Spermatozoa of the Anomalodesmata (Bivalvia, Mollusca) with special reference to relationships within the group

Sperm ultrastructure in the marine bivalve order Anomalodesmata is considered in the light of new information for Australian Myochama anomioides and Cuspidaria latesulcata . In M. anomioides , the acrosomal complex lies posterior to the nucleus, in contact with the asymmetrical midpiece mitochondria – an unusual configuration reported from most of the studied Anomalodesmata. Spermatozoa of M. anomioides resemble those of Myadora brevis (both in family Myochamidae). Myochamid spermatozoa are considerably less modified than those of the Lyonsiidae or Laternulidae, and may prove a basal type within the non-septibranch anomalodesmatans. In contrast, C. latesulcata differs from other examined anomalodesmatans in having an anterior acrosomal complex and radial midpiece mitochondria (classic aquasperm features). Sperm data for the Anomalodesmata are limited but congruent with the most recent phylogenetic analyses that recognize distinct 'thraciid' and 'lyonsiid' clades. Results for C. latesulcata suggest septibranch origins before the development of a posteriorly positioned acrosomal complex and mitochondrial asymmetry.     

Patterns of evolutionary transformation in the petrosal bone and some basicranial features in marsupial mammals, with special reference to didelphids

Twelve petrosal and four nonpetrosal characters were coded for representatives of all 15 extant genera of Didelphidae and for 16 additional genera of marsupials representing all extant orders. Three basal metatherians were used as outgroup comparison. Histological sections of a subset of the data were examined. An intermediate position of the hiatus Fallopii supports the monophyly of Didelphidae. Several basicranial regions support different clades within the Didelphidae that recent molecular work has identified, including a sister group relationship of Caluromys and Caluromysiops , the monophyly of large opossums, a Lestodelphys-Thylamys clade, and a Lestodelphys-Thylamys-Gracilinanus-Marmosops clade. Glironia lacks petrosal and jaw synapomorphies of Caluromys and Caluromysiops. The transverse canal, a synapomorphy of the crown-group Marsupialia, opens as a single foramen anterior to the carotid foramen in most marsupials or as numerous foramina in the pterygoid fossa in diprotodontians. It is either intramural (most marsupials) or simply endocranial (most diprotodontians excluding koalas and wombats). Loss of a deep sulcus in the anterior pole of the promontorium for the internal carotid artery and a rostral tympanic process of the petrosal also characterize the groundplan of the crown group Marsupialia. Pouch-young wombats show a groove in the anterior pole of the petrosal for the internal carotid artery. The absence of a prootic canal foramen in the tympanic side of the petrosal of adults supports the monophyly of Australidelphia. Some pouch-young marsupials possess a prootic canal that is later lost in ontogeny. A rather flat promontorium and a crest running medio-distally in the middle of the promontorium characterize Macropodidae.     

Complete Mitochondrial Genome Sequences of the South American and the Australian Lungfish: Testing of the Phylogenetic Performance of Mitochondrial Data Sets for Phylogenetic Problems in Tetrapod Relationships

We determined the complete nucleotide sequences (16403 and 16572 base pairs, respectively) of the mitochondrial genomes of the South American lungfish, Lepidosiren paradoxa, and the Australian lungfish, Neoceratodus forsteri (Sarcopterygii, Dipnoi). The mitochondrial DNA sequences were established in an effort to resolve the debated evolutionary positions of the lungfish and the coelacanth relative to land vertebrates. Previous molecular phylogenetic studies based on complete mtDNA sequences, including only the African lungfish, Protopterus dolloi, sequence were able to strongly reject the traditional textbook hypothesis that coelacanths are the closest relatives of land vertebrates. However, these studies were unable to statistically significantly distinguish between the two remaining scenarios: lungfish as the closest relatives to land vertebrates and lungfish and coelacanths jointly as their sister group (Cao et al. 1998; Zardoya et al. 1998; Zardoya and Meyer 1997a). Lungfish, coelacanths, and the fish ancestors of the tetrapod lineage all originated within a short time window of about 20 million years, back in the early Devonian (about 380 to 400 million years ago). This short divergence time makes the determination of the phylogenetic relationships among these three lineages difficult. In this study, we attempted to break the long evolutionary branch of lungfish, in an effort to better resolve the phylogenetic relationships among the three extant sarcopterygian lineages. The gene order of the mitochondrial genomes of the South American and Australian lungfish conforms to the consensus gene order among gnathostome vertebrates. The phylogenetic analyses of the complete set of mitochondrial proteins (without ND6) suggest that the lungfish are the closest relatives of the tetrapods, although the support in favor of this scenario is not statistically significant. The two other smaller data sets (tRNA and rRNA genes) give inconsistent results depending on the different reconstruction methods applied and cannot significantly rule out any of the three alternative hypotheses. Nuclear protein-coding genes, which might be better phylogenetic markers for this question, support the lungfish–tetrapod sister-group relationship (Brinkmann et al. 2004).This article contains online supplementary material.Reviewing Editor: Dr. Rafael Zardoya     

