Species delimitation in sharpnose sharks (genus <Emphasis Type="Italic">Rhizoprionodon</Emphasis>) in the western Atlantic Ocean using mitochondrial DNA

Despite Springer’s (1964) revision of the sharpnose sharks (genus Rhizoprionodon), the taxonomic definition and ranges of Rhizoprionodon in the western Atlantic Ocean remains problematic. In particular, the distinction between Rhizoprionodon terraenovae and R. porosus, and the occurrence of R. terraenovae in South American waters are unresolved issues involving common and ecologically important species in need of fishery management in Caribbean and southwest Atlantic waters. In recent years, molecular markers have been used as efficient tools for the detection of cryptic species and to address controversial taxonomic issues. In this study 415 samples of the genus Rhizoprionodon captured in the western Atlantic Ocean from Florida to southern Brazil were examined for sequences of the COI gene and the D-loop and evaluated for nucleotide differences. The results on nucleotide composition, AMOVA tests, and relationship distances using Bayesian-likelihood method and haplotypes network, corroborates Springer’s (1964) morphometric and meristic finding and provide strong evidence that supports consideration of R. terraenovae and R. porosus as distinct species.     

A new circumscription of the lichen genus <Emphasis Type="Italic">Nephromopsis</Emphasis> (Parmeliaceae,lichenized Ascomycetes)

The phylogeny of the cetrarioid lichens with bifusiform spermatia and dorsiventral thalli which contain usnic acid is reanalysed using three parts of the genome, ITS rDNA, β-tubulin and GAPDH sequences. Molecular data from five cetrarioid species are presented for the first time, and 13 new sequences are combined with sequences from the gene bank to delimit the genus Nephromopsis. A monophyletic clade of Nephromopsis, Tuckneraria, ‘Cetraria’ leucostigma and ‘C.’ melaloma is identified and circumscribed as one genus, Nephromopsis, which now includes 19 species. Four new combinations are presented. A key to the species is provided.     

The “<Emphasis Type="Italic">Tetrahymena pyriformis</Emphasis>” complex of cryptic species

Cryptic species are common among protists and have long been known in ciliates. The ciliate genus Tetrahymena contains a large group of morphologically indistinguishable species referred to as the ‘T. pyriformis’ complex. These species include those reproductively isolated by mating type as well as asexual species characterized by the absence of the germinal micronucleus. This paper examines the molecular diversity of the species and describes the biogeography of ‘T. pyriformis’ species. Most species are globally distributed, though the best studied species, T. thermophila, is confined to North America and gives evidence of population structure in local populations. Selfers and asexual species are common and arise from sexual species, a possible exploitation of nuclear dimorphism. It is argued that the cryptic species likely have different ecological roles and that the biodiversity of Tetrahymena in particular, and ciliates in general, is underestimated. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Cryptic species of <Emphasis Type="Italic">Notophyllum</Emphasis> (Polychaeta: Phyllodocidae) in Scandinavian waters

The phyllodocid polychaete Notophyllum foliosum occurs in two colour morphs in Swedish and Norwegian waters, one palish yellow to grey form with black patches that is restricted to deeper waters and often associated with reefs of the deep-water coral Lophelia pertusa, and one usually yellow-orange form with black patches and white spots that is usually encountered on more shallow bottoms. We have sampled the two forms from sympatric occurrences in Norway, and the shallow form from the Swedish west coast. Phylogenetic and haplotype analyses based on the mitochondrial cytochrome c oxidase subunit I (COI) gene and the nuclear internal transcribed spacer region (ITS1-5.8SrDNA-ITS2) unequivocally indicate that the two forms represent different species. We apply the name N. foliosum (Sars, 1835) to the ‘shallow form’, and propose N. crypticum n. sp. for the ‘deep form’. A lectotype is fixed for N. foliosum.     

DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus

Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p‐distance, 0.115–0.235; k2p, 0.128–0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity.     

Population genetic structure and taxonomy of the common dolphin (Delphinus sp.) at its southernmost range limit: New Zealand waters

New Zealand is the southernmost limit of the common dolphin's (genus Delphinus) distribution in the Pacific Ocean. In this area, common dolphins occur in both coastal and oceanic habitats, exhibit seasonal and resident occurrence, and present high morphological variability. Here we investigated the population structure and the taxonomic identity of common dolphins (Delphinus sp.) within New Zealand waters using 14 microsatellite loci, 577 bp of the mtDNA control region, and 1,120 bp of the mtDNA cytochrome b gene across 90 individuals. We found high genetic variability and evidence of population expansion. Phylogenetic analyses conducted to clarify the taxonomic status of New Zealand common dolphins did not show any clustering reflecting geographic origin or morphotypes. The microsatellite analysis showed genetic differentiation between Coastal and Oceanic putative populations, while mtDNA revealed significant genetic differentiation only between the Hauraki Gulf and other putative groups. Our results suggest that differences in habitat choice and possible female site fidelity may play a role in shaping population structure of New Zealand common dolphins.     

