Limitations of relative apparent synapomorphy analysis (RASA) for measuring phylogenetic signal.

In this paper we use hypothetical and empirical data matrices to evaluate the ability of relative apparent synapomorphy analysis (RASA) to measure phylogenetic signal, select outgroups, and identify terminals subject to long-branch attraction. In all cases, except for equal character-state frequencies, RASA indicated extraordinarily high levels of phylogenetic information for hypothetical data matrices that are uninformative regarding relationships among the terminals. Yet, regardless of the number of characters or character-state frequencies, RASA failed to detect phylogenetic signal for hypothetical matrices with strong phylogenetic signal. In our empirical example, RASA indicated increasing phylogenetic signal for matrices for which the strict consensus of the most parsimonious trees is increasingly poorly resolved, clades are increasingly poorly supported, and for which many relationships are in conflict with more widely sampled analyses. RASA is an ineffective approach to identify outgroup terminal(s) with the most plesiomorphic character states for the ingroup. Our hypothetical example demonstrated that RASA preferred outgroup terminals with increasing numbers of convergent character states with ingroup terminals, and rejected the outgroup terminal with all plesiomorphic character states. Our empirical example demonstrated that RASA, in all three cases examined, selected an ingroup terminal, rather than an outgroup terminal, as the best outgroup. In no case was one of the two outgroup terminals even close to being considered the optimal outgroup by RASA. RASA is an ineffective means of identifying problematic long-branch terminals. In our hypothetical example, RASA indicated a terminal as being a problematic long-branch terminal in spite of the terminal being on a zero-length branch and having no possibility of undergoing long-branch attraction with another terminal. RASA also failed to identify actual problematic long-branch terminals that did undergo long-branch attraction, but only after following Lyons-Weiler and Hoelzer's (1997) three-step process to identify and remove terminals subject to long-branch attraction. We conclude that RASA should not be used for any of these purposes.     

Systematics of Chaetocerotaceae (Bacillariophyceae). I. A phylogenetic analysis of the family

In order to construct a model of evolutionary relationships within the diatom family Chaetocerotaceae, 37 species of Chaetoceros Ehrenberg, representing all subgenera and 21 of 22 subgeneric sections of the genus, plus three Bacteriastrum Shadbolt species, representing both of its subgeneric sections, were subjected to cladistic analysis. One species each of Eucampia Ehrenberg, Cerataulina Peragallo, Hemiau‐lus Ehrenberg, Attheya West and Gonioceros H. & M. Peragallo were used as outgroups. A matrix of 65 binary and multistate morphological characters was constructed, with data being gathered from original observation of material in the light and electron microscopes, and from the published literature. The analysis yielded 36 most‐parsimonious cladograms of 316 steps; incongruence between trees is largely restricted to some taxa representing undersampled sections of Chaetoceros subg. Hyalochaete. The robustness of this hypothesis was examined in several ways. To assess the effect of character weighting, the bootstrap was used to randomly weight characters. The parsimony criterion was relaxed via a decay index, and finally, the tree length was compared to that of trees randomly generated from the data matrix. The majority of investigated species of Chaetoceros subg. Phaeoceros, Chaetoceros subg. Hyalochaete and Bacteriastrum appear to belong to a continuous grade, rather than comprising individual clades. Chaetoceros is paraphyletic. Thus, the traditional classification does not accurately reflect the hypothesized phylogenetic relationships of this family.     

apTreeshape: statistical analysis of phylogenetic tree shape

apTreeshape is a R package dedicated to simulation and analysis of phylogenetic tree topologies using statistical imbalance measures. It is a companion library of the R package 'ape', which provides additional functions for reading, plotting, manipulating phylogenetic trees and for connecting to public phylogenetic tree databases. One strength of the package is to include appropriate corrections of classical shape statistics as well as new tests based on the statistical theory of likelihood ratios.     

Mitochondrial DNA phylogenetic analysis of the genus Laparocerus (Coleoptera, Curculionidae, Entiminae). I. The Madeiran clade

