Phylogenetic analysis of the Amphitritinae (Polycnaeta: Terebellidae)

The phylogenetic relationships of the Amphitritinae (Polychaeta: Terebellidae) were studied using parsimony analysis of 22 external morphological characters. To choose outgroups to polarize the characters, I carried out a preliminary analysis of the relationships of the four terebellid subfamilies and the Trichobranchidae. The single most parsimonious tree from the analysis supports monophyly of the Terebellidae by the presence of ventral glandular shields. However, this character is homoplasious within the Terebellomorpha, and further evaluation of the Terebellidae is recommended. Artacama and Thelepus were chosen as outgroups for the analysis of amphitritine genera. The generic level analysis yielded seven equally parsimonious trees, which are consistent in their topologies except for the relationships among seven genera in one large clade. In all trees, Artacama is the sister taxon to a large clade within the Amphitritinae; the Artacaminae is therefore synonymized with the Amphitritinae, which is diagnosed by the presence of double rows of uncini. Within the Amphitritinae, the status of several monotypic genera is questioned; plesiomorphic character states indicated by the analysis are discussed. The results presented are offered as working hypotheses of the relationships among amphitritine genera. The large number of homoplasies indicated by the analysis emphasizes the need to further evaluate these hypotheses using additional characters. With a robust phylogenetic hypothesis of amphitritine relationships, a re-classification of the group based on apomorphic character states can be undertaken, and questions regarding the evolution of morphological characters, reproductive modes, or biogeographical patterns can be properly addressed.     

The phylogenetic position of the Clitellata and the Echiura - on the problematic assessment of absent characters*

Absent characters (negative characters) are difficult to assess and their correct interpretation as symplesiomorphies, synapomorphies or convergencies (homoplasies) is one of the greatest challenges in phylogenetic systematics. Different phylogenetic assessments often result in contradictory phylogenetic hypotheses, in which the direction of evolutionary changes is diametrically opposed. Especially in deciding between primary (plesiomorphic) and secondary (apomorphic) absence, false conclusions may be reached if only the outgroup comparison and the principle of parsimony are employed without attempting any biological evaluation or interpretation of characters. For example, in the higher‐level systematization of the Annelida and related taxa different assessments of absent characters have led to conflicting hypotheses about the phylogenetic relationships and the ground pattern of the annelid stem species. Varying phylogenetic interpretations regarding the absence of the chemosensory nuchal organs in the clitellates and their presence in polychaetes initiated a controversy that produced two alternative phylogenetic hypotheses: (1) the Clitellata are highly derived Annelida related to a subtaxon within the, in this case, paraphyletic ‘Polychaeta’ or (2) the Clitellata are comparatively primitive Annelida representing the sister group of a monophyletic taxon Polychaeta. In the former, the absence of nuchal organs in the Clitellata is regarded as a secondary character, in the latter as primary. As most Clitellata are either limnetic or terrestrial, we must ask which characters are plesiomorphies, taken from their marine stem species without changes. In addition to a thorough investigation and evaluation of clitellate characters, a promising approach to these questions is to look for such characters in limnetic and terrestrial annelids clearly not belonging to the Clitellata. A similar problem applies to the evaluation of the position of the Echiura, which lack both segmentation and nuchal organs. Evidence is presented that in both taxa these absent characters represent derived, apomorphic character states. The consequences for their phylogenetic position and the questionable monophyly of the Polychaeta are discussed. The conclusion drawn from morphological character assessments is in accordance with recently published hypotheses based on molecular data.     

Phylogenetic interrelationships of the barbets (Aves: Capitonidae) and toucans (Aves: Ramphastidae) based on morphology with comparisons to DNA-DNA hybridization