Spatial patterns of genetic differentiation in <Emphasis Type="Italic">Brachionus</Emphasis> <Emphasis Type="Italic">calyciflorus</Emphasis> species complex collected from East China in summer

In this study, the mtDNA COI genes of 124 individuals in Brachionus calyciflorus complex were sequenced and analyzed. Overall, 84 mtDNA haplotypes were defined, and were split into three clades by the phylogenetic trees. The divergences of COI gene sequence among the three clades ranged from 11.4 to 22.5%, indicating the occurrence of three cryptic species (cryptic species 1, cryptic species 2, and cryptic species 3). Within cryptic species 3, a remarkable degree of differentiation (F _st = 0.0947) might be attributable to habitat fragmentation, restricted gene flow, and founder effect, most probably together with local adaptation. The more shared haplotypes were observed, and a non-significant correlation existed between geographic and genetic distance, suggesting that some ancestral haplotypes might be involved in a past range expansion, and as founders give a similar distribution pattern among geographic populations. The networks were also in agreement with the pattern of genetic differentiation in B. calyciflorus species complex revealed by molecular phylogeny. The nested clade analysis suggested a slight geographic structure in the network I, network II, and the highest nesting clade levels within the network III. Under the possible effect of the Younger Dryas Event, the three cryptic species might have survived in multiple relict refugia throughout the south of China. The co-occurrence of cryptic species 2 and 3 might be found in Guangzhou and Hainan due to the possible interference of the barrier and contiguous range expansion. After the Younger Dryas Event, cryptic species 3 with high colonization ability might have arrived and colonized whole habitats at first, and reduce effective gene flow among cryptic species, thus effectively increasing persistence of founder events. Cryptic species 2 might, respectively, have expanded their ranges into Wuhu and Nanjing regions only because of the probable barrier of the Yangtze River, its weak colonization abilities and the ‘priority effects’ of cryptic species 3. Cryptic species 1 distributed exclusively in Danzhou probably failed to expand its ranges into mainland China because of small population size, weaker dispersal capacity, and the barrier of the Qiongzhou Strait.     

Comparison of the developmental stages of some European allocreadiid trematode species and a clarification of their life-cycles based on ITS2 and 28S sequences

Genetic data were used to examine the diversity in some allocreadiid trematodes. Nuclear ribosomal DNA (ITS2 and partial sequences of 5.8S and 28S) was sampled from sexual adult and ‘larval’ stages. From these and previous reference datasets phylogenetic trees were constructed. The results uncovered genetically distinct lineages within Bunodera luciopercae (Müller, 1776), suggesting that the two Palaearctic subspecies, B. l. luciopercae and B. l. acerinae Roitman & Sokolov, 1999, and Nearctic B. luciopercae from Perca flavescens may represent distinct species with a restricted host-specificity. Identical rDNA was revealed for the sexual adult of B. l. acerinae and ‘larval’ B. luciopercae described by Wiśniewski (1958). An unexpected match between the rDNA sequences of adult B. l. luciopercae and ‘larval’ Allocreadium isoporum (sensu Wiśniewski, 1958) was also detected. The adult A. isoporum (Looss, 1894) differs significantly from the ‘larval’ A. isoporum, the level of rDNA sequence divergence between them (8.6 % for 5.8S-ITS2-28S sequences and 6.26% for 28S) being consistent with the level expected for intergeneric variation. These results revealed the possible existence of a cryptic species complex within the nominal species B. luciopercae and a clear need for reconsideration of some of the accepted, but largely untested, tenets regarding allocreadiid life-cycles.     

