Taxonomic revision of the dolphin genus Lagenorhynchus

Evolutionary relationships among cetaceans within the family Delphinidae have been difficult to resolve due to the high number of species and their relatively rapid radiation. This is the case for the dolphin species currently placed in the genus Lagenorhynchus, and their relations to Cephalorhynchus and Lissodelphis species. Phylogenetic relationships among these species have been investigated using multiple lines of evidence, and that evidence consistently suggests that the six species currently assigned to Lagenorhynchus do not form a monophyletic group. Here, we summarize findings from studies of morphology, genetics, historical biogeography, and acoustics that offer insight into the phylogenetics of these taxa. We present the taxonomic basis for revision of Lagenorhynchus, propose retention of Lagenorhynchus albirostris and reassignment of the remaining five species into other existing generic names, namely Leucopleurus acutus, Sagmatias australis, Sagmatias cruciger, Sagmatias obliquidens, and Sagmatias obscurus. Making these revisions now so that the taxonomy better reflects evolutionary relationships among these species will ensure that future studies include the most appropriate taxa for investigating the complex phylogenetic and systematic relationships among cetaceans. However, comprehensive analyses using multiple lines of evidence are still needed to clarify the phylogenetic relationships within and among the Lissodelphininae genera Cephalorhynchus, Lissodelphis, and Sagmatias.     

Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution

Background  

Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relationships were poorly resolved. In this study, we present a combined-analysis phylogenetic hypothesis for Lagenorhynchus and members of the subfamily Lissodelphininae, which is derived from two nuclear and two mitochondrial data sets and the addition of 34 individuals representing 9 species. In addition, we characterize with parsimony and Bayesian analyses the phylogenetic utility and interaction of characters with statistical measures, including the utility of highly consistent (non-homoplasious) characters as a conservative measure of phylogenetic robustness. We also explore the effects of removing sources of character conflict on phylogenetic resolution.     

POLYPHYLY OF THE BLACKBIRD GENUS AGELAIUS AND THE IMPORTANCE OF ASSUMPTIONS OF MONOPHYLY IN COMPARATIVE STUDIES

A phylogeny for Agelaius blackbirds was constructed using sequence data from an 890 base-pair (bp) region of the mitochondrial cytochrome-b gene in nine species of Agelaius and a single species from all but 1 of the 28 described blackbird genera and subgenera. The genus was found to be polyphyletic with the South American members of Agelaius more closely related to other South American blackbird genera. Application of bootstrap and jackknife manipulations supports this conclusion. That this relatively well-known genus is polyphyletic represents a warning to those attempting to construct phylogenies without first demonstrating monophyly of the ingroup. The conclusion that Agelaius is polyphyletic necessitates (1) the reinterpretation of previous studies that assumed monophyly and (2) the initiation of a variety of new comparative behavioral and ecological studies suggested by this finding.     

Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA

Following taxonomic revisions in recent years, the originally large family Grapsidae MacLeay, 1838 has become a relatively small and morphologically homogeneous family in terms of adult and larval morphology. Most available molecular studies including more than one genus of the family have also suggested monophyly of the corresponding taxa. However, no single phylogenetic study has ever included all constituent genera of the Grapsidae. In the current study, a molecular phylogeny based on sequences of the mitochondrial 16S rRNA gene from all eight grapsid genera and 34 species is presented and suggests that up to four genera are not monophyletic. This is mainly due to the polyphyletic nature of the genus Pachygrapsus which can be found in six different lineages of the phylogeny, suggesting that the genus currently does not represent a single evolutionary lineage and is in need of taxonomic revision. Amphi-atlantic and trans-isthmian species pairs or populations in four genera are compared and reveal relatively constant and pronounced divergences across the Panama Isthmus as opposed to moderate divergences across the Atlantic Ocean, thereby suggesting occurrence of gene flow across the Atlantic Ocean during the past three million years.     

