EXACT INDICES, CRITERIA TO SELECT FROM MINIMUM LENGTH TREES

Abstract— Modifications of the consistency, retention and rescaled consistency indices are introduced. These apply to particular transformations of a character state rather than all of the transformations of a character. For example, if one observes relatively many losses in a character state over a suite of minimum length trees, a low weight is applied to the transformation to a loss; however, these observations infer nothing on the probability of the character state being gained independently. If the same character state shows few or no convergent gains on the suite of minimum length cladograms, then gains receive a relatively high weight. Conversely, if for a particular character state, convergent gains are common and losses rare, the transformation to a loss is given a higher weight than the transformation to a gain. For multistate characters, each possible transformation is weighted independently. Three indices are proposed, i.e. the exact consistently index, the exact retention index and the exact rescaled consistency index. The consistency index is modified to deal with characters with unknown entries.
The methods outlined not only select (or generate) preferred tree topologies but they also choose character optimizations, even for trees of identical topology.     

Meta-analysis of character utility and phylogenetic information content in cladistic studies of ammonoids

While previous workers have argued persuasively that ammonoid workers should use cladistic approaches to reconstruct phylogeny, relatively few cladistic studies have been published to date. An essential yet challenging part of cladistic analysis is the selection of characters. Are certain types of characters more likely to show homoplasy? Are certain aspects of shell anatomy more likely to contain phylogenetically informative characters? Are datasets with more characters inherently better? To answer these questions, a meta-analysis of character data from published ammonoid phylogenies was performed. I compiled 14 datasets, published between 1989 and 2007, representing parsimony-based phylogenetic analyses of ammonoids. These studies defined a combined total of 323 characters, which were grouped into categories reflecting different aspects of anatomy: shell size and shape, ornament, suture, early ontogeny, body chamber and apertural modifications. Tree searches were re-run to determine overall tree statistics, parsimony permutation tail probability (PTP) tests were calculated to assess the phylogenetic information content of the matrices, and retention and rescaled consistency indices for each character were calculated. My analyses revealed that studies with higher character/taxon ratios did not necessarily produce trees with more information content and less homoplasy, as measured by retention or rescaled consistency indices, because additional characters were often parsimony-uninformative. Rather, studies with relatively few characters could produce high-quality trees if the characters were well-chosen and character states carefully defined. Characters related to the body chamber and adult aperture typically had retention indices of either 0 or 1, rarely in between, indicating that they either worked perfectly or not at all. Suture characters tended to have higher indices than shell shape or ornament characters, suggesting more phylogenetic information and less homoplasy in the suture line than in shell traits. These results should aid in the selection of characters for future cladistic studies of ammonoids.     

PARSIMONY AND THE CHOICE BETWEEN DIFFERENT TRANSFORMATIONS FOR THE SAME CHARACTER SET

Abstract— When phylogeneticists choose among alternative hypotheses, they choose the one that requires the fewest ad hoc assumptions, i.e. the one that is the most parsimonious. For some systematists, choosing among alternative transformation series for the same set of taxa is equivalent to attaining trees with shorter length and minimal homoplasy. Homoplasy is shown to be composed of hierarchical discordance and scattering, which are recognized and described for the first time. Neither the consistency nor retention indices can be used in assessing different theories of multistate character transformation because both are affected by the shape of the transformation series rather than the character state distribution on a tree. Fits of transformations to a tree are better assessed by comparing the transformation to the cladogram character and the nearest neighbor network. Nearest neighbor networks are graphical representations of the nearest neighbor matrix. Transformations with the closest greatest number of matches between cladogram characters and the least complexity in the nearest neighbor network are preferred. These transformations are shown to make the fewest number of ad hoc statements and hence to be the most parsimonious. A means for obtaining cladogram characters and nearest neighbor matrices using a widely distributed microcomputer program is presented.     

