Genetic studies facilitated management decisions on the invasion of the ruddy duck in Europe

The ruddy duck (Oxyura jamaicensis), a stifftail native to the Americas, was introduced to the UK in the 1950s and has since been recorded in 22 western Palearctic countries. By 2000, the UK population peaked at nearly 6,000 individuals. In 1991, hybridisation with the native and globally threatened (IUCN Endangered) white-headed duck (Oxyura leucocephala), a stifftail restricted to the Mediterranean and Asia, was recorded in Spain and culling of hybrids and ruddy ducks began. Here we report on a series of genetic studies that have enabled and supported management decisions to the benefit of the white-headed duck. First, genetic data confirmed that these are two distinct species, each of which is more closely related to other stifftail species. Second, molecular studies indicated that ruddy ducks in Spain, Iceland and elsewhere in Europe were of captive origin and not descendants from vagrants from their native North America. Third, genetic methods were used to distinguish among different hybrid generations in Spain and detected no ruddy duck introgression in birds identified morphologically as white-headed ducks. Collectively, these results supported management decisions to eradicate ruddy ducks from Europe. Subsequently, a control programme reduced the UK population by over 95 % by 2010, and the arrival of ruddy ducks to Spain decreased from 21 birds in 2003 to two sightings in 2010–2011. However, increased efforts to control small ruddy duck populations elsewhere in Europe and Morocco are still required to ensure conservation of the white-headed duck. This case of invasion by hybridization demonstrates that successful control is feasible given early detection followed by a rapid response plan; it also shows the contribution of research to management and that to guarantee the conservation of an endangered native species action may be required in countries outside its distribution range.     

Is homoplasy or lineage sorting the source of incongruent mtdna and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oxyura)?

We evaluated the potential effects of homoplasy, ancestral polymorphism, and hybridization as obstacles to resolving phylogenetic relationships within Nomonyx-Oxyura stiff-tailed ducks (Oxyurinae; subtribe Oxyurina). Mitochondrial DNA (mtDNA) control region sequences from 94 individuals supported monophyly of mtDNA haplotypes for each of the six species and provided no evidence of extant incomplete lineage sorting or inter-specific hybridization. The ruddy ducks (O. j. jamaicensis,O. j. andina, O. j. ferruginea) are each others' closest relatives, but the lack of shared haplotypes between O. j. jamaicensis and O. j. ferruginea suggests long-standing historical isolation. In contrast, O. j. andina shares haplotypes with O. j. jamaicensis and O. j. ferruginea, which supports Todd's (1979) and Fjelds?'s (1986) hypothesis that O. j. andina is an intergrade or hybrid subspecies of O. j. jamaicensis and O. j. ferruginea. Control region data and a much larger data set composed of approximately 8800 base pairs of mitochondrial and nuclear sequence for each species indicate that the two New World species, O. vittata and O. jamaicensis, branch basally within Oxyura. A clade of three Old World species (O. australis, O. maccoa, O. leucocephala) is well supported, but different loci and also different characters within the mtDNA data support three different resolutions of the Old World clade, yielding an essentially unresolved trichotomy. Fundamentally different factors limited the resolution of the mtDNA and nuclear gene trees. Gene trees for most nuclear loci were unresolved due to slow rates of mutation and a lack of informative variation, whereas uncertain resolution of the mtDNA gene tree was due to homoplasy. Within the mtDNA, approximately equal numbers of characters supported each of three possible resolutions. Parametric and nonparametric bootstrap analyses suggest that resolution of the mtDNA tree based on ~4300 bp per taxon is uncertain but that complete mtDNA sequences would yield a fully resolved gene tree. A short internode separating O. leucocephala from (O. australis, O. maccoa) in the best mtDNA tree combined with long terminal branches and substantial rate variation among nucleotide sites allowed the small number of changes occurring on the internode to be obscured by homoplasy in a significant portion of simulated data sets. Although most nuclear loci were uninformative, two loci supported a resolution of the Old World clade (O. maccoa, O. leucocephala) that is incongruent with the best mtDNA tree. Thus, incongruence between nuclear and mtDNA trees may be due to random sorting of ancestral lineages during the short internode, homoplasy in the mtDNA data, or both. The Oxyura trichotomy represents a difficult though likely common problem in molecular systematics. Given a short internode, the mtDNA tree has a greater chance of being congruent with the history of speciation because its effective population size (N(e)) is one-quarter that of any nuclear locus, but its resolution is more likely to be obscured by homoplasy. In contrast, gene trees for more slowly evolving nuclear loci will be difficult to resolve due to a lack of substitutions during the internode, and when resolved are more likely to be incongruent with the species history due to the stochastic effects of lineage sorting. We suggest that researchers consider first whether independent gene trees are adequately resolved and then whether those trees are congruent with the species history. In the case of Oxyura, the answer to both questions may be no. Complete mtDNA sequences combined with data from a very large number of nuclear loci may be the only way to resolve such trichotomies.     

