eDNA metabarcoding reveals the role of habitat specialization and spatial and environmental variability in shaping diversity patterns of fish metacommunities.

Information is scarce on how environmental and dispersal processes interact with biological features of the organisms, such as their habitat affinity, to influence patterns in biodiversity. We examined the role of habitat specialist vs. generalist species, and the spatial configuration, connectivity, and different environmental characteristics of river-floodplain habitats to get a more mechanistic understanding of alpha and beta diversity of fish metacommunities. We used environmental DNA metabarcoding to characterize species (taxa) richness and composition in two separate floodplains of the river Danube (Austria and Hungary) during two different hydrological conditions. Results showed that differences in the number of generalist and specialist species and their responses to connectivity and environmental gradients influenced patterns in alpha and beta diversity. Of the components of beta diversity, richness difference (nestedness) showed consistently higher values than replacement (turnover), mainly due to the decrease of specialist species along the connectivity gradient (i.e., from the mainstem to the most isolated oxbows). Variance in both alpha and beta diversity could be well predicted by a set of local and regional variables, despite high environmental variability, which characterizes river-floodplain ecosystems. Of these, the joint or shared variance fractions proved to be the most important, which indicates that the effects of local and regional processes cannot be unambiguously separated in these river-floodplain systems. Local scale environmental variables were more important determinants of both alpha and beta diversity in the low water period than in the high water period. These results indicate the differential role of local and regional processes in community organization during different hydrological conditions. Maintenance of both local and regional scale processes are thus important in the preservation of alpha and beta diversity of floodplain fish metacommunities, which should be considered by environmental management.

Scale of population synchrony confirms macroecological estimates of minimum viable range size.

Global ecosystems are facing a deepening biodiversity crisis, necessitating robust approaches to quantifying species extinction risk. The lower limit of the macroecological relationship between species range and body size has long been hypothesized as an estimate of the relationship between the minimum viable range size (MVRS) needed for species persistence and the organismal traits that affect space and resource requirements. Here, we perform the first explicit test of this assumption by confronting the MVRS predicted by the range-body size relationship with an independent estimate based on the scale of synchrony in abundance among spatially separated populations of riverine fish. We provide clear evidence of a positive relationship between the scale of synchrony and species body size, and strong support for the MVRS set by the lower limit of the range-body size macroecological relationship. This MVRS may help prioritize first evaluations for unassessed or data-deficient taxa in global conservation assessments.

Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR.

Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.

Hydrology is a major influence on amphibian abundance in a large European floodplain.

River-floodplain ecosystems play a crucial role in connecting landscape patches through hydrological connectivity, but they are among the most threatened ecosystems. Floodplains provide important habitat for amphibians by connecting aquatic and terrestrial habitats. Modifications to floodplain hydrology can impact amphibian communities, yet few studies have examined amphibian metacommunities in floodplain wetlands.In this study, we assessed patterns in amphibian breeding abundance in one of the largest floodplains of the Danube River, Hungary, relative to hydrological connectivity and multi-scale variables at 30 waterbody sites. Our aim was to determine whether these patterns aligned with the pond-permanence gradient hypothesis, where breeding amphibian abundance is predicted to be highest in ephemeral ponds without large predatory fish. We used Bayesian hierarchical modelling to estimate multi-species abundance from repeated survey (count) data collected over one breeding season.We detected the eggs and larvae of four amphibian species. The best model of abundance included covariates describing two principal component axes associated with waterbody hydrology and landscape composition within a 500-m radius of a site. There was a positive relationship between mean community abundance at a site and hydrological disconnection from the main river channel; however, the common toad (Bufo bufo) was associated with hydrologically connected waterbodies. There was a positive relationship between mean community abundance and a high proportion of forest cover and low cover of agricultural land within a 500-m radius around a site, although this relationship was clear for only two species. There was no support for models containing the number of large predatory fish species detected at a site.Although our results showed that amphibian abundance declined with hydrological connectivity, based on model selection we could not ascribe this relationship to an increased number of large predatory fish species detected in waterbodies close to the main river channel. Differences in life history and habitat requirements are likely to have explained interspecific responses to hydrological connectivity. Our results underscore the importance of addressing amphibian abundance at multiple spatial scales in floodplain wetlands, as landscape composition partly explained patterns in abundance.Application of multi-species abundance modelling allowed us to investigate environmental relationships for common and infrequently detected species. Habitat restoration programmes in floodplains should provide waterbodies disconnected from main river channels as potential amphibian breeding sites and protect or restore forest as terrestrial habitat.

