Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

Cladistic and phenetic studies of genera of Afrotropical Cryptobiina (Coleoptera,Staphylinidae, Paederinae) II. The phenetic approach

The phenetics of 12 genera of Afrotropical Cryptobiina have been analysed by multivariate statistics. Three analyses (principal component analysis, canonical discriminant analysis and cluster analysis) have been used to determine the relative positions of the taxa in a morphospace. These analyses have allowed us to confirm the generic divisions based on alpha-systematic and phylogenetic grounds. While phenetic systematics and cladistic systematics have often been opposed, this study shows that both approaches are, in the end, complementary. Phenetical analysis allow, in addition to a quantitative definition of the genera, the isolation of ethological or ecological characters, while the cladistic approch gives to them precision and a phylogenetic sense. The three types of analyses point out the importance in Cryptobiina of the size, length of the scapus and width of the neck, all three characters which were also designated as significant characters by the phylogenetic analysis.     

An investigation into the usefulness of a cladistic approach to the study of the origin of anatomically modern humans

Cladistic analyses for the study of hominid evolution become very common during the last two decades, but little attention has been given to the appropriateness of the approach to studies being undertaken. This paper discusses how cladistic analyses have been used in studies of late Middle and Upper Pleicostocene hominids without due consideration of the problems inherent within the approach. It is concluded that in studies of the origin of anatomicaly modern humans a strict cladistic approach is inappropriate because it takes too narrow a view (presence/absence) of morphology, and in doing so does not allow for morphological variation. A phenetic approach which is interested in overall morphological similarity based on many characters and attempts to sample the total morphological variability evident within a sample would seem a more appropriate approach in such studies.     

Preliminary cladistic analysis of genera of the cestode order Trypanorhyncha Diesing, 1863

A preliminary cladistic analysis was carried out on the 49 currently recognised genera of the order Trypanorhyncha. Forty-four characters were analysed; a functional outgroup was used for scolex and strobilar characters, while Nybelinia was utilised to polarise characters related to the rhyncheal system. Eight well-resolved clades were evident in the resultant cladogram, which is compared with existing phenetic classifications. An analysis of families resulted in a similar clustering of taxa to that observed in the case of the genera. The results suggest that two key characters used in existing classifications, namely the presence of sensory fossettes on the bothridia and the development of atypical heteroacanth and poeciloacanth armatures from typical heteroacanth armatures, have occurred on several occasions. Some clades provide support for the arrangements used in current classifications. Suggestions are made for future avenues of research which might provide more robust phylogenetic data for the Trypanorhyncha.     

Isozyme criteria in the testing of phyletic relationships between species of Gobius and related eastern Atlantic-Mediterranean genera (Teleostei: Gobüdae)

Horizontal starch gel electrophoresis was employed to investigate allozyme variation at 19 isozyme loci, in nine closely-related Atlantic-Mediterranean gobiid fish species, to assess genetic relationships, and to compare this with a phyletic hypothesis based on morphological apo-morphies. The species examined were Gobius niger, G. auratus, G. cruentatus, G. paganellus, Mauligobius maderensis, Zosterisessor ophiocephalus, Thorogobius ephippiatus, Padogobius martensii and P. nigricans . Various phenetic and cladistic analyses were performed on isozyme and morphological data. The phenetic and cladistic results from morphological data, and the cladistic results from isozyme data, were largely comparable, with P. martensü and P. nigricans forming a sister group to all the other taxa, species of Cobius forming a crown group within the latter, and stem lines formed by Mauligobius, Zosterisessor and Thorogobius , respectively. The isozymic estimates of genetic distance differed from these chiefly in the relative positions of Zosterisessor and G. auratus , which appear less similar to other species of Gohius. G. auratus shows many alleles which are unique within the genus Gobius ; possible explanations for this are put forward. The position of nigricans as congeneric with Padogobius martensü is confirmed by both phenetic and cladistic analyses of isozyme data.     