Hidden diversity of Euscorpius (Scorpiones: Euscorpiidae) in Greece revealed by multilocus species‐delimitation approaches

Phylogenetic analysis of the genus Euscorpius (Scorpiones: Euscorpiidae) across the Mediterranean region (86 specimens, 77 localities, four DNA markers: 16S rDNA, COI, COII, and ITS1), focusing on Greek fauna, revealed high variation, deep clade divergences, many cryptic lineages, paraphyly at subgenus level, and sympatry of several new and formerly known lineages. Numerous specimens from mainland and insular Greece, undoubtedly the least studied region of the genus' distribution, have been included. The reconstructed phylogeny covers representative taxa and populations across the entire genus of Euscorpius. The deepest clades detected within Euscorpius correspond (partially) to its current subgeneric division, outlining subgenera Tetratrichobothrius and Alpiscorpius. The rest of the genus falls into several clades, including subgenus Polytrichobothrius and a paraphyletic subgenus Euscorpius s.s. Several cryptic lineages are recovered, especially on the islands. The inadequacy of the morphological characters used in the taxonomy of the genus to delineate species is discussed. Finally, the time frame of differentiation of Euscorpius in the study region is estimated and the distributional patterns of the lineages are contrasted with those of other highly diversified invertebrate genera occurring in the study region. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 728–748.     

Native plant/herbivore interactions as determinants of the ecological and evolutionary effects of invasive mammalian herbivores: the case of the common brushtail possum

In their native range, mammalian herbivores exist in a suite of direct and indirect ecological and evolutionary relationships with plant populations and communities. Outside their native range these herbivores become embedded in a multitude of new ecological and evolutionary interactions with native plant species in the new range. Sound knowledge of the plant/herbivore interactions in the herbivores’ native range provides an ideal framework to better understand their effects in the introduced range. The example of the common brushtail possum (Trichosurus vulpecula) and its introduction to New Zealand from Australia provides an excellent case study. In Australia, the common brushtail possum is a widespread generalist herbivore and it is thought that this generalist lifestyle has equipped the species well for successful colonisation of New Zealand. In Australia the brushtail possum has co-existed with highly chemically defended foliage since the Oligocene and recent papers have supported the role of possums as agents of selection on eucalypt defences. While the chemical profile of New Zealand foliage is comparatively poorly understood, possums do show clear selectivity between and within populations and some of these interactions may be mediated by the animals ability to ‘cope’ with PSMs, coupled with maintaining its generalist diet. While possums have had less time to effect evolutionary change in New Zealand species, their impacts on plant fitness have been well documented. However, further knowledge on variation and heritability of foliage traits driving possum preferences is needed to elucidate the ecological and evolutionary plant/possum interactions in the invasive range.     

Low genetic diversity and lack of genetic structure in the giant jellyfish Nemopilema nomurai in Chinese coastal waters

The giant jellyfish Nemopilema nomurai is a scyphozoan species well-known in East Asian Marginal Seas for its damage to fisheries. The genetic diversity and population structure of N. nomurai, collected from five geographic regions in Chinese coastal seas, were examined based on mitochondrial cytochrome c oxidase subunit I (COI) gene and nuclear internal transcribed spacer one (ITS1) sequences. A total of 26 and five unique haplotypes were recovered from the COI and ITS1 genes, respectively. The overall genetic diversity of N. nomurai calculated by the COI and ITS1 sequences was low (haplotype diversity 0.727% and 0.108%, nucleotide diversity 0.212% and 0.039%). The median-joining network analysis revealed a star-like haplotype network. The hierarchical Analysis of Molecular Variance (AMOVA) of COI haplotypes showed that N. nomurai populations form a single population, with a low F_ST (0.0149, p?=?0.1036). The dispersal ability, together with the biological characteristics, could be important factors for the lack of a geographically structured pattern in N. nomurai in Chinese coastal waters.     

Systematics and distribution of the New Zealand onychoteuthid fauna (Cephalopoda: Oegopsida), including a new species, Notonykia nesisi sp. nov.

Onychoteuthid squids are among the most common cephalopods found in New Zealand waters, and comprise a major portion of the regional diets of teuthophagous marine mammals. Although several recent publications have addressed aspects of various species’ biology and reproduction, the systematics of the group remains poorly understood. Herein the ontogenetic and adult morphologies of regionally occurring known species of the genera Moroteuthis, Onychoteuthis, and Notonykia are redescribed, and Notonykia nesisi sp. nov. is described for the first time. Ontogenetic and sexually dimorphic variation in characters and character states associated with body proportions, and beak, radula, tentacular hook, palatine tooth and gladius morphologies are also described and compared between local onychoteuthid taxa for the first time.     

