The phylogenetic relationships of sauropod dinosaurs

A data-matrix of 205 osteological characters for 26 sauropod taxa is subjected to cladistic analysis. Two most parsimonious trees are produced, differing only in the relationships between Euhelopus, Omeisaurus and Mamenchisaurus. The monophyly of the Euhelopodidae (including Shunosaurus) is supported by seven synapomorphies. The Cetiosauridae (Patagosaurus, Cetiosaurus and Haplocanthosaurus) is paraphyletic with respect to the Neosauropoda. The latter clade divides into two major radiations–the ‘Brachiosauria’ (Camarasaurus, brachiosaurids and titanosauroids), and the Diplodocoidea (nemegtosaurids, dicraeosaurids, diplodocids and Rebbachisaurus). Further evidence for the inclusion of Opisthocoelwaudia in the Titanosauroidea is presented. Phuwiangosaurus, a problematic sauropod from Thailand, may represent one of the most plesiomorphic titanosauroids. ‘Peg’-like teeth have evolved at least twice within the Sauropoda. The postspinal lamina, on the neural spines of middle and caudal dorsal vertebrae, represents a neomorph rather than a fusion of pre-existing structures. Forked chevrons may have evolved convergently in the Euhelopodidae and the diplodocid-dicraeosaurid clade, or they may have been acquired early in sauropod evolution and subsequently lost in the ‘Brachiosauria’. The strengths and weaknesses of the data-matrix and tree topologies are explored using bootstrapping, decay analysis and randomization tests. Several nodes are only poorly supported, but this seems to reflect the large proportion of missing data in the matrix (～46%), rather than an abnormally high level of homoplasy. The results of the randomization tests indicate that the ‘data-matrix’ probably contains a strong phylogenetic ‘signal’. The relationships of some forms, such as Haplocanthosaurus, are influenced by the inclusion or exclusion of certain taxa with unusual combinations of character states. Such a result suggests that there are dangers inherent in the view that ‘higher’ level sauropod phylogeny can be accurately reconstructed using only a small number of well-known taxa.     

The phylogenetic relationships within the Chamaeleonidae, with comments on some aspects of cladistic analysis

The phylogenetic relationships of the African mainland species of the genus Rhampholeon (formerly referred to the genus Brookesia ) with respect to Brookesia superciliaris, Bradypodion pumilus , and the genus Chamaeleo are analysed. Rhampholeon constitutes a genus well separated from Brookesia and may itself be subdivided in two subgroups on the basis of characters derived from the nasal and parietal complexes. A final section investigates problems of cladistic analysis, viz. the relationship of parsimony to character weighting, and pattern versus process as complementary perspectives of character analysis and coding.     

Cladistic analysis of phylogenetic relationships among tribes Cicereae, Trifolieae, and Vicieae (Leguminosae)

A cladistic analysis of tribes Cicereae, Trifolieae, and Vicieae was carried out using 33 morphological, anatomical, karyological, and chemotaxonomical characteristics. Transformation polarities of the character states were developed by comparison with the character states of the genus Galega, the sister group of the tribes. Cicereae and Vicieae were found to be a monophyletic group, and Trifolieae was its sister group. The seven synapomorphic characters of Cicereae and Vicieae were presumed to be: germination hypogeal vs. epigeal; first leaf in seedlings scarious vs. laminous; leaves paripinnately and tendrilous vs. imparipinnately and etendrilous; postchalazal vascular bundle present in seed coats vs. absent; a cotyledon flap present at antihilar side vs. absent; radicles short in seeds vs. long; and plumules long in seeds vs. short.     

The ethmoidal region of Dibamus taylori (Squamata: Dibamidae), with a phylogenetic hypothesis on dibamid relationships within Squamata

The nasal capsule and nasal sac of Dibamus taylori are described based on a plate reconstruction of serially sectioned material and are compared with several other squamate taxa. The ethmoidal region of D. taylori is characterized by a short nasal vestibule, a well developed concha, a much reduced and nearly functionless Jacobson's organ, an incomplete nasal roof, and a true nasopharyngeal duct with a complicated secondary palate. Cartilaginous and epithelial structures of the ethmoidal region provide many informative and useful characters for a phylogenetic analysis. Different anatomical features of D. taylori are compared with other burrowing forms ( Acontias meleagris, Annietta, pulchra Voetzkowia mira, Feylinia curron ) and discussed functionally and phylogenetically. Phylogenetic analysis of all higher squamate taxa using 144 available data derived from many regions of the body indicates relative relationships as (((Dibamidae, Amphisbaenia) Serpentes) Scleroglossa).     