Distance decay 2.0 - A global synthesis of taxonomic and functional turnover in ecological communities.

Aim: Understanding the variation in community composition and species abundances (i.e., ß-diversity) is at the heart of community ecology. A common approach to examine ß-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments. Location: Global. Time period: 1990 to present. Major taxa studied: From diatoms to mammals. Method: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features. Results: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances. Main conclusions: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments.

From meta-system theory to the sustainable management of rivers in the Anthropocene.

Regional-scale ecological processes, such as the spatial flows of material, energy, and organisms, are fundamental for maintaining biodiversity and ecosystem functioning in river networks. Yet these processes remain largely overlooked in most river management practices and underlying policies. Here, we propose adoption of a meta-system approach, where regional processes acting at different levels of ecological organization - populations, communities, and ecosystems - are integrated into conventional river conservation, restoration, and biomonitoring. We also describe a series of measurements and indicators that could be assimilated into the implementation of relevant biodiversity and environmental policies. Finally, we highlight the need for alternative management strategies that can guide practitioners toward applying recent advances in ecology to preserve and restore river ecosystems and the ecosystem services they provide, in the context of increasing alteration of river network connectivity worldwide.

Estimating nutrient thresholds for eutrophication management: Novel insights from understudied lake types.

Nutrient targets based on pressure-response models are essential for defining ambitions and managing eutrophication. However, the scale of biogeographical variation in these pressure-response relationships is poorly understood, which may hinder eutrophication management in regions where lake ecology is less intensively studied. In this study, we derive ecology-based nutrient targets for five major ecoregions of Europe: Northern, Central-Baltic, Alpine, Mediterranean and Eastern Continental. As a first step, we developed regressions between nutrient concentrations and ecological quality ratios (EQR) based on phytoplankton and macrophyte communities. Significant relationships were established for 13 major lake types; in most cases, these relationships were stronger for phosphorus than for nitrogen, and stronger for phytoplankton than for macrophytes. Using these regressions, we estimated the total phosphorus (TP) and total nitrogen (TN) concentrations at which lakes of different types are likely to achieve good ecological status. However, in the very shallow lakes of the Eastern Continental region, relations between nutrient and biological communities were weak or non-significant. This can be attributed to high nutrient concentrations (in the asymptotic zone of phosphorus-phytoplankton models) suggesting other factors (light, grazing) limit primary production. However, we also show that fish stocking is a major pressure on Eastern Continental lakes, negatively affecting ecological status: lakes with low fish stocking show low chlorophyll-a concentrations and good ecological status despite high nutrient levels, while the lakes with high fish stocking show high chlorophyll-a and low ecological status. This study highlights the need to better understand lakes in biogeographic regions that have been, for historical reasons, less studied. This, in turn, helps reveal factors that challenge the dominant paradigms of lake assessment and management.

European fish-based assessment reveals high diversity of systems for determining ecological status of lakes.

Triggered by the adoption of the Water Framework Directive, a variety of fish-based systems were developed throughout Europe to assess the ecological status of lakes. This paper provides a comprehensive overview of all existing systems and summarizes sampling methods, fish community traits (metrics) and the relevant anthropogenic pressures assessed by them. Twenty-one European countries developed fish-based assessment systems. Three countries each developed two distinct systems to approach different ecoregions, either to use different data, or to assess different lake types leading to a total number of 24 systems. The most common approach for the setting of reference conditions, used in seventeen systems, was the utilisation of fish communities in comparably undisturbed natural lakes as reference. Eleven used expert judgment, nine historical data and eight modelled relationships. Fourteen systems combined at least two approaches. The most common fish sampling method was a standardized fishing procedure with multimesh-gillnets. Many countries applied combinations of fishing methods, e.g. non-standard gillnets, fyke nets and electrofishing. Altogether 177 metrics were used for index development and each system combined 2-13 metrics. The most common ones were total standardized catches of number and biomass, relative abundance of Perca fluviatilis, Rutilus rutilus, and Abramis brama, feeding preferences, sensitive species, and non-natives. The pressure-response-relationships for these metrics were supported with both correlations established during system development and scientific publications. However, the metrics and their combinations were highly diverse and no metric was applied universally. Our analysis reveals that most fish-based assessment systems address multiple pressures (eutrophication, hydromorphological alterations, fishery pressure and occurrence of non-natives), whilst few are pressure-specific, tackling only eutrophication or acidification. We argue that the value of fish-based systems for lakes lies in their capacity to capture the effect of many different pressures and their interactions which is lacking for most assessment systems based on other biota.

