Warming during embryogenesis induces a lasting transcriptomic signature in fishes.

Exposure to elevated temperatures during embryogenesis can influence the plasticity of tissues in later life. Despite these long-term changes in plasticity, few differentially expressed genes are ever identified, suggesting that the developmental programming of later life plasticity may occur through the modulation of other aspects of transcriptomic architecture, such as gene network organisation. Here, we use network modelling approaches to demonstrate that warm temperatures during embryonic development (developmental warming) have consistent effects in later life on the organisation of transcriptomic networks across four diverse species of fishes: Scyliorhinus canicula, Danio rerio, Dicentrarchus labrax, and Gasterosteus aculeatus. The transcriptomes of developmentally warmed fishes are characterised by an increased entropy of their pairwise gene interaction networks, implying a less structured, more 'random' set of gene interactions. We also show that, in zebrafish subject to developmental warming, the entropy of an individual gene within a network is associated with that gene's probability of expression change during temperature acclimation in later life. However, this association is absent in animals reared under 'control' conditions. Thus, the thermal environment experienced during embryogenesis can alter transcriptomic organisation in later life, and these changes may influence an individual's responsiveness to future temperature challenges.

Ontogeny reveals the origin of Gemminger bones in Mormyridae.

Mormyridae are well known and intensively studied for their weak electric organ discharges, which facilitate communication and orientation. The Gemminger bones of Mormyridae are located next to the electrical organ in the caudal peduncle; however, they have not attracted much interest until recently. Therefore, we investigated the diversity of Gemminger bones in mormyrids and studied their ontogenetic development in Mormyrus rume proboscirostris. Gemminger bones are paired, thin, elongated ossifications lying on the dorsal and ventral sides of the caudal peduncle, and usually reach anterior well below the dorsal and anal fin bases. Ontogeny revealed that they are not intermuscular ossifications, as suspected based on the anatomical position of this structure and the systematic position of the mormyrids. Instead, they are membrane ossifications that originate from the fin stays of the dorsal and anal fins.

Molecular phylogenetics of the Clupeiformes based on exon-capture data and a new classification of the order.

The Clupeiformes, including among others herrings, anchovies, shads and menhadens are ecologically and commercially important, yet their phylogenetic relationships are still controversial. Previous classification of Clupeiformes were based on morphological characters or lack of synapomorphic characters. More recent studies based on molecular data as well as new morphological evidence are keeping challenging their phylogenetic relations and there is still no consensus on many interrelationships within the Clupeiformes. In this study, we collected nuclear sequence data from 4,434 single-copy protein coding loci using a gene-capture method. We obtained a robust phylogeny based on 1,165 filtered loci with less than 30 % missing data. Our major findings include: 1) reconfirmation of monophyly of the Clupeiformes, that is, Denticipitidae is sister to all other clupeiforms; 2) the polyphyletic nature of dussumieriids and early branching of Spratelloididae from all other clupeoids were confirmed using datasets curated for less missing data and more balanced base composition in the respective taxa. The next branching clade is the monophyletic Engraulidae. Pristigasteridae also is monophyletic, but it was nested in the previously defined "Clupeidae". Within Pristigasteridae there is no support for monophyletic Pelloninae. Chirocentrus is close to Dussumieria and not to engraulids. The miniaturized Sundasalanx is placed close to the ehiravine Clupeonella, however, with a relatively deep split. The genus Clupea, is not part of the diverse "Clupeidae", but part of a clade containing additionally Sprattus and Etrumeus. Within the crown group clades, Alosidae and Dorosomatidae are retrieved as sister clades. Based on new fossil calibration points, we found that major lineages of the clupeiforms diverged in the late Cretaceous and early Paleogene. The extinction event at the end of the Cretaceous may have created ecological niches, which could have fueled the diversification of clupeiform fishes. Based on the strong evidence of the present study, we propose an updated classification of Clupeiformes consisting of ten families: Denticipitidae; Spratelloididae; Engraulidae (Engraulinae + Coiliinae); Clupeidae; Chirocentridae; Dussumieriidae; Pristigasteridae; Ehiravidae; Alosidae, Dorosomatidae.

Morphological characters in light of new molecular phylogenies: the caudal-fin skeleton of Ovalentaria.

