Coral and fish distribution patterns in Mafia Island Marine Park, Tanzania: fish–habitat interactions

We examined coral reef communities at 11 sites within Mafia Island Marine Park using a point count method for substrate and visually censused belt transects for fish populations. Multivariate ordinations showed that the benthic habitat differed among reefs. The patterns were mainly attributed to variations in depth, hydrodynamics and benthic composition. In total, the substratum was dominated by dead coral (49%) and algae (25%), with a live coral cover of only 14%. Three hundred and ninety-four fish species belonging to 56 families were recorded. According to MDS-ordinations and RELATE procedures, fish assemblage composition varied among sites in concordance with the habitats provided. Sites with highest proportion of dead coral exhibited highest degree of dispersion in the multivariate ordinations of fish assemblages. Stepwise multiple regression was used to determine the proportion of variance among sites which could be explained by depth, exposure, rugosity, substrate diversity, branching substrate, live coral cover, dead coral cover and different types of algae. The results showed that habitat variables explained up to 92% of the variation in species numbers and in total, and taxon-specific, abundance. Live coral cover was the foremost predictor of both numerical and species abundance, as well as of corallivores, invertivores, planktivores and of the families Pomacentridae, Chaetodontidae and Pomacanthidae. Our results suggest that habitat characteristics play a dominant role in determining fish assemblage composition on coral reefs.     

Donsol: an important reproductive habitat for the world's largest fish Rhincodon typus?

Little is known about the reproductive ecology of the whale shark Rhincodon typus. On 15 March 2020, a free-swimming neonate whale shark was found in the shallow, coastal waters of Donsol, Philippines. The total length of the male shark was 60 cm, falling within the species known size-at-birth. This is the third occurrence of neonatal whale sharks reported in the area, and coupled with the occurrence of juveniles and adults, and anecdotal mating and precopulatory behaviour reported herein, the importance of the site for this endangered species is highlighted.     

Do relaxed selection and habitat temperature facilitate biased mitogenomic introgression in a narrowly endemic fish?

Introgression might be exceptionally common during the evolution of narrowly endemic species. For instance, in the springs of the small and isolated Cuatro Ciénegas Valley, the mitogenome of the cichlid fish Herichthys cyanoguttatus could be rapidly introgressing into populations of the trophically polymorphic H. minckleyi. We used a combination of genetic and environmental data to examine the factors associated with this mitochondrial introgression. A reduced representation library of over 6220 single nucleotide polymorphisms (SNPs) from the nuclear genome showed that mitochondrial introgression into H. minckleyi is biased relative to the amount of nuclear introgression. SNP assignment probabilities also indicated that cichlids with more hybrid ancestry are not more commonly female providing no support for asymmetric backcrossing or hybrid‐induced sex‐ratio distortion in generating the bias in mitochondrial introgression. Smaller effective population size in H. minckleyi inferred from the SNPs coupled with sequences of all 13 mitochondrial proteins suggests that relaxed selection on the mitogenome could be facilitating the introgression of “H. cyanoguttatus” haplotypes. Additionally, we showed that springs with colder temperatures had greater amounts of mitochondrial introgression from H. cyanoguttatus. Relaxed selection in H. minckleyi coupled with temperature‐related molecular adaptation could be facilitating mitogenomic introgression into H. minckleyi.     

Predicting spatially explicit coral reef fish abundance, richness and Shannon–Weaver index from habitat characteristics

