A molecular phylogeny of warbling-finches (Poospiza): paraphyly in a neotropical Emberizid genus

We investigated the phylogenetic relationships of 12 species within a single genus of neotropical passerine (Poospiza) using 849 bp (283 codons) of the cytochrome b mitochondrial gene. We further explored evolutionary affinities of these taxa using sequence from an additional 47 thraupine (tanagers) and 7 emberizine (sparrows and buntings) genera, members of the predominantly New World family Emberizidae. Poospiza have traditionally been considered part of the emberizine radiation. However, our analyses suggest that members of this genus are more closely related to some thraupine lineages than they are to the other neotropical emberizine genera included in our study (Atlapetes, Embernagra, Melopyrrha, Phrygilus, Saltatricula, Tiaris). Although member taxa are closely related, the genus Poospiza appears to be paraphyletic with representatives of 6 thraupine genera (Cnemoscopus, Cypsnagra, Hemispingus, Nephelornis, Pyrrhocoma, Thylpopsis) interspersed among four well-supported Poospiza clades. The majority of species within this Poospiza-thraupine clade have geographic ranges that are exclusive to, or partially overlap with, the Andes Mountains. It is probable that these mountains have played an important role in driving cladogenesis within this group. Sequence divergence (transversions only; mean 4.7+/-1.3%) within the clade suggests that much of this diversification occurred within the late Miocene and Pliocene, a period coincident with major orogenic activity in central-western South America.     

Spore morphology of Serpocaulon A.R.Sm. and related taxa from Brazil (Polypodiaceae)

The epiphytic fern genus Serpocaulon (Polypodiaceae) comprises 42 species nested within the neotropical clade of the family together with genera such as Campyloneurum, Grammitis, Microgramma, Niphidium, Pleopeltis, Pecluma, Polypodium and Terpsichore. Although Serpocaulon is a well-supported genus, its intra-specific relationships are still not completely resolved. The morphological dataset for Serpocaulon and related genera is therefore expanded here with information on spore morphology to provide additional information for phylogenetic consideration. Spores have been collected from herbarium vouchers and acetolysed for light and scanning electron microscopy. All members of the neotropical clade have monolete spores, except for Grammitis and Terpsichore, which have trilete spores. Both verrucate and papillate ornamentation types are recognised. The palynological analysis shows close similarity between spores of Serpocaulon, Campyloneurum, Pleopeltis and Polypodium and supports close phylogenetic relationships between these taxa. Species of the grammitid clade, although nested within the Polypodiaceae, have spore morphology that supports a separate position.     

Phylogenetic study of the Characinae (Teleostei: Characiformes: Characidae)

The Characinae is a subunit of the Characidae of special significance in including Charax, the type genus of the family and the order Characiformes. Twelve genera and 79 species have been traditionally assigned to the Characinae, but the subfamily still lacks a phylogenetic diagnosis. Herein, a data matrix including 150 morphological characters and 64 taxa (35 species representing all genera of the Characinae and 29 included in other lineages within the Characiformes) was submitted to two cladistic analyses that differ in the inclusion/exclusion of Priocharax due to the difficulty of coding most of the character states in the miniature species of this genus. Both analyses resulted in a non‐monophyletic Characinae and this subfamily is herein restricted to only seven of the original 12 genera forming the clade (Phenacogaster((Charax Roeboides)(Acanthocharax(Cynopotamus(Acestrocephalus Galeocharax))))), which is supported by ten non‐ambiguous synapomorphies and is more closely related to other genera of the Characidae than those traditionally placed in the subfamily. A second clade includes the members of the tribe Heterocharacini (Lonchogenys(Heterocharax Hoplocharax)) as the sister‐group of Gnathocharax, supported by seven non‐ambiguous synapomorphies. This clade is more closely related to a taxon formed by Roestes and Gilbertolus based on seven non‐ambiguous synapomorphies. Results do not corroborate a close relationship between Roestes–Gilbertolus and the Cynodontinae. Inclusion of the genus Priocharax suggests that it is related more closely to the Heterocharacini, but the profound modifications in its anatomy possibly related to ontogenetic truncations obscure a better understanding of its relationships. A new classification of the Characinae and the Heterocharacinae is proposed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 809–915.     

