Phylogenetic relationships of the genera of Theaceae based on morphology

This work represents the first phylogenetic analysis of all genera belonging to the plant family Theaceae (sensu lato). The study is based on 60 morphological characters derived from herbarium specimens and an extensive literature review of 37 genera (including the outgroup). In contrast to the results from molecular data, Theaceae is here found to consist of one clade in which the recognition of two families or subfamilies would leave Theaceae s.s. paraphyletic. Within that clade, Ternstroemiaceae is supported as monophyletic and includes Adinandra, Anneslea, Archboldiodendron, Balthasaria, Cleyera, Eurya, Euryodendron, Ficalhoa, Freziera, Symplococarpon, Ternstroemia and Visnea. The paraphyletic Theaceae s.s. includes Apterosperma, Camellia, Dankia, Gordonia, Pyrenaria, Schima, and Stewartia. Tetrameristaceae (Pentamerista and Tetramerista) are supported as a monophyletic family, with Pellicieraceae (Pelliciera) as sister group, and that clade is sister to the rest of the taxa. Bonnetiaceae (Archytaea and Bonnetia) and Kielmeyeroideae of the Clusiaceae (Caraipa, Haploclathra, Kielmeyera, Mahurea, Marila, and Neotatea) are also supported as monophyletic. Given the differences between the results obtained from morphological and molecular data, we consider that there is still a need for further research, including combined analyses.     

Abundance and utilization of Pyrenacantha sylvestris in Budongo Forest Reserve,western Uganda

Pyrenacantha sylvestris S. Moore (Icacinaceae), locally known as Kateganende, has been extensively harvested by local people yet poorly managed. This has created a gap between its utilization and conservation. A study was therefore conducted to document its abundance and utilization in Budongo Forest Reserve. Abundance was assessed in ten systematically sampled plots of 20 × 50 m. Five of the plots were established in logged forest (compartment N2) and the other five in the nature reserve (compartment N15). Individual P. sylvestris and trellises were recorded and their respective diameter at breast height measured. Questionnaires designed to capture information on the utilization of P. sylvestris were administered to 40 systematically selected respondents adjacent to the forest reserve. Abundance was highest in logged areas of the forest (χ² = 14.8, d.f. = 4, P < 0.01). Individuals in the diameter class 0.1–0.5 cm were the most abundant. Pyrenacantha sylvestris in the forest were mostly hosted in the trellises of the diameter class 1.0–10 cm. Over‐reliance and use of P. sylvestris threaten the survival of the species. There is a need to create awareness and regulate its harvesting. In addition, research needs to be conducted on the possibility of propagating and domesticating this plant.     

Phylogenetic relationships of Polyporus and morphologically allied genera

Polyporus accommodates morphologically heterogeneous species and is divided into six infrageneric groups based on macromorphological characters. On the other hand allied genera have macro- and microscopic characters similar to those of Polyporus. The phylogenetic relationships of Polyporus and allied genera were established from sequences of RNA polymerase II second largest subunit (RPB2), nuclear ribosomal large subunit (nucLSU) and mitochondrial ATPase subunit 6 (ATP6). The molecular phylogenetic trees confirmed that Polyporus is a polyphyletic genus and recognized six major clades (1-6) containing species of Polyporus and several allied genera. Among the clades one contained three infrageneric groups of Polyporus and two allied genera, Datronia and Pseudofavolus while one other contained group Polyporellus and Lentinus. Five of the six major clades contained species belonging to a single infrageneric group, Favolus, Melanopus, Polyporellus or Polyporus. This suggests that morphological characters used to define these groups have phylogenetic significance and reveals the need for a taxonomic revision of Polyporus and its allied genera.     

