Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid ecological speciation of an incipient species flock

The rapid rise of phenotypic and ecological diversity in independent lake‐dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260 000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species groups and to evaluate the relationships and genetic structure among five closely related, endemic, co‐occurring species (the Uruguay River species flock; URSF). Additionally, we evaluated ecological divergence of the URSF based on body and lower pharyngeal jaw (LPJ) shape and gut contents. Across the genus, we recovered novel relationships among the species groups. We found strong support for the monophyly of the URSF; however, relationships among these species remain problematic, likely because of the rapid and recent evolution of this clade. Clustered co‐ancestry analysis recovered most species as well delimited genetic groups. The URSF species exhibit species‐specific body and LPJ shapes associated with specialized trophic roles. Collectively, our results suggest that the URSF consists of incipient species that arose via ecological speciation associated with the exploration of novel trophic roles.     

Stable isotopes, mesocosms and gut content analysis demonstrate trophic differences in two invasive decapod crustacea

1. Improving our understanding of dietary differences among omnivorous, benthic crustacea can help to define the scope of their trophic influence in benthic food webs. In this study, we examined the trophic ecology of two non‐native decapod crustaceans, the Chinese mitten crab (Eriocheir sinensis) (CMC) and the red swamp crayfish (Procambarus clarkii) (RSC), in the San Francisco Bay ecosystem to describe their food web impacts and explore whether these species are functionally equivalent in their impacts on aquatic benthic communities. 2. We used multiple methods to maximise resolution of the diet of these species, including N and C stable isotope analysis of field data, controlled feeding experiments to estimate isotopic fractionation, mesocosm experiments, and gut content analysis (GCA). 3. In experimental enclosures, both CMC and RSC caused significant declines in terrestrially derived plant detritus (P < 0.01) and algae (P < 0.02) relative to controls, and declines in densities of the caddisfly Gumaga nigricula by >50% relative to controls. 4. Plant material dominated gut contents of both species, but several sediment‐dwelling invertebrate taxa were also found. GCA and mesocosm results indicate that CMC feed predominantly on surface‐dwelling invertebrates, suggesting that trophic impacts of this species could include a shift in invertebrate community composition towards sediment‐dwelling taxa. 5. Stable isotope analysis supported a stronger relationship between CMC and both algae and algal‐associated invertebrates than with allochthonous plant materials, while RSC was more closely aligned with terrestrially derived detritus. 6. The trophic ecology and life histories of these two invasive species translate into important differences in potential impacts on aquatic food webs. Our results suggest that the CMC differs from the RSC in exerting new pressures on autochthonous food sources and shallow‐dwelling invertebrates. The crab's wide‐ranging foraging techniques, use of intertidal habitat, and migration out of freshwater at sexual maturity increases the distribution of the impacts of this important invasive species.     

Quantitative diet analysis of four mesopredators from a coral reef

The diets of four common mesopredator fishes were examined in the back‐reef habitat of a subtropical fringing reef system during the summer months. Quantitative gut content analyses revealed that crustaceans, represented >60% of ingested prey (% mass) by the latticed sand‐perch Parapercis clathrata, brown dottyback Pseudochromis fuscus and half‐moon grouper Epinephelus rivulatus. Dietary analyses also provided insights into ontogenetic shifts. Juvenile P. fuscus ingested large numbers of crustaceans (amphipods and isopods); these small prey were rarely found in larger individuals (<1% of ingested mass). Fishes also made an important contribution to the diets of all three species representing 10–30% of ingested mass. Conversely, the sand lizardfish Synodus dermatogenys fed exclusively on fishes including clupeids, gobies and labrids. Differences in the gut contents of the four species recorded were not apparent using stable isotope analysis of muscle tissues. The similarity of δ¹³C values in muscle tissues suggested that carbon within prey was derived from primary producers, with comparable carbon isotope signatures to corals and macroalgae, whilst similarities in δ¹⁵N values indicated that all four species belonged to the same trophic level. Thus, interspecific differences between mesopredator diets were undetectable when using stable isotope analysis which suggests that detailed elucidation of trophic pathways requires gut content analyses.     

Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes

Of the 5000 fish species on coral reefs, corals dominate the diet of just 41 species. Most (61%) belong to a single family, the butterflyfishes (Chaetodontidae). We examine the evolutionary origins of chaetodontid corallivory using a new molecular phylogeny incorporating all 11 genera. A 1759‐bp sequence of nuclear (S7I1 and ETS2) and mitochondrial (cytochrome b) data yielded a fully resolved tree with strong support for all major nodes. A chronogram, constructed using Bayesian inference with multiple parametric priors, and recent ecological data reveal that corallivory has arisen at least five times over a period of 12 Ma, from 15.7 to 3 Ma. A move onto coral reefs in the Miocene foreshadowed rapid cladogenesis within Chaetodon and the origins of corallivory, coinciding with a global reorganization of coral reefs and the expansion of fast‐growing corals. This historical association underpins the sensitivity of specific butterflyfish clades to global coral decline.     

Ichthyosporidium weissii n. sp. (Microsporidia) infecting the arrow goby (Clevelandia ios)

Gonadal infections by a novel microsporidium were discovered in 34% (13/38) of arrow gobies, Clevelandia ios, sampled over a 3‐yr period from Morro Bay Marina in Morro Bay, California. Gonadal tumors had been reported in arrow gobies from this geographic area. The infected gonads, found primarily in females, typically appeared grossly as large, white‐gray firm and lobulated masses. Histological examination revealed large, multilobate xenomas within the ovaries and no evidence of neoplasia. Typical of the genus Ichthyosporidium, the large xenomas were filled with developmental stages and pleomorphic spores. Wet mount preparations showed two general spore types: microspores with mean length of 6.2 (7.0–4.9, SD = 0.6, N = 20) μm and mean width of 4.3 (5.3–2.9, SD = 0.8) μm; and less numerous macrospores with mean length of 8.5 (10.1–7.1, SD = 1.0, N = 10) μm and mean width of 5.5 (6.2–4.8, SD = 0.5) μm. Transmission electron microscopy demonstrated stages consistent with the genus and 35–50 turns of the polar filament. Small subunit rDNA gene sequence analysis revealed that the parasite from arrow gobies was most closely related to, but distinct from Ichthyosporidium sp. based on sequences available in GenBank. We conclude that this microsporidium represents a new species of Ichthyosporidium, the first species of this genus described from a member of the family Gobiidae and from the Pacific Ocean.     

Occurrence of non‐native fishes in the Danube east of Vienna (Austria) and potential interactions of invasive gobiids with native fishes

Non‐native fish species pose a major threat to local fish populations and aquatic ecosystems in general. Invasive gobies are a particular focus of research, but with partly inconsistent results. While some studies reported severe detrimental impacts on native species, others have concluded less serious or neutral effects. We provide results from a large‐scale, multi‐annual fish monitoring program on the occurrence and abundance of non‐native fishes in the main stem of a free‐flowing section of the Austrian Danube. Special emphasis was placed on identifying positive or negative interactions of invasive gobies with native species. Whereas most non‐native species occurred too sporadically or were too few in number to infer a direct threat on the local fish community, invasive gobies were among the most common fishes throughout all sampling years. Co‐occurrence analyses revealed species‐ and mesohabitat type‐specific associations of gobies with native species, which were primarily positive. Notably, native predators such as asp, burbot, or perch probably benefit from the ubiquitous gobies. Two characteristic fluvial fishes revealed negative associations with invasive gobies, namely barbel (Barbus barbus) and Danube whitefin gudgeon (Romanogobio vladykovi): they appear to avoid habitats occupied by gobies. Accordingly, high abundances of round and bighead goby most likely resulted in population losses of barbel and whitefin gudgeon, respectively. Overall, our results indicate a limited negative impact of non‐native species in the sampling area. This is because only two out of 51 occurring species were found to be adversely affected by gobies, the share of co‐occurrences with native species was high, and other non‐native species were generally rare. Nevertheless, invasions are highly dynamic, and new non‐native species are likely to occur in the Austrian Danube, calling for continued monitoring and awareness.     

DNA‐based identification of preys from non‐destructive,total DNA extractions of predators using arthropod universal primers

Here, I show that prey sequences can be detected from DNA of tiger beetles of the genus Rivacindela using whole specimens, nondestructive methods, and universal cytochrome b primers for arthropods. BLAST searches of the obtained sequences against public databases revealed that the diet of Rivacindela is mostly composed of flies but also termites and other beetles. Accurate determination of order, family and even genus was achieved in most cases but rarely to species level. Results suggest that stored DNA samples extracted from whole predatory specimens could be an alternative to dissected gut contents as starting source for DNA‐based dietary studies.     

Three terrestrial Pleistocene coucals (Centropus: Cuculidae) from southern Australia: biogeographical and ecological significance

Coucals are large, predatory, primarily ground‐dwelling cuckoos of the genus Centropus, with 26 extant species ranging from Africa to Australia. Their evolutionary and biogeographical history are poorly understood and their fossil record almost non‐existent. Only one species (Centropus phasianinus) currently inhabits Australia, but there is now fossil evidence for at least three Pleistocene species. One of these (Centropus colossus) was described from south‐eastern Australia in 1985. Here we describe additional elements of this species from the same site, and remains of two further extinct species from the Thylacoleo Caves of the Nullarbor Plain, south‐central Australia. The skeletal morphology and large size of the three extinct species indicates that they had reduced capacity for flight and were probably primarily ground‐dwelling. The extinct species include the two largest‐known cuckoos, weighing upwards of 1 kg each. They demonstrate that gigantism in this lineage has been more marked in a continental context than on islands, contrary to the impression gained from extant species. The evolutionary relationships of the Australian fossil coucals are uncertain, but our phylogenetic analysis indicates a possible close relationship between one of the Nullarbor species and extant Centropus violaceus from the Bismarck Archipelago. The presence of three coucals in southern Australia markedly extends the geographical range of the genus from tropical Australia into southern temperate regions. This demonstrates the remarkable and consistent ability of coucals to colonize continents despite their very limited flying ability.     

Does your lip stick? Evolutionary aspects of the mouth morphology of the Indo‐Pacific clinging goby of the Sicyopterus genus (Teleostei: Gobioidei: Sicydiinae) based on mitogenome phylogeny

Sicydiinae gobies have an amphidromous life cycle. Adults grow, feed, and reproduce in rivers, while larvae have a marine dispersal phase. Larvae recruit back to rivers and settle in upstream habitats. Within the Sicydiinae subfamily, the Sicyopterus genus, one of the most diverse (24 species), is distributed in the tropical islands of the Indo‐Pacific. One of the characters used to determine Sicyopterus species is the upper lip morphology, which can be either smooth, crenulated, or with papillae, and with (2 or 3) or without clefts. The mouth is used as a secondary locomotor organ along with the pelvic sucker. It is thus strongly related to the climbing ability of species and is of major importance for the upstream migration and the colonization of insular freshwater systems. The mouth also has an important role in the feeding mechanism of these herbivorous species. In this paper, we have established a molecular phylogeny of the genus based on the 13 mitochondrial protein‐coding genes to discuss the relationship between 18 Sicyopterus species. There is a well‐supported dichotomy in the molecular phylogeny of the Sicyopterus genus and this separation into two clades is also morphologically visible, with the distinction of species with three clefts and species with 0 or 2 clefts on the upper lip. The mouth morphology can thus be separated with regard to the molecular phylogeny obtained. The evolution of the mouth morphology is discussed in terms of the adaptation of the Sicyopterus genus to settlement and life in tropical insular river systems.     

