New records of Alvinocarididae (Crustacea: Decapoda: Caridea) from the southwestern Pacific hydrothermal vents,with descriptions of one new genus and three new species

Three new species of the caridean family Alvinocarididae are described from hydrothermal vents in the Southwest Pacific, namely, Chorocaris parva sp. nov. (Manus Basin, 1305–1684 m), Chorocaris variabilis sp. nov. (Manus and North Fiji basins and Vanuatu, 1305–2480 m) and Manuscaris acuminatus gen. et sp. nov. (Manus Basin, 1310 m). Morphological affinities of these three species are discussed. Molecular genetic analysis using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene supports the recognition of the two new species assigned to Chorocaris Martin and Hessler, 1990. The generic diagnosis of Chorocaris is slightly emended to accommodate the two new species. Opaepele susannae Komai, Gierre and Segonzac, 2007 is transferred to Chorocaris. Alvinocaris komai Zelnio and Hourdez, 2009, originally described from the Lau Basin, is newly recorded from the North Fiji Basin and Vanuatu (Nifonea vent field), at depths of 1740–2750 m.

http://zoobank.org/urn:lsid:zoobank.org:pub:4BFC8C31-C006-4738-BED7-B13D3296A7CA     

Repeated sampling adds to the genetic diversity of Lepidochelys olivacea (Eschscholtz 1829) olive ridley sea turtle

ABSTRACT

First sampled in the late 1990s, Campamento Tortuguero La Gloria, in Jalisco, Mexico, was resampled for olive ridley sea turtle (Lepidochyles olivacea Eschscholtz) diversity 10 years later. A comparison with all previously reported mitochondrial sequences revealed that these new samples added to the known genetic diversity for this species, and revealed unexpectedly high genetic diversity among turtles nesting on this beach. The results highlight the importance of systematic resampling in known nesting rookeries to verify the genetic diversity of study populations. Three new olive ridley haplotypes are reported, all more closely related to Baja Californian haplotypes than to Australian haplotypes. Significant genetic divergence is reported within populations, within ocean basins (Atlantic, Pacific, Indian and Indo-Pacific), and between ocean basins. Furthermore, this is the first study that integrates satellite tagging data to demonstrate diverse post-nesting migration patterns of turtles with identical haplotypes, and it demonstrates flexibility in post-nesting migratory behaviour for olive ridley sea turtles of the same genetic provenance.     

Phylogenetic divergence in a desert fish: differentiation of speckled dace within the Bonneville, Lahontan, and upper Snake river basins

Historical events have had a great impact on the biogeography of fishes of western North America. We examined the genetic variation of the speckled dace ( Rhinichthys osculus ) to determine the effects on this species of extensive hydrological changes during the last 10 million years in the Bonneville and Lahontan basins of the Great Basin and the upper Snake River Basin. Eight hundred sixty-nine base pairs of the mitochondrial gene cytochrome b were sequenced from 97 individuals representing 22 populations within these 3 basins, as well as from 2 individuals of longnose dace ( Rhinichthys cataractae ) that served as outgroups. Additionally, 13 speckled dace sequences representing 3 Bonneville populations were used from GenBank. Phylogenetic relationships were reconstructed using maximum parsimony and maximum likelihood criteria. Analysis of molecular variance was used to determine population structure and to estimate the amount of gene flow across the community boundaries. Three distinct clades were reconstructed representing the Lahontan Basin, the northern Bonneville and upper Snake River basins, and the southern Bonneville Basin. Additionally, most of the population structuring was explained by variation among basins (65.33%). Speckled dace demonstrated high genetic variation. As hypothesized, the northern and southern Bonneville specimens formed separate clades; however, the southern Bonneville clade was basal to a sister clade formed by the northern Bonneville/upper Snake River and Lahontan clades. These relationships indicate that Pliocene connections between the Snake, Lahontan, and Bonneville drainages, rather than more recent Pleistocene connections, best explain population structuring in speckled dace.     

