Habitat Partitioning Research Articles

Ecomorphological divergence and habitat lability in the context of robust patterns of modularity in the cichlid feeding apparatus

BackgroundAdaptive radiations are characterized by extreme and/or iterative phenotypic divergence; however, such variation does not accumulate evenly across an organism. Instead, it is often partitioned into sub-units, or modules, which can differentially respond to selection. While it is recognized that changing the pattern of modularity or the strength of covariation (integration) can influence the range or rate of morphological evolution, the relationship between shape variation and covariation remains unclear. For example, it is possible that rapid phenotypic change requires concomitant changes to the underlying covariance structure. Alternatively, repeated shifts between phenotypic states may be facilitated by a conserved covariance structure. Distinguishing between these scenarios will contribute to a better understanding of the factors that shape biodiversity. Here, we explore these questions using a diverse Lake Malawi cichlid species complex, Tropheops, that appears to partition habitat by depth.ResultsWe construct a phylogeny of Tropheops populations and use 3D geometric morphometrics to assess the shape of four bones involved in feeding (mandible, pharyngeal jaw, maxilla, pre-maxilla) in populations that inhabit deep versus shallow habitats. We next test numerous modularity hypotheses to understand whether fish at different depths are characterized by conserved or divergent patterns of modularity. We further examine rates of morphological evolution and disparity between habitats and among modules. Finally, we raise a single Tropheops species in environments mimicking deep or shallow habitats to discover whether plasticity can replicate the pattern of morphology, disparity, or modularity observed in natural populations.ConclusionsOur data support the hypothesis that conserved patterns of modularity permit the evolution of divergent morphologies and may facilitate the repeated transitions between habitats. In addition, we find the lab-reared populations replicate many trends in the natural populations, which suggests that plasticity may be an important force in initiating depth transitions, priming the feeding apparatus for evolutionary change.

Distribution patterns, carbon sources and niche partitioning in cave shrimps (Atyidae: Typhlatya)

Cave shrimps of the Typhlatya genus are common and widespread in fresh, brackish and marine groundwater throughout the Yucatan Peninsula (Mexico). These species are ideal models to test niche partitioning within sympatric species in oligotrophic systems. Nevertheless, their food sources remain unidentified, and despite their frequency and functional importance, distribution and abundance patterns of these species within caves have not been fully recognized. Here, we describe the abundance of three Typhlatya species in different temporal and spatial scales, investigate changes in water conditions, and potential sources of carbon as an indication of food origin. Species composition and abundance varied markedly in space and time revealing patterns that differed from one system to another and in relation to environmental parameters. Isotope analysis showed that each species reflects a particular δ13C and Δ14C fingerprint, suggesting they feed in different proportions from the available carbon sources. Overall, our findings suggest a niche partitioning of habitat and feeding sources amongst the three Typhlatya species investigated, where environmental characteristics and physiological differences could play an important role governing their distribution patterns.

Linking Antarctic krill larval supply and recruitment along the Antarctic Peninsula.

Antarctic krill (Euphausia superba) larval production and overwinter survival drive recruitment variability, which in turn determines abundance trends. The Antarctic Peninsula has been described as a recruitment hot spot and as a potentially important source region for larval and juvenile krill dispersal. However, there has been no analysis to spatially resolve regional-scale krill population dynamics across life stages. We assessed spatiotemporal patterns in krill demography using two decades of austral summer data collected along the North and West Antarctic Peninsula since 1993. We identified persistent spatial segregation in the summer distribution of euphausiid larvae (E. superba plus other species), which were concentrated in oceanic waters along the continental slope, and E. superba recruits, which were concentrated in shelf and coastal waters. Mature females of E. superba were more abundant over the continental shelf than the slope or coast. Euphausiid larval abundance was relatively localized and weakly correlated between the North and West Antarctic Peninsula, while E. superba recruitment was generally synchronized throughout the entire region. Euphausiid larval abundance along the West Antarctic Peninsula slope explained E. superba recruitment in shelf and coastal waters the next year. Given the localized nature of krill productivity, it is critical to evaluate the connectivity between upstream and downstream areas of the Antarctic Peninsula and beyond. Krill fishery catch distributions and population projections in the context of a changing climate should account for ontogenetic habitat partitioning, regional population connectivity, and highly variable recruitment.

