A baited underwater video technique to assess shallow-water Mediterranean fish assemblages: Methodological evaluation

A baited underwater video (BUV) system for the study of reef-associated fish populations on shallow (10-20 m) rocky habitats in the western Mediterranean was assessed at four locations in Spain and two in France. We describe the apparatus and optimal deployment times for video sampling. Different species had different response times to the bait, with four response groups identified. Examination of species accumulation curves and fish abundance estimates over time revealed that a period of approximately 20 min deployment was sufficient to capture most species on video. The technique sampled a wide variety of species, with 51 species belonging to 33 families recorded. Nine species of fish appeared regularly at the bait in relatively high numbers, and consist of six carnivores (Serranus cabrilla, Serranus scriba, Coris julis, Diplodus annularis, Diplodus vulgaris, Thalassoma pavo), two planktivores (Chromis chromis, Boops boops) and one omnivore (Oblada melanura). However, abundance estimates for other species were generally very low (mean < 1 per location). Comparison of results from BUV with those obtained by Underwater Visual Census (UVC) at the same locations suggests that although BUV estimates species richness reliably, UVC is the more suitable technique for estimating the abundance of shallow-water reef fish in the Mediterranean. BUV improvements are suggested to optimise its use in deeper waters where UVC using scuba is inoperable.     

Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) trawls for assessments of fish biodiversity in inter-reefal areas of the Great Barrier Reef Marine Park

A field comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) trawls was made to assess the sampling options for describing patterns of fish biodiversity in the lagoonal waters of the Great Barrier Reef Marine Park. Replicated comparisons were made during the day and night on trawl grounds with different biophysical characteristics. Each trawl was made close and parallel to a long-shore set of five BRUVS set at regular intervals along one nautical mile. For each species, the sum of the maximum number of fish sighted on BRUVS at any one time (∑MaxN_{1, …, 5}) was compared with the number of fish caught in trawls (N).The two techniques recorded significantly different components of the fish fauna on the trawl grounds. Trawls caught mainly small (≤300 mm), sedentary or cryptic, demersal species—such as flatfishes, apogonids, synodontids, triglids and callionymids. The BRUVS recorded more larger, mobile species from a much wider size range of families, including large elasmobranchs, more fusiform pelagic species (such as carangids and scombrids), and numerous eels. Species accumulation curves were parallel and very similar in shape for both techniques, but were separated by about 11 extra species in trawls. Fifty-two species in 17 families were caught only in trawls and 38 species in 15 families were recorded only by BRUVS. The occurrence of 38 small mobile species in 21 families was common to both techniques, but most of these showed marked differences in relative abundance. Trawls recorded higher species richness at all sites, and at night, but the average number of species and individuals recorded per transect were only about 26% and 19% lower for the BRUVS. The BRUVS consistently recorded more species during the day than trawls, and are limited most by water clarity. Multivariate analyses showed that both techniques indicated the presence of six fish assemblages based on day and night in three locations, despite sampling quite different components of the fauna. The six assemblages accounted for 78.9% of the variation in the BRUVS data compared to 68.9% of the variation in the trawl data, and there was a lower error rate in discriminating the six assemblages in the BRUVS data.BRUVS are non-extractive and can be used on complex topographies and in sensitive habitats in most or all zones of the Marine Park, but models of bait plumes are needed to convert fish sightings to density estimates. They may have a particular role in studies of larger, rarer elasmobranchs and teleosts of special conservation interest. Trawls can be used in any level of water clarity and provide direct estimates of fish density, particularly those smaller teleosts most vulnerable to the effects of trawling. The complementary use of prawn trawls and BRUVS would enable a more comprehensive assessment of teleost and elasmobranch diversity in the variety of inter-reef seabed topographies and management zones comprising the Marine Park.     

