Molecular systematics of threadfin breams and relatives (Teleostei,Nemipteridae)

Threadfin breams and relatives of the family Nemipteridae comprise 69 currently recognized species in five genera. They are found in the tropical and subtropical Indo‐West Pacific and most are commercially important. Using recently developed molecule‐based approaches exploiting DNA sequence variation among species/specimens, this study reconstructed a comprehensive phylogeny of the Nemipteridae, examined the validity of species and explored the cryptic diversity of the family, and tested previous phylogenetic hypotheses. A combined data set (105 taxa from 41 morphospecies) with newly determined sequences from two nuclear genes (RAG1 and RH) and one mitochondrial gene (COI), and a data set with only COI gene sequences (329 newly obtained plus 328 from public databases from a total of 53 morphospecies) were used in the phylogenetic analysis. The latter was further used for species delimitation analyses with two different tools to explore species diversity. Our phylogenetic results showed that all the currently recognized genera were monophyletic. The monotypic genus Scaevius is the sister group of Pentapodus and they together are sister to Nemipterus. These three genera combined to form the sister group of the clade comprising Parascolopsis and Scolopsis. The validity of most of the examined species was confirmed except in some cases. The combined evidence from the results of different analyses revealed a gap in our existing knowledge of species diversity in the Nemipteridae. We found several currently recognized species contain multiple separately evolving metapopulation lineages within species; some lineages should be considered as new species for further assignment. Finally, some problematic sequences deposited in public databases (probably due to misidentification) were also revised in this study to improve the accuracy for prospective DNA barcoding work on nemipterid fishes.     

浙江省温岭海区虾类资源调查

于1999－2001年间对温岭海区虾类进行了调查,调查表明,该海区计有虾24种,分属7科16属。其中,对虾科8种12种;樱虾科1属2种;玻璃虾科1属1种;鼓虾科1属3种;长臂虾科2属3种;藻虾科2属2种;龙虾科1属1种。对该海区的虾类资源作了评价,并提出了资源开发保护的建议。     

Cryptic species in the Neotropical fish genus Curimatopsis (Teleostei,Characiformes)

Detritivores of the fish family Curimatidae are assigned to eight genera, one of which, the Curimatopsis, with only five species, is the least speciose genus and sister to other seven genera in the family. Ongoing morphological investigations reveal, however, the likely existence of additional species. In this study, fifty‐one specimens of Curimatopsis from multiple rivers of the Amazon, Paraguay and Suriname drainages were identified morphologically according to the present species concepts and then barcoded using the universal cytochrome c oxidase subunit I (COI) mitochondrial marker. Species delimitation analyses were conducted using Bayesian methods through the general mixed Yule‐coalescent analysis combined with conventional likelihood, genetic distance and haplotypic diversity approaches. We found eleven well‐supported clusters that represent four of the named species and seven cryptic, undescribed species of Curimatopsis. Our results show a clear delimitation of species boundaries constrained by distinct Amazonian river ecotones that may have promoted intrageneric lineage diversification. This is the first of a series of genetic studies applicable to future taxonomic, phylogenetic and evolutionary studies across the Curimatidae.     

A molecular phylogeny of marine amphipods in the herbivorous family Ampithoidae

Ampithoid amphipods dominate invertebrate assemblages associated with shallow‐water macroalgae and seagrasses worldwide and represent the most species‐rich family of herbivorous amphipod known. To generate the first molecular phylogeny of this family, we sequenced 35 species from 10 genera at two mitochondrial genes [the cytochrome c oxidase subunit I (COI) and the large subunit of 16 s (LSU)] and two nuclear loci [sodium–potassium ATPase (NAK) and elongation factor 1‐alpha (EF1)], for a total of 1453 base pairs. All 10 genera are embedded within an apparently monophyletic Ampithoidae (Amphitholina, Ampithoe, Biancolina, Cymadusa, Exampithoe, Paragrubia, Peramphithoe, Pleonexes, Plumithoe, Pseudoamphithoides and Sunamphitoe). Biancolina was previously placed within its own superfamily in another suborder. Within the family, single‐locus trees were generally poor at resolving relationships among genera. Combined‐locus trees were better at resolving deeper nodes, but complete resolution will require greater taxon sampling of ampithoids and closely related outgroup species, and more molecular characters. Despite these difficulties, our data generally support the monophyly of Ampithoidae, novel evolutionary relationships among genera, several currently accepted genera that will require revisions via alpha taxonomy and the presence of cryptic species.     

