David John Rees

Amphipod genome sizes: first estimates for Arctic species reveal genomic giants

The genome sizes of 8 species of amphipods collected from the Canadian Arctic were estimated by flow cytometry. Haploid genome sizes ranged from 2.94 +/- 0.04 pg DNA in Acanthostepheia malmgreni (Oedicerotidae) to 64.62 +/- 2.85 pg in Ampelisca macrocephala (Ampeliscidae). The value for Ampelisca macrocephala represents the largest crustacean genome size recorded to date (and also the largest within the Arthropoda) and indicates a 400-fold variation in genome size among crustaceans. The presence of such large genomes within a relatively small sample of Arctic amphipods is striking and highlights the need to further explore the relationships between genome size, development rates, and body size in both Arctic and temperate amphipods.

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

BackgroundA skewed assemblage of two epi-, meso- and bathypelagic fish families makes up the order Myctophiformes – the blackchins Neoscopelidae and the lanternfishes Myctophidae. The six rare neoscopelids show few morphological specializations whereas the divergent myctophids have evolved into about 250 species, of which many show massive abundances and wide distributions. In fact, Myctophidae is by far the most abundant fish family in the world, with plausible estimates of more than half of the oceans combined fish biomass. Myctophids possess a unique communication system of species-specific photophore patterns and traditional intrafamilial classification has been established to reflect arrangements of photophores. Myctophids present the most diverse array of larval body forms found in fishes although this attribute has both corroborated and confounded phylogenetic hypotheses based on adult morphology. No molecular phylogeny is available for Myctophiformes, despite their importance within all ocean trophic cycles, open-ocean speciation and as an important part of neoteleost divergence. This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements.ResultsMitogenomic evidence from DNA sequences and unique gene orders are highly congruent concerning phylogenetic resolution on several myctophiform classification levels, corroborating evidence from osteology, larval ontogeny and photophore patterns, although the lack of larval morphological characters within the subfamily Lampanyctinae stands out. Neoscopelidae is resolved as the sister family to myctophids with Solivomer arenidens positioned as a sister taxon to the remaining neoscopelids. The enigmatic Notolychnus valdiviae is placed as a sister taxon to all other myctophids and exhibits an unusual second copy of the tRNA-Met gene – a gene order rearrangement reminiscent of that found in the tribe Diaphini although our analyses show it to be independently derived. Most tribes are resolved in accordance with adult morphology although Gonichthyini is found within a subclade of the tribe Myctophini consisting of ctenoid scaled species. Mitogenomic sequence data from this study recognize 10 reciprocally monophyletic lineages within Myctophidae, with five of these clades delimited from additional rearranged gene orders or intergenic non-coding sequences.ConclusionsMitogenomic results from DNA sequences and unique gene orders corroborate morphology in phylogeny reconstruction and provide a likely scenario for the phylogenetic history of Myctophiformes. The extent of gene order rearrangements found within the mitochondrial genomes of myctophids is unique for phylogenetic purposes.

Are they still viable? Physical conditions and abundance of Daphnia pulicaria resting eggs in sediment cores from lakes in the Tatra Mountains

All species of Daphnia (Cladocera) produce, at some stage in their life cycle, diapausing eggs, which can remain viable for decades or centuries forming a “seed bank” in lake sediments. Because of their often good preservation in lake sediment, they are useful in paleolimnology and microevolutionary studies. The focus of this study was the analysis of cladoceran resting eggs stored in the sediment in order to examine the ephippial eggs bank of Daphnia pulicaria Forbes in six mountain lakes in the High Tatra Mountains, the Western Carpathians (northern Slovakia and southern Poland). Firstly, we analyzed distribution, abundance and physical condition of resting eggs in the sediment for their later used in historical reconstruction of Daphnia populations by genetic methods. To assess changes in the genetic composition of the population through time, we used two microsatellite markers. Although DNA from resting eggs preserved in the High Tatra Mountain lake sediments was extracted by various protocols modified for small amounts of ancient DNA, DNA from eggs was not of sufficient quality for microsatellite analyses. Distribution curves of resting eggs from sediment cores correspond to the environmental changes that have occurred in the High Tatra Mountains area during last two centuries (atmospheric acid deposition, fish introduction) and demonstrate their influence on natural populations. Evaluation of ephippia physical condition (the most common category was empty ephippial covers) suggests that the majority of resting eggs hatched to produce a new generation of Daphnia or may be due to failed deposition of resting eggs by Daphnia to the chitinous case. In conclusion, age, low quantity and poor physical condition of resting eggs from these Tatra lake sediments proved to be unsuitable not just for use in genetic analyses, but also the possibilities of autogenous restoration of Daphnia populations from the resting egg banks in the Tatra sediments are negligible.

On the origin of a novel parasitic-feeding mode within suspension-feeding barnacles.