Species relationships in Lactuca s.l. (Lactuceae, Asteraceae) inferred from AFLP fingerprints

An AFLP data set comprising 95 accessions from 20 species of Lactuca s.l. (sensu lato) and related genera was generated using the primer combinations E35/M48 and E35/M49. In phenetic analyses of a data subset, clustering with UPGMA based on Jaccard's similarity coefficient resulted in the highest cophenetic correlation, and the results were comparable to those of a principal coordinates analysis. In analyses of the total data set, phenetic and cladistic analyses showed similar tree topologies for the well-supported parts of the trees. The validity of cladistic analysis of AFLP data is discussed. The results do not support a distinction among the serriola-like species L. sativa, L. serriola, L. dregeana, and L. altaica, which is in line with previous results. Therefore, we postulate that these species are conspecific. The serriola-like species L. aculeata occupies a clearly separate position, making it an ideal outgroup for studies of the closest relatives of L. sativa. The subsect. Lactuca as a group is well supported by our data, but the positions of L. saligna and L. virosa relative to the serriola-like species remain unclear. The close relationship between the sect. Mulgedium species L. tatarica and L. sibirica is corroborated by the present AFLP results and by additional crossability data.     

Cladistic and phenetic analysis of allozyme data for nine species of sea anemones of the family Actiniidae (Cnidaria: Anthozoa)

The aim of this study was to infer from allozyme data the phylogenetic relationships of nine species of actiniid sea anemones, and also use these data to assess the various methods (phenetic and cladistic) available for phylogenetic analysis. Starch gel electrophoresis was used to obtain genetic data from 13 gene loci. The anemone Metridium senile, from the family Metridiidae, was used as an outgroup. For the phenetic analysis a matrix of pairwise unbiased genetic distances was computed and, from this, dendrograms were produced both by the Wagner distance and the UPGMA methods. For the cladistic analyses three different approaches were used: the first was to treat the allele as a binary character; this was investigated using a Wagner parsimony algorithm. Another approach used was to consider the locus as an unordered character, using the alleles as states. Finally, we used the locus as an ordered multistate character, where mutation, fixation and elimination of each allele were treated as evolutionary novelties, and the heterozygotes were used as cues for the construction of transformation series. The trees produced by the phenetic and cladistic methods were highly congruent. This result suggests that allozymes can be used to produce phylogenetic hypotheses at higher taxonomic levels than those at which they are more usually employed. The Solé difference between the various trees was the relative positions of Bunodosoma caissarum and Bunodactis verrucosa in relation to the two species of Urticina. This difference was probably due to a high rate of anagenic change in B. verrucosa, which distorted the UPGMA dendrogram. The genera Actinia and Urticina appeared monophyletic in all of the trees produced. Also, the sea anemones with specialized column structures such as verrucae and vesicles (U.felina, U. eques, B. verrucosa, B. caissarum) formed a monophyletic cluster, a result compatible with the suggestion that these structures may have appeared only once in the evolutionary history of the Actiniidae.     

Phylogenetic analyses of Lapita decoration do not support branching evolution or regional population structure during colonization of Remote Oceania

Intricately decorated Lapita pottery (3100-2700 BP) was made and deposited by the prehistoric colonizers of Pacific islands, east of the main Solomon's chain. For decades, analyses of this pottery have focused on the ancestor-descendant relationships of populations and the relative degree of interaction across the region to explain similarities in Lapita decoration. Cladistic analyses, increasingly used to examine the evolutionary relationships of material culture assemblages, have not been conducted on Lapita artefacts. Here, we present the first cladistic analysis of Lapita pottery and note the difficulties in using cladistics to investigate datasets where a high degree of horizontal transmission and non-branching evolution may explain observed variation. We additionally present NeighborNet and phenetic distance network analyses to generate hypotheses that may account for Lapita decorative similarity.     

The subfamilies and tribes of the family Bovidae

In this paper 112 skeletal characters in 27 living species of bovids are used in cladistic and phenetic analyses of the relationships among the tribes in the family. Consideration and modification of the cladistic analysis leads to the conclusion that bovids cluster around four foci in ascending evolutionary sequence: Boselaphini and allies; Antilopini and some Neotragini; the Caprinae; and a group of African antelopes containing Aepyceros , Alcelaphini, Reduncini and Hippotragini. This conclusion is quite closely compatible with the phenetic distance analysis of the same data, provided die latter is read as if primitive or early bovids share more similarities than divergently advanced ones and hence associate more closely. Given the primitiveness of Boselaphini and allies, the crucial finding is that Caprinae link with African antelopes and that Antilopini are more remote. Cladistic and phenetic analyses of 32 characters in 12 extinct bovid species produce similar groupings, but also throw doubt on the classification of Aepyceros , Reduncini and Hippotragini alongside Alcelaphini within a clade of African antelopes. As a result of these two sets of studies, of living and of extinct bovids, minimal alterations are proposed to the arrangement of bovid tribes. In addition, Saiga is placed in the Antilopini, and, with less assurance, Pelea in the Neotragini, Aepyceros in the Alcelaphinae, and Pantholops in the Caprinae. The contribution of the fossil record to understanding bovid evolution is considered.     