Phylogeny,classification and evolution of the water scavenger beetle tribe Hydrobiusini inferred from morphology and molecules (Coleoptera: Hydrophilidae: Hydrophilinae)

The water scavenger beetle tribe Hydrobiusini contains 47 species in eight genera distributed worldwide. Most species of the tribe are aquatic, although several species are known to occur in waterfalls or tree mosses. Some members of the tribe are known to communicate via underwater stridulation. While recent morphological and molecular‐based phylogenies have affirmed the monophyly of the tribe as currently circumscribed, doubts remain about the monophyly of included genera. Here we use morphological and molecular data to infer a species‐level phylogeny of the Hydrobiusini. The monophyly of the tribe is decisively supported, as is the monophyly of most genera. The genus Hydrobius was found to be polyphyletic, and as a result the genus Limnohydrobius stat. rev. is removed from synonymy with Hydrobius, yielding three new combinations: L. melaenus comb.n. , L. orientalis comb.n. , and L. tumbius comb.n. Recent changes to the species‐level taxonomy of Hydrobius are reviewed. The morphology of the stridulatory apparatus has undergone a single remarkable transformation within the lineage, from a simple, unmodified pars stridens to one that is highly organized and complex. We present an updated key to genera, revised generic diagnoses and a list of the known distributions for all species within the tribe.     

Comparative seed morphology of <Emphasis Type="Italic">Leandra</Emphasis> (Miconieae,Melastomataceae)

The seed morphology of 79 species of neotropical Miconieae (Melastomataceae) is presented. These species have been chosen, in majority, from the polyphyletic genus Leandra. A few other species from the polyphyletic genera Miconia, Ossaea, and Clidemia were also sampled, because of potential similarities. Sixteen morphological seed types are defined after analysis through light microscopy and scanning electron microscopy. The seed morphology appears to possess a great deal of variability on the level of the overall shape as well as the structure and the surface of the testa. The different types defined here do not match with genera or sections, but rather are composed of species coming from different genera. In comparison with a preliminary molecular phylogeny study done on Leandra, some types of seeds are related to well supported clades. In some cases seed morphology corresponds with natural groups of species, thus being of high phylogenetic importance.     

Molecular phylogeny of Moenkhausia (Characidae) inferred from mitochondrial and nuclear DNA evidence

Moenkhausia is one of the most speciose genera in Characidae, currently composed of 75 nominal species of small fishes distributed across South American hydrographic basins, primarily the Amazon and Guyanas. Despite the large number of described species, studies involving a substantial number of its species designed to better understand their relationships and putative monophyly are still lacking. In this study, we analysed a large number of species of Moenkhausia to test the monophyly of the genus based on the phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes. The in‐group included 29 species of Moenkhausia, and the out‐group was composed of representatives of Characidae and other members of Characiformes. All species of Moenkhausia belong to the same clade (Clade C); however, they appear distributed in five monophyletic groups along with other different genera, which means that Moenkhausia is polyphyletic and indicates the necessity of an extensive revision of the group.     

The demise of Leptotheca Thélohan, 1895 (Myxozoa: Myxosporea: Ceratomyxidae) and assignment of its species to Ceratomyxa Thélohan, 1892 (Myxosporea: Ceratomyxidae), Ellipsomyxa K?ie, 2003 (Myxosporea: Ceratomyxidae), Myxobolus Bütschli, 1882 and Sphaerospora Thélohan, 1892 (Myxosporea: Sphaerosporidae)

A revision of Leptotheca Thélohan, 1895 is presented. The boundaries that separate Leptotheca from Ceratomyxa Thélohan, 1892 and Sphaerospora Thélohan, 1892 are vague and have been highlighted as an area of concern within myxosporean classification. A survey of the literature revealed 63 species that are currently assigned to Leptotheca and a further 11 species that have been relegated as synonyms in Ceratomyxa, Sphaerospora or Myxobolus Bütschli, 1882. The placement of some species in the genus is unclear and demonstrates the need for a revision. The type-species of Leptotheca (L. agilis Thélohan 1892) has many Ceratomyxa-like characters, such that a minor amendation of the diagnosis of Ceratomyxa will then accept the type-species of Leptotheca, rendering the latter genus its synonym. We propose the suppression of Leptotheca, with all species currently assigned to that genus reassigned to Ceratomyxa, Ellipsomyxa K?ie, 2003, Myxobolus or Sphaerospora on the basis of appropriate morphological and biological traits. The diagnoses of Ceratomyxa and Ellipsomyxa are amended appropriately. Molecular analysis may change the placement of some species in the future; however, the aim of this review was to eliminate the ambiguity of assignment of species in the genera Leptotheca, Ceratomyxa and Sphaerospora by suppressing Leptotheca.     