The assessment of biodiversity in coral reefs requires the application of geographic information systems (GIS), remote sensing and analytical tools in order to make cost-effective spatially explicit predictions of biodiversity over large geographic areas. Here we present a spatially explicit prediction for coral reef fish diversity index, as well as habitat classification according to reef fish diversity index values in Chinchorro Bank Biosphere Reserve, one of the most important plain/atoll type reef systems in the Caribbean. We have used extensive ecological data on depth, fish and habitat characteristics to perform such prediction. Fish species assemblages and different biotic variables of benthic organisms were characterized using visual censuses and video-transects, respectively at 119 sampling stations. The information was integrated in a GIS, along with satellite imagery (LANSDAT 7 ETM+) and a digital bathymetric model. From the recorded data and a hierarchical classification procedure, we obtained nine different classes of habitats. We used a generalized regression analysis and spatial prediction methodology to create predictive maps (GIS layers) of the different reef benthic components, and a second modeling run produced predictive maps of coral reef fish diversity index. Predictive accuracy of the diversity index map presented a good correlation coefficient (r = 0.87), with maximum diversity index values en reefscapes composed of aggregation of coral colonies with seagrass beds. The implementation of our application was successful for the prediction of fish diversity hot spots and surrogate habitats.     

The heterospecific habitat copying hypothesis: can competitors indicate habitat quality?

According to the "habitat copying" hypothesis, animals use thereproductive performance of conspecifics to assess habitat suitabilityand choose their future breeding site. This is because conspecificsshare ecological needs and thus indicate habitat suitability.Here, we propose the "heterospecific habitat copying" hypothesis,which states that animals should use public information (i.e.,information derived from the performance of others) from con-and heterospecifics sharing ecological needs. In a correlationalapproach we test some assumptions and predictions of this hypothesiswith a data set from two sympatric bird populations, rollers(Coracias garrulus) and kestrels (Falco tinnunculus), usingthe same nest-boxes and exploiting similar food resources. Sincekestrels are residents and breed earlier, we assumed that theyare dominant over rollers for nest-box acquisition. The environmentappears to be patchy for both species and temporally predictablefor kestrels only. Two results suggest that the use of heterospecificpublic information in breeding habitat selection may be at work:(1) an increase in the reoccupancy probability by kestrels ofprevious roller nests with increasing nest success, and (2)an increase in roller breeding population with increasing localkestrel success. Most of the other observed patterns could beexplained by alternative mechanisms such as natal philopatry,breeding fidelity, conspecific attraction, intraspecific habitatcopying, and the effect of interspecific competition.     

Control of freshwater fish and crayfish community structure in Taranaki,New Zealand: dams,diadromy or habitat structure?

1. Freshwater fish and crayfish communities were surveyed along elevational gradients in streams radiating from Mount Taranaki, New Zealand. Six of the 38 streams surveyed had dams or weirs and 32 of the 85 sites were above these barriers. 2. Of the 15 fish and one crayfish species captured, 14 were native. The number of species declined with increasing elevation and distance from the sea. Species richness was also lower above dams even when effects of elevation and distance from the sea were accounted for. 3. Linear regression models using sites without dams were constructed to predict the effect of elevation on fish and crayfish community structure and to allow the effect of dams to be evaluated. The number of species predicted by these models was consistently higher than the number of species found at the above-dam sites. 4. Four fish community groups were classified using two-way indicator species analysis (TWINSPAN). One high elevation group of sites consisted of short steep streams on the west side of the mountain and a second contained longer, lower gradient streams on the east side. The other two groups (3 and 4) consisted of mid-elevation sites and low-elevation sites, respectively. 5. Discriminant analysis was used to predict biotic group membership using the environmental data. Overall, 80% of sites were classified correctly. Correlation of environmental variables with axis scores in the canonical variate analysis revealed that distance from the sea, site elevation and presence of dams were most strongly associated with fish distribution patterns.     

Endotoxin recognition: in fish or not in fish?

