Phylogenetic analysis of Macrobiotidae (Eutardigrada, Parachela): a combined morphological and molecular approach

Combined analyses of morphological and molecular data were used to resolve phylogenetic relationships within Macrobiotidae (Eutardigrada). Morphological data were analysed using a cladistic approach with a matrix comprising 15 taxa with 17 characters to obtain a phylogenetic reconstruction. Molecular data were obtained by sequencing the cytochrome c oxidase subunit I gene in seven species of Macrobiotidae and one of Eohypsibiidae (used as outgroup). The morphological character defining the family, symmetrical claw on each leg, turns out to be plesiomorphic. Moreover, neither morphological nor molecular analyses supports a monophyletic clade for the subfamily Macrobiotinae, whereas both support a well defined evolutionary line (Murrayinae) within the family. We propose elevating the latter to family level (Murrayidae) while temporarily retaining as valid the family Macrobiotidae (amending its diagnosis, including within it only Macrobiotinae). Murrayidae opens an interesting evolutionary prospective, because the entire line has differentiated without sexual reproduction, constituting an example of evolution of asexual lineages.     

Cuticle structure and systematics of the Macrobiotidae (Tardigrada, Eutardigrada)

The cuticle of tardigrades is characterized by three main layers: epicuticle, intracuticle and procuticle. Pillars are present in the epicuticle of almost all heterotardigrades, but these structures are also known in a few species of eutardigrades. The apparent heterogeneity of the cuticular ultrastructure in several species of the Macrobiotidae (Eutardigrada) prompted us to analyse the structure of the cuticle in this family. Eleven species in several genera were investigated with light and/or electron microscopy. All the species of the genera Murrayon and Dactylobiotus showed pillars in the epicuticle, whereas the examined species of Macrobiotus , Richtersius and Xerobiotus completely lacked pillars. Therefore, in the Macrobiotidae, in contrast to what appears with light microscopy, the cuticle is homogeneous within each genus examined at the electron microscopic level. Considering the absence of pillars in the Macrobiotidae a synapomorphy, we propose the erection of two new subfamilies. Macrobiotinae subfam. n. is characterized by the absence of pillars in the epicuticular layer and includes, in addition to the genera Macrobiotus, Xerobiotus and Richtersius, the genera Pseudohexapodibius, Adorybiotus, and probably also Minibiotus, Calcarobiotus and Pseudodiphascon . Murrayinae subfam. n. is characterized by the presence of pillars in the epicuticular layer and includes the genera Murrayon, Dactylobiotus and, probably, Macroversum.     

CHROMOSOME NUMBERS IN THE LEGUMINOSAE II: AFRICAN SPECIES,INCLUDING PHYLETIC INTERPRETATIONS

Turner , B. L., and O. S. Fearing . (U. Texas, Austin.) Chromosome numbers in the Leguminosae. II. African species, including phyletic interpretations. Amer. Jour. Bot. 46(1) : 49-57. Illus. 1959.—Chromosome numbers for 30 African legume species have been reported. These include first reports for 28 taxa, including 12 genera (Bolusanthus, Calpurnia, Melolobium, Lessertia, Sulherlandia, Colophospermum, Guibourtia, Burkea, Julbernardia, Schotia, Piliostigma and Swartzia). The counts are discussed with respect to those previously reported for related groups, and this chromosomal information was used to construct hypothetical phyletic lines at the tribal level within the subfamilies Papilionoideae and Caesalpinioideae. A phyletic scheme for the Leguminosae (excluding the Mimosoideae) based on this evidence from chromosome studies is presented. Notable departures from previously suggested phyletic treatments include: (1) Suggestion for inclusion of genera of the Galegeae and Hedysareae with base numbers of x = 10 and 11 with the Phaseoleae and Dalbergieae. (2) Derivation of the Papilionoideae through caesalpinoid prototypes, possibly from Swartzia-like ancestors. (3) Recognition of several very old chromosomal lines stemming from the subfamily Caesalpinioideae, and the suggestion that parts of the tribes Sclerolobieae, Cynometreae, Swartzieae and Sophoreae are, perhaps, more closely related to each other and to the Papilionoideae than they are to the remaining caesalpinoid tribal lines.     