Biogeography of Plagiochila (Hepaticae): natural species groups span several floristic kingdoms

Aim This paper presents a synthesis of our recent results regarding the biogeography of Plagiochila using a molecular approach, and documents intercontinental ranges within this largest genus of the hepatics. Methods A maximum likelihood analysis of sixty‐one nrITS sequences of Plagiochila was performed and the molecular topology obtained was compared with morphological, phytochemical and geographical data. Results Our molecular data set allowed the identification of eleven Plagiochila sections, the majority of which cover at least two floristic kingdoms. Seven sections have species in Europe (sect. Arrectae, Carringtoniae, Fuscoluteae, Glaucescentes, Plagiochila, Rutilantes, Vagae). Plagiochila species from Atlantic Europe are usually close to or conspecific with neotropical taxa, whereas species widespread in Europe are closely related to Asian ones and not to those in the Neotropics. Plagiochila sect. Arrectae represents a neotropical – Atlantic European clade. The section is not closely related – as has often been suggested – to the morphologically similar sect. Zonatae from Asia and western North America. Sequence data show that the African P. integerrima and the neotropical P. subplana are members of the Asian sect. Cucullatae (sect. Ciliatae, syn. nov.), which becomes pantropical in distribution. An ITS sequence of P. boryana from Uganda confirms the Afro‐American range of the primarily neotropical sect. Hylacoetes. Similarities in sporophyte morphology between the sect. Cucullatae and sect. Hylacoetes are the result of parallel evolution. Main conclusions Our results indicate that intercontinental ranges at section and species level are common in Plagiochila. Carl's (1931) subdivision of Plagiochila into sections restricted to one floristic kingdom is outdated. Biogeographical patterns in Plagiochila are not dissimilar to those of other groups of bryophytes but elucidation of the geographical ranges of the taxa requires a molecular approach. Contrary to earlier belief, most Plagiochila species from Atlantic Europe do not have close relatives in Asia but are conspecific with or closely related to species from tropical America.     

Phylogeny of Oedogoniales (Chlorophyceae, Chlorophyta) inferred from 18S rDNA sequences with emphasis on the relationships in the genus Oedogonium based on ITS-2 sequences

The phylogeny of Oedogoniales was investigated by using nuclear 18S rDNA sequences. Results showed that the genus Oedocladium, as a separated clade, was clustered within the clade of Oedogonium; whereas the genus Bulbochaete was in a comparatively divergent position to the other two genera. The relationship among the species of Oedogonium was discussed, focusing on ITS-2 phylogeny analyzed combining with some morphological characteristics. Our results showed that all the dioecious nannandrous taxa involved in this study were resolved into one clade, while all the monocious taxa were clustered into another clade as a sister group to the former. The report also suggests that the dioecious macrandrous taxa form a paraphyly and could be more basally situated than the dioecious nannandrous and the monoecious taxa by means of molecular phylogeny and morphotype investigations.     

A Total Evidence Phylogeny of the Arctoidea (Carnivora: Mammalia): Relationships Among Basal Taxa

A total evidence phylogenetic analysis was performed for 14 extant and 18 fossil caniform genera using a data matrix of 5.6 kbp of concatenated sequence data from six independent loci and 80 morphological characters from the cranium and dentition. Maximum parsimony analysis recovered a single most parsimonious cladogram (MPC). The topology of the extant taxa in the MPC agreed with previous molecular phylogenies. Phylogenetic positions for fossil taxa indicate that several taxa previously described as early members of extant families (e.g., Bathygale and Plesictis) are likely stem taxa at the base of the Arctoidea. Taxa in the “Paleomustelidae” were found to be paraphyletic, but a monophyletic Oligobuninae was recovered within this set of taxa. This clade was closely related to the extant genera Gulo and Martes, therefore, nested within the extant radiation of the family Mustelidae. This analysis provides a resolution to several discrepancies between phylogenies considering either fossil taxa or extant taxa separately, and provides a framework for incorporating fossil and extant taxa into comprehensive combined evidence analyses.     

Comparative morphology of the venom apparatus in the braconid wasp subfamily Rogadinae (Insecta, Hymenoptera, Braconidae) and related taxa

