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.     

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 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 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.     

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 .     

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.     

A phylogenetic analysis of the palm subtribe Oncospermatinae (Arecaceae) based on morphological characters

Subtribe Oncospermatinae (Arecaceae: Arecoideae: Areceae) is a diverse group of spiny Old World palms. The subtribe includesOncosperma, a widespread Asian genus of five species, along with seven monotypic genera, all endemic to the Seychelles and Mascarene Islands of the western Indian Ocean. A phylogenetic analysis was conducted in order to test the monophyly of subtribe Oncospermatinae with respect to other Old World genera of tribe Areceae. A matrix of 38 morphological characters was scored for 29 taxa, including 11 species of the Oncospermatinae. A single most parsimonious tree was found, resolving the subtribe as a polyphyletic group of two distinct clades. One clade containingAcanthophoenix, Deckenia, Oncosperma, andTectiphiala was placed as sister to a large group that includes members of subtribes Archontophoenicinae, Arecinae, Iguanurinae, and Ptychospermatinae. The other clade of Oncospermatinae, including the Seychelles endemic generaNephrosperma, Phoenicophorium, Roscheria, andVerschaffeltia, was resolved as sister to the Madagascar endemic subtribe Masoalinae, and may have arisen in the western Indian Ocean region.     

A phylogenetic study of the Galappidae H. Milne Edwards 1837 (Crustacea: Brachyura) with a reappraisal of the status of the family

The systematic status of the family Calappidae and the phylogenetic relationships of its four component subfamilies are re-evaluated based on a cladistic analysis of 78 adult morphological characters. A single tree was produced (CI = 0.654). The monophyly of the Calappidae sensu lato is rejected. The data suggest that the Calappinae and Hepatinae form a single lineage which is closer to some xanthids than to the Matutinae or Orithyiinae. A close link between the Matutinae and some leucosiids and between the Orithyiinae. and some dorippids is also apparent, with a suggestion that these four taxa all belong to a single lineage. A revised classification of the Oxystomata emend , and Calappidae is proposed.     

Some taxonomic corrections in the subtribe Bulbophyllinae (Orchidaceae)

Garay, Hamer and Siegerist (1994) propose numerous new taxa and combinations in the genus Bulbophyllum . Their opinions are often contradicting those expressed in Vermeulen (1991, 1993a. 1993b). A reason for this can be sought in the different basic principles both authors apply when delimiting species and higher taxonomic entities. Some of the taxa proposed by Garay, Hamer and Siegerist (1994) are analysed, and taxonomic changes are proposed.     

New species of the subtribe Goodyerinae (Orchidaceae) from Colombia

Seven new species of the subtribe Goodyerinae, six of Microchilus and one of Aspidogyne, are described and illustrated based on Colombian material. The information about the distribution and ecology of the new entities as well as brief taxonomic notes are provided.     

Phylogenetics of Stelis and closely related genera (Orchidaceae: Pleurothallidinae)

Stelis, one of the largest genera within Pleurothallidinae, was recently recircumscribed to include a few hundred more species, most of which had previously been assigned to Pleurothallis. Here, a new phylogenetic analysis of Stelis and closely related genera based on DNA sequences from nuclear ITS and chloroplast matK, based on a much larger sample, is presented; it includes more than 100 species assigned to Stelis and covers all proposed groupings within the genus, many of which have not previously been represented. Clades are proposed to enable easier discussion of groups of closely related species; each clade is characterized morphologically, ecologically, and geographically to explain the evidence found in the molecular analysis. Discussion of the evolutionary trends of character states found in the genus in its broad sense is given. The current taxonomy of the group is given and the possible taxonomical implications of the findings presented here are discussed.     

Stem structure and its bearing on the systematics of Pleurothallidinae (Orchidaceae)