A palaeontological and phylogenetical analysis of squaliform sharks (Chondrichthyes: Squaliformes) based on dental characters

Squaliformes comprise the major proportion of modern deep-water sharks, yet their fossil history and phylogenetic relationships are still poorly understood. New analyses have been undertaken, however, and new living and fossil species have been discovered during the past 10 years. A cladistic analysis involving 29 dental characters has been made and most living and fossil genera are included. On the basis of their dental morphology, the monophyly of the Squaliformes can be supported if the fossil genus Protospinax is excluded. The traditional phylogenetic positions of most living genera, Protosqualus, Cretascymnus and Eoetmopterus, are confirmed despite the fact that the Oxynotidae, Etmopterinae, Palaeomicroides, Proetmopterus and Microetmopterus have some atypical phylogenetic relationships within the Squaliformes. The addition of the palaeontological data in a phylogenetic tree including fossil and living Squaliformes demonstrates some gaps in the fossil record. Nevertheless, and as a consequence of that stratigraphy-phylogeny inference, two particular events can be pinpointed in the history of the Squaliformes: the first one occurs after the major Cenomanian-Turonian anoxic event and the second one after the Cretaceous/Tertiary crisis. The first radiation involves the majority of the living Squaliformes (Somniosinae, Centrophorinae, most of the Etmopterinae, Oxynotinae) in deep-sea waters, the second, the more epipelagic sharks (most of the Dalatiidae), suggesting a secondary adaptation to more shallow environments.     

木灵藓科分类与系统学研究：历史、问题和展望

木灵藓科(Orthotrichaceae)是藓类植物中的第3大科。该科不仅种类多, 生态类型特殊, 而且是世界公认的多样化程度高、分类难度大、系统关系复杂的类群。当代木灵藓科植物分类系统学研究主要集中在该科的地区志编写和专属分类修订。目前, 除了热带美洲、热带非洲的变齿藓属(Zygodon)和火藓属(Schlotheimia)部分类群外, 木灵藓科主要类群的分类修订工作已基本完成, 但是有关亚科和属的划分和地位以及各属之间的关系等方面仍存在众多争议。木灵藓科分支系统学研究也不够系统全面, 有的仅应用了单个基因片段, 或者只涉及少数类群。因此, 需要基于更多的分子和形态学性状, 进一步开展世界木灵藓科植物的系统发育研究, 建立一个更趋自然的木灵藓科分类系统。     

Phylogeny of the millipede genus Sphaeriodesmus Peters, 1864 (Polydesmida: Sphaeriodesmidae) based on morphological characters

In order to understand the evolutionary relationships among the species encompassed within the genus Sphaeriodesmus Peters, 1864, a cladistic analysis including 63 species was conducted. Ninety-five morphological characters were used for the phylogenetic reconstruction. The results suggested that the current composition of the genus Sphaeriodesmus does not circumscribe a monophyletic group; instead, the genera Eusphaeriodesmus, Colobodesmus, and Proeilodesmus are here synonymized under Sphaeriodesmus. Although raw morphological data had suggested the genus Lophocyclus as the sister taxon of Sphaeriodesmus, the phylogenetic analysis under implied weight identified the genus Cyphodesmus as the taxon most closely related to Sphaeriodesmus. Sphaeriodesmus isolatus Chamberlin, 1940 is a subjective synonym of Sphaeriodesmus conformans Chamberlin, 1925. The putative subdivisions previously proposed within Sphaeriodesmus do not hold as monophyletic either. Low stability was observed concerning the higher-level phylogenetic relationships of Sphaeriodesmus. Sphaeriodesmus crucis (Loomis, 1974), S. mecistonyx (Hoffman, 1990), and S. triramus (Kraus, 1954) are new combinations.     

The diversification of the northern temperate woody flora – A case study of the Elm family (Ulmaceae) based on phylogenomic and paleobotanical evidence

Ulmaceae is a woody family widespread in northern temperate forests. Despite the ecological importance of this family, its phylogeny and biogeographic history are poorly understood. In this study, we reconstruct phylogenetic relationships within the family and infer spatio-temporal diversification patterns based on chloroplast genome (complete cpDNA) and nuclear ribosomal DNA sequences (nrDNA). The seven Ulmaceae genera are resolved in two main clades (temperate vs. tropical) by both cpDNA and nrDNA sequences. The temperate clade includes four genera, Hemiptelea, Zelkova, Planera, and Ulmus. The relationships among Planera and other genera are controversial because of inconsistent topologies between plastid and nuclear data. The tropical clade includes three genera ((Ampelocera, Phyllostylon), Holoptelea). Molecular dating and diversification analyses show that Ulmaceae originated in the Early Cretaceous (ca. 110–125 Ma) with the main lineages establishing from the Late Cretaceous to the early Eocene. The diversification rate slowed during the middle to the late Paleogene (ca. 23–45 Ma), followed by a rapid diversification of the East Asian temperate group in the Neogene, congruent with a global cooling event. The ancestral state optimization analysis suggests an East Asian origin of the temperate Ulmaceae clade during the Paleocene, which is consistent with the fossil record. Both phylogenomic and fossil evidence support East Asia as a center of origin and diversification for the temperate woody lineages.     