A phylogenetic analysis of the interrelationships of the barbets (Capitonidae) and the toucans (Aves: Ramphastidae, Superfamily Ramphastoidea) is presented. Thirty-two morphological characters from the literature and independent osteological observations were analysed. Character polarity was determined by outgroup comparison to the Picidae, Indicatoridae, Galbulidae, Bucconidae and Coraciiformes. Four alternative phylogenetic hypotheses were compared: (1) the overall most parsimonious morphological phylogeny, (2) the most parsimonious morphological phylogeny in which the capitonids and ramphastids were hypothesized as monophyletic sister groups, and (3) and (4) the most parsimonious hypotheses for the evolution of the morphological characters within two proposed DNA-DNA hybridization phylogenies of the ramphastoids. The analysis focused on the higher level relationships of ramphastids and capitonids and interrelationships among capitonid genera. Two cladistic analyses were performed using 26 phylogenetically informative characters, and the PAUP and CONTREE computer alogorithms. The most parsimonious morphological phylogeny required fewer character changes and had a lower consistency index than any of the alternative hypotheses but congruence between the most parsimonious phylogeny and the second, revised DNA-DNA hybridization hypothesis was very high. Based on these results the monophyly of the Capitonidae is rejected. The ramphastids and the Neotropical capitonids form a well corroborated clade within the pantropical ramphastoid radiation. Neither the African, Asian nor New World capitonids is monophyletic. The genus Trachyphonus is the sister group to all other capitonids and ramphastids. The sister group to the ramphastids is the genus Semnornis. The interrelationships of the Old World capitonids excluding Trachyphonus are not completely resolved by these morphological data but one of the alternative phylogenetic resolutions is presented as a preliminary hypothesis. The clades in this resolved phylogeny are diagnosed and the palaeontology and biogeography of the ramphastoids arc-reviewed in light of this new evidence. A phylogenetic classification is proposed in which the Capitonidae is rejected and the capitonids and ramphastids are placed in seven subfamilies of the Ramphastidae.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.     

Live history evolution in Serpulimorph polychaetes: a phylogenetic analysis

The widely accepted hypothesis of plesiomorphy of planktotrophic, and apomorphy of lecithotrophic, larval development in marine invertebrates has been recently challenged as a result of phylogenetic analyses of various taxa. Here the evolution of planktotrophy and lecithotrophy in Serpulimorph polychaetes (families Serpulidae and Spirorbidae) was studied using a hypothesis of phylogenetic relationships in this group. A phylogenetic (parsimony) analysis of 36 characters (34 morphological, 2 developmental) was performed for 12 selected serpulid and 6 spirorbid species with known reproductive/developmental strategies. Four species of Sabellidae were used in the outgroup. The analysis yielded 4 equally parsimonious trees of 78 steps, with a consistency index (CI) of 0.654 (CI excluding uninformative characters is 0.625). Under the assumption of unweighted parsimony analysis, planktotrophic larvae are apomorphic and non-feeding brooded embryos are plesiomorphic in serpulimorph polychaetes. The estimated polarity of life history transitions may be strengthened by further studies demonstrating an absence of a unidirectional bias in planktotrophy-lecithotrophy transition in polychaetes.     

Morphology-based phylogeny of the treehopper family Membracidae (Hemiptera: Cicadomorpha: Membracoidea)

A parsimony‐based phylogenetic analysis of eighty‐three morphological characters of adults and immatures of seventy representatives of the tribes and subfamilies of Membracidae and two outgroup taxa was conducted to evaluate the status and relationships of these taxa. Centrotinae apparently gave rise to Nessorhinini and Oxyrhachini (both formerly treated as subfamilies, now syn.n. and syn.reinst., respectively, of Centrotinae). In contrast to previous analyses, a clade comprising Nicomiinae, Centronodinae, Centrodontinae, and the unplaced genera Holdgatiella Evans, Euwalkeria Goding and Antillotolania Ramos was recovered, but relationships within this clade were not well resolved. Nodonica bispinigera, gen.n. and sp.n., is described and placed in Centrodontini based on its sister‐group relationship to a clade comprising previously described genera of this tribe. Membracinae and Heteronotinae were consistently monophyletic. Neither Darninae nor Smiliinae, as previously defined, was monophyletic on the maximally parsimonious cladograms, but constraining both as monophyletic groups required only one additional step. The monophyly of Stegaspidinae, including Deiroderes Ramos (unplaced in Membracidae), was supported on some but not all equally parsimonious cladograms. More detailed analyses of individual subfamilies, as well as morphological data on the undescribed immatures of several membracid tribes and genera, will be needed to elucidate relationships among tribes and genera. A key to the subfamilies and tribes is provided.     