Inflorescence diversification in the "finger millet clade" (Chloridoideae, Poaceae): a comparison of molecular phylogeny and developmental morphology

Within the Poaceae, inflorescence diversification and its bearing on phylogeny and evolution are exceedingly complex. We used phylogenetic information of the "finger millet clade," a group of grasses with digitate inflorescences, to study the inflorescence diversification. This clade appears monophyletic in the morphological and molecular phylogenetic analyses. Three well-supported clades are shown in our cpDNA-derived phylogeny, with clades I and III consisting of species of Chloris and Microchloa, respectively, and clade II including species of Cynodon, Dactyloctenium, and Eleusine. Variation appears at different times throughout development. Changes involving primordium number and arrangement occur very early, changes involving duration of primordium activity occur much later. Characters derived from the comparison of developmental sequences were optimized onto the most parsimonious tree. The developmental characters were congruent with the molecular phylogeny. Two developmental characters may not be homologous in the Chloris subclade and the Cynodon subclade.     

Phylogenetic relationships within the Laridae (Charadriiformes: Aves) inferred from mitochondrial markers

Gulls (Aves: Laridae) constitute a recent and cosmopolite family of well-studied seabirds for which a robust phylogeny is needed to perform comparative and biogeographical analyses. The present study, the first molecular phylogeny of all Larids species (N=53), is based on a combined segment of mtDNA (partial cytochrome b and control region). We discuss our phylogenetic tree in the light of previous suggestions based on morphological, behavioral, and plumage characters. Although the phylogeny is not fully resolved, it highlights several robust species groups and confirms or identifies for the first time some sister relationships that had never been suggested before. The Dolphin Gull (Leucophaeus scoresbii) for instance, is identified as the sister species of the Grey Gull (Larus modestus) and the Ross's Gull (Rhodostethia rosea) forms a monophyletic group with the Little Gull (Larus minutus). Our results clearly demonstrate that the genus Larus as currently defined is not monophyletic, since current taxonomy of gulls is based on the use of convergent phenotypic characters. We propose a new systematic arrangement that better reflects their evolutionary history.     

五味子科的系统发育:核糖体DNA ITS区序列证据

The Schisandraceae is one of the most important taxa for understanding the origin and evolution of primitive angiosperms due to its basal position in the recent cladograms of the angiosperm based both on several gene sequences and on morphological characters, but phylogenetic relationships within the family are still unresolved. The sequences of nrDNA ITS region of 15 species representing four sections of Schisandra Michx., two sections of Kadsura Kaempf. ex Juss. and one outgroup, Illicium fargesii Finet et Gagnep., were used to reconstruct the phylogeny of Schisandraceae. Fourteen most parsimonious trees (Length=259, CI=0.934 and RI=0.889) were obtained from the analysis with I．fargesii as the outgroup. In the consensus tree, the genus Schisandra was found to be divided into three clades. Sect. Pleiostema formed a clade together with sect. Maximowiczia, sect. Sphaerostema was weakly supported to be the sister group of a clade comprising S. bicolor var. tuberculata and Kadsura species. In particular, S. bicolor var. tuberculata, a species of sect. Schisandra, was nested within Kadsura. It seems from this result and the morphological characters that Schisandra might not be a monophyletic group. According to the present molecular phylogeny, both elongated hypocarpium and deciduous habit originated independently at least twice in the Schisandraceae, and therefore, the value of the present morphological characters used in the classification of the family Schisandraceae should be reevaluated.     

