Molecular Systematics of Trilliaceae I. Phylogenetic Analyses of Trillium Using matK Gene Sequences

matK was conducted using 41 Trillium taxa and two out-group taxa (Veratrum maackii and Helonias bullata). A total of 1608 base pairs were analyzed and compared., and then there were 61 variable (36 informative) sites among Trillium species. Fifteen insertion/deletion events (indels) of six or fifteen base pairs were also detected. Phylogenetic analyses of the sequence data revealed that the subgenus Phyllantherum (sessile-flowered species) forms a distinct monophyletic group, whereas the subgenus Trillium (pedicellate-flowered species) does not form a monophyletic group, and is composed of three distinct groups and three basally located species in the tree: (1) the Erectum group, (2) the Grandiflorum group, and (3) the Pusillum group and (4) the three species, including T. govanianum, T. undulatum, and T. rivale. T .rivale appears to be the most basally diverged and a very specialized taxon among the ingroup members. Our matK data indicated that the closest relative of the subgenus Phyllantherum is the Grandiflorum group. The results are concordant with the results of the RFLP analysis of cpDNA and also more or less with those of the cladistic analysis of morphological characters. Received 11 September 1998/ Accepted in revised form 25 December 1998     

Molecular systematics of Trilliaceae II. Phylogenetic analyses of Trillium and its allies using sequences of rbcL and matK genes of cpDNA and internal transcribed spacers of 18S–26S nrDNA

Coding regions of the rbcL and matK genes of cp DNA and internal transcribed spacers (ITS) of nuclear ribosomal DNA were sequenced to study phylogenetic relationships within and among all four genera of Trilliaceae: Trillium, Paris, Daiswa and Kinugasa . The rbcL gene has evolved much slower than matK and in particular ITS; hence the phylogenetic trees based on the rbcL gene show a much lower resolution than trees based on either matK or ITS. The general topology of phylogenetic trees resulting from separate parsimony analyses of the matK and ITS sequences are relatively congruent, with the exception of the placement of T. pusillum . Both matK and ITS phylogenies reveal that T. rivale diverges at the base of the trees. In both trees, Paris, Daiswa and Kinugasa form a relatively weakly supported group. Within this group, the allo-octaploid Kinugasa japonica is the sister group of Daiswa species. The Paris–Daiswa – Kinugasa group, the major Trillium group, and T. undulatum and T. govanianum showed a loosely related topology, but their affinities are not evident according to these two molecular markers. However, phylogenetic analysis of amino acid sequences derived from matK shows that T. rivale together with clades T. undulatum–T. govanianum, Daiswa–Kinugasa and Paris is basally diverged as a sister group to the remainder of Trillium .     

Life History Studies on the Genus Trillium (Liliaceae) V. Reproductive Biology and Survivorship of Three Declinate-flowered Species

Absract Three pedicellate-declinate-flowered species of Trillium (Liliaceae), T. vaseyi and T. flexipes , were studied for their life history characteristics, e.g., stage class structures of natural populations and reproductive features, including energy allocation to reproductive activities. The populations structures of all three species showed similar depletion structures characterized by a conspicuous decrease of individuals in the small juvenile stages, as was also observed in pedicellate-erect-flowered Trillium species However, with respect to reproductive characteristics, these three declinate-flowered species showed different features from erect-flowered species, although they belong to the same pedicellate-flowered group. That is, these declinate-flowered Trillium species exhibited low seed setting rates of 30% in T. catesbaei , 45% in T. vaseyi and 34% in T. flexipes , suggesting that they possess different mating systems from erect-flowered species which showed high seed setting rates of 50–90%.     

Life History Studies on the Genus Trillium (Liliaceae) I. Reproductive Biology of Four Japanese Species

Abstract Four Japanese Trillium (Liliaceae) species which are representative perennial herbs of the temperate deciduous forests— Trillium kamtschaticum (2x), T. apetalon (4x), T. tschonoskii (4x) and T. smallii (6x)—were studied for their reproductive characteristics, e.g., patterns of reproductive resource allocation and reproductive output.
In spite of the differences in ploidy levels (from 2x to 6x), all four species showed very similar reproductive traits. It became evident that in response to the increase in reproductive allocation to total reproductive organs (RA), the number of seeds produced per plant (P_N) clearly increased. This trend is well in accord with the relationship found in four North American species and also several temperate woodland perennial herbs which occur in closed, stable and predictable environments, and possess typical xenogamous breeding systems. Although there is no conspicuous trend between ploidy levels and P_N, one of the significant differences noted in this study was in seed weight, which ranged from 2.93 mg in diploids, to 3.42–3.45 mg in tetraploids, and to 4.47 mg in hexaploids.     

