18S rDNA phylogeny of the Tubificidae (Clitellata) and its constituent taxa: dismissal of the Naididae

The phylogeny of the Tubificidae, and of most of its subfamilies and some of its genera, is revisited, on the basis of sequences of 18S ribosomal DNA in a selection of species. Forty-six new 18S sequences of Naididae (6), Tubificidae (37), Phreodrilidae (1), Lumbriculidae (1), and Enchytraeidae (1) are reported and aligned together with corresponding sequences of 21 previously studied taxa. The 18S gene of Insulodrilus bifidus provides the first molecular evidence that phreodrilids are closely related to tubificids, corroborating previous conclusions based on morphology. The data further support the monophyletic status of Tubificidae, provided that the "Naididae" is regarded a part of this family; "naidids" may not even constitute a monophyletic group. It is thus suggested that the family name Naididae is formally suppressed as a junior synonym of the Tubificidae. The 18S gene also resolves a number of relationships within the tubificids. Among the subfamilies, Tubificinae is supported, Rhyacodrilinae and Phallodrilinae are revealed as nonmonophyletic, and Limnodriloidinae remains unresolved. Most tubificid genera tested for monophyly are corroborated by the data, only one (Tubifex) is refuted, and two (Tubificoides and Limnodriloides) are unresolved from other taxa. It is concluded that it will be valuable to expand the taxonomic sampling for 18S rDNA in clitellates, and in annelids in general, as this is likely to improve the resolution at many levels. However, it will be equally important to combine the annelid 18S data with other gene sequences and nonmolecular characters, to estimate the phylogeny of these common and diverse worms with greater precision.     

Brassicaceae phylogeny and trichome evolution

To estimate the evolutionary history of the mustard family (Brassicaceae or Cruciferae), we sampled 113 species, representing 101 of the roughly 350 genera and 17 of the 19 tribes of the family, for the chloroplast gene ndhF. The included accessions increase the number of genera sampled over previous phylogenetic studies by four-fold. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the Shimodaira-Hasegawa test (S-H test) to compare the phylogenetic results with the most recent tribal classification for the family. The resultant phylogeny allowed a critical assessment of variations in fruit morphology and seed anatomy, upon which the current classification is based. We also used the S-H test to examine the utility of trichome branching patterns for describing monophyletic groups in the ndhF phylogeny. Our phylogenetic results indicate that 97 of 114 ingroup accessions fall into one of 21 strongly supported clades. Some of these clades can themselves be grouped into strongly to moderately supported monophyletic groups. One of these lineages is a novel grouping overlooked in previous phylogenetic studies. Results comparing 30 different scenarios of evolution by the S-H test indicate that five of 12 tribes represented by two or more genera in the study are clearly polyphyletic, although a few tribes are not sampled well enough to establish para- or polyphyly. In addition, branched trichomes likely evolved independently several times in the Brassicaceae, although malpighiaceous and stellate trichomes may each have a single origin.     

Reconstructing the phylogeny of the Sipuncula

Sipunculans are marine spiralian worms with possible close affinities to the Mollusca or Annelida. Currently 147 species, 17 genera, 6 families, 4 orders and 2 classes are recognized. In this paper we review sipunculan morphology, anatomy, paleontological data and historical affiliations. We have conducted cladistic analyses for two data sets to elucidate the phylogenetic relationships among sipunculan species. We first analyzed the relationships among the 45 species of Phascolosomatidea with representatives of the Sipunculidea as outgroups, using 35 morphological characters. The resulting consensus tree has low resolution and branch support is low for most branches. The second analysis was based on DNA sequence data from two nuclear ribosomal genes (18S rRNA and 28S rRNA) and one nuclear protein-coding gene, histone H3. Outgroups were chosen among representative spiralians. In a third analysis, the molecular data were combined with the morphological data. Data were analyzed using parsimony as the optimality criterion and branch support evaluated with jackknifing and Bremer support values. Branch support for outgroup relationships is low but the monophyly of the Sipuncula is well supported. Within Sipuncula, the monophyly of the two major groups, Phascolosomatidea and Sipunculidea is not confirmed. Of the currently recognized families, only Themistidae appears monophyletic. The Aspidosiphonidae, Phascolosomatidae and Golfingiidae would be monophyletic with some adjustments in their definition. The Sipunculidae is clearly polyphyletic, with Sipunculus nudus as the sister group to the remaining Sipuncula, Siphonosoma cumanense the sister group to a clade containing Siphonosoma vastumand the Phascolosomatidea, and Phascolopsis gouldi grouping within the Golfingiiformes, as suggested previously by some authors. Of the genera with multiple representatives, only Phascolosoma and Themiste are monophyletic as currently defined. We are aiming to expand our current dataset with more species in our molecular database and more detailed morphological studies.     