Rooting with Multiple Outgroups: Consensus Versus Parsimony

Using outgroup(s) is the most frequent method to root trees. Rooting through unconstrained simultaneous analysis of several outgroups is a favoured option because it serves as a test of the supposed monophyly of the ingroup. When contradiction occurs among the characters of the outgroups, the branching pattern of basal nodes of the rooted tree is dependent on the order of the outgroups listed in the data matrix, that is, on the prime outgroup (even in the case of exhaustive search). Different equally parsimonious rooted trees (=cladograms) can be obtained by permutation of prime outgroups. An alternative to a common implicit practice (select one outgroup to orientate the tree) is that the accepted cladogram is the strict consensus of the different equally parsimonious rooted trees. The consensus tree is less parsimonious but is not hampered with extra assumption such as the choice of one outgroup (or more) among the initial number of outgroup terminals. It also does not show sister-group relations that are ambiguously resolved or not resolved at all.     

TRIBAL PLACEMENT OF MARSHALLIA (ASTERACEAE) USING CHLOROPLAST DNA RESTRICTION SITE MAPPING

The examination of morphological traits has failed to resolve the tribal placement of Marshallia. Suggested relationships for this anomalous genus have, at various times, included Eupatorieae, Heliantheae, Vemonieae, and Inuleae. Chloroplast DNA restriction site mapping, using Bamadesiinae (Mutisieae) as the outgroup, revealed 981 restriction site mutations, 332 of which were phylogenetically informative, for 60 genera representing 15 tribes of Asteraceae. Wagner parsimony produced 36 equally parsimonious tress of 729 steps, and Dollo parsimony produced 34 equally parsimonious trees of 759 steps. Monophyletic groups, resulting from the Wagner analysis, were further tested with the bootstrap method. The placement of Marshallia in the Heliantheae-Tageteae-Coreopsideae-Eupatorieae complex was consistent for all trees produced. Tageteae and Coreopsideae form the sister group to paraphyletic Heliantheae, with Marshallia sharing its most recent common ancestor with Galinsoga, Palafoxia, and Bahia. The Eupatorieae form a monophyletic clade that is derived from helianthoid ancestors.     

Phylogeny of the Anomala (Crustacea, Decapoda, Reptantia) based on the ossicles of the foregut

We present a cladistic analysis of the Anomala based on 66 ingroup species and 5 outgroup representatives. Based on a comparative analysis of the morphology of the foregut we scored 124 characters related to size, shape, and fusion of foregut ossicles and other foregut structures. Our parsimony analysis resulted in 30 equally parsimonious trees which differ mainly at the lower hierarchical level. Our study reveals two large clades within Anomala. One large clade consists of Galatheoidea and Chirostyloidea. The internal relationships show a monophyletic Porcellanidae nested within a group comprising paraphyletic Galatheidae, and Munididae as well as Munidopsidae. The other large clade contains Aegla as sister group to a monophyletic group consisting of the Hippoidea and a clade formed by Lomis and the Paguroidea. Coenobitidae are nested within paraphyletic Diogenidae and Lithodidae are nested within paraphyletic Paguridae. The results are discussed in the context of other morphological and molecular analyses. Furthermore, some aspects of carcinization are touched upon; in particular, an anomalan stem species with a, at least to some extent, ventrally folded pleon is suggested.     

THE EFFECT OF ORDERED CHARACTERS ON PHYLOGENETIC RECONSTRUCTION

Abstract Morphological structures are likely to undergo more than a single change during the course of evolution. As a result, multistate characters are common in systematic studies and must be dealt with. Particularly interesting is the question of whether or not multistate characters should be treated as ordered (additive) or unordered (non-additive). In accepting a particular hypothesis of order, numerous others are necessarily rejected. We review some of the criteria often used to order character states and the underlying assumptions inherent in these criteria.
The effects that ordered multistate characters can have on phylogenetic reconstruction are examined using 27 data sets. It has been suggested that hypotheses of character state order are more informative then hypotheses of unorder and may restrict the number of equally parsimonious trees as well as increase tree resolution. Our results indicate that ordered characters can produce more, equal or less equally parsimonious trees and can increase, decrease or have no effect on tree resolution. The effect on tree resolution can be a simple gain in resolution or a dramatic change in sister-taxa relationships. In cases where several outgroups are included in the data matrix, hypotheses of order can change character polarities by altering outgroup topology. Ordered characters result in a different topology from unordered characters only when the hierarchy of the cladogram disagrees with the investigator's a priori hypothesis of order. If the best criterion for assessing character evolution is congruence with other characters, the practice of ordering multistate characters is inappropriate.     

