ANALYSIS OF A PLASTID MULTIGENE DATA SET AND THE PHYLOGENETIC POSITION OF THE MARINE MACROALGA CAULERPA FILIFORMIS (CHLOROPHYTA)1

Molecular phylogenetic relationships within the Chlorophyta have relied heavily on rRNA data. These data have revolutionized our insight in green algal evolution, yet some class relationships have never been well resolved. A commonly used class within the Chlorophyta is the Ulvophyceae, although there is not much support for its monophyly. The relationships among the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae are also contentious. In recent years, chloroplast genome data have shown their utility in resolving relationships between the main green algal clades, but such studies have never included marine macroalgae. We provide partial chloroplast genome data (～30,000 bp, 23 genes) of the ulvophycean macroalga Caulerpa filiformis (Suhr) K. Herig. We show gene order conservation for some gene combinations and rearrangements in other regions compared to closely related taxa. Our data also revealed a pseudogene (ycf62) in Caulerpa species. Our phylogenetic results, based on analyses of a 23‐gene alignment, suggest that neither Ulvophyceae nor Trebouxiophyceae are monophyletic, with Caulerpa being more closely related to the trebouxiophyte Chlorella than to Oltmannsiellopsis and Pseudendoclonium.     

Histochemical analysis of oligochaete body wall

The body wall muscle fibers of Rinchelmis limosella and Enchytraeus albidus have been hystochemically characterized. The results have been compared with similar data on Lumbricus terrestris and Hirudo medicinalis. The various enzymatic activities have been correlated with the ultrastructural data and a possible functional meaning of the different muscle layers has been proposed.     

New approaches to estimating the mutagenic potential of chemicals

New developments in mutagenic risk assessment have appeared in the past few years. New methods have been developed such asin vitro micronucleus assay for chromosomal alterations, comet assay for primary DNA damage, use of transgenic animals to detectin vivo gene mutations, and fluorescent in situ hybridization method to detect aneuploidy. Other new methods will be developed in the few next years, including the use of DNA chips and the use of molecular biological methods. Several micromethods have been developed to test a great number of chemical compounds. New concepts have appeared concerning interpretation of data, and particularly of thresholds especially in the case of aneugens; in some cases metabolic or mechanistic thresholds were demonstrated. Genotoxic studies are best integrated into toxicological testing: for example, some genotoxicity tests can be integrated into subacute toxicology; interpretation of data includes metabolism; and toxicokinetic data relate to other toxicological studies. Conversely, genotoxicity data can be used to interpret toxicology studies. This revised version was published online in July 2006 with corrections to the Cover Date.     

Brief communication: Ectocranial suture closure in Pongo: Pattern and phylogeny

Ectocranial suture fusion patterns have been shown to contain biological and phylogenetic information. Previously the patterns of Homo, Pan, and Gorilla have been described. These data reflect the phylogenetic relationships among these species. In this study, we applied similar methodology to Pongo to determine the suture synostosis progression of this genus, and to allow comparison to previously reported data on other large‐bodied hominoids. We hypothesized these data would strengthen the argument that suture synostosis patterns reflect the phylogeny of primate taxa. Results indicate that the synostosis of vault sutures in Pongo is similar to that reported for Gorilla (excluding Pan and Homo). However, the lateral‐anterior pattern of fusion, in which there is a strong superior to inferior pattern, for Pongo is unique among these species, reflecting its phylogenetic distinctness among great ape taxa. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians

Species of Valerianaceae are a common component of the alpine flora throughout the Northern Hemisphere as well as the Andes of South America. Sequence data from three chloroplast markers (psbA-trnH intron, trnK-matK intron, and the trnL-F region) along with the internal transcribed spacer region (ITS) of nuclear ribosomal DNA were used to infer relationships within Valerianaceae. Both genomes, as well as a combined data set, provide support for the major clades within the group and do not support a monophyletic Valeriana. In addition, these data indicate that Plectritis is nested within South American Valeriana, as opposed to being sister to Centhranthus as previously hypothesized. Valerianaceae appear to have originated in Asia, probably in the Himalayas, and subsequently to have dispersed several times to Europe and to the New World. Our results imply that Valerianaceae colonized South America on multiple occasions from the north. In one of these cases there appears to have been a substantial and rapid radiation, primarily in the high elevation paramo habitat. A variety of methods were used to estimate divergence times to determine when Valerianaceae might have colonized South America. Regardless of the method and fossil constraints applied, our estimates suggest that Valerianaceae colonized South America prior to the formation of the Isthmus of Panama.     