Evolutionary implications of a rRNA-based phylogeny of Harpellales

The Harpellales (Trichomycetes) are endosymbiotic microfungi, mostly unculturable and predominantly associated with larval aquatic insects worldwide. Molecular phylogenies including ‘gut fungi’ have included at most only four axenic isolates of the 38 genera of Harpellales. Cladistic analyses were used to infer the phylogeny of the Harpellales using partial 18S or 28S nu-rRNA sequences generated for 16 genera of Harpellales, with 64 of 72 sequences generated from unculturable samples. Both analyses placed Orphella outside an otherwise monophyletic group of Harpellales, more closely allied to the Kickxellales. The current classification recognizing two families is not corroborated and continued use of the family Legeriomycetaceae may not be supportable. The largest genera of Harpellales, Smittium and Stachylina, were polyphyletic and the 28S rRNA sequences separate Smittium culisetae from the remainder of its genus. The cladograms did not support the consistent mapping of important morphological taxonomic characters, including trichospore shape and zygospore type or appendage numbers for both. This study demonstrates the use of microscopic thalli from host guts for molecular phylogenies and suggests the need for more data from the remaining Harpellales, especially with the future inclusion of protein-coding genes.     

Ptolemeba n. gen., a Novel Genus of Hartmannellid Amoebae (Tubulinea,Amoebozoa); with an Emphasis on the Taxonomy of Saccamoeba

Hartmannellid amoebae are an unnatural assemblage of amoeboid organisms that are morphologically difficult to discern from one another. In molecular phylogenetic trees of the nuclear‐encoded small subunit rDNA, they occupy at least five lineages within Tubulinea, a well‐supported clade in Amoebozoa. The polyphyletic nature of the hartmannellids has led to many taxonomic problems, in particular paraphyletic genera. Recent taxonomic revisions have alleviated some of the problems. However, the genus Saccamoeba is paraphyletic and is still in need of revision as it currently occupies two distinct lineages. Here, we report a new clade on the tree of Tubulinea, which we infer represents a novel genus that we name Ptolemeba n. gen. This genus subsumes a clade of hartmannellid amoebae that were previously considered in the genus Saccamoeba, but whose mitochondrial morphology is distinct from Saccamoeba. In accordance with previous research, we formalize the clade as distinct from Saccamoeba. Transmission electron microscopy of our isolates illustrate that both molecularly discrete species can be further differentiated by their unique mitochondrial cristal morphology.     

Toward Modern Classification of Eustigmatophytes,Including the Description of Neomonodaceae Fam. Nov. and Three New Genera1

The class Eustigmatophyceae includes mostly coccoid, freshwater algae, although some genera are common in terrestrial habitats and two are primarily marine. The formal classification of the class, developed decades ago, does not fit the diversity and phylogeny of the group as presently known and is in urgent need of revision. This study concerns a clade informally known as the Pseudellipsoidion group of the order Eustigmatales, which was initially known to comprise seven strains with oval to ellipsoidal cells, some bearing a stipe. We examined those strains as well as 10 new ones and obtained 18S rDNA and rbcL gene sequences. The results from phylogenetic analyses of the sequence data were integrated with morphological data of vegetative and motile cells. Monophyly of the Pseudellipsoidion group is supported in both 18S rDNA and rbcL trees. The group is formalized as the new family Neomonodaceae comprising, in addition to Pseudellipsoidion, three newly erected genera. By establishing Neomonodus gen. nov. (with type species Neomonodus ovalis comb. nov.), we finally resolve the intricate taxonomic history of a species originally described as Monodus ovalis and later moved to the genera Characiopsis and Pseudocharaciopsis. Characiopsiella gen. nov. (with the type species Characiopsiella minima comb. nov.) and Munda gen. nov. (with the type species Munda aquilonaris) are established to accommodate additional representatives of the polyphyletic genus Characiopsis. A morphological feature common to all examined Neomonodaceae is the absence of a pyrenoid in the chloroplasts, which discriminates them from other morphologically similar yet unrelated eustigmatophytes (including other Characiopsis-like species).     