Demography and reproductive strategies of a polycarpic perennial, Trillium apetalon (Trilliaceae)

To investigate the connection between demographic strategies and reproductive strategies of a polycarpic perennial herb, Trillium apetalon Makino, we conducted three studies. First, we monitored the fate of individuals and the flowering behavior of T. apetalon for 12 years and used a transition matrix model to analyze the demography of the population. The analysis revealed that it takes a long time for individuals to go through one-leaf stage in juveniles. Elasticity analysis showed that the survival of flowering individuals was a decisive factor in the dynamics of the population. Furthermore, we found that the average remaining lifetime of flowering individuals was high relative to the other three stages. Second, to elucidate the demographic consequences of organ preformation, we investigated the development of flower buds for future years. We observed three to six flower buds per rhizome, suggesting that flower buds for the next 3–6 years were ready in advance in this plant. Third, the results of breeding experiments clarified that although this species appears to have a substantial capacity for both inbreeding and outbreeding, inbreeding plays an important role in seed production, and that crossing experiments (direct cross-pollination and self pollination) yielded similar seed-ovule ratios to those obtained from open-pollinated individuals. Our three studies suggest that the adult survival and continuous flowering strategies of T. apetalon obtained from demographic analysis are closely interlinked with breeding systems and preformation of flower buds.     

Phylogeny and co-speciation in feather mites of the subfamily Avenzoariinae (Analgoidea: Avenzoariidae)

A cladistic analysis of phylogenetic relationships is carried out for the feather mite subfamily Avenzoariinae. The analysis is made at two different taxonomic levels, for 19 genera of the all family Avenzoariidae and for taxa of species rank for the Avenzoaria and Bychovskiata generic groups. A subsequent comparative analysis of phylogenetic hypotheseis for the subfamily Avenzoariinae and recently accepted phylogenetic hypotheses of the shorebirds Charadriiformes indicates co-speciation of feather mites with their hosts. As a result of the comparative analysis it is suggested, that the subfamily Avenzoariinae originated from an ancestor of the order Charadriiformes and co-speciated with this host order. The expected pattern of parallel evolution is disturbed by different evolutionary events, such as host shifts, extinction of mites and differential evolutionary rates of mite lineages in different phyletic branches of feather parasites.     

Life History Studies on the Genus Trillium (Liliaceae) IV. Stage Class Structures and Spatial Distribution of Four Japanese Species

Abstract The population struaures, spatial and temporal distributions of individual plants, and survivorship were investigated in four Japanese Trillium species (Liliaceae), T. kamtschaticum, T. tschonoskii, T. apetaion and T. smallii.
The stage class structures of these four species based on leaf area categories all showed similar depletion curves associated with an increase in stnge class. That is, there occurs a conspicuous decrease in early juvenile stages, subsequent leveling-off in the intermediate stages and a slight decrease again in the larger stages. The high mortality in juvenile stages was also confirmed by continuous observations in the permanent plots established on the forest floor for T. kamtschaticum and T. apetalon. Furthermore, the analysis of spatial distribution patterns for T. kamtschaticum and T. apetalon revealed successive distributional changes from under-dispersed (aggregated) to random or overdispersed with the progress of the growth stage.     

Life History Studies on the Genus Trillium (Liliaceae) III. Reproductive Biology of Six Sessile-flowered Species Occurring in the Southeastern United States with Special Reference to Vegetative Reproduction

Abstract Life history characteristics, e.g., stage class structures of natural populations and associated reproductive characteristics, were studied for six sessile-flowered, diploid Trillium (Liliaceae) species that are restricted to the Coastal Plain region of the southeastern United States.
These sessile-flowered species reproduce primarily by vegetative propagation. Leaf area measurements were used to categorize stage class distributions of natural populations. Populations propagating mainly by vegetative reproduction had non-sigmoidal, convex-shaped population structures with most plants being in the intermediate stage classes. Low numbers of individuals in smaller stage classes and an abundance of intermediate sized individuals are due to the fact that vegetative propagules are the primary method for maintenance of local populations.
Characteristics associated with sexual reproduction were also examined. Seed output averaged about 20 seeds per plant, except for T. lancifolium which produced 9.7 seeds on the average. Seed setting rates varied between 15.61–44.15% and mean seed weight varied from 4.89 to 10.75 mg. The dominance of vegetative versus sexual reproduction may be due to the fact that all six species occur in ecologically unstable flood plain habitats.     