A COMPUTER ASSISTED ANALYSIS OF THE RELATIONSHIPS OF THE HIGHER CATEGORIES OF TURTLES

Abstract— A character matrix of 39 characters for 14 supregeneric categories of living and extinct turtles was examined using PAUP 2.41 and 3.0L. The Branch and Bound algorithm found a single most parsimonious cladogram of 55 steps, consistency index of 0.709, retention index of 0.848 and a rescaled consistency index of 0.601. The cladogram is identical to that proposed by Gaffney and Meylan (1988). The Pleurodira and Cryptodira are each shown to be monophyletic and are supported by synapomorphies involving complex structures of the basicranium and adductor musculature. These synapomorphies are judged to be relatively well-tested homologies. A paraphyletic Cryptodira occurs in 18% of 38 equally parsimonious trees 57 steps in length, but these trees are based on characters, such as absence of pterygoid teeth, that are susceptible to homoplasy in amniotes. We re-iterate the notion that it is better to choose fewer, well-analysed characters than large numbers of poorly analysed characters.     

Phylogenetic relationships of Holarctic Teleiodini (Lepidoptera: Gelechiidae) based on analysis of morphological and molecular data

Abstract Phylogenetic relationships of 25 genera of Holarctic Teleiodini (Gelechiidae) are postulated based on morphology and molecular characters, including CO‐I, CO‐II, and 28S genes. The phylogenetic analysis of the morphology matrix yielded four equal most‐parsimonious trees (length 330 steps, CI = 0.36, RI = 0.55) and a strict consensus tree (length 335 steps, CI = 0.36, RI = 0.54) with one polytomy and one trichotomy. The phylogenetic analysis of the combined morphology and CO‐I + CO‐II + 28S matrices yielded two equally most‐parsimonious trees (length 1184 steps, CI = 0.50, RI = 0.42) and a strict consensus tree (length 1187 steps, CI = 0.50, RI = 0.42) that reinforced results from the morphological analysis and resolved the one polytomy present in the morphology consensus tree. Teleiodini are defined as a monophyletic clade with a Bremer support value greater than 5 in the consensus tree based on morphological and molecular data. Twenty‐three clades of genera are defined with Bremer support values provided. An analysis of larval host‐plant preferences based on the consensus tree for combined data indicates derivation of feeding on woody hosts from genera feeding on herbaceous hosts and a single origin of feeding on coniferous hosts. An area cladogram indicates five independent origins of Nearctic genera from Holarctic ancestors and one origin from a Palearctic genus.     

Morphological, palaeontological and molecular aspects of ichneumonoid phylogeny (Hymenoptera, Insecta)

Ichneumonoid phylogeny is revised on the basis of morphological, palaeontological and molecular evidence. The only previous formal cladistic study of the phylogeny of the families of the superfamily Ichneumonoidea made many assumptions about what families lower taxa belonged to and was based on a very limited set of characters, nearly all of which were uninformative at family level. We have subdivided both Ichneumonidae and Braconidae into major groups, investigated several new character systems, reinterpreted some characters, scored several character states for extinct taxa by examining impression fossils using environment chamber scanning electron microscopy, and included data for a significant new subfamily of Braconidae from Cretaceous amber of New Jersey. Sixteen different variants of the data set were each subjected to parsimony analysis without weighting and with successive approximations weighting employing both maximum and minimum values of both the retention and rescaled consistency indices. Each analysis resulted in one of seven different strict consensus trees. Consensus trees based on subsets of these trees, selected on the basis of the optimal character compatibility index (OCCI), resulted in an eighth distinct tree. All trees had the Braconidae monophyletic with the Trachypetinae as the basal clade, and also had a clade comprising various arrangements of Apozyginae, the Rhyssalinae group, Aphidiinae and 'other cyclostomes', but relationships among the remaining braconid groups varied between trees. Only one of the consensus trees had the Ichneumonidae (including Tanychorella ) monophyletic. The Eoichneumonidae + Tanychora are the sister group the Braconidae in two of the consensus trees. Paxylommatinae were basal in the clade comprising the Eoichneumonidae + Tanychora and the Braconidae. The preferred tree, based on the highest OCCI was used for interpreting character state transitions.     