Phylogenetic status and timescale for the diversification of Steno and Sotalia dolphins

Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the phylogenetic placement of Sotalia and Steno within the Delphinidae, we sequenced three new delphinid mitogenomes. Our analyses support three delphinid clades: one joining Steno and Sotalia (supporting the revised subfamily Stenoninae); another placing Sousa within the Delphininae; and a third, the Globicephalinae, which includes Globicephala, Feresa, Pseudorca, Peponocephala and Grampus. We also conclude that Orcinus does not belong in the Globicephalinae, but Orcaella may be part of that subfamily. Divergence dates were estimated using the relaxed molecular clock calibrated with fossil data. We hypothesise that the timing of separation of the marine and Amazonian Sotalia species (2.3 Ma) coincided with the establishment of the modern Amazon River basin.     

Phylogenetic analysis of the New World Ptininae (Coleoptera: Bostrichoidea)

A phylogenetic analysis of the New World Ptininae (Anobiidae) was conducted with representatives of nine of ten New World genera, several Old World genera and seven more of the ten subfamilies of Anobiidae. One hundred and two characters (forty‐three multistate) from thirty‐four taxa were used. The single cladogram shows Ptininae as monophyletic and the sister group of the remaining Anobiidae, supporting their placement as subfamilies of a monophyletic Bostrichidae. Genus Niptus Boieldieu is polyphyletic supporting recognition of Pseudeurostus Heyden and the creation of a new genus to encompass the remaining New World species of Niptus. Flightlessness has evolved a minimum of three times within Ptininae and myrmecophily has probably evolved three times within just the New World taxa. The classifications of Ptininae and the remaining Anobiidae are examined and the evolution of feeding habits, myrmecophily and wing loss are discussed.     

Evaluating the utility of cox1 for cetacean species identification

The mitochondrial cytochrome c oxidase I (cox1) gene has been promoted as a universal reference gene, or barcode, to identify organisms to the species level. We evaluated whether cox1 would be appropriate to diagnose cetacean species. The 5′ end of cox1 (686 base pairs, bp) was sequenced for 46 of 86 recognized species of cetaceans. In addition, we included 105 sequences from GenBank, increasing our taxonomic coverage to 61 species. Particular focus was placed on sampling two subfamilies that contain closely related taxa: the Delphininae and the Globicephalinae. Species‐specific sequences were observed for all but three taxa (Delphinus delphis, D. capensis, and Stenella coeruleoalba). Although correct assignment was seen for most species, significant overlap between intra‐ and interspecific variation makes cox1 an imperfect barcode for cetaceans. The efficacy of cox1 was compared to the 5′ end of the cytochrome b (cytb) gene, a mitochondrial region routinely used for cetacean species identification. Although cytb performed better than cox1 for some species, this marker could not differentiate other closely related taxa (Eubalaena spp.). Species identification for taxa not reliably identified using cox1 or cytb might be best addressed through use of multiple mitochondrial DNA fragments or other newly developed markers.     

Molecular Systematics of Threatened Seed Plant Species Endemic in the Caribbean Islands

A review of available Caribbean Island red-lists species (CR and EN categories based on the IUCN guidelines from 2001, and E category established according to the IUCN guidelines from 1980) is presented. A database of over 1,300 endemic species that are either Critically Endangered or Endangered sensu IUCN was created. There are molecular systematic studies available for 112 of them. Six of these species (in six genera) are the only members of early divergent lineages that are sister to groups composed of a large number of clades. Seven of the species (in seven genera) belong to clades that have a small number of taxa but are sister to species/genus-rich clades. Ten of the species (in six genera) are sister to taxa restricted to South America or nested in clades endemic to this region. Fifty-seven of the species (in 35 genera) are sister to Caribbean Island endemic species. Erigeron belliastroides, an Endangered (EN) Cuban endemic, is sister to the Galapagos genus Darwiniothamnus. The phylogenetic placement of four of the threatened species resulted in changes in their taxonomic placement; they belong to polyphyletic or paraphyletic genera.     