Investigating the behavioural responses of trapped fishes using underwater video surveillance

An underwater video surveillance system known as TrapCam was used to continuously record (15 ×c. 24 h periods) fish behaviour within and immediately surrounding an experimental fish trap situated in a coral reef ecosystem in the United States Virgin Islands. Of the 100 fishes (18 species, 12 families) trapped, surgeonfishes (Acanthuridae) and snappers (Lutjanidae) were most common. Thirteen distinctively identifiable behaviours were observed for trapped fishes. Species did not differ significantly in the proportion of time allocated to different behaviours (ANOSIM, R = 0·142). Doctorfish Acanthurus chirurgus and grey angelfish Pomacanthus arcuatus allocated the largest proportion of their recorded time to enter and exit the trap. Fishes spent an average of 15 min in the trap before escaping. Sixty‐seven per cent of trap approaches consisted of an individual of the same species as one already trapped suggesting that conspecific attraction may have occurred. Fifteen per cent of trapped species were observed with abrasions to the head and 70% were observed approaching the trap corners. The results of this study provide a greater understanding of the behavioural interactions between fishes and traps that can help explain patterns of catch composition, the physical condition of fishes in traps and inform design of gear modifications to optimize by‐catch reduction in the trap fishery.     

Growth of reef fishes in response to live coral cover

Although the global decline in coral reef health is likely to have profound effects on reef associated fishes, these effects are poorly understood. While declining coral cover can reduce the abundance of reef fishes through direct effects on recruitment and/or mortality, recent evidence suggests that individuals may survive in disturbed habitats, but may experience sublethal reductions in their condition. This study examined the response of 2 coral associated damselfishes (Pomacentridae), Chrysiptera parasema and Dascyllus melanurus, to varying levels of live coral cover. Growth, persistence, and the condition of individuals were quantified on replicate coral colonies in 3 coral treatments: 100% live coral (control), 50% live coral (partial) and 0% live coral (dead). The growth rates of both species were directly related to the percentage live coral cover, with individuals associated with dead corals exhibiting the slowest growth, and highest growth on control corals. Such differences in individual growth between treatments were apparent after 29 d. There was no significant difference in the numbers of fishes persisting or the physiological condition of individuals between different treatments on this time-scale. Slower growth in disturbed habitats will delay the onset of maturity, reduce lifetime fecundity and increase individual's vulnerability to gape-limited predation. Hence, immediate effects on recruitment and survival may underestimate the longer-term impacts of declining coral on the structure and diversity of coral-associated reef fish communities.     

Comparative phylogeography of reef fishes from the Gulf of Aden to the Arabian Sea reveals two cryptic lineages

The Arabian Sea is a heterogeneous region with high coral cover and warm stable conditions at the western end (Djibouti), in contrast to sparse coral cover, cooler temperatures, and upwelling at the eastern end (southern Oman). We tested for barriers to dispersal across this region (including the Gulf of Aden and Gulf of Oman), using mitochondrial DNA surveys of 11 reef fishes. Study species included seven taxa from six families with broad distributions across the Indo-Pacific and four species restricted to the Arabian Sea (and adjacent areas). Nine species showed no significant genetic partitions, indicating connectivity among contrasting environments spread across 2000 km. One butterflyfish (Chaetodon melannotus) and a snapper (Lutjanus kasmira) showed phylogenetic divergences of d = 0.008 and 0.048, respectively, possibly indicating cryptic species within these broadly distributed taxa. These genetic partitions at the western periphery of the Indo-Pacific reflect similar partitions recently discovered at the eastern periphery of the Indo-Pacific (the Hawaiian and the Marquesan Archipelagos), indicating that these disjunctive habitats at the ends of the range may serve as evolutionary incubators for coral reef organisms.