The interaction between pathogens and their multicellular hosts is initiated by activation of pathogen recognition receptors (PRRs). These receptors, that include most notably members of the toll-like receptor (TLR) family, recognize specific pathogen-associated molecular patterns (PAMPs). TLR4 is a central part of the receptor complex that is involved in the activation of the immune system by lipopolysaccharide (LPS) through the specific recognition of its endotoxic moiety (Lipid A). This is a critical event that is essential for the immune response to Gram-negative bacteria as well as the etiology of endotoxic shock. Interestingly, compared to mammals, fish are resistant to endotoxic shock. This in vivo resistance concurs with in vitro studies demonstrating significantly lowered sensitivity of fish leukocytes to LPS activation. Further, our in vitro analyses demonstrate that in trout mononuclear phagocytes, LPS fails to induce antiviral genes, an event that occurs downstream of TLR4 and is required for the development of endotoxic shock. Finally, an in silico approach that includes mining of different piscine genomic and EST databases, reveals the presence in fish of all of the major TLR signaling elements except for the molecules specifically involved in TLR4-mediated endotoxin recognition and signaling in mammals. Collectively, our analysis questions the existence of TLR4-mediated cellular responses to LPS in fish. We further speculate that other receptors, in particular beta-2 integrins, may play a primary role in the activation of piscine leukocytes by LPS.     

Creation and maintenance of habitat downstream from a weir for the greenside darter, Etheostoma blennioides – a rare fish in Canada

The biology, microhabitat use and migratory behaviour of the greenside darter, Etheostoma blennioides, was studied at the Mannheim Weir on the Grand River, Ontario during the summer of 1995 and 1996. Officially listed as vulnerable in Canada, greenside darters reached maturity at age 1 and lived up to 4 years. They were found in riffle habitats that consisted of cobble and loose boulders, with large mats of Cladophora. This type of unembedded substrate is uncommon in the Grand River watershed. However, local abundance of greenside darters immediately downstream from the Mannheim Weir was likely due to high water velocities from weir discharge, freshets and ice scour which help maintain unembedded riffle areas. Trap data indicated that greenside darters temporally partition this habitat with the stonecat, Noturus flavus. Other darter species were not commonly found in areas with greenside darters, whose depth selection and habitat choices were influenced by predators and morphology. Denil fishways at the Mannheim Weir rarely passed greenside darters due to prohibitively high water velocities and exclusion by larger fish. This revised version was published online in August 2006 with corrections to the Cover Date.     

How do habitat amount and habitat fragmentation drive time-delayed responses of biodiversity to land-use change?

Land-use change is a root cause of the extinction crisis, but links between habitat change and biodiversity loss are not fully understood. While there is evidence that habitat loss is an important extinction driver, the relevance of habitat fragmentation remains debated. Moreover, while time delays of biodiversity responses to habitat transformation are well-documented, time-delayed effects have been ignored in the habitat loss versus fragmentation debate. Here, using a hierarchical Bayesian multi-species occupancy framework, we systematically tested for time-delayed responses of bird and mammal communities to habitat loss and to habitat fragmentation. We focused on the Argentine Chaco, where deforestation has been widespread recently. We used an extensive field dataset on birds and mammals, along with a time series of annual woodland maps from 1985 to 2016 covering recent and historical habitat transformations. Contemporary habitat amount explained bird and mammal occupancy better than past habitat amount. However, occupancy was affected more by the past rather than recent fragmentation, indicating a time-delayed response to fragmentation. Considering past landscape patterns is therefore crucial for understanding current biodiversity patterns. Not accounting for land-use history ignores the possibility of extinction debt and can thus obscure impacts of fragmentation, potentially explaining contrasting findings of habitat loss versus fragmentation studies.     

More genes in fish?

Certain species of fish have recently become important model systems in comparative genomics and in developmental biology, in certain instances because of their small genome sizes (e.g., in the pufferfish) and, in other cases, because of the opportunity they provide to combine an easily accessible and experimentally manipulable embryology with the power of genetic approaches (e.g., in the zebrafish). The resulting accumulation of genomic information indicates that, surprisingly, many gene families of fish consist of more members than in mammals. Most modern fish, including the zebrafish and medakka, are diploid organisms; however, the greater number of genes in fish was possibly caused by additional ancient genome duplications which happened in the lineage leading to modern ray-finned fishes but not along the lineage leading to tetrapods. Since these two lineages shared their last common ancestor (in the Devonian about 360 million years ago) individual duplicated members of gene families were later lost in fish. Interestingly, comparative data indicate that, in some cases, genes in mammals even serve somewhat different functions than their homologues in fish, highlighting that the degree of evolutionary relatedness of genes is not always a reliable predictor of their evolutionary conservation and their similarity of function. Since fish are phenotypically probably not more complex than mammals, it is possible that evolution took alternative paths to the “economics of genomics” through alternative solutions to gene regulation. It is suggested that the more complex genomic architecture of fish permitted them to adapt and speciate quickly in response to changing selective regimes. BioEssays 20 :511–515, 1998. © 1998 John Wiley & Sons, Inc.     