In his monograph on Cirripedia from 1851, Darwin pointed to a highly unusual, plateless, and most likely parasitic barnacle of uncertain phylogenetic affinity. Darwins barnacle was Anelasma squalicola, found on deep-water sharks of the family Etmopteridae, or lantern sharks. The barnacle is uncommon and is therefore rarely studied. Recent observations by us have shown that they occur at an unusually high prevalence on the velvet belly lantern shark, Etmopterus spinax, in restricted fjord areas of western Norway. A phylogenetic analysis based on ribosomal DNA data (16S, 18S, and 28S) from 99 selected barnacle species, including all available pedunculate barnacle sequences from GenBank, shows that A. squalicola is most closely related (sister taxon) to the pedunculate barnacle Capitulum mitella. Both C. mitella and species of Pollicipes, situated one node higher in the tree, are conventional suspension feeders from the rocky intertidal. Our phylogenetic analysis now makes it possible to establish morphological homologies between A. squalicola and its sister taxon and provides the evolutionary framework to explain the unprecedented transition from a filter-feeding barnacle to a parasitic mode of life.

Control region sequences indicate that multiple externae represent multiple infections by Sacculina carcini (Cirripedia: Rhizocephala)

The rhizocephalan barnacle, Sacculina carcini, is a common parasite of the European shore crab, Carcinus maenas, in which it causes significant detrimental physical and behavioral modifications. In the vast majority of cases, the external portion of the parasite is present in the form of a single sac-like externa; in rare cases, double or even triple externae may occur on the same individual host. Here, we use a highly variable DNA marker, the mitochondrial control region (CR), to investigate whether multiple externae in S. carcini represent infection by multiple parasites or asexual cloning developed by a single parasite individual. Sequences for multiple externae from C. maenas hosts from the Danish inlet, Limfjorden, and from the mud flates at Roscoff, France, were compared. In almost all cases, double or triple externae from an individual host yielded different haplotypes. In the few cases where identical haplotypes were identified from externae on a multiple-infected host, this always represented the most commonly found haplotype in the population. This indicates that in Sacculina carcini, the presence of multiple externae on a single host reflects infection by different individual parasites. A haplotype network of CR sequences also suggests a degree of geographical partitioning, with no shared haplotypes between the Limfjorden and Roscoff. Our data represent the first complete CR sequences for a rhizocephalan, and a unique gene order was also revealed. Although the utility of CR sequences for population-level work must be investigated further, the CR has proved a simple to use and highly variable marker for studies of S. carcini and can easily be applied to a variety of studies in this important parasite.

Molecular and morphological variation in saddled fathead sculpins (Psychrolutidae: Cottunculus) of the north-east Atlantic Ocean, with a synonymy of three species

On the basis of 104 individuals of Cottunculus from the Norwegian coast, the Barents Sea, Svalbard and north-east Greenland waters, this paper evaluates the descriptive taxonomic characters of three species Cottunculus sadko, Cottunculus microps and Cottunculus konstantinovi and links the character variation to genetic characterizations. Eleven morphological characters used as diagnostic characters in the original descriptions of these species were analysed in pair-wise character comparisons. All characters show cross-species traits when in combination with each other, and all individuals show traits of more than one of the species. Partial cytochrome oxidase c subunit I (coI) gene sequences from 21 individuals, covering the morphological variation among the specimens, show little variation among the individuals. From these results, it is concluded that the descriptive characters do not support the maintenance of more than one species. It is recommended that C. microps remains the name for this species, with C. sadko and C. konstantinovi as junior synonyms.

Lack of taxonomic information from parietal spine size invalidates subspecies in the Atlantic hookear sculpin Artediellus atlanticus.

An analysis of 107 individuals of Atlantic hookear sculpin Artediellus atlanticus from the Barents Sea-Svalbard region and from north-east Greenland shows that the state of the parietal spines, although not randomly distributed geographically, occurs sympatrically. They do not diagnostically describe populations. They are therefore inept for subspecies delimitation into Artediellus atlanticus atlanticus, Artediellus atlanticus corniger and Artediellus atlanticus europaeus. Sympatric occurrence of parietal spine states called for a molecular approach to look for differences at a species level. Sequencing the mitochondrial genes, cytochrome oxidase c subunit I (coI) and cytochrome b (cytb), shows no difference between individuals with different parietal spine size. Thus, there is no evidence of the spine states representing species-level variation. The study shows that parietal spine size has no taxonomic information for this species. The patterns of variation in parietal spine size differ to some degree between the sexes.

On a New Species of Parasitic Barnacle (Crustacea: Rhizocephala), Sacculina shiinoi sp. nov., Parasitizing Japanese Mud Shrimps Upogebia spp. (Decapoda: Thalassinidea: Upogebiidae), Including a Description of a Novel Morphological Structure in the Rhizocephala

The rhizocephalan Sacculina shiinoi sp. nov. parasitizes three species of Upogebia in Japan. It is described morphologically and compared with another Upogebia parasite, Sacculina upogebiae Shiino, 1943 from Japan and Korea. These two species are the only sacculinids that parasitize mud shrimps. DNA analyses clearly show the two species to be separate and not closely related. The cuticle differs in being provided with close-set, branched, and spiny excrescences in S. shiinoi, while it lacks excrescences, but forms small scales in S. upogebiae. In S. upogebiae, the bulbous sperm-producing part and the narrow receptacle duct are separated by a compartmentalized mid portion, which is missing in S. shiinoi. A ridge, having a thickened, fluffy cuticle with a U-shaped course, passes across the visceral mass between the two receptacle openings in S. shiinoi. Such a structure has never been described in other rhizocephalans, and its function is uncertain.