Zaldivar‐River ó n, A., Areekul, B., Shaw, M. R. & Quicke, D. L. J. (2004). Comparative morphology of the venom apparatus in the braconid wasp subfamily Rogadinae (Insecta, Hymenoptera, Braconidae) and related taxa. —Zoologica Scripta, 33, 223–237. The morphology of the venom apparatus intima in representatives of 38 genera of the problematic braconid wasp subfamily Rogadinae and other cyclostome braconids was investigated and a preliminary phylogenetic analysis for the group was performed with the information obtained. Despite the limited number of characters, the data suggest several relationships at various taxonomic levels. The venom apparatus in the Clinocentrini and the Stiropiini is relatively unmodified and similar to that found in other genera previously placed within a broader concept of the Rogadinae (e.g. genera of Lysitermini, Pentatermini, Tetratermini, Hormiini) and also to that of the Betylobraconinae. The presence of a cone of filaments located inside the secondary venom duct near to its insertion on the venom reservoir/primary venom duct is proposed as a synapomorphy for the tribe Rogadini to the exclusion of Stiropiini, Clinocentrini and Yeliconini. Other features of the secondary venom duct and its insertion on the venom reservoir/primary venom duct support a number of relationships between the genera of the Rogadini and also within the large genus Aleiodes. A clade containing 15 Rogadini genera (Bathoteca, Bathotecoides, Bulborogas, Canalirogas, Colastomion, Conspinaria, Cystomastacoides, Macrostomion, Megarhogas, Myocron, Pholichora, Rectivena, Rogas, Spinaria and Triraphis) is supported by the presence of a thickened and short secondary venom duct, whereas the different members of Aleiodes (excluding members of the subgenus Heterogamus) and Cordylorhogas are distinguished by having a recessed secondary venom duct with well‐defined and numerous internal filaments. New World Rogas species exhibit a unique venom apparatus and may not be closely related to the Old World ones. Features of the venom apparatus of the enigmatic genus Telengaia and the exothecine genera Shawiana and Colastes suggest that the Telengainae and Exothecinae are both closely related to the Braconinae, Gnamptodontinae, and possibly to the Opiinae and Alysiinae. An unsculptured venom reservoir was found in one specimen of the type species of Avga, A. choaspes, which is consistent with it occupying either a very basal position within the cyclostome braconids or belonging to a recently recognized ‘Gondwanan’ clade that also includes the Aphidiinae.     

Molecular Phylogenetics of Gadidae and Related Gadiformes Based on Mitochondrial DNA Sequences

Mitochondrial DNA sequences of selected regions of the small subunit and large subunit ribosomal RNAs and cytochrome b genes were analyzed for 10 gadid species, representing 8 genera within Gadidae, and 10 species representing 5 other gadiform families. Phylogenetic analyses revealed that Gadiculus is the most basal gadid genus, and that Trisopterus and Micromesistius constitute a relatively basal clade. Lotidae was identified as the family most closely related to Gadidae. Estimation of divergence times indicated that the most ancient Gadidae split between Gadiculus and the remaining gadid genera occurred about 20 million years ago. The clade including the most recent species (Gadus, Boreogadus, Merlangius, Melanogrammus, and Pollachius) diverged from the Trisopterus/Micromesistius clade approximately 12 million years ago.     

MOLECULAR PHYLOGENY OF SELECTED MEMBERS OF THE ORDER THALASSIOSIRALES (BACILLARIOPHYTA) AND EVOLUTION OF THE FULTOPORTULA1

Recent phylogenetic studies of the diatoms indicate that members of the order Thalassiosirales occupy an interesting position in the diatom evolutionary tree. Despite their radial morphology and scaly auxospores, they are consistently recovered in molecular analyses as a member of subdivision Bacillariophytina and a sister clade to non‐fultoportulate and non‐radial lithodesmioids. This study included 46 species from nine traditionally accepted extant genera, and analyzed 43 nuclear small subunit (SSU) rRNA sequences in parallel with a survey of the variation in fultoportula structure. Three possible scenarios leading to the evolution of the fultoportula are discussed in the context of molecular and morphological similarities between the examined Thalassiosirales and their SSU rRNA sister clade Lithodesmiales. We speculate that the fultoportula might be derived by a modification of either a cribrum in an areola (fultoportula within an areola), or structures similar to marginal ridges now seen in lithodesmioids around a cluster of poroids (fultoportula in a tube), or finally, that the central fultoportula may have an origin different from the marginal fultoportulae. Our data confirm that fultoportula‐bearing diatoms constitute a natural phylogenetic group. The families Thalassiosiraceae, Skeletonemaceae, and Stephanodiscaceae and the genus Thalassiosira Cleve were unexpectedly found to be paraphyletic. Further, Cyclotella Kutz. and Stephanodiscus Ehr. may not be closely related and some species of these genera are more closely allied to other species of Thalassiosira. The generitype, T. nordenskioeldii, is embedded within a large poorly structured cluster of species that includes several members of Thalassiosira, Planktoniella sol, Minidiscus trioculatus, and two members of Stephanodiscus. An emendment of the order Lithodesmiales and the family Lauderiaceae are proposed.     