The evolution of the laterophysic connection with a revised phylogeny and taxonomy of butterflyfishes (Teleostei: Chaetodontidae)

The higher‐level relationships of butterflyfishes were examined using 37 morphological characters. This analysis combines characters derived from a histological study describing variation in the morphology of the laterophysic connection (an association between the swim bladder and the lateral‐line canals) with previously described morphological characters. The phylogenetic analysis resulted in four equally parsimonious trees that only differed in the placement of two of the 11 chaetodontid genera (Amphichaetodon and Forcipiger). We compare our analysis with previous hypotheses, present a new taxonomy consistent with the proposed cladistic relationships, and diagnose Chaetodon with five unreversed synapomorphies, including the evolution of characters composing the laterophysic connection. A new character‐based diagnosis of Chaetodon is provided and species are allocated accordingly; Chaetodon now includes the former Parachaetodon ocellatus and excludes the former subgenera Prognathodes and Roa. The evolution of the laterophysic connection is examined by optimizing character‐state transformations on the new hypothesis of relationships.     

Phylogenetic relationships among families of the Scaphopoda (Mollusca)

Phylogenetic relationships among families in the molluscan class Scaphopoda were analysed using morphological characters and cladistic parsimony methods. A maximum parsimony analysis of 34 discrete characters, treated as unordered and equally weighted, from nine ingroup terminal taxa produced a single most parsimonious tree; supplementary analyses of tree length frequency distribution and Bremer support indices indicate a strong phylogenetic signal from the data and moderate to minimally supported clades. The traditional major division of the class, the orders Dentaliida and Gadilida, is supported as both taxa are confirmed as monophyletic clades. Within the Dentaliida, two clades are recognized, the first comprised of the families Dentaliidae and Fustiariidae, the second of the Rhabdidae and Calliodentaliidae; together, these groups comprise a third clade, which has the Gadilinidae as sister. Within the Gadilida, a nested series of relationships is found among [Entalinidae, [Pulsellidae, [Wemersoniellidae, Gadilidae]]]. These results lend cladistic support to earlier hypotheses of shared common ancestry for some families, but are at variance with other previous hypotheses of evolution in the Scaphopoda. Furthermore, analysis of constituent Gadilinidae representatives provide evidence for paraphyly of this family. The relationships supported here provide a working hypothesis that the development of new characters and greater breadth of taxonomic sampling can test, with a suggested primary goal of establishing monophyly at the family level.     

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 nereidids (Polychaeta, Nereididae) with paragnaths

A phylogenetic analysis was conducted of the Nereidinae — those members of the Nereididae (Polychaeta) with pharyngeal paragnaths. We had two objectives: to test the monophyly of currently accepted genera, subgenera and informal subgeneric groupings within the Nereidinae, and, if warranted, to propose a more natural classification of the Nereidinae. Parsimony analyses were undertaken, including 52 terminal taxa from all genera and informal groupings from the large heterogeneous genera Nereis , Ceratonereis , Neanthes and Perinereis . Analyses of a character set of 52 informative characters yielded more than 10 000 equally parsimonious trees with a length of 176 steps (consistency index [CI] = 0.34, retention index [RI] = 0.66). Reweighting three times resulted in 445 most parsimonious trees with length 54.62 (CI = 0.59, RI = 0.79). Many characters widely used in nereidid systematics were found to exhibit high levels of homoplasy. The most parsimonious trees could not be rooted such that the selected ingroup, 'Nereididae with paragnaths', was monophyletic, causing us to reject the monophyly of the Nereidinae as currently defined. The following genera were well supported by the parsimony analyses and are newly diagnosed: Alitta , Ceratonereis , Pseudonereis , Simplisetia , Solomononereis and Unanereis . Alitta succinea , Pseudonereis cortezi , Pseudonereis noodti and Pseudonereis pseudonoodti are proposed as new combinations. The parsimony analysis supported the monophyly of neither Composetia , Neanthes , Nereis and Perinereis nor of any new groupings of remaining species presently placed in those genera. It is these poorly supported genera that comprise most species of Nereididae.     

