Romance of the three domains:how cladistics transformed the classifi cation of cellular organisms

Cladistics is a biological philosophy that uses genealogi-cal relationship among species and an inferred sequence of divergence as the basis of classifi cation.This review critically surveys the chronological development of bio-logical classification from Aristotle through our post-genomic era with a central focus on cladistics.In 1957,Julian Huxley coined cladogenesis to denote splitting from subspeciation.In 1960,the English translation of Willi Hennig’s 1950 work,Systematic Phylogenetics,was published,which received strong opposition from phenet-icists,such as numerical taxonomists Peter Sneath and Robert Sokal,and evolutionary taxonomist,Ernst Mayr,and sparked acrimonious debates in 1960-1980.In 1977-1990,Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellu-lar life and established major prokaryotic phyla.Cladistics has since dominated taxonomy.Despite being compatible with modern microbiological observations,i.e.organisms with unusual phenotypes,restricted expression of charac-teristics and occasionally being uncultivable,increasing recognition of pervasiveness and abundance of horizon-tal gene transfer has challenged relevance and validity of cladistics.The mosaic nature of eukaryotic and prokary-otic genomes was also gradually discovered.In the mid-2000s,high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life.While genomics only indirectly leads to understanding of func-tional adaptations to ecological niches,computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged.Controversies are not expected to settle as taxonomic classifi cations shall remain subjective to serve the human scientist,not the classifi ed.

Cladistic Analysis of the Cyprinid Subgenus Cyprinus (Mesocyprinus) Fang (Teleostei: Cyprinidae)

Phylogeny of the cyprinid subgenus Cyprinus (Mesocyprinus ) is elucidated based on both external and osteological features. All five species of Cyprinus (Mesocyprinus ) are including in the ingroup in addition to two Cyprinus (Cyprinus ) species. Procypris merus was treated as outgroup in comparison. A total of 48 characters were identified as variable among ingroup and outgroup. Phylogenetic analysis was accomplished using Parsimony and Bootstrap methods with Branch and Bound search of PAUP *. There are 28 characters remaining useful after excluding unpolarized characters and autapomorphies of terminal taxa. Analysis of the characters resulted in one tree with a length of 69 steps, Consistency Index (CI) of 0 7246, CI excluding uninformative characters of 0 6122, and Retention Index (RI) of 0 6346. It is apparent that the Mesocyprinus group consisting of five species is a polyphyletic group. This result suggests that subgenus Cyprinus (Mesocyprinus ) should be suspended.

Morphological Phylogeny of the Water Snake Subfamily Homalopsinae (Serpent: Colubridae)

The morphological phylogeny of the water snake subfamily Homalopsinae, containing 10 genera, of which seven are monotypic, was not reported up until now. Here fourteen morphological characters were selected for the cladistic analysis. Using software Hennig 86, two phylogenetic trees were inferred and the results showed that the subfamily Homalopsinae was divided into two groups. Compared with the molecular phylonenetic tree of Voris et al （2002）, the genera Gerarda and Fordonia are sister groups in both studies; both studies also yielded the same monophyletic lineage, which contained three genera （Cerberus ＋ Erpeton ＋ Homalopsis ）. However, the position of the genus Cantoria is distinctly different with the study of Voris et a1（2002）.

A Cladistic Analysis on the Genera of Tinginae (Hemiptera:Heteroptera:Tingidae) from Northern China

In the present paper,the cladistics method is used to analyze the phylogenetic relationship of 16 genera of Tinginae (Hemiptera:Heteroptera:Tingidae) from northern China. 33 characters with 88 states were chosen based on the morphological comparison. The character matrix was formed through ingroup and outgroup analysis and computed using the computer programs MacClad (version 3 0 1), AutoDecay (version 3 0), PAUP (version 3 1 1) and Hennig 86 (version 1 5),and the same most parsimonious tree and Nelson consensus cladogram were obtained from both computation to explain the phylogenetic relationship among the genera (L=118,CI=0 454,RI=0 529). We categorized these genera involved in the analysis phylogenetically into 6 groups according to the results. They are Agramma group,Leptoypha group,Dictyla group,Catoplatus group,Physatocheila group and Derephysia group. The phylogenetic relationship among the involved genera is presented as (((((Derephysia group=( Lasiacantha ,( Acalypta ,( Galeatus ,( Dictyonota ,( Derephysia,Sphaerista ))))),Physatocheila group =(( Elasmotropis,Tingis ),(( Oncochila,Cochlochila ), Physatocheila ))),Catoplatus group= Catoplatus ),Dictyla group=( Monosteira,Dictyla )),Leptoypha group= Leptoypha ),Agramma group= Agramma ). These groups will not be regarded as higher classific taxa until more genera and data are available and further analysis are carried out.

