PAUP Analysis Research Articles

Analysis of Genetic Diversity Between Eriobotrya japonica (Thunb.) Lindl. (Rosaceae) Populations Growing in the Aegean Region of Turkey

In this study, we performed a genetic diversity using RAPD (Random amplified polymorphic DNA) and ISSR (Inter-simple sequence repeats) markers for some Eriobotrya japonica populations grown in the Aegean region of Turkey. PCR was performed with all DNA samples and primers with ability of scoring band. Phylogenetic analysis and pairwise genetic distance between the populations were calculated by using the PAUP analysis program. According to the RAPD data, a total of 33 bands were obtained and 21 of them were polymorphic. The closest genetic distance (0.09677) was found between Aydın and Nazilli populations, while the most distant value was found 0.44000 between Salihli and Nazilli populations. According to the ISSR data, a total of 43 bands were obtained and 18 of them were polymorphic. The closest genetic distance (0.09302) was found between İzmir and Aydın populations, while the most distant values (0.48276) were found between Denizli and Nazilli populations. As a result of this study, the rate of polymorphism obtained in ISSR technique was found to be lower than the RAPD technique.

A molecular phylogeny of Callianassidae and related families (Crustacea : Decapoda : Axiidea) with morphological support

The axiidean families Callianassidae and Ctenochelidae, sometimes treated together as Callianassoidea, are shown to represent a monophyletic taxon. It comprises 265 accepted species in 74 genera, twice this number of species if fossil taxa are included. The higher taxonomy of the group has proved difficult and fluid. In a molecular phylogenetic approach, we inferred evolutionary relationships from a maximum-likelihood (ML) and Bayesian analysis of four genes, mitochondrial 16S rRNA and 12S rRNA along with nuclear histone H3 and 18S rRNA. Our sample consisted of 298 specimens representing 123 species plus two species each of Axiidae and Callianideidae serving as outgroups. This number represented about half of all known species, but included 26 species undescribed or not confidently identified, 9% of all known. In a parallel morphological approach, the published descriptions of all species were examined and detailed observations made on about two-thirds of the known fauna in museum collections. A DELTA (Description Language for Taxonomy), database of 135 characters was made for 195 putative species, 18 of which were undescribed. A PAUP analysis found small clades coincident with the terminal clades found in the molecular treatment. Bayesian analysis of a total-evidence dataset combined elements of both molecular and morphological analyses. Clades were interpreted as seven families and 53 genera. Seventeen new genera are required to reflect the molecular and morphological phylograms. Relationships between the families and genera inferred from the two analyses differed between the two strategies in spite of retrospective searches for morphological features supporting intermediate clades. The family Ctenochelidae was recovered in both analyses but the monophyly of Paragourretia was not supported by molecular data. The hitherto well recognised family Eucalliacidae was found to be polyphyletic in the molecular analysis, but the family and its genera were well defined by morphological synapomorphies. The phylogram for Callianassidae suggested the isolation of several species from the genera to which they had traditionally been assigned and necessitated 12 new generic names. The same was true for Callichiridae, with stronger ML than Bayesian support, and five new genera are proposed. Morphological data did not reliably reflect generic relationships inferred from the molecular analysis though they did diagnose terminal taxa treated as genera. We conclude that discrepancies between molecular and morphological analyses are due at least in part to missing sequences for key species, but no less to our inability to recognise unambiguously informative morphological synapomorphies. The ML analysis revealed the presence of at least 10 complexes wherein 2–4 cryptic species masquerade under single species names.