     

Phylogeography of the invasive seaweed Asparagopsis (Bonnemaisoniales, Rhodophyta) reveals cryptic diversity

The rhodophyte seaweed Asparagopsis armata Harvey is distributed in the northern and southern temperate zones, and its congener Asparagopsis taxiformis (Delile) Trevisan abounds throughout the tropics and subtropics. Here, we determine intraspecific phylogeographic patterns to compare potential causes of the disjunctions in the distributions of both species. We obtained specimens throughout their ranges and inferred phylogenies from the hypervariable domains D1-D3 of the nuclear rDNA LSU, the plastid spacer between the large and small subunits of RuBisCo and the mitochondrial cox 2-3 intergenic spacer. The cox spacer acquired base changes the fastest and the RuBisCo spacer the slowest. Median-joining networks inferred from the sequences revealed the absence of phylogeographic structure in the introduced range of A. armata, corroborating the species' reported recent introduction. A. taxiformis consisted of three nuclear, three plastid and four mitochondrial genetically distinct, lineages (1-4). Mitochondrial lineage 3 is found in the western Atlantic, the Canary Islands and the eastern Mediterranean. Mitochondrial lineages 1, 2, and 4 occur in the Indo-Pacific, but one of them (lineage 2) is also found in the central Mediterranean and southern Portugal. Phylogeographic results suggest separation of Atlantic and Indo-Pacific lineages resulted from the emergence of the Isthmus of Panama, as well as from dispersal events postdating the closure event, such as the invasion of the Mediterranean Sea by mitochondrial lineages 2 and 3. Molecular clock estimates using the Panama closure event as a calibration for the split of lineages 3 and 4 suggest that A. taxiformis diverged into two main cryptic species (1 + 2 and 3 + 4) about 3.2-5.5 million years ago (Ma), and that the separation of the mitochondrial lineages 1 and 2 occurred 1-2.3 Ma.     

Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae)

Hypotheses on the taxonomic status of two Bolivian Pristimantis with taxonomic problems are assessed by an integrative taxonomic approach that integrates three independent lines of evidence: external morphology, prezygotic reproductive barriers (advertisement calls) and reciprocal monophyly (phylogenetic analyses of partial 16S mtDNA sequences). Central Andean Bolivian populations previously assigned to either P. peruvianus or P. dundeei, and lowland Amazonian populations from southern Peru and northern Bolivia previously considered P. peruvianus do not correspond to these species. Indeed, multivariate analyses of qualitative and quantitative morphological and bioacoustic characters, and phylogenetic analyses support the hypothesis that they represent different, previously unknown, cryptic lineages. They are herein described as new species. The former is a sibling species of P. fenestratus that inhabits the Amazonian and semideciduous forests of the Andean foothills in central Bolivia. The latter is sibling to the Andean species P. danae and is parapatric to it in the Amazonian lowland forests and adjacent foothills of northern Bolivia, southern Peru and adjacent Brazil. Most species of Neotropical frogs, and especially Pristimantis, have been described by using external qualitative morphological characters only. An extended integrative taxonomic approach, as exemplified herein, may lead to the discovery of many other cryptic and sibling lineages that would increase the species numbers of tropical areas. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 97–122.     

In-stream behaviour of threatened fishes and their food organisms based on remote video monitoring

Can remote underwater video be used to investigate the in-stream behaviour of small fishes and decapods? Diel activity of two threatened freshwater fishes (Macquaria australasica and Gadopsis bispinosus), a palaemonid prawn and an atyid shrimp, was established from remote underwater video in a pool of an upland stream in the current study. Decapods and large fishes (>5 cm TL) were nocturnal, whereas, small fishes (<5 cm TL) were diurnal. The suitability of using underwater video to quantify short-term (seconds) behavioural interaction among individuals was also demonstrated, with early-juvenile-phase Gadopsis bispinosus exhibiting interference competition on 35% of occasions when two or more individuals were observed. This study demonstrates that remote underwater video is useful for observing the in-stream behaviour of threatened freshwater fauna where other techniques are not viable, and presents sub-sampling of video as a means of reducing video processing time in assessing fish diel activity patterns.     