Feeding ecology of two subspecies of bottlenose dolphin: a tooth tale

Two subspecies of bottlenose dolphins are observed, not simultaneously, in a narrow coastal area of the western South Atlantic Ocean. However, their trophic interaction is unknown. Such information can be explored using stable isotope composition in teeth, warranting time series data. We analyzed carbon and nitrogen isotopic values (δ13C and δ15N) of dentin growth layer groups in teeth of Tursiops truncatus truncatus and Tursiops truncatus gephyreus stranded along this area of potential co-occurrence in order to investigate the trophic, spatial and temporal dimensions of their isotopic niches. For each subspecies, we calculated isotopic niche width and the possible overlap in resource use between them. We modeled δ13C and δ15N according to age to verify ontogenetic variations in resources use. We also measured the ratio of individual variation by that of the population to estimate the degree of individual specialization within each subspecies. Mean isotopic values differed only for carbon values (δ13CTtg = − 12.7‰; δ13CTtt = − 14.3‰), and a small overlap in resource use between subspecies was observed. Individual specialization was evident in both subspecies suggesting temporal consistency in resource use and indicating they forage upon various preys. Although weaning age and feeding habit seem similar, subspecies diverge especially in habitat use, indicating they adapted for feeding in different environments. These results show a clear habitat partitioning between subspecies and only a small overlap on resource use within the area, reinforcing the hypothesis of a parapatric distribution with very occasional contacts in this region of the western South Atlantic Ocean.

Habitat partitioning of two closely related pond frogs, Pelophylax nigromaculatus and Pelophylax porosus brevipodus, during their breeding season

Parapatric distributions of closely related species are common in many taxonomic groups. However, habitat overlap in sympatric areas within both species’ ranges is complex and driven by the nature of the interactions between species as well as each species’ ecological requirements. We therefore investigated the distribution of breeding habitats for two congeneric frogs, Pelophylax nigromaculatus and Pelophylax porosus brevipodus, in a region of Japan where these species co-occur, based on observation of mating calls as an index of the abundance of males engaging in reproductive activities. Among a total of 381 surveyed sites, P. nigromaculatus and P. porosus brevipodus were found at 171 and 229 sites, respectively. Pelophylax porosus brevipodus was widely distributed throughout the study area and was more abundant than P. nigromaculatus in sympatric sites. Analysis using cumulative link mixed models revealed that the abundance of calling males was negatively affected by the presence of calling males of the other species and by landscape factors. Interspecific differences in this negative effect appear to favor P. porosus brevipodus over P. nigromaculatus in our study area. Due to differences in the primary habitat preferences of the two species during the non-breeding season, habitat partitioning during the breeding season is likely driven by negative interspecific interactions during the reproductive process (i.e., reproductive interference).

Non-volant mammals of the Ibura National Forest, northeastern Brazil

Less than 10% of the original Atlantic Forest cover now remains standing in the Brazilian state of Sergipe, although few scientific studies have focused on its mammalian diversity. The present study describes the diversity of non-volant mammals found in the Ibura National Forest (INF), based on live trapping, and direct and indirect observations. We sampled the IBF on six days per month between June 2012 and August 2013, using live-traps (Sherman-type) positioned in pairs (ground and understory). We equally sampled semideciduous forest and an abandoned Eucalyptus plantation with dense understory (over 30 years). We also used non-systematics methods (direct observations, vestiges, camera-trap, and opportunistic captures). We recorded 18 species, from 12 families and 7 orders considering all the applied methods. Among recorded species, Bradypus torquatus and Lontra longicaudis are considered threatened of extinction. Considering only the live-trapping (totaling 3,240 trapping nights), we captured 125 individuals (3.85% success) from four species, Marmosa demerarae (52%), Didelphis albiventris (19.2%), Cerradomys vivoi (15.2%), and M. murina (13.6%). Estimated and observed richness was the same, suggesting a satisfactory effort. Didelphis albiventris and M. demerarae showed significantly higher captures in the dry seasons. Didelphis albiventris and C. vivoi showed significantly higher captures in the substratum, and M. demerarae higher in the understory. Cerradomys vivoi showed significantly higher captures in the Eucalyptus phytophysiognomy. Non-Metric Multidimensional Scaling and the ANOSIM showed a significant difference in the captured species among semidecidual forest and Eucalyptus. Despite the small area (144 ha), the INF still houses a relatively high mammalian diversity. Further investigations may help to understand the role of habitat reduction in the diversity and habitat partitioning among mammal species in the Atlantic Forest of Northeastern Brazil.