Genetic variation and molecular relationships taxa of Conringia heist. ex Fabr. (Brassicaceae) based on RAPD markers in Turkey

In this study, genetic variation and phylogenetic analysis of 13 populations of 6 species belonging to Conringia genus spreading in Turkey were performed using RAPD markers. Genomic DNA isolation from the leaves of the Conringia plant samples was performed via using a commercial kit. Seven RAPD primers were used to identify the genetic diversity between the populations. Polymerase Chain Reaction (PCR) was performed using DNA samples and primers. PCR products were resolved using agarose gel electrophoresis and visualized under UV light. All gel images were analyzed, and the absence and presence of polymorphic bands were scored. The total of 34 DNA bands were detected by seven RAPD primers. PAUP 4.0b10 analysis program was used to calculate phylogenetic tree and genetic distances between the species. The phylogenetic tree was obtained using the UPGMA algorithm and it was composed of two clades. According to the PAUP analysis, the species having the closest distance between each other are C. planisiliqua (Ankara-Aya?) and C. planisiliqua (Ankara-Nall?han) with the value of 0.000 and those having the longest distance are C. grandiflora (Akseki ?ukurk?y) and C. orientalis (Elaz??-Baskil) with the value of 0.6000. The results suggest that the RAPD markers are useful tools to demonstrate the genetic relationships between populations of the Conringia species.

Phylogenetic Analysis of Chrysochamela (Fenzl) Boiss. (Brassicaceae) Taxa Growing in Turkey

In this study, we performed a genetic diversity analysis using RAPD (Random Amplified Polymorphic DNA) and ISSR (Inter simple sequence repeat) markers for some Chrysochamela species growing in Turkey. PCR was performed using RAPD and ISSR primers and genomic DNA samples from each specimen, and the resulting bands were scored. Phylogenetic relationships and genetic distances between the studied taxa were calculated using the PAUP analysis program. According to the RAPD analysis, the closest genetic distance was found to be 0.20000 between C. noeana populations, while the most distant values were found as 0.60000 between C. noeana and C. elliptica. The ISSR analysis also revealed the closest genetic distance as 0.34043 between C. noeana populations, while the most distant values were found to be 0.55319 between C. noeana and C. elliptica. UPGMA (unweighted pair group method with arithmetic mean) dendrogram generated for both RAPD and ISSR analyses consisted of two groups. As a result, it was found that RAPD data were more appropriate for comparison with the previous anatomical and morphological data of the studied taxa.

Molecular Characterization of Vitex agnus-castus L. (Verbenaceae) Populations Grown in Aydin, Turkey

In this study, we performed a genetic diversity analysis using RAPD markers for some Vitex agnus-castus populations grown in Aydin, Turkey. Total genomic DNA isolation from the leaves of Vitex agnus-castus was performed using a commercial kit. Seven RAPD primers (OPA-02, OPA-05, OPA-13, OPA-15, OPA-16, OPA-18, OPA-20) were used to determine genetic diversity among populations. Polymerase Chain Reaction (PCR) was performed with all genomic DNA samples and primers. PCR products were run in agarose gel electrophoresis and visualized under UV light. The amplified products were scored as bands (1) and no bands (0) for all gel images and their matrix files were generated. A total of 36 characters were obtained from the primers. Phylogenetic relationships and genetic distances between the cultivars were calculated by using the PAUP* (Phylogenetic Analysis Using Parsimony and other methods) program. According to PAUP analysis, the closest genetic distances were between Çine pink flower and Çakmar purple flower, and Çakmar pink flower and Çakmar purple flower populations with a value of 0.05556; and the greatest genetic distance was between Çakmar pink flower and Köşk purple flower populations with a value of 0.36111. In the phylogenetic analysis obtained using UPGMA algorithms, the phylogenetic tree consisted of four groups. The results suggest that RAPD markers are useful tools for determining genetic relationships among Vitex agnus-castus genotypes.

Comparative morphology of antennae in Cicadoidea (Insecta: Hemiptera), with respect to functional, taxonomic and phylogenetic implications