Freshwater systems and ecosystem services: Challenges and chances for cross-fertilization of disciplines.

Freshwater ecosystems are among the most threatened in the world, while providing numerous essential ecosystem services (ES) to humans. Despite their importance, research on freshwater ecosystem services is limited. Here, we examine how freshwater studies could help to advance ES research and vice versa. We summarize major knowledge gaps and suggest solutions focusing on science and policy in Europe. We found several features that are unique to freshwater ecosystems, but often disregarded in ES assessments. Insufficient transfer of knowledge towards stakeholders is also problematic. Knowledge transfer and implementation seems to be less effective towards South-east Europe. Focusing on the strengths of freshwater research regarding connectivity, across borders, involving multiple actors can help to improve ES research towards a more dynamic, landscape-level approach, which we believe can boost the implementation of the ES concept in freshwater policies. Bridging these gaps can contribute to achieve the ambitious targets of the EU's Green Deal.

A global agenda for advancing freshwater biodiversity research.

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.

The mixed phylogenetic origin of northern pike (Esox lucius Linnaeus 1758) populations in the Middle Danubian drainage.

BACKGROUND: Pikes, members of genus Esox, are widespread freshwater predators of the northern hemisphere, and important sport fish also. From the Carpathian basin only one species, the northern pike (E. lucius) is noted. At the same time the pike stocks living in this area show high level of phenotypic variance (e.g. various body pattern) and its growth varies highly both among and within populations. These features usually explained by the environmental diversity of the area. Whereas we think that genetic reasons -e.g. the appearance of other/new pike species in the area- may also be responsible for these observed features. Since as no detailed information have been published from the pike populations of this area, so far; we conducted phylogenetic and morphological assay on 88 pike specimens, collected from 49 Middle Danubian sampling sites. RESULTS: Our phylogenetic surveys showed that the northern pike appear in the study area solely, but all the three of its major lineages (Northern, Circumpolar, Southern) were indicated. Only six specimens represent the Northern lineage, collected from the western part of the study area. The Circumpolar and Southern lineages were common in the Carpathian basin, but the Southern lineage showed higher levels of haplotype diversity than the Circumpolar clade. Which indicates that only the Southern lineage is native in the area, while the other two groups could have appeared in the Middle Danubian system either spontaneously or by human introduction. Moreover, the different clades appeared in the same populations, suggesting the opportunity of inter-lineage hybridisation. From the studied morphologicalal features, the number of scales on the lateral line and the head length showed significant differences among the lineages. At the same time the body pattern of the studied individuals seems to be rather influenced by the ontogenic changes than phylogeny. CONCLUSIONS: The high phenotypic variability of Middle Danubian northern pike populations may be due that all of its three major clades appeared and came in secondary contact in the area. In the within watershed spread of the non-native lineages the human stocking/transfer may play a considerable role.

A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions.

The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium- and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a 'very high risk' of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate 'rapid' management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement.

The geography of metapopulation synchrony in dendritic river networks.

Dendritic habitats, such as river ecosystems, promote the persistence of species by favouring spatial asynchronous dynamics among branches. Yet, our understanding of how network topology influences metapopulation synchrony in these ecosystems remains limited. Here, we introduce the concept of fluvial synchrogram to formulate and test expectations regarding the geography of metapopulation synchrony across watersheds. By combining theoretical simulations and an extensive fish population time-series dataset across Europe, we provide evidence that fish metapopulations can be buffered against synchronous dynamics as a direct consequence of network connectivity and branching complexity. Synchrony was higher between populations connected by direct water flow and decayed faster with distance over the Euclidean than the watercourse dimension. Likewise, synchrony decayed faster with distance in headwater than mainstem populations of the same basin. As network topology and flow directionality generate fundamental spatial patterns of synchrony in fish metapopulations, empirical synchrograms can aid knowledge advancement and inform conservation strategies in complex habitats.