Phylogeny and classification of the Scopulini moths (Lepidoptera: Geometridae, Sterrhinae)

The phylogenetic relationships of the genera in the geometrid tribe Scopulini (Lepidoptera: Sterrhinae) were examined using 141 characters of adult morphology and ecology. The study material included 92 species, representing all previously recognized genera and covering the morphological variation and full geographical range of the tribe. The cladistic analysis resulted in 20 equally parsimonious trees and a strict consensus cladogram based on these was well resolved. A majority of the recovered synapomorphic characters have been used previously in the taxonomy of the tribe. However, many novel characters were found in the sclerotized structures of the thorax. Many previously recognized genera were found to be nonmonophyletic and based on the present revised, synapomorphy-based classification, the number of recovered genera is reduced considerably. Twenty new generic synonyms and 90 new or revived species combinations are proposed. Seven genera are considered valid, with the large genus Scopula Schrank including over 85% of all species in the tribe. The taxonomic history of the tribe is reviewed and the problems of earlier classifications are discussed. A key to the genera is presented, although an informal diagnosis is preferred. All recognized genera are illustrated and a revised world checklist of the Scopulini is presented.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 473−530.     

Phylogeny and biogeography of the Vitrinidae (Gastropoda: Stylommatophora)

The phylogeny of the Vitrinidae is reconstructed in a cladistic analysis based on characters of the genitalia, the copulation behaviour and the radula. The genera with an atrial stimulator turned out to be the earliest branches of the Vitrinidae, whereas the genera with a glandula amatoria form a monophyletic, taxonomically apomorphic group. The differences between the proposed phylogeny and previous hypotheses are discussed. The ancestral areas of the Vitrinidae and its sister group, the limacoid slugs Boettgerillidae–Limacidae–Agriolimacidae, are estimated using weighted ancestral area analysis. The Vitrinidae and the limacoid slugs might have originated by a vicariance event between Central Europe and the Near East. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 134 , 347–358.     

Timing of canopy closure influences carbon translocation and seed production of an understorey herb, Trillium apetalon (Trilliaceae)

BACKGROUND AND AIMS: The light availability on a temperate, deciduous-forest floor varies greatly, reflecting the seasonal leaf dynamics of the canopy trees. The growth and/or reproductive activity of understorey plants should be influenced by the length of the high-irradiance period from snowmelt to canopy closure. The aim of the present study was to clarify how spring-blooming species regulate the translocation of photosynthetic products to current reproduction and storage organs during a growing season in accordance with the changing light conditions. METHODS: Growth pattern, net photosynthetic rate, seed production, and shoot and flower production in the next year of Trillium apetalon were compared between natural and experimentally shaded conditions. Furthermore, translocation of current photosynthetic products within plants was assessed by a labelled carbon-chase experiment. KEY RESULTS: During the high-irradiance period, plants showed high photosynthetic ability, in which current products were initially used for shoot growth, then reserved in the rhizome. Carbon translocation to developing fruit occurred after canopy closure, but this was very small due to low photosynthetic rates under the darker conditions. The shading treatment in the early season advanced the time of carbon translocation to fruit, but reduced seed production in the current year and flower production of the next year. CONCLUSIONS: Carbon translocation to the storage organ had priority over seed production under high-irradiance conditions. A shortened bright period due to early canopy closure effectively restricts carbon assimilation, which greatly reduces subsequent reproductive output owing to low photosynthetic products for fruit development and small carbon storage for future reproduction. As populations of this species are maintained by seedling recruitment, acceleration of canopy closure timing may influence the maintenance and dynamics of populations.     

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.     

Phylogenetic analysis and revision of the linyphiid spider genus Solenysa (Araneae: Linyphiidae: Erigoninae)

In this paper we carry out a taxonomic revision and phylogenetic analysis of the linyphiid spider genus Solenysa Simon, 1894. A total of 12 species is treated here, including five new species collected from China and Japan: Solenysa akihisai Tu sp. nov., Solenysa lanyuensis Tu sp. nov., Solenysa retractilis Tu sp. nov., Solenysa tianmushana Tu sp. nov. , and Solenysa yangmingshana Tu sp. nov. Solenysa circularis Gao, Zhu & Sha, 1993 is a junior synonym of Solenysa protrudens Gao, Zhu & Sha, 1993. We have assembled two different character matrices to reconstruct the phylogenetic relationships of Solenysa. In the first matrix (Matrix 1), five representative species of Solenysa were added to the morphological dataset of Miller & Hormiga to test the monophyly of the genus and its placement within Linyphiidae. The genitalic structures and somatic morphology of Solenysa were studied by means of scanning electron microscopy for the first time. To infer the species‐level phylogenetic relationships of Solenysa we produced a second matrix (Matrix 2) that includes all 12 Solenysa species and six outgroup species chosen from the results of the analysis of the first matrix. The two most parsimonious trees from the analysis of Matrix 1 support the monophyly of Solenysa and its placement within the ‘Distal Erigonines’ clade. The single most parsimonious tree resulting from the analysis of the second matrix suggests that the Solenysa clade includes four monophyletic groups, each group represented by a distinct genitalic pattern. The morphology of Solenysa, both somatic and genitalic, is highly autapomorphic. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 484–530.     