Cladistics and the comparative morphology of linyphiid spiders and their relatives (Araneae, Araneoidea, Linyphiidae)

This paper provides the first quantitative cladistic analysis of linyphiid morphology. Classical and novel homology hypotheses for a variety of character systems (male and female genitalia, somatic morphology, spinneret silk spigot morphology, etc.) are critically examined and studied within a phylogenetic context. Critical characters have been illustrated. A sample of linyphiid taxa (nine genera in four subfamilies), five species of Pimoa (Pimoidae), and two other araneoid families (Tetragnathidae and Araneidae, represented by Tetragnatha and Zygiella , respectively) were used to study the implications of the phylogeny of Pimoidae for the systematics of linyphiids. The phylogenetic relationships of these 16 exemplar taxa, as coded for the 47 characters studied, were analysed using numerical cladistic methods. In the preferred cladogram Pimoidae and Linyphiidae are sister groups, Stemonyphantinae are sister group to the remaining linyphiids, and Mynogleninae are sister group to the clade composed of Erigoninae plus Linyphiinae. These results agree with the relationships recently proposed by Wunderlich, except by finding erigonines as the sister group to linyphiines rather than to mynoglenines.     

Morphological phylogenetic analysis of Ophrys (Orchidaceae): insights from morpho‐anatomical floral traits into the interspecific relationships in an unresolved clade

Reconstructing the phylogeny of the sexually deceptive orchid genus Ophrys is crucial to our understanding of the evolution of its complex floral morphology. Molecular phylogenetic analyses showed that section Pseudophrys forms a well supported clade with Ophrys bombyliflora, O. tenthredinifera and O. speculum, but were unable to elucidate the relationships between these four groups of taxa. Here we conduct a morphological phylogenetic analysis of this unresolved clade of Ophrys based on a data matrix of 45 macro‐ and micromorphological and anatomical floral characters, using maximum parsimony and Bayesian inference. Our cladistic analysis yielded a single most parsimonious tree and a Bayesian 50% majority‐rule consensus tree which differed in their overall topology but agreed that O. tenthredinifera and O. bombyliflora are not sister groups. The phylogenetic placement of O. tenthredinifera was ambiguous since it shares six valid synapomorphies each with the cluster of O. speculum–O. bombyliflora and with section Pseudophrys. In contrast, O. bombyliflora is most likely the sister group to O. speculum, a finding that rejects an earlier morphological phylogenetic hypothesis and favours the existing molecular trees based on nuclear ITS rather than plastid data. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 454–476.     

The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters

Consensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.     

Phylogeny of Polygonia, Nymphalis and related butterflies (Lepidoptera: Nymphalidae): a total-evidence analysis

We investigated the phylogeny of butterflies in the tribe Nymphalini sensu Harvey 1991, comprising the genera Vanessa, Cynthia, Bassaris, Aglais, Inachis, Nymphalis, Polygonia, Kaniska, Antanartia, Hypanartia, Symbrenthia, Mynes and Araschnia . Evidence from the mitochondrial gene ndl, the nuclear gene 'wingless' and from morphology/ ecology/behaviour were used separately and combined to analyse relationships. Phylogenies based on the different types of data agreed in many aspects of basic topology. We show that an analysis of only wing pattern characters (based on Nijhout's homology system) results in a topology broadly similar to the one resulting from analysis of the complete matrix. We found support for a monophyletic Nymphalini, where Hypanartia may be the sister clade to all other genera. Mynes, Symbrenthia and Araschnia together seem to form another basal clade. Evidence presented gives only moderate support for a monophyletic Vanessa in the wide sense, including also Cynthia and Bassaris , but strong support for the monophyly of the largely holarctic clade Aglais + Inachis + Nymphalis + Polygonia + Kaniska + Roddia . Within the latter group there is strong support for a clade consisting of Aglais + Inachis and for a second clade which includes Nymphalis, Polygonia (and its sister clade, the monotypic Kaniska) as well as Roddia l-album (= Nymphalis vaualbum ). As a consequence of this topology, Aglais is recognized as a taxon separate from Nymphalis . We present a hypothesis of species relationships within the focal group of genera. We also analyse and discuss the implications of excluding or including ecological data in phylogenetic tree construction, when the tree is to be used for studies in phylogenetic ecology.     