Mating behavior,spawning, parental care,and embryonic development of some marine pseudocerotid flatworms (Platyhelminthes: Rhabditophora: Polycladida) in Singapore

The reproductive biology of tropical marine cotylean polyclads is presently poorly known. Reproductive aspects of 16 polyclad species from the family Pseudocerotidae in the genera Acanthozoon, Nymphozoon, Phrikoceros, Pseudobiceros, Pseudoceros, Thysanozoon, and Tytthosoceros from Singapore were documented for the first time. Penis fencing was observed to be just a mating ritual and not necessary for insemination, not always aggressive, and could also result in eventual reciprocal insemination. Results showed that all species underwent similar embryonic developmental stages and hatched as Müller's larvae. Only Pseudoceros concinnus and Pseudoceros laingensis, with mean developmental times of >20 days and mean brood sizes of <1,000 eggs, displayed long‐term parental care. Polyclads producing larger brood sizes had shorter developmental times and only covered their egg masses for about one day. Phrikoceros baibaiye and Pseudobiceros spp. produced egg capsules with pointed opercula, whereas all other species possessed smooth, rounded opercula. All genera hatched with brownish‐orange larvae, except for Pseudoceros spp., which hatched with reddish‐purple larvae regardless of the initial embryo color (either grayish‐yellow or reddish‐purple). These could potentially complement current taxonomic characters in distinguishing polyclad genera and species.     

A Molecular Phylogenetic Investigation of Bakuella,Anteholosticha, and Caudiholosticha (Protista,Ciliophora, Hypotrichia) Based on Three‐Gene Sequences

Traditionally classifications of the Urostyloida have been mainly based on morphology and morphogenesis. Recent molecular phylogenetic analyses have been largely based on single‐gene data for a limited number of taxa. Consequently, incongruence has arisen between the morphological/morphogenetic and the molecular data. In this study, the three phylogenetic markers (SSU rDNA, ITS1‐5.8S‐ITS2 region, and LSU‐rDNA) of three urostyloid genera represented by four species (Bakuella granulifera, Anteholosticha monilata, Caudiholosticha sylvatica, and C. tetracirra) were sequenced to investigate their phylogeny. The results show that: (1) all three genera should be regarded as the members of the order Urostyloida within the subclass Hypotrichia, as indicated by morphological characters; (2) phylogenetic analyses and sequence similarities both indicate that neither Anteholosticha nor Caudiholosticha are monophyletic and the systematic assignment of both genera awaits further evaluation; and (3) Bakuella has a closer relationship with Urostyla than with bakuellids (e.g. Apobakuella and Metaurostylopsis), suggesting Bakuella may belong to the family Urostylidae rather than the family Bakuellidae.     

Les Lagomerycidae (Artiodactyla, Mammalia) de FranceThe French Lagomerycidae (Cervoidea, Artiodactyla, Mammalia)

The Lagomerycidae, a small family of the Cervoidea, is known in France by the genera Lagomeryx, Ligeromeryx and Stephanocemas. Lagomeryx contains three species, the other two genera one species only. This family is known from MN3 to MN5.     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

Comparative morphology,biology and phylogeny of terminal‐instar larvae of the European species of Toryminae (Hym., Chalcidoidea,Torymidae) parasitoids of gall wasps (Hym. Cynipidae)

We present a phylogenetic and taxonomic study of the morphology and biology of the terminal‐instar larval stage of 19 species representing all the genera of Torymidae parasitoids of gall wasps in Europe, with the single exception of Megastigmus. The genera studied include Adontomerus Nikol'skaya, Idiomacromerus Crawford, Chalcimerus Steffan & Andriescu, Glyphomerus Förster, Pseudotorymus Masi and Torymus Dalman. We primarily used chaetotaxy and some head structures. The terminal‐instar larvae of all studied species are thoroughly described for the first time and illustrated with SEM images. We provide diagnostic characters for the family and the genera studied, and keys to genera and species for the identification of torymid larvae associated with cynipid galls. The majority of the torymid larvae studied are solitary monophagous parasitoids. Finally, to assess the potential use of larval characters in systematic studies of the family, a phylogenetic analysis of the studied taxa based on 42 larval morphological characters is proposed and compared with the current taxonomy of Torymidae. Our results suggest that body chaetotaxy, and characters of the head and mouthparts could be used for genera and species discrimination. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 676–721.     

