A Review of Current Theories and Methods in Cladistics and a Cladistic Study of Twelve Lindera Species in Eastern China

Cladistics has become a widely used method for phylogenetic reconstruction．Because of rapid improvement Of cladistic theories and methodologies,and application of new data,especially,molecular data,it is becoming realistic to reconstruct phylogenies of organisms,and to establish natural classifications based on these phylogenies．This paper reviews some current cladistic theories and methods in a practical way,such as choosing characters,defining character states,polarizing characters,analyzing data matrices, calculating consensus cladograms,choosing among multiple equally most parsimonious cladograms,estimating reliability of cladograms,and applying cladograms to classification, character evolution,and biogeography． Based on 36 morphological characters．a parsimony analysis of 12 species representing six sections in subgenus Lindera and an outgroup species from subgenus lteodaphne of the genus Lindera(Lauraceae)was conducted．The results suggest a close relationship between section Lindera and section Sphaerocarpae,which is different from the previous phylogenetic hypothesis within the genus．In the strict consensus cladogram,two species,L．megaphylla and L.chienii,from section Cupuliformes are in the most primitive and the most advanced clades respectively,indicating that the section is polyphyletic．The cladogram also suggests that section Lindera be a polyphyletic group．     

In search of historical biogeographic patterns in the western Mediterranean terrestrial fauna

A cladistic biogeographic study of the western Mediterranean terrestrial fauna is made using taxon-area cladograms of ten groups of animals showing high levels of endemicity in the area. The groups analysed are the Nephrotoma flavescens group, the Tipula (Acutipula) maxima group, the T. (Lunatipula) bullata and falcata group, the subgenus T. (Mediotipula) , the T. (Savtshenkia) goriziensis group, the T. (S) signata group (Insecta, Diptera, Tipulidae), the Protonemura corsicana group (Insecta, Plecoptera, Nemouridae), the genus Speonemadus (Insecta, Coleoptera, Cholevidae), and the subgenera Triturus (Palaeotriton) and Triturus (Triturus) (Urodela, Salamandridae). The groups contain a total of 123 species and subspecies. Detailed distribution maps of 94 species and subspecies of Tipulidae included in the study are given. Based on the distributions of 74 endemic species and subspecies, 13 areas of endemism in the Mediterranean are recognized. The geology of the western Mediterranean since the late Oligocene is discussed with reference to a number of maps showing kinematic reconstructions of the area. Five methods for cladistic biogeographic purposes were employed, viz. Brooks Parsimony Analysis, Component Compatibility Analysis, Component Analysis, Three-Area Statements Analysis, and Paralogy-free Subtree Analysis. General area cladograms produced by computer implementations of the five methods show low levels of congruence. Geological area cladograms are fully compatible with some of the results of Brooks Parsimony Analysis only.     

CLADISTIC AND BIOGEOGRAPHIC ANALYSES OF THE WEEVIL GENUS LISTRODERES SCHOENHERR (COLEOPTERA: CURCULIONIDAE)

Abstract— The weevil genus Listroderes Schoenherr is a monophyletic group defined by the body vestiture consisting of subcircular to suboval scales, and comprises 35 species endemic to southern South America. A cladistic analysis of the genus was carried out using 44 characters from external morphology, body vestiture, and male and female genitalia. The curvipes (three species), nodifer (five species) and robustus (four species) species groups and the 23 species of the costirostris species group were considered terminal taxa. Apomorphic states were identified using the genus Hyperoides Marshall as outgroup. The analysis yielded 122 equally parsimonious cladograms, each with 89 steps and a consistency index of 0.42; a successive weighting procedure resulted in nine cladograms (consistency index of 0.69 and retention index of 0.85). In the general consensus cladogram, nodifer-robustus and curvipes-costirostris are two pairs of sister species groups. The costirostris group comprises the subgroups foveatus, angusticeps, costirostris, delaiguei, bimaculatus and elegans , in phylogenetic order. A distributional analysis of the species of Listroderes led to identification of four areas of endemism, namely central Chile, sub-Antarctic, central Argentina and Chaco. A vicariance biogeographic analysis of these areas, based on area cladograms of Listroderes, Hyperoides, Naupactus taeniatulus species group (Coleoptera: Curculionidae), and Lucilia generic group (Asteraceae) was carried out applying the three-area statements technique. According to the general area cladogram the sequence of area-fragmentation is as follows: (central Chile (sub-Antarctic (central Argentina, Chaco))). This sequence is congruent with the history hypothesized for the region, where the uplift of the Andes (Oligocene-Pliocene) led to a progressive aridification, replacing the ancient subtropical forest by open-country environments.     