Phylogenomic study of Amorphophallus (Alismatales; Araceae): When plastid DNA gene sequences help to resolve the backbone subgeneric delineation

Encompassing ca. 200 species distributed in paleotropical Africa and Asia, Amorphophallus is one of the largest genera of Araceae. In spite of the great economic interest in its glucomannan production, only a few studies have attempted to grasp the evolutionary history of this genus. In the current state of knowledge, four main clades, mostly linked to biogeographical delineation, have been identified from phylogenies based on a few genes. However, relationships among and within these clades still remain unclear, due to the rapid radiation that occurred during the early evolutionary history of the genus. Here, we generated genome skimming libraries for 43 specimens from 36 species distributed across the 4 clades, which allowed us to produce a phylogenetic matrix for a set of 71 plastid genes. Our phylogenies confirm the monophyly of these clades but show a new and well-resolved arrangement among these clades. Our analyses therefore provide a new scenario and timeline for the evolution of the main Amorphophallus clades, consistent with the morphological characteristics of the clades. The inferred scenario is also in agreement with climate dynamics and the onset of long-distance dispersal by the earliest migratory birds near the Oligocene/Miocene transition around 23 million years ago. Our study provides an up-to-date baseline to understand biogeographic and ecological processes that shaped the current diversity and distribution of Amorphophallus, paving the way for larger-scale phylogenomic studies based on plastid and nuclear genomes.     

The non-monophyletic origin of the tRNA molecule

The hypothesis that the tRNA molecule may have originated from the assembly of two similar RNA hairpin structures is utilised to understand the evolutionary period in which this molecule originated. Consistent with the exon theory of genes is the observation that the introns in tRNA genes are found almost exclusively in the anticodon loop and "stitched together" the two halves of the molecule, which originally may have been simply two hairpin structures and which can still be observed in the three-dimensional structure of tRNAs. This theory therefore considers these hairpin structures as minigenes on which complex protein synthesis may have been achieved. This in turn leads to the belief that the organisation of the genetic code may have been determined by use of the hairpin structures but not the complete tRNA molecule. In view of this, it can be conjectured that tRNA molecules might have been assembled only after the establishment of the main phyletic lines. If this is all true, then the origin of the tRNA molecule might have been non-monophyletic, i.e. a tRNA specific for a certain amino acid might have been assembled in different phyletic lines with a second and different hairpin structure. This leads to the belief that tRNAs specific for different amino acids but belonging to the same phyletic line might have been more similar to one another than to tRNAs specific for the same amino acid but belonging to different phyletic lines. This prediction seems to be supported by phylogenetic analysis making major use of the bootstrap technique performed on the tRNA sequences and by analysis already existing in the literature which supports the non-monophyletic origin of the tRNA molecule. The main conclusion of this paper is that if the tRNA molecule was assembled in the main phyletic lines this would imply a still rapidly evolving translation apparatus which, in turn, seems to imply that the last universal common ancestor was a progenote.     

Chemotaxonomy of Gentianopsis: Xanthones, C-glycosylflavonoids and carbohydrates

In the genus Gentiana s.l. (Gentianaceae), the status of the section Crossopetalum Froel, is still very much debated. On Morphological grounds. Ma regarded this section as an independent genus which he called Gentianopsis. In this paper we discuss this proposal, taking into account chemotaxonomic data (xanthones, carbohydrates and C-glycosylflavones) arising from an examination of leaves and flowers of 13 species including the type-species Gentianopsis barbata. Isoscoparin, primeverose. 1,3,7- and 1,3,7,8-O-substituted xanthones were present in all species, while 1,3,5,8-O-substituted xanthones were absent. These criteria clearly differentiate the group from Gentianella (occurrence of 1,3,5,8-O-substituted xanthones, absence of 1,3,7-O-substituted xanthones, presence of swertisin, absence of primeverosel in which they were previously included. Furthermore, a comparison of Crossopetalum with two species belonging to Gentiana s.s. (the type G. lutea L. and G. orbicularis Schur.) discloses some analogy with respect to xanthone composition (only 1,3,7- or 1,3,7,8-substitution, respectively). However, the presence of gentianoise in Gentiana s.s., in contrast to its absence in Gentianopsis, indicates that the latter should be excluded from Gentiana. The assessment on morphological grounds of the validity of the genus Gentianopsis Ma is thus reinforced. The evolutionary signification of the chemical characters and the phyletic relationships of Gentianopsis with the other genera of the Gentianinae are discussed.     

