A comparative analysis of nested subset patterns of species composition

We present a broad comparative assessment of nested subsets in species composition among ecological communities. We assembled presence-absence data from a broad range of taxa, geographic regions, and spatial scales; and subjected this collection of datasets to common analyses, including a variety of metrics for measuring nestedness and null hypotheses against which to evaluate them. Here we identify ecological patterns in the prevalence and strength of nested subset structure, and assess differences and biases among the available methodologies. In all, we compiled 279 presence-absence matrices, of which 163 do not overlap in their coverage of species and sites. The survey includes studies on vertebrates, arthropods, mollusks, plants, and other taxa; from north temperate, tropical, and south temperate latitudes. Our results were as follows. Statistically significant nestedness was common. Assemblages from landbridge archipelagos were strongly nested, and immigration experiments were least nested. This adds further empirical support to the hypothesis that extinction plays a major role in producing nested structure. Nestedness was positively correlated with the ratio of the areas of the largest and smallest sites, suggesting that the range in area of sites affects nestedness. Taxonomic differences in nestedness were weak. Higher taxonomic levels showed stronger nesting than their constituent lower taxa. We observed no effect of distance of isolation on nestedness; nor any effects of latitude. With regard to methodology, the metrics Nc and Ut yielded similar results, although Nc proved slightly more flexible in use, and deals differently with tied sites. Similarities also exist in the behavior of N0 (“N”) and Up, and between N1 and Ua. Standardized nestedness metrics were mostly insensitive to matrix size, and were useful in comparative analyses among presence-absence matrices. Most metrics were affected by the proportion of presences in the matrix. All analyses of nestedness, therefore, should test for bias due to matrix fill. We suggest that the factors controlling nested subset structure can be thought of as four filters that species pass to occur at a site: a sampling filter, a distance filter, a habitat filter, and an area filter – and three constraints on community homogeneity: evolutionary history, recent history, and spatial variation in the environment. The scale of examination can also have important effects on the degree of nestedness observed. Received: 13 September 1996 / Accepted: 16 September 1997     

Flow-related patterns in abundance and composition of the fish fauna of a degraded Australian lowland river

1. A 7‐year study was conducted in three hydrologically distinct sections within the highly regulated, lowland Campaspe River to investigate the influence of hydrology on temporal and spatial patterns in fish composition, abundance and recruitment. One section had 6 months, one section 2 months and one section no months of increased flow due to storage releases. The fish fauna of the less regulated, nearby Broken River served as a reference to which that of the Campaspe River was compared for the last 3 years of the study to allow insight into the relative effects of hydrology, barriers to movement and other environmental characteristics. The study included one high‐flow year, a moderate‐flow year and five low‐flow years. 2. A total of 16 fish species – 10 native and six alien – were caught in the Campaspe River, although of the native species, only three are considered to have self‐sustaining populations. The remaining species are either itinerants or a result of stocking. Alien species comprised approximately 64% of the total biomass of all fish caught. 3. Overall composition of the fish fauna did not differ significantly by year, but did by section of river. Species richness and the abundance of most of the dominant species also differed significantly by river section, but there was little inter‐annual variation in the abundance of any species, except for European perch and for common carp; the latter showing an increase in abundance following a high‐flow event during the spring of 2000 as a result of recruitment. 4. Overall faunal composition was not influenced by hydrology. However, multiple regression indicated that species richness, abundance of the dominant species and abundance of young‐of‐year (YOY) of golden perch, European perch and common carp all were influenced significantly by hydrological variables. The nature of the relationships was dependent on river section and hydrological season (‘winter’ or ‘spring/summer’). Of note was the result that the total abundance of fish and that of YOY common carp were significantly positively related to the number of spells above the threshold for movement upstream through the lower two weirs in the Campaspe River. Only one significant relationship between hydrological and fish‐related variables was found for the upper river section, whereas seven and five were found for the lower and middle sections respectively. 5. Comparisons with fish collected in the Broken River over 3 years suggest that the fauna of the Broken River is in a more natural state than that of the Campaspe River. Since the two rivers do not differ substantially in water quality, and since both contain significant weirs, which act as barriers to movement of fish, flow regulation is most likely to be the major reason for the poor state of the fauna in the Campaspe River.     