Molecular Phylogeny and Evolutionary Relationships between the Ciliate Genera Peniculistoma and Mytilophilus (Peniculistomatidae,Pleuronematida)

Peniculistoma mytili and Mytilophilus pacificae are placed in the pleuronematid scuticociliate family Peniculistomatidae based on morphology and ecological preference for the mantle cavity of mytiloid bivalves. We tested this placement with sequences of the small subunit rRNA (SSUrRNA) and cytochrome c oxidase subunit 1 (cox1) genes. These species are very closely related sister taxa with no distinct genetic difference in the SSUrRNA sequence but about 21% genetic difference for cox1, supporting their placement together but separation as distinct taxa. Using infection frequencies, M. pacificae, like its sister species P. mytili, does not interact with Ancistrum spp., co‐inhabitants of the mantle cavity. On the basis of these ecological similarities, the fossil record of host mussels, and features of morphology and stomatogenesis of these two ciliates, we argue that M. pacificae derived from a Peniculistoma‐like ancestor after divergence of the two host mussels. Our phylogenetic analyses of pleuronematid ciliates includes the SSUrRNA gene sequence of Sulcigera comosa, a Histiobalantium‐like ciliate from Lake Baikal. We conclude: (i) that the pleuronematids are a monophyletic group; (ii) that the genus Pleuronema is paraphyletic; and (iii) that S. comosa is a Histiobalantium species. We transfer S. comosa to Histiobalantium and propose a new combination Histiobalantium comosa n. comb.     

Molecular Phylogeny and Species Identification of Pufferfish of the Genus Takifugu (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships and species identification of pufferfishes of the genus Takifugu were examined by use of randomly amplified polymorphic DNA (RAPD) and sequencing of the amplified partial mitochondrial 16S ribosomal RNA genes. Amplifications with 200 ten-base primers under predetermined optimal reaction conditions yielded 1962 reproducible amplified fragments ranging from 200 to 3000 bp. Genetic distances between 5 species of Takifugu and Lagocephalus spadiceus as the outgroup were calculated from the presence or absence of the amplified fragments. Approximately 572 bp of the 16S ribosomal RNA gene was amplified, using universal primers, and used to determine the genetic distance values. Topological phylogenic trees for the 5 species of Takifugu and outgroup were generated from neighbor-joining analysis based on the data set of RAPD analysis and sequences of mitochondrial 16S rDNA. The genetic distance between Takifugu rubripes and Takifugu pseudommus was almost the same as that between individuals within each species, but much smaller than that between T. rubripes, T. pseudommus, and the other species. The molecular data gathered from both analysis of mitochondria and nuclear DNA strongly indicated that T. rubripes and T. pseudommus should be regarded as the same species. A fragment of approximately 900 bp was amplified from the genome of all 26 T. pseudommus individuals examined and 4 individuals of intermediate varieties between T. rubripes and T. pseudommus. Of the 32 T. rubripes individuals, only 3 had the amplified fragment. These results suggest that this fragment may be useful in distinguishing between T. rubripes and T. pseudommus. Received September 29, 2000; accepted February 26, 2001.     

Redescription of Antetintinnidium mucicola (Claparède and Lachmann, 1858) nov. gen., nov. comb. (Alveolata,Ciliophora, Tintinnina)

Tintinnid ciliates have traditionally been described and classified exclusively based on their lorica features. Although information on the cell characters is urgently needed for a natural classification, more molecular than cytological data has been accumulated over recent years. Apparently, the tintinnids developed in the marine environment and entered freshwater several times independently. Typical freshwater tintinnids belong to the genera Tintinnidium and Membranicola. The species are comparatively well‐known regarding their morphology and characterised by two unusual de novo originating ciliary rows, the ventral organelles. In contrast, the cell features in the marine/brackish Tintinnidium species, specifically their somatic ciliary patterns, are insufficiently known or not known at all. Therefore, the morphology of a common marine/brackish representative, Tintinnidium mucicola, is redescribed based on live observation and protargol‐stained material. Furthermore, biogeographical and autecological data of the species are compiled from literature and own records. The phylogenetic relationships of T. mucicola are inferred and the diversity of the family Tintinnidiidae is assessed from 18S rDNA sequences. The study shows that T. mucicola is not only molecularly distinct, but also characterised by many plesiomorphic features, for instance, it does not possess a verifiable homologue to the ventral organelles. Hence, a new genus, Antetintinnidium nov. gen., is established for T. mucicola. The new insights into the diversity of Tintinnidiidae shed light on the early evolution of tintinnids and might provide clues on their adaptions to freshwater.