A phylogenetic analysis of subtribe Pleurothallidinae (Orchidaceae)

A cladistic analysis of subtribe, Pleurothallidinae (Orchidaceae) is based on 45 anatomical/ morphological characters. The ingroup members comprise 24 genera; the large genus Pkurothallis consists of two subgenera and ten species complexes. Three taxa representing subtribes Laeliinae and ArpophyUinae are designated as outgroup. Eight most parsimonious trees were discovered using computer assisted software (length = 230; CI = 0.27). The hypothesis that subtribe Pleurothallidinae has undergone a unilinear reduction in the number of pollinia is not supported by this study. Although the eight-pollinia state as represented by Octomeria apparently is plesiomorphic, the two-pollinia and four-pollinia states arose early in the phytogeny of the subtribe. Both two-and four-pollinia states subsequently reappeared as parallelisms. The six-pollinia state exhibited in Brachionidium is autapomorphic. This cladistic analysis suggests that Pkurothallis is not a natural genus and, perhaps may be divided into several discrete genera.     

Pollen morphology of the subtribe Pleurothallidinae Lindl. (Orchidaceae)

Pollinia of 21 pleurothallid genera were examined with SEM. To detect the polarity in sculpture evolution, pollinia of three species (Restrepia elegans, Myoxanthus ceratothallis, Octomeria grandiflora) were studied with TEM. Compared with other taxa of the subfamily Epidendroideae, the Pleurothallidinae reveal a strong tendency towards sporoderm reduction. Besides a primitive surface there are 5 derived types which have evolved along two major morphological lines: psilate-reticulate-octomerioid and psilate-granulatelepanthoid/hamulate/gemmate. Caudicular regions generally show an undifferentiated exinous layer. Even 'primitive' representatives of the subtribe have a reduced stratification compared with the classic angiospermous tectate-columellate pollen wall. Starting with a partially baculate sporoderm, which already lacks the nexine (Restrepia) we find a highly reduced pollen wall with a compact sporopollenin-layer and a stratified intine in Octomeria and Myoxanthus . Pollen walls of the inner pollinium consist only of a bi-layered intine. In Octomeria inner tetrads are separated by a partially perforated cell wall comparable to the callose wall of the pollen mother cell. Palynological data and their systematic implications are summarized in a diagram. Except for Pleurothallis and Masdevallia, which seem to be paraphyletic, surface types are consistent with the genera. However, some of them have apparently evolved independently several times. Reduction patterns coincide with major trends of orchidaceous sporoderm evolution. Some of the surface types, however, have been undocumented in the family so far. They show the subtribe as a highly derived natural taxon, which is still actively evolving. Adaptations to very small pollinators (dipterans) and short dispersal distances of the pollen, along with the high humidity of the natural habitat, have apparently triggered the reduction processes of the pleurothallid sporoderm.     

A phylogenetic analysis of the land plants

Phylogenetic systematics (cladistics) is a theory of phylogeny reconstruction and classification widely used in zoology. Taxa are grouped hierarchically by the sharing of derived (advanced) characters. The information is expressed in a cladogram, a best estimate of a phylogeny. Plant systematists generally use a phenetic system, grouping taxa on overall similarity which results in many groups being formed, at least in part, on the basis of shared primitive characters.
The methods of phylogenetic systematics are used to create a preliminary cladogram of land plants. The current classification of land plants is criticized for its inclusion of many groups which are not monophyletic.
Objections to the use of phylogenetic systematics in botany, apparent convergences within major groups and frequent hybridization, are shown to be invalid. It is concluded that cladistic analysis presents the best estimate of die natural hierarchy of organisms, and should be adopted by plant systematists in their assessment of plant interrelationships.     

以礼草属系统发育的分析

基于分支系统学的原理和方法。对禾本科以礼草属进行了系统发育分析,以礼草属是个单系在群,它的３２个外部性状选作极性分析。鹅观草属中的肃草作为外类群,采用ＰＡＵＰ程序对矩阵进行运算,获得了１个最简约的谱系分支图。在分支图上,以民礼草属２６个种可以归为３个组,但不适合于划分系,３个组中各组包含的种数分别与传统分类的３个组基本吻合,从而支持了传统分类的结果。同时,分支图还展示了各个类群间的亲缘演化关系,其     

Phylogeny of subfamily Epidendroideae (Orchidaceae) inferred from ndhF chloroplast gene sequences