The Ovalentaria is a taxon of teleosts that has been proposed based on molecular analyses only. Previously widely separated families are assembled in this taxon. For the first time, the Ovalentaria are analysed using a comparative morphological approach. The caudal-fin skeleton of 355 species covering all 48 ovalentarian families are examined in cleared and stained specimens, µCT datasets and X-ray images as well as from the literature. A total of 38 morphological characters are evaluated and used for ancestral character state reconstructions and phylogenetic analyses. Results provide hypotheses for a scenario of the evolution of the caudal-fin skeleton and its ground plan in Ovalentaria. An evolutionary trend towards the reduction of skeletal elements in the caudal fin is observed. Connections between the evolution of the caudal-fin skeleton and modes of locomotion found in ovalentarian taxa are discussed. Phylogenetic analyses based on the caudal-fin morphology provide topologies for intra-ovalentarian relationships that largely agree with molecular hypotheses.

Development of the caudal-fin skeleton reveals multiple convergent fusions within Atherinomorpha.

BACKGROUND: The caudal fin of teleosts is a highly diverse morphological structure and a valuable source of information for comparative analyses. Within the Atherinomorpha a high variation of conditions of the caudal-fin skeleton can be found. These range from complex but basal configurations to simple yet derived configurations. When comparing atherinomorph taxa, it is often difficult to decide on the homology of skeletal elements if only considering adult specimens. However, observing the development of caudal-fin skeletons allows one to evaluate complex structures, reveal homologies and developmental patterns, and even reconstruct the grundplan of the examined taxa. RESULTS: We studied the development of the caudal-fin skeleton in different atheriniform, beloniform and cyprinodontiform species using cleared and stained specimens. Subsequently we compared the development to find similarities and differences in terms of 1) which structures are formed and 2) which structures fuse during ontogeny. For many structures, i.e., the parhypural, the epural(s), the haemal and neural spines of the preural centra and the uroneural, there were either no or only minor differences visible between the three taxa. However, the development of the hypurals revealed a high variation of fusions within different taxa that partly occurred independently in atheriniforms, beloniforms and cyprinodontiforms. Moreover, comparing the development of the ural centra exposed two ways of formation of the compound centrum: 1) in atheriniforms and the beloniforms Oryzias and Hyporhamphus limbatus two ural centra develop and fuse during ontogeny while 2) in cyprinodontiforms and Exocoetidae (Beloniformes) only a single ural centrum is formed during ontogeny. CONCLUSIONS: We were able to reconstruct the grundplan of the developmental pattern of the caudal-fin skeleton of the Atheriniformes, Beloniformes and Cyprinodontiformes as well as their last common ancestors. We found two developmental modes of the compound centrum within the Atherinomorpha, i.e., the fusion of two developing ural centra in atheriniforms and beloniforms and the development of only one ural centrum in cyprinodontiforms. Further differences and similarities for the examined taxa are discussed, resulting in the hypothesis that the caudal-fin development of a last common ancestor to all atherinomorphs is very much similar to that of extant atheriniforms.

Fatty Acid Composition in Blubber, Liver, and Muscle of Marine Mammals in the Southern Baltic Sea.

To date, only limited results on the fatty composition in different tissues of the top predators in the Baltic Sea are available. In the current study, tissue samples of blubber, skeletal muscle, and liver from 8 harbour porpoise (Phocoena phocoena) and 17 grey seals (Halichoerus grypus) in the Baltic Sea off Mecklenburg-Western Pomerania were included in the investigation. While the total fatty acid content in liver and blubber tissue revealed no differences between both species, the total fatty acid content of muscle tissue was significantly differentand showed higher concentrations in harbour porpoise muscle compared with grey seals. The most abundant fatty acids in the blubber of grey seals and harbour porpoises (18:1cis-9, 16:1cis-9, 16:0 and 22:6n-3) were present in similar quantities and ratios to each other as known from other marine top predators. If future studies can show that differences in tissue fatty acid content are caused by variation in the nutritional status, and this may lead to the development of a more objective assessment of body condition in seals and porpoises recovered via stranding schemes.

Ocean warming and hypoxia affect embryonic growth, fitness and survival of small-spotted catsharks, Scyliorhinus canicula.

Elasmobranchs are key to a healthy marine ecosystem but are under threat from human activities, such as destructive fisheries and shark finning. Embryos of oviparous elasmobranchs may be further challenged during development by rising temperatures and falling dissolved oxygen concentrations in their intertidal environment. However, the impact of climate change on survival and growth of oviparous elasmobranchs is still poorly understood. Here, we investigate the effects of temperature and hypoxia on the growth and survival of small-spotted catshark (Scyliorhinus canicula) embryos by incubating eggs in normoxia 15°C, normoxia 20°C, hypoxia 15°C, or hypoxia 20°C. Incubation under the elevated temperature increased the embryonic growth rate, yolk consumption rate and Fulton's condition factor at hatching, whilst decreasing the total length and body mass of newly hatched sharks. Under low oxygen conditions (50% air saturation) the survival rate of S. canicula embryos dropped significantly and the temperature-induced increase in Fulton's condition factor was reversed. Together, these data demonstrate both the individual and compound effects of elevated temperature and hypoxia on the survival and growth during early ontogeny of a ubiquitous, coastal elasmobranch, S. canicula.