Laparocerus are plant‐chewing flightless weevils distributed on oceanic islands in Macaronesia, with a single species in Morocco. The genus has a complicated taxonomic history with several subgenera described. To assist in a taxonomical revision of the group, a molecular study was undertaken. In this first contribution, the species from the Azores and Madeira archipelagos are studied together with representatives of subgenera from the Canary Islands and the single known continental species (46 OTUs). Phylogenetic analyses are based on sequence data from mitochondrial cytochrome oxidase II (COII) and the ribosomal 16S ribosomal RNA (16S rRNA) genes (combined data set 1023 bp), with additional data from the nuclear elongation factor 1α (EF‐1α) for some selected species. Maximum likelihood (ML) and Bayesian analyses show that all Madeiran species are monophyletic and form a monophyletic group with the Afro‐Canarian samples. Species of the genus Lichenophagus appear within the Madeiran and Canarian Laparocerus clades, but separated in accordance with their respective island origin. Thus, Lichenophagus is here restricted to Madeiran species and proposed as subgenus (status novo) of Laparocerus. Conversely, the Laparocerus subgenus Drouetius from the Azores is revealed to be a separate and distant outgroup, in agreement with its morphological distinctiveness, deserving an independent genus status. Internal relationships within the Madeiran clade are discussed and compared with morphologically defined species groups. The Madeiran monotypic subgenus Cyphoscelis is not supported by the genetic data and synonymized (nov. syn.) with Laparocerus. Subgenera Laparocerus and Atlantis prove to be polyphyletic. Consequently a restriction to monophyletic and morphologically congruent clades is proposed. A cryptic species vicariant of Laparocerus morio was detected and recognized as L. chaoensis, status novo. Other cases of discrepancy between the genetic results and the traditional taxonomy are discussed in detail in the light of mitochondrial introgression, incomplete lineage sorting or poor taxonomy hypotheses.     

The phylogenetic signal of diversification rates

Hypotheses to explain the causes of diversity gradients have increasingly focused on the factors that actually change species numbers, namely speciation, extinction and dispersal. A common assumption of many of these hypotheses is that there should be phylogenetic signal in diversification rates, yet this assumption has rarely been tested explicitly. In this study, we compile a large data set including 328,219 species of plants, mammals, amphibians and squamates to assess the level of phylogenetic signal in their diversification rates. Significant phylogenetic signal was detected in all data sets, except for squamates, suggesting not only that closely related clades indeed might share similar diversification rates, but also that the level of phylogenetic signal might vary considerably between them. Moreover, there were intriguing differences among taxa in the rate of decay in phylogenetic autocorrelation over time, underscoring the existence of taxon-specific patterns of phylogenetic autocorrelation. These results have important implications for the development of more realistic models of species diversification.     

The signal recognition particle database (SRPDB).

The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and 9 archaeal homologs) and a total of 20 protein sequences representing SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72. The offerings also include representative RNA secondary structure diagrams.     

The signal recognition particle database (SRPDB).

The SRPDB (signal recognition particle database) provides annotated SRP RNA sequences from Eucaryotes and Archaea, phylogenetically ordered and aligned with their bacterial equivalents. We also make available representative RNA secondary structure diagrams, where each base pair is proven by comparative sequence analysis. New to this release are 17 SRP RNA sequences (a total of 64 sequences) and alignments of proteins SRP19 and SRP54 with their RNA binding sites.     

Genome-wide analysis of SINA family in plants and their phylogenetic relationships(dagger).

SINA genes in plants are part of a multigene family with 5 members in Arabidopsis thaliana, 10 members in Populus trichocarpa, 6 members in Oryza sativa, at least 6 members in Zea mays and at least 1 member in Physcomitrella patens. Six members in maize were confirmed by RT-PCR. All SINAs have one RING domain and one SINA domain. These two domains are highly conserved in plants. According to the motif organization and phylogenetic tree, SINA family members were divided into 2 groups. In addition, through semi-quantitative RT-PCR analysis of maize members and Digital Northern analysis of Arabidopsis and rice members, we found that the tissue expression patterns are more diverse in monocot than in Arabidopsis.     

Structure of poly (I).poly (A).poly (I)

The molecular structure of poly (I).poly (A).poly (I) has been determined and refined using the continuous intensity data on layer lines in the x-ray diffraction pattern obtained from an oriented fiber of this polymorphic RNA complex. The polymer forms a 12-fold right-handed triple-helix of pitch 39.7A and each base-triplet is stabilized by quasi Crick-Watson-Hoogsteen hydrogen bonds. The ribose rings in all the three strands have C3'-endo conformations. The final R-value for this best structure is 0.24 and the x-ray fit is significantly superior to all the alternative structures where the different chains might have different furanose conformations. This all-purine triple-helix, counter-intuitively, has a diameter roughly 3A shorter than that of DNA and RNA triple-helices containing a homopurine and two complementary homopyrimidine strands. Its compact, grooveless cylindrical shape is consistent with the lack of lateral organization.     