Phylogenetic relationships among genera of the Tetrabothriidae (Eucestoda)

Cladistic analysis of the generic-level relationships within the family Tetrabothriidae was conducted. A single cladogram resulted from evaluation of 28 homologous transformation series representing 41 character states. The genus Tetrabothrius was recognized as plesiomorphic followed by Chaetophallus and Trigonocotyle. The latter was considered as the sister group for the remaining tetrabothriid genera of marine mammals. Anophryocephalus, Strobilocephalus, and Priapocephalus are among the most highly derived genera and are postulated as having close evolutionary affinities. Comparisons to previous explicit hypotheses for relationships among the genera indicated the present analysis was the most efficient phylogenetic statement (consistency index = 85.4%) for the 28 attributes evaluated. The recognition of Tetrabothrius as primitive and a natural grouping of Anophryocephalus, Strobilocephalus, and Priapocephalus in part confirmed results of previous studies of the Tetrabothriidae.     

Phylogenetic relationships between Bryum and supposedly closely related genera

Abstract

The phylogeny of the genus Bryum was studied using cladistic analyses under the maximum parsimony criterion of evolution of anatomical and morphological characters. Three analyses were made with 32 Bryum species plus 20 species from genera supposedly closely related to Bryum, and with Amblyodon dealbatus (Sw. ex Hedw.) Bruch & Schimp., Meesia uliginosa Hedw., and Leptostomum macrocarpum (Hedw.) Bach. Pyl., as outgroups. It is here suggested that under earlier systematic concepts the genus Bryum is paraphyletic. A clade with Bryum billarderi Schwägr., B. capillare Hedw., B. donianum Grev., B. russulum Broth. & Geh., Rhodobryum giganteum (Schwägr.) Paris, and R. keniae (Müll. Hal.) Broth. are circumscribed by spathulate stem leaves that are crowded in the stem apex, suggesting that the rosulate species of Bryum are more closely related to Rhodobryum than to the rest of Bryum. Stem leaf costae without stereids and spores that mature in the winter are synapomorphies for a clade with Anomobryum julaceum (P. Gaertn. et al.) Schimp. and Bryum argenteum (Hedw.). The tropical species B. cellulare Hook. and B. flaccum Wilson ex Mitt. appear in a clade with Plagiobryum zieri (Dicks. ex Hedw.) Lindb. and Synthetodontium pringlei Cardot. In one analysis, B. limbatum Müll. Hal., Epipterygium tozeri (Grev.) Lindb., Leptobryum pyriforme (Hedw.) Wilson, and Roellia roellii (Broth. ex Röll) H.A. Crum came out in a clade with Mniobryum atropurpureum (Wahlenb.) I. Hagen, Mnium hornum Hedw., Pohlia cruda (Hedw.) Lindb., P. longicollis (Hedw.) Lindb., and Pseudopohlia didymodontia (Mitt.) A.L.Andrews. It is here suggested that gametophytic features, such as the orientation and anatomy of the stem leaves and the appearance of vegetative propagules, are important for the internal relationships within the studied ingroup, whereas characters related to the sporophyte, especially those of the peristome, may obscure phylogenetic relationships. Most of the subgenera and the sections of Bryum, as defined by earlier authors, appear to be paraphyletic. However, due to the low stability of most clades it is suggested that analyses including anatomical, morphological, and molecular data are needed.     

Phylogenetic relationships of the genera Arthroderma and Nannizzia inferred from mitochondrial DNA analysis

The phylogenetic relationship of the genera Arthroderma and Nannizzia, was investigated by mitochondrial DNA analysis based on the restriction-fragment-length polymorphisms. Phylogenetic trees made on ten species. A. benhamiae, A. insingulare, A. quadrifidum, A. simii, A. vanbreuseghemii, N. fulva, N. grubyia, N. gypsea, N. incurvata and N. otae showed no definite distinctions between the genera Arthroderma and Nannizzia. These results support the conclusion of Weitzman et al. that the genera Arthroderma and Nannizzia are congeneric.     

Phylogenetic relationships among Heliconiinae genera based on morphology (Lepidoptera: Nymphalidae)

Abstract.  Phylogenetic relationships among Heliconiinae genera are proposed based on early-stage and adult morphology. Parsimony analyses of forty-nine species in twenty-nine genera indicate that Heliconiinae can be divided into four main groups: (1) Pardopsis , Acraea and Actinote ; (2) Cethosia plus Neotropical genera; (3) Oriental genera and (4) fritillaries. Analyses of adult characters suggested that Oriental genera form a monophyletic group, whereas those of adult plus early-stage characters artificially split this group into three separate lineages. Our character set does not contain enough phylogenetic information to resolve relationships among fritillary genera with confidence, and further studies of this group are needed. The classification of the Heliconiinae is revised based on our results.     