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.     

Restriction enzyme analysis of the nuclear 45s ribosomal DNA of six cultivated Alliums (Alliaceae)

Estimates of the phylogenetic relationships among cultivated and wildAllium species would benefit from identification of objective molecular characters. Restriction fragment length polymorphisms in the nuclear 45s ribosomal DNA (rDNA) were identified among two of five accessions of each of six cultivated Alliums. Restriction enzyme sites forBamHI,DraI,EcoRI,EcoRV,SacI, andXbaI were mapped. Different lengths of the rDNA repeat unit among the cultivated Alliums were due to sizes of the intergenic spacer. Nineteen polymorphic restriction enzyme sites were discovered and used to estimate phylogenetic relationships. Cladistic analyses based on Wagner parsimony were completed without an outgroup and resulted in two equally most parsimonious trees of 22 steps. A combined analysis of differences at RE sites in the ribosomal (19 characters) and chloroplast (15 characters) DNA generated a single most parsimonious tree of 39 steps. Single trichotomies were observed at 40 and 41 steps. Strict consensus of the three trees of 41 or fewer steps consisted of a lineage forA. tuberosum, a second forA. ampeloprasum andA. sativum, and a third forA. cepa, A. fistulosum, andA. schoenoprasum. Estimates of phylogenetic relationships based on variability at restriction enzyme sites in the rDNA and chloroplast DNA agree with the classification scheme ofTraub. Because of the predominance of autapomorphies, restriction enzyme analysis of the nuclear 45s rDNA is of limited use in estimating phylogenies amongAllium sections. However it is useful in the establishment of interspecific hybridity.     

A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology

A cladistic analysis, primarily based on morphology, is presented from 40 diploid taxa representing the 24 monogenomic genera of the Triticeae. General problems related to the treatment of hybrids and supposedly allopolyploid heterogenomic taxa are highlighted. Special emphasis is given to taxa not traditionally included in Aegilops s.J. Most of the 33 characters used in the analysis are coded as binary. The only four multistate characters in the matrix are treated as unordered. Three diploid species of Bromus are used as outgroup. The number of equally parsimonious trees found is very large (approx. 170000; length = 107, ci = 0.36, ri = 0.75) and the strict consensus tree has an expectedly low level of resolution. However, most of the equally parsimonious trees owe their existence to an unresolved Aegilops clade. If this clade is replaced by its hypothetical ancestor, the number of equally parsimonious trees drops dramatically (48; length = 78, ci = 0.45, ri = 0.76). When trees for which more highly resolved compatible trees exist are excluded, only two trees remain. Bremer support is used as a measure of branch support. The trees based on morphology and on molecular data are largely incongruent.     

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．     

A preliminary cladistic study of the families of the superorder Lamiiflorae

LU AN-MING, 1990. A preliminary cladistic study of the families of the superorder Lamiiflorae. A preliminary cladistic analysis was undertaken to evaluate the relationships between families of the superorder Lamiiflorae sensu Dahlgren. Several character complexes were surveyed, and ultimately 29 informative characters were used for the study. Three families, Clethraceae, Oleaceae and Solanaceae were selected for outgroup comparison and polarization of the characters. A data matrix was constructed for the 23 ingroup families. The data matrix was analysed with the cladistic parsimony program Hennig86. Three equally parsimonious cladograms were found. Many family interrelationships could not be resolved, although several groups were common to all three cladograms, as shown by a strict consensus tree. The Retziaceae emerged as the sister group to the remaining families. About half of those appeared in a large polytomy in the consensus tree. There was also one possibly monophyletic complex of families involving the Lamiales with the families Verbenaceae, Lamiaceae, Phrymaceae and Callitrichaceae as well as the three isolated families Trapellaceae, Hippuridaceae, and Hydrostachyaceae. Within this complex, Verbenaceae and Lamiaceae came out as sister groups, as did Callitrichaceae and Hydrostachyaceae, with Hippuridaceae as sister group to them. However, the results must be regarded as tentative.