This project undertakes the first molecular-based phylogenetic study of subfamily Epidendroideae (Orchidaceae). Approximately 1200 nucleotides (from the 3' half of the chloroplast gene ndhF for 34 orchid taxa and a lilioid monocot, Clivia miniata (Amaryllidaceae), were subjected to phylogenetic analysis using parsimony and maximum likelihood methods. Oryza sativa (Poaceae), a nonlilioid monocot, was designated as outgroup. Trees from both parsimony and maximum likelihood methods suggest that subfamily Epidendroideae is monophyletic, with Listera (Neottieae) as sister. Although subtribal relationships are typically well resolved and have strong branch support, intertribal relationships are generally poorly resolved. Perhaps this general lack of resolution among tribes reflects a rapid species radiation that coincided with anatomical, physiological, and anatomical adaptations that initiated large-scale epiphytism in the ancestral Epidendroideae. Six taxa in this study exhibit deletions that are not evenly divisible by three and result in extensive sequence frameshifts. For example, one deletion is 227 bp in length and is flanked by the short direct repeat sequence; TCAATAGGAATTTCTTTT. Multiple deletions and frameshifts suggest that ndhF may be a pseudogene, in at least some orchid taxa.     

A phylogenetic analysis of the Conchostraca and Cladocera (Crustacea, Branchiopoda, Diplostraca)

A computer-assisted cladistic analysis on morphological characters of the Diplostraca (Conchostraca and Cladocera) has been undertaken for the first time. The morphological information has been obtained from literature and transformed into 56 suitable characters. The analysis included 47 ingroup taxa, comprising five conchostracan taxa (four families of the Spinicaudata and the Laevicaudata) and 42 genera of the Cladocera. A detailed character discussion is presented which will be a useful working base for future phylogenetic studies on the group. A number of systematic groups were, with differing degrees of certainty, supported in all 218 equally short trees. These are the Diplostraca, Cladocera, Gymnomera (Onychopoda and Haplopoda), Onychopoda, Podonidae, Cercopagididae, Anomopoda, Daphniidae, Moininae, Scapholeberinae, Chydoridae, Chydorinae and Sididae. The Spinicaudata were only supported on some of the 218 equally short trees while no support was found for the Conchostraca. Two taxa—the Macrothricidae and Aloninae—were relatively strongly indicated to be paraphyletic. A suggested classificatory hierarchy, without indication of absolute rank, is presented.     

A comparison of phenetic and phylogenetic methods applied to the systematics of Oligochaeta

A comparative study of naidid subfamilies shows that a combination of ordination, Jaccard/Average Linkage cluster analysis and Wagner parsimony provides a useful basis for a rational phylogeny but that this does not differ markedly from the original proposed by Sperber nearly four decades ago. Hennig rules, modified by Wiley, permit a preliminary phylogeny and classification of the Annelida to be made by hand. An error in earlier versions suggested that the Dorydrilidae lacked prostate glands, and this is corrected.     

A unifying theory for methods of systematic analysis

A unifying theory for systematic analysis states that a number of methods should be used jointly to cope with various kinds of data; also that groups should be as consistent as possible, be made with least information loss, and where needed, be polythetic. A test of relationship, homogeneity, can use various kinds of data. It can take account of the internal variation of aggregate items such as genera. It can give due emphasis to smaller clusters that have likely important contexts of external items. It helps in analysing trends, cores and hazes in dendrograms. A proposed detector for formal groups can be based on measures of isolation, identifiability and inclusiveness. Non-mathematical, inter-item reaction tests such as hybridization and serology can also be used in grouping. All relationship data are used polythetically to reveal natural groups. This leads to a unified informational concept for taxa. This is more useful than the biological species concept that is restricted to inter-breeding data. All the methods appear to be analogues of the powerful human grouping instinct. The resulting compatibility is important as precise methods are needed mainly when the data are too complex for the mind to use reliably. Cladograms can be made by self-graded deweighting of homogeneity and agglomerative clustering. Unlike classical cladistics this can reveal any polythetic group. Finding the derived states for making cladograms is often much too hypothetical for a fully cladistic approach to be properly precise. Instead, where the evidence is weak, a milder strength of graded deweighting is used for the cladistic properties, which help to show relationships along with the others. Axiomatic failures of other classes of grouping methods are discussed. Unavoidable remnants of instinctive processing lower the precision of all the methods. The Uniter computer program, based on the theory, is tested with finely graded values of artificially ‘evolved’ items and with coarsely coded cladistic data. The results show that with natural data, the program should act as a fairly sensitive probe of past evolutionary branching. Another test shows how specimens from species complexes can be grouped and how distinctions between groups are analysed.     