中国疱衣属地衣的初步研究

报道了中国疱衣科疱衣属一新记录种：类喜马拉雅疱衣(Phlyctis subhimalayensis S. Joshi&Upreti),提供了该种的形态特征描述和DNA数据支撑。还对中国已知的疱衣属物种进行了简要描述。同时讨论了近似种,编制了分种检索表,为疱衣属的进一步研究提供了基础资料。     

Phylogenetic position of Cyperus clandestinus (Cypereae,Cyperaceae) clarified by morphological and molecular evidence

Extreme morphological reduction and convergent evolution can obscure taxonomic relationships. This phenomenon is frequently encountered in Cyperaceae, where characters traditionally used to diagnose genera have been shown to have evolved independently multiple times. The Ethiopian high‐altitude perennial first described as Cyperus clandestinus was subsequently moved to Ficinia because it has spiral glume arrangement, unlike typical Cyperus species, which have distichous glume arrangement. However, this position has remained uncertain as no nutlets have previously been studied to establish the presence or absence of the gynophore – the synapomorphy for Ficinia. We resolve this 140‐year‐old puzzle by describing the morphology of the nutlet, which lacks a gynophore, and use DNA sequence data to resolve the taxon within Cyperus. Cyperus clandestinus was found to be closely related to Remirea maritima and Cyperus cyperoides in the C₄Cyperus clade, whose members predominantly have distichously arranged glumes. This provides further evidence for the unreliability of glume arrangement as a character to distinguish between members of the Cyperus and Ficinia clades, whereas gynophore presence is more congruent with molecular data.     

A new phylogeny of Stegosauria (Dinosauria,Ornithischia)

The stegosaurs are some of the most easily recognizable dinosaurs, but are surprisingly rare as fossils. Consequently much remains unknown about their palaeobiology, and every new stegosaurian find contributes to our understanding of the evolution of the clade. Since the last attempt to examine the evolutionary relationships of Stegosauria, new specimens have come to light, including the most complete individual of Stegosaurus ever found, new taxa have been described and, perhaps most importantly, new methods for analysis of cladistic datasets have been produced. In the light of these new data and technological advances, the phylogenetic relationships of the stegosaurs and basal armoured dinosaurs are investigated. The inclusion of continuous data results in much better resolution than was previously obtained, and the resulting single most parsimonious tree supports re‐erection of the genera Miragaia and Hesperosaurus, which had previously been synonymized with Dacentrurus and Stegosaurus respectively. The recently described genus Alcovasaurus is resolved as a basal thyreophoran, but this is most likely a consequence of a very high degree of missing data and the questionable ontogenetic stage of the specimen. Examination of the effects of continuous data on the analysis suggest that while it contains a phylogenetic signal congruent with that of discrete data and provides better resolution than discrete data alone, it can affect topologies in unpredictable ways, particularly in areas of the tree where there are large amounts of missing data. The phylogeny presented here will form the basis for future work on the palaeobiology of the plated dinosaurs.     

An assessment of the geological evidence for previous Acanthaster outbreaks

Much debate has surrounded the notion that outbreaks of the crown-of-thorns starfish (Acanthaster planci) have occurred in the geological past and hence are natural phenomena. As this debate has recently been renewed, we have reassessed statistically data presented by Frankel (1977, 1978) as evidence for the occurrence of past outbreaks. This was done using Frankel's data as well as those from extensive starfish surveys conducted prior to the commencement of his research. Our analysis of these data indicates that the occurrence of A. planci remains in recent sediments is independent of whether or not the reef from which the sample was collected had experienced a recent outbreak. Based on this premise, it is not possible to infer from Frankel's data the occurrence of past outbreaks from similar material in much older sediments. Thus while the data presented by Frankel (1977, 1978) may show that A. planci has existed within the Great Barrier Reef for at least several thousand years it does not demonstrate that outbreaks of this starfish have occurred in the geological past.     

Piper protrusum (Piperaceae), a new species from southern Thailand based on morphological and molecular evidence

Abstract Piper protrusum Chaveer. & Tanee, sp. nov. is described and illustrated. It dominantly comprises three branching types with three different types of leaf blades, bases, and apexes. The critical distinguishing character is the protruded receptacle having a bract and nine stamens. Individual plants have been discovered in areas of Southern Thailand since 2004 without reproductive parts. The investigated sites were revisited several times, and an individual with flowers was finally found in July 2009. Phylogenetic analysis of the new species and five similar species is carried out based on DNA fingerprinting. The genetic distances between the new species and five similar species range from 0.25 to 0.35, supporting new species designation. Molecular data conform to morphological data in validating that it is a new species. Additionally, its DNA barcodes have been provided for further identification in case the morphological data is unclear. The sequence data have been submitted to the GenBank database under accession numbers GU980898 (rpoB gene), GU980899 (rpoC1 gene), and GU980900 (psbA‐trnH region).     