Polemoniaceae phylogeny and classification: implications of sequence data from the chloroplast gene ndhF

The chloroplast gene ndhF was used to study phylogenetic relationships of the Polemoniaceae at two levels: among members of the Ericales and among genera of the family. Sequence data for interfamilial analyses consisted of 2266 bp for 14 members of the Ericales, including four species of the Polemoniaceae, plus three outgroup taxa. The Polemoniaceae were found to be related to Diospyros, Fouquieria, the Primulales, Rhododendron, and Impatiens, but relationships among taxa were generally not well supported. The precise position of the Polemoniaceae within the Ericales remains obscure. Data for intrafamilial analyses consisted of 1031 bp for 27 species of the Polemoniaceae, including at least one species from most genera of the family, plus five outgroup taxa. A single most parsimonious tree was identified. The analyses suggested that subfamily Cobaeoideae, excluding Loeselia, is monophyletic and that Huthia is sister to Cantua. Acanthogilia was sister to the remainder of subfamily Cobaeoideae. Subfamily Polemonioideae plus Loeselia formed four subclades that were strongly supported as monophyletic and represent the major lineages of the subfamily.     

The phylogeny and classification of Embioptera (Insecta)

A phylogenetic analysis of the order Embioptera is presented with a revised classification based on results of the analysis. Eighty‐two species of Embioptera are included from all families except Paedembiidae Ross and Embonychidae Navás. Monophyly of each of the eight remaining currently recognized families is tested except Andesembiidae Ross, for which only a single species was included. Nine outgroup taxa are included from Blattaria, Grylloblattaria, Mantodea, Mantophasmatodea, Orthoptera, Phasmida and Plecoptera. Ninety‐six morphological characters were analysed along with DNA sequence data from the five genes 16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase I and histone III. Data were analysed in combined analyses of all data using parsimony and Bayesian optimality criteria, and combined molecular data were analysed using maximum likelihood. Several major conclusions about Embioptera relationships and classification are based on interpretation of these analyses. Of eight families for which monophyly was tested, four were found to be monophyletic under each optimality criterion: Clothodidae Davis, Anisembiidae Davis, Oligotomidae Enderlein and Teratembiidae Krauss. Australembiidae Ross was not recovered as monophyletic in the likelihood analysis in which one Australembia Ross species was recovered in a position distant from other australembiids. This analysis included only molecular data and the topology was not strongly supported. Given this, and because parsimony and the Bayesian analyses recovered a strongly supported clade including all Australembiidae, we regard this family also as monophyletic. Three other families – Notoligotomidae Davis, Archembiidae Ross and Embiidae Burmeister, as historically delimited – were not found to be monophyletic under any optimality criterion. Notoligotomidae is restricted here to include only the genus Notoligotoma Davis with a new family, Ptilocerembiidae Miller and Edgerly, new family, erected to include the genus Ptilocerembia Friederichs. Archembiidae is restricted here to include only the genera Archembia Ross and Calamoclostes Enderlein. The family group name Scelembiidae Ross is resurrected from synonymy with Archembiidae (new status) to include all other genera recently placed in Archembiidae. Embiidae is not demonstrably monophyletic with species currently placed in the family resolved in three separate clades under each optimality criterion. Because taxon sampling is not extensive within this family in this analysis, no changes are made to Embiidae classification. Relationships between families delimited herein are not strongly supported under any optimality criterion with a few exceptions. Either Clothodidae Davis (parsimony) or Australembiidae Ross (Bayesian) is the sister to the remaining Embioptera taxa. The Bayesian analysis includes Australembiidae as the sister to all other Embioptera except Clothididae, suggesting that each of these taxa is a relatively plesiomorphic representatative of the order. Oligotomidae and Teratembiidae are sister groups, and Archembiidae (sensu novum), Ptilocerembiidae, Andesembiidae and Anisembiidae form a monophyletic group under each optimality criterion. Each family is discussed in reference to this analysis, diagnostic combinations and taxon compositions are provided, and a key to families of Embioptera is included.     

Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

The cyprinid tribe Labeonini (sensuRainboth, 1991) is a large group of freshwater fishes containing around 40 genera and 400 species. They are characterized by an amazing diversity of modifications to their lips and associated structures. In this study, a total of 34 genera and 142 species of putative members of this tribe, which represent most of the generic diversity and more than one third of the species diversity of the group, were sampled and sequenced for four nuclear genes and five mitochondrial genes (totaling 9465bp). Phylogenetic relationships and subdivision of this tribe were investigated and the placement and status of most genera are discussed. Partitioned maximum likelihood analyses were performed based on the nuclear dataset, mitochondrial dataset, combined dataset, and the dataset for each nuclear gene. Inclusion of the genera Paracrossochilus, Barbichthys, Thynnichthys, and Linichthys in the Labeonini was either confirmed or proposed for the first time. None of the genera Labeo, Garra, Bangana, Cirrhinus, and Crossocheilus are monophyletic. Taxonomic revisions of some genera were made: the generic names Gymnostomus Heckel, 1843, Ageneiogarra Garman, 1912 and Gonorhynchus McClelland, 1839 were revalidated; Akrokolioplax Zhang and Kottelat, 2006 becomes a junior synonym of Gonorhynchus; the species Osteochilus nashii was found to be a member of the barbin genus Osteochilichthys. Five historical hypotheses on the classification of the Labeonini were tested and rejected. We proposed to subdivide the tribe, which is strongly supported as monophyletic, into four subtribes: Labeoina, Garraina, Osteochilina, and Semilabeoina. The taxa included in each subtribe were listed and those taxa that need taxonomic revision were discussed.     

Molecular phylogeny of the green lacewings (Neuroptera: Chrysopidae)

Abstract  The first quantitative analysis of phylogenetic relationships of green lacewings (Chrysopidae) is presented based on DNA sequence data. A single nuclear and two mitochondrial genes are used in the analysis: carbomoylphosphate synthase (CPS) domain of carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase (CAD) (i.e. rudimentary locus), large subunit ribosomal gene (16S) and cytochrome oxidase I (COI). This study represents the first use of the CAD gene to investigate phylogenetic relationships of the lacewings. DNA sequences for 33 chrysopid species from 18 genera, representing all subfamilies and tribes, were compared with outgroups sampled from families Hemerobiidae, Osmylidae and Polystoechotidae. Parsimony analyses of the combined data set recovered all of the previously established subfamilial and tribal groups as monophyletic clades (although relatively weakly supported) except Apochrysinae sensu lato . The enigmatic Nothancyla verreauxi Navás has historically been difficult to place in a subfamily group based on morphological characteristics; molecular data presented herein do not adequately resolve this problem.     

Molecular phylogeny of grapsoid crabs (Decapoda, Brachyura) and allies based on two mitochondrial genes and a proposal for refraining from current superfamily classification

Grapsoid and ocypodoid crabs receive a lot of attention in the literature due to their predominance and important role as primary and secondary consumers in intertidal as well as supratidal marine habitats. They are especially species‐rich in the tropics, where they have been found to repeatedly invade terrestrial and freshwater habitats. However, the systematics of the crabs belonging to these two superfamilies is still not settled, despite recent steps clarifying phylogenetic relationships and introducing new taxa. In this study, a molecular phylogeny of grapsoid crabs primarily based on East African representatives is constructed based on DNA sequences of the mitochondrial small and large ribosomal subunits (12S and 16S rRNA), thus complementing previous molecular taxonomic studies that had been carried out with the American and East Asian fauna. In addition, selected representatives of all ocypodoid families and subfamilies were included. The monophyly of Grapsidae, Ocypodidae (sensu stuctu), Sesarmidae and Varunidae is well confirmed, if the genera Cyclograpsus, Helice are considered Varunidae and Euchirograpsus a Plagusiidae, as previously suggested. The monophyly of the family Gecarcinidae cannot be supported with our data. The family Plagusiidae in its present composition is polyphyletic. Special attention was given to the large family Sesarmidae, which has many endemic genera in the Indo‐West Pacific. According to this study, two of the most speciose genera, Chiromantes and Parasesarma, are not monophyletic and need to be redefined. On the higher taxonomic level, it becomes evident that both superfamilies, Grapsoidea and Ocypodoidea, are not monophyletic in their current composition, as exemplified by a proposed sister group relationship of Varunidae and Macrophthalmidae. These results confirm those from previous molecular studies and we therefore propose to refrain from the traditional use of the Grapsoidea and Ocypodoidea as monophyletic superfamilies and treat the constituent families separately.     