THE ENVIRONMENTAL QUALITY OF THE SEWAGEDISCHARGE AREA OF QINGDAO COVE--ACLADISTIC ANALYSIS

This study on the environmental quality of the Qingdao Cove intertidal zone sewage discharge area is based on data obtained from the December of 1989 and 1990 macrobenthos investigations there, and uses pollution indicator species and computer aided cladistic analysis to divide the area into a polluted area and a semi-polluted area. The study showed the environmental quality in 1990 improved over that in 1989.

Phylogenetic Relationships Among Species Subgroups in the Drosophila saltans Group (Diptera: Drosophilidae): Can Morphology Solve a Molecular Conflict?

Proper phylogenetic reconstruction is crucial for understanding many evolutionary phenomena. In spite of the great success of molecular phylogenetics, DNA signal still may be limited by some intrinsic constraints such as codon usage bias. The phylogenetic relationships between the five species subgroups of the Drosophila saltans group are a good example of conflicting molecular phylogenies drawn from different genes due to an ancestral substitutional shift. Here, forty morphological characters were analyzed using the same set of species used in previous molecular studies, with at least a single representative of each subgroup. The cladistic analysis was in disagreement with most of the previous hypotheses in placing the sturtevanti subgroup as an early branch, whereas the four remaining subgroups form a well supported clade that can be further subdivided into two sister clades： one containing the cordata and the elliptica subgroups, whereas the second includes the parasaltans and the saltans subgroups. The molecular evolution （codon usage bias） of the saltans group were revised in light of the present finding. The analysis highlights the important role of morphology in phylogeny reconstruction and in understanding molecular evolutionary phenomena.

THE PHYLOGENY OF YEASTS--A CLADISTIC ANALYSIS

Cladistic analysis was used to clarify the phylogeny of 16 genera of yeasts whose great morphological differences and inclusion in different classification systems resulted in controversies over the taxonomy of seven genera such as Crypeococcus, etc. Some scholars suggest that they belong to Ascomycetes. but others think they belong to fungi imperfecti. After comprehensive cladistic analysis of many genetic characters, the authors consider that the above-mentioned seven genera of yeasts developed in parallel with Ascomycetes so that they should belong to one and the same developmental system.

Phylogeny of Devonian Lycopsids Inferred from Bayesian Phylogenetic Analyses

To investigate the phylogeny of early lycopsids,cladistic analyses using both parsimony and Bayesian approaches are presented,with a data matrix of 33 morphological characters across 25 taxa. The resulting parsimony and Bayesian trees showed overall similarities in tree topologies.In the Bayesian tree,the Protolepidodendrales and the heterosporous lycopsids are recognized as two monophyletic groups,and within the latter group,the Isoetales sensu lato forms a subclade.This topology implies that the acquisition of a ligulate character evolved twice in the lycopsids,once in the protolepidodendralean Leclercqia Banks et al.,and once in the heterosporous lycopsid clade. Phylogenetic positions of several lycopsid plants previously reported from the Mid-Upper Devonian of South China,which have uncertain ordinal affinities,were estimated by the cladistic analyses;cf. Longostachys Xue et Hao,Longostachys Zhu et al.,Monilistrobus Wang et Berry,and Yuguangia Hao et al.fall well within the Isoetales clade,as earliest members of this order,while Minostrobus Wang and Wuxia Berry et al.are nested within the basal part of the heterosporous lycopsids.Bayesian analyses are a very useful approach in systematic studies and can be applied in analyzing paleobotanical data sets as well.

ANALYSIS OF EVOLUTIONARY RELATIONSHIP BETWEEN ASTASIA LONGA AND EUGLENA GRACILIS BY USING RAPD TECHNIQUE AND CLADISTIC ANALYSIS

Although both Astasia longa and Euglena gracilis belong to different genera, they share many morphological characters except that A. longa has no chloroplast. In the 1940’s, on the basis of the finding that in darkness or upon addition of some chemicals, E. gracilis would fade reversibly or irreversibly, some scholars hypothesised that A. longa evolved from E. gracilis by losing chloroplast. The authors’ use of RAPD and cladistic analyses in a study on the evolutionary relationship between A .longa and E. gracilis showed that the A. longa ’s relationship with E. gracilis was closer than that with other green euglenoids. This proves the hypothesis that A. longa evolved from E. gracilis is reasonable. The results of this study suggest that saprophytic colorless euglenoids were transformed from green euglenoids by losing their choroplasts.