A Cladistic Analysis of the Genus Cyttaria (Fungi-Ascomycotina)*

Abstract—Cyttaria Berkeley (Cyttariaceae, Cyttariales, Class Discomycetes), is a genus of eleven species, seven from South America and four from Australasia (Australia, Tasmania, and New Zealand). Cyttaria is a monophyletic genus defined by the following synapomorphies: fleshy to gelatinous stromata with endostromatic apothecia; and complete lack of fungal chitin in the cell walls, having instead β-1–3-glucan. All Cyttaria are exclusive parasites of Nothofagus species. A cladistic analysis of the genus was performed using 18 characters from macromorphology, micro-morphology, and phenology. Polarity of characters is based on the outgroup comparison method (using the Class Discomycetes as a whole) and on the ontogenetic criterion. A hypothetical outgroup was constructed using all plesiomorphic states. Two equally parsimonious cladograms were produced, each with 40 steps and a consistency index of 0.70. These differed in the position of the South American species C. hookeri and C. johowii. In one cladogram, C. hookeri is the sister group to the rest of the genus, and in the other, both species form a monophyletic group (ascospores ovoid) that is the sister group of the rest of the genus. Our analysis of the two characters causing this difference (position of apothecia on stroma, and shape of ascospores) supports the latter hypothesis. In both cladograms, all of the Australasian species form a monophyletic group (thick ectostroma), and, within that, two subgroups are defined: C. gunnii-C. pallida (papillae present), and C. nigra-C. septentrionalis (ectostroma with black incrustations). The Australasian species form a monophyletic group (spermatangia absent) with C. berteroi , and this last group forms a monophyletic group (conidia absent) with C. espinosae. Cytlaria darwimi and C. exigua form another monophyletic group (very thick ectostroma). Excluding C. hookeri and C. johowii, C. hariotii is the sister group to the remaining eight species.     

分支系统学当前的理论和方法概述及华东地区山胡椒属十二个种的分支系统学研究

本文概述了当前分支系统学研究中涉及的主要理论和方法,包括性状的选取、性状状态和极性的确定、数据矩阵的分析计算、结果分支图的处理、分支图可靠性的评价及分支图的应用。本文同时以华东地区樟科山胡椒属Linderal2个种的分支系统学研究为例,讨论了用形态性状进行分支系统学研究中可能遇到的问题,也揭示了一些分支系统学与传统的系统学在应用性状推导进化关系上的不同点。对这12个种的分支系统学研究得出了一些不同于传统系统学方法所推测的山胡椒属内的系统发育关系,如分支系统学研究显示山胡椒组和球果组很近缘。在严格一致性分支图上,杯托组的黑壳楠和江浙山胡椒分别位于最原始和最进化的分支,表明这个组是复系类群。分支图也显示山胡椒组可能是复系类群。     

Systematics of the genus Cidaria Treitschke (Lepidoptera, Geometridae, Larentiinae)

The genus Cidaria Treitschke is revised. Eight species of the genus which occur widely in the Palaearctic and northern India, are recognized, of which one, Cidaria luteata sp. nov. , is described as new while two subspecies of C. fulvata (Forster) are elevated to species, C. nugata Felder stat. rev., and C. distinctata Staudinger stat. nov. C. ochripennis Prout is proposed as a junior synonym of C. ochreata Staudinger. C. deletaria Hampson is excluded from the genus. All species of Cidaria and their genitalia are described and illustrated. The cladistic analysis of these eight species of Cidaria is carried out using two data matrices, the first comprising morphological characters alone and the second morphological and distributional characters. The most parsimonious cladogram of Cidaria is selected, and its monophyly defined. The character analysis shows that some distribution characters contribute to resolving the in group node. The choice of multiple trees is discussed.     