Trans‐Atlantic,trans‐Pacific and trans‐Indian Ocean dispersal in the small Gondwanan Laurales family Hernandiaceae

Aim To investigate the historical biogeography of the pantropical flowering plant family Hernandiaceae (Laurales), which today comprises 62 species in five genera. Location Hernandiaceae occur in Africa (9 species), Madagascar (4), the Neotropics (25), Australia (3), southern China, Indochina, Malesia, and on numerous Pacific Islands (32). These numbers include two widespread species, Hernandia nymphaeifolia, which ranges from East Africa to the Ogasawara Islands and New Caledonia, and Gyrocarpus americanus, thought to have a pantropical range. Methods We sampled 37 species from all genera, the widespread ones with multiple accessions, for a chloroplast DNA matrix of 2210 aligned nucleotides, and used maximum likelihood to infer species relationships. Divergence time estimation relied on an uncorrelated‐rates relaxed molecular clock calibrated with outgroup fossils of Lauraceae and Monimiaceae. Results The deepest split in the family is between a predominantly African–Madagascan–Malesian lineage comprising Hazomalania, Hernandia and Illigera, and an African–Neotropical lineage comprising Gyrocarpus and Sparattanthelium; this split may be 122 (110–134) Myr old. The stem lineages of the five genera date back at least to the Palaeocene, but six splits associated with transoceanic range disjunctions date only to the Oligocene and Miocene, implying long‐distance dispersal. It is inferred that Hernandia beninensis reached the West African islands of São Tomé and Bioko from the West Indies or the Guianas; Hernandia dispersed across the Pacific; and Illigera madagascariensis reached Madagascar from across the Indian Ocean. Main conclusions The disjunct ranges and divergence times of sister clades in the Hernandiaceae are partly congruent with the break‐up of West Gondwana, but mostly with later transoceanic dispersal. An exceptional ability to establish following prolonged oceanic dispersal may be largely responsible for the evolutionary persistence of this small clade.     

Historical biogeography and cryptic diversity in the Callichthyinae (Siluriformes,Callichthyidae)

The family Callichthyidae, divided into the subfamilies Corydoradinae and Callichthyinae, contains more than 200 species of armoured catfishes distributed throughout the Neotropics, as well as fossil species dating from the Palaeocene. Both subfamilies are very widely distributed throughout the continent, with some species ranges extending across multiple hypothesized biogeographical barriers. Species with such vast geographical ranges could be made up of multiple cryptic populations that are genetically distinct and have diverged over time. Although relationships among Callichthyinae genera have been thoroughly investigated, the historical biogeography of the Callichthyinae and the presence of species complexes have yet to be examined. Furthermore, there is a lack of fossil‐calibrated molecular phylogenies providing a time frame for the evolution of the Callichthyinae. Here, we present a novel molecular data set for all Callichthyinae genera composed of partial sequences of mitochondrial and nuclear markers. These data were used to construct a fossil‐calibrated tree for the Callichthyinae and to reconstruct patterns of spatiotemporal evolution. All phylogenetic analyses [Bayesian, maximum likelihood and maximum parsimony (MP)] resulted in a single fully resolved and well‐supported hypothesis for the Callichthyinae, where Dianema is the sister group of all the remaining genera. Results suggest that the ancestry of most Callichthyinae genera originated in the Amazonas basin, with a number of subsequent ancestral dispersal events between adjacent basins. High divergences in sequences and time were observed for several samples of Hoplosternum littorale, Megalechis picta and Callichthys callichthys, suggesting that these species may contain cryptic diversity. The results highlight the need for a taxonomic revision of species complexes within the Callichthyinae, which may reveal more diversity within this relatively species‐poor lineage.     

Phylogenetic relationships within Nephtyidae (Polychaeta,Annelida)

Ravara, A., Wiklund, H., Cunha, M. R. & Pleijel, F. (2010). Phylogenetic relationships within Nephtyidae (Polychaeta, Annelida). —Zoologica Scripta, 39, 394–405. We present the first phylogeny of nephtyids, a common, soft‐bottom living polychaete family comprising five genera and over 100 species. Characters used to distinguish nephtyid genera are a matter of controversy and considerable confusion remains as to the generic delineations. The phylogeny is estimated with molecular data from the mitochondrial genes cytochrome oxidase I and 16S rDNA, the nuclear genes 18S rDNA and 28S rDNA and morphological data. The results reveal two well‐supported major clades, corresponding in part to the two main genera of the family, Aglaophamus and Nephtys. The species Nephtys pulchra and Nephtys australiensis are transferred to Aglaophamus, and new diagnoses for the genera are provided. Dentinephtys is synonymized with Nephtys, and Nephtys cornuta is sister to the remaining nephtyids and is referred to the new genus Bipalponephtys, together with Nephtys danida and Micronephthys neotena. Micronephthys is sister to Nephtys and Inermonephtys is of uncertain position.     