Species of <Emphasis Type="Italic">Neohaliotrema</Emphasis> Yamaguti, 1965 (Monogenea: Ancyrocephalidae) from the pomacentrid <Emphasis Type="Italic">Abudefduf vaigensis</Emphasis> (Quoy &; Gaimard) off Pulau Langkawi,Malaysia, with a revised diagnosis of the genus and a key to its species

Four new and one unidentified species of Neohaliotrema Yamaguti, 1965 were obtained from the gills of the Indo-Pacific sergeant Abudefduf vaigensis (Quoy & Gaimard) off Pulau Langkawi, Malaysia. The five species, N. malayense n. sp., N. bombini n. sp., N. andamanense n. sp., N. parvum n. sp. and an unidentified Neohaliotrema sp. (similar to N. macracanthum Zhukov, 1976), are described and distinguished based mainly on features of the haptor. Species of this genus are divisible into two groups, the ‘maomao group’, with two pairs of morphometrically modified ‘marginal’ hooks and a fenestrated haptor, and the ‘gracile group’, with morphologically similar marginal hooks and an entire haptor. With the exception of N. bombini n. sp., the species described fit within the ‘maomao group’. It is suggested that the more complex Neohaliotrema species of the ‘maomao group’ have modified hooks 1 and 2 on a haptoral ‘isthmus’ between two large apertures, i.e. ‘windows’, whereas the less complex species lacking these features are those of the ‘gracile group’. Neohaliotrema spp. have only a single pair of pigmented eye-spots. A fenestrated haptor is unique to the Neohaliotrema spp. of the ‘maomao group’. The generic diagnosis of Neohaliotrema is amended to include new data and a key to its known species is presented.     

Mycorrhiza status of Gnetum spp. in Cameroon: evaluating diversity with a view to ameliorating domestication efforts

A field survey was carried out to investigate the diversity of mycorrhizal fungi associated with Gnetum spp. in Cameroon. The extent and variation of ectomycorrhizal colonisation as well as the degree of host specificity were evaluated. Gnetum spp. were found to be almost always ectomycorrhizal in all sites visited. There were just two ectomycorrhizal morphotypes (‘yellow’ and ‘white’) associated with this plant. Such low diversity is unusual for an ectomycorrhizal plant. The yellow morphotype was the most widespread and prevalent and was identified by morphological and molecular methods to have been formed with Scleroderma sinnamariense. Propagules of this fungus were present in soil collected from farm lands, cocoa plantations, Chromolaena and bush fallows, as well as in a relatively undisturbed forest harbouring ectomycorrhizal legumes. The fungus responsible for the white morphotype was identified as also belonging to the genus Scleroderma by ITS sequence similarity. Arbuscular mycorrhizal structures were absent in cleared and stained portions of the roots.     

Utilization of polychaete tubes as spawning substrate by the sea raven Hemitripterus villosus (Scorpaeniformes)

Synopsis The sea raven, Hemitripterus villosus, deposits its eggs on polychaete tubes (Salmacina sp.) in the coastal waters of Usujiri, southern Hokkaido, Japan. This is contradictory to investigations in the Bay of Peter the Great, Soviet Union, where eggs are deposited in narrow clefts. The egg masses are found among the bunchy worm tubes or between the base of the colony and the substrate. The spawning habit of H. villosus is distinct from ‘spawner in live invertebrates’ such as the little dragon sculpin Blepsias cirrhosus, which specifically associates with a sponge. That of H. villosus is classified as a ‘cavity spawner’.     

Phylogenetic Diversity of New Zealand Gelidiales as Revealed by rbcL Sequence Data

Diversity and phylogenetic relationships of New Zealand representatives of the red algal order Gelidiales have been examined using rbcL sequence data. Extensive field collections have been made from throughout the New Zealand region. Six genera have been reported previously from New Zealand (Capreolia, Gelidium, Pterocladia, Pterocladiella, Pterocladiastrum, Ptilophora). This research has revealed species with very restricted local distributions, as well as the discovery of several undescribed, cryptic taxa. The common and widespread Gelidium caulacantheum is confirmed to be more closely related to Capreolia than to other species of Gelidium. The generic concept of Capreolia, based on life history characters, will need to be modified to accommodate additional species possessing “Gelidium” life histories. A species endemic to New Zealand, Gelidium ceramoides, has been found to differ significantly from all other members of the Gelidiales and requires reclassification in another genus and order. Examination of field collections and herbarium specimens in addition to molecular sequence data have led us to conclude that specimens previously placed in the genera Ptilophora and Pterocladiastrum belong within Pterocladia lucida.     

Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in <Emphasis Type="Italic">Paramacrobiotus</Emphasis> (Tardigrada)

Species within the tardigrade genus Paramacrobiotus could be distinguished via an analysis of internal transcribed spacer 2 (ITS2) secondary structures. Sequences of P. richtersi and four populations previously treated under provisional names (Paramacrobiotus ‘richtersi group’ 1 to 4) from different continents were determined and annotated, and their secondary structures were predicted. A tree based on a combined sequence-structure alignment was reconstructed by Neighbor-Joining. The topology obtained is consistent with a tree based on a distance matrix of compensatory base changes (CBCs) between all ITS2 sequence-structure pairs in the global multiple alignment. The CBC analysis, together with 18S rDNA sequences, physiological, biochemical and biophysical data identified three species new to science that are morphologically indistinguishable from P. richtersi. These are formally described under the names Paramacrobiotus fairbanksi sp. nov., P. kenianus sp. nov., and P. palaui sp. nov.     

Observations of a distinctive morphotype of killer whale (Orcinus orca), type D, from subantarctic waters

Studies have shown that killer whale (Orcinus orca) communities in high latitudes regularly comprise assemblages of sympatric ‘ecotypes’—forms that differ in morphology, behavior, and prey preferences. Although they can appear superficially similar, recent genetic evidence suggests that breeding is assortative among ecotypes within individual communities, and species-level divergences are inferred in some cases. Here, we provide information on a recently recognized ‘type D’ killer whale based on photographs of a 1955 mass stranding in New Zealand and our own six at-sea sightings since 2004. It is the most distinctive-looking form of killer whale that we know of, immediately recognizable by its extremely small white eye patch. Its geographic range appears to be circumglobal in subantarctic waters between latitudes 40°S and 60°S. School sizes are relatively large (mean 17.6; range 9–35; n = 7), and although nothing is known about the type D diet, it is suspected to include fish because groups have been photographed around longline vessels where they reportedly depredate Patagonian toothfish (Dissostichus eleginoides).     

Taxonomy and host-specificity of Gyrodactylus aideni n. sp. and G. pleuronecti (Monogenea: Gyrodactylidae) from Pseudopleuronectes americanus (Walbaum) in Passamaquoddy Bay, New Brunswick, Canada

Wild and cultured winter flounder Pseudopleuronectes americanus (Walbaum) from Passamaquoddy Bay were surveyed for species of Gyrodactylus Nordmann, 1832. Two species were found: G. pleuronecti Cone, 1981 and G. aideni n. sp, both members of Malmberg’s ‘groenlandicus group’. Although the hard parts in the haptor are very similar in the two species, hamuli of G. aideni are consistently shorter than those of G. pleuronecti. The two species differed by 35 base pairs in the ITS 1, 5.8 and ITS 2 region. A BLAST search identified a variety of species of Gyrodactylus from marine fishes in the Atlantic Ocean as closest matches, indicating the ‘groenlandicus group’ is part of a major marine lineage within Gyrodactylus (sensu lato) that has successfully radiated among coastal percid, pleuronectid, cottid and anarhichadid fishes. Exposure experiments suggested that winter flounder is the primary host of both species of parasites and that three other pleuronectid species in the bay may potentially serve only as occasional transport hosts.     

Complete sequence and gene organization of the mitochondrial genome of scaly-sided merganser (<Emphasis Type="Italic">Mergus squamatus</Emphasis>) and phylogeny of some Anatidae species

The scaly-sided merganser (Mergus squamatus) is an endangered bird species on the IUCN Red List with the estimated global population of less than 2,500 individuals at present. In the present study, we studied the complete mitochondrial genome (mtDNA) and the phylogenetic of M. squamatus by PCR amplification and GenBank data. The genome was 16,595 bp in length and contained 37 genes (13 protein coding genes, two rRNAs, and 22 tRNAs) and a non-coding control region (D-loop). All protein-coding genes of M. squamatus mtDNA start with a typical ATG codon, except ND1, COI, and COII uses GTG as their initial codon. TAA, T- and TAG as the terminate codon occurred very commonly in the sequence. All tRNA genes can be folded into canonical cloverleaf secondary structure except for tRNA^Ser (AGY) and tRNA^Leu (CUN), which lose ‘‘DHU’’ arm. The genome sequences had been deposited in GenBank under accession number HQ833701. Based on the concatenated nucleotide sequences of mtDNA genes (Cyt b and D-loop), we reconstructed phylogenetic trees and discussed the phylogenetic relationships among ten Anatidae species. The results are different from the present classification, and we support Lophodytes cucullatus and Mergullus albellus to be members of the genus Mergus.