A cladistic analysis of the genus Lopezia (Onagraceae)

Lopezia, a genus of 22 species largely restricted to Mexico, forms a monophyletic group defined by the possession of two stamens in tetramerous flowerS. A cladistic analysis of the genus was performed using 16 characters from morphology, anatomy and embryology. Twenty of the 22 species were considered the terminal taxa. Polarity of the characters was based on the outgroup comparison method, using three alternative outgroups: the genus Fuchsia, Onagraceae excluding Ludwigia, and Epilobieae-Onagreae. Using Fuchsia as outgroup, 29 equally parsimonious cladograms were produced, each with 24 steps and a consistency index of 0.75. A successive weighting procedure was applied, resulting in 15 cladograms with consistency index of 0.85. The strict consensus cladogram defines eight monophyletic groups and supports most of the current sectional classification of Lopezia, with the exception that no synapomorphy defines section Jehlia. The larger sections Lopezia and Pelozia, although well-defined as clades, are not fully resolved internally. All cladograms support section Riesenbachia as monophyletic. The two alternative hypotheses for outgroups produced similar results: 61 most parsimonious trees, reduced after the successive weighting procedure to 15, which are identical to those produced with Fuchsia as outgroup. These results are discussed in the context of data on cytology and pollination biology.     

PHYLOGENY OF THE NEMERTEAN SUBCLASS PALAEONEMERTEA (ANOPLA, NEMERTEA)

Abstract— A cladistic analysis based on 50 morphological characters was performed for 49 of the 98 species currently assigned to the subclass Palaeonemertea (phylum Nemertea), and six additional undescribed species. Thirty-five species were excluded from the parsimony analysis because of the high number of unknowns in the character matrix, and one species since it was considered a nomen nudum . An initial analysis suggested that the subclass Hoplonemertea is the sistergroup to the clade Palaeo- and Heteronemertea and the ingroup cladograms are rooted using a paraphyletic outgroup based on this information. Seventy-two equally most parsimonious cladograms were found; the consistency index was low but tree-length distribution for the character set is skewed to the left, and the cladograms are invariably shorter than trees based on random data. These cladograms suggested a character transformation series for the cerebral organ where this complex character reappeared several times after being absent. We considered this biologically implausible and the final discussion is based on three cladograms, one step longer than the most parsimonious, where the evolution of this character appears to be more realistic. The cladistic analysis indicates that many previously recognized genera (e.g. Cephalothrix, Procephalothrix and Cephalotrichella ), and higher taxa, are paraphyletic. It furthermore indicates that the previously suggested hypothesis of the Archinemertea as a monophyletic sistertaxon to Palaeonemertea is unsupported.     

Revision of the genus Xylomoia Staudinger (Lepidoptera: Noctuidae), with descriptions of two new species

Seven species are included in the genus Xylomoia Staudinger, two of which are new: X. retinax sp.n. from the Novosibirsk area, Western Siberia, and from the Chelyabinsk area, southern Ural Mountains, and X. stangelmaieri sp.n. from Caorle, Venezia Giulia, on the Adriatic coast. A North American species, Chortodes didonea (Smith) comb.n., is removed from the genus. According to a cladistic analysis, the genus Xylomoia comprises one plesiomorphic species group, the chagnoni group, and two apomorphic groups: the graminea and strix groups. The latter are exclusively temperate Palaearctic. Xylomoia chagnoni (Barnes & McDunnough) is the only Nearctic species of the genus, and the loosely related X. apameaoides (Hacker) was recently described from Turkey. In geographical isolation, these two species have retained many ancestral features. In the more central area, the common ancestor of the graminea and strix groups has evolved into at least five species. The locality and rarity of the species of Xylomoia seemingly result from adaptation of the species to moist habitats, the larvae probably bore inside grass stems (the case of X. chagnoni ). What are called lock-and-key mechanisms may lead to the use of non-independent character states in a cladistic analysis; particularly in the case of homoplasy this kind of double-weighting may result in erroneous cladograms. In Xylomoia , deleting female lock-and-keys affected only the number of cladograms produced, whereas omitting the corresponding male characters had profound effects on the cladogram.     