The evolution of euhermaphroditism in caridean shrimps: a molecular perspective of sexual systems and systematics

Background  

The hippolytid genus Lysmata is characterized by simultaneous hermaphroditism, a very rare sexual system among Decapoda. Specialized cleaning behavior is reported in a few pair-living species; these life history traits vary within the genus. Unfortunately, the systematics of Lysmata and the Hippolytidae itself are in contention, making it difficult to examine these taxa for trends in life history traits. A phylogeny of Lysmata and related taxa is needed, to clarify their evolutionary relationships and the origin of their unique sexual pattern. In this study, we present a molecular phylogenetic analysis among species of Lysmata, related genera, and several putative hippolytids. The analysis is based upon DNA sequences of two genes, 16S mtDNA and nuclear 28S rRNA. Phylogenetic trees were estimated using Bayesian Inference, Maximum Likelihood, and Maximum Parsimony.     

Molecular and morphological characterization of a poorly known marine ciliate, Myoschiston duplicatum precht 1935: implications for phylogenetic relationships between three morphologically similar genera -- Zoothamnium, Myoschiston, and Zoothamnopsis (Ciliophora, Peritrichia, Zoothamniidae)

We studied the morphology and molecular phylogeny of Myoschiston duplicatum, a peritrich ciliate that has been recorded as an epibiont of crustaceans, but which we also identified on marine algae from Korea. The important morphological characteristics revealed by silver staining of Myoschiston species have not been described because they are rarely collected. Using morphological methods, we redescribed the type species of the genus, Myoschiston duplicatum, and provided an improved diagnosis of Myoschiston. In addition, the coding regions for nuclear small subunit (SSU) rRNA and internal transcribed spacer 1‐5.8S‐internal transcribed spacer 2 sequences were sequenced. Phylogenetic analyses that included available SSU rDNA sequences of peritrichs from GenBank strongly supported a position of M. duplicatum within the family Zoothamniidae. In addition, phylogenetic analyses were performed with single datasets (ITS1‐5.8S‐ITS2) and combined datasets (SSU rDNA + ITS1‐5.8S‐ITS2) to explore further the phylogenetic relationship in the family Zoothamniidae between the three morphologically similar genera—Zoothamnium, Myoschiston, and Zoothamnopsis.     

Multi‐locus phylogeny of African pipits and longclaws (Aves: Motacillidae) highlights taxonomic inconsistencies

The globally distributed avian family Motacillidae consists of five to seven genera (Anthus, Dendronanthus, Tmetothylacus, Macronyx and Motacilla, and depending on the taxonomy followed, Amaurocichla and Madanga) and 66–68 recognized species, of which 32 species in four genera occur in sub‐Saharan Africa. The taxonomy of the Motacillidae has been contentious, with variable numbers of genera, species and subspecies proposed and some studies suggesting greater taxonomic diversity than currently recognized (five genera and 67 species). Using one nuclear (Mb) and two mitochondrial (cyt b and CO1) gene regions amplified from DNA extracted from contemporary and museum specimens, we investigated the taxonomic status of 56 of the currently recognized motacillid species and present the most taxonomically complete and expanded phylogeny of this family to date. Our results suggest that the family comprises six clades broadly reflecting continental distributions: sub‐Saharan Africa (two clades), the New World (one clade), Palaearctic (one clade), a widespread large‐bodied Anthus clade, and a sixth widespread genus, Motacilla. Within the Afrotropical region, our phylogeny further supports recognition of Wood Pipit Anthus nyassae as a valid species, and the treatment of Long‐tailed Pipit Anthus longicaudatus and Kimberley Pipit Anthus pseudosimilis as junior subjective synonyms of Buffy Pipit Anthus vaalensis and African Pipit Anthus cinnamomeus, respectively. As the disjunct populations of Long‐billed Pipit Anthus similis in southern and East Africa are genetically distinct and geographically separated, we propose a specific status for the southern African population under the earliest available name, Nicholson's Pipit Anthus nicholsoni. Further, as our analyses indicate that Yellow‐breasted Pipit Anthus chloris and Golden Pipit Tmetothylacus tenellus are both nested within the Macronyx longclaws, we propose transferring these species to the latter genus.     