Assessing phylogenetic signal with measurement error: a comparison of mantel tests, blomberg et Al.'s k, and phylogenetic distograms

In macroevolutionary studies, different approaches are commonly used to measure phylogenetic signal-the tendency of related taxa to resemble one another-including the K statistic and the Mantel test. The latter was recently criticized for lacking statistical power. Using new simulations, we show that the power of the Mantel test depends on the metrics used to define trait distances and phylogenetic distances between species. Increasing power is obtained by lowering variance and increasing negative skewness in interspecific distances, as obtained using Euclidean trait distances and the complement of Abouheif proximity as a phylogenetic distance. We show realistic situations involving "measurement error" due to intraspecific variability where the Mantel test is more powerful to detect a phylogenetic signal than a permutation test based on the K statistic. We highlight limitations of the K-statistic (univariate measure) and show that its application should take into account measurement errors using repeated measures per species to avoid estimation bias. Finally, we argue that phylogenetic distograms representing Euclidean trait distance as a function of the square root of patristic distance provide an insightful representation of the phylogenetic signal that can be used to assess both the impact of measurement error and the departure from a Brownian evolution model.     

Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities

Abouheif adapted a test for serial independence to detect a phylogenetic signal in phenotypic traits. We provide the exact analytic value of this test, revealing that it uses Moran's I statistic with a new matrix of phylogenetic proximities. We introduce then two new matrices of phylogenetic proximities highlighting their mathematical properties: matrix A which is used in Abouheif test and matrix M which is related to A and biodiversity studies. Matrix A unifies the tests developed by Abouheif, Moran and Geary. We discuss the advantages of matrices A and M over three widely used phylogenetic proximity matrices through simulations evaluating power and type-I error of tests for phylogenetic autocorrelation. We conclude that A enhances the power of Moran's test and is useful for unresolved trees. Data sets and routines are freely available in an online package and explained in an online supplementary file.     

The marsupial placenta: a phylogenetic analysis

The structure, physiology, and endocrinology of the yolk sac placenta of different marsupial groups is compared and phylogenetically analyzed to provide information on placental characters in the marsupial stem species. We conclude that the marsupial stem species possessed a functional yolk sac placenta. Histotrophic nutrition by uterine secretion decreased during late pregnancy and at least half of the yolk sac was vascularized at the time of shell coat rupture. Due to yolk sac fusion, the larger part of the avascular, bilaminar yolk sac could not serve as a placenta at late gestation in the polyovular marsupial stem species. The bilaminar yolk sac gained a relatively greater importance for nutrition in monovular australidelphians. In macropodids a greater proportion of the yolk sac remained bilaminar at the time of shell coat rupture than in the stem species. Another derived feature of macropodids is the sustained plasma progesterone synthesis that is in turn responsible for an extended secretory phase of the uterus and a lengthened gestation. The placenta of the marsupial stem species was probably capable of metabolising histo- and hemotrophes. Recognition of pregnancy during early stages of development is a derived character of macropodids that we suggest did not occur in the marsupial stem species. However, birth and birth behaviour were apparently induced by prostaglandins in the marsupial stem species. Although the yolk sac formed the definitive placenta, it is likely that the allantois provided a supplementary placental function in the marsupial stem species, but that the role of the allantois became progressively less important during the evolution of marsupial placentation.     

The ribophorin I from Penaeus monodon shrimp: cDNA cloning, expression and phylogenetic analysis

Ribophorin I, a 67 kDa subunit of the oligosaccharyl transferase complex, is involved in facilitating N-linked glycosylation of polypeptides. We have isolated a full length Penaeus monodon cDNA encoding an insect/mammalian ribophorin I homologue by screening a lymphoid cDNA library and by performing rapid amplification of cDNA ends polymerase chain reaction of lymphoid RNA. The cDNA clone of shrimp ribophorin I (PmRibI) consists of 2263 nucleotides encoding 601 amino acid residues. Primary structure analysis of PmRibI indicated that it is a type I transmembrane protein, comprising a cleavable signal sequence of 23 residues at the amino terminus, preceding 434 residues of the luminal domain, 17 residues of the transmembrane domain, and 150 residues of the cytoplasmic domain at the carboxy terminus. The protein has a calculated molecular mass of 67.98 kDa with a pI of 6.05. This putative PmRibI cDNA clone was also expressed as PmRibI-6His in Sf9 cells. The recombinant PmRibI has an apparent molecular weight of 70 kDa, similar to the MW calculated from the deduced cDNA sequence. The inferred protein sequence of PmRibI has 52% identity with that of Strongylocentrotus purpuratus, 49% identity with that of Danio rerio, and 47% identity with mammalian ribophorin I. Phylogenetic analysis showed that PmRibI is most closely related to the echinoderm ribophorin I. The expression of the ribophorin I gene is tissue specific, with its mRNA highly abundant in hemocytes, gill, lymphoid organ and hepatopancreas.     