Distribution patterns and chorological analysis of fish fauna of the Arctic Region

Chorological structure of ichthyofauna of the Arctic Region is described. Distribution patterns of 504 fish-like vertebrates and fish species are characterized. One hundred and eighty-nine range types are defined, which are combined into eight main categories: 1—Arctic; 2—Atlantic-Arctic; 3—transitional subarctic zone of Atlantic sector; 4—Pacific-Arctic; 5—transitional subarctic subarctic zone of Pacific sector, 6—Pacific-Atlantic (amphiboreal); 7—bipolar; 8—continental (fresh and brackish waters). Arctic and boreal regions are bordered by transitional (subarctic) zones, which are the areas of intermutual penetration of faunas. The distribution of most fish species that penetrate into to the Arctic Region from the southern areas is limited by these transitional zones. The benthic fish species prevail in the group of autochthonous Arctic species (which includes 64 species or 14% of marine fauna). The demersal fauna of the Arctic preudoabyssal is presented by endemic species. Ten variations of amphiboreal distribution patterns are revealed. Three areas may be defined within the Atlantic-subarctic zone in regard to the fish fauna and range types, i.e., Labrador-Greenland region, the Barents Sea region, and Icelandic (transitional) region.     

Species composition and distribution of the freshwater fish fauna of Southern Vietnam

Two hundred and fifty-five fish species occurring in freshwaters in the South of Vietnam are listed. Their geographical distribution is briefly discussed.     

Global scale patterns of fish species richness in rivers

Explanations of spatial and temporal variation in species richness is a central theme in community ecology Until recently, most research has focused on small-scale phenomena, often emphasizing on local environmental factors and, thus, poorly reflecting large-scale processes that organize species richness In this paper, we analyze variations in species richness of indigeneous freshwater fish on a worldwide scale We show that factors related to species-area and species-energy theories statistically explain most of the variation in freshwater fish species richness across continents Historical events supposed to influence present distributions offish are of little assistence in explaining variations in fish species richness at the global scale Our model, which uses easily measured factors, should also be of practical value to aquatic conservation biology and natural resource management     

Surveillance of fish species composition using environmental DNA

Prompt and accurate methods for assessing the species composition of given areas are indispensable in addressing the rapid loss of biodiversity. Here, we propose a method for the surveillance of fish species composition in freshwater using environmental DNA as species markers. First, the applicability of the method was demonstrated through aquarium experiments. DNA was extracted from 120?ml aquarium water, and the degenerated primers targeting the fish mitochondrial cytochrome b gene were used for amplification. PCR-amplified fragments were analysed by random cloning, and all species reared in the aquarium were detected. Next, this method was applied to natural freshwater environments. Water samples were collected from three sites in the Yura River, Japan; DNA was concentrated from 2?l of environmental water, and then amplified and cloned. Up to four species of fish were detected by sequencing 47 randomly selected clones from a single water sample. Overall, the results were consistent with previous knowledge of fish habitat utilisation. Using this method, the surveillance of fish species composition can be conducted less laboriously than with traditional methods.     

Changes in fish species composition in Lake Naivasha,Kenya

The fish species composition in Lake Naivasha has been modified during recent years. Out of seven introduced and one indigenous species reported in 1962, only three introduced ones are found today. The elimination of species has been brought about by predation and changing ecological conditions. The most common fish species today is Sarotherodon leucosticuus. The hybridization found by previous workers between S. leucostictus x S. spilurus niger has stopped, as S. s. niger is no longer found in the lake. Most of the hybrid characters have been lost by the few surviving hybrids due to backcrossing between hybrids and between hybrids and S. leucostictus. The hybrids now mostly resemble S. leucostictus.     