Cladistic and phenetic analysis of relationships in Vicia subgenus Vicia (Fabaceae) by morphology and isozymes

 Variation of 80 multistate morphological characters and isozymes encoded by 13 loci among 23 vetch species of the type subgenus of the genus Vicia in comparison with V. dumetorum, V. pisiformis and V. sylvatica of the subgenus Cracca is described and analyzed with cladistic parsimony and phenetic neighbour-joining methods by using two different ways of coding. Morphological analyses showed the subgenus Vicia monophyletic and revealed subgroups in a general agreement with traditionally recognized sections, except showing V. faba nested within section Narbonensis and ambiguity in the position of V. lathyroides and V. bithynica. Parsimony analysis of orthozymes as presence/absence characters revealed in the subgenus two basic monophyletic clades: 1) V. faba and three species of the section Peregrinae, V. michauxii, V. aintabensis and V. peregrina, in one subclade linked with species of the Narbonensis and Hyperchusa sections together with V. pisiformis of subgenus Cracca in a second subclade; 2) species belonging to sections Vicia, Sepium, Pseudolathyrus and Lathyroides together with V. sylvatica of the subgenus Cracca. Neighbour-joining analysis of orthozymes revealed the same two basic groups, differing only in the relative position of some species in subclusters. Both isozyme analyses showed paraphyly of the subgenera Vicia and Cracca. Parsimony analysis of orthozymes as character states of isozymes yielded a largely unresolved strict consensus cladogram of 209 most parsimonious trees, and reweighting of characters failed to produce a stable tree. Phylogenetic congruence and discordance among morphological and isozyme analyses, coding ways, homoplasy and weighting of characters are discussed. Received November 20, 2001 Accepted January 31, 2002     

Vegetative anatomy of subtribe Orchidinae (Orchidaceae)

Leaves in Orchidinae are essentially glabrous; anticlinal walls of foliar epidermal cells arc basically straight-sided to curvilinear, and cells arc fundamentally polygonal on both surfaces; adaxial cells are larger than abaxial cells. Stomata arc anomocytic and usually only abaxial and superficial; substomatal chambers are small to moderate; outer and inner guard cell ledges are mostly small. There is no hypodermis nor are there fibre bundles. Mesophyll is homogeneous, chlorcnchyma cells arc thin-walled, and intercellular spaces numerous. Crystalliferous idioblasts abound. Vascular bundles are collateral, organized in a single series. and lack associated sclerenchyma. Bundle sheath cells are thin-walled and chlorophyllous. Stems are glabrous; stomata arc frequent in one species, lacking in others. Cortical cells are oval to circular, thick-walled, and interspersed with triangular intercellular spaces. Ground-tissue cells are circular, and triangular intercellular spaces are present. Vascular bundles arc collateral and scattered throughout the ground-tissue or are absent from the central ground-tissue. Epidermis in absorbing roots is one-layered and non-velamcntous. Exodcrmal cells are thin-walled and dead cell walls bear tenuous scalariform bars; some species lack an exodermis. Outer cortical cells are polygonal and lack intercellular spaces; middle layer cortical cells are rounded with triangular intercellular spaces; inner layer cells are polygonal and lack intercellular spaces. Endodermis and pericycle are thin-walled and one-layered. Vascular cylinder is mostly 7–9-arch with xylcm and phloem components alternating regularly; vascular tissue is embedded in parenchyma; pith cells are parenchymatous, polygonal, thin-walled and lack intercellular spaces. Root tubers generally bear a velamen of variable thickness; bulbous-based unicellular hairs frequently form a dense mat; exodermal cells are thin-walled; dead cells have scalariform bars, passage cells are sparse. Ground-tissue consists of rounded water-storage and assimilatory cells interspersed with triangular or quadrangular intercellular spaces; peripheral cells arc polygonal lacking intercellular spaces. Vascular tissue consists of monarch to pentarch meristeles distributed thoughout the ground-tissue each surrounded by a uniscriale endodermis of thin-walled cells. Thin roots ofPlalanthera exhibit a typical central cylinder surrounded by a homogeneous cortex uninterrupted by meristeles; thicker roots show a central vascular cylinder and cortex in which meristeles are also present; in globoid root tubers there is no central cylinder, and the ground-tissue is replete with scattered meristeles. Because the central vascular cylinder in Platanthera gives rise to branches (meristeles), these represent components of a single vascular system and are not separate stelar entities as implied by the use of the term ‘polystele’.     