STERN, W. L., PRIDGEON, A. M. & LUER, C. A., 1985. Stem structure and its bearing on the systematics of Pleurothallidinae (Orchidaceae) . Pleurothallids comprise a subtribe of numerous orchids consisting of mostly diminutive New World epiphytes. The cauline system involves a branching rhizome bearing unifoliate ramicauls. The inflorescence usually originates from an adaxial invagination toward the apex of the ramicaul. Two or more cycles of vascular bundles traverse the ramicaul; typically, there is an outer, branching series of smaller strands and an inner, non-branching series of larger strands. In the ultimate internode subtending the leaf the smaller, outer bundles migrate between the larger, inner bundles and become aggregated in the medullary region. They bend adaxially to vascularize the inflorescence. The leaf is articulated at an abscission layer to the prolongated apex of the ramicaul more or less distal to the cauline invagination. In some pleurothallids, a cauline annulus appears at the insertion of the inflorescence and cither below or at the attachment of the leaf to the apex of the ramicaul. Anatomical studies show that the annulus is the external manifestation of an intercalary meristem. Except for Pleurothallis , genera are consistent in having or lacking an annulus. Genera with two pollinia either possess or lack the annulus; those with four to eight pollinia always lack the annulus. It is suggested that the intercalary meristem is a derived characteristic providing survival value and a selective advantage to those pleurothallids in which it occurs. Presence of the intercalary meristem is correlated with other structural features considered to represent specializations.     

A phylogenetic analysis of the orb-weaving spider family Araneidae (Arachnida, Araneae)

We present the first cladistic analysis focused at the tribal and subfamily level of the orb-weaving spider family Araneidae. The data matrix of 82 characters scored for 57 arancid genera of 6 subfamilies and 19 tribes (and 13 genera from 8 outgroup families) resulted in 16 slightly different, most parsimonious trees. Successive weighting corroborated 62 of the 66 informative nodes on these cladograms; one is recommended as the 'working' araneid phylogcny. The sister group of Araneidae is all other Araneoidea. Araneidae comprises two major clades: the subfamily Araneinae, and the 'argiopoid' clade, which includes all other subfamilies and most tribes (((Gasteracanthinae, Caerostreae), (((Micratheninae, Xylcthreae), Eruyosaccus ), (Eurycorminae, Arciinae)), Cyrlarachninae), ((Argiopinae, Cyrtophorinae), Arachnureae)). Cyrtarachneae and Mastophoreae are united in a new subfamily, Cyr-tarachninae. The spiny orb-weavers alone (Gasteracanthinae and Micratheninae) are not monophyletic. The mimetid subfamily Arciinae and the 'tetragnathid' genus Zygiella are araneids, but .Nephila (and other tetragnathids) are not. On the preferred tree, web decorations (stabilimenta) evolved 9 times within 15 genera, and were lost once. The use of silk to subdue prey evolved once in cribellate and four times in ecribillate orb weavers. Sexual size dimorphism evolved once in nephilines, twice in araneids, and reverted to monomorphism five times. Evolution in other genitalic and somatic characters is also assessed; behavioral and spinneret features arc most consistent (male genitalia, leg and prosomal features least consistent) on the phylogeny.     

The role of parsimony,outgroup analysis,and theory of evolution in phylogenetic systematics

It is argued that both the principle of parsimony and the theory of evolution, especially that of natural selection, are essential analytical tools in phylogenetic systematics, whereas the widely used outgroup analysis is completely useless and may even be misleading. In any systematic analysis, two types of patterns of characters and character states must be discriminated which are referred to as completely and incompletely resolved. In the former, all known species are presented in which the characters and their states studied occur, whereas in the latter this is not the case. Dependent on its structure, a pattern of characters and their states may be explained by either a unique or by various conflicting, equally most parsimonious hypotheses of relationships. The so-called permutation method is introduced which facilitates finding the conflicting, equally most parsimonious hypotheses of relationships. The utility of the principle of parsimony is limited by the uncertainty as to whether its application in systematics must refer to the minimum number of steps needed to explain a pattern of characterts and their states most parsimoniously or to the minimum number of evolutionary events assumed to have caused these steps. Although these numbers may differ, the former is usually preferred for simplicity. The types of outgroup analysis are shown to exist which are termed parsimony analysis based on test samples and cladistic type of outgroup analysis. Essentially, the former is used for analysing incompletely resolved patterns of characters and their states, the latter for analysing completely resolved ones. Both types are shown to be completely useless for rejecting even one of various conflicting, equally most parsimonious hypotheses of relationships. According to contemporary knowledge, this task can be accomplished only by employing the theory of evolution (including the theory of natural selection). But even then, many phylogenetic-systematic problems will remain unsolved. In such cases, arbitrary algorithms like those offered by phenetics can at best offer pseudosolutions to open problems. Despite its limitations, phylogenetic systematics is superior to any kind of aphylogenetic systematics (transformed cladistics included) in approaching a (not: the) “general reference system” of organisms.