Nested subset structure of larval mycophagous fly assemblages: nestedness in a non-island system

Nested subset structure has been studied in archipelagoes and fragmented habitats, and has been attributed to differential colonization and extinction rates among species and nested environmental tolerances. In this experiment, we tested for nestedness in assemblages of mycophagous fly larvae. Twenty mushrooms in each of three size classes (4.8–6.0 g, 10–15 g, 21–32 g) were placed on moist potting soil in experimental cups. The cups were placed in oak and pine forests in Greenville, S.C., USA for 5 days, where they were available to ovipositing flies. Upon collection, the mushrooms were incubated in the laboratory for 3 weeks and all emerging flies were sorted by species, counted, and weighed. A random placement analysis was conducted to determine whether the species richness pattern was a sampling artifact of the species abundance distributions. The actual species richness pattern did not conform to the random placement model; most mushrooms contained significantly fewer species than predicted by random sampling. The communities were strongly nested as measured by two different indices, and the nestedness pattern was related to mushroom size. Small mushrooms usually produced no flies or a single species, Dohrniphora sp. (Phoridae). Medium and large mushrooms typically produced more species-rich communities that usually contained the phorid and Drosophila putrida, D. tripunctata, and Leucophenga varia. This core guild was nested within a more diverse assemblage that included D. falleni, Mycodrosophila dimidiata, a muscid, and two Leptocera sp. (sphaeroceridae). These patterns are tentatively explained in the context of nested desiccation tolerances, mediated by differences in mushroom size.     

Species composition and distribution of the freshwater fish fauna of the North of Vietnam

Two hundred and three fish species and subspecies occurring in fresh water in the North of Vietnam are listed. The geographical and ecological problems connected with these fishes are discussed.     

Trematode fauna patterns of the freshwater fish on the border of the geographical range

The trematode fauna of the fishes inhabiting Lake Ladoga are represented by forty-six species; nine species of which are found here on the northern boudary of their geographic range. The depauperization of the trematode fauna compared to the southern pools is a result both of the decreasing impact of the Pont-Caspian group and of the introduction of the boreal piedmont species complex. The increase in the biological productivity of Lake Ladoga for the last 50-year period leads to enrichment of the species biodiversity. The same process increases the invasion extensiveness by trematodes, which use fish as an intermediate host. The Diplostomida, the presence of which is crucial for the young fish survival rate, dominate among the trematodes.     

The biochemical composition of chyme in fish species with different diets

The chyme contents of the main biochemical components in fish with different diets vary. Proteins are dominant in the chyme of piscivorous fish (burbot and pike). In the chyme of benthivores (roach and bream), ash is the dominating component. Typical for all fish is the descending lipid gradients with maxima in the proximal section and the ascending ash gradients with maxima in the distal section. The maximum amount of protein was found in the medial part of the intestine. As a rule, there are higher contents of lipids in the chyme of the proximal section and proteins in the chyme of the medial section than in the whole body of fish prey.     

Patterns in the species composition of fish assemblages among Wisconsin streams

Synopsis To better understand patterns of fish assemblage composition in Wisconsin streams in relation to major environmental gradients, I carried out multivariate direct gradient analysis (canonical correspondence analysis) of two large independent datasets on fish species abundance in Wisconsin streams. Analysis of the two datasets yielded similar results, suggesting that observed patterns and relationships were real. Stream sites were distributed along fish species-environment gradients, but segregation into distinct stream temperature and geographic groups was also evident. The strongest gradient in both datasets was related to summer water temperature patterns, and encompassed a transition from small, coldwater streams dominated by salmonids, cottids, certain cyprinids, and few other species, to both small and large, warmwater streams dominated by a high diversity of different cyprinids, catostomids, ictalurids, centrarchids, and percids. A second gradient in both datasets was complex but largely geographic. Within it, sites from each of the four ecoregions that occupy Wisconsin formed fairly discrete groups. The strongest differences were between sites in the two southern Wisconsin ecoregions, the Driftless Area and the Southeastern Wisconsin Till Plains, that were dominated by certain cyprinids, ictalurids, and centrarchids, and sites in the two northern Wisconsin ecoregions, the North Central Hardwood Forests and the Northern Lakes and Forests, that were dominated by a different set of cyprinids and ictalurids, plus some petromyzontids, salmonids, catostomids, and percids. Sites from the Driftless Area that were mostly higher-gradient (steep stream slope) and had many riffle-dwelling species could also be distinguished from sites in the Southeastern Wisconsin Till Plains that were mostly lower-gradient and had many pool-dwelling species. The patterns of fish assemblage composition among sites and the associated fish species-environment relationships that were revealed by the analyses provided a framework for developing an ecologically meaningful hierarchical classification of Wisconsin stream sites based on stream thermal regime, ecoregion, stream size, and stream gradient.     