Use of a mechanistic growth model in evaluating post-restoration habitat quality for juvenile salmonids.

Individual growth data are useful in assessing relative habitat quality, but this approach is less common when evaluating the efficacy of habitat restoration. Furthermore, available models describing growth are infrequently combined with computational approaches capable of handling large data sets. We apply a mechanistic model to evaluate whether selection of restored habitat can affect individual growth. We used mark-recapture to collect size and growth data on sub-yearling Chinook salmon and steelhead in restored and unrestored habitat in five sampling years (2009, 2010, 2012, 2013, 2016). Modeling strategies differed for the two species: For Chinook, we compared growth patterns of individuals recaptured in restored habitat over 15-60 d with those not recaptured regardless of initial habitat at marking. For steelhead, we had enough recaptured fish in each habitat type to use the model to directly compare habitats. The model generated spatially explicit growth parameters describing size of fish over the growing season in restored vs. unrestored habitat. Model parameters showed benefits of restoration for both species, but that varied by year and time of season, consistent with known patterns of habitat partitioning among them. The model was also supported by direct measurement of growth rates in steelhead and by known patterns of spatio-temporal partitioning of habitat between these two species. Model parameters described not only the rate of growth, but the timing of size increases, and is spatially explicit, accounting for habitat differences, making it widely applicable across taxa. The model usually supported data on density differences among habitat types in Chinook, but only in a couple of cases in steelhead. Modeling growth can thus prevent overconfidence in distributional data, which are commonly used as the metric of restoration success.

Habitat zonation on coral reefs: Structural complexity, nutritional resources and herbivorous fish distributions.

Distinct zonation of community assemblages among habitats is a ubiquitous feature of coral reefs. The distribution of roving herbivorous fishes (parrotfishes, surgeonfishes and rabbitfishes) is a particularly clear example, with the abundance of these fishes generally peaking in shallow-water, high-energy habitats, regardless of the biogeographic realm. Yet, our understanding of the factors which structure this habitat partitioning, especially with regards to different facets of structural complexity and nutritional resource availability, is limited. To address this issue, we used three-dimensional photogrammetry and structure-from-motion technologies to describe five components of structural complexity (rugosity, coral cover, verticality, refuge density and field-of-view) and nutritional resource availability (grazing surface area) among habitats and considered how these factors are related to herbivorous fish distributions. All complexity metrics (including coral cover) were highest on the slope and crest. Nutritional resource availability differed from this general pattern and peaked on the outer-flat. Unexpectedly, when compared to the distribution of herbivorous fishes, none of the complexity metrics had a marked influence in the models. However, grazing surface area was a strong predictor of both the abundance and biomass of herbivorous fishes. The strong relationship between grazing surface area and herbivorous fish distributions indicates that nutritional resource availability may be one of the primary factors driving the distribution of roving herbivorous fishes. The lack of a relationship between complexity and herbivorous fishes, and a strong affinity of herbivorous fishes for low-complexity, algal turf-dominated outer-flat habitats, offers some cautious optimism that herbivory may be sustained on future, low-complexity, algal turf-dominated reef configurations.

Does habitat partitioning by sympatric plovers affect nest survival?