Evaluation of target strength–fish length equation choices for estimating estuarine fish biomass

In the Gulf of Mexico (GOM), fish biomass estimates are necessary for the evaluation of habitat use and function following the mandate for ecosystem-based fisheries management in the recently reauthorized Sustainable Fisheries Act of 2007. Acoustic surveys have emerged as a potential tool to estimate fish biomass in shallow-water estuaries, however, the transformation of acoustic data into an index of fish biomass is not straightforward. In this article, we examine the consequences of equation selection for target strength (TS) to fish length relationships on potential error generation in hydroacoustic fish biomass estimates. We applied structural equation models (SEMs) to evaluate how our choice of an acoustic TS–fish length equation affected our biomass estimates, and how error occurred and propagated during this process. To demonstrate the magnitude of the error when applied to field data, we used SEMs on normally distributed simulated data to better understand the sources of error involved with converting acoustic data to fish biomass. As such, we describe where, and to what magnitude, error propagates when estimating fish biomass. Estimates of fish lengths were affected by measurement errors of TS, and from inexact relationships between fish length and TS. Differences in parameter estimates resulted in significant differences in fish biomass estimates and led to the conclusion that in the absence of known TS–fish length relationships, Love’s (J Acoust Soc Am 46:746–752, 1969) lateral-aspect equation may be an acceptable substitute for an ecosystem-specific TS–fish length relationship. Based upon SEMs applied to simulated data, perhaps the most important, yet most variable, component is the mean volume backscattering strength, which significantly inflated biomass errors in approximately 10% of the cases. Handling editor: M. Power     

Conservation of remnant populations of Colchicum autumnale – The relative importance of local habitat quality and habitat fragmentation

Semi-natural habitat is extremely vulnerable to habitat fragmentation and degradation since its socio-economic value has decreased substantially during the last century in most parts of Europe. We evaluated the relative effects of habitat fragmentation and local environmental conditions on population structure and reproductive performance of the long-lived corm geophyte Colchicum autumnale in 17 highly fragmented populations. Habitat isolation did not affect patch occupancy, population structure or plant performance. In contrast, population size and local environment strongly affected population structure and reproductive performance. Densities of all life stages increased with increasing population size. Large populations also showed a higher reproductive performance and a larger proportion of new recruits. Relationships with local growth conditions pointed towards the importance of an open grassland sward for flower and fruit set and the presence of microsites for successful sexual recruitment. These results suggest that the distribution of C. autumnale consists of an assemblage of basically unconnected populations that are remnants of formerly larger populations. This is in accordance with the species' ability to grow clonally, allowing long-term persistence under deteriorating conditions that occurred during a long period of habitat fragmentation. In conclusion, our results indicate that local habitat and population size are more important than habitat fragmentation (i.e. calcareous grassland isolation and surface area) and argue in favour of a management that is primarily focused on local habitat restoration. This is preferentially accomplished by reintroducing grazing practices, complemented by regular setback of spontaneous succession towards forest.     

What is a fish species?