Phylogenetic relationships of four endemic genera of the Phasianidae in China based on mitochondrial DNA control-region genes

The taxonomic status of some genera within the Phasianidae remains controversial. To demonstrate the phylogenetic relationships of four endemic genera (Tetraophasis, Ithaginis, Crossoptilon and Chrysolophus) and other 11 genera of Phasianidae in China, a total of 1070 nucleotides of mitochondrial DNA (mtDNA) control-region genes were sequenced. There are 376 variable sites including 345 parsimony sites. The genetic distance ranged from 0.067 (Chrysolophus and Phasianus) to 0.181 (Perdix and Bambusicola) among the 15 genera. Maximum likelihood method was used to construct a phylogenetic tree, which grouped all the genera into two deeply divergent clades. Perdix was shown to be a non-partridge genus. Alternatively, it appears ancestral to either partridges or pheasants. The sibling taxa of the four endemic genera were Lophophorus, Tragopan, Lophura and Phasianus, respectively. Calibrated rates of molecular evolution suggested that the divergence time between the four genera and related taxa was 4.00–5.00 million years ago, corresponding to the Pliocene. Considering their molecular phylogenetics, fossil and geographical distribution patterns, the four endemic genera might have originated in the southwestern mountains in China.     

Wood and stem anatomy of Lardizabalaceae, with comments on the vining habit, ecology and systematics

CARLQUIST, S., 1984. Wood and stem anatomy of Lardizabalaceae, with comments on the vining habit, ecology and systematics. Qualitative and quantitative data, based mostly upon liquid-preserved specimens, are presented for Akebia, Roquila, Decaisnea, Holbodia, Lardizabala, Sinofranchetia and Stauntonia . Because Decaisnea is a shrub whereas the other genera are vines, anatomical differences attributable to the scandent habit can be considered. These include exceptionally wide vessels, a high proportion of vessels to tracheids (or other imperforate trdcheary elements) as seen in transection, simple perforation plates, multiseriate rays which are wide and tall, and pith which is partly or wholly sclerenchymatous. With respect to ecology, two features are discussed: spirals in narrower vessels may relate to adaptation to freezing in the species of colder areas, and crystalliferous sclereids seem adapted in morphology and position to deterrence of phytophagous insects or herbivores. The wood may provide mechanisms for maintaining conduction even if wider vessels are deactivated temporarily by formation of air embolisms. Wood and stem anatomy of Lardizabalaceae compare closely to those of Berberidaceae and of Clematis (Ranunculaceae), as well as to other families of Berberidales. Decaisnea is more primitive than these in having consistently sralariform perforation plates and in having scalariform pitting on lateral walls of vessels. A tentative listing of anatomical features which may correspond to generic limits is given.     

Phylogenetic relationships of three genera in Anacardiaceae: Bonetiella, Pseudosmodingium, and Smodingium

Phylogenetic analyses were conducted to determine the relationships between and characterize the morphological variation among three genera of Anacardiaceae:Bonetiella, Pseudosmodingium, andSmodingium. The first two genera are endemic to Mexico and the third to South Africa.Bonetiella andSmodingium are monotypic.Pseudosmodingium has eight species, six extant and two fossil, and all were included in the analyses. Fifty-six anatomical characters for leaves, wood, and fruit, as well as morphological characters, were considered. Our results indicate thatSmodingium is not closely related toPseudosmodingium andBonetiella, and that these last two genera are sister taxa.Pseudosmodingium is a monophyletic group and the two fossil species are related to species from the same geographical area of central Mexico where they were found. Fruit anatomical characters were significant at the generic level, while leaf anatomical characters were important at the species level inPseudosmodingium.