Phylogeny of the vipers of the Caucasus (Reptilia, Viperidae)

Phylogenetic relationships for five taxa of Palearctic vipers (genus Vipera ) from the Caucasian region were revealed by cladistic analyses of separate and combined morphological and biochemical characters. The different data sets yielded largely congruent cladograms. Vipera berus from Sweden was included as an ingroup and V. aspis was used for outgroup comparison. For V. kaznakovi and V. dinniki , three and four different sub-populations, respectively, were treated as independent terminal taxa in the analyses. The most parsimonious cladograms confirmed the systematic positions of these populations, discussed in a recent study, and support the hypothesis that the montane populations of the western main Caucasus comprise one polymorphie species: V. dinniki.
Analyses of combined biochemical and morphological data generated two equally parsimonious cladograms (for all ingroups compared), but yielded only one fully resolved topology when ingroups were condensed to the species level: ( berus ((renardi ('ursinii'-eriwanensis )))( dinnikikaznakovi )).     

A Cladistic Analysis of the New World Species of Lotus L. (Fabaceae, Loteae)

The genus Lotus L. is a monophyletic group diagnosed by the possession of a standard claw with thickened infolded margin, stamens diadelphous, and the style hardened from the base. It comprises approximately 200 species distributed throughout the world. A cladistic analysis of the New World species was performed using 39 morphological and anatomical characters (29 from seed morphology and anatomy, 1 from plant habit, 1 from leaf morphology, 6 from flower morphology, and 2 from fruit morphology). Dorycnium, Edentolotus, Krokeria , and Pedrosia , of the Old World, and 28 species of the New World were considered terminal taxa. Tetragonolobus Scop. was chosen to root the cladograms and Dorycnium Mill. to reroot them. With Tetragonolobus the analysis yielded 15 equally parsimonious trees, each with a length of 74 steps, a consistency index of 0.62, and a retention index of 0.89. The 15 initial trees and the strict consensus tree defined 12 monophyletic groups. All terminal taxa form a monophyletic group diagnosed by the presence of a radicular lobe discernible to conspicuous (character 10); rim aril thick (character 13); stipules absent (character 31); and style simple and nondilated (character 36). The New World species form a monophyletic group on the basis of the seed relationship of length to width in hilar view 1.5:1 to 2:1 (character 5); micropyle linear-deltoid to bifurcate (character 19); and keel erostrate (character 33). Identical monophyletic groups were obtained when Dorycnium was used as root. These results are discussed in the context of data on cytology and morphology.     

A cladistic analysis of Nassauvia Comm. ex Juss. (Asteraceae, Mutisieae) and related genera