Recent rapid speciation and ecomorph divergence in Indo‐Australian sea snakes

The viviparous sea snakes (Hydrophiinae) are a young radiation of at least 62 species that display spectacular morphological diversity and high levels of local sympatry. To shed light on the mechanisms underlying sea snake diversification, we investigated recent speciation and eco‐morphological differentiation in a clade of four nominal species with overlapping ranges in Southeast Asia and Australia. Analyses of morphology and stomach contents identified the presence of two distinct ecomorphs: a ‘macrocephalic’ ecomorph that reaches >2 m in length, has a large head and feeds on crevice‐dwelling eels and gobies; and a ‘microcephalic’ ecomorph that rarely exceeds 1 m in length, has a small head and narrow fore‐body and hunts snake eels in burrows. Mitochondrial sequences show a lack of reciprocal monophyly between ecomorphs and among putative species. However, individual assignment based on newly developed microsatellites separated co‐distributed specimens into four significantly differentiated clusters corresponding to morphological species designations, indicating limited recent gene flow and progress towards speciation. A coalescent species tree (based on mitochondrial and nuclear sequences) and isolation‐migration model (mitochondrial and microsatellite markers) suggest between one and three transitions between ecomorphs within the last approximately 1.2 million to approximately 840 000 years. In particular, the macrocephalic ‘eastern’ population of Hydrophis cyanocinctus and microcephalic H. melanocephalus appear to have diverged very recently and rapidly, resulting in major phenotypic differences and restriction of gene flow in sympatry. These results highlight the viviparous sea snakes as a promising system for speciation studies in the marine environment.     

Comparison of current-velocity tolerance among six stream gobies of the genus Rhinogobius

Tolerance to current velocity was compared among six stream gobies of the genus Rhinogobius (cross-band, dark, large-dark, cobalt, and orange types, and R. flumineus). Each individual of the six gobies was exposed to incremental increases in current velocity within a laboratory flume. The current velocity at which each individual was dislodged was recorded and compared by species. Results from comparisons showed that the tolerance of gobies declined in the following order: cobalt, large-dark, dark, cross-band, R. flumineus, and orange type. This interspecific difference in velocity tolerance is consistent with their habitat segregation patterns as previously reported by field observations.     

The Toxicity of Skin Secretions from Coral-Dwelling Gobies and their Potential Role as a Predator Deterrent

Coral-dwelling gobies in the genus Gobiodon (family Gobiidae) posses toxic skin secretions. We used bioassays to investigate interspecific variation in the toxicity of skin secretions from six species of Gobiodon from Lizard Island on the Great Barrier Reef. We then used feeding experiments with two common species of predatory fish to test if skin secretions might act as a chemical defence against predation. The skin secretions of all species were toxic to the bioassay species, Apogon fragilis, but there were marked differences in toxicity among Gobiodon species. Feeding experiments showed that both small- and large-gaped predators avoided food items to which goby skin secretions, or a whole goby, had been added. These experiments indicate that skin toxins could function as a predator deterrent in coral-dwelling gobies.     

Identifying the core microbial community in the gut of fungus‐growing termites

Gut microbes play a crucial role in decomposing lignocellulose to fuel termite societies, with protists in the lower termites and prokaryotes in the higher termites providing these services. However, a single basal subfamily of the higher termites, the Macrotermitinae, also domesticated a plant biomass‐degrading fungus (Termitomyces), and how this symbiont acquisition has affected the fungus‐growing termite gut microbiota has remained unclear. The objective of our study was to compare the intestinal bacterial communities of five genera (nine species) of fungus‐growing termites to establish whether or not an ancestral core microbiota has been maintained and characterizes extant lineages. Using 454‐pyrosequencing of the 16S rRNA gene, we show that gut communities have representatives of 26 bacterial phyla and are dominated by Firmicutes, Bacteroidetes, Spirochaetes, Proteobacteria and Synergistetes. A set of 42 genus‐level taxa was present in all termite species and accounted for 56–68% of the species‐specific reads. Gut communities of termites from the same genus were more similar than distantly related species, suggesting that phylogenetic ancestry matters, possibly in connection with specific termite genus‐level ecological niches. Finally, we show that gut communities of fungus‐growing termites are similar to cockroaches, both at the bacterial phylum level and in a comparison of the core Macrotermitinae taxa abundances with representative cockroach, lower termite and higher nonfungus‐growing termites. These results suggest that the obligate association with Termitomyces has forced the bacterial gut communities of the fungus‐growing termites towards a relatively uniform composition with higher similarity to their omnivorous relatives than to more closely related termites.     