Accounting for missing data in the estimation of contemporary genetic effective population size (Ne)

Theoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error. One commonly used solution for the calculation of contemporary effective population size (N_e) is to calculate the effective sample size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (N_e). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known N_e and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed‐inverse variance‐weighted harmonic mean) consistently performed the best for both single‐sample and two‐sample (temporal) methods of estimating N_e and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per‐locus sample size components.     

PHYLOGENY OF THE BASAL LINEAGES OF STREPTOPHYTA BASED ON RBCL AND ATPB GENE SEQUENCE DATA

The streptophytes comprise the Charophyceae sensu Mattox and Stewart (a morphologically diverse group of fresh‐water green algae) and the embryophytes (land plants). Several charophycean groups are currently recognized. These include the Charales, Coleochaetales, Chlorokybales, Klebsormidiales and Zygnemophyceae (Desmidiales and Zygnematales). Recently, SSU rRNA gene sequence data allied Mesostigma viride (Prasinophyceae) with the Streptophyta. Complete chloroplast sequence data, however, placed Mesostigma sister to all green algae, not with the streptophytes. Several morphological, ultrastructural and biochemical features unite these lineages into a monophyletic group including embryophytes, but evolutionary relationships among the basal streptophytes remain ambiguous. To date, numerous studies using SSU rRNA gene sequences have yielded differing phylogenies with varying degrees of support dependent upon taxon sampling and choice of phylogenetic method. Like SSU data, chloroplast DNA sequence data have been used to examine relationships within the Charales, Coleochaetales, Zygnemophyceae and embryophytes. Representatives of all basal streptophyte lineages have not been examined using chloroplast data in a single analysis. Phylogenetic analyses were performed using DNA sequences of rbcL (the genes encoding the large subunit of rubisco) and atpB (the beta‐subunit of ATPase) to examine relationships of basal streptophyte lineages. Preliminary analyses placed the branch leading to Mesostigma as the basal lineage in the Streptophyta with Chlorokybus, the sole representative of the Chlorokybales, branching next. Klebsormidiales and the enigmatic genus Entransia were sister taxa. Sister to these, the Charales, Coleochaetales, embryophytes and Zygnemophyceae formed a monophyletic group with Charales and Coleochaetales sister to each other and this clade sister to the embryophytes.     

Paternal age and Down's syndrome data from prenatal diagnoses (DFG)

Summary From prenatal diagnosis data obtained on mothers aged 35 years and above in the Federal Republic of Germany (DFG data), older fathers are demonstrated to have an increased risk of having trisomy 21 offspring. For paternal ages of 41 years upward, the age effect is quite strong. The risk for a fetus to have any de novo chromosomal aberration increases more with advancing paternal age for older mothers than for younger ones. Thus the ages of both parents have to be taken into account as an indication for prenatal diagnosis. Risk figures for trisomy 21 and for any de novo chromosomal aberration are given, together with preliminary recommendations for prenatal diagnosis for different combinations of parental ages.     

The phylogenetic position of Apterosperma (Theaceae) based on morphological and karyotype characters

Classifications of Theaceae have usually placed the endangered monotypic genus Apterosperma in tribe Schimeae (x=18), whereas recent molecular phylogenetic evidence supports its transfer to tribe Theeae (x=15). Molecular data have not resolved the phylogenetic position of Apterosperma within Theeae. We investigated the chromosome number and karyotype of Apterosperma in the context of molecular and morphological phylogenetic evidence to provide further insight into the placement of Apterosperma within Theaceae. The chromosome number and karyotype was found to be 2n = 30 = 26m + 4sm, consistent with the transfer of Apterosperma to tribe Theeae. When the chromosome data were incorporated into a data set of 46 other nonmolecular characters, Apterosperma was placed as the first-diverging lineage within the clade comprising tribe Theeae. This supports its placement based on molecular data. The low intrachromosomal asymmetry (type 1A) of Apterosperma, presumably ancestral for the family, is also consistent with this placement. Character optimization strongly supports a base chromosome number of x=15 for tribe Theeae. Because of variable and sometimes conflicting chromosome count reports of species in tribes Schimeae and Stewartieae, the base chromosome number of Theaceae could be either x=15 or 17.     