FREIRE, S. E., CRISCI, J. V. & KATINAS, L., 1993. A cladistic analysis of Nassauvia Comm. ex Juss. (Asteraceae, Mutisieae) and related genera. Nassauvia and the most closely related genera Calopappus and Triptilion from the southern Andes and Patagonia of South America, form a monophyletic group diagnosed by the following synapomorphies: cypsela trichomes single two-celled, cypsela testa with strengthened cells, pollen grains spheroidal to spheroidal-oblate, colpi membrane with sexine processes, pappus bristles two to six, and pappus deciduous. Furthermore, Nassauvia, Triptilion, and Calopappus form a group with two other Andean genera, Moscharia and Polyachyrus, diagnosed by occurrence of pseudocephalia and a reduction in the number of flowers to five, three or one. A cladistic analysis of the group was undertaken using 35 characters from morphology, anatomy, and palynology. The monophyletic terminal taxa were the 38 species of Nassauvia, the genus Triptilion, the monotypic genus Calopappus, the genus Polyachyrus, and the genus Moscharia. Character polarity was based on outgroup comparison using Cephalopappus. The analysis resulted in 223 equally parsimonious cladograms, each with 70 steps and a consistency index of 0.57. A successive weighting procedure was applied, resulting in 15 cladograms with a consistency index of 0.82. Results of the cladistic analysis support most of the current systematic classification of Nassauvia, with three exceptions: (1) Nassauvia (excluding Calopappus) is paraphyletic; (2) section Masligophorus appears to be a polyphyletic group (N. pygmaea does not cluster with the remaining species of the section); (3) section Panargyrum (without N. lagascae= section Caloptilium) appears to be a paraphyletic group. The capitula arranged in cymose conflorescences in Triptilion are regarded as a primitive condition which gave rise to all stages present in Nassauvia (conflorescence spicate, pseudocephalium, capitula solitary). The capitula arranged in pseudocephalia in Moscharia and Polyachyrus are regarded as a parallel development to the pseudocephalium found in Nassauvia. Nassauvia, subgenus Strongyloma appears as the most primitive taxon, with its spicate conflorescence, whereas section Masligophorus with its solitary capitulum is thought-derived. These results correspond well with cytological data where species of the subgenus Strongyloma have n= 11 and the species of section Masligophorus are tetraploids (n = 22).     

Cladistic analysis of Enkianthus with notes on the early diversification of the Ericaceae

The genus Enkianthus (Ericaceae) has been subject to a cladistic analysis of morphological, anatomical, embryological, and cytological data, using two species of Clethra as outgroup. In order to evaluate the monophyly of Enkianthus , the genera Epigaea and Phyllodoce from the subfamily Rhododendroideae, and the genus Andromeda from the subfamily Vaccinioideae were also included in an initial analysis which yielded 20 equally parsimonious cladograms. The results indicated that Enkianthus is monophyletic, and a subsequent analysis with only the outgroup taxa and 14 species of Enkianthus yielded two equally parsimonious cladograms with a more resolved topology. In order to obtain strictly monophyletic taxa, the current subgeneric classification of Enkianthus is revised, recognizing four sections: Enkianthus (9 spp.), Andromedina (2 spp.), Meisteria (2 spp.), and Enkiantella (4 spp.). The paper provides a key, illustrations of representative taxa, a cladogram, and strict consensus trees.     

The genus Cynara L. (Asteraceae-Cardueae)

WIKLUND, A., 1992. The genus Cynara L. (Asteraceae-Cardueae). This study includes a taxonomic revision of the genus Cynara. Eight species and four subspecies are recognized, viz. C. algarbiensis, C. auranitica, C. baetica including subsp. baetica and subsp. maroccana (formerly known as C. hystrix), C. cardunculus including subsp. cardunculus and subsp. flavescens, C. cornigera, C. cyrenaica, C. humilis (formerly sometimes in the genus Bourgaea) and C. syriaca. The cultivated artichoke (formerly C. scolymus) and cardoon are both included in C. cardunculus. One species, C. tournefortii , is excluded from Cynara. A cladistic study of the genus is also undertaken and its morphology, anatomy and phytogeography are discussed.     

On phylogeny of Hippophae (Elaeagnaceae)

A cladistic analysis of the genus Hippophae (Elaeagnaceae) was undertaken. based on 37 characters. The five species of the genera Shepherdia and Elaeagnus were included in the analysis as the outgroup taxa. The operational taxonomic units of Hippophae were the species H. gyantsensis, H. neurocarpa, Hsalicifolia and H. tibetana plus eight subspecies of H. rhamnoides . The analysis revealed 117 or 14 equally parsimonious trees depending on whether the multistate characters were treated as ordered whenever possible, or all characters were treated as unordered. The results are not directly in accordance with any of the formerly proposed taxonomies. After successive weighting only two trees were retained both with ordered and unordered characters and the combinable component (semistrict) consensus trees give support to recognition of the two species in the genus, H. rhamnoides and Hsalicifolia . Three new combinations H. rhamnoides ssp. neurocarpa, H. salicifolia ssp. sinensis and H. salicifolia ssp. yunnanensis (Rousi) Hyvönen are proposed.     