Hylid frog phylogeny and sampling strategies for speciose clades

How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships. We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S). Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being > 90% incomplete. Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree. Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis. The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family. They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera. A new classification of hylid frogs is proposed. Several potentially misleading signals in the morphological data are discussed.     

Toward a global phylogeny of the Brassicaceae

The Brassicaceae is a large plant family (338 genera and 3,700 species) of major scientific and economic importance. The taxonomy of this group has been plagued by convergent evolution in nearly every morphological feature used to define tribes and genera. Phylogenetic analysis of 746 nrDNA internal transcribed spacer (ITS) sequences, representing 24 of the 25 currently recognized tribes, 146 genera, and 461 species of Brassicaceae, produced the most comprehensive, single-locus-based phylogenetic analysis of the family published to date. Novel approaches to nrDNA ITS analysis and extensive taxonomic sampling offered a test of monophyly for a large complement of the currently recognized tribes and genera of Brassicaceae. In the most comprehensive analysis, tribes Alysseae, Anchonieae plus Hesperideae, Boechereae, Cardamineae, Eutremeae, Halimolobeae, Iberideae, Noccaeeae, Physarieae, Schizopetaleae, Smelowskieae, and Thlaspideae were all monophyletic. Several broadly defined genera (e.g., Draba and Smelowskia) were supported as monophyletic, whereas others (e.g., Sisymbrium and Alyssum) were clearly polyphyletic. Analyses of ITS data identified several problematic sequences attributable to errors in sample identification or database submission. Results from parsimony ratchet and Bayesian analyses recovered little support for the backbone of the phylogeny, suggesting that many lineages of Brassicaceae have undergone rapid radiations that may ultimately be difficult to resolve with any single locus. However, the development of a preliminary supermatrix including the combination of 10 loci for 65 species provides an initial estimate of intertribal relations and suggests that broad application of such a method will provide greater understanding of relationships in the family.     

Weighted parsimony phylogeny of the family Characidae (Teleostei: Characiformes)

The family Characidae, including more than 1000 species, lacks a phylogenetic diagnosis, with many of its genera currently considered as incertae sedis . The aims of the present study are to propose a phylogenetic diagnosis and to assess higher-level relationships of and within Characidae. In this regard, 360 morphological characters are studied for 160 species of Characidae and related families. Phylogenetic analyses under implied weighting and self-weighted optimization are presented, exploring a broad range of parameters. The analysis under self-weighted optimization is innovative for this size of matrices. Familial status of Serrasalmidae is supported, and Acestrorhynchidae and Cynodontidae are included in a monophyletic Characidae. Engraulisoma taeniatum is transferred from Characidae to Gasteropelecidae. Thus constituted, the monophyly of Characidae is supported by seven synapomorphies. A new subfamily, Heterocharacinae, is proposed, and the subfamilies Aphyocharacinae, Aphyoditeinae, Characinae, Gymnocharacinae, and Stevardiinae are redefined. The Glandulocaudinae are included in Stevardiinae together with remaining members of "clade A" ( sensu Malabarba and Weitzman, 2003 . Comun. Mus. Ciênc. Tecnol. PUCRS, Sér. Zool. 16, 67–151.) and the genera Aulixidens and Nantis . Most incertae sedis genera are assigned, at least tentatively, to a phylogenetically diagnosed clade.     

A molecular phylogeny of celtidaceae and ulmaceae (Urticales) based onrbcL Nucleotide sequences

On the basis of 1,290 bp sequences of the chloroplast generbcL, a molecular phylogeny of seven of nine genera of the Celtidaceae and four of six genera of the Ulmaceae was produced. These data were analyzed together with some other urticalean genera using three methods (i.e., maximum parsimony, maximum likelihood, and neighbor joining methods). Maximum likelihood topology among 18 trees obtained indicated that the Urticales are monophyletic with its common clade splitting basally into two: one leading to a line comprisingAmpelocera (traditionally placed in Celtidaceae) and Ulmaceae, and the other leading to a line comprising the remaining genera of Celtidaceae, Moraceae, and other Urticales. Ulmaceae, to whichAmpelocera is a sister group, are monophyletic, as supported by many lines of morphological evidence. In contrast to Ulmaceae, the monophyly of Celtidaceae (excludingAmpelocera) was not supported, and resolution of relationships of Celtidaceae with other Urticales, as well as of those within the family, is left for future study.     