Phylogenetics of paniceae (poaceae)

Paniceae demonstrate unique variability of photosynthetic physiology and anatomy, including both non-Kranz and Kranz species and all subtypes of the latter. This variability suggests hypotheses of independent origin or reversals (e.g., from C(4) to C(3)). These hypotheses can be tested by phylogenetic analysis of independent molecular characters. The molecular phylogeny of 57 species of Paniceae was explored using sequences from the grass-specific insert found in the plastid locus rpoC2. Phylogenetic analyses confirmed some long-recognized alliances in Paniceae, some recent molecular phylogenetic results, and suggested new relationships. Broadly, Paniceae were found to be paraphyletic with Andropogoneae, Panicum was found to be polyphyletic, and Oplismenus hirtellus was resolved as the sister group to the remaining ingroup species. A particularly well-supported clade in the rpoC2 tree included four genera with non-Kranz species and three with distinctively keeled paleas. As previously suggested, the PCK (phosphoenol pyruvate carboxykinase) C(4) subtype arose once within Paniceae. All clades with non-Kranz species had Kranz ancestors or sister taxa suggesting repeated loss of the Kranz syndrome.     

Molecular phylogeny of Malagasy reed frogs, Heterixalus, and the relative performance of bioacoustics and color-patterns for resolving their systematics

The members of the genus Heterixalus constitute one of the endemic frog radiations in Madagascar. Here we present a complete species-level phylogeny based on DNA sequences (4876 base pairs) of three nuclear and four mitochondrial markers to clarify the phylogenetic relationships among and within all known species of this genus, as well as the phylogenetic position of the monospecific Seychellean Tachycnemis seychellensis. Although the performance to resolve supported clades of Heterixalus species differed among the investigated gene fragments when analyzed separately, we could identify five well-supported species groups within Heterixalus in the combined analysis of all gene fragments. Our data strongly support a Heterixalus-Tachycnemis clade, and indicate the probable monophyly of Heterixalus placed sister to Tachycnemis. However, the diversification of these lineages may have happened in a short interval of time, leading to an unstable placement of Tachycnemis in the single-gene fragment phylogenies. Referring to the hitherto existing classification of Heterixalus, which is predominantly based on chromatic and bioacoustic characters, we examined the relative performance of these data sets relative to our molecular phylogeny. A Bayesian tree reconstructed with a bioacoustic data set yielded a higher resemblance to the molecular phylogeny than a tree constructed using a chromatic data set, which supports the importance of bioacoustic characters for systematic analyses of these anurans.     

Phylogenetic evidence for loss of sound production and a shift in sexual recognition signals in Hamadryas butterflies (Nymphalidae: Biblidinae)

The neotropical butterfly genus Hamadryas Hübner comprises 20 species that exhibit an intriguing variation in their natural history traits. Although revised in 1983, no phylogenetic hypothesis was presented: the first phylogenetic hypothesis is estimated here based on 93 characters and including species from the three other genera in the tribe Ageroniini. The phylogeny is used to test the monophyly of the genus, establish the sister group of Hamadryas and identify its apomorphies. The tree allows the inference of patterns of character change in sound production and sexual dimorphism. Implied weights show that Hamadryas is monophyletic and corroborate Ectima Doubleday as a sister genus. Previously suggested subgenera for Hamadryas were non‐monophyletic, with the exception of the laodamia clade, supported by the presence of a complete sterigma. Sound production is inferred to be a derived condition in Hamadryas that has been lost in the laodamia clade. This, plus the presence of androconial organs and sexual dimorphism in the laodamia clade, suggests a shift in sexual recognition signalling. Furthermore, the phylogeny indicates that the colour pattern of males in the laodamia clade is novel, supporting a Darwinian origin of sexual dimorphism.     