Phylogenetic reconstruction and phenetic taxonomy

Cladistic analysis should not be equated with phylogenetic reconstruc Instead it is a means of describing character-state distributions among organisms and in this it resembles phenetic analysis. However, the claim that cladistic methods meet phenetic ('Gilmour-natural') criteria for classification as well as or better than traditional phenetic ones is shown to be based on an inadequate interpretation of these criteria. Instead, a new measure of naturalness is proposed in which the most natural classification is that which describes the distribution of all character states by the smallest number of statements. The possibility of extending this measure to provide a criterion for an optimally simple classification is noted. It is concluded that phylogenetic reconstruction must not only reflect the branching patterns suggested by cladistic analysis but also take account of the tionary history that is reflected in an optimal phenogram.     

Phylogeny of the water strider genus Rheumatobates (Heteroptera: Gerridae)

The genus Rheumatobates comprises thirty‐seven species and subspecies of New World water striders belonging to subfamily Rhagadotarsinae. Among species, males vary dramatically in the degree and nature of modifications of the antennae, three pairs of legs and abdominal and genital segments. Characters describing this modification have traditionally been used to differentiate and group species. The general assumption has been that modified species belong to one group and unmodified species to another. These two ‘species groups’ are subdivided into ‘subgroups’, but little effort has been made to resolve relationships among them. We conduct the first numerical cladistic analysis of Rheumatobates using a data set comprised of 102 characters, primarily describing modification of male external morphology. To address concerns about the inclusion of characters to be optimized on the phylogeny, characters describing modification of antennae and hind legs were included and then excluded in separate analyses. A preferred phylogeny was chosen from the four equally parsimonious cladograms found after successive reweighting of characters. There was good resolution at all levels of the phylogeny. Most of the major clades and terminal relationships were moderately to strongly supported, whereas the basal relationships were less well supported. The general assumption that unmodified and modified species form two monophyletic groups was not supported. However, traditionally recognized ‘subgroups’ within the modified species group were largely upheld. The analysis also suggested several major clades and relationships among these clades that were not previously recognized. The exclusion of characters describing modification of antennae and hind legs did not change the resolved major clades of the reconstructed phylogeny.     

Evolution and character congruence in some western Indian Ocean Phelsuma: Numerical analysis of biochemistry, shape and scalation

The evolution of five island populations of Green gecko, representing inter- and intra-specific divergence, was studied using biochemical data, scalation and shape. The data were numerically analysed using ordination analyses for the phenetic classification and Wagner trees to hypothesize the phylogeny. These studies revealed three phenetic groups corresponding to three mono-phyletic lineages. The numerical analysis of morphological data agreed with the numerical analysis of biochemical data. It is concluded that the classification based on biochemical affinities differed from the previous classification based on conventional analysis of morphology due to methodological and philosophical differences rather than differences between morphological and biochemical evolution.
The ordination analyses were very congruent between data sets (biochemical, shape, scalation, total) and the Wagner trees were generally congruent between data sets. Some Wagner trees based on scalation data were incongruent. The phenetic and cladistic classifications corresponded to each other but differed from the conventional classification. The phylogenetic analysis of the total data set indicated that the three specific lineages showed relatively equal anagenesis. However, anagenic divergence differed markedly between character types. It is suggested that a range of character types be used when studying anagenesis.     

Dinoflagellates in evolution. A molecular phylogenetic analysis of large subunit ribosomal RNA

Summary The sequence of the large subunit ribosomal RNA (LsuRNA) gene of the dinoflagellateProrocentrum micans has been determined. The inferred rRNA sequence [3408 nucleotides (nt)] is presented in its most probable secondary structure based on compensatory mutations, energy, and conservation criteria. No introns have been found but a hidden break is present in the second variable domain, 690 nt from the 5 end, as judged by agarose gel electrophoresis and primer extension experiments.Prorocentrum micans LsuRNA length and G+C content are close to those of ciliates and yeast. The conserved portions of the molecule (1900 nt) have been aligned with corresponding sequences from various eukaryotes, including five protista, one metaphyta, and three metazoa. An extensive phylogenetic study was performed, comparing two phenetic methods (neighbor joining on difference matrix, and Fitch and Margoliash on Knuc values matrix) and one cladistic (parsimony). The three methods led to similar tree topologies, except for the emergence of yeast that groups with ciliates and dinoflagellates when phenetic methods are used, but emerges later in the most parsimonious tree. This discrepancy was checked by statistical analyses on reduced trees (limited to four species) inferred using parsimony and evolutionary parsimony methods. The data support the phenetic tree topologies and a close relationship between dinoflagellates, ciliates, and yeast.     

Phenetic and cladistic relationships among tenebrionid beetles (Coleoptera)

Abstract. The higher classification of Tenebrionidae is analysed using numerical phenetic, numerical cladistic and traditional Hennigian methods. In all, eighty characters are examined for about 335 taxa; definitive analyses are made on combinations of eighteen to seventy characters for thirty-three OTUs. At lower levels of relationship (genera and closely related tribes) phenetic and cladistic classifications are shown to be congruent, but at higher levels (tribes and subfamilies) there is marked discordance with phenetic results being more stable. A consensus classification is more similar to the Hennigian cladogram than is any single computer generated cladogram. Two main tribal groups – the Lagrioid and Tenebrionoid groups – are suggested which differ in defensive glands, female anatomy, wing and mouthpart morphology, larval characters and other features. The Tenebrionoid group consists of three main subdivisions – the tenebrionine, coelometopine and diaperine lineages. Changes in classificatory position are recommended for eighty-seven genera and tribes (listed in Appendix E) and implied for numerous others.     

Congruence between larval ventromental plate ultrastructure and immature morphology in Yama Sublette & Martin and some Oceanian species of Chironomus Meigen (Diptera: Chironomidae)

The morphology of the larval ventromental plates of Y. tahitiensis Sublette & Martin and four Oceanian species of Chironomus Meigen, C. hawaiiensis Grimshaw, C. javanus Kieffer, C. magnivalva Kieffer and C. samoensis Edwards, has been studied by scanning electron micrography. Data on ventromental plate ultrastructure are used in phenetic and cladistic analyses of the relationships of T. tahitiensis and the Oceanian Chironomus to other species in Chironomus and additional genera. The results of these analyses support the current generic status of T. tahitiensis but indicate that Yama is less closely related to Chironomus than previously supposed, a finding that is supported by a reexamination of 'traditional' morphological features.     

Characterisation of cDNAs for ribulose bisphosphate carboxylase small subunit genes in different species of Avena (Poaceae)

ABSTRACT

We report the cloning and sequencing of 14 rbcS cDNAs in six species of Avena (Poaceae) with different genome and ploidy levels. The nucleotide sequences 504 bp long were aligned with the published sequences of cultivated hexaploid oat, wheat, barley, rye, rice and corn and subjected to cladistic and phenetic analyses. The parsimonious analysis generated a tree with a topology very similar to the phenogram generated by the Neighbor-Joining analysis based on the Jukes and Cantor distances. Within the monophyletic assemblage of the tribe Aveneae, consistent clades composed of rbcS clones belonging to different species are recognized. It is suggested that they correspond to orthologous genes belonging to different subfamilies, and that the “within-species?d homogenisation may have occurred at a slow rate with respect to species evolution. In the monophyletic group of Pooideae, the topologies place barley rbcS sequences closer to wheat and rye than to oat sequences. This grouping agrees with most taxonomic and phylogenetic views.     

Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa

Over the past 10 years, the phylogenetic relationships among higher-level artiodactyl taxa have been examined with multiple data sets. Many of these data sets suggest that Artiodactyla (even-toed ungulates) is paraphyletic and that Cetacea (whales) represents a highly derived "artiodactyl" subgroup. In this report, phylogenetic relationships between Cetacea and artiodactyls are tested with a combination of 15 published data sets plus new DNA sequence data from two nuclear loci, interphotoreceptor retinoid-binding protein (IRBP) and von Willebrand factor (vWF). The addition of the IRBP and vWF character sets disrupts none of the relationships supported by recent cladistic analyses of the other 15 data sets. Simultaneous analyses support three critical clades: (Cetacea + Hippopotamidae), (Cetacea + Hippopotamidae + Ruminantia), and (Cetacea + Hippopotamidae + Ruminantia + Suina). Perturbations of the combined matrix show that the above clades are stable to a variety of disturbances. A chronicle of phylogenetic results over the past 3 years suggests that cladistic relationships between Cetacea and artiodactyls have been stable to increased taxonomic sampling and to the addition of more than 1,400 informative characters from 15 data sets.     

Notes on the position of the true freshwater crabs within the brachyrhynchan Eubrachyura (Crustacea: Decapoda: Brachyura)

Cladistic and phenetic relationships of 51 eubrachyuran crab genera, comprising 36 genera of marine crabs and 18 genera of true freshwater crabs from 7 families, were investigated using 121 parsimony-informative adult morphological characters. The data matrix was subjected to four different treatments: (1) a cladistic analysis with a combination of unordered and ordered characters, (2) a cladistic analysis with all characters unordered, (3) neighbour-joining, and (4) UPGMA phenetic analyses. The parsimony analysis conducted with a combination of ordered and unordered characters produced a set of hypotheses which supported monophyly of a Pseudothelphusidae+Potamoidea clade. Furthermore, exemplar genera of the Bythograeidae and Pinnotheridae formed an unresolved polytomy with the Pseudothelphusidae+Potamoidea group, the Thoracotremata. The trichodactylid freshwater crabs were positioned as the sister taxon of the basal portunoid Carcinus, but were unresolved relative to other portunoids and geryonids. Second, the parsimony analysis conducted with all characters unordered resulted in a [bythograeid, pseudothelphusid+potamoid, pinnotherid, thoracotreme] group with no hierarchical resolution, which in turn formed a polytomy with a goneplacid+portunoid clade and a polyphyletic Xanthoidea. And third, phenetic groupings of the eubrachyuran genera invariably placed the pseudothelphusids with the potamoids, and this clustered with a group containing the thoracotremes (either in whole or part). Support was thus found for morphological connections among the nontrichodactylid freshwater crabs, thoracotremes, bythograeids, and pinnotherids, and for the placement of the trichodactylids within the Portunoidea. These two latter findings (that used a range of genera from each family) are broadly congruent with a previous cladistic analysis of selected eubrachyuran familial groundpatterns that used a basal exemplar of each marine and freshwater crab family (Sternberg et al., 1999). However, it is clear that the large scale homoplasy identified here may nullify any reliable hypothesis of brachyrhynchan groupings at this stage.     

Cladistics and polychaetes

A series of cladistic analyses assesses the status and membership of the taxon Polychaeta. The available literature, and a review by Fauchald & Rouse (1997), on the 80 accepted families of the Polychaeta are used to develop characters and data matrices. As well as the polychaete families, non-polychaete taxa, such as the Echiura, Euarthropoda, Onychophora, Pogonophora (as Frenulata and Vestimentifera), Clitellata, Aeolosomatidae and Potamodrilidae, are included in the analyses. All trees are rooted using the Sipuncula as outgroup. Characters are based on features (where present) such as the prostomium, peristomium, antennae, palps, nuchal organs, parapodia, stomodaeum, segmental organ structure and distribution, circulation and chaetae. A number of analyses are performed, involving different ways of coding and weighting the characters, as well as the number of taxa included. Transformation series are provided for several of these analyses. One of the analyses is chosen to provide a new classification. The Annelida is found to be monophyletic, though weakly supported, and comprises the Clitellata and Polychaeta. The Polychaeta is monophyletic only if taxa such as the Pogonophora, Aeolosomatidae and Potamodrilidae are included and is also weakly supported. The Pogonophora is reduced to the rank of family within the Polychaeta and reverts to the name Siboglinidae Caullery, 1914. The new classification does not use Linnaean categories, and the Polychaeta comprises two clades, the Scolecida and Palpata. The Palpata has the clades Aciculata and Canalipalpata. The Aciculata contains the Phyllodocida and Eunicida. The Canalipalpata has three clades; the Sabellida (including the Siboglinidae) Spionida and Terebellida. The position of a number of families requires further investigation.