The number of nucleotides required to determine the branching order of three species,with special reference to the human-chimpanzee-gorilla divergence

Summary A mathematical theory for computing the probabilities of various nucleotide configurations among related species is developed, and the probability of obtaining the correct tree (topology) from nucleotide sequence data is evaluated using models of evolutionary trees that are close to the tree of mitochondrial DNAs from human, chimpanzee, gorilla, orangutan, and gibbon. Special attention is given to the number of nucleotides required to resolve the branching order among the three most closely related organisms (human, chimpanzee, and gorilla). If the extent of DNA divergence is close to that obtained by Brown et al. for mitochondrial DNA and if sequence data are available only for the three most closely related organisms, the number of nucleotides (m^*) required to obtain the correct tree with a probability of 95% is about 4700. If sequence data for two outgroup species (orangutan and gibbon) are available, m^* becomes about 2600–2700 when the transformed distance, distance-Wagner, maximum parsimony, or compatibility method is used. In the unweighted pair-group method, m^* is not affected by the availability of data from outgroup species. When these five different tree-making methods, as well as Fitch and Margoliash's method, are applied to the mitochondrial DNA data (1834 bp) obtained by Brown et al. and by Hixson and Brown, they all give the same phylogenetic tree, in which human and chimpanzee are most closely related. However, the trees considered here are gene trees, and to obtain the correct species tree, sequence data for several independent loci must be used.     

A molecular perspective on the phylogeny of placental mammals based on mitochondrial 12S rDNA sequences,with special reference to the problem of the Paenungulata

Part of the 12S rDNA gene was amplified and sequenced for 11 placental mammals, 3 marsupials, and 2 monotremes. Multiple alignments for these sequences and nine additional placental sequences taken from GenBank were obtained using CLUSTAL. Phylogenetic analyses were performed using standard parsimony, transversion parsimony, and Lake's method of invariants. All of our analyses uniteLoxodontia withDugong. Procavia, in turn, is a sister group to these taxa, thus supporting the monophyly of the Paenungulata. Perissodactyls are a sister group to paenungulates when transitions and transversions are both included but not when transitions are omitted. Likewise, cetaceans are a sister group to artiodactyls on minimum length trees under standard parsimony but not under transversion parsimony. Rodent monophyly and bat monophyly also receive mixed support, as does a putative alliance between primates and lagomorphs. Interestingly, the percentage divergence between the echidna and the platypus is less than for the rat and mouse.     

Scapania paraphyllia,a new synonym of Scapania koponenii (Marchantiophyta,Scapaniaceae) with special reference to paraphyllia,pseudoparaphyllia, and paraphyses

Scapania paraphyllia T.Cao, C.Gao, J.Sun & B.R.Zuo and S. koponenii Potemkin are both endemic to China. They share considerable morphological similarities except that the former species has pseudoparaphyllia. In order to elucidate the taxonomic status of the two species, we investigated morphological characters possessed by their type specimens and additional collections, and reconstructed a species phylogeny for S. koponenii, S. paraphyllia, and closely related species. The phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference analyses based on the nuclear marker nrITS and the plastid markers trnL-F region and atpB-rbcL spacer. Both morphological and molecular evidence contradicted the hypothesis that S. paraphyllia and S. koponenii are separate species. The pseudoparaphyllia reported for S. paraphyllia are confirmed as paraphyses. The paraphyllia, paraphyses, and pseudoparaphyllia in Scapania are discussed.     