The osteology of the golden grey mullet Liza aurata (Teleostei: Mugiliformes: Mugilidae) including interactive three-dimensional reconstructions.

Grey mullets are remarkably characterized by their overall uniform external morphology. Identifying species as well as positioning the Mugiliformes in a phylogenetic context is rather difficult. Most recently they were placed in the newly erected Ovalentaria, but more detailed relationships to potential sister taxa were not resolved. Studying the internal morphology, especially the osteology, might provide new insights into the evolution of the Mugiliformes as well as help clarify their phylogenetic position within the Ovalentaria. A detailed osteology of the golden grey mullet Liza aurata is presented. The use of cleared and stained specimens allowed for a complete examination of bony and cartilaginous structures, and a 3D reconstruction from a µCT data set provided additional information on the positional relationships of the bones. Following this, the data obtained were compared with different mugilid species, particularly with the flathead grey mullet Mugil cephalus. Several differences between these species could be identified, such as the position of the basisphenoid, the shape of the hyomandibular and the composition of the branchial arches. These characters might help in understanding the evolutionary changes happening within the mugiliforms and will provide the basis to study this taxon in detail, finally allowing the reconstruction of the body plan of grey mullets.

Twins! Microsatellite analysis of two embryos within one egg case in oviparous elasmobranchs.

Elasmobranchs display various reproductive modes, which have been key to their evolutionary success. In recent decades there has been a rise in the number of reported cases of foetal abnormalities including fertilised, double-embryos held within one egg capsule, hereafter referred to as twins. Previously, the occurrences of twin egg cases have been reported in two batoid and one shark species. We report the first cases of twins in three species of oviparous elasmobranchs: the undulate ray (Raja undulata), the nursehound (Scyliorhinus stellaris), and the small-spotted catshark (Scyliorhinus canicula). We investigated the genetic relationships between the twins in S. stellaris, and S. canicula using microsatellite markers. Whilst the S. stellaris twins displayed the same genotypes, we found that the S. canicula twin individuals arose through heteropaternal superfecundation. This is the first reported incidence of such a paternity in elasmobranchs. The relationship between environmental change and reproductive strategy in elasmobranchs is unclear and further research is needed to determine its effect on the prevalence and mechanisms of formation of elasmobranch twins.

Recognition software successfully aids the identification of individual small-spotted catsharks Scyliorhinus canicula during their first year of life.

Eighteen captive small-spotted catsharks Scyliorhinus canicula were successfully identified from hatching to 1 year of age using the free computer recognition software, I3 S classic. The effect of increasing the time interval between recognition attempts on the accuracy of the software was investigated, revealing that recognition fiedelity decreases with increasing time intervals for younger (0 to 15 weeks), but not older (15 weeks onwards) sharks. Identification by I3 S was validated using genetic analyses of seven microsatellite markers, revealing a 100% success rate. Thus, this non-invasive recognition method can be used as an inexpensive and effective alternative to invasive tagging, improving animal welfare and complementing ex-situ conservation methods.

A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies.