Phylogeny and circumscription of the near-endemic Brazilian tribe Microlicieae (Melastomataceae)

The members of tribe Microlicieae in the flowering plant family Melastomataceae are nearly all endemic to the cerrado biome of Brazil. Traditional classifications of the Melastomataceae have attributed between 15 and 17 genera to the Microlicieae, but subsequent revisions have circumscribed the tribe more narrowly. The monophyly and intergeneric relationships of the Microlicieae were evaluated through phylogenetic analyses with molecular and morphological data sets. Incorporation of DNA sequences from the intron of the chloroplast gene rpl16 into a previously generated family-wide data set yielded a clade comprising Chaetostoma, Lavoisiera, Microlicia, Rhynchanthera, Stenodon, and Trembleya ("core Microlicieae"), with Rhynchanthera as the first-diverging lineage. The other four genera of Microlicieae sampled are placed in other clades: Eriocnema with Miconieae; Siphanthera with Aciotis, Nepsera, and Acisanthera of Melastomeae; Castratella as sister to Monochaetum of Melastomeae; and Cambessedesia as part of an unresolved polytomy in a large clade that includes most Melastomataceae. Analyses of the chloroplast genes rbcL and ndhF that included three core genera produced similar results, as did the combined analysis of all three data sets. Combined parsimony analyses of DNA sequences from rpl16 and the nuclear ribosomal intercistronic transcribed spacer (ITS) region of 22 species of core Microlicieae yielded generally low internal support values. Lavoisiera, recently redefined on the basis of several morphological characters, was strongly supported as monophyletic. A morphological phylogenetic analysis of the Microlicieae based on 10 parsimony-informative characters recovered a monophyletic core Microlicieae but provided no further resolution among genera. Penalized likelihood analysis with two calibration time windows produced an age estimate of 3.7 million years for the time of initial divergence of strictly Brazilian core Microlicieae. This date is in general agreement with the estimated age of the most active stage of development of cerrado vegetation and implies an adaptive shift from hydric to seasonally dry habitats during the early evolution of this group.     

Multi-locus phylogeny clarifies the systematics of the Australo-Papuan robins (Family Petroicidae, Passeriformes)

The Australo-Papuan family Petroicidae (Aves: Passeriformes) has been the focus of much systematic debate about its relationships with other passerine families, as well as relationships within the family. Mostly conservative morphology within the group limits the effectiveness of traditional taxonomic analyses and has contributed to ongoing systematic debate. To assess relationships within the family, we sampled 47 individuals from 26 species, representing the majority of genera and species, for four loci: 528 base pairs (bp) of C-myc, 501 bp of BA20454 and 336 bp of BA23989 from nuclear DNA and 1005 bp of the mitochondrial ND2 gene. There was consensus between individual loci and overall support for major lineages was strong. Partitioned Bayesian analyses of all four loci produced a fully resolved and very well-supported phylogeny that addresses many of the previous systematic debates in this group. The Eopsaltriinae as construed is monophyletic with the exception of Eopsaltria flaviventris, which is nested within Microeca as an unremarkable member of that genus. This relationship is corroborated by morphology and egg color and pattern. Petroicinae as currently construed was not monophyletic and comprised two lineages that are paraphyletic with respect to each other. The third subfamily, Drymodinae, remains incertae sedis. The mangrove robin, Peneonanthe pulverulenta, of tropical Australia and New Guinea is nested within a clade that also contained the sampled species of Peneothello and Melanodryas, a novel relationship. Preliminary biogeographic and divergence time estimates from these results are discussed and a new subfamily arrangement proposed.     

Molecular phylogeny of the cyrtophorid ciliates (Protozoa, Ciliophora, Phyllopharyngea)

Evolutionary relationships of cyrtophorian ciliates are poorly known because molecular data of most groups within this subclass are lacking. In the present work, the SS rRNA genes belonging to 17 genera, 7 families of Cyrtophoria were sequenced and phylogenetic trees were constructed to assess their inter-generic relationships. The results indicated: (1) the assignment of cyrtophorians into two orders is consistently confirmed in all topologies; (2) the order Dysteriida is an outlined monophyletic assemblage while Chlamydodontida is paraphyletic with three separate monophyletic families; (3) Microxysma, which is currently assigned within the family Hartmannulidae, should be transferred to the family Dysteriidae; (4) the systematic position of Plesiotrichopidae remains unclear, yet the two genera that were placed in this family before, Pithites and Trochochilodon, should be transferred to Chlamydodontida; (5) a new family, Pithitidae n. fam., based on the type genus Pithites was suggested; and (6) the sequence of Isochona sp., the only available data of Chonotrichia so far, is probably from a misidentified species. In addition, three group I introns of SS rRNA gene were discovered in Aegyriana oliva, among which Aol.S516 is the first IE group intron reported in ciliates.     