Variability in behaviour of four fish species attracted to baited underwater cameras in the North Sea

Baited underwater camera (BUC) systems to estimate demersal fish abundance are becoming increasingly considered as an alternative to traditional survey methods, particularly in environments that contain sensitive habitats or protected species. Based on 27 replicate deployments of BUCs at 100 m depth in the northern North Sea, in rank order of abundance, hagfish (Myxine glutinosa), flatfish mainly dabs (Limanda limanda), whiting (Merlangius merlangus) and haddock (Melanogramus aeglefinus) were observed consistently at baits. Higher maximum numbers (N _max) occurred during daytime in all species with the most significant effect in flatfish, 18 in daytime and 5 at night-time. Bottom current had no significant effect on numbers of whiting, flatfish or haddock. The N _max of hagfish was strongly related to current speed in a non-linear way with an increase in numbers up to 10 cm s⁻¹ and then decrease in N _max at higher water speeds. Understanding and accounting for such species-specific influences is important in the design of long term monitoring surveys using baited cameras.     

The origins of limnetic forms and cryptic divergence in Gnathopogon fishes (Cyprinidae) in Japan

The cyprinid species of the genus Gnathopogon, exhibiting flexible morphological and ecological variation, include limnetic life forms. We examined the origin of the limnetic forms and the population divergence of the Japanese Gnathopogon species, using molecular phylogenetic and phylogeographic analyses. A Bayesian phylogenetic inference approach based on mtDNA cytochrome b sequence data revealed three major lineages in G. elongatus. One of them formed a monophyletic group with the limnetic species G. caerulescens, which is endemic to an ancient lake, Lake Biwa. The divergence of the G. caerulescens lineage was estimated to date back to the early Pleistocene. This precedes the formation of the extensive pelagic environment in the present Lake Biwa. However, the recent genetic divergence of G. caerulescens was inferred to originate in the present Lake Biwa in the late Pleistocene. Another lacustrine population in the Mikata Lakes was shown to belong to a different lineage from G. caerulescens. The majority of the population possessed unique, but non-monophyletic, haplotypes, suggesting a short evolutionary history. One of the cryptic lineages of G. elongatus discovered in the Ina Valley, the lower area of Lake Suwa, might be related to the extinct lacustrine subspecies G. elongatus suwae, which has been replaced by introduced congeners. The previous and ongoing introductions of Gnathopogon fishes would have produced genetic disturbance to the indigenous populations.     

The distribution of macrobenthic epifauna in the Far Eastern Marine Reserve based on remote underwater video data

The spatial distribution of epifauna in the Far Eastern Marine Reserve was examined using a remotely operated vehicle. The abundance and distribution patterns of the sea stars Patiria pectinifera, Distolasterias nipon, and Asterias amurensis, as well as those of brittle stars, the black sea cucumber Cucumaria japonica, the sea urchin Strongylocentrotus intermedius, the ascidian Halocynthia aurantium, hermit crabs, and the Japanese scallop Mizuhopecten yessoensis were determined in the South Section of the Reserve. The average biomass of five dominant epifaunal species ranged from 51.0 to 87.4% of the average biomass of the softbottom communities.     

AFLP reveals cryptic population structure in migratory European red admirals (Vanessa atalanta)

1. The genetic differentiation in a migratory butterfly, the red admiral (Vanessa atalanta), was investigated to discern patterns of migratory routes used across Europe. AFLP profiles showed significant differences between almost all sampled locations, but there was no clear pattern of isolation‐by‐distance. 2. Using the software STRUCTURE 2.2, we found two distinct genotype clusters present in different frequencies at all study sites. The frequencies of these genotypic clusters varied significantly between years within the same site. Remarkably few individuals were of mixed ancestry, indicating that some isolating mechanisms are present. Twenty‐seven mtDNA haplotypes were identified but they showed no geographic structure, nor were they related to either of the two genotype clusters identified in the AFLP data. 3. Most field observations of migrating red admirals suggest a regular north–south migration pattern in Europe. Our data indicate both long‐distance migration and a more variable pattern in orientation, since the composition of the two genotypic clusters shows dramatic variation between sites and years in the northern part of the distribution range.     