The formal processes of alpha-taxonomy ensure that species have uniquenames and can be identified. No similar process is mandatory forinfraspecific variation, so the species is a uniquely importantpractical term. At present, there is little agreement of the definitionof a species. In the last 30 years, numerous concepts have beenproposed. The nature of fish species is reviewed. Clonal inheritance ofnuclear genes occurs in several lineages. Hybridization is frequent,often leading to introgression, which may lead to extinction of species.Species may have hybrid origins. There is good evidence for parallelspeciation in similar habitats. There are clearly exceptions to thecladistic assumption of dichotomous branching during speciation. Siblingspecies may exist with no discernible niche differentiation.Basic assumptions are violated for the recognition, phylogenetic,ecological and some formulations of the evolutionary species concepts.The most satisfactory definitions are two of the earliest proposed inthe light of evolutionary theory. The Darwinian view is that species arerecognizable entities which are not qualitatively distinct fromvarieties. A restatement of this concept in genetic terms provides ameans of dealing with all forms of species known in present-day fishes.This modified Darwinian concept is operated through the application offuzzy logic rather than rigid definition. This involves a search fordiscontinuities between species, rather than an a priori definition ofhow boundaries are to be determined. A subset of Darwinian species areMayrian or biological species, which are characterized by theirdemonstrable reproductive isolation from other species. The status of apopulation as a Mayrian species is a testable hypothesis. Moleculartechniques allow this hypothesis to be tested more easily thanpreviously, at least when dealing with sympatric populations.     

Stream habitat fragmentation — a threat to biodiversity

Biodiversity is undisturbed rhithral streams in central Europe is high, with about 1000 resident metazoan species; over 600 insect species occur in the Fulda river (Germany). Longitudinal downstream shift of dominance from rheobiontic to rheophilous and finally to ubiquituos rheoxenic taxa in the potamal is described. Present downstream importance of ubiquituous species probably results from replacement of original potamal communities, present faunas being surrogates. Species losses through human impact are well documented for fish. The case of Plecoptera (10 potamal species either altogether extinct, extinct in Central Europe or extremely endangered) suggests that potamal invertebrates suffered as severe losses as did fish.Human impact on major rivers was so severe also because they occur at distances beyond average dispersal capacity of the fauna, i.e. are widely separate ecological islands, with known risk of species losses. In contrast, faunal exchange between adjacent headwater streams in mountains with intact stream nets is easy, certainly for amphibious insects. However, damage to rhithral streams is becoming increasingly frequent. This fragments stream nets, turning also upper parts of drainage systems into ecological islands, with danger of extinctions. Rhithral biodiversity is thought to be much more endangered by human impact than is presently recognized.     

Fish ladders select fish traits on migration–still a growing problem for natural fish populations

We investigated the potential selective effect of fish ladders on physiological and morphological profiles of the curimbatá, Prochilodus lineatus, during reproductive migration in Brazil. We registered sex, body weight and length, plasma glucose, hepatosomatic and gonadosomatic indices (HSI and GSI, respectively), hematocrit, leucocrit, blood cell and nucleus areas, and the diameter of white and red muscle fibers in fish sampled at the bottom (downstream) and at the top (upstream) of a fish ladder at a hydroelectric dam. Males and females at the top of the ladder showed higher size (weight and length), white muscle fiber diameters, plasma glucose levels and lower hematocrit when compared with those at the bottom. These size and muscle traits assist fish to overcome the ladder barrier and bypass the dam, an effort that might be reflected in the glucose levels. Females also showed higher GSI at the top of the fish ladder, a trait possibly facilitating their reproduction upstream. These results indicate that a dam system favors fish with specific morphological–physiological profile. This may have a strong influence upon upstream fish populations over generations and implies the presence of artificial selective pressure.     