Diet of harbor porpoises along the Dutch coast: A combined stable isotope and stomach contents approach

High stranding frequency of porpoises, Phocoena phocoena, along the Dutch coast since 2006 has led to increased interest in the ecology of porpoises in the North Sea. Stranded porpoises were collected along the Dutch coast (2006–2008) and their diet was assessed through stomach content and stable isotope analysis (δ¹³C and δ¹⁵N) of porpoise muscle and prey. Stable isotope analysis (SIAR) was used to estimate the contribution of prey species to the porpoises' diet. This was compared to prey composition from stomach contents, to analyze differences between long‐ and short‐term diet. According to stomach contents, 90.5% of the diet consisted of gobies, whiting, lesser sandeel, herring, cod, and sprat. Stable isotope analysis revealed that 70‐83% of the diet consisted of poor cod, mackerel, greater sandeel, lesser sandeel, sprat, and gobies, highlighting a higher importance of pelagic, schooling species in the porpoises' diet compared to stomach contents. This could be due to prey distribution as well as differences in behavior of porpoises and prey between the coastal zone and offshore waters. This study supports the need for multi‐method approaches. Future ecological and fishery impact assessment studies and management decisions for porpoise conservation should acknowledge this difference between the long‐ and short‐term diet.     

Haramonas viridissp. nov. (Raphidophyceae, Heterokontophyta), a new sand-dwelling raphidophyte from cold temperate waters

A new, marine, sand‐dwelling raphidophyte from Sylt, Germany, Haramonas viridis Horiguchi et Hoppenrath sp. nov. is described. This represents a second species in the previously monotypic genus Haramonas, which was originally described from a sand sample from a mangrove river mouth in tropical Australia, based on the type species, H. dimorpha. This new species from a cold temperate region: (i) possesses a tubular invagi‐nation in the posterior part of the cell; (ii) produces copious amounts of mucilage in culture; (iii) possesses both motile and non‐motile stages in its life cycle; and (iv) has overlapping discoidal chloroplasts, all of which are diagnostic features of the genus Haramonas. Therefore, it is indisputable that this species belongs to this genus. However, the species from Sylt differs from the type species of the genus in: (i) having a larger cell size; (ii) possessing a larger number of chloroplasts; and (iii) being greenish in color. The ultrastructural study revealed that the structure of the tubular invagi‐nation was the same as that of the type species.     

Parental defence on the reef: antipredator tactics of coral‐reef fishes against egg‐eating seasnakes

On coral reefs in New Caledonia, the eggs of demersal‐spawning fishes are consumed by turtle‐headed seasnakes (Emydocephalus annulatus). Fish repel nest‐raiding snakes by a series of tactics. We recorded 232 cases (involving 22 fish species) of antipredator behaviour towards snakes on a reef near Noumea. Blennies and gobies focused their attacks on snakes entering their nests, whereas damselfish (Pomacentridae) attacked passing snakes, as well as nest‐raiders (reflecting territorial defence). Biting the snake was the most common form of attack, although damselfish and blennies also slapped snakes with the tail, or (blennies only) plugged the nest entrance with the parent fish's body. Gobies rarely defended the nest, although they sometimes bit or threw sand at the snake. A snake was more likely to flee if it was attacked before it began feeding rather than after it found the eggs (82% versus 3% repelled) and if bitten on the head rather than the body (68% versus 53%). Tail‐slaps were not effective, although plugging the burrow and throwing sand often caused snakes to flee. These strong patterns reflect phylogenetic variation in fish behaviour (e.g. damselfish detect a snake approach sooner than do substrate‐dwelling blennies and gobies) coupled with intraspecific variation in snake diets. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 415–425.     