Quantifying the influence of small omnivorous fishes on seagrass epiphyte load

The influence of two cryptic, seagrass‐inhabiting omnivorous fishes, the fan‐bellied leatherjacket Monacanthus chinensis and the variable sabretoothed blenny Petroscirtes variabilis, on seagrass epiphyte biomass are described. Overall, M. chinensis significantly reduced epiphyte biomass by 35·1% after 18 h in experimental aquaria, whilst P. variabilis showed a non‐significant 15·7% reduction. It is concluded that some cryptic omnivorous species play an important role in epiphyte removal in seagrass beds.     

A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic species

This study examined genetic variation across the range of Brachidontes variabilis to produce a molecular phylogeography. Neighbour joining (NJ), minimum evolution (ME) and maximum parsimony (MP) trees based on partial mitochondrial DNA sequences of 16S-rDNA and cytochrome oxidase (COI) genes revealed three monophyletic clades: (1) Brachidontes pharaonis s.l. from the Mediterranean Sea and the Red Sea; (2) B. variabilis from the Indian Ocean; (3) B. variabilis from the western Pacific Ocean. Although the three clades have never been differentiated by malacologists employing conventional morphological keys, they should be ascribed to the taxonomic rank of species. The nucleotide divergences between Brachidontes lineages (between 10.3% and 23.2%) were substantially higher than the divergence between congeneric Mytilus species (2.3–6.7%) and corresponded to interspecific divergences found in other bivalvia, indicating that they should be considered three different species. Analysis of the 16S-rDNA sequences revealed heteroplasmy, indicating dual uniparental inheritance (DUI) of mtDNA in the species of Brachidontes collected in the Indian Ocean, but not in the species in the Pacific nor in the species in the Red Sea and the Mediterranean Sea. When we employed the conventional estimate of the rate of mitochondrial sequence divergence (2% per million years), the divergence times for the three monophyletic lineages were 6–11 Myr for the Indian Ocean and Pacific Ocean Brachidontes sp. and 6.5–9 Myr for the Red Sea and Indian Ocean Brachidontes sp . Thus, these species diverged from one another during the Miocene (23.8–5.3 Myr). We infer that a common ancestor of the three Brachidontes species probably had an Indo-Pacific distribution and that vicariance events, linked to Pleistocene glaciations first and then to the opening of the Red Sea, produced three monophyletic lineages.     

Comparison of remote video and diver's direct observations to quantify reef fishes feeding on benthos in coral and rocky reefs

This study compared remote underwater video and traditional direct diver observations to assess reef fish feeding impact on benthos across multiple functional groups within different trophic categories (e.g. herbivores, zoobenthivores and omnivores) and in two distinct reef systems: a subtropical rocky reef and a tropical coral reef. The two techniques were roughly equivalent, both detecting the species with higher feeding impact and recording similar bite rates, suggesting that reef fish feeding behaviour at the study areas are not strongly affected by the diver's presence.     