Taxonomy-based differences in feeding guilds of fish

It has been taken for granted that feeding guilds and behavior in animals are linked to the taxonomic relatedness of species,but empirical evidence supporting such relationship is virtually missing.To examine the importance of taxonomy on trophic ecology,I here present the first well-resolved dietary taxonomy analysis based on feeding guilds(predation,herbivory,and filtering)among families and genera within the fish order Perciformes.Taxonomic relatedness in feeding did not vary with ecosystem dimension(marine vs.freshwater).Although predation dominates among Perciformes fishes,this study shows that in most cases taxonomic units(family or genus)are composed by species with several feeding guilds.Related species are more similar in feeding compared with species that are taxonomically more distant demonstrating that there is a greater variation of feeding guilds within families than genera.Thus,there is no consistency in feeding guilds between family-and genus-level taxonomy.This study provides empirical support for the notion that genera are more informative than families,underlining that family-level taxonomy should be avoided to infer feeding habits of fish species at finer taxonomic resolution.Thus,the choice of taxonomic resolution(family or genus level)in ecological studies is key to avoid information loss and misleading results.I conclude that high-rank taxonomic units(i.e.,above the generic level)are not appropriate to test research hypotheses about the feeding of fish.     

Prey catching in the archer fish: does the fish use a learned correction for refraction?

An answer to the question of how the archer fish hits an aerial insect, despite the refraction of light at the surface of the water has not yet been found. The aims of the present studies are to find out: (1) whether the fish applies a learned correction with the virtual image as a point of reference; (2) whether deprivation of practice in squirting affects performance. For the first aim the accuracy of squirts was measured in 30 subjects. Contrary to suggestions from the literature, elevation failures were prominent but the frequencies of over- and under-squirting did not differ, which does not support the idea that the fishes applied a learned correction for refraction by using feedback from the efficacy of squirts. For the second aim, five experimental subjects were deprived of practice, whereas six control subjects got daily practice, during 6 months. The only significant difference, found thereafter, was that during the first session experimental subjects aimed more often before squirting than control subjects did, but hitting was not affected. A number of subjects developed abnormal mandibles which inevitably led to squirting too high. Our findings do not support the hypothesis that the archer fish uses learned corrections for refraction.     

Otolith chemistry of prey fish consumed by a fish predator: does digestion hinder Russian doll techniques?

The effect of digestion by a predatory fish (largemouth bass Micropterus salmoides) on stable isotopic (δ¹³C and δ¹⁸O) and trace elemental (Sr:Ca and Ba:Ca) compositions of prey fish (bluegill Lepomis macrochirus) otoliths was investigated in a laboratory experiment. Trace element and stable‐isotopic signatures of L. macrochirus otoliths were not significantly altered for up to 16 h after L. macrochirus were consumed by M. salmoides. Prey fish otoliths recovered from predator digesta can retain environmental stable isotopic and trace elemental signatures, suggesting that determination of environmental history for prey fishes by stable‐isotope and trace‐element analysis of otoliths recovered from stomachs of piscivorous fishes will be feasible.     

Population regulation by habitat heterogeneity or individual adjustment?

1. The habitat heterogeneity (HHH) and individual adjustment (IAH) hypotheses are commonly proposed to explain a decrease in reproduction rate with increasing population density. Higher numbers of low-quality territories with low reproductive success as density increases lead to a decrease in reproduction under the HHH, while more competition at high density decreases reproduction across all territories under the IAH. 2. We analyse the influence of density and habitat heterogeneity on reproductive success in eight populations of long-lived territorial birds of prey belonging to four species. Sufficient reliability in distinguishing between population-wide, site-specific and individual quality effects on reproduction was granted through the minimal duration of 20 years of all data sets and the ability to control for individual quality in five of them. 3. Density increased in five populations but reproduction did not decrease in these. Territory occupancy as a surrogate of territory quality correlated positively with reproductive success but only significantly so in large data sets with more than 100 territories. 4. Reproductive success was always best explained by measures of territory quality in multivariate models. Direct or delayed (t-1) population density entered very few of the best models. Mixed models controlling for individual quality showed an increasing reproductive performance in older individuals and in those laying earlier, but measures of territory quality were also always retained in the best models. 5. We find strong support for the habitat heterogeneity hypothesis but weak support for the individual adjustment hypothesis. Both individual and site characteristics are crucial for reproductive performance in long-lived birds. Proportional occupancy of territories enables recognition of high-quality territories as preferential conservation targets.