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Resumen  En este trabajo se llevaron a cabo análisis filogenéticos para determinar las relaciones filogenéticas así como caracterizar la variación morfológica de tres géneros de Anacardiaceae:Bonetiella, Pseudosmodingium ySmodingium. Los dos primeros son endémicos a México y el terceroo a Sudáfrica.Bonetiella ySmodingium son monotípicos.Pseudosmodingium incluye ocho especies, dos fósiles y el resto vivientes, y todas fueron consideradas en los análisis. Se consideraron 56 caracteres tanto anatómicos como morfológicos de hojas, madera y frutos. Nuestros resultados indican queSmodingium no está cercanamente relacionado aPseudosmodingium yBonetiella, y que estos dos últimos géneros son taxa hermanos.Pseudosmodingium es un grupo monofilético y las dos especies fósiles están relacionadas a especies que crecen en las mismas áreas geográficas del centro de México, donde fueron descubiertas. Los caracteres anatómicos del fruto fueron significativos a nivel genérico, mientras que los de hoja fueron importantes a nivel de especies enPseudosmodingium.

     

Phylogenetic relationships of African killifishes in the genera Aphyosemion and Fundulopanchax inferred from mitochondrial DNA sequences

We have analyzed the phylogenetic relationships of 52 species representing all defined species groups (J. J. Scheel, 1990, Atlas of Killifishes of the Old World, 448 pp.) of the African aplocheiloid fish genera Aphyosemion and Fundulopanchax in order to examine their interrelationships and to reveal trends of karyotypic evolution. The data set comprised 785 total nucleotides from the mitochondrial 12S rRNA and cytochrome b genes. The molecular-based topologies analyzed by both maximum parsimony and neighbor-joining support the monophyly of most previously defined species groups within these two killifish genera. The genus Aphyosemion is monophyletic except for the nested position of Fundulopanchax kunzi (batesi group; subgenus Raddaella) within this clade, suggesting that this taxon was improperly assigned to Fundulopanchax. The remaining Fundulopanchax species sampled were supported as being monophyletic in most analyses. Relationships among the species groups in both genera were not as strongly supported, suggesting that further data will be required to resolve these relationships. Additional sampling from the 16S rRNA gene allowed further resolution of relationships within Fundulopanchax, more specifically identifying the nonannual scheeli group as the basal lineage of this otherwise annual genus. Chromosomal evolution within Aphyosemion has been episodic, with the evolution of a reduced n = 9-10 metacentric complement having occurred in multiple, independent lineages. Polarity of chromosomal reductions within the elegans species group appears to support previous hypotheses concerning mechanisms of karyotypic change within the genus Aphyosemion.     

Phylogenetic relationships in Orchis and some related genera: an approach using chloroplast DNA

A chloroplast DNA restriction fragment length polymorphism analysis has been carried out on representatives species of Orchis (Orchidaceae) and of the allied genera Aceras, Dactylorhiza , and Anacamptis . One species of Cephalanthera and one of Serapias were used as outgroups. The consensus tree from a cladistic analysis showed that Orchis , as presently defined, is paraphyletic, as it contains also Aceras anthropophorum and Dactylorhiza saccifera . The genus Orchis is divided in two clades: one including O. laxiflora, O. papilionacea, O. coriophora , and O. morio in a ladderized sequence, the other showing D. saccifera at the base, followed by a clade in which a collapse of O. mascula, O. pauciflora, O. quadripunctata is sister group to a clade composed by O. italica, O. simia , and A. anthropophorum . These results, which agree to a great extent with literature evidence on chromosomes and isozymes, have been compared with various traditional systematic hypotheses for the genus.     

Phylogenetic relationships in the Ranidae. Independent origin of direct development in the genera Philautus and Taylorana

Phylogenetic relationships within a group of Ranidae were studied, particularly between the genera Philautus and Taylorana, to determine whether their original reproductive mode (direct development) appeared independently. To study these relationships, we used the DNA sequences of the 5' end of the gene coding for mitochondrial ribosome small subunit in 28 species. Parsimony analysis resulted in two equiparsimonious trees, 867 steps long (CI = 0.382; RI = 0.429). Data saturation was studied and we applied weighting (weight of 5 for transversions and 1 for transitions) to enhance the phylogenetic information. The tree we obtained (2,212 steps long, CI = 0.408; RI = 0.482) is best supported and allows us to determine clearly that direct development has appeared independently in Philautus and Taylorana. In addition, it is confirmed that the genus Rana sensu lato is heterogeneous. The genera Occidozyga and Phrynoglossus form a clade basal to all the group but this position is not supported. The inclusion of the Rhacophorinae in the Ranidae is confirmed. Finally, this study confirms that the relationships within the group Tomopterna sensu Boulenger, 1918 should be re-evaluated.     

