Relative apparent synapomorphy analysis (RASA). I: The statistical measurement of phylogenetic signal

We have developed a new approach to the measurement of phylogenetic signal in character state matrices called relative apparent synapomorphy analysis (RASA). RASA provides a deterministic, statistical measure of natural cladistic hierarchy (phylogenetic signal) in character state matrices. The method works by determining whether a measure of the rate of increase of cladistic similarity among pairs of taxa as a function of phenetic similarity is greater than a null equiprobable rate of increase. Our investigation of the utility and limitations of RASA using simulated and bacteriophage T7 data sets indicates that the method has numerous advantages over existing measures of signal. A first advantage is computational efficiency. A second advantage is that RASA employs known methods of statistical inference, providing measurable sensitivity and power. The performance of RASA is examined under various conditions of branching evolution as the number of characters, character states per character, and mutations per branch length are varied. RASA appears to provide an unbiased and reliable measure of phylogenetic signal, and the general approach promises to be useful in the development of new techniques that should increase the rigor and reliability of phylogenetic estimates.      

Temporal niche dynamics, relative abundance and phylogenetic signal of coexisting species

The coexistence of similar species accounts for some 30% of diversity within communities, yet the coexistence and relative abundance of similar species is a continuing ecological conundrum. Using close phylogenetic relatedness as a measure of similarity, we previously demonstrated that neither classic niche theory nor neutral theory can explain the relative abundances of co-occurring pairs of similar tree species in a diverse tropical forest. Here, we show that the stable, focused competition of a temporal niche dynamic fits the distribution of observed fractional abundances (pairwise relative abundances). Previously published, independent evidence of temporal dynamics in this community supports our results; our model identifies additional criteria for field tests of differential sensitivity (DS) temporal dynamics. The success of temporal dynamics at explaining the observed distribution—and the failure of alternative hypotheses to do so—indicates that current diagnostics of community structure and assembly needs general re-examination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A device for measuring relative angular displacement.

A simple, inexpensive, and accurate way to measure relative segmental rotations resulting from torsional loadings locally is described. To measure these rotations, we fabricated a planar spatial linkage (open-loop kinematic chain) requiring only one rotational displacement transducer. This paper describes this device, defines its kinematics, and examines its accuracy.     

Methods of systematic analysis: the relative superiority of phylogenetic systematics

The superiority of cladistic methods to both synthetic and phenetic methods is briefly advanced and reviewed. Cladistics creates testable hypotheses of phylogeny that also give a highly informative summary of available data. Thus it best fits the criteria for a method for determining the general reference classification in biology. For protistologists in particular, cladistics is especially useful. Inundated by an abundance of ultrastructural, biochemical, and cell biological information, protistologists could be greatly helped by the informative way in which cladistics orders and summarizes the data. In addition to classifying protist taxa, hypotheses about the evolution of cell organelles and cellular could be scientifically formulated and tested by cladistics . Because cladistic classifications best summarize the data, they would also be best for making predictions about taxa and characters. They would, for the same reason, be the most stable. Widespread adoption of cladistic methods would serve to stabilize the now fluid state of protist taxonomy. It is for all of these reasons that such methods best suit the needs of the evolutionary protistologist .     

Methods of systematic analysis: The relative superiority of phylogenetic systematics

The superiority of cladistic methods to both synthetic and phenetic methods is briefly advanced and reviewed. Cladistics creates testable hypotheses of phylogeny that also give a highly informative summary of available data. Thus it best fits the criteria for a method for determining the general reference classification in biology.For protistologists in particular, cladistics is especially useful. Inundated by an abundance of ultrastructural, biochemical, and cell biological information, protistologists could be greatly helped by the informative way in which cladistics orders and summarizes the data. In addition to classifying protist taxa, hypotheses about the evolution of cell organelles and cellular could be scientifically formulated and tested by cladistics. Because cladistic classifications best summarize the data, they would also be best for making predictions about taxa and characters. They would, for the same reason, be the most stable. Widespread adoption of cladistic methods would serve to stabilize the now fluid state of protist taxonomy. It is for all of these reasons that such methods best suit the needs of the evolutionary protistologist.     