Vegetative anatomy of subtribe Habenariinae (Orchidaceae)

Leaves of Habenariinae are characterized by anomocytic stomatal apparatuses, homogeneous mesophyll, collateral vascular bundles in a single series, and thin-walled bundle sheath cells. There is no foliar sclerenchyma nor a hypodermis. Cauline cortex consists of thin-walled living cells among which are large and numerous intercellular spaces. The ground tissue is bordered externally by a layer of thick-walled living cells, except in Habenaria repens. Central ground tissue cells are living, and usually thin-walled surrounding intercellular spaces of various dimensions. These are conspicuously large in H. repens. Collateral vascular bundles are scattered across the ground tissue. Sclerenchyma is absent. Absorbing roots are generally velamentous, exodermal dead cells are diin-walled, and passage cells usually have a thickened outer wall. A regular vascular cylinder is present, and vascular tissue is embedded in parenchyma. Root tubers are velamentous, exodermal cells are usually thin-walled, and passage cells frequently have thickened outer walls. Vascular tissue of root tubers is organized into two classes: (1) those with a single vascular cylinder surrounded by a cortex and (2) those with a series of meristeles dispersed throughout the ground tissue. In group (1) cortex is homogeneous either with or without mucilage cells except in Stenoglattis where the cortex is heterogeneous, consisting of water-storage and assimilatory cells, and lacks mucilage cells. In group (2) the ground tissue consists of larger mucilage-containing cells and smaller assimilatory cells.     

A phylogenetic analysis of Diplodocoidea (Saurischia: Sauropoda)

Diplodocoidea includes some of the first well‐known sauropod dinosaurs, including such late 19^th century and early 20^th century discoveries as Apatosaurus, Diplodocus, and Dicraeosaurus. As a consequence of their long history of study, the basic set of suprageneric diplodocoid interrelationships is well resolved, and the diagnostic features of each genus are well established. However, intergeneric relationships are less resolved, including the relationships of putatively basal taxa like Amphicoelias and Haplocanthosaurus, the flagellicaudatan Suuwassea, and the highly specialized rebbachisaurids. For the rebbachisaurids, this uncertainty is coupled with a recent surge in the discovery of new taxa. Comparative cladistic methods demonstrate that character and taxon sampling need to be improved before greater phylogenetic resolution can be expected. Here, I present a new phylogenetic analysis that resolves many of the outstanding questions regarding the relationships within Diplodocoidea and examines palaeobiogeographical trends within the group. Suuwassea is recovered as a basal dicraeosaurid (the only Laurasian member of the group), and two distinct clades of rebbachisaurids are identified: a group closely allied with Nigersaurus and a clade associated with Limaysaurus. Amphicoelias, Amazonsaurus, and Haplocanthosaurus are provisionally placed as successively less‐derived taxa at the base of Diplodocoidea. A North American origin for Diplodocoidea and Flagellicaudata is hypothesized based on the geographical and temporal distribution of those taxa. Rebbachisaurid taxa demonstrate a South American/African vicariance pattern, but the timing of the event pre‐dates the proposed final rifting of those continents by c. 40 million years; the meaning of this discrepancy is uncertain. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 872–915.     

Phylogenetic analysis of the tribe Bovini (Mammalia: Artiodactyla)

A matrix of 57 (mainly cranial) characters and 32 taxa of fossil and Recent Bovini (buffaloes, bison and cattle) has been analysed using the parsimony program HENNIG86. Among the best established results are the exclusion of Parabos , polyphyly of Leptobos , monophyly of the Bos sensu lato + buffaloes group (a clade including all Recent Bovini), probable monophyly of the Bubalina and Syncerina, and the close relationship between bison and yak. Some other interesting questions raised include the apparent absence of a close link between Pliocene African bovines (except "Leptobos" syrticus ) and later African buffaloes, and the possible monophyly of Pelorovis oldowayensis+Bos sensu lato .     