AbstractThe vertical structure and composition of vegetation can influence the quantity and quality of potential nesting sites for birds. Interspecific competition for high-quality nesting habitat may force some individuals into suboptimal habitat and lead to reduced reproductive success, eventually leading to changes in distribution or abundance. Large climate-mediated shifts in vegetation, including the rapid expansion of shrubs onto tundra, are occurring in the Arctic across important breeding grounds of many shorebird species of conservation concern. We investigated effects of vegetation structure and composition on nest-site selection and nest success of sympatrically breeding American Golden-Plovers (Pluvialis dominica) and Pacific Golden-Plovers (P. fulva), which nest along an elevational gradient ranging from coastal tundra meadows to alpine tundra. Both species strongly selected nest sites with less cover of tall shrubs and other tall vegetation than available at random sites within their territories. American Golden-Plovers selected territories and nest sites that were higher in elevation and had more rocky substrates and less graminoid vegetation than those selected by Pacific Golden-Plovers. The daily nest survival rate was equivalent in the 2 species (0.966, 95% CI: 0.955, 0.975) and similar to that found in other Arctic-breeding shorebirds; however, contrary to predictions, nest survival was not associated with habitat features selected for nest sites for either species. Strong selection of open habitat for nest sites suggests that continued climate-related shrub expansion may reduce the amount of suitable breeding habitat for both species, but partitioning along the elevational gradient and differences in body size suggest that impacts may be more severe for Pacific Golden-Plovers. Additional research is needed to determine if differential selection of nesting habitat is related to survival of the adults or their young.

Classical and computed tomographic anatomical analyses in a not-so-cryptic Alviniconcha species complex from hydrothermal vents in the SW Pacific

The chemosymbiotic gastropod Alviniconcha (Provannidae), first described in 1988, is one of the most emblematic hydrothermal-vent taxa described from the Central Indian Ridge and the Southwest (SW) Pacific. Symbiotic bacteria found in the gill of Alviniconcha are thought to be their principal source of nutrition. In the SW Pacific, species distributions for A. kojimai, A. boucheti – and to a lesser extent A. strummeri – overlap. While Alviniconcha species do not appear to truly co-exist in these highly energetic but spatially limited habitats, certain species regularly co-occur within a single vent field and in rare instances, the same edifice. Past research suggests that SW-Pacific Alviniconcha species might aggregate around fluids with distinct geothermal profiles. These small-scale distribution patterns have been attributed to differences in their symbiont assemblages or host physiologies. However, little is known about the anatomy of most Alviniconcha species, beyond that detailed for the type species Alviniconcha hessleri, whose geographic range does not overlap with other congeners. In fact, species within this genus are currently described as cryptic, despite the absence of any comparative morphological studies to assess this. To test whether the genus is genuinely cryptic and identify any functional differences in host anatomy that might also mediate habitat partitioning in SW Pacific species, the current study examined the morphoanatomy of A. kojimai, A. boucheti and A. strummeri from the Fatu Kapa vent field, an area of hydrothermal activity recently discovered north of the Lau Basin near the Wallis and Futuna Islands and the only known example where all three species occur within adjacent vent fields. A combination of detailed dissections, histology and X-ray computed tomography demonstrate that A. kojimai, A. strummeri and A. boucheti are readily identifiable based on shell morphology and ornamentation alone, and therefore not truly cryptic. These traits provide a rapid and reliable means for species identification. However, aside from some subtle differences in radular morphology, these species of Alviniconcha exhibit conserved anatomical features, providing no evidence that functional host anatomy is implicated in habitat partitioning. This provides support for the current belief that host-species distributions are probably governed by symbiont-mediated physiological factors.

Tidal effects on marsh habitat use by three fishes in the San Francisco Estuary

Little is known about the ecological importance of low-order tidal marsh channels to fishes in the San Francisco Estuary, California. We conducted a passive mark-recapture study to compare residency, site fidelity, and movement patterns of fishes in a small intertidal channel (0.1 km2) in a large tidal marsh reserve (4.25 km2). We coupled continuous, high-frequency data on movements of fish tagged with Passive Integrated Transponder (PIT) tags and abiotic conditions from a PIT-detector and datasonde, respectively. Novel insights were gained by employing TidalTrend, a software program that characterizes tidal time-series data for ecological interpretation. Overall, we found that fishes exhibited different patterns of intertidal habitat use: the resident species, tule perch (Hysterocarpus traski), consistently spent more time per visit, per day, and per season using the intertidal channel, except during the reproductive window in spring; the transient species, Sacramento splittail (Pogonichthys macrolepidotus) and striped bass (Morone saxatilis), were more opportunistic and exhibited higher individual variation in movement patterns. Generalized additive mixed models indicated that tide height, rate of change in tide height, tidal inequality, time of day, lunar phase, and water temperature better predicted fish detections than other variables, but their effects varied across species. Based on our findings, we posit that time, through tides, allows habitat partitioning among fish species and individuals with different life-history types. Furthermore, functional connectivity between subtidal and intertidal channels in tidal marshes is a feature of the estuarine mosaic that should be integrated into habitat restoration designs in the San Francisco Estuary.