Phenetic and phylogenetic analysis of Reinhardtia (Palmae)

Principal component analysis and cluster analysis of morphometric data divide specimens of Reinhardtia into six groups, corresponding to the six species recognized in the most recent revisions. Discriminant analysis classifies specimens into these six species with 100% success. Five species occur in lowland to montane moist forests in Central America, from Mexico to Panama, and just reach Colombia; one species occurs in montane moist forests in Hispaniola. Three species have large stems and are rare, patchily distributed, and seldom collected. The other three species have small stems, are common and frequently collected, but also patchily distributed. One species of small plants, R. gracilis, exhibits considerable variability. Within this species, seven distinct groups can be recognized, although sample size is limited. Among species, there is a phyletic decrease in size of plants, from the basal species with large stems to derived species with small stems. For leaves and inflorescences there is also an associated decrease in size, but one species does not follow this trend. In this species, R. latisecta, there is evidence of a large ontogenetic change in leaf development. Phyletic decrease in size corresponds to a latitudinal and elevational gradient suggesting speciation has taken place from north to south and from high to low elevation. However, this pattern is obscured disjunct distributions in some species.     

A phylogenetic analysis of subtribe Pleurothallidinae (Orchidaceae)

A cladistic analysis of subtribe, Pleurothallidinae (Orchidaceae) is based on 45 anatomical/ morphological characters. The ingroup members comprise 24 genera; the large genus Pleurothallis consists of two subgenera and ten species complexes. Three taxa representing subtribes Laeliinae and Arpophyllinae are designated as outgroup. Eight most parsimonious trees were discovered using computer assisted software (length = 230; CI = 0.27). The hypothesis that subtribe Pleurothallidinae has undergone a unilinear reduction in the number of pollinia is not supported by this study. Although the eight-pollinia state as represented by Octomeria apparently is plesiomorphic, the two-pollinia and four-pollinia states arose early in the phylogeny of the subtribe. Both two-and four-pollinia states subsequently reappeared as parallelisms. The six-pollinia state exhibited in Brachionidium is autapomorphic. This cladistic analysis suggests that Pleurothallis is not a natural genus and, perhaps may be divided into several discrete genera.     

A phylogenetic analysis of subtribe Pleurothallidinae (Orchidaceae)

A cladistic analysis of subtribe, Pleurothallidinae (Orchidaceae) is based on 45 anatomical/ morphological characters. The ingroup members comprise 24 genera; the large genus Pkurothallis consists of two subgenera and ten species complexes. Three taxa representing subtribes Laeliinae and ArpophyUinae are designated as outgroup. Eight most parsimonious trees were discovered using computer assisted software (length = 230; CI = 0.27). The hypothesis that subtribe Pleurothallidinae has undergone a unilinear reduction in the number of pollinia is not supported by this study. Although the eight-pollinia state as represented by Octomeria apparently is plesiomorphic, the two-pollinia and four-pollinia states arose early in the phytogeny of the subtribe. Both two-and four-pollinia states subsequently reappeared as parallelisms. The six-pollinia state exhibited in Brachionidium is autapomorphic. This cladistic analysis suggests that Pkurothallis is not a natural genus and, perhaps may be divided into several discrete genera.     

A phylogenetic analysis ofLeucaena (Leguminosae: Mimosoideae)

Chloroplast DNA restriction fragment length polymorphisms have been used to reconstruct the maternal phylogeny of all the known taxa in the small neotropical legume genusLeucaena. Three major plastome clades were recognized, but these did not conform with relationships between the taxa proposed on other characters from morphology, cytology or hybridization. The maternal parentage of tetraploids within the genus has been proposed. Evidence for introgression was found between diploidL. diversifolia and tetraploidL. diversifolia. The implications of these results for the origin of the cultivated taxa are discussed.     