Phylogenetic relationships of African microhylid frogs inferred from DNA sequences of mitochondrial 12S and 16S rRNA genes

The phylogenetic relationships of microhylid frogs are poorly understood. The first molecular phylogeny for continental African microhylids is presented, including representatives of all subfamilies, six of the eight genera, and the enigmatic hemisotid Hemisus. Mitochondrial 12S and 16S rRNA sequence data were analysed using parsimony, likelihood and Bayesian methods. Analyses of the data are consistent with the monophyly of all sampled subfamilies and genera. Hemisus does not nest within either brevicipitines or non-brevicipitines. It is possibly the sister group to brevicipitines, in which case brevicipitines might not be microhylids. Phrynomantis and Hoplophryne potentially group with non-African, non-brevicipitine microhylids, in agreement with recent morphological and molecular data. Within brevicipitines, Breviceps is recovered as the sister group to a clade of Callulina+Spelaeophryne+Probreviceps. The relationships among the genera within this latter clade are unclear, being sensitive to the method of analysis. Optimal trees suggest the Probreviceps macrodactylus subspecies complex might be paraphyletic with respect to P. uluguruensis, corroborating preliminary morphological studies indicating that P. m. rungwensis may be a distinct species. P. m. loveridgei may be paraphyletic with respect to P. m. macrodactylus, though this is not strongly supported. Some biogeographic hypotheses are examined in light of these findings.     

C-Glycosylflavones and xanthones in leaves of Rigidella,sessilanthera and Fosteria

Four New World genera are included in the tribe tigrideae of the Iridaceae. These genera, which have been the subject of recent systematic treatments [1–4], share many characteristics; e.g. a haploid complement of two large and 12 small chromosomes and bisulcate pollen grains. However, the taxonomic and phyletic relationships within and between these genera have been based strictly on floral morphology and may simply reflect the primary pollinators of these genera [4,5].The flavonoid chemistry of eight species in three of the four genera, Rigidella, Sessilanthera and Fosteria, was investigated as part of a systematic study of Tigrideae. Our results are summarized in Table 1 nad Fig. 1. Although a recurrent pattern of $\text{C-}\text{glycosylflavones}$ and xanthones characterize the leaves of these taxa, each species exhibits a distinctive array of compounds. The same classes of compounds occur in other tribes of the Iridaceae: $\text{C-}\text{glycosylflavones}$ occur in the Irideae [6,7], Cipureae, and Mariceae and xanthones in Irideae [6] and Sisyrinchieae [6].     

Scale and squamation character polarity and phyletic assessment in the family Cichlidae

Scale and squamation characters have proved to be useful in investigating phyletic relationships in the family Cichlidae. To provide a sound basis for a cladistic analysis the plesiomorphic states have to be determined. This has been done for the family as a whole as well as for some phyletic lineages. Based on those characters the phylogeny within the family has been investigated.     

Strontium isotope stratigraphy of Cretaceous hippuritid rudist bivalves: rates of morphological change and heterochronic evolution

Strontium isotope stratigraphy of 17 localities of rudist formations in the region of the former Mediterranean Tethys has provided a reliable and precise stratigraphical frame for the evaluation of morphological change in hippuritid rudist bivalves during the Coniacian–Campanian. The phyletic lineage Vaccinites cornuvaccinum (Bronn)–Vaccinites chaperi (Douvillé) evolved from the Early Coniacian until the Early Campanian and is characterized by phyletic size increase and allometric growth, as shown by morphometrical measurements of 102 shells. These chronospecies intergrade in the Late Coniacian so that V. cornuvaccinum is considered to be a reliable marker species for the Coniacian. The taxonomy of Vaccinites alpinus (Douvillé) is discussed and the species is recognized as a senior synonym of Vaccinites ultimus (Milovanovi ). It appears first in the Late Santonian and the last appearance is probably in Late Campanian. Both lineages are characterized by phyletic size increase and peramorphic evolution involving hypermorphosis. A doubling of the length of the mantle margin occurred within 5 m.y. in both lineages. The results demonstrate that the combination of morphometric analyses and stratigraphical precision provides an important tool for the delineation of tempo and mode of evolution in rudist bivalves. Strontium isotope stratigraphy resulted in a considerable revision of the ranges of the species investigated. As the stratigraphy of many Tethyan carbonate platforms relies on the distribution of rudist bivalves, and the species investigated are abundant in many rudist formations, the history of many Late Cretaceous carbonate platforms must be re-evaluated.     