Habitat Partitioning in Sympatric Delphinids Around the Falkland Islands: Predicting Distributions Based on a Limited Data Set

Spatial modelling based on line transect data is a standard method for characterising marine mammal distributions and habitat preference. However, collecting the data required is costly and may be difficult in remote areas. Models based on habitat variables offer the potential to predict where the species will occur in areas outside the area of a localised survey. This has important implications for spatial management where decisions have to be made that affect wide areas over which comprehensive survey efforts may not be feasible. This study demonstrates that it is possible, using a spatially limited data set, to characterise habitat use and predict the distribution of two poorly known sympatric delphinids around the Falkland (Malvinas) Islands (FI), Commerson’s dolphins (Cephalorhynchus commersonnii) and Peale’s dolphins (Lagenorhynchus australis). We used a Hurdle model approach to investigate the relationship between dolphin sightings (from a spatially restricted boat-based line transect survey) and environmental covariates. We then used the modelled relationships to predict the distribution and relative abundance of Commerson’s and Peale’s dolphins over the entire FI inshore waters. We compared the predicted distribution maps to independent sightings from a subsequent island-wide aerial line transect survey, and found a close match between predicted and observed distributions. Commerson’s dolphins preferred nearshore waters with strong tidal mixing and were most numerous close to river mouths and in upper inlets or channels. In contrast, Peale’s dolphins preferred deeper, well-stratified areas further from shore as well as nearshore waters with extensive kelp beds. While the two dolphin species are often considered sympatric, our results indicate fine-scale habitat partitioning based on specific habitat preferences, which is important to consider in further studies and marine spatial planning. We provide several methodological refinements to prepare transect sighting data for spatial analysis and implement Hurdle models more easily using the new ‘dshm’ R-package. We also show the usefulness of such refinements applied to a carefully chosen spatially limited dataset as a cost-effective approach to elucidating species distribution patterns. Our methodology and software implementations can be easily applied to transect survey data of other marine and terrestrial taxa.

Pelagic Habitat Partitioning of Late-Larval and Juvenile Tunas in the Oceanic Gulf of Mexico

Tunas are ecologically important in pelagic ecosystems, but due to their high economic value, large-bodied species are overfished. Declines in fishery landings of large-bodied tuna species in the Gulf of Mexico (GoM) are expected to increase fishing pressures on unmanaged, small-bodied tuna species, whose life history traits are less known. While predicting spawning stocks and recruitment success typically focuses on estimates of larval abundances, juveniles may provide a better estimate of future adult stock sizes, as they are more likely to survive to adulthood because mortality rates scale inversely with body size. However, distributional studies on juveniles are rare, leading to a gap in our understanding of tuna ecology. In the present study, tuna early life stages were collected across the GoM from January-September 2011. The size class examined in this study, representing large larvae and small juveniles, is larger than that of previous larval tuna studies in the GoM. Faunal composition, abundance, frequency of occurrence, and diel catchability were investigated. Generalized additive models (GAMs) were used to examine spatiotemporal distributions of the family Scombridae and the three most-abundant tuna species in the GoM’s epipelagic waters with respect to location, oceanographic features, and temporal change. In total, 11 of the 16 scombrid species inhabiting the GoM were collected, with small-bodied tuna species (Euthynnus alletteratus, Thunnus atlanticus, Auxis thazard) dominating the assemblage. Overall, scombrids were caught at higher abundances and frequencies at night than during the day, demonstrating that nighttime sampling generates a more accurate representation of faunal abundance and distribution. Abundance and presence-absence GAMs identified a coastal group (E. alletteratus and A. thazard) associated with productive continental shelf/slope environments (low salinity, higher chlorophyll a concentrations, nearer to shelf break) and an oceanic group (represented by T. atlanticus) associated with offshore, oligotrophic habitats (high salinity, lower chlorophyll a concentrations, further from shelf break). These results demonstrate that over a broad spatiotemporal domain, large larvae and juvenile tunas partition pelagic habitat on the mesoscale in addition to the temporal partitioning of adult spawning. These factors are important for spatially and temporally explicit modeling aimed at predicting tuna stock sizes.