Global patterns and predictors of tropical reef fish species richness

In the marine realm, the tropics host an extraordinary diversity of taxa but the drivers underlying the global distribution of marine organisms are still under scrutiny and we still lack an accurate global predictive model. Using a spatial database for 6336 tropical reef fishes, we attempted to predict species richness according to geometric, biogeographical and environmental explanatory variables. In particular, we aimed to evaluate and disentangle the predictive performances of temperature, habitat area, connectivity, mid‐domain effect and biogeographical region on reef fish species richness. We used boosted regression trees, a flexible machine‐learning technique, to build our predictive model and structural equation modeling to test for potential ‘mediation effects’ among predictors. Our model proved to be accurate, explaining 80% of the total deviance in fish richness using a cross‐validated procedure. Coral reef area and biogeographical region were the primary predictors of reef fish species richness, followed by coast length, connectivity, mid‐domain effect and sea surface temperature, with interactions between the region and other predictors. Important indirect effects of water temperature on reef fish richness, mediated by coral reef area, were also identified. The relationship between environmental predictors and species richness varied markedly among biogeographical regions. Our analysis revealed that a few easily accessible variables can accurately predict reef fish species richness. They also highlight concerns regarding ongoing environmental declines, with region‐specific responses to variation in environmental conditions predicting a variable response to anthropogenic impacts.     

Marine elements in fish fauna of southeastern Ethiopia

The eel Anguilla bengalensis labiata (Peters) is reported from the middle reaches of the Genale River drainage in southeastern Ethiopia based on our own samples, as well as, on prevously undesribed or poorly described samples obtained by earlier investigators. The Anguilla eels from the Indian Ocean appeared to be the only group of diadromous fishes in Ethiopian fauna. An occurrence of the goby Glossogobius giuris (Hamilton) in the same drainage is reported based on four specimens from the lower reaches of the Genale River. Gross morphology of Ethiopian eels and gobies was described in relation to their identification. The distribution of other saltwater dispersants in the Ethiopian waters is briefly discussed.     

Studies on the bottom fauna in a tropical freshwater fish pond

Summary Quantitative samples of the bottom fauna obtained from a tropical freshwater fish pond during a period of two years were studied with regard to species composition, zonal variation and seasonal fluctuation. Two different zones with differences in faunal composition could be distinguished. The littoral zone was dominated by Mollusca, whereas Oligochaetes were predominant in the profundal zone. Most of the organisms showed their peaks in the months January to April. Breeding activities ofVivipara bengalensis, Digoniostoma cerameopoma, Melanoides granifera andPisidium clarkeanum as evidenced by presence of younger length groups in the populations were also observed during the same period (January to April). The influence of environmental factors as temperature, alkalinity and food were discussed as probable causes for the peaks in abundance. The average number of total organisms per square metre was found to be comparatively high indicating a high standing crop. Differences observed in the total number of organisms present have been attributed to inflow of water resulting in sudden alteration of the nutrient condition of the bottom mud. The seasonal variations of the standing crop of bottom fauna during both the years have been found to be influenced by fluctuations of the bivalve mollusc,Lamellidens corrianus. The availability of sufficient amount of benthic fauna for consumption by bottom feeding fishes has been indicated.This work formed part of a thesis submitted for the Degree of Doctor of Philosophy to the University of Calcutta, India in 1964.     