Plastomes of Betulaceae and phylogenetic implications

Betulaceae is a well‐defined family of Fagales, including six living genera and more than 160 modern species. Species of the family have high ecological and economic value for the abundant production of wood. However, phylogenetic relationships within Betulaceae have remained partly unresolved, likely due to the lack of a sufficient number of informative sites used in previous studies. Here, we re‐investigate the Betulaceae phylogeny with whole chloroplast genomes from 24 species (17 newly assembled), representing all genera of the family. All the 24 plastomes are relatively conserved with four regions, and each genome is ∼158–161 kb long, with 111 genes. The six genera are all monophyletic in the plastome tree, whereas Ostrya Scop. is nested in the Carpinus clade in the internal transcribed spacer tree. Further incongruencies are also detected within some genera between species. Incomplete lineage sorting and/or hybrid introgression during the diversification of the family could account for such incongruencies. Our dating analysis, based on four fossils, suggests that the most recent common ancestors of the extant genera date back to the mid‐ to late Miocene, and confirms that Betulaceae started to diversify in the upper Cretaceous/early Paleocene. Our results highlight the significance of using more informative sites in resolving phylogenetic relationships. Plastome data and increased taxon sampling will help to better understand the evolutionary history of Betulaceae in the future.     

A phylogeny of sparoid fishes (Perciformes, Percoidei) based on morphology

 The putative percoid superfamily Sparoidea includes the Nemipteridae, Lethrinidae, Sparidae, and Centracanthidae. Although a rigorous cladistic analysis has never been attempted, two hypotheses regarding relationships among these families have been proposed. One early noncladistic hypothesis considered the Sparidae to be intermediate between the more primitive Nemipteridae and the more derived Lethrinidae. A later nonformal phylogenetic treatment provided evidence for a close relationship between Sparidae and Centranthidae and suggested a closer affinity between the Nemipteridae and Lethrinidae. We examine 54 osteological, ligament, and squamation characters in representatives of all 45 genera of these families and 4 outgroup taxa. The results of our cladistic analysis are congruent with a cladistic interpretation of the earlier hypothesis, with strong support for the phyletic sequence Nemipteridae, Lethrinidae, Sparidae plus Centracanthidae, with placement of centracanthids unresolved with respect to sparid genera. Received: May 21, 2001 / Revised: October 26, 2001 / Accepted: November 19, 2001     

Evolutionary history of the Tricladida and the Platyhelminthes: an up-to-date phylogenetic and systematic account

Within the free-living platyhelminths, the triclads, or planarians, are the best-known group, largely as a result of long-standing and intensive research on regeneration, pattern formation and Hox gene expression. However, the group's evolutionary history has been long debated, with controversies ranging from their phyletic structure and position within the Metazoa to the relationships among species within the Tricladida. Over the the last decade, with the advent of molecular phylogenies, some of these issues have begun to be resolved. Here, we present an up-to-date summary of the main phylogenetic changes and novelties with some comments on their evolutionary implications. The phylum has been split into two groups, and the position of the main group (the Rhabdithophora and the Catenulida), close to the Annelida and the Mollusca within the Lophotrochozoa, is now clear. Their internal relationships, although not totally resolved, have been clarified. Tricladida systematics has also experienced a revolution since the implementation of molecular data. The terrestrial planarians have been demonstrated to have emerged from one of the freshwater families, giving a different view of their evolution and greatly altering their classification. The use of molecular data is also facilitating the identification of Tricladida species by DNA barcoding, allowing better knowledge of their distribution and genetic diversity. Finally, molecular phylogenetic and phylogeographical analyses, taking advantage of recent data, are beginning to give a clear picture of the recent history of the Dugesia and Schmidtea species in the Mediterranean.