Character transformation and relationships in Corallorhiza (Orchidaceae: Epidendroideae). II. Morphological variation and phylogenetic analysis

Morphological and anatomical study of Corallorhiza, a genus of primarily New World leafless mycoparasitic orchids, was undertaken in order to produce a hypothesis of relationships among the species and to gain some understanding of character transformations. Cladistic analysis of the resulting data set gave two most parsimonious trees. Analysis of combined plastid DNA and morphological data yielded a single topology, identical to one of the two from the analysis of morphological data alone. Molecular data do not conflict with the morphological data set, and provide more resolution within the C. maculata complex. The combined data indicate that C. striata is the sister group to the remainder of the genus; the circumboreal C. trifida also occupies a basal position. Corallorhiza wisteriana and C. odontorhiza comprise the sister group to the C. maculata + C. mertensiana + C. bulbosa clade. Only two synapomorphies, presence of the coralloid rhizome and loss of leaves, unite the species of Corallorhiza. The coralloid rhizome appears to be a paedomorphic development, due to its similarity to a protocorm; if so, it too is a loss character and may be considered only weak support for monophyly of the genus. Predominant autogamy, seen in C. trifida and cleistogamous C. odontorhiza, has probably arisen independently in these taxa.     

A molecular analysis of the phylogenetic affinities of Saccoglossus cambrensis Brambell & Cole (Hemichordata).

Traditional approaches to phylogeny reconstruction have not allowed precise resolution of the evolutionary relationships between the major deuterostome phyla (chordates, hemichordates, echinoderms). Here we report the use of a molecular approach to investigate deuterostome phylogeny. We have used a polymerase chain reaction-based strategy to amplify, clone and sequence parts of the genes coding for 18S ribosomal RNA from Saccoglossus cambrensis (Hemichordata), Arbacia sp. (Echinodermata) and, for comparison, Mytilus edulis (Mollusca). We report the results of phylogenetic reconstructions using these, and homologous sequences from other eukaryotes. The results of our analyses are consistent with the hypothesis that S. cambrensis and vertebrates share a common ancestor not shared by echinoderms.     

Treeness triangles: visualizing the loss of phylogenetic signal

It is well known that molecular data "saturates" with increasing sequence divergence (thereby losing phylogenetic information) and that in addition the accumulation of misleading information due to chance similarities or to systematic bias may accompany saturation as well. Exploratory data analysis methods that can quantify the extent of signal loss or convergence for a given data set are scarce. Such methods are needed because genomics delivers very long sequence alignments spanning substantial phylogenetic depth, where site saturation may be compounded by systematic biases or other alternative signals. Here we introduce the Treeness Triangle (TT) graph, in which signals detectable by Hadamard (spectral) analysis are summed into 3 categories--those supporting 1) external and 2) internal branches in the optimal tree, in addition to 3) the residuals (potential internal branches not present in the optimal tree). These 3 values are plotted in a standard ternary coordinate system. The approach is illustrated with simulated and real data sets, the latter from complete chloroplast genomes, where potential problems of paralogy or lateral gene acquisition can be excluded. The TT uncovers the divergence-dependent loss of phylogenetic signal as subsets of chloroplast genomes are investigated that span increasingly deeper evolutionary timescales. The rate of signal loss (or signal retention) varies with the gene and/or the method of analysis.     

The ovaries of scale insects (Hemiptera, Coccinea). Morphology and phylogenetic conclusions

Coccoids (Coccinea, Coccoidea, Coccomorpha, scale insects, scales) are a highly diverse group of ectoparasitic insects. They comprise 2 subgroups: primitive archaeococcoids (= Orthezioidea sensu Koteja) and advanced neococcoids (= Coccoidea sensu Koteja). The ovaries of coccoids consist of numerous short telotrophic-meroistic ovarioles. The ovarioles of all investigated species share common characters (e.g. the same mechanism of ovariole development, lack of terminal filaments, occurrence of single oocytes in the vitellaria) supporting the concept of monophyletic origin of this group. Despite these characteristics, the ovaries of archaeococcoids and neococcoids differ in the number of germ cells (oocytes + trophocytes) constituting a single ovariole. In primitive families (Ortheziidae, Margarodidae), this number is relatively large (15-58), whereas in advanced ones (Pseudococcidae, Kermesidae, Eriococcidae, Cryptococcidae, Coccidae, Diaspididae) it is small and usually does not exceed 8. The comparative analysis of the ovary structure in the representatives of Coccinea and closely related Aphidinea (aphids) has revealed that: (1) the organization of archaeococcoid ovaries is more similar to those of aphids than to neococcoids and (2) during the evolution of Coccinea a gradual reduction in the number of germ cells in ovarioles took place.