Cryptic speciation in the ectocommensal Bdelloura candida (Platyhelminthes, Tricladida, Maricola) follows habitat specialization of the American horseshoe crab, Limulus polyphemus

AbstractIn strict symbiotic associations, the genetic structure of the symbiont often mirrors that of its host, with interesting implications for population dynamics and phylogeography. An unresolved case of symbiotic specificity and phylogeographic consequence is the relationship between the marine triclad Bdelloura candida and its host, the American horseshoe crab, Limulus polyphemus. A recent study by Riesgo et al. (2017, Marine Biology, 164, 111) identified a strong genetic break between populations of B. candida in the Gulf of Mexico and the Atlantic Ocean but had minimal sampling around the Florida peninsula such that the exact location of the boundary zone was not specified. To solve this, a comprehensive analysis of 16S rRNA and ITS2 genetic markers was conducted from new collections around the Florida peninsula. A clear and significant genetic break was identified between populations of supposed B. candida between Cumberland Island, Georgia, and Mosquito Lagoon, Florida. This genetic break establishes two cryptic lineages, an Atlantic population as far south as Georgia and a Floridian population inclusive of the entire peninsula and Gulf of Mexico, potentially due to niche partitioning of the unique intertidal habitats of its horseshoe crab hosts in Florida. This result directly refutes the previous hypothesis that a population break exists between the coasts of the Atlantic Ocean and Gulf of Mexico, and instead matches the genetic break of its host. Furthermore, a third cryptic lineage was identified in Key West. Overall, this work demonstrates the challenges in maintaining genetic connections between populations of both B. candida and L. polyphemus across their distributions, and poses meaningful implications for both species in the larger context of marine conservation and biodiversity.

Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding

Lutjanus erythropterus and L. malabaricus are sympatric, sister taxa that are important to fisheries throughout the Indo-Pacific. Their juveniles are morphologically indistinguishable (i.e. cryptic). A DNA metabarcoding dietary study was undertaken to assess the diet composition and partitioning between the juvenile and adult life history stages of these two lutjanids. Major prey taxa were comprised of teleosts and crustaceans for all groups except adult L. erythropterus, which instead consumed soft bodied invertebrates (e.g. tunicates, comb jellies and medusae) as well as teleosts, with crustaceans being notably absent. Diet composition was significantly different among life history stages and species, which may be associated with niche habitat partitioning or differences in mouth morphology within adult life stages. This study provides the first evidence of diet partitioning between cryptic juveniles of overlapping lutjanid species, thus providing new insights into the ecological interactions, habitat associations, and the specialised adaptations required for the coexistence of closely related species. This study has improved our understanding of the differential contributions of the juvenile and adult diets of these sympatric species within food webs. The diet partitioning reported in this study was only revealed by the taxonomic resolution provided by the DNA metabarcoding approach and highlights the potential utility of this method to refine the dietary components of reef fishes more generally.

Estuarine-terrestrial habitat gradients enhance nursery function for resident and transient fishes in the San Francisco Estuary

Nursery functions of US West Coast drowned river valley estuaries are not well understood. Using long-term fish-monitoring data (1995-2017) in Suisun Marsh, San Francisco Estuary, California, USA, we examined spatial and temporal trends in abundance and apparent growth of fishes with diverse life-history types. Focal species were Sacramento splittail Pogonichthys macrolepidotus, striped bass Morone saxatilis, tule perch Hysterocarpus traski, and starry flounder Platichthys stellatus, which collectively represented 55% of total catch (n = 140092). We identified keystone habitat patches that functioned as nursery hotspots during the peak young-of-the-year recruitment window. Deep, flow-through sloughs close to the open estuary were important nursery habitats for the marine transient starry flounder. In contrast, splittail and striped bass mostly migrated through such corridors to rear in shallow, dead-end sloughs bisecting tidal marsh plains, managed tidal ponds, and uplands. Tule perch were concentrated in shallow, interior sloughs, reflecting their resident life-history type and adaptations to variable conditions in a small home range. Interactions among freshwater flows and stationary habitat features (e.g. channel depth, land-to-open-water ratio) were related to fish abundance; however, species and age classes differed in their relationships to these interactions, suggesting a mechanism for habitat partitioning in space and time. Overall, we inferred that habitat connectivity—longitudinal, lateral, and vertical—along the estuarine-terrestrial gradient was a driver of fish species diversity and productivity. Consideration of seascape-landscape dynamics across multiple spatial and temporal scales in estuaries should help maintain or increase fish populations and ecological resilience in the face of rising sea levels and other environmental stressors.