Molecular phylogeny of major lineages of the avian family Phasianidae inferred from complete mitochondrial genome sequences

Phasianidae is a large family of birds which contains most of the gallinaceous birds of the world. So far, the taxonomic status of many genera within Phasianidae has been controversial. The complete mitochondrial genome sequence of the white-eared pheasant (Crossoption crossoptilon) was determined in this study. Combining this with other previously published mitochondrial genome sequences, we reconstructed the phylogenetic relationships of Phasianidae and related species using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All analyses yielded a similar and well-supported topology, in which Crossoptilon grouped with Lophura. Perdix dauurica was sister taxon to the gallopheasants with high support, and Pucrasia was sister to this clade and separate from the other tragopans. Tetraophasis and Lophophorus grouped together, with Tragopan as the sister taxon. In addition, our results indicated that Meleagris clustered with Bonasa forming a monophyletic clade embedded in the pheasant‐partridge clade and the turkey–grouse lineage should be considered a part of the pheasant–partridge radiation.     

Relationships of the South African lizards assigned to Aporosaura,Meroles and Pedioplanis (Reptilia: Lacertidae)

Phylogenetic analyses, using parsimony and compatibility methods, were carried out on the South African lacertid lizards assigned in recent times to Aporosaura, Meroles and Pedioplanis. These were based on 80 primary and 102 binary morphological characters which were drawn from osteology, external features, muscles, kidneys and reproductive systems. Contrary to some previous interpretations, there are two well-defined clades: Meroles plus Aporosaura, and Pedioplanis; these form successive branches on the main stem of the phylogeny of advanced lacertids. The clades show considerable parallel development of derived features, presumably because they had very similar initial genetic potential. Relationships within the two groups are shown on p. 800 and p. 802. As Aporosaura anchietae is sister taxon to a clade consisting of three of the seven species of Meroles, it has been transferred to that genus. Relationships in Meroles-Aporosaura are very well substantiated, in contrast to the situation in Pedioplanis. This difference appears to be related to the different kinds of evolutionary history that the two groups have had. The Meroles-Aporosaura clade has spread progressively into increasingly stringent and singular aeolian sand environments which have elicited the production of many, often unique, derived character states related to the functional problems of survival in such situations. As these states are rarely duplicated in outgroups, the characters concerned are easily polarized. This, together with their abundance, means that a robust basis for phylogenetic inference is available. In contrast, Pedioplanis exhibits relatively limited ecological radiation of a kind that also occurs in related groups, and the functionally related derived states elicited are fewer and less distinctive. In fact, production of a phylogeny for Pedioplanis is very dependent on genital characters which seem to be substantially independent of the main ecological changes that have occurred in the genus. The premaxilla is embraced dorsally by the anterior processes of the maxillae in most lacertids, but the processes are less extensive in two sister species of Pedioplanis, P. burchelli and P. laticeps. This modified condition also occurs in the genera Eremias, Acanthodactylus, Mesalina and Ophisops, which together constitute a clade that forms the sister group of Pedioplanis. The modification provides extra evidence for the holophyly of the clade, even though presence in some Pedioplanis shows it to be homoplasious.     

On the taxonomic status of the highly endangered Ponto-Caspian gastropod genus Caspia (Gastropoda: Hydrobiidae: Caspiinae)

Caspia is an endemic Ponto-Caspian Basin genus of hydrobiid gastropods. Around a dozen nominal species of Caspia have been described to inhabit the Caspian Sea while four species occupy a restricted zone in the lower part of the rivers flowing into the Black Sea and the Sea of Azov. Scanning electron microscopic study of the protoconch and radula morphology of two Caspia species from the Azov–Black Sea Basin allows re-evaluation of the taxonomic rank and attribution of the genus. The adult shell geometry and characters of ornamentation do not enable clear demarcation of these species of Caspia but the protoconch parameters do allow their differentiation. Available morphological data on Caspia and the related genus Caspiohydrobia are interpreted here as confirmation of the subfamilial rank of Caspiinae in the family Hydrobiidae, in contrast to the previous affiliation of this group with Pyrgulidae.     