Phylogenetic analysis of the Monocotylidae (Monogenea) inferred from 28S rDNA sequences

The current classification of the Monocotylidae (Monogenea) is based on a phylogeny generated from morphological characters. The present study tests the morphological phylogenetic hypothesis using molecular methods. Sequences from domains C2 and D1 and the partial domains C1 and D2 from the 28S rDNA gene for 26 species of monocotylids from six of the seven subfamilies were used. Trees were generated using maximum parsimony, neighbour joining and maximum likelihood algorithms. The maximum parsimony tree, with branches showing less than 70% bootstrap support collapsed, had a topology identical to that obtained using the maximum likelihood analysis. The neighbour joining tree, with branches showing less than 70% support collapsed, differed only in its placement of Heterocotyle capricornensis as the sister group to the Decacotylinae clade. The molecular tree largely supports the subfamilies established using morphological characters. Differences are primarily how the subfamilies are related to each other. The monophyly of the Calicotylinae and Merizocotylinae and their sister group relationship is supported by high bootstrap values in all three methods, but relationships within the Merizocotylinae are unclear. Merizocotyle is paraphyletic and our data suggest that Mycteronastes and Thaumatocotyle, which were synonymized with Merizocotyle after the morphological cladistic analysis, should perhaps be resurrected as valid genera. The monophyly of the Monocotylinae and Decacotylinae is also supported by high bootstrap values. The Decacotylinae, which was considered previously to be the sister group to the Calicotylinae plus Merizocotylinae, is grouped in an unresolved polychotomy with the Monocotylinae and members of the Heterocotylinae. According to our molecular data, the Heterocotylinae is paraphyletic. Molecular data support a sister group relationship between Troglocephalus rhinobatidis and Neoheterocotyle rhinobatidis to the exclusion of the other species of Neoheterocotyle and recognition of Troglocephalus renders Neoheterocotyle paraphyletic. We propose Troglocephalus incertae sedis. An updated classification and full species list of the Monocotylidae is provided.     

A phylogenetic analysis of the tropidurine lizards (Squamata: Tropiduridae), including new characters of squamation and epidermal microstructure

Characters of scale surface microstructure are combined with 'traditional'morphological characters in a phylogenetic analysis of the Tropidurini. Tropidurid lizards show variation in types of coarse and fine scale surface microstructure, in the anatomical distribution of different scale surface features, and in scale organ morphology and distribution. The morphology of the inner surface zone of scales is here described for the first time using scanning electron microscopy. Our phylogeny differs considerably from those proposed in earlier studies. New characters and frequency coding of polymorphic characters help resolve the problematic relationships of several species. Statistical confidence supports recognition of one large cis-Andean and one large trans-Andean clade of species. Based on our results, we synonymize Plesiomicrolophus with Microlophus and Uranoscodon with Tropidurus. The phylogenetic relationships of newly discovered Tropidurus are resolved: T. caltathelys is the sister species of T. melanopleurus; T. xanthochilus is the sister species of T. spinulosus. Tropidurus spinulosus is found to be more closely related to T. strobilurus and a clade of Amazonian species than to T. melanopleurus. The species previously placed in Uracentron are more closely related to species previously placed in Plica than to 77 strobilurus as previously thought.     

An improved phylogeny of the Andean tit-tyrants (Aves, Tyrannidae): more characters trump sophisticated analyses

The phylogeny of the flycatcher genus Anairetes was previously inferred using short fragments of mitochondrial DNA and parsimony and distance-based methods. The resulting topology spurred taxonomic revision and influenced understanding of Andean biogeography. More than a decade later, we revisit the phylogeny of Anairetes tit-tyrants using more mtDNA characters, seven unlinked loci (three mitochondrial genes, six nuclear loci), more closely related outgroup taxa, partitioned Bayesian analyses, and two coalescent species-tree approaches (Bayesian estimation of species trees, BEST; Bayesian evolutionary analysis by sampling trees, (*)BEAST). Of these improvements in data and analyses, the fourfold increase in mtDNA characters was both necessary and sufficient to incur a major shift in the topology and near-complete resolution. The species-tree analyses, while theoretically preferable to concatenation or single gene approaches, yielded topologies that were compatible with mtDNA but with weaker statistical resolution at nodes. The previous results that had led to taxonomic and biogeographic reappraisal were refuted, and the current results support the resurrection of the genus Uromyias as the sister clade to Anairetes. The sister relationship between these two genera corresponds to an ecological dichotomy between a depauperate humid cloud forest clade and a diverse dry-tolerant clade that has diversified along the latitudinal axis of the Andes. The species-tree results and the concatenation results each reaffirm the primacy of mtDNA to provide phylogenetic signal for avian phylogenies at the species and subspecies level. This is due in part to the abundance of informative characters in mtDNA, and in part to its lower effective population size that causes it to more faithfully track the species tree.     

Molecular phylogeny of grouse: individual and combined performance of W-linked,autosomal, and mitochondrial loci

The phylogeny of grouse (Aves: Tetraoninae) was reconstructed using four noncoding loci: two were W-linked, one was autosomal, and one was the mitochondrial control region (CR). The rapidly evolving CR provided resolution throughout the tree, whereas the slowly evolving nuclear loci failed to resolve deeper nodes. The tree based on all four loci combined was almost identical to the CR tree and did not improve resolution or bootstrap support. The stemminess and imbalance of the trees were good determinants of the quality of the phylogenetic signal. The skewness of the tree score distribution (g(1)) behaved contrary to prediction; loci that had a more symmetric tree score distribution produced trees that had greater stemminess and balance. The quality of the phylogenetic signal was related to the evolutionary rate. Four clades of grouse were discovered. Two of these clades corresponded to currently recognized genera Bonasa and Lagopus. Bonasa was the sister to other grouse and Lagopus was the sister to the other two non-Bonasa clades. The third clade included Falcipennis, Tetrao, and Lyrurus. The fourth clade included the genera Centrocercus, Dendragapus, and Tympanuchus. The data support recognition of Falcipennis canadensis franklinii and Dendragapus obscurus fuliginosus as species.     

Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding

The labyrinthulomycetes, also known as the 'Labyrinthulomycota' are saprotrophic or less frequently parasitic stramenopilan protists, usually in marine ecosystems. Their distinguishing feature is an 'ectoplasmic net,' an external cytoplasmic network secreted by a specialized organelle that attaches the cell to its substrate and secretes digestive enzymes for absorptive nutrition. In this study, one of our aims was to infer the phylogenetic position of the labyrinthulomycetes relative to the non-photosynthetic bicoeceans and oomycetes and the photosynthetic ochrophytes and thereby evaluate patterns of change from photosynthesis to saprotrophism among the stramenopiles. For the labyrinthulomycetes, we determined sequences of the actin, beta-tubulin, and elongation factor 1-alpha gene fragments and where necessary, ribosomal small subunit (SSU) genes. Multilocus analysis using standard tree construction techniques not only strongly supported the oomycetes as the sister group to the phototrophic stramenopiles, but also, for the first time with moderate statistical support, showed that the labyrinthulomycetes and the bicoecean as sister groups. The paraphyly of the non-photosynthetic groups was consistent with independent loss of photosynthesis in labyrinthulomycetes and oomycetes. We also wished to develop a phylogenetically based hypothesis for the origin of the gliding cell bodies and the ectoplasmic net found in some labyrinthulomycetes. The cells of species in Labyrinthula and Aplanochytrium share a specialized form of motility involving gliding on ectoplasmic tracks. Before our study, only ribosomal DNA genes had been determined for these genera and their phylogenetic position in the labyrinthulomycetes was equivocal. Multilocus phylogenies applying our newly determined protein-coding sequences divided the labyrinthulomycetes between sister clades 'A' and 'B' and showed that the monophyletic group containing all of the gliding species was nested among non-gliding species in clade B. This phylogeny suggested that species that glide via an ectoplasm evolved from species that had used the ectoplasm mainly for anchorage and assimilation rather than motility.     