Haustorial synergids: an important character in the systematics of danthonioid grasses (Arundinoideae: Poaceae)?

The mature ovule and megagametophyte of 42 grass species (23 genera), mostly from the taxonomically troublesome subfamily Arundinoideae, was investigated. Haustorial synergids, first described from the Arundineae, are reported for a further 26 species (ten genera) of danthonioid grasses, a group for which they appear to be synapomorphic. The evolution of this character and a suite of associated integument and nucellar characters is discussed. The danthonioid clade, as defined by haustorial synergids, includes Cortaderia (often treated as nondanthonioid) but excludes a number of taxa currently contained in the Arundineae. The full extent of the group remains undetermined, however, since several of its potential members remain unstudied. The data provide some indication of phylogenetic structure within the clade. At least two of the species of Merxmuellera studied appear to occupy a basal position, while three do not, suggesting that this genus may be paraphyletic, or even polyphyletic. Also, the reduction or absence of synergid haustoria in Prionanthium, Pentaschistis, and Pentameris is considered to be secondarily derived and weakly corroborates the monophyly of this generic cluster as indicated by spikelet morphology.     

PHYLOGENYOF CHLOROMONAS (CHLOROPHYCEAE): A STUDY OF 185 RIBOSOMAL RNA GENE SEQUENCES1

The unicellular, biflagellate genus Chloromonas differs from its ally, Chlamydomonas, primarily by the absence of pyrenoids in the vegetative stage of the former. As with most green flagellate genera, little is known about phylogenetic affinities within and among Chloromonas species. Phylogenetic analyses of nuclear-encoded small-subunit ribosomal RNA gene sequences demonstrate that a sampling of five Chloromonas taxa, obtained from major culture collections, do not form a monophyletic group. However, only three of these isolates, Chloromonas clathrata, Chloromonas serbinowi, and Chloromonas rosae, are diagnosable morphologically as Chloromonas species by the absence of a pyrenoid in the vegetative stage. The three diagnosable Chloromonas taxa form an alliance with two pyrenoid-bearing chlamydomonads, Chlamydomonas augustae and Chlamydomonas macrostellata. With the exception of Chloromonas serbinowi, which represents the basal lineage within the clade, each of the diagnosable Chloromonas taxa and their pyrenoidbearing Chlamydomonas allies were isolated originally from mountain soils, snow, or cold peat. These observations suggest that habitat, independent of pyrenoid status, may be most closely linked to the natural history of this clade of chlamydomonad flagellates.     

Phylogeny and biogeography of the staghorn fern genus Platycerium (Polypodiaceae, Polypodiidae)

The genus Platycerium is one of the few pantropical epiphytic fern genera with six species in Afro-Madagascar, 8-11 Australasian species, and a single species in tropical South America. Nucleotide sequences of four chloroplast DNA markers are employed to reconstruct the phylogeny of these ferns and to explore their historical biogeography. The data set was designed to resolve conflicting hypotheses on the relationships within the genus that were based on previous phylogenetic studies exploring morphological evidence. Our results suggest a basal split of Platycerium into two well-supported clades. One clade comprises species occurring in Africa, Madagascar, and South America, whereas the second clade contains exclusively Australasian species. The latter clade is further divided into a clade corresponding to P. bifurcatum and its putative segregates and a clade of seven species occurring from Indochina throughout the Malesian region to New Guinea and Australia. The Afro-Madagascan clade includes a clade of two species found in tropical Africa and a clade of four species that includes three species endemic to Madagascar. The single neotropical species of this genus, P. andinum, is nested within the Afro-Madagascan clade but is not closely related to any extant species.     

The geometry of gender: hyper‐diversification of sexual systems in Urtica L. (Urticaceae)

Urtica L. (Urticaceae) is generally reported as a genus of monoecious and dioecious taxa. However, the gender information found in the literature does not at all reflect the actual diversity of gender patterns in Urtica. Dioecy appears to be truly absent from Urtica, but otherwise there has been a major diversification in the geometry of gender and no comparable patterns exist in other plant groups. Thus, we here define technical terms for all unique architectural types of monoecy found in Urtica and closely related genera and reconstruct the ancestral gender states in a Bayesian framework. Our studies are based on a near‐comprehensive sampling, including 61 of the 63 Urtica species recognized. We report polygamy, two types of gynodioecy and five different architectural types of monoecy. A total of 15 switches appear to have taken place within the genus. Although gender characteristics have diversified strongly, they are relatively conserved within clades. Monoecy is the predominant sexual system within Urtica and specifically basiandrous monoecy (i.e. basal inflorescence branches of each individual male only, apical branches female) is the most widespread type, reported for 11 different clades. In particular, it characterizes the basally branching pilulifera‐clade and the sister genus Zhengyia, and may thus represent the plesiomorphic condition for Urtica. Gender distribution and gross morphology appear to evolve largely independently from each other and gender distribution is largely independent of growth habit. However, polygamous taxa are most common amongst rhizomatous perennials (one‐third of the taxa).     