Ultrastructural observations on the spermatozoa of a species of <Emphasis Type="Italic">Lepidodasys</Emphasis> (Gastrotricha,Macrodasyida)

The ultrastructure of the spermatozoon of a species in the marine gastrotrich genus Lepidodasys is described. The filiform cell is composed of a cork-screw acrosome, a long single mitochondrion surrounded by a helical nucleus, and a flagellum with a 9 × 2 + 2 axonemal arrangement. The structure of the sperm of this species from Denmark appears closely similar to those of the other two species of Lepidodasys studied so far from Italy and Florida (US). Peculiar features (cylindrical nucleus, absence of a periaxonemal sheath) place this genus far from the others in the family Lepidodasyidae. The absence of synapomorphies between Lepidodasys and other genera of Lepidodasyidae suggests that the family is polyphyletic. The sperm ultrastructure fully fits the species of Lepidodasys into the marine order Macrodasyida, with the sperm ground plan of which its sperm shares a number of details.     

Molecular data to elucidate the taxonomy of Seseli sect. Seseli (Apiaceae) in east Mediterranean and southern Europe

The taxonomy of the type section of the genus Seseli is revised based on newly obtained molecular data. The type species of the genus, Seseli tortuosum, is shown to be a polyphyletic taxon and is split into two species: the western Mediterranean S. tortuosum and the eastern Mediterranean S. arenarium. The Turkish endemics S. hartvigii, S. serpentinum and S. andronakii, and the Transcaucasian S. grandivittatum form a complex of closely related species together with S. arenarium. The results of the molecular analysis confirm the specific rank of S. corymbosum, S. phrygium and S. paphlagonicum and the status of S. gummiferum as distinct from either of these three. The latter species is strictly endemic to Crimea and does not occur in Turkey.     

Phylogeny of Adramini (Diptera,Tephritidae) based on integrative evidence

Species of the tribe Adramini (Tephritidae: Trypetinae) are usually slender, and some specific species have eyes borne at the ends of their long stalks. This tribe is mainly distributed in the tropics and subtropics of the Afrotropical, Oriental and Australasian Regions; relatively few species occur in the Palearctic and Nearctic Regions. The phylogeny of the tribe Adramini is presented here based on analysis of morphological and molecular information (DNA sequences of nuclear 28S rDNA, mitochondrial COI and COII, and 16S rDNA genes) for its representative species in most genera. Three monophyletic groups (Adrama‐com‐group, Pelmatops‐com‐group and Dimeringophrys‐com‐group) were discovered in the combined morphological and molecular tree. The results showed moderate support for the monophyly of Adramini and strong support for most of its genera. However, Euphranta appears to be polyphyletic. Sapadrama, Celidodacus and Euphranta are basal taxon, and Coelopacidia, Soita and Trypanophion are closely related to the stalk‐eyed fruit flies (Pelmatops + Pseudopelmatops). A hypothesis regarding the morphology–function relationships for two main groups of Adramini (Adrama‐group and Pelmatops‐group) with different evolving probabilities is inferred. Sapadrama is proposed be removed from Adramini; a new genus, Ichneumonomacula Chen gen. n. and a new species Ichneumonmacula wangyongi Chen sp. n., are recognized and described, and a key to recognize the genera of Adramini around the world is provided.     

The phylogeny of Branchiobdellida (Annelida, Clitellata) assessed by sperm characters

Data on the spermatozoa of Branchiobdellida were taken from the published literature: sperm models of 25 species belonging to 13 different branchiobdellidan genera have been compared with the aim of supplying further evidences for a phylogenetic analysis of the group. The species considered were representative of all traditional branchiobdellidan families, excluding the monotypic Caridinophilidae. Branchiobdellidan spermatozoa are complex cells, thus it was possible to analyse the variation of 20 characters within the group. A parsimony analysis has yielded nine minimal trees, eight of which are very similar to one another. The main conclusions of the phylogenetic analysis are: (a) the monophyly of the taxon Branchiobdellida is confirmed; (b) the most speciose branchiobdellidan genus, Cambarincola is polyphyletic; (c) none of the traditional ‘families’ are supported; (d) the genus Branchiobdella is monophyletic, but the position of one species, B. kobayashi, albeit basal to the whole genus, is not resolved; (e) the other two genera analysed for which more than one species was available, Pterodrilus and Xironogiton, are monophyletic; (f) there seems to be a ‘trend’ in the whole group towards an increase of acrosome length. Our results partly parallel those obtained by Gelder and Siddall (2000) with a combined analysis of molecular and somatic characters, and point to the need for a comprehensive revision of the Branchiobdellida based on a combination of molecular, somatic and spermatological data sets.