Molecular phylogenetic analysis ofChrysosplenium (Saxifragaceae) in Japan

The phylogeny of Japanese species ofChrysosplenium (Saxifragaceae) was examined using variation in DNA sequences. Sequences ofrbcL andmatK genes were compared for their feasibility for reconstructing the phylogeny ofChrysosplenium, and thematK sequences was found to give greater resolution. All but one of the 17 Japanese species have been examined formatK gene sequences and phylogenetic analysis of these data resulted in eight most parsimonious trees of 390 steps and a consistency index (Cl) of 0.823. The molecular phylogeny obtained was generally in agreement with Hara's (1957) classification based upon phenotypic similarity, although a conclusion needs extensive examination of the genus on a world-wide level. Using the phylogenetic data, character evolution was examined, especially in the characters traditionally used for grouping infrageneric taxa. Differentiation of opposite and alternate phyllotaxis appears to have occurred only once in the course of evolution ofChrysosplenium.     

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.     

Floral morphology and phylogenetic analysis inCrossostylis (Rhizophoraceae)

Floral morphology in all ten species ofCrossostylis, one of the inland genera of Rhizophoraceae and is distributed in the South Pacific Islands, was studied to increase our knowledge on floral features of individual species as well as on relationships among the species. Flowers ofCrossostylis, unlike those of the other Rhizophoraceae, always have semi-inferior ovaries and entire petals, but are diversified concerning the number and arrangement of stamens and carpels, the presence or absence of staminodia, sexuality and the structure of nectaries. Despite some doubt of the presence of apomorphies restricted to the whole genus, we tentatively definedCrossostylis by a combination of the presence of the semi-inferior ovary, entire petals, and arillate seeds, and then performed cladistic analysis on the basis of 24 floral and other morphological characters and withCarallia andGynotroches as outgroups. Our phylogenetic analysis suggested that the species ofCrossostylis are divided into two monophyletic groups: one comprising six species distributed in the Solomon Islands, Vanuatu and the Fiji Islands, and the other comprising four species distributed in New Caledonia and Polynesia.     

Multilocus phylogenetic analysis of true morels (Morchella) reveals high levels of endemics in Turkey relative to other regions of Europe

The present study was conducted to better understand how the phylogenetic diversity of true morels (Morchella) in Turkey compares with species found in other regions of the world. The current research builds on our recently published surveys of 10 Turkish provinces and the northern hemisphere in which DNA sequence data from 247 and 562 collections respectively were analyzed phylogenetically. Herein we report on phylogenetic analyses of 243 additional collections made in spring 2009 and 2010 from eight additional provinces in the Aegean, Black Sea, central Anatolia, eastern Anatolia and Marmara regions of Turkey. Our analysis revealed that five species within the Esculenta clade (yellow morels) and 15 species within the Elata clade (black morels) were present in Turkey. Our preliminary results also indicate that M. anatolica, recently described from a collection in Mu?la province in the Aegean region of Turkey, is a closely related sister of M. rufobrunnea; these two species comprise a separate evolutionary lineage from the Esculenta and Elata clades. Nine species of Morchella currently are known only from Turkey, four species were present in Turkey and other European countries and seven species might have been introduced to Turkey anthropogenically. Three of the putatively exotic species in Turkey appear to be endemic to western North America; they are nested within a clade of fire-adapted morels that dates to the late Oligocene, 25 000 000 y ago. Our results indicate that there are roughly twice as many Morchella species in Turkey compared with the other regions of Europe sampled. Knowledge of Morchella species diversity and their biogeographic distribution are crucial for formulating informed conservation policies directed at preventing species loss and ensuring that annual morel harvests are sustainable and ecologically sound.     