Kauriphanes n. gen., a new genus of braconid parasitoid wasp (Hymenoptera: Braconidae: Doryctinae) from New Zealand

A new genus belonging to the braconid wasp subfamily Doryctinae, Kauriphanes n. gen. (type species K. khalaimi n. sp.), is described from New Zealand. This genus is placed within the doryctine subtribe Caenophanina. The extent of this subtribe is discussed and the phylogenetic relationships of three of its genera were investigated using one mitochondrial and one nuclear DNA sequence markers. Similar to previous studies, the Bayesian analyses performed significantly support a clade with the included members of Caenophanina as a sister group of a clade with the examined species of Spathiini sensu stricto. The placement of the Caenophanini within Doryctini, however, is left pendant to further exhaustive phylogenetic studies. A key to genera and subgenera belonging to Caenophanina is given.     

Evolution in the High Andes: The Phylogenetics of Muscisaxicola Ground-Tyrants

Phylogenetic relationships within the genus Muscisaxicola, a primarily Andean group of tyrant-flycatchers, were studied using complete sequences of the mitochondrial genes COII and ND3. Relationships among Muscisaxicola species were found to differ substantially from those of previous views, suggesting convergence in traditional avian taxonomic characters within the genus. The 11 species of large, gray, “typical” Muscisaxicola flycatchers (including M. grisea, newly restored to species status) formed a distinct clade, consisting of two major groups: a clade of 6 species breeding primarily in the central Andes and a clade of 5 species breeding primarily in the southern Andes. The other 2 species traditionally placed in this genus, M. fluviatilis, an Amazonian species, and M. maculirostris, were both rather divergent genetically from the typical species, although M. maculirostris may be the sister taxon to the typical clade. The patterns of sympatry exhibited by Muscisaxicola species in the high Andes appear to be the consequence of speciation and secondary contact within regions of the Andes, rather than a result of dispersal between regions. Diversification of the typical Muscisaxicola species appears to have occurred during the middle and late Pleistocene, suggesting generally that taxa of the high Andes and Patagonia may have been greatly influenced by mid-to-late Pleistocene events. There were likely several independent developments of migration within this genus, but migration is probably ancestral in the southern clade, with subsequent loss of migration in two taxa.     

Molecular phylogenetics and generic assessment in the tribe Morindeae (Rubiaceae–Rubioideae): How to circumscribe Morinda L. to be monophyletic?

Most of the species of the family Rubiaceae with flowers arranged in head inflorescences are currently classified in three distantly related tribes, Naucleeae (subfamily Cinchonoideae) and Morindeae and Schradereae (subfamily Rubioideae). Within Morindeae the type genus Morinda is traditionally and currently circumscribed based on its head inflorescences and syncarpous fruits (syncarps). These characters are also present in some members of its allied genera, raising doubts about the monophyly of Morinda. We perform Bayesian phylogenetic analyses using combined nrETS/nrITS/trnT-F data for 67 Morindeae taxa and five outgroups from the closely related tribes Mitchelleae and Gaertnereae to rigorously test the monophyly of Morinda as currently delimited and assess the phylogenetic value of head inflorescences and syncarps in Morinda and Morindeae and to evaluate generic relationships and limits in Morindeae. Our analyses demonstrate that head inflorescences and syncarps in Morinda and Morindeae are evolutionarily labile. Morinda is highly paraphyletic, unless the genera Coelospermum, Gynochthodes, Pogonolobus, and Sarcopygme are also included. Morindeae comprises four well-supported and morphologically distinct major lineages: Appunia clade, Morinda clade (including Sarcopygme and the lectotype M. royoc), Coelospermum clade (containing Pogonolobus and Morinda reticulata), and Gynochthodes–Morinda clade. Four possible alternatives for revising generic boundaries are presented to establish monophyletic units. We favor the recognition of the four major lineages of Morindeae as separate genera, because this classification reflects the occurrence of a considerable morphological diversity in the tribe and the phylogenetic and taxonomic distinctness of its newly delimited genera.