菝葜科基于形态学证据的系统发育分析

对全世界范围分布的菝葜科Smilacaceae的79个代表种(包括了全部的属和组), 以分布于南美洲的Philesia Comm. ex Juss.和Lapageria Ruiz &; Pav.属为外类群, 选取包括花粉和染色体性状在内的47个广义的形态学性状进行了分支分类系统发育分析, 同时以表征分类的方法构建了距离树(NJ)辅助分析, 首次对世界分布的菝葜科各属间及属内的系统发育关系作了探讨。(1)Ripogonum与菝葜属Smilax +肖菝葜属Heterosmilax互为姐妹群, 但是距离较远, 支持将类菝葜属(新拟中文名)Ripogonum独立为科的观点; (2)肖菝葜属在菝葜科内处于较为进化的分支上, 并与菝葜属土茯苓组sect. Coilanthus的部分种组成一个具较高支持率(88%)的单系分支, 分析表明肖菝葜属并非是一个好属, 应归入菝葜属; (3)菝葜属6个组的划分大都没有得到支持, 只有东亚北美间断分布的草本菝葜组sect. Nemexia的单系得到很好的支持(93%); (4)分布于南美洲巴西的种类聚为一个单系类群, 表明它们可能有共同的起源, 但由于取样局限, 南美洲种类的系统地位有待进一步研究。     

Cladistic analysis of Simulium (Trichodagmia) and Simulium (Thyrsopelma) (Diptera: Simuliidae)

A cladistic analysis of Simulium ( Trichodagmia ) sensu Crosskey and Howard, using 34 morphological characters of larvae (6 characters), pupa (5) and adults (23), yields nine most parsimonious trees under equal weights (length 101 steps CI 0.49 RI 0.73). Successive weighting based on the maximal rescaled consistency index preferred one of the nine (31.37 steps CI 0.62 RI 0.87 total fit_con3= 235.8), which was also one of two trees found under implicit weights with concavity values of 3–6. The cladogram justifies the recognition of two subgenera. Simulium ( Trichodagmia ) sensu stricto (containing S. muiscorum, sumapazense, S. wygodzinskyorum, S. nigrimanum, S. chalcocoma, S. huairayacu and S. lahillei ) is supported by the branchial tip sclerotization and the presence of cibarial teeth, larval body tegument covered with lanceolate hairs, female with simple claw, and gonapophysis size. Simulium ( Thyrsopelma ) (containing S. scutistriatum, S. hirtipupa, S. orbitale, S. guianense, S. perplexum and S. itaunense ) is supported by the hypostomial teeth.     

Comparison of the Cladograms Produced by Li's Method and Farris' Method

In order to avoid producing many equally most parsimonious trees, Li (1990) developed a new cladistic method, the Median Elimination Series (MES), to construct a single cladogram for a given data set. However, we found that Li's method can produce more than one tree if two or more taxa have the same advancement index (which is the total number of apomorphies for a taxon in a given data set), because there is no objective method to decide which taxon should be connected first and different orders of connection can produce different trees. Li claimed that the result produced by his method did not apply the principle of simplicity (parsimony). Nevertheless, Zhang (1991) recognised that Li's method actually accepted the principle of parsimony. Here we demonstrated that Li's method also can produce the minimum-length trees. We conclude that Li's method could produce more than one tree and the tree(s) may be the minimum-length possible. However, the length of tree(s) depends on the order of connection of the taxa. The major problems in using Li's methodare discussed.     

Partitioned Bremer support and multiple trees

Partitioned Bremer support (PBS) is a valuable means of assessing congruence in combined data sets, but some aspects require clarification. When more than one equally parsimonious tree is found during the constrained search for trees lacking the node of interest, averaging PBS for each data set across these trees can conceal conflict, and PBS should ideally be examined for each constrained tree. Similarly, when multiple most parsimonious trees (MPTs) are generated during analysis of the combined data, PBS is usually calculated on the consensus tree. However, extra information can be obtained if PBS is calculated on each of the MPTs or even suboptimal trees.     

Trees and/or networks to display intraspecific DNA sequence variation?

Phylogenetic trees and networks are both used in the scientific literature to display DNA sequence variation at the intraspecific level. Should we rather use trees or networks? I argue that the process of inferring the most parsimonious genealogical relationships among a set of DNA sequences should be dissociated from the problem of displaying this information in a graph. A network graph is probably more appropriate than a strict consensus tree if many alternative, equally most parsimonious, genealogies are to be included. Within the maximum parsimony framework, current phylogenetic inference and network‐building algorithms are both unable to guarantee the finding of all most parsimonious (MP) connections. In fact, each approach can find MP connections that the other does not. Although it should be possible to improve at least the maximum parsimony approach, current implementations of these algorithms are such that it is advisable to use both approaches to increase the probability of finding all possible MP connections among a set of DNA sequences.     

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.     

