A phylogenetic analysis of the nursery-web spider family Pisauridae, with emphasis on the genera Architis and Staberius (Araneae: Lycosoidea)

This study presents a general cladistic analysis of pisaurid genera, with emphasis on the Neotropical genera Architis Simon and Staberius Simon. The analysis was based on a matrix with 21 terminal taxa: eight species of Architis , Staberius spinipes (Taczanowski), seven exemplars of other pisaurid genera and five outgroup taxa. These terminals were scored for 59 morphological and three behavioural characters. An analysis with all characters equally weighted resulted in two most parsimonious trees, differing only in the position of Architis colombo Santos. In both trees Pisauridae arouse as a monophyletic group, and the exemplars of Architis composed a clade with S. spinipes . Contrary to hypotheses from the literature, Thalassius Simon emerged as sister-group of all remaining pisaurids, not as a close relative of Dolomedes Latreille. The genera Tinus F.O.P. -Cambridge and Thaumasia Perty appeared in the trees as the closest relatives of Architis and Staberius Simon. The analysis strongly supported S. spinipes as the sister-group of A. helveola (Simon), indicating that Architis as currently delimited is paraphyletic. Based on these results, Staberius is considered a subjective junior synonym of Architis . Additionally, the genus Mimicosa Petrunkevitch, originally described in Tetragnathidae, is transferred to Pisauridae and considered a junior synonym of Architis . Two species are proposed as junior synonyms of A. spinipes comb.n. Mimicosa spinosa Petrunkevitch and Staberius lemoulti Caporiacco.     

A molecular phylogenetic study of southern African Apiaceae

It has been suggested that southern Africa is the origin of the predominantly herbaceous Apiaceae subfamily Apioideae and that the woody habit is plesiomorphic. We expand previous molecular phylogenetic analyses of the family by considering all but three of the approximately 38 genera native to southern Africa, including all genera whose members, save one, have a woody habit. Representatives of five other genera are included because they may be closely related to these southern African taxa. Chloroplast DNA rps16 intron and/or nuclear rDNA ITS sequences for 154 accessions are analyzed using maximum parsimony, Bayesian, and maximum likelihood methods. Within Apioideae, two major clades hitherto unrecognized in the subfamily are inferred. The monogeneric Lichtensteinia clade is sister group to all other members of the subfamily, whereas the Annesorhiza clade (Annesorhiza, Chamarea, and Itasina) plus Molopospermum (and Astydamia in the ITS trees) are the successive sister group to all Apioideae except Lichtensteinia. Tribe Heteromorpheae is expanded to include Pseudocarum, "Oreofraga" ined., and five genera endemic to Madagascar. The southern African origin of subfamily Apioideae is corroborated (with subsequent migration northward into Eurasia along two dispersal routes), and the positions of the herbaceous Lichtensteinia and Annesorhiza clades within the subfamily suggest, surprisingly, that its ancestor was herbaceous, not woody.     

A phylogenetic analysis of the family Dermatophilaceae

The comparative analysis of the 16S ribosomal ribonucleic acid (rRNA) of Geodermatophilus obscurus DSM 43060 and Dermatophilus congolensis DSM 43037 revealed that these members of the family Dermatophilaceae were only remotely related. While G. obscurus represented an individual and separate line of descent within the phylogenetically defined order Actinomycetales, D. congolensis was closely related to representatives of Arthrobacter, Micrococcus, Cellulomonas, Brevibacterium, Promicromonospora and Microbacterium.     

A molecular phylogenetic assessment of the advanced Asiatic and Malesian didymocarpoid Gesneriaceae with focus on non-monophyletic and monotypic genera

Based on a considerably enlarged sampling, a phylogenetic analysis of the largest group of didymocarpoid Gesneriaceae, the ??advanced Asiatic and Malesian genera??, was performed, covering all but 3 of the 60 genera presently recognised in this group (20 of these, mostly from China, are monotypic). The results suggest that no fewer than 17 out of the 57 genera examined are poly- (or rarely para-)phyletic. Highly polyphyletic are Briggsia, Chirita, Henckelia and Raphiocarpus. Only a dozen of the non-monotypic genera (including the three species-richest genera, Cyrtandra, Aeschynanthus and Agalmyla) are confirmed as monophyletic entities, though some exhibit considerable genetic variation. For eight genera, no statement can be made, as only one (of two or several) species was included in the analysis. For a dozen of the (particularly Chinese) monotypic genera a close relationship (or possible congenerity) with other genera was found. In China, only Allostigma, Cathayanthe, Conandron and Metapetrocosmea seem to have no strong affinities to other genera, indicating that they represent phylogenetically isolated lineages or represent remnants of previously larger and earlier diversified groups. The present study forms the foundation for targeted molecular, morphological and phytogeographic studies of the polyphyletic and monotypic genera and particular of clades of genera with interrelations uncovered here for the first time.     

A phylogenetic analysis of the lipocalin protein family

The lipocalins are a family of extracellular proteins that bind and transport small hydrophobic molecules. They are found in eubacteria and a great variety of eukaryotic cells, in which they play diverse physiological roles. We report here the detection of two new eukaryotic lipocalins and a phylogenetic analysis of 113 lipocalin family members performed with maximum-likelihood and parsimony methods on their amino acid sequences. Lipocalins segregate into 13 monophyletic clades, some of which are grouped in well-supported superclades. An examination of the G + C content of the bacterial lipocalin genes and the detection of four new conceptual lipocalins in other eubacterial species argue against a recent horizontal transfer as the origin of prokaryotic lipocalins. Therefore, we rooted our lipocalin tree using the clade containing the prokaryotic lipocalins. The topology of the rooted lipocalin tree is in general agreement with the currently accepted view of the organismal phylogeny of arthropods and chordates. The rooted tree allows us to assign polarity to character changes and suggests a plausible scenario for the evolution of important lipocalin properties. More recently evolved lipocalins tend to (1) show greater rates of amino acid substitutions, (2) have more flexible protein structures, (3) bind smaller hydrophobic ligands, and (4) increase the efficiency of their ligand-binding contacts. Finally, we found that the family of fatty-acid-binding proteins originated from the more derived lipocalins and therefore cannot be considered a sister group of the lipocalin family.     

A molecular phylogeny of apple snails (Gastropoda, Caenogastropoda, Ampullariidae) with an emphasis on African species

Ampullariids are widespread in Africa, Asia, South- and Central America, and the Caribbean Islands. Basal phylogenetic relationships of the African genera Afropomus and Saulea have been inferred based on anatomical evidence. Until recently the Viviparidae was regarded as the sister-group of Ampullariidae, but recent molecular data infer a sister-group relationship with Campanilidae. We have used members of both families as outgroups in the present investigation on ampullariid phylogeny. We have used data from portions of five molecular loci, that is, the nuclear genes 18S rRNA, 28S rRNA and H3, and the mitochondrial genes 16S rRNA and COI. Our data most often infer a basal position of Afropomus . The West African species Saulea is inferred as the basal member of a clade including the South American Marisa and Pomacea . We hypothesize that evolutionary lineages leading to Saulea and the American genera were isolated from each other by vicariance events (Gondwanaland break-up 130–110 Mya). Our individual gene analyses inferred two major clades of the African Lanistes . However, in some analyses they were not inferred as sister-groups making Lanistes paraphyletic. The African and Asian genus Pila is most often inferred to be monophyletic (except for the generally unresolved 28S). Our analyses most often inferred a sister-group relationship between Lanistes and Pila . The very low genetic diversity of the endemic radiation of Lanistes in Lake Malawi suggests that the morphological divergence has happened much faster than the molecular divergence as is also evidenced from the cichlid radiations.     

A phylogenetic analysis of the Gruiformes (Aves) based on morphological characters,with an emphasis on the rails (Rallidae)

The order Gruiformes, for which even familial composition remains controversial, is perhaps the least well understood avian order from a phylogenetic perspective. The history of the systematics of the order is presented, and the ecological and biogeographic characteristics of its members are summarized. Using cladistic techniques, phylogenetic relationships among fossil and modern genera of the Gruiformes were estimated based on 381 primarily osteological characters; relationships among modern species of Grues (Psophiidae, Aramidae, Gruidae, Heliornithidae and Rallidae) were assessed based on these characters augmented by 189 characters of the definitive integument. A strict consensus tree for 20,000 shortest trees compiled for the matrix of gruiform genera (length = 967, CI = 0.517) revealed a number of nodes common to the solution set, many of which were robust to bootstrapping and had substantial support (Bremer) indices. Robust nodes included those supporting: a sister relationship between the Pedionomidae and Turnicidae; monophyly of the Gruiformes exclusive of the Pedionomidae and Turnicidae; a sister relationship between the Cariamidae and Phorusrhacoidea; a sister relationship between a clade comprising Eurypyga and Messelornis and one comprising Rhynochetos and Aptornis; monophyly of the Grues (Psophiidae, Aramidae, Gruidae, Heliornithidae and Rallidae); monophyly of a clade (Gruoidea) comprising (in order of increasingly close relationship) Psophia, Aramus, Balearica and other Gruidae, with monophyly of each member in this series confirmed; a sister relationship between the Heliornithidae and Rallidae; and monophyly of the Rallidae exclusive of Himantornis. Autapomorphic divergence was comparatively high for Pedionomus, Eurypyga, Psophia, Himantornis and Fulica; extreme autapomorphy, much of which is unique for the order, characterized the extinct, flightless Aptornis. In the species-level analysis of modern Grues, special efforts were made to limit the analytical impacts of homoplasy related to flightlessness in a number of rallid lineages. A strict consensus tree of 20,000 shortest trees compiled (length = 1232, CI = 0.463) confirmed the interfamilial relationships resolved in the ordinal analysis and established a number of other, variably supported groups within the Rallidae. Groupings within the Rallidae included: monophyly of Rallidae exclusive of Himantornis and a clade comprising Porphyrio (including Notornis) and Porphyrula; a poorly resolved, basal group of genera including Gymnocrex, Habroptila, Eulabeornis, Aramides, Canirallus and Mentocrex; an intermediate grade comprising Anurolimnas, Amaurolimnas, and Rougetius; monophyly of two major subdivisions of remaining rallids, one comprising Rallina (paraphyletic), Rallicula, and Sarothrura, and the other comprising the apparently paraphyletic ''long-billed'' rails (e.g. Pardirallus, Cyanolimnas, Rallus, Gallirallus and Cabalus and a variably resolved clade comprising ''crakes'' (e.g. Atlantisia, Laterallus and Porzana, waterhens (Amaurornis), moorhens (Gallinula and allied genera) and coots (Fulica). Relationships among ''crakes'' remain poorly resolved; Laterallus may be paraphyletic, and Porzana is evidently polyphyletic and poses substantial challenges for reconciliation with current taxonomy. Relationships among the species of waterhens, moorhens and coots, however, were comparatively well resolved, and exhaustive, fine-scale analyses of several genera (Grus, Porphyrio, Aramides, Rallus, Laterallus and Fulica) and species complexes (Porphyrio porphyrio -group,Gallirallus philippensis -group and Fulica americana -group) revealed additional topological likelihoods. Many nodes shared by a majority of the shortest trees under equal weighting were common to all shortest trees found following one or two iterations of successive weighting of characters. Provisional placements of selected subfossil rallids (e.g. Diaphorapteryx, Aphanapteryx and Capellirallus ) were based on separate heuristic searches using the strict consensus tree for modern rallids as a backbone constraint. These analyses were considered with respect to assessments of robustness, homoplasy related to flightlessness, challenges and importance of fossils in cladistic analysis, previously published studies and biogeography, and an annotated phylogenetic classification of the Gruiformes is proposed.     

A phylogenetic analysis of 100+ genera and 50+ families of euasterids based on morphological and molecular data with notes on possible higher level morphological synapomorphies

 A data matrix of 143 morphological and chemical characters for 142 genera of euasterids according to the APG system was compiled and complemented with rbcL and ndhF sequences for most of the genera. The data were subjected to parsimony analysis and support was assessed by bootstrapping. Strict consensus trees from analyses of morphology alone and morphology + rbcL + ndhF are presented. The morphological data recover several groups supported by molecular data but at the level of orders and above relationships are only superficially in agreement with molecular studies. The analyses provide support for monophyly of Gentianales, Aquifoliales, Apiales, Asterales, and Dipsacales. All data indicate that Adoxaceae are closely related to Dipsacales and hence they should be included in that order. The trees were used to assess some possible morphological synapomorphies for euasterids I and II and for the orders of the APG system. Euasterids I are generally characterised by opposite leaves, entire leaf margins, hypogynous flowers, “early sympetaly” with a ring-shaped corolla primordium, fusion of stamen filaments with the corolla tube, and capsular fruits. Euasterids II often have alternate leaves, serrate-dentate leaf margins, epigynous flowers, “late sympetaly” with distinct petal primordia, free stamen filaments, and indehiscent fruits. It is unclear which of these characters represent synapomorphies and symplesiomorphies for the two groups, respectively, and there are numerous expections to be interpreted as reversals and parallelisms. Received August 28, 2000 Accepted August 7, 2001     

A molecular phylogenetic investigation of Opisthonecta and related genera (Ciliophora, Peritrichia, Sessilida)

The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs.     

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed.     

Seed plant genera endemic to the Caribbean Island biodiversity hotspot: A review and a molecular phylogenetic perspective

The Caribbean Island Biodiversity Hotspot is composed primarily of the Bahamas and Greater and Lesser Antilles. A total of 180 genera (727 spp., ca. 9% of the species endemic to the Antilles) are restricted to this hotspot. Most of these genera are unispecific (51%), a pattern that is also found on other islands of the world. The majority of the endemic genera belong to the “Core Eudicot” clade, and they were published in two time periods (1854–1878 and 1904–1928). There are molecular phylogenies available for 63 of the endemic genera. However, phylogenetic reconstructions of only 21 genera are based on more than one independent DNA region and have well-supported clades and good taxonomic sampling. Six of the endemic genera form part of early-branching groups. We could not infer biogeographical conclusions from the molecular phylogenies of most of the endemic genera (43: 68%). There is an urgent need for (1) additional field studies to learn the conservation status of these genera, (2) effective protection of the habitats where the most endangered genera occur, and (3) additional biological and systematic studies of the least understood genera.     

A molecular phylogenetic analysis of strombid gastropod morphological diversity

The shells of strombid gastropods show a wide variety of forms, ranging from small and fusiform to large and elaborately ornamented with a strongly flared outer lip. Here, we present the first species-level molecular phylogeny for strombids and use the resulting phylogenetic framework to explore relationships between species richness and morphological diversity. We use portions of one nuclear (325 bp of histone H3) and one mitochondrial (640 bp of cytochrome oxidase I, COI) gene to infer relationships within the two most species-rich genera in the Strombidae: Strombus and Lambis. We include 32 species of Strombus, representing 10 of 11 extant subgenera, and 3 of the 9 species of Lambis, representing 2 of 3 extant subgenera. Maximum likelihood and Bayesian analyses of COI and of H3 and COI combined suggest Lambis is nested within a paraphyletic Strombus. Eastern Pacific and western Atlantic species of Strombus form a relatively recent monophyletic radiation within an older, paraphyletic Indo-West Pacific grade. Morphological diversity of subclades scales positively with species richness but does not show evidence of strong phylogenetic constraints.     

A molecular phylogenetic investigation of Pseudoamphisiella and Parabirojimia (Protozoa, Ciliophora, Spirotrichea), two genera with ambiguous systematic positions

The gene coding for the small subunit ribosomal RNA molecule was sequenced in three marine spirotrichs: Pseudoamphisiella lacazei, P. alveolata, and Parabirojimia similis, the systematic positions of which remain unclear in spite of recent progress. Phylogenetic trees were constructed by means of neighbor-joining (NJ), least-squares (LS), maximum parsimony (MP), and Bayesian inference (BI) methods in order to test previously inferred phylogenetic assignments of Pseudoamphisiella and Parabirojimia based on morphological and morphogenetic data. The main results are that: (1) all trees constructed have similar topologies in which the genus Parabirojimia derives at the base of the class Stichotrichia, which suggests that it might represent a unique taxon at about suborder or even-order level near urostylids; (2) the present study supports the conclusion reported by previous researchers that urostylids could be a paraphyletic assemblage and that Uroleptus and Paruroleptus should be removed from the order Urostylida; (3) Pseudoamphisiellidae/Pseudoamphisiella always clusters with Prodiscocephalus borrori rather than with urostylids, which indicates that they might represent an ancestral form for both discocephaline and urostylid species; (4) the monophyly of the traditional suborder Discocephalina and typical euplotids is consistently rejected. Based on both morphological/morphogenetical and molecular data obtained, a new suborder Parabirojimina n. subord. is suggested, which currently includes one family, Parabirojimidae n. fam., and the single genus Parabirojimia.     