Only one can remain? Environmental and spatial factors influencing habitat partitioning among invasive and native crayfishes in the Pannonian Ecoregion (Hungary).

Biological invasions have increasingly threatened indigenous species, influence metacommunity organisation and consequently, global biodiversity. World-wide expansion of non-indigenous crayfish (NICS) is associated with dramatic changes in species poor indigenous crayfish (ICS) assemblages challenging conservation planning. We analysed long-term changes of crayfish occurrences from the pre-invasion state, through the first appearance of NICS, to their intensive spread in Hungarian waters. Further, we analysed present-day crayfish metacommunity patterns for co-occurrences and influence of spatial and environmental factors. Historic data revealed a marked pre-invasion decline in indigenous noble crayfish Astacus astacus and stone crayfish Austropotamobius torrentium populations, but not in the narrow-clawed crayfish Pontastacus leptodactylus. Historic data provided no direct evidence for the impact of NICS on ICS, rather it supported that NICS often entered areas where ICS had been extinct or were not present at all. Crayfish species extremely rarely co-occurred which could indicate their strong competition and be related to utilization of empty sites by NICS. Crayfish metacommunities were predominantly spatially structured indicating the primary influence of ongoing invasion. Crayfish species also exhibited different environmental preferences mainly along the altitude and temperature gradients. We conclude that the invasion is still in the expanding phase and without an effective conservational program the future of ICS is doubtful in Hungary. Conservation policy should focus on the preservation and reintroduction of the stone and noble crayfishes in highland refugees. Expansion of NICS should be prevented in refugee areas by utilizing possibilities provided by natural and artificial barriers, and education and strict ban should be simultaneously applied to prevent further illegal releases by aquarists.

Scavenging behaviour and size-dependent carcass consumption of the black bullhead (Ameiurus melas).

This study examined the size-dependent scavenging behaviour of black bullheads Ameiurus melas under laboratory conditions, using common bleak Alburnus alburnus and pumpkinseed Lepomis gibbosus carcasses. Video camera observations showed that the activity of A. melas was higher at night, but substantial daytime activity was also recorded. Larger A. melas were more active than their smaller conspecifics, especially at night. All size classes exhibited a well-defined sequence of consuming different parts of the carcasses independent of size, but larger individuals tended to consume carcasses more efficiently. Carcasses of the softer-bodied A. alburnus were consumed more readily than those of the bonier L. gibbosus, independent of size. This scavenging behaviour of A. melas might facilitate the invasion success of the species.

Multiple stressor effects on alpha, beta and zeta diversity of riverine fish.

We examined the effects of regional scale land use and local scale environmental and biotic stressors on alpha, beta and zeta diversities of native fish communities in wadeable streams and non-wadeable rivers in the Danube basin, Hungary. Relationships among land use and local scale environmental and biotic stressors were weak both in streams and rivers, suggesting that these stressors act relatively independently. Alpha diversity decreased strongly with increasing local scale environmental stressor intensity in rivers. On the contrary, its response to stressors was more obscure in streams, where the best-fit statistical model indicated the importance of the interaction between land use, local scale environmental and biotic stressors, while the secondly ranked model highlighted the negative impact of local scale environmental stressors. Analysis of variance using distance matrices provided evidence that stressors alone and in interactions explained compositional differences of pairs of study sites (beta diversity). Considering the degree of overall degradation, both local (alpha) and among-site (beta and zeta) diversity indices responded to increasing stressor intensity, generally negatively. Riverine fish communities showed higher degrees of similarity (lower beta and higher zeta) than stream fish communities. They also showed increasing similarity (i.e. homogenization) with increasing overall stressor intensity, unlike stream fish communities, which showed no relationship with overall stressor intensity. Our results suggest that the relationships between land use and local scale environmental and biotic stressors can be complex and so do their effects on biodiversity. While stressor specific indices can provide information on the role of specific stressors in some cases, the examination of overall stressor effects is needed to assess realistically the effects of anthropogenic disturbances on native fish diversity. Diversity indices that quantify among-site changes in species composition, such as measures of beta and zeta diversity, can be fruitful for better understanding the role of multiple stressors in structuring ecological communities.