Immune response of fishes to ciliates

Ciliates are highly evolved protists comprising a phylum of diverse species, many of which are opportunistic or obligate parasites. Ciliates parasitic to fish consist of salt and freshwater forms with endo- or ectoparasitic modes of infection. Some of the more commonly encountered genera include Chilodonella, Brooklynella, Ophryoglenina, Ichthyophthirius, Cryptocaryon, Uronema, Tetrahymena, Epistylus, and Trichodina. Species range from obligate parasites and commensals to opportunistic, facultative forms. Some parasitic ciliates are highly pathogenic and fishes in closed environments such as aquaria and farm ponds are particularly susceptible to high mortalities. Nevertheless, fish have evolved an immune system capable of mounting an effective protective response against parasite challenge. Much of the experimental research on immunity against ciliates has been carried out with Ichthyophthirius multifiliis, on obligate parasite that invades surface epithelia of virtually all freshwater fish species. Interest in the immune response against I. multifiliis stems from the fact that convalescent fish become resistant to subsequent challenge (suggesting the possibility of immunoprophylaxis), and the need to curtail severe losses caused by this parasite in intensively farmed fishes. Furthermore, I. multifiliis has proven to be a useful experimental model because it is amenable to study under laboratory conditions. In this review cellular and humoral factors involved in both innate and acquired immunity against ciliates are covered and include natural killer cells, phagocytic cells, and antibody responses. Current ideas on the mechanisms of antibody-mediated cutaneous immunity against I. multifiliis are discussed and approaches toward the development of vaccines against this and other ciliate parasites are presented.     

Phylogeny of European Pyrochroa (Coleoptera,Pyrochroidae) reveals cryptic taxa and different glacial histories

Only three saproxylic species of Pyrochroinae (Coleoptera: Pyrochroidae) are distributed in Europe, two of which belonging to Pyrochroa: P. coccinea and P. serraticornis. However, P. serraticornis is polytypic, for the presence of the endemic subspecies P. s. kiesenwetteri in southern Italy. Using both molecular and morphological data, we explored the phylogeny of the European Pyrochroa species. A multilocus (COI, CAD, 28S) phylogenetic analysis helped highlight different evolutionary histories for the two examined species. First, P. coccinea, distributed throughout Europe, showed a high differentiation among Italian and European populations. Furthermore, three different taxonomic entities were identified within P. serraticornis, among which the cryptic species Pyrochroa bifoveata sp. n. from central Europe is described and illustrated. A comprehensive identification key to the European Pyrochroinae is also provided. Our results also suggested an historical survival of P. coccinea and P. s. kiesenwetteri in glacial refugia in Italy, and a subsequent post-glacial spread of the former species throughout the Peninsula. In contrast, the current distribution of P. s. serraticornis likely originated from a post-glacial colonization of western European relict populations, while the survival of P. bifoveata plausibly occurred in more eastern glacial refugia (e.g. Carpathian or Balkan regions). Similarly, the European populations of P. coccinea could have originated from relict populations in glacial refugia out from the Italian Peninsula. More comprehensive data on the taxonomy, ecology and biogeography of Pyrochroa are needed to learn more about these species and to help preserve the European saproxylic fauna.     

A multilocus sequencing approach reveals the cryptic phylogeographical history of Phyllodoce nipponica Makino (Ericaceae)

Discordant phylogeographical patterns among species with similar distributions may not only denote specific biogeographical histories of different species, but also could represent stochastic variance of genealogies in applied genetic markers. A multilocus investigation representing different genomes can be used to address the latter concern, allowing robust inference to biogeographical history. In the present study, we conducted a multilocus phylogeographical analysis to re‐examine the genetic structuring of Phyllodoce nipponica, in which chloroplast (cp)DNA markers exhibited a discordant pattern compared to those of other alpine plants. The geographical structure of sequence variation at five nuclear loci was not consistent with that of cpDNA and showed differentiation between the northern and southern parts of the range of this species. Its demographic history inferred from the isolation‐with‐migration model suggests that the north–south divergence originated from Pleistocene vicariance. In addition, the demographic parameters showed a lack of chloroplast‐specific gene flow, suggesting that stochastic variance in genealogy resulted in the discordant geographical structure. Thus, P. nipponica probably experienced Pleistocene vicariance between its southern and northern range parts in concordance with other alpine plants in the Japanese archipelago. The findings of the present study demonstrates the importance of using a multilocus approach for inferring population dynamics, as well as for reconciling discordant phylogeographical patterns among species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 214–226.