The antennae of 25 cicada species were examined using light and scanning electron microscopies, with particular attention given to the structures and arrangement of antennal sensilla in phylogenic analysis. Eight morphologically different types of sensilla were observed: sensilla trichodea (subtypes I, II and III), sensilla basiconica, sensilla coeloconica (subtypes I, II and III), sensilla styloconica, foramen olfactorium, sensilla cavitata-peg (subtypes I and II), sensilla campaniformia and cuticular spines. The arrangement of antennal sensilla tends to be a highly regular distribution model, i.e., sensilla trichodea and sensilla basiconica mainly spread in the scape and pedicel, while sensilla coeloconica, foramen olfactorium and/or sensilla styloconica merely spread in the flagellum. The overall topology of phylogeny of Cicadidae based on antennal characters using PAUP, WinClada and IQtree analyses is compatible with the classification of previously related studies, but shows that the genus Karenia Distant, 1888 is more allied to the members of Cicadinae, and that the tribe Cicadatrini Distant, 1905 is located in the subfamily Cicadettinae instead of Cicadinae, which is consistent with the results of a recent molecular phylogenetic study of Cicadidae. The results imply that the traditional grouping of Cicadinae and Cicadettinae based on the presence or absence of timbal covers is unsound, which also supports related previous analyses based on morphology of Cicadidae. Related genera and tribes in Cicadidae need to be further addressed by phylogenetic analysis based on more morphological features combined with molecular data.

New exceptionally well-preserved specimens of “Zangerlia” neimongolensis from Bayan Mandahu, Inner Mongolia, and their taxonomic significance

Two exceptionally well-preserved specimens of “Zangerlia” neimongolensis provide additional information on the structure of the skull, shell and limbs of this taxon. These specimens show that the carapace is more similar to that of Hanbogdemys than was previously recognized. A PAUP analysis results in a single most parsimonious cladogram in which the type species of Zangerlia, Zangerlia testudinimorpha is separated from other species that have been included in that genus while “Z.” neimongolensis, “Zangerlia” ukaachelys and “Zangerlia” dzamynchondi and Jiangxichelys are grouped together. Both specimens are exceptional in being preserved in a life-like position: one is preserved with the skull in a retracted position; the other with the head and left forelimb both protracted and in a raised position. These positions suggest that they were entombed while still alive. Thus these specimens provide additional examples of rapid burial of vertebrates in the Bayan Mandahu locality, most likely from either by sand storms that dumped massive amounts of sand over a short period of time or by collapse of individuals in burrows.

The captorhinid reptile Captorhinikos valensis from the lower Permian Vale Formation of Texas, and the evolution of herbivory in eureptiles

ABSTRACT Captorhinikos valensis is a poorly known, multiple-tooth-rowed captorhinid reptile from the Lower Permian Vale Formation of Texas. Our reappraisal of C. valensis reveals it to be a small moradisaurine, exhibiting a maximum of five rows of bullet-shaped teeth in the multiple-rowed region of both the maxilla and the dentary. The slightly radiating organization of the tooth rows distinguishes C. valensis from the parallel arrangement of the tooth rows exhibited by all other moradisaurines. Captorhinikos valensis is also distinguishable from the coeval moradisaurine Labidosaurikos meachami by a more conspicuously denticulated, broader, ‘U’-shaped transverse flange of the pterygoid, a plesiomorphic morphology shared with the large, single-rowed captorhinid Labidosaurus hamatus. Postcranial information is limited to two short series of presacral vertebrae not associated with the cranial materials; open neurocentral sutures are present in one specimen, indicating immaturity at death. We investigated the relationships of C. valensis to other captorhinids by adding it to the data matrix of a previously published analysis that included several moradisaurine captorhinids. A branch-and-bound PAUP analysis discovered a single optimal tree. Whereas a previous analysis of captorhinid interrelationships found the (undifferentiated) genus Captorhinikos to fall outside of a clade composed of L. hamatus and the large moradisaurines, our analysis recovered C. valensis in a clade with the genera Labidosaurikos, Gansurhinus, Moradisaurus, and Rothianiscus (i.e., Moradisaurinae sensu stricto), and Captorhinikos chozaensis as the sister species of a clade that includes L. hamatus and Moradisaurinae s.s.; Captorhinikos chozaensis is no longer classifiable as a moradisaurine (according to our phylogenetic definition for the group), and should be assigned to a new genus. Stratigraphic calibration of our captorhinid phylogeny indicates that moradisaurines evolved by the middle Kungurian (middle Leonardian). SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP

Composite Single Cell Genetics and Clonal Phylogeny in Acute Lymphoblastic Leukaemia

AbstractAbstract 122Cancer clone development is widely regarded as an evolutionary or Darwinian process of genetic diversification and natural (or therapeutic) selection within tissue ecosystems. Emerging studies are providing strong evidence that dynamic and complex branching sub-clonal genetic architectures are a common feature of cancer (Greaves M and Maley CC Nature 2012). This complexity may underpin the intransigence of advanced cancer to therapeutic control, particularly as the critical ’driver’ cells – cancer or leukaemic stem cells, also appear to be genetically diverse within individual patients (Anderson K et al Nature 2011, Notta F et al Nature 2011). Sub-clonal architecture can only be fully determined through the study of large numbers of single cells uniformly sampled from the individual cancer of interest and assessed for composite genotype. Various technologies and approaches from fluorescent in situ hybridisation (FISH) to whole-genome sequencing of single cells have been applied to cancer and leukaemic cells but each approach has limitations. We have developed a novel multiplex microfluidic Q-PCR approach that allows unbiased single cell sampling, high throughput analysis of hundreds of individual cells and simultaneous detection of multiple genetic alterations in a single cell, including fusion genes, DNA copy number alterations (CNAs) and sequence-based mutations.As a proof of principle study we have applied this technique to REH, an acute lymphoblastic leukaemia (ALL) cell line that harbors the ETV6-RUNX1 fusion and a SNP in the EPO receptor gene, which we used as a surrogate mutation. We further determined a detailed sub-clonal genetic architecture for two ETV6-RUNX1 positive ALL patient samples with multiple point mutations and copy number alterations (determined by whole-genome sequencing) by interrogating approximately 400 flow cytometry sorted single cells with validation by FISH and standard sequencing. Briefly, single cells were lysed prior to multiplex specific (DNA) target amplification (STA) and Q-PCR using the 96.96 dynamic microfluidic array and the BioMarkï HD (Fluidigm, UK). Phylogenetic trees were constructed using maximum parsimony with PAUP analysis software.Interrogation of REH revealed that all single cells registered the ETV6-RUNX1 fusion and EPO receptor SNP, but 42% of cells gained either 1 or 2 additional copies of chromosome 21. Patient sample data revealed branching sub-clonal architectures in Case A in which all leukaemic cells harbored the fusion with additional point mutations but only sub-clones showed CNAs. In contrast, the sub-clonal architecture of Case B showed that whilst the ETV6-RUNX1 fusion was the earliest (or universal) genomic event, CNAs were relatively early events preceding the acquisition of point mutations (Figure 1). In both cases, the numerically predominant sub-clone harbored both point mutations and CNAs in addition to the presumptive initiating lesion, ETV6-RUNX1.These detailed and complex sub-clonal architectures would be masked by other genetic techniques. Single cell genetics coupled with deep genome sequencing is now technically feasible and provides an accurate portrait of the dynamic clonal complexity in leukaemia (and other cancers). Variegated genetics and clonal complexity in individual leukaemias has important implications for our understanding of molecular pathogenesis and for therapeutic targeting. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

First report of Phytophthora cinnamomi associated with stem cankers of Quercus cerris in South Africa