Bythinella Moquin-Tandon, 1856 (Gastropoda: Rissooidea: Bythinellidae) in Romania: species richness in a glacial refugium

The buff-throated partridge, Tetraophasis szechenyii Madarász, 1885, is a species endemic to west China. The complete mitochondrial genome of this species was sequenced. It was 16,706 base pairs (bp) in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The phylogenetic relationships of the buff-throated partridge and 19 other Phasianidae species were inferred by Bayesian inference and maximum likelihood analyses based on 12 protein-coding genes. With the exception of a few nodes, most internal branches were supported by a high Bayesian posterior probability (BPP?=?1.0). The resulting trees clarified the phylogenetic position of T. szechenyii within Phasianidae. The genetic diversity and population structure of the Pamulin population of T. szechenyii were examined based on the mitochondrial DNA CR. Nucleotide sequence analysis defined 18 haplotypes in 24 individuals. Haplotype diversity (h) was 0.953 and nucleotide diversity (π) was 0.0044. The results revealed that the genetic diversity of this population was not particularly low. Combined with the field work conducted by our lab, we found that members of the Pamuling population are cooperative breeders and the population may contain individuals from neighbouring groups. Our work provided genetic background information for the conservation and management of this species.     

A new species of arboreal salamander (Caudata: Plethodontidae: Pseudoeurycea) from the mountains of Oaxaca,Mexico

Recent surveys of the plethodontid salamander fauna of Oaxaca, Mexico, disclosed the existence of a new, morphologically distinct arboreal species of the genus Pseudoeurycea. The new species, described here, is from the Sierra Mazateca in northern Oaxaca. Sequences of 1833 base pairs of the 16S, cytochrome b and ND4 mitochondrial DNA (mtDNA) genes from the new taxon were used to assess its phylogenetic position. Previous phylogenetic analyses based on mtDNA supported recognition of four clades within Pseudoeurycea: P. bellii, P. gadovii, P. juarezi and P. leprosa-Lineatriton species groups. One additional species, P. unguidentis, was not closely allied to any of the four groups. Re-analysis including the additional sequences reported here establishes a sister-group relationship between the new species and P. unguidentis. Moreover, it supports this clade as part of the P. juarezi species group.     

Sipunculans and echiurans from the deep Angola Basin

Sipunculans and echiurans collected by the “DIVA 1” expedition by RV Meteor (Cruise M48/1) to the deep‐sea bottom of the Angola Basin are recorded. Seven species from five genera and two separate phyla are recognized; only the echiuran Pseudoikedella achaeta has not been recorded hitherto in the southern sector of the Atlantic Ocean. A gradient analysis using redundancy analysis (RDA) under the CANOCO package indicates the existence of a neat latitudinal gradient of sipunculans along the Angola Basin from the southernmost stations towards the northern ones. The local abundance of abandoned horny tubes of polychaetes at some of the sampling sites of the northernmost stations explains the dense aggregations of Nephasoma diaphanes. This species exhibits an opportunistic lifestyle inside empty polychaete tubes on the abyssal plains of the Angola Basin.     

New taxa of the parasitic quill mites associated with accipitrid birds indicating close relationship of falconid birds to Psittaci–Columbi clade

Two new species of syringophilid mites (Acari: Prostigmata: Cheyletoidea: Syringophilidae) associated with accipitrid diurnal raptors (Falconiformes: Accipitridae) are described and figured: Megasyringophilus aquilus sp. nov. from two host species of the genus Aquila, A. rapax (Temminck, 1828) and A. pomarina Brehm, 1831, and Peristerophila accipitridicus sp. nov. from Terathopius ecaudatus (Daudin, 1800). Relationships between birds of prey and Psittaci–Columbi clade are briefly discussed.     

Sequence variation of mitochondrial DNA ND5 in captive South China tigers (Panthera tigris amoyensis)

This paper represents the first study of the genetic diversity of captive South China tigers Panthera tigris amoyensis by sequence variation in a fragment of mitochondrial DNA (mtDNA) NADH dehydrogenase subunit 5 (ND5) gene. Two haplotypes (haplotype I and haplotype II) were identified and the captive population had a bias towards haplotype I. This subspecies as a whole demonstrated an extremely low level of genetic diversity with the nucleotide diversity of 0.057±0.021%. The mtDNA ND5 variations detected in the present study could provide significant information to the studbook data of the South China tiger.     

