional data, our cumulative diversity elucidated similar temporal fluctuations in native fish diversity, characterized by a consistent decrease in cAlpha and an initial increase in cBeta followed by a precipitous decline.By incorporating the latitude of individual lakes into the analysis, the cumulative diversity effectively disclosed the spatial distribution pattern of integrated native fish diversity.Notably, the cAlpha and cBeta of native fish residing within lakes across the Japanese archipelago exhibited highly significant correlations, albeit inverse, with the latitudinal gradient at any period.Specifically, islands situated at the northern-and southernmost of the Japanese archipelago (namely, Hokkaido at higher latitudes and Kyushu at lower latitudes) displayed pronounced dissimilarities in native fish compositions, despite their low species richness.This observation suggests the presence of distinct endemic fishes on these two geographically distant islands.In contrast, the larger Honshu Island, located centrally, harbours a substantial number of native fish species, with lakes exhibiting similar species compositions.The geographical isolation of Hokkaido and Kyushu from Honshu by the Tsugaru Strait and Kanmon Strait, respectively, represents a significant barrier to the dispersion and exchange of freshwater fish among these regions.Hence, the fish species are only able to within freshwater habitats on their respective islands and have facilitated the emergence of fish community structures distinct from those on other islands.Although our study does not explicitly quantify the contribution of geographical isolation imposed by the two straits on the fish community structures of the distinct islands through mathematical modelling, the highly significant latitudinal distribution patterns identified by our cumulative diversity results provide compelling evidence in favour of limitation hypothesis, which posits that geographic isolation and limited dispersal are key factors in maintaining species distribution patterns(da Silva et al., 2018;de Oliveira et al., 2020).By way of contrast, the lakes on Honshu Island exhibit a greater similarity in fish composition.The network of freshwater systems on the larger island promotes fish mobility among habitats and broadens the spatial distribution of fish, thereby enhancing the probability of fish species establishment in a larger number of lakes.Furthermore, Honshu, with a population exceeding 100 million, is the most densely populated island in Japan.Human activities such as fish introduction and removal, stocking, waterbody management and environmental changes have significantly contributed to global fish homogenization.Specifically, the introduction of nonnative species through stocking, along with habitat alterations from water management practices, has led to the spread of generalist species and the decline of unique, local species.Pollution, climate change and overfishing further exacerbate this trend by selectively impacting sensitive species and favouring more adaptable, often non-native species.This considerable human footprint . The significant U-shaped curve between integrated LCBD values and the latitudinal position of the lakes also signifies the high endemism of Hokkaido and Kyushu fishes in the historical period.The diminished variation in cLCBD values, evidenced by a flattening curve against latitudes, indicates degeneration of the high endemism of Hokkaido and Kyushu fish assemblages in the following periods.The principal mechanism driving the homogenous location contribution to nationwide fish dissimilarity is the reduced occurrence of unique fish species, predominantly attributable to the preferential extinction of the threatened species.Conversely, lakes situated in the southern region of Honshu Island are anticipated to supersede Hokkaido and Kyushu as the location with the pinnacle cLCBD values.These lakes usually boast high species richness and interwoven ecosystems, making them more resistant and stable in response to external changes.
our study accentuates that by integrating these recommendations and combining a holistic comprehension of biogeography, genetics and functional ecology, conservation endeavours can be optimized, thereby contributing to the efficacious preservation of biodiversity and ecosystems.ACK N OWLED G EM ENTS B. Dai receives financial and administrative support for his doctoral research from the Japanese Government (MEXT) Scholarship [No.: 211538] and the China Scholarship Council (CSC) [No.: 202006500004].