Population dynamics of Farfantepenaeus subtilis (Pérez-Farfante, 1967) and Litopenaeus schmitti (Burkenroad, 1936) (Decapoda: Penaeidae) and evidence of habitat partitioning in the northeast of Brazil

The population structure, sex ratio, size at the onset of sexual maturity, growth rates, and longevity of Farfantepenaeus subtilis and Litopenaeus schmitti were studied in the State of Sergipe, Brazil. The distribution pattern of juveniles and reproductive females was compared to investigate whether habitat partitioning takes place between these species. The sampling occurred monthly, from September/2013 to August/2014, in nine stations of three transects (5 m, 15 m, and 30 m deep) using a shrimp fishing boat. In total, 1076 F. subtilis and 499 L. schmitti individuals were captured. The sex ratio of F. subtilis was skewed toward females, while L. schmitti had a 1:1 sex ratio. Females of both species were larger than the males. The size at the onset of sexual maturity of F. subtilis females was large than that of males, while the opposite occurred in L. schmitti. The estimated growth parameters of F. subtilis males were: CL∞=33.24 mm, k = 2.30/year and longevity = 2.0 years. For the females, they were: CL∞=42.49 mm, k = 2.15/year and longevity = 2.12 years. The growth parameters of L. schmitti males were: CL∞=32.48 mm, k = 2.41/year and longevity = 1.91 years. For the females, they were: CL∞=38.78 mm, k = 2.01/year and longevity = 2.29 years. The distribution patterns of juveniles and reproductive females differed between species. F. subtilis females predominated in deeper waters. Juveniles of L. schmitti were aggregated in shallow waters (5 m), while F. subtilis aggregated at 15 m. Considering that (1) the relationship between the environmental factors and the abundance of juveniles and females was not evident, and (2) the reproductive and recruitment periods of these species are synchronized, our results suggest that habitat partitioning takes place to decrease the interspecific competition.

EDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.

Seasonal occurrence and habitat partitioning of two oriental weather loaches, the alien Misgurnus dabryanus and the endemic M. anguillicaudatus, in Shiga, central Japan

Seasonal occurrence and habitat partitioning of two oriental weather loaches, the alien Misgurnus dabryanus and the endemic M. anguillicaudatus, in Shiga, central Japan

Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)

Abstract Fish are the most diverse vertebrate group, and they have evolved equally diverse visual systems, varying in terms of eye morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and opsin gene expression levels. This variation is mainly due to adaptations driven by two factors: differences in the light environments and behavioural tasks. However, while the effects of large‐scale habitat differences are well described, it is less clear whether visual systems also adapt to differences in environmental light at the microhabitat level. To address this, we assessed the relationship between microhabitat use and visual system features in fishes inhabiting coral reefs, where habitat partitioning is particularly common. We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology. We found that cardinalfishes display six types of microhabitat partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix. Species predominantly found in exposed microhabitats had higher expression of the short‐wavelength‐sensitive violet opsin (SWS2B) and lower expression of the dim‐light active rod opsin (RH1). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue‐green central part of the light spectrum (SWS2As and RH2s), while fishes entirely hidden in the reef substrate had a higher expression of the long‐wavelength‐sensitive red opsin. We also found that eye size relative to body size differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure. Retinal topography did not show co‐adaptation with microhabitat use, but data suggested co‐adaptation with feeding mode. We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems—and possibly those of other (reef) fishes—have also adapted to the light intensity and the light spectrum of their preferred diurnal microhabitats. A free Plain Language Summary can be found within the Supporting Information of this article.