Molecular phylogeny of Palaearctic genera of Gomphocerinae grasshoppers (Orthoptera, Acrididae)

Abstract.  Molecular phylogenetic methods were used to examine morphologically based hypotheses concerning the taxonomic structure and relationships of the grasshopper subfamily Gomphocerinae. Two mitochondrial gene (cytochrome b and cytochrome oxidase subunit I) sequences were determined for twenty-five species representing eleven Palaearctic genera. The studied Gomphocerinae species constituted a monophyletic group; furthermore, the earlier division of Gomphocerinae into tribes was supported, with each tribe monophyletic. There was no support for various systems uniting Stenobothrini and Gomphocerini into one tribe. Two separate clusters were discerned in Gomphocerini and two tribes were distinguished – Gomphocerini (genera Aeropus , Stauroderus , Chorthippus ) and Stenobothrini (genera Omocestus , Stenobothrus ).     

Systematics of Amaryllidaceae based on cladistic analysis of plastid sequence data

Cladistic analyses of plastid DNA sequences rbcL and trnL-F are presented separately and combined for 48 genera of Amaryllidaceae and 29 genera of related asparagalean families. The combined analysis is the most highly resolved of the three and provides good support for the monophyly of Amaryllidaceae and indicates Agapanthaceae as its sister family. Alliaceae are in turn sister to the Amaryllidaceae/Agapanthaceae clade. The origins of the family appear to be western Gondwanaland (Africa), and infrafamilial relationships are resolved along biogeographic lines. Tribe Amaryllideae, primarily South African, is sister to the rest of Amaryllidaceae; this tribe is supported by numerous morphological synapomorphies as well. The remaining two African tribes of the family, Haemantheae and Cyrtantheae, are well supported, but their position relative to the Australasian Calostemmateae and a large clade comprising the Eurasian and American genera, is not yet clear. The Eurasian and American elements of the family are each monophyletic sister clades. Internal resolution of the Eurasian clade only partially supports currently accepted tribal concepts, and few conclusions can be drawn on the relationships of the genera based on these data. A monophyletic Lycorideae (Central and East Asian) is weakly supported. Galanthus and Leucojum (Galantheae pro parte) are supported as sister genera by the bootstrap. The American clade shows a higher degree of internal resolution. Hippeastreae (minus Griffinia and Worsleya) are well supported, and Zephyranthinae are resolved as a distinct subtribe. An Andean clade marked by a chromosome number of 2n = 46 (and derivatives thereof) is resolved with weak support. The plastid DNA phylogenies are discussed in the context of biogeography and character evolution in the family.     

Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages.     

Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes)

Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively little phylogenetic attention. Our results suggest that the genus Echinorhinus is not a squaliform, but rather related to the saw sharks, a hypothesis that might be supported by both groups sharing 'spiny' snouts. In sum, our results offer the most detailed species-level phylogeny of sharks to date and a tool for comparative analyses.     

A multilocus phylogeny of the Sulidae (Aves: Pelecaniformes)

Gene trees will often differ from the true species history, the species tree, as a result of processes such as incomplete lineage sorting. New methods such as Bayesian Estimation of the Species Tree (BEST) use the multispecies coalescent to model lineage sorting, and directly infer the species tree from multilocus DNA sequence data. The Sulidae (Aves: Pelecaniformes) is a family of ten booby and gannet species with a global distribution. We sequenced five nuclear intron loci and one mitochondrial locus to estimate a species tree for the Sulidae using both BEST and by concatenating nuclear loci. We also used fossil calibrated strict and relaxed molecular clocks in BEAST to estimate divergence times for major nodes in the sulid phylogeny. Individual gene trees showed little phylogenetic conflict but varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. On the other hand, both the BEST and concatenated species trees were highly resolved, strongly supported, and topologically consistent with each other. The three sulid genera (Morus, Sula, Papasula) were monophyletic and the relationships within genera were mostly consistent with both a previously estimated mtDNA gene tree and the mtDNA gene tree estimated here. However, our species trees conflicted with the mtDNA gene trees in the relationships among the three genera. Most notably, we find that the endemic and endangered Abbott's booby (Papasula abbotti) is likely basal to all other members of the Sulidae and diverged from them approximately 22 million years ago.