Juraphididae,a new family of aphids and its significance in aphid evolution

A revision of the Jurassic aphid family Genaphididae revealed that the type genus Genaphis did not have the characteristics usually attributed to this family. This discovery led to a series of taxonomic decisions. The diagnosis of the family Genaphididae is emended. The genera Aphaorus, Juraphis and Pterotella are moved to the Juraphididae, fam.n. The new family is included in the superfamily Palaeoaphidoidea. Additionally, two new species, Juraphis karataviensis sp.n. and Pterotella shartegensis sp.n. , are described. Phylogenetic relationships among the taxa of Juraphididae, the position of the family, and the distribution and palaeoecology of the taxa are discussed. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:411C1D8C‐AA45‐4311‐AA2D‐4469E44B6EDF .     

A phylogeny reconstruction of the Dendrophylliidae (Cnidaria,Scleractinia) based on molecular and micromorphological criteria,and its ecological implications

Recent molecular phylogenetic studies have shown that most traditional families of zooxanthellate shallow‐water scleractinians are polyphyletic, whereas most families mainly composed of deep‐sea and azooxanthellate species are monophyletic. In this context, the family Dendrophylliidae (Cnidaria, Scleractinia) has unique features. It shows a remarkable variation of morphological and ecological traits by including species that are either colonial or solitary, zooxanthellate or azooxanthellate, and inhabiting shallow or deep water. Despite this morphological heterogeneity, recent molecular works have confirmed that this family is monophyletic. Nevertheless, what so far is known about the evolutionary relationships within this family, is predominantly based on skeleton macromorphology, while most of its species have remained unstudied from a molecular point of view. Therefore, we analysed 11 dendrophylliid genera, four of which were investigated for the first time, and 30 species at molecular, micromorphological and microstructural levels. We present a robust molecular phylogeny reconstruction based on two mitochondrial markers (COI and the intergenic spacer between COI and 16S) and one nuclear (rDNA), which is used as basis to compare micromorphogical and microstructural character states within the family. The monophyly of the Dendrophylliidae is well supported by molecular data and also by the presence of rapid accretion deposits, which are ca. 5 μm in diameter and arranged in irregular clusters, and fibres that thicken the skeleton organized in small patches of a few micrometres in diameter. However, all genera represented by at least two species are not monophyletic, Tubastraea excluded. They were defined by traditional macromorphological characters that appear affected by convergence, homoplasy and intraspecific variation. Micromorphogical and microstructural analyses do not support the distinction of clades, with the exception of the organization of thickening deposits for the Tubastraea clade.     

British Bryological Society Expedition to Mulanje Mountain,Malawi. 17 Sematophyllaceae (Bryopsida): Part 1

Abstract

The family Sematophyllaceae is a difficult family to treat in Africa because of the large number of species described without any subsequent revision or monography and, despite the many collections mentioned in this paper, only two species had previously been identified from Malawi. A total of four species in four genera (Gammiella, Mρacrohymenium, Radulina and Wijkia) are recorded in this paper, all but one new to Malawi. The two remaining genera (Sematophyllum and Trichosteleum) present additional difficulties of identification, and will be dealt with separately.     

Isolation and identification of Rhizoctonia-like fungi from roots of three orchid genera, Paphiopedilum, Dendrobium, and Cymbidium, collected in Chiang Rai and Chiang Mai provinces of Thailand

Three orchid genera, Paphiopedilum, Cymbidium, and Dendrobium, are among the most heavily traded ornamental plants in Thailand. In this study, 27 isolates of Rhizoctonia-like fungi were isolated from root sections of mature orchids in the three orchid genera, collected from diverse horticultural settings in Chiang Mai and Chiang Rai provinces of Thailand. Fungal identification was done by the morphological characterization, the comparison of the internal transcribed spacer and 5.8S ribosomal DNA sequences, and the phylogenetic analysis. Epulorhiza repens was found to be the most common species found in the roots of various species of all three orchid genera, whereas Epulorhiza calendulina-like isolates were strictly found in the roots of Paphiopedilum species. We have also isolated and described an anamorph of Tulasnella irregularis, four new anamorphic species in the genus Tulasnella, and a new anamorphic species in the family Tulasnellaceae. Our study provides information on diversity of root-associated fungi of the orchid genera and at the sampling sites that were rarely addressed in the previous studies.