MALDI‐TOF MS identification of microbiota associated with pest insect Diabrotica speciosa

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Ankistrodinium armigerum sp. nov. (Dinophyceae), a new species of heterotrophic marine sand‐dwelling dinoflagellate from Japan and Australia

A new heterotrophic sand‐dwelling dinoflagellate, Ankistrodinium armigerum K. Watanabe, Miyoshi, Kubo, Murray et Horiguchi sp. nov., is described from Ishikari Beach, Hokkaido, Japan and Port Botany, NSW, Australia. The dinoflagellate is laterally compressed, possessing a short triangular epicone and a large sac‐like hypocone. It possesses a right‐handed cingulum and a deeply‐incised sulcus. The sulcus descends towards the posterior of the cell where it becomes much deeper and wider, resulting in a bilobed ventral side to the hypocone, with a greater excavation of the left lobe than the right. In addition, the right lobe of the hypocone is shorter than the left lobe, which allows a partial view of the left sulcal wall when the cell is viewed from its right side. The sulcus ascends in the epicone to form an apical groove. The apical groove is linear but terminates in an ellipsoid fashion and its extremity approaches, but does not form a closed loop with the apical end of the linear portion. The dinoflagellate possesses two distinct size classes of trichocysts. The large trichocysts are located in the posterior part of the cell, while small trichocysts are distributed throughout the cell. The dinoflagellate shares morphological characteristics with the heterotrophic sand‐dwelling dinoflagellate, Ankistrodinium semilunatum, the type species of the genus. These include a laterally compressed cell, a right‐handed cingulum, a deeply‐incised sulcus and the same basic structure to the apical groove. Molecular phylogenetic analyses based on small and large subunits of rDNA showed that in both trees, A. semilunatum and A. armigerum formed a robust clade, suggesting that these two species are closely related. Because no organism with the characteristics of this species exists and because this species is closely related to A. semilunatum, we concluded that this species should be described as a second species of the genus Ankistrodinium.     

Electric fishes of the genus Sternarchorhynchus (Teleostei,Ostariophysi, Gymnotiformes); phylogenetic and revisionary studies

Analysis of 88 characters of external and internal body systems yielded a phylogenetic reconstruction of the Neotropical electric knifefish genus Sternarchorhynchus (Apteronotidae; Gymnotiformes). The results support a hypothesis of Sternarchorhynchus as the sister group to Platyurosternarchus. A series of synapomorphies, many involving major innovations of the neurocranium, jaws, suspensorium, and associated systems that permit an unusual mode of grasp‐suction feeding, support the monophyly of both genera. Synapomorphies largely resolve relationships within Sternarchorhynchus with basal nodes strongly supported by characters pertinent to prey capture and initial processing of food items. These possible key innovations may provide Sternarchorhynchus with a competitive advantage over other clades of the Apteronotidae and account for the species diversity of the genus in Neotropical rivers. Adaptive radiation in Sternarchorhynchus was analysed. Habitat preference transitions repeatedly occurred in the genus between deep‐river channel dwelling species and rheophilic species with preferences for higher energy setting including rapids and swift‐flowing fluviatile settings. Twenty‐two species of Sternarchorhynchus are described as new based on samples that originated in the smaller rivers draining into the Golfo de Paria, the Marowijne and Essequibo River basins, the Río Orinoco and in particular the Amazon River basin. The 32 species in Sternarchorhynchus make it the most speciose genus in the Apteronotidae. No claim to original US government works. Journal compilation © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 223–371.