Quercus cerris (Turkey oak) is native to the orient and southeastern Europe (Balci & Halmschlager, 2003a). These trees are also commonly planted as non-native ornamentals in countries including South Africa. Recently, bleeding cankers on the stems, typical of Phytophthora infection, were found on Q. cerris trees growing on the Vergelegen Estate near Somerset West in the Western Cape Province of South Africa (Fig. 1). Phytophthora species have been recognised as being involved in the decline of Quercus spp., including Q. cerris, in eastern and north-central USA and Europe (Balci et al., 2007). Species isolated from soil associated with declining Q. cerris include P. citricola, P. cryptogea, P. quercina, and P. syringae (Balci & Halmschlager, 2003a,b), while P. ramorum and P. cinnamomi have been isolated directly from sapwood of trees showing bleeding cankers in Europe (Brown & Brasier, 2007). Isolations were made from diseased tissues of four Q. cerris trees using selective medium (Jung et al., 1996). Single hyphal tip cultures of putative Phytophthora spp. were transferred to V8 agar and stored in the culture collection (CMW) of the Forestry and Agricultural Biotechnology Institute at the University of Pretoria. DNA of all isolates was extracted and the ITS gene regions amplified and compared with sequences downloaded from GenBank (Accession Nos. AF266764, AY302148, AY302149, EF055303). The most parsimonious tree was obtained by PAUP analysis of the ITS dataset. The morphological characteristics for the four isolates from Q. cerris were the same as those described for P. cinnamomi, with typical corraloid hyphae. The sequences (GU799635, GU799636, GU799637, GU799638) of all isolates were identical to that of authenticated P. cinnamomi sequences. Four isolates (CMW 33386, 33387, 33388, 333889) identified as P. cinnamomi were tested for mating type by pairing these with known P. cinnamomi mating tester strains. Results of these pairings showed that isolate CMW33386 was of the A1 mating type and the remaining three isolates were of the A2 mating type. Plerotic oospores (38.5 μm in average diameter) were formed after seven days on V8 agar. Amphigynous antheridia were uni- or bicellular (16.2 times 17.6 μm average) (Fig. 2). It was impossible to obtain Q. cerris seedlings in South Africa so inoculation trials were conducted on six seedlings each of Q. robur and Q. suber and additionally 30 Q. palustris trees to determine whether the isolates collected were pathogenic to Quercus spp. A mycelial agar plug (6 mm) representing isolates of two different mating types were inserted into the stems of trees including an equal number for each isolate and a control inoculation with a sterile V8 agar plug. The seedlings were kept in a greenhouse at 25-30°C for two weeks. Necrotic lesions that developed were measured and photographed. The P. cinnamomi isolates produced lesions on all three Quercus species (Fig. 3). Lesions on Q. suber and Q. palustris were similar in length for both isolates. However, CMW33387 produced significantly larger lesions than CMW33386 on Q. robur. Phytophthora cinnamomi was re-isolated from all the lesions using the same selective medium. Results of this study have shown that P. cinnamomi is the most likely cause of the disease on Q. cerris. To the best of our knowledge, this is the first report of P. cinnamomi on Q. cerris in South Africa.

New material of the Late Cretaceous deltatheroidan mammal Sulestes from Uzbekistan and phylogenetic reassessment of the metatherian-eutherian dichotomy

Sulestes karakshi Nessov, 1985b (= Deltatheroides kizylkumensisNessov, 1993 = Marsasia aenigmaNessov, 1997) from the Late Cretaceous (Turonian) Bissekty local fauna, Kyzylkum Desert, Uzbekistan, is revised based on additional material from the type locality. It is characterized by an absence of palatal vacuities, double-rooted P1, an asymmetrical M3 with reduced metastylar lobe, an unreduced M4 and m4, obliquely oriented p1, anterior wall of the upper canine alveolus formed by premaxilla, and Meckelian groove on the dentary. PAUP analyses using a data matrix modified from Rougier et al. (1998, 2004) places Sulestes within Deltatheridiidae in an unresolved trichotomy with the Mongolian Campanian Deltatheridium and Deltatheroides. Oklatheridium from the Early Cretaceous of North America is sister taxon to these Late Cretaceous Asiatic deltatheridiidans. Deltatheridiidae is the sister group to other Metatheria including the crown clade Marsupialia. A Deltatheroides-like taxon from the Maastrichtian at Guriliin Tsav, Mongolia, is not related to the Stagodontidae but is sister taxon to other Boreometatheria. The North American Early Cretaceous Atokatheridium, Pappotherium, and Montanalestes are stem tribosphenic mammals, while Holoclemensia is at the base of the eutherian lineage.