Phylogenetic relationships within the tropical soft coral genera Sarcophyton and Lobophytum (Anthozoa, Octocorallia)

Abstract. The alcyonacean soft coral genera Sarcophyton and Lobophytum are conspicuous, ecologically important members of shallow reef communities throughout the Indo-West Pacific. Study of their ecology is, however, hindered by incomplete knowledge of their taxonomy: most species cannot be identified in the field and the two genera cannot always be distinguished reliably. We used a 735-bp fragment of the octocoral-specific mitochondrial protein-coding gene msh1 to construct a phylogeny for 92 specimens identified to 19 species of Lobophytum and 16 species of Sarcophyton . All phylogenetic methods used recovered a tree with three strongly supported clades. One clade included only morphologically typical Sarcophyton species with a stalk distinct from the polypary, poorly formed club-shaped sclerites in the colony surface, and large spindles in the interior of the stalk. A second clade included only morphologically typical Lobophytum colonies with lobes and ridges on the colony surface, poorly formed clubs in the colony surface, and interior sclerites consisting of oval forms with regular girdles of ornamental warts. The third distinct clade included a mix of Sarcophyton and Lobophytum nominal species with intermediate morphologies. Most of the species in this mixed clade had a polypary that was not distinct from the stalk, and the sclerites in the colony surface were clubs with well-defined heads. Within the Sarcophyton clade, specimens identified as Sarcophyton glaucum belonged to six very distinct genetic sub-clades, suggesting that this morphologically heterogeneous species is actually a cryptic species complex. Our results highlight the need for a complete taxonomic revision of these genera, using molecular data to help confirm species boundaries as well as to guide higher taxonomic decisions.     

Phylogenetic relationships of vespertilionid genera (Mammalia: Chiroptera) as revealed by karyological analysis

Banded karyotypes of 50 species belonging to 23 genera were analyzed. The diploid chromosome numbers ranged from 26 to 50. For karyotypic comparison we used a 44 chromosomes karyotype, consisting of 4 metacentric and 17 acrocentric autosomes, as “basic karyotype”. Almost all of its 25 autosomal arms could be identified in each individual karyotype. In 8 chromosomes, i. e. 1/2, 7, 11, 12, 13, 15, 23 and X, small inversions were detected. As a result, each of the chromosomes mentioned occurs in two states which differ slightly in their banding patterns. These were used as character states in the cladistic analysis together with other chromosomal rearrangements. The implications drawn from the cladogram obtained are: The Miniopterinae clearly belong to the Vespertilionidae but are the first to branch off from the common stem. The tribe Myotini should be raised to the rank of a subfamily. Within the largest subfamily Vespertilioninae, one autapomorphic chromosomal character was found for each of the tribes Vespertilionini and Pipistrellini. In addition, both tribes are distinguished from the other Vespertilioninae tribes by two synapomorphic features. These results allow for the first time an unequivocal classification of the systematically difficult “pipistrelloid” species. The species of the genus Pipistrellus (sensu Hill and Harrison 1987) are spread over the Pipistrelllni and Vespertilionini. We therefore suggest the splitting of this heterogenous genus into at least four genera. Only the members of the previous subgenus Pipistrellus constitute the genus Pipistrellus and belong to the Pipistrellini. The previous subgenera Hypsugo, Vespadelus and Falsistrellus, given generic rank in some recent studies, belong to the tribe Vespertilionini and are not closely related to Pipistrellus. For the genera Eptesicus and Hesperoptenus, which belong neither to the Vespertilionini nor to the Pipistrellini, the tribe Eptesicini was established. The phylogenetic relations of this tribe and the status of the presumably polyphyletic tribe “Nycticeiini” could not be solved.     

Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters

The taxonomy of the coelomycetous fungus Pestalotiopsis and other closely related genera based on morphological characters has been equivocal. To gain insight in the phylogenetic relationships of Pestalotiopsis and its allies, part of the large subunit (28S) ribosomal DNA region was examined and compared with existing morphological information. Phylogenetic analyses were conducted using parsimony, distance, and likelihood criteria. Results of the analyses showed that Bartalinia, Pestalotiopsis, Seimatosporium, and Seiridium represent distinct monophyletic groups with high bootstrap support. However, Truncatella species are paraphyletic with Bartalinia, sharing a common ancestor. Pestalotia species sequenced clustered together with Pestalotiopsis. These genera should be recognized as distinct natural groups except for Monochaetia and Discosia, which need to be further resolved. Tree topologies are generally in concordance with previous morphological hypotheses, most notably the placement of all Pestalotia species, except the type P. pezizoides, in Pestalotiopsis. Well-supported clades corresponding to groupings based on conidial morphology were resolved and the relative importance of morphological characters for generic delimitation is discussed. Molecular data also provide further evidence to support the association of these coelomycetes with the Amphisphaeriaceae.     

Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences

Internal transcribed spacer (ITS-1) sequences from 97 accessions representing 23 species of Lactuca and related genera were determined and used to evaluate species relationships of Lactuca sensu lato (s.l.). The ITS-1 phylogenies, calculated using PAUP and PHYLIP, correspond better to the classification of Feráková than to other classifications evaluated, although the inclusion of sect. Lactuca subsect. Cyanicae is not supported. Therefore, exclusion of subsect. Cyanicae from Lactuca sensu Feráková is proposed. The amended genus contains the entire gene pool (sensu Harlan and De Wet) of cultivated lettuce (Lactuca sativa). The position of the species in the amended classification corresponds to their position in the lettuce gene pool. In the ITS-1 phylogenies, a clade with L. sativa, L. serriola, L. dregeana, L. altaica, and L. aculeata represents the primary gene pool. L. virosa and L. saligna, branching off closest to this clade, encompass the secondary gene pool. L. virosa is possibly of hybrid origin. The primary and secondary gene pool species are classified in sect. Lactuca subsect. Lactuca. The species L. quercina, L. viminea, L. sibirica, and L. tatarica, branching off next, represent the tertiary gene pool. They are classified in Lactuca sect. Lactucopsis, sect. Phaenixopus, and sect. Mulgedium, respectively. L. perennis and L. tenerrima, classified in sect. Lactuca subsect. Cyanicae, form clades with species from related genera and are not part of the lettuce gene pool.     

Phylogenetic relationships among genera in theLiliaceae-Asparagoideae-Polygonatae s.l. inferred fromrbcL gene sequence data

The chloroplast gene encoding ribulose-1,5-bisphosphate-carboxylase (rbcL) was sequenced for phylogenetic analysis of 13 species (10 genera) in the tribePolygonatae s.l. of theLiliaceae-Asparagoideae. The data were analysed using maximum parsimony and neighbour-joining methods. There were 233 phylogenetically informative sites out of 1368 base pairs compared. The results suggest that there are three monophyletic groups withinPolygonatae s.l. with high bootstrap confidence values. Group A representsPolygonatae s.str., with generaMaianthemum, Smilacina, Convallaria, Disporopsis, andPolygonatum. Group B containsUvularia andDisporum and group C includesStreptopus, Tricyrtis, Clintonia, andProsartes. The study suggests thatPolygonatae s.l. are not a monophyletic group, including at least three groups of different phylogenetic origin. Monophyly of the taxa within groups A, B, and C is supported by the high bootstrap confidence values (85–100%) of the bootstrap replications for both parsimony and neighbour-joining methods. The differences between each group (calculated as 100x base substitutions per site) were 6.99–9.03 for group A and B, 4.92–7.35 for A and C, and 6.66–7.57 for B and C.