PHYLOGENY OF CARTERIA (CHLOROPHYCEAE) INFERRED FROM MOLECULAR AND ORGANISMAL DATA1

Comparative ultrastructural data have shown that at least two distinct groups exist within Carteria. Similarly, interpretations of variation in gross morphological features have led to the discovery of morphologically distinct groups within the genus. Partial sequences from the nuclear-encoded small- and large-subunit ribosomal RNA molecules of selected Carteria taxa were studied as a means of 1) testing hypotheses that distinct groups of species exist within the genus and 2) assessing monophyly of the genus. Parsimony analysis of the sequence data suggests that three Carteria species, C. lunzensis, C. crucifera, and C. olivieri, form a monophyletic group that is the basal sister group to all other ingroup flagellate taxa (including species of Chlamydomonas, Haematococcus, Stephanosphaera, Volvox, and Eudorina). Two other Carteria taxa, C. radiosa and Carteria sp. (UTEX isolate LB 762), form a clade that is the sister group to a clade that includes Haematococcus spp., Chlamydomonas spp., and Stephanosphaera. Thus, the sequence data support the interpretations of ultrastructural evidence that described two distinct Carteria lineages. Moreover, the sequence data suggest that these two Carteria groups do not form a monophyletic assemblage. Parsimony analysis of a suite of organismal (morphological, ultra-structural, life history, and biochemical) character data also suggest two distinct lineages among the five Carteria taxa; however, the organismal data are ambiguous regarding monophyly of these Carteria taxa. When the two independent data sets are pooled, monophyly of Carteria is not supported; therefore, the weight of available evidence, both molecular and organismal, fails to support the concept of Carteria as a natural genus.     

Phylogenetic Studies in the Monocot Subclass Alismatidae: Evidence for a Reappraisal of the Aquatic Order Najadales

Within the angiosperm subclass Alismatidae (= superorder Alismatiflorae), contemporary taxonomists have often assigned the families Hydrocharitaceae and Najadaceae to different orders. The Najadaceae are presumably allied to a variety of aquatic families in the order Najadales, whereas the Hydrocharitaceae have been segregated as the order Hydrocharitales or placed within the order Alismatales. Analyses of DNA sequence data from the chloroplast gene rbcL, however, indicate that Najadaceae have a much closer phylogenetic relationship to Hydrocharitaceae than to families of the "Najadales" (Cymodoceaceae, Potamogetonaceae, Ruppiaceae, Scheuchzeriaceae, Zannichelliaceae, Zosteraceae). This association supports previous studies based upon examination of floral structure and seed coat anatomy. The rbcL sequence data also indicate that the Zosteraceae and Potamogetonaceae are closely related families. The rbcL sequence of Zostera is actually more similar to that of Potamogeton richardsonii than is the sequence of the latter to a congener, Potamogeton amplifolius. The marine, dioecious, hydrophilous genus Zostera has acquired a number of distinctive adaptations, but probably diverged relatively rapidly from freshwater Potamogetonaceae. Molecular data place Ruppiaceae as a sister group to the marine Cymodoceaceae and do not support the commonly accepted merger of Ruppiaceae and Potamogetonaceae.     

Haplotypic polymorphisms of the TNFB gene

The NTFB genes from two major histocomptibility complex (MHC) ancestral haplotypes have been compared. The genes carried by the ancestral haplotypes 8.1 (A1,B8,BfS,C4AQ0, C4B1,DR3) and 57.1 (A1,B57, BfS,C4A6,C4B1,DR7) were cloned and sequenced to determine the degree of polymorphism. In this report we show that the r e spective TNF genes are allelic and have unique nucleotide sequences. The data demonstrate the presence of three nucleotide differences between the TNFB alleles of 8.1 and 57.1. Two of the differences occur in untranslated regions of the gene but the third nucleotide change results in amino acid differences in the mature TNFB protein. These polymorphisms may have implications with respect to differential regulation in disease-and nondisease-associated haplotypes.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M55913.     

Breeding abundance of threatened raptors as estimated from occurrence data

A model derived from the negative binomial distribution (NBD) has been proposed to solve the problem of predicting abundance of species from occurrence maps. The viability of NBD was explored for predicting the breeding abundance of five threatened species of raptor: Bonelli's Eagle Hieraaetus fasciatus, Golden Eagle Aquila chrysaetos, Peregrine Falco peregrinus, Lanner Falco biarmicus and Lesser Kestrel Falco naumanni. First, the accuracy of the NBD was tested in a reference area where the species abundance and occurrence were known through intensive field surveys. Next, an estimation of regional abundance derived from NBD was made for each species. These estimates were then compared to the existing regional data for the five raptors. The spatial distributions of the species were strongly aggregated, with F. peregrinus correctly showing the most widespread area of occupancy. The NBD gave a good approximation of the breeding abundance of the raptors, but tended to overestimate real data, particularly the regional data for falcons. Difficulties in species detection, insufficient sampling effort (F. biarmicus) or data collected over long time spans when population size increased (F. naumanni) may have reduced the NBD's resolution power. The ability of the method to predict local abundances over large areas from readily available presence‐absence data, with relatively low fieldwork effort, could have considerable applications in conservation biology.