Reiszorhinus olsoni, a new single-tooth-rowed captorhinid reptile from the Lower Permian of Texas

ABSTRACT A new genus and species of captorhinid reptile from the Lower Permian Waggoner Ranch formation of north-central Texas, Reiszorhinus olsoni, is described on the basis of well-preserved cranial material. The holotypic specimen, consisting of a partial skull and mandible, was misidentified by S. W. Williston in 1917 as Labidosaurus hamatus. Autapomorphies of the new taxon include recurved teeth and the possession of an extremely large Meckelian foramen on the medial surface of the lower jaw. The new taxon retains the primitive condition of a single row of dentary and maxillary marginal teeth. It is distinguished from other single-tooth-rowed captorhinids, with the exception of Labidosaurus hamatus, by its large size, and it lacks the marked cheek expansion found in other large captorhinids. PAUP and Bayesian analyses suggest the new genus is the most basal of described captorhinid genera with the exceptions of Romeria, Concordia, and Protocaptorhinus. The description of a new, large, single-tooth-rowed form suggests that, in addition to multiple tooth rows, relatively larger size evolved more than once in the basal reptilian family Captorhinidae.

Xeradipterus hatcheri, a new dipnoan from the Late Devonian (Frasnian) Gogo Formation, Western Australia, and other new holodontid material

ABSTRACT A new holodontid lungfish, Xeradipterus hatcheri, gen. et sp. nov., is described from the Late Devonian (Frasnian) Gogo Formation, Western Australia. The material comprises a single specimen preserved in a large concretion, represented by elements of the skull roof, cheek, lower jaw, palate, shoulder girdle, and parts of the postcranial skeleton. Xeradipterus, gen. nov., differs from other holodontids by its broad crushing dentition, prearticular tooth plates with pronounced heel, lack of prominent teeth, and ordered tooth rows, and by its parasphenoid morphology. Results of PAUP analyses of 82 characters for 33 dipnoan taxa revealed that the new genus is a member of the Holodontidae, suggesting a possible endemic radiation of holodontids within the Gogo fauna. In addition, new “Holodipterus” elderae material examined shows the shape and extent of the nasal capsules, and the presence of an anterior median callus for the first time.

PHYTOREOVIRUS-LIKE SEQUENCES ISOLATED FROM SALIVARY GLANDS OF THE GLASSY-WINGED SHARPSHOOTER HOMALODISCA VITRIPENNIS (HEMIPTERA: CICADELLIDAE)

The salivary glands of the Glassy-winged sharpshooter (GWSS), Homalodisca vitripennis Germar 1821, (syn. H. coagulata, Hemiptera: Cicadellidae) were collected and used to produce a cDNA library. Examination by BLASTX analyses identified 2 viral sequences, one a 610-base pair fragment and a second 839-base pair fragment, both of which had significant homology to viruses within the genus Phytoreovirus. Resequencing of the fragments confirmed sequence validities. These sequences were used for in silico protein translation and BLASTP analysis confirming the established homology. While the GWSS is the primary vector of Pierce’s disease of grapes, this is the first report that GWSS may be a vector of a phytoreoviruses. Phylogenetic and homology comparisons with BLASTX, BLASTP, and PAUP analyses indicated that the viral sequences isolated from GWSS were closely related to the viruses in the Family Reoviridae, Genus Phytoreovirus, specifically Rice Dwarf Phytoreovirus (RDV). RDV is the only plant reovirus that is not limited to the phloem. Phytoreoviruses are transmitted in a propagative manner by cicadellid leafhoppers (Hemiptera: Cicadellidae), which acquire and transmit them during feeding. Phytoreoviruses have been reported from Agallian, Agalliopsis, Nephotettix, and Recilia, genera of leafhoppers, with evidence for transovarial transmission. The GWSS, although considered to feed primarily from the xylem, ingests from other plant tissues, such as the phloem and mesophyll during probing similar to other leafhoppers. The feeding behavior and wide host range of the GWSS provides an overlapping condition for these two organisms, leafhopper and virus. GWSS will feed from grasses as a transitory host, and on herbaceous and woody plants as primary hosts, which may favor the acquisition and transmission of Phytoreovirus by this leafhopper. Monitoring for an increase of Phytoreovirus spread in graminaceous crops that are in proximity to vineyards or tree crop orchards, where GWSS occurs, such as in southern California, will provide a better understanding of the potential role of the GWSS as a disease vector in the spread of phytoreoviruses and other plant pathogens. The sequences have been deposited in NCBI database under the accession numbers (EF058280) for GWSS-V1, WHSg013C11 and (EF058281) for GWSS-V2, WHSg024H02.