Effects of fragmentation on genetic variation in populations of the terrestrial earthworm Drawida japonica Michaelsen, 1892 (Oligochaeta,Moniligastridae) in Shandong and Liaodong peninsulas,China

Earthworms are excellent indicators of landscape fragmentation due to their widespread distribution and poor dispersal abilities over water. Based on field studies conducted in the Shandong and Liaodong peninsulas and their associated islands during summer 2009, we analysed the genetic variation of Drawida japonica Michaelsen, 1892 (Oligochaeta, Moniligastridae) using DNA sequences of the 16S and 28S ribosomal genes in samples obtained from 13 localities, 12 of which were islands, one artificially connected to the mainland by man (Yangma SC). We identified 55 haplotypes among 79 samples, based on 1094 bp, including 47 unique haplotypes. The phylogenetic tree topologies showed two distinct clades. A multiple-apex Poisson distribution using a mismatch analysis of nucleotides was also detected. Results of a Tajima D neutral test were not significant (p > 0.05). Genetic divergence among populations was much larger than within populations. A positive relationship between genetic diversity and island area was revealed, but no significant correlation between genetic diversity and distance to the nearest larger landmass was found. These results indicate that the intraspecific genetic diversity of D. japonica has been influenced by geographic isolation (i.e. island habitat). Passive transport via anthropogenic activities or nonhuman vertebrates (birds or mammals) may also play a key role in dispersal.     

Phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the boreal island of Hokkaido,Japan

To test postglacial population expansion in small arboreal mammals dependent on boreal and subboreal forests, we used complete mitochondrial cytochrome b gene sequences (1140 bases) to investigate the phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the Hokkaido Island of Japan. This subspecies is common in the boreal and subboreal forests of Hokkaido. We examined 61 specimens from 27 localities in Hokkaido. Phylogenetic relationships among 29 haplotypes found in the Hokkaido populations were not associated with geographic distribution of sampling localities. There were four mitochondrial DNA phylogroups. Phylogeographic analyses support sudden expansion of S. vulgaris orientis from restricted refugium in the southern part of Hokkaido during the last glacial period. The phylogeographic structure of this subspecies directly reflects the boreal and subboreal forest dynamics occurring in Hokkaido.     

Chaetognaths from Alvin dives in the Santa Catalina Basin (California), with description of two new Heterokrohnia species

Six species of deep-water chaetognaths have been caught near the bottom (at about 1300 m) during four dives of the submersible Alvin in the Santa Catalina Basin (California). Although few samples were taken, they are very interesting. New morphological data are presented on a supposed very well-known planktonic species (Sagitta macrocephala) and two new benthoplanktonic species of the genus Heterokrohnia are described. Details on the morphology and reproduction of the family Heterokrohniidae, and also on the bathymetric and zoogeographic distributions of Heterokrohnia species of the ‘longidentata’ group are given.     

Phylogenetic relationships among genera in the Calanidae (Crustacea: Copepoda) based on morphology

Cladistic analysis of Calanidae recovered two major clades: a tropical epipelagic clade composed of species without ontogenetic vertical migration (Canthocalanus + Cosmocalanus + Nannocalanus + Undinula); and a clade of ontogenetically migrating genera (Neocalanus + Calanoides + Calanus + Mesocalanus). The latter clade is least well supported although its Calanoides and Neocalanus lineages are well supported. Morphology-based topologies are largely congruent with published molecular trees, differing chiefly in the positions of Mesocalanus and Calanus. Independent homoplasious trends in character states in the male leg 5 include: reduction in segmentation and number of setae, increasing asymmetry as well as the probable retention of larval characteristics. The monophyly of Calanoides, Neocalanus and Calanus is well supported. It is postulated that Calanidae radiated during the mid to late Triassic from a bathypelagic megacalanid which was adapted to low oxygen conditions. High latitude locations may have been the first epipelagic environments to be recolonized.