Spatial autocorrelation,phylogenetic constraints,and the causes of sexual dimorphism in primates

Cheverud et al. (1985) apply the important and relatively new methodology of spatial autocorrelation to the quantification of phylogenetic constraints on adaptation and illustrate the use of these methods in an allometric study of sexual dimorphism in body size among extant nonhuman primates. Though of potentially broad applicability, the technique was completely overlooked in a recent review of methods to control for the effects of common descent in comparative studies (Bell, 1989). Their approach therefore deserves a wider recognition. However, their specific conclusion, that phytogeny is the primary determinant of patterns of sexual dimorphism among primates, has been uncritically accepted. We present four main methodological problems with their approach that should temper the interpretation of their analysis: biased phylogenetic relatedness scores, biased sample selection, size dependence in sex dimorphism measurement, and deficiencies in selection of a structural path model. We conclude that, even in terms of the analysis by Cheverud and co-workers (1985), phylogenetic inertia is not the primary reason for body size dimorphism.     

用matK序列分析探讨木兰属植物的系统发育关系

用木兰科Magnoliaceae 57种植物的matK基因序列构建了该科的系统发育分支图。结果表明: (1)木兰属Magnolia L.是一个因为性状的趋同演化而建立的多系类群; (2)木兰亚属subgen. Magnolia和玉兰亚属subgen. Yulania (Spach) Reichenb.亲缘关系较远, 支持将后者从该属中分出建立玉兰属Yulania Spach, 木兰亚属作为木兰属保留; (3)木兰亚属的sect. Splendentes Dandy ex Vazquez组与皱种组sect. Rytidospermum Spach的两个美洲种M. macrophylla Michaux和M. dealbata Zucc.亲缘关系较近, 荷花玉兰组sect. Theorhodon Spach与常绿组sect. Gwillimia DC.的亲缘关系较近; (4)盖裂木属Talauma Juss.可以成立, 而其分布于亚洲的Blumiana Blume组可归入木兰属; (5)拟单性木兰属Parakmeria Hu &; Cheng、华盖木属Manglietiastrum Law以及单性木兰属Kmeria (Pierre) Dandy形成一个单系群, 与玉兰亚属和含笑属Michelia L.的亲缘关系较近。花的着生位置不足以作为木兰科的分族依据, 含笑族Michelieae和木兰族Magnolieae的特征及其界定应做修改。将玉兰亚属从木兰属分出后, 木兰属与含笑属无性状交叉,成为两个区别明显的属。     

Phylogenetic relationships between and within sections Hypechusa, Narbonensis and Peregrinae of genus Vicia (Fabaceae) based on evidence from isozymes and morphology

Previous studies of vetch species belonging to sections Hypechusa, Narbonensis and Peregrinae have revealed controversies and open questions that deserve revisiting with the use of contemporary approaches. The paper extends the previous work of Leht and Jaaska (2002) by describing variation of 16 isozymes and 86 morphological characters among 17 Vicia species belonging to sections Hypechusa, Narbonensis and Peregrinae of the type subgenus in comparison with V. bithynica of section Pseudolathyrus. Three more isozymes and 12 new morphological characters are included to improve the resolution of phylogenetic relationships. The maximum parsimony trees based on isozymes and morphology revealed essentially the same four clusters of species that correspond to series Hypechusa and Hyrcanicae of section Hypechusa, to sections Narbonensis and Peregrinae of current taxonomy, except that the isozyme tree placed V. lutea of series Hypechusa into a separate clade. Isozyme variation in V. mollis, V. noeana, V. sericocarpa and V. ciliatula of section Hypechusa is described for the first time. Twenty-three species-specific isozymes that may be used for species identification by analysis of seeds are described. Two new isozymes that distinguish V. serratifolia from V. narbonensis are described that further support their specific status. Series Hypechusa and Hyrcanicae of section Hypechusa, sections Narbonensis and Peregrinae of traditional taxonomy are monophyletic groups that deserve sectional status within the genus Vicia. The phylogenetic position and sectional placement of V. lutea warrants further study with independent sets of DNA characters.     

Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles

Molecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlier studies did not include representatives from all taxonomic classes. We used a five-gene (nuclear encoded SSU rRNA; plastid encoded rbcL, psaA, psbA, psbC) analysis with a subset of 89 taxa representing all 16 heterokont classes to infer a phylogenetic tree. There were three major clades. The Aurearenophyceae, Chrysomerophyceae, Phaeophyceae, Phaeothamniophyceae, Raphidophyceae, Schizocladiophyceae and Xanthophyceae formed the SI clade. The Chrysophyceae, Eustigmatophyceae, Pinguiophyceae, Synchromophyceae and Synurophyceae formed the SII clade. The Bacillariophyceae, Bolidophyceae, Dictyochophyceae and Pelagophyceae formed the SIII clade. These three clades were also found in a ten-gene analysis. The approximately unbiased test rejected alternative hypotheses that forced each class into either of the other two clades. Morphological and biochemical data were not available for all 89 taxa, however, existing data were consistent with the molecular phylogenetic tree, especially for the SIII clade.     

Assessing current adaptation and phylogenetic inertia as explanations of trait evolution: the need for controlled comparisons

The determination of whether the pattern of trait evolution observed in a comparative analysis of species data is due to adaptation to current environments, to phylogenetic inertia, or to both of these forces requires that one control for the effects of either force when making an assessment of the evolutionary role of the other. Orzack and Sober (2001) developed the method of controlled comparisons to make such assessments; their implementation of the method focussed on a discretely varying trait. Here, we show that the method of controlled comparisons can be viewed as a meta-method, which can be implemented in many ways. We discuss which recent methods for the comparative analysis of continuously distributed traits can generate controlled comparisons and can thereby be used to properly assess whether current adaptation and/or phylogenetic inertia have influenced a trait's evolution. The implementation of controlled comparisons is illustrated by an analysis of sex-ratio data for fig wasps. This analysis suggests that current adaptation and phylogenetic inertia influence this trait.     

Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia

The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene,GlTop 2 was identified. It is a single copy gene with a 4476 bp long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a -100 aa longer central domain; a ~200 aa shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the ““amitochondriate““ G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G, lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.     

A genome-wide phylogenetic reconstruction of family 1 UDP-glycosyltransferases revealed the expansion of the family during the adaptation of plants to life on land

For almost a decade, our knowledge on the organisation of the family 1 UDP‐glycosyltransferases (UGTs) has been limited to the model plant A. thaliana. The availability of other plant genomes represents an opportunity to obtain a broader view of the family in terms of evolution and organisation. Family 1 UGTs are known to glycosylate several classes of plant secondary metabolites. A phylogeny reconstruction study was performed to get an insight into the evolution of this multigene family during the adaptation of plants to life on land. The organisation of the UGTs in the different organisms was also investigated. More than 1500 putative UGTs were identified in 12 fully sequenced and assembled plant genomes based on the highly conserved PSPG motif. Analyses by maximum likelihood (ML) method were performed to reconstruct the phylogenetic relationships existing between the sequences. The results of this study clearly show that the UGT family expanded during the transition from algae to vascular plants and that in higher plants the clustering of UGTs into phylogenetic groups appears to be conserved, although gene loss and gene gain events seem to have occurred in certain lineages. Interestingly, two new phylogenetic groups, named O and P, that are not present in A. thaliana were discovered.     

A new genus of red‐toothed shrew (Mammalia,Soricidae) from the Early Pleistocene of Gran Dolina (Atapuerca,Burgos, Spain), and a phylogenetic approach to the Eurasiatic Soricinae

This paper describes a new genus and species of shrew from the Pleistocene (levels 4, 5, and 6) of the Gran Dolina site, located in the Sierra de Atapuerca (Burgos, Spain). Dolinasorex glyphodon gen. et sp. nov. (Mammalia, Soricidae) is a type of large‐sized soricine, endemic in character, which inhabited the Sierra de Atapuerca in the last part of the Early Pleistocene (c. 780–900 kya). Morphometric and phylogenetic analyses indicate that the new species is more closely related to Asiatic forms than to the species Beremendia fissidens with its primarily European distribution. The main palaeoecological and palaeobiogeographical implications of the new taxon in the area around Atapuerca and in the Iberian Peninsula in general are discussed. The paper also presents a tentative phylogeny for the Soricinae subfamily in Eurasia, including for the first time exclusively fossil species, producing results that may prove to be of great interest for more complete studies in the future. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 904–925.