Phylogenetic analysis by RFLP and sequencing of mitochondrial DNA in a Korean population

Analysis of molecular nature of mitochondrial DNA (mtDNA) could be powerful marker for anthropological studies of modern populations. While population genetic studies on mtDNA have been reported for several ethnic groups, no such study has been documented for the Korean population. We surveyed mtDNA polymorphisms in the HVS I of noncoding D-loop region and its upstream region from 430 unrelated healthy Korean population by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing analysis. PCR product with 2,790 bp spanning the specific mtDNA region (mt13715-16504) was subjected to RFLP analysis using 6 restriction enzyme (Hinf I, Hae III, Alu I, Dde I, Mbo I, Rsa I). On the PAUP analysis of PCR-RFLP results, 38 mtDNA haplotypes (Hap 1-38) were detected in the Korean populations, which were classified into 11 haplogroups (Grp 1-11) of related haplotypes encompassing all 38 haplotypes. In comparison of sequencing data with Anderson's reference sequence, the transition type was more prevalent than the transversion type. Insertions or deletions were not found. In addition, three of the polymorphic sites (A16240C, A16351G, G16384A) in HVS-I region are determined newly. The polymorphic sites were distributed randomly in the region, though the frequency at each site was variable. Thus, this research might be required for the genealogical study of Orientals.

Postcranial anatomy of Haldanodon exspectatus (Mammalia, Docodonta) from the Late Jurassic (Kimmeridgian) of Portugal and its bearing for mammalian evolution

The postcranium of the Late Jurassic docodont Haldanodon exspectatus Kuhne & Krusat, 1972 is represented by a partial skeleton and isolated bones of other individuals from the Late Jurassic (Kimmeridgian) of the Guimarota coal mine in Portugal. Haldanodon exhibits adaptations for a fossorial lifestyle such as stout and short limb bones and humeri with greatly expanded distal joints and strong deltopectoral crests. Short first and second phalanges and moderately curved and laterally compressed terminal phalanges with lateral grooves suggest that Haldanodon was a scratch-digger. The dorso-ventrally elongated, triangular scapula has a convex transverse profile with strongly laterally reflected anterior and posterior scapula margins, enclosing a deep trough-like ‘infraspinous fossa’. A supraspinous fossa is not developed. The saddle-shaped glenoid facet is mainly formed by the coracoid and orientated antero-ventrally indicating a sprawling gait. No epiphyses were detected and the wide size range of humerus and femur possibly indicate a lifelong growth. Haldanodon is more derived than Morganucodon by complete reduction of the procoracoid, absence of the procoracoid foramen, and a peg-like coracoid. It shares with monotremes a postscapular fossa that is absent in Morganucodon . A PAUP analysis based on 280 cranio-dental and postcranial characters corroborated the position of Haldanodon above morganucodontids and below Hadrocodium . © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 145 , 219‐248.

Amazonian malaria vector anopheline relationships interpreted from ITS2 rDNA sequences

Species identification of anopheline mosquitoes (Diptera: Culicidae) can be problematic because many of them belong to complexes of morphologically similar species, often with contrasted ecology, behaviour and vectorial importance. The application of DNA-based diagnostics has proved to be useful for distinguishing between such species. We determined ribosomal DNA sequences of the second internal transcribed spacer (ITS2) from samples of 16 species of Anopheles captured in the Amazon Basin, Brazil. Length of the ITS2 varied from 323 to 410 base pairs, with GC content ranging from 50.7% to 66.5% and sequence identity from 25% to 99% between species. Maximum-likelihood paup analysis separated two distinct groups of species conforming with the recognized subgenera Anopheles (represented by eiseni, mattogrossensis, mediopunctatus and peryassui) and Nyssorhynchus (represented by 12 spp.). For the latter group, the neighbour-joining tree generated from rDNA sequence ITS2 relationships is compatible with the morphological taxonomic key established for these Amazonian species: albitarsis, aquasalis, benarrochi, braziliensis, darlingi, deaneorum, dunhami, evansae, nuneztovari, oswaldoi, rangeli and triannulatus. These ITS2 sequence data proved to be a useful tool for species identification and, potentially, to solve taxonomic problems.