Sparing and sharing land for maintaining the multifunctionality of large floodplain rivers.

Large floodplain rivers (LFRs) are among the most threatened ecosystems on Earth and their utilization is expected to grow. Therefore, the need to develop more effective spatial prioritization tools to maintain their multifunctionality becomes increasingly important. We present a novel approach to land use design and conservation planning of LFRs and demonstrate its applicability using a case study for the Danube River, Central-Europe. Specifically, we use indicators of habitat naturalness and complexity to define four main land use functions for LFRs: (1) relatively intact areas with high habitat complexity, which are of high priority for conservation (C), (2) degraded and simplified areas, which are not suited for conservation, but for human utilization (HU), (3) relatively natural areas with low habitat complexity, which are suited both for conservation and for sustainable use of goods and services (LS), (4) degraded areas with relatively high habitat complexity potential, which should be used for rehabilitation (R). While C and HU spare land primarily for conservation and for human utilization, respectively, categories LS and R share land both for biodiversity conservation and for human use and well-being. Results of the case study show that the different land use functions did not clearly separate spatially along the evaluated segment, but distributed relatively equally. Area weighted indices highlighted the importance of large floodplains, while non-weighted indices indicated the importance of many smaller segments with narrow floodplain riparian zone, which can still be important for conservation or rehabilitation purposes. Our multiscale analysis revealed how land use categorizations depend on index use, index weightings and spatial resolution of land use function maps, which should be considered by management. The suggested methodology provides a transparent framework to any stakeholder groups on how to plan out management actions in the context of land conservation and ecosystem services delivery of LFRs.

Population Genetic Patterns of Threatened European Mudminnow (Umbra krameri Walbaum, 1792) in a Fragmented Landscape: Implications for Conservation Management.

The European mudminnow (Umbra krameri) is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs) and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80-90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed.

Human effects on ecological connectivity in aquatic ecosystems: Integrating scientific approaches to support management and mitigation.

Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change. Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and management, is best achieved via data synthesis from multiple analytical approaches. We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology; population structure; movement characteristics; and environmental tolerance/phenotypic plasticity. Structuring empirical research around these four broad data requirements, and using this information to parameterise appropriate models and develop management approaches, will allow for mitigation of the effects of anthropogenic disturbance on ecological connectivity in aquatic ecosystems.

Genetic heterogeneity reveals on-going speciation and cryptic taxonomic diversity of stream-dwelling gudgeons (Teleostei, Cyprinidae) in the middle Danubian hydrosystem (Hungary).

Although stream-dwelling gudgeons (Cyprinidae, genus: Gobio) are widespread in Central Europe, the taxonomy of this group and the distribution of its species are still unexplored in detail. The aims of our study are to ascertain taxonomic composition and distribution of the former Gobio gobio superspecies in the inner area of the Carpathian Basin. Since the presence of cryptic species is suspected in this area, we examined the taxonomic and phylogenetic relationships of Central European Gobio taxa by sequencing the mitochondrial DNA control region (mtCR). Additionally, we characterized the genetic structure of 27 stream-dwelling gudgeon populations of this area by Amplified Fragment Length Polymorphism (AFLP). Results of mtCR analysis proved the presence of three species already known as G. obtusirostris (dominant in NW-Hungary), G. gobio (sporadic) and G. carpathicus (sporadic). Additionally, the analysis revealed the existence of one doubtful taxon, G. sp1 (dominant in NE-Hungary), and a new isolated haplogroup (dominant in SW-Hungary). Although Network analysis showed significant detachment among haplogroups, their genetic distances were quite small. Therefore Bayesian phylogenetic analysis showed weak nodal support for the branching pattern both for newly described haplotypes, and for the already accepted species. AFLP data showed distinct population structure and a clear pattern of isolation was revealed by distance of stocks. At the same time, level of separation was not affected by the altitudinal position of sites. Moreover we found three major clusters of populations which were separated according to hydrographic regions, and corresponded to the findings of mtCR analysis. Our results suggest the on-going speciation of gudgeons in the Carpathian Basin, however the separation of haplogroups seems to only be an intermediate phase. The discovered natural pattern seems to be only slightly influenced by anthropogenic impacts. Additionally our results put into question the suitability of the recently accepted within Gobio genus taxonomy.