Effects of site and species characteristics on nested patterns of species composition in sedge meadows

Biotas of both geographical islands and habitat islands are often nested subsets of the biotas of successively more species-rich islands within the same system. The life history characteristics of a species may determine how that species contributes to the general pattern of species nestedness. Here, I investigate the floras of 56 sedge meadow wetlands in northern Illinois (USA) in order to characterize the degree of nestedness in these communities, determine which individual plant species contribute to the nested pattern, and investigate species characteristics that might be related to nonrandom patterns of distribution in individual plant species. The entire assemblage of species at all sedge meadows was significantly nested. Species richness and area were significantly correlated, and the nested pattern was closely related to site area, suggesting that species drop out of the assemblage in a predictable order as site area decreases. Some individual species exhibited nonrandom distributions across the sites, occurring more often in large, species-rich sites. Large sites were more likely than smaller sites to contain conservative species, i.e., those typical of pristine natural habitat, whereas nonconservative species were distributed more randomly among sites. Nested patterns of distribution of conservative species with respect to site area may result from their high probability of extinction on small sites or from a tendency for required habitats to co-occur on the same large sites. This revised version was published online in June 2006 with corrections to the Cover Date.     

Movement patterns and habitat use of three declining littoral fish species in a north-temperate mesotrophic lake

We explored patterns of habitat use and movement of three declining fish species intolerant to eutrophication in a north-temperate (Minnesota, USA) glacial lake: the blackchin shiner Notropis heterodon, blacknose shiner Notropis heterolepis, and banded killifish Fundulus diaphanus. We marked individuals with elastomer tags and estimated movement distances of recaptured individuals. Estimated home ranges for all species ranged from 3,264 to 19,525 m², which covered 0.8 and 5.0% of our study lake’s total littoral area. Individuals of all species traveled to opposite ends of the lake over periods of time as short as 24 h. Using Geographic Information System (GIS) overlays and generalized additive models, we found fish species occurrences to be positively associated with macrophyte biovolume greater than 20% and with a high probability of occurrence of Chara. The magnitude of main and interaction effects varied among years and species. Overall, blackchin shiner occurrence was most strongly associated with biovolume. In other species by year combinations, biovolume and Chara explained varying degrees of variance in fish probability of occurrence. Our results suggest that controlling lake eutrophication and protecting of refuge areas of dense macrophytes and Chara may be needed to conserve these species.     

Temporal and spatial variation in the species composition of trawl samples from a demersal fish community

The temporal variation in species and size structure of the demersal fish community of a 70–150m deep open coastal locality of SW Norway was studied by multivariate analysis of bottom trawl data both from surveys and from fixed locations sampled repeatedly through 48-h periods. The trawl data were related to echo recordings from individual tows made during the 48-h experiments, Between-site variation was greater than short-term variation at single sites. Short-term variation was largely cyclical, diel variation, involving several species. Catches of the numerically dominating species, Sebastes viviparus and Trisopterus esmarki , did not follow any diel patterns. Acoustical recordings suggested that these species undertook diel vertical migrations largely within the lower 5 m of the water column. This corresponds to the vertical opening of the trawl.     

Effect of the removal of cleaner fish on the abundance and species composition of reef fish

The ecological significance of cleaner fish on coral reefs was investigated. I removed all cleaner fish, Labroides dimidiatus, from eight small reefs, measured the subsequent effect on the abundance and species composition of all reef fish after 3 and 6 months, and compared it with eight control reefs with cleaner fish. The removal of cleaner fish had no detectable effect on the total abundance of fish on reefs and the total number of fish species at both times. Multivariate analysis by non-metric multidimensional scaling and ANOSIM pairwise tests based on 191 fish species revealed no effect of cleaners on the community structure of fish. Similar results were obtained using principal components analysis on subsets of the data using the 33 most common fish species and the 15 most abundant species (≥5 individuals per reef ) with both log10 (x + 1) transformed data and with fish numbers standardized for abundance. This study demonstrates that the removal of cleaner fish for 6 months did not result in fish suffering increased mortality nor in fish leaving reefs to seek cleaning elsewhere. Received: 28 October 1996 / Accepted: 7 February 1997