Phylogenetic Relationship of Osmia spp. in Korea Based on Mitochondrial COI Gene Sequences (Hymenoptera: Megachilidae)

The mitochondrial cytochrome oxidase subunit I (COI) sequences of 610bp were determined for seven species of the genus Osmia from Korea and two species of outgroups. The sequences were extremely rich in A+T (75.1% on the average), especially in the third codon position. The transversion/transition ratio was > 1 and most transversions were occurred between A and T. The sequence divergence in pairwise comparisons among seven Osmia species ranged from 6% to 26%. The phylogenetic trees estimated from the nine sequences through PAUP and PHYLIP analyses formed two clades, which was supported by high bootstrap values of both analyses. The phylogenetic trees, appeared to conform most satisfactorily with the traditional views of taxonomic relationships within this group of Osmia mason bees, were produced. There was no difference between Korean and Japanese O. cornifrons (Radoszkowsi) and O. taurus Smith in COI sequences used this study.

A Revision Of Paramblypterid And Amblypterid Actinopterygians From Upper Carboniferous–Lower Permian Lacustrine Deposits Of Central Europe

The descriptions and diagnoses of the type species of ParamblypterusParamblypterusdecorus, and the type species of Amblypterus Amblypterus latus, which is very similar to Paramblypterus, are revised. The skulls of Paramblypterusdecorus P. duvernoyi, and A. latus are restored in three‐dimensional models, and their diagnoses are emended. Intra‐specific variation of P.decorusP. duvernoyi concerns dermohyal, ‘suborbital’ and extrascapular bones, and dermohyal, rostral, parietal and extrascapular bones, respectively. Owing to poor preservation, patterns of variation could only be recognised in one specimen of A. latus regarding the extrascapular series and the posterior edges of the scales. All data on AmblypterusParamblypterus were entered into a PAUP analysis. Fifty taxa of lower actinopterygians were analysed for 57 characters. According to this analysis, ParamblypterusAmblypterus are contained in the same family, the Amblypteridae. P. gelbertiP. duvernoyi are the sister group of P. rohani and P. decorus, and the genus Paramblypterus is the sister taxon of the genus Amblypterus. Key words. morphology, intra‐specific variation, systematics, lower actinopterygians, amblypterids, paramblypterids, Permo‐Carboniferous.

Skeletal ultrastructure and phylogeny of cyclostome bryozoans

Recent research on the ultrastructure of the calcareous skeleton in the bryozoan order Cyclostomata is summarized and updated, based on field emission SEM studies of 87 species. Six fundamental ultrastructural fabrics are recognized which differ in the crystallographic orientations, shapes and prevailing growth directions of the constituent crystallites. During the growth of individual walls a succession of fabrics is secreted, defining a fabric suite. Five fabric suites are described in interior walls and four in exterior walls. Nine ultrastructural characters were combined with 37 other skeletal characters in a PAUP analysis of the relationships between 28 post-Palaeozoic cyclostomes chosen to include representatives of all suborders. A single tree of length 142 steps was found. Comparison of tree statistics for three categories of characters showed ultrastructural characters to be more homoplastic than zooidal characters, and the latter more homoplastic than colonial characters. Rooting the tree on the paleotubuliporine Cuffeyella gave four transitions from fixed- to free-walled organization and no reversals. With respect to the five extant suborders of cyclostomes, this first, preliminary analysis implies that Rectangulata and Cancellata are monophyletic groups, whereas Articulata are diphyletic, and both Tubuliporina and Cerioporina paraphyletic.