A phylogenetic analysis of the 18S ribosomal RNA sequence of the coelacanth Latimeria chalumnae

Synopsis Approximately 98% of the sequence of the 18S ribosomal RNA (rRNA) of the coelacanth Latimeria chalumnae was determined by a combination of direct RNA sequencing and sequencing of rRNA genes amplified by the polymerase chain reaction. This sequence was compared with 18S rRNA sequences of similar length from seven other vertebrate species, representing the taxa Petromyzontiformes, Holocephali, Elasmobranchii, Actinopterygii, Dipnoi, Amphibia, and Amniota, in order to determine the most likely sister group of the coelacanth. Maximum parsimony analysis of these sequences resulted in a single most parsimonious tree containing a number of anomalous relationships among these groups. A bootstrap analysis showed that none of the relationships in this tree was significantly supported at the 95% level, however. Addition of data from 15 other vertebrates (providing multiple representatives of most of the higher taxa) resulted in similar ambiguous groupings, as did a number of methods of editing the sites compared (designed to eliminate rapidly evolving positions). These results may be due to a relatively rapid radiation of the major lineages of osteichthyans, the resolution of which will require molecular information from a larger portion of the coelacanth genome.     

Molecular phylogenetics of soricid shrews (Mammalia) based on mitochondrial cytochrome b gene sequences: with special reference to the Soricinae

Molecular phylogeny of soricid shrews (Soricidae, Eulipotyphla, Mammalia) based on 1140 bp mitochondrial cytochrome b gene (cyt b ) sequences was inferred by the maximum likelihood (ML) method. All 13 genera of extant Soricinae and two genera of Crocidurinae were included in the analyses. Anourosorex was phylogenetically distant from the main groupings within Soricinae and Crocidurinae in the ML tree. Thus, it could not be determined to which subfamily Anourosorex should be assigned: Soricinae, Crocidurinae or a new subfamily. Soricinae (excluding Anourosorex ) should be divided into four tribes: Neomyini, Notiosoricini, Soricini and Blarinini. However, monophyly of Blarinini was not robust in the present data set. Also, branching orders among tribes of Soricinae and those among genera of Neomyini could not be determined because of insufficient phylogenetic information of the cyt b sequences. For water shrews of Neomyini ( Chimarrogale , Nectogale and Neomys ), monophyly of Neomys and the Chimarrogale – Nectogale group could not be verified, which implies the possibility of multiple origins for the semi-aquatic mode of living among taxa within Neomyini. Episoriculus may contain several separate genera. Blarinella was included in Blarinini not Soricini, based on the cyt b sequences, but the confidence level was rather low; hence more phylogenetic information is needed to determine its phylogenetic position. Furthermore, some specific problems of taxonomy of soricid shrews were clarified, for example phylogeny of local populations of Notiosorex crawfordi , Chimarrogale himalayica and Crocidura attenuata .     

A morphological classification of plants,with special reference to the New Zealand alpine flora

Abstract. A plant is a complex of integrated systems (leaves, leaf groups, stems, roots, inflorescences), coexisting side by side or superimposed on each other to produce the life form (orphysiognomy) of the individual. The classic Raunkiaer classification based fundamentally on one character (apex position) is insufficient for the purpose of a functional classification. Five keys are given to determine the categories of:

• 1) the plant silhouette or general shape resulting from a combination of other systems, with 11 categories proposed;
• 2) the leaf group, with 14 categories;
• 3) the stem, with 27 categories;
• 4) the root, with 5 categories; and
• 5) the inflorescence, with 3 categories.

Each plant can be named according to the category or model of each of the five different systems that they most resemble, or by using only the name(s) of systems which are more conspicuous than others. Characters are selected primarily for their influence on form and secondarily on size. This scheme allows for detailed studies of a flora in terms of morphological characteristics (alone or in systems), expressed as frequency of occurrence of each character in the flora. Characters can be analysed separately (e.g. entire margined leaves), as a combination of characters (e.g. leaf groups) or as a combination of systems (e.g. rosettes without stems). Thus correlations between environmental variables and plants canbe made with more precision than in previous classification schemes. The classification also serves as the framework for including additional morphological data and incorporating new models. The New Zealand alpine flora is used as a test case and to exemplify the classification.