A preliminary molecular historical biogeography of Caragana (Leguminosae) based on ITS and trnL-F DNA sequence data

The nrDNA internal transcribed spacer (ITS) and cpDNA trnL-F internal spacer (IGS) sequence data of Caragana eight species and one outgroup Halimodendron halodendron, was employed to reconstruct a phylogenetic tree, then the area relationship was analyzed by means of component analysis (CA), Brooks parsimony analysis (BPA), and dispersal-vicariance analysis (DIVA), six areas were selected from two divided distributions of East Asia and Tethys in Caragana. The phylogenetic tree indicated that there were three distinctive groups, which were attributed to some morphological characters, first with pinnate foliage and deciduous rachis, second with palmate foliage and persistent sclerotic stick rachis, and third with pinnate foliage and persistent sclerotic stick rachis. The results of CA and BPA illustrated general area relationships. An explicit area relationship should be Altai-Sayan, Far East NE China and North China (Hengduan Mountains). DIVA recognized several explanatory vicariance and dispersal events. As the scenario of Caragana distribution pattern, it looks like the vicariance versus dispersal plays more important role. In vicaraince, there are not only the isolated far-distance vicariance, but also the adjacent vicariance especially a vicariance between Hengduan Mountains and North China.

A new species of Friesea(Collembola:Neanuridae) from Hebei Province, North China and a cladistic analysis

Friesea incognita sp. nov. is described from China. This new species is characterized by the combination of: 2 + 2 eyes, no capitate tenent hairs on tibiotarsi, three anal spines, furcula without mucro and dens with 3 setae. Total dorsal and ventral chaetotaxy of the new species is given. A revised key for identification of the species of this genus with 2 + 2 eyes is given. Forty-seven characters of antennal sensilla, eyes and body chaetotaxy are chosen for the cladistic analysis performed for 18 species of this genus, including 12 with 2+2 eyes. Results indicate the new species F. incognita seems to be related to F. nauimetztli from Mexico. The phylogenetic relationships of the species are not well resolved due to the presence of many homoplasies among different species that adapt to a similar soil habitat.

Numerical Taxonomic Study of Some Tribes of Gramineae from Egypt

A systematic study for eleven tribes of Gramineae surveyed 34 characters including fruit morphology, fruit anatomy and palynology. The results were conducted to some numerical analysis aspects. On the basis of UPGMA (Unpaired Group Method of Average) clustering and PCA (Principal component analysis), the results show congruence between the UPGMA clustering and PCA method, in suggesting two major clads/groups and five subclads.

Latest progress in graptolitic phylogeny studies——Cladistic analysis of Ashgillian Dicellograptus

The graptolites studied here were collected from the Ashgillian Wufeng Formation in Wuning County, Jiangxi Province, which included 9 species of Dicellograptus, 2 species of Tangyagraptus and 1 species of Dicranograptus . The polarity and states of 8 selected characters are analyzed based on the morphological features and stratigraphic sequences of the 12 species and a parsimonious cladogram is reconstructed by using the monothetic method proposed by Camin and Sokal. A phyloneny tree of evolutionary significance formed by adding a time_axis to the cladogram indicates that the Ashgillian Dicellograptus in the investigated area includes two independent evolutionary lineages starting to diverge as early as in the Caradocian and, within the main lineage composed of the dicellograptids with square or subsquare basal portion, two clades represented respectively by Dicellograptus complexus and D. turgidus mark the highest stage of the Ashgillian dicellograptid evolution.

Determination of phylogenetic position of Pipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS ) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.

Increasing the number of discrete character states for continuous characters generates well-resolved trees that do not reflect phylogeny

Since the introduction of the cladistic method in systematics,continuous characters have been integrated into analyses but no methods for their treatment have received unanimous support.Some methods require a large number of character states to discretise continuous characters in order to keep the maximum level of informa­tion about taxa differences within the coding scheme.Our objective was to assess the impact of increasing the character state number on the outcomes of phylogenetic analyses.Analysis of a variety of simulated datasets shows that these methods for coding continuous characters can lead to the generation of well-resolved trees that do not reflect a phylogenetic signal.We call this phenomenon the flattening of the tree-length distribution;it is influenced by both the relative quantity of continuous characters in relation to discrete characters,and the num­ber of characters in relation to the number of taxa.Bootstrap tests provide a method to avoid this potential bias.