Buccal capsule development as a consideration for phylogenetic analysis of Rhabditida (Nemata)

 Bacterial feeding nematodes in the order Rhabditida including Zeldia punctata (Cephalobidae) and Caenorhabditis elegans (Rhabditidae) differ profoundly in the buccal capsule parts and associated cells. We carried out a range of tests to determine which buccal capsule parts and cells are evolutionarily homologous between the representative species of the two families. Tests included reconstruction of the buccal capsule and procorpus with transmission electron microscopy (TEM), nuclei position and morphology using 4,6-diamidino-2-phenylindole (DAPI) staining, and cell lineage using four dimensional (4D) microscopy. The lining of the buccal capsule of Z. punctata and additional Cephalobidae includes four sets of muscular radial cells, ma, mb, mc and md, in contrast to C. elegans and additional Rhabditidae, which has two sets of epithelial cells (e1, e3) and two sets of muscle cells (m1, m2). Cell lineage of a nematode closely related to Z. punctata, Cephalobus cubaensis, supports the hypothesis that in cephalobids the e1 and e3 cells become hypodermal cells or are programmed to die. Our findings contradict all previous hypotheses of buccal capsule homology, and suggest instead that ma and mb in Z. punctata are homologous to m1 and m2 in C. elegans respectively. We also hypothesize that ma and mb could be homologous to primary and secondary sets of stylet-protractor muscle cells in the plant parasitic Tylenchida. Received: 24 March 1998 / Accepted: 24 July 1998     

A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae): implications for insect phylogenetic studies

We assessed the utility of eight DNA sequence markers (5.8S rDNA, 18S rDNA, 28S rDNA, ITS regions, long-wavelength opsin, elongation factor 1-alpha, cytochrome b, and cytochrome oxidase I) in reconstructing phylogenetic relationships at various levels of divergence in gallwasps (Hymenoptera: Cynipidae), using a set of eight exemplar taxa. We report sequence divergence values and saturation levels and compare phylogenetic results of these sequences analyzed both separately and combined to a well-corroborated morphological phylogeny. Likelihood ratio tests were used to find the best evolutionary model fitting each of the markers. The likelihood model best explaining the data is, for most loci, parameter rich, with strong A-T bias for mitochondrial loci and strong rate heterogeneity for the majority of loci. Our data suggest that 28S rDNA, elongation factor 1-alpha, and long-wavelength opsin may be potentially useful markers for the resolution of cynipid and other insect within-family-level divergences (circa 50-100 mya old), whereas mitochondrial loci and ITS regions are most useful for lower-level phylogenetics. In contrast, the 18S rDNA marker is likely to be useful for the resolution of above-family-level relationships.     

Preliminary phylogenetic analysis of the Protanisoptera (Insecta: Odonatoptera)

The Permian suborder Protanisoptera (Insecta: Odonatoptera) is revised and a new phylogenetic hypothesis proposed after analyses based on wing venation and different outgroups. After our study the families Camptotaxineuridae and Kaltanoneuridae are excluded from the Protanisoptera. After a new phylogenetic analysis, the family Permaeschnidae is redefined and the families Pholidoptilidae, Polytaxineuridae, Callimokaltaniidae and Hemizygopteridae are restored, as already proposed for the latter three families by Bechly (1996). The new genus Proditaxineura is described. The genus Gondvanoptilon RÖSLER et al., 1981 is excluded from the Meganisoptera: Erasipteridae and re-included in the Permaeschnidae, as already proposed by Bechly (1998). Permaeschna proxima MARTYNOV, 1931 is considered as a junior synonym of Permaeschna dolloi MARTYNOV, 1931. Pholidoptilon camense ZALESSKY, 1931 is excluded from Permaeschna MARTYNOV, 1931 and the genus Pholidoptilon [Zalessky, 1931a] and [Zalessky, 1931b] is restored. Ditaxineurella stigmalisMARTYNOV, 1940 is excluded from the Hemizygopteridae and considered as a Protanisoptera Incertae sedis.