RFLP analysis of mtDNA from six platyrrhine genera: phylogenetic inferences

This study investigates the phylogenetic relationships of 10 species of platyrrhine primates using RFLP analysis of mtDNA. Three restriction enzymes were used to determine the restriction site haplotypes for a total of 276 individuals. Phylogenetic analysis using maximum parsimony was employed to construct phylogenetic trees. We found close phylogenetic relationships between Alouatta, Lagothrix and Ateles. We also found a close relationship between Cebus and Aotus, with Saimiri clustering with the atelines. Haplotype diversity was found in four of the species studied, in Cebus albifrons, Saimiri sciureus, Lagothrix lagotricha and Ateles fusciceps. These data provide additional information concerning the phylogenetic relationships between these platyrrhine genera and species.     

Morphological review ofPelvetia andSilvetia (Fucaceae, Phaeophyta) with an emphasis on phylogenetic relationships

We compared the morphology of all four members ofPelvetia andSilvetia (Fucaceae, Phaeophyta), with an emphasis on phylogenetic relationships.Silvetia is segregated fromPelvetia because it has two, longitudinally divided eggs in the oogonium. In contrast, the eggs of the genusPelvetia are transversally divided. A cladistic analysis, based on 17 morphological features, shows thatPelvetia is closely related toHesperophycus andPelvetiopsis, as are three species ofSilvetia. We can infer from the cladistic tree and biogeographic information that some silvetian ancestor populations from the northern Pacific region likely evolved toS. babingtonii in northern Japan and then moved to Korea and California (USA), whereS. siliquosa andS. compressa, respectively, diverged. Our morphological study corroborates the DNA-based phytogeny and the ensuing taxonomy for the two genera. These results demonstrate the necessity for systematically revising the family Fucaceae to emphasize egg development, rather than egg number, in the oogonium, as a diagnostic character.     

A phylogenetic dissection of the family micrococcaceae

A comparative analysis of 16S ribosomal RNA sequences in the Micrococcaceae shows the family not to be a phylogenetically coherent unit. In fact, at least two of its three genera are themselves not valid phylogenetic units. Species, of the genusMicrococcus are phylogenetically inseparable from those ofArthrobacter. The genusPlanococcus groups specifically with certain members ofBacillus, andStaphylococcus is also related to the genusBacillus, though more peripherally. These findings question the validity of spherical shape as a valid indicator of phylogenetic relationships on all but the lowest levels.     

Expression analysis of the CLCA gene family in mouse and human with emphasis on the nervous system

Background  

Members of the calcium-activated chloride channel (CLCA) gene family have been suggested to possess a variety of functions including cell adhesion and tumor suppression. Expression of CLCA family members has mostly been analyzed in non-neural tissues. Here we describe the expression of mouse and human CLCA genes in the nervous system.     

A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information

The insulin receptor (IR), the insulin-like growth factor 1 receptor (IGF1R) and the insulin receptor-related receptor (IRR) are covalently-linked homodimers made up of several structural domains. The molecular mechanism of ligand binding to the ectodomain of these receptors and the resulting activation of their tyrosine kinase domain is still not well understood. We have carried out an amino acid residue conservation analysis in order to reconstruct the phylogeny of the IR Family. We have confirmed the location of ligand binding site 1 of the IGF1R and IR. Importantly, we have also predicted the likely location of the insulin binding site 2 on the surface of the fibronectin type III domains of the IR. An evolutionary conserved surface on the second leucine-rich domain that may interact with the ligand could not be detected. We suggest a possible mechanical trigger of the activation of the IR that involves a slight 'twist' rotation of the last two fibronectin type III domains in order to face the likely location of insulin. Finally, a strong selective pressure was found amongst the IRR orthologous sequences, suggesting that this orphan receptor has a yet unknown physiological role which may be conserved from amphibians to mammals.