BACKGROUND: Previous molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, we perform target gene capturing and subsequent next generation sequencing of putative ortholog exons of major clupeocephalan lineages. Sequence information for the RNA bait design was derived from publicly available genomes of bony fishes. Newly acquired sequence data comprising > 800 exon sequences was subsequently used for phylogenetic reconstructions. RESULTS: Our results support monophyletic Otomorpha comprising Alepocephaliformes. Within Ostariophysi, Gonorynchiformes are sister to a clade comprising Cypriniformes, Characiformes, Siluriformes and Gymnotiformes, where the interrelationships of Characiformes, Siluriformes and Gymnotiformes remain enigmatic. Euteleosts comprise four major clades: Lepidogalaxiiformes, Protacanthopterygii, Stomiatii, and Galaxiiformes plus Neoteleostei. The monotypic Lepidogalaxiiformes form the sister-group to all remaining euteleosts. Protacanthopterygii, comprising Argentini-, Esoci- and Salmoniformes, is sister to Stomiatii (Osmeriformes and Stomiatiformes) and Galaxiiformes plus Neoteleostei. CONCLUSIONS: Several proposed monophyla defined by morphological apomorphies within the Clupeocephalan phylogeny are confirmed by the phylogenetic estimates presented herein. However, other morphologically described groups cannot be reconciled with molecular phylogenies. Thus, numerous morphological apomoprhies of supposed monophyla are called into question. The interpretation of suggested morphological synapomorphies of otomorph fishes is strongly affected by the inclusion of deep-sea inhabiting, and to that effect morphologically adapted Alepocephaliformes. Our revision of these potential synapomorphies, in the context that Alepocephaliformes are otomorph fishes, reveals that only a single character of the total nine characters proposed as synapomorphic for the group is clearly valid for all otomorphs. Three further characters remain possible apomorphies since their status remains unclear in the deep-sea adapted Alepocephaliformes showing developmental lag and lacking a swim bladder. Further, our analysis places Galaxiiformes as sister group to neoteleosts, which contradicts some previous molecular phylogenetic studies. This needs further investigation from a morphological perspective, as suggested synapomophies for several euteleostean lineages are challenged or still lacking. For the verification of results presented herein, a denser phylogenomic-level taxon sampling should be applied.

Lessons from the first dorsal fin in atheriniforms-A new mode of dorsal fin development and its phylogenetic implications.

The median fins in extant actinopterygians are the product of millions of years of evolution. During this time, different developmental patterns for the dorsal and anal fins emerged leading to a high variation in median fin morphology and ontogeny. In this study, the development of anal and dorsal fins in atheriniforms is described and its consequences for the current phylogenetic hypothesis are discussed. Developmental series of five atheriniform species were investigated using clearing and staining as well as antibody staining. The skeletal elements of the second dorsal fin and the anal fin emerge in a bidirectional pattern. The first dorsal fin, however, arises separately in front of the second dorsal fin after this one is almost completely formed. The pterygiophores of the first dorsal fin, including the interdorsal pterygiophores, develop from caudal to rostral, but the fin-spines of the first dorsal fin form in the opposite direction. This new mode of fin development has been found in all examined atheriniform species with two dorsal fins. Several morphological characters of atheriniforms, including interdorsal pterygiophores, are also found in one other taxon: the Mugiliformes. Thus, several dorsal fin characteristics may provide evidence for a closer relationship of these two taxa.

Description of two new Bathyaethiops species (Teleostei: Alestidae) from the Congo basin.

Two new species of Bathyaethiops (Teleostei: Characiformes: Alestidae) are described. Bathyaethiops baka n. sp. is a dwarf species with the largest known specimen being only 24.4 mm SL. The species is characterized by an incomplete squamation and a large humeral spot. Bathyaethiops baka n. sp. is known so far only from the Ngoko River of Southeastern Cameroon, a tributary of the Sangha River in the northern Congo basin. The second species, Bathyaethiops flammeus n. sp., shows a diagnostic spot in front of the dorsal-fin base, which is devoid of melanophores and bright red in life. The species is described from the Bakéré River at Yambula-Bakéré, a locality north-west of Kisangani in the Central Congo basin. Other records of Bathyaethiops flammeus n. sp. from the Tshuapa respectively Ruki River at Boende and Eala, Central Congo basin, suggests a wider geographic distribution. A key to all species of Bathyaethiops is provided.

Continental diversification of an African catfish radiation (Mochokidae: Synodontis).

Despite African rivers containing high species diversity, continental-scale studies investigating the mechanisms generating biological diversity of African riverine faunas are limited compared with lacustrine systems. To investigate the build-up of diversity in a tropical aquatic continental radiation, we test different models of lineage diversification and reconstruct the biogeographic history in a species-rich siluriform genus, Synodontis (~130 species), with a broad distribution across all major tropical African drainage basins. The resulting robust species-level phylogeny (~60% complete, based on a multigene data set) exhibits a near constant rate of lineage accumulation throughout the mid-Cenozoic to recent, irrespective of missing species and despite the changing environmental conditions that were prevalent during this time period. This pattern contrasts with the findings for species-level diversification of large clades that commonly show an early burst of cladogenesis followed by declining rates through time. The identification of distinct biogeographic clades demonstrates a correlation between river hydrology and cladogenesis, although there is evidence of recent repeat dispersal into the southern range of the focal group. We conclude that diverse freshwater fish radiations with tropical continental distributions represent important organisms to test hypotheses of diversification and investigate the effects of palaeo-landscapes and climates on present day biodiversity.