Phylogeny of the nuthatches of the Sitta canadensis group and its evolutionary and biogeographic implications

A phylogeny of ten species of nuthatch (Sittidae), including the newly described Kabylie Nuthatch Sitta ledanti of North Africa, was constructed using a sequence of 491 bp of the cytochrome-b gene of mtDNA. On the basis of trees derived using parsimony analysis and neighbour-joining methods, and assessments of robustness based on bootstrap analysis, the following phylogenetic relationships were inferred: the five species of the Sitta canadensis group are a monophyletic group, within which S. canadensis, S. whiteheadi and S. villosa form the sister clade of S. krueperi and S. ledanti; the other relations are not so well supported. These phylogenetic relationships are congruent with morphology. Differences in behavioural and ecological characters as well as biogeographic patterns are discussed.     

Phylogenies from genetic and morphological characters do not support a revision of Gigasporaceae (Glomeromycota) into four families and five genera

The family Gigasporaceae consisted of the two genera Gigaspora and Scutellospora when first erected. In a recent revision of this classification, Scutellospora was divided into three families and four genera based on two main lines of evidence: (1) phylogenetic patterns of coevolving small and large rRNA genes and (2) morphology of spore germination shields. The rRNA trees were assumed to accurately reflect species evolution, and shield characters were selected because they correlated with gene trees. These characters then were used selectively to support gene trees and validate the classification. To test this new classification, a phylogenetic tree was reconstructed from concatenated 25S rRNA and β-tubulin gene sequences using 35% of known species in Gigasporaceae. A tree also was reconstructed from 23 morphological characters represented in 71% of known species. Results from both datasets showed that the revised classification was untenable. The classification also failed to accurately represent sister group relationships amongst higher taxa. Only two clades were fully resolved and congruent among datasets: Gigaspora and Racocetra (a clade consisting of species with spores having one inner germinal wall). Other clades were unresolved, which was attributed in part to undersampling of species. Topology of the morphology-based phylogeny was incongruent with gene evolution. Five shield characters were reduced to three, of which two were phylogenetically uninformative because they were homoplastic. Therefore, most taxa erected in the new classification are rejected. The classification is revised to restore the family Gigasporaceae, within which are the three genera Gigaspora, Racocetra, and Scutellospora. This classification does not reflect strict topology of either gene or morphological evolution. Further revisions must await sampling of additional characters and taxa to better ascertain congruence between datasets and infer a more accurate phylogeny of this important group of fungi.     

Phylogenetic analysis of the Monocotylidae (Monogenea) inferred from 28S rDNA sequences

The current classification of the Monocotylidae (Monogenea) is based on a phylogeny generated from morphological characters. The present study tests the morphological phylogenetic hypothesis using molecular methods. Sequences from domains C2 and D1 and the partial domains C1 and D2 from the 28S rDNA gene for 26 species of monocotylids from six of the seven subfamilies were used. Trees were generated using maximum parsimony, neighbour joining and maximum likelihood algorithms. The maximum parsimony tree, with branches showing less than 70% bootstrap support collapsed, had a topology identical to that obtained using the maximum likelihood analysis. The neighbour joining tree, with branches showing less than 70% support collapsed, differed only in its placement of Heterocotyle capricornensis as the sister group to the Decacotylinae clade. The molecular tree largely supports the subfamilies established using morphological characters. Differences are primarily how the subfamilies are related to each other. The monophyly of the Calicotylinae and Merizocotylinae and their sister group relationship is supported by high bootstrap values in all three methods, but relationships within the Merizocotylinae are unclear. Merizocotyle is paraphyletic and our data suggest that Mycteronastes and Thaumatocotyle, which were synonymized with Merizocotyle after the morphological cladistic analysis, should perhaps be resurrected as valid genera. The monophyly of the Monocotylinae and Decacotylinae is also supported by high bootstrap values. The Decacotylinae, which was considered previously to be the sister group to the Calicotylinae plus Merizocotylinae, is grouped in an unresolved polychotomy with the Monocotylinae and members of the Heterocotylinae. According to our molecular data, the Heterocotylinae is paraphyletic. Molecular data support a sister group relationship between Troglocephalus rhinobatidis and Neoheterocotyle rhinobatidis to the exclusion of the other species of Neoheterocotyle and recognition of Troglocephalus renders Neoheterocotyle paraphyletic. We propose Troglocephalus incertae sedis. An updated classification and full species list of the Monocotylidae is provided.