Generic interrelationships within the Spionidae (Annelida: Polychaeta)

The phylogenetic relationships of spionid genera are estimated from parsimony analyses of morphological characters, with Trochochaetidae, Poecilochaetidae and Uncispionidae as outgroups. A first analysis of currendy recognised genera proved inconclusive and even exclusion of six of the most polymorphic genera resulted in 13 305 equally parsimonious trees and a fully collapsed consensus tree. A second analysis using only the type species of each genus, yielded four equally parsimonious trees; reduced to two after successive weighting. The topologies of these two trees indicated division of the family into four main groups: (1) Aonidella and Xandaros; (2) Prionospio (sensu fato)-complex, Laonice, Spiophanes and Aonides; (3) a large assemblage of genera, including Polydora-{senm late), Scolelepis, Malacoceros and Spio; (4) Atherospio, Pseudatherospio and Pygospiopsis. Earlier literature classifications of the group are evaluated and compared with die new results.     

A new species of Trichosalpinx (Orchidaceae: Pleurothallidinae) from Costa Rica

Trichosalpinx sanctuarii, a new species of Orchidaceae, subtribe Pleurothallidinae, is described and illustrated. It most resembles T. ringens, from which it is distinguished in the text. The new species is endemic to Costa Rica.     

Phylogenetics and evolution of a circumarctic species complex (Gladocera: Daphnia pulex)

The evolutionary history of freshwater zooplankton is still relatively unknown. However, studies of the microcrustacean Daphnia have revealed interesting patterns; the daphniids that dominate ponds and lakes in the northern hemisphere may have recent origins, likely associated with the glacial advances and retreats during the Pleistocene. Moreover, they form species complexes that actively engage in hybridization and introgression. The present study examines the phylogenetic relationships among circumarctic members of the Daphnia pulex complex, through the analysis of sequence diversity in 498 nt of the ND5 mitochondrial gene. Our results suggest that the complex is composed of three major clades, two of which are subdivided into at least eight different lineages. Clearly, species in the complex show genetic discontinuity. Many lineages originated during the Pleistocene, but at least three lineages diverged during the Pliocene. Two taxa ( D. pulex, D. pulicaria ), thought to be broadly distributed in the northern hemisphere, are shown to be endemic to single continents. In general, the diversification of the pulex complex is characterized by rapidly dispersed lineages spanning enormous distances and also by endemism in temperate areas. Gene flow among lineages from the temperate region of different continents are restricted to rare intercontinental migrations across a polar bridge followed by convergent morphological evolution.     

Infrageneric relationships within Pogostemon Desf. (Labiatae)

Cladistic and phenetic analyses of the morphology of 79 species of Pogostemon Desf. sens lato have been undertaken. The cladistic analysis included 135 character state differences encoded as 41 binary or multistate characters. The phenetic analysis included 52 metric variables and 54 binary variables. There is a very good correspondence between the results of cladistic and phenetic analyses based on different data sets. The existence of several clearly marked clades/clusters has been demonstrated. Some groups/clades are similar to those previously taxonomically recognized but the relationships and membership of infra-generic groups have been clarified by these analyses, validating a revised infra-generic classification which has been proposed.     

Chloroplast DNA phylogeny of subtribe Dendrobiinae (Orchidaceae): Insights from a combined analysis based onrbcL sequences and restriction site variation

Phylogenetic analyses using two chloroplast DNA data sets, derived from variation of the ribulose-bisphosphate carboxylase gene (rbcL) and restriction sites, were performed to examine relationships among 13 taxa in subtribe Dendrobiinae, one of the most taxonomically complicated groups in Orchidaceae, and its putative sister groups. Owing to a limited number of informative substitutions, therbcL data set did not provide conclusive evidence in itself. The data set combiningrbcL and restriction site mutations, however, provided the following insights: (1)Pseuderia belongs with tribe Podochileae rather than tribe Dendrobieae. (2) Subtribe Dendrobiinae is monophyletic ifPseuderia is excluded. (3) ExcludingPseuderia, Dendrobiinae comprises three major clades: Clade 1 (Dendrobium sectionSpatulata, Cadetia, Diplocaulobium, andFlickingeria); Clade 2 (Dendrobium sectionsDendrobium andCallista); and Clade 3 (Epigeneium). (4)Epigeneium diverged early from the lineage including Clades 1 and 2. (5) Relative toCadetia, Diplocaulobium, andFlickingeria, Dendrobium is shown to be para-/polyphyletic. (6)Diplocaulobium andFlickingeria constitute a monophyletic clade, from which cladeDendrobium sectionSpatulata andCadetia form succesive sister groups. Among these results, (1) and (5) are especially stable in view of the congruence between the separate and combined analyses as well as robust internal support.