Cecropia as a food resource for bats in French Guiana and the significance of fruit structure in seed dispersal and longevity

Cecropia (Cecropiaceae) is a Neotropical genus of pioneer plants. A review of bat/plant dispersal interactions revealed that 15 species of Cecropia are consumed by 32 species of bats. In French Guiana, bats were captured in primary and secondary forests, yielding 936 fecal samples with diaspores, among which 162 contained fruits of C. obtusa, C. palmata, and C. sciadophylla. A comparative morphological and anatomical study of fruits and seeds taken directly from herbarium specimens, bat feces, and an experimental soil seed bank was made. Contrary to previous reports, the dispersal unit of Cecropia is the fruit not the seed. Bats consume the infructescence, digest pulp derived from the enlarged, fleshy perianth, and defecate the fruits. The mucilaginous pericarp of Cecropia is described. The external mucilage production of Cecropia may facilitate endozoochory. The exocarp and part of the mesocarp may be lost after passage through the digestive tract of bats, but fruits buried for a year in the soil seed bank remain structurally unchanged. Fruit characters were found to be useful for identifying species of bat-dispersed Cecropia. Bat dispersal is not necessary for seed germination but it increases seed survival and subsequent germination. Fruit structure plays a significant role in seed longevity.     

A monograph of the genus Colignonia (Nyctaginaceae)

Species of the neotropical genus Colignoniu are perennial herbs, subshrubs and lianas from 1 m to c. 15 m tall. The genus ranges from c. 5°N in Colombia to c. 28°S in Argentina and comprises six species. It occurs in the Andean montane rain forest and cloud forest, often in disturbed areas. The flowers are of two types and divide the genus into two sections, viz. Pterocarpae (3 spp) with a 3-lobed perianth, and Colignonia (3 spp) with a 5-lobed perianth. C. pentoptera is described as new. C. biumbellata is reduced to subspecific status under C. parviflora. C. acutifolia , originally described by Heimerl as a variety of C. glomerata , is referred to C. parviflora as a distinct variety of ssp. biumbellata . Several names are reduced to synonymy. The chromosome number 2 n = 34 is recorded for three species (Sect. Colignoniu ) and 2 n= 32 for three species (Sect. Pterocarpae ). The correlation between chromosome numbers and perianth type supports the subdivision of the genus. Considerable morphological variation, correlated with changes in temperature and altitude, was observed in the field and in plants under cultivation. Pollen morphology and relationships to other genera in the Nyctaginaceae are discussed. Colignonia seems most closely related to Mirabilis, Commicarpus, Boerhaaviu , and Pisoniella .     

Preliminary comments on a phylogenetic study of the order Diphyllidea van Beneden in Carus, 1863

The basis for a preliminary analysis of the relationships within the monophyletic Diphyllidea is outlined. Information on morphological characters and their interpretation within a phylogenetic context are presented. A cladistic analysis at the species level was conducted based on a matrix of 21 morphological characters. Character polarity was determined by taxonomic outgroup analysis relative to the basal orders, Pseudophyllidea and Haplobothriidea. The phylogeny for the diphyllideans was found to be poorly resolved based on characters currently available for evaluation. Computer assisted cladistic analysis found three equally parsimonious trees with a consistency index of 0.54. The topology of these trees shows that Ditrachybothridium macrocephalum is the basal taxon and the putative sister group for species of Echinobothrium; Macrobothridium rhynchobati is grouped among species of Echinobothrium. If the classification is to be consistent with this tree, M. rhynchobati should be included in the genus Echinobothrium. This observation should be carefully examined, considering the relative paucity of useful morphological characters currently available for this group.