Data decisiveness,data quality,and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences

We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.     

The basicranium of dicynodonts (Synapsida) and its use in phylogenetic analysis

Current phylogenetic hypotheses for the dicynodonts conflict, probably because the characters used, especially those of the jaws and facial region, show considerable convergence. Characters of the braincase and basipterygoid articulation of the Late Permian–Middle Triassic dicynodonts Diictodon , Dicynodon , Kingoria, Lystrosaurus , Rechnisaurus , and 14 other genera, may have phylogenetic value. Parsimony analysis and the character compatability permutation test suggest, at the highest possible confidence level, that the data set contains significant hierarchical structure, interpreted as a result of phylogeny. The most parsimonious tree broadly agrees with all recent hypotheses on the relationships among dicynodonts. However, it conflicts with the recent suggestion that Lystrosaurus is part of a clade of Middle–Late Triassic dicynodonts, but supports the basal position of Kingoria . The use of Eodicynodon as an outgroup does not perturb the parsimonious relationship of the included taxa. Topological constraints reveal that phylogenetic hypotheses based only on basicranial characters are not robust. Characters of the basipterygoid articulation and inner braincase have high consistency and retention indices, which suggests that the main evolutionary transformations in the dicynodont basicranium occurred within these structures.     

Seabird and louse coevolution: complex histories revealed by 12S rRNA sequences and reconciliation analyses

We investigated the coevolutionary history of seabirds (orders Procellariiformes and Sphenisciformes) and their lice (order Phthiraptera). Independent trees were produced for the seabirds (tree derived from 12S ribosomal RNA, isoenzyme, and behavioral data) and their lice (trees derived from 12S rRNA data). Brook's parsimony analysis (BPA) supported a general history of cospeciation (consistency index = 0.84, retention index = 0.81). We inferred that the homoplasy in the BPA was caused by one intrahost speciation, one potential host-switching, and eight or nine sorting events. Using reconciliation analysis, we quantified the cost of fitting the louse tree onto the seabird tree. The reconciled trees postulated one host-switching, nine cospeciation, three or four intrahost speciation, and 11 to 14 sorting events. The number of cospeciation events was significantly more than would be expected from chance alone (P < 0.01). The sequence data were used to test for rate heterogeneity for both seabirds and lice. Neither data set displayed significant rate heterogeneity. An examination of the codivergent nodes revealed that seabirds and lice have cospeciated synchronously and that lice have evolved at approximately 5.5 times the rate of seabirds. The degree of sequence divergence supported some of the postulated intrahost speciation events (e.g., Halipeurus predated the evolution of their present hosts). The sequence data also supported some of the postulated host-switching events. These results demonstrate the value of sequence data and reconciliation analyses in unraveling complex histories between hosts and their parasites.     

Systematics of New World Monkeys (Platyrrhini, Primates) Based on 16S Mitochondrial DNA Sequences: A Comparative Analysis of Different Weighting Methods in Cladistic Analysis

In order to investigate the effects of different weighting methods on a phylogeny reconstruction based on DNA sequences and to evaluate the phylogenetic information content of various secondary structures, a fragment of the large ribosomal mitochondrial gene (16S) was sequenced from 13 species of New World monkeys, three species of catarrhines, and Tarsius. The data were analyzed cladistically without weighting characters or changes, and with different weighting methods: a priori differential weights for transitions and transversions, two variants of dynamic weighting for each kind and direction of change, and successive approximations, using both the character consistency index (CI) and the rescaled consistency index (RC). The results were compared with published trees constructed from nuclear sequences of ε-globins and morphological characters by different authors. The result of the analysis of the mtDNA data set with successive approximations, using the RC as weighting function, was the closest to the topology on which all molecular and morphological trees concur. Other relationships were unique to this tree. "Loops" were the type of secondary structure that showed maximum variation in sequence length and sites with the lowest character CI and RC. A large number of sites within loops showed high values for these indices, however, which suggests that uniform downweighting of these regions represents a large loss of phylogenetic information. Successive weighting, which assigns a weight for each particular character, seems to be a desirable alternative to this practice. We propose a new variant of dynamic weighting, which we call homoplasy-correcting dynamic weighting, that like dynamic weighting, is applicable to any kind of sequence, coding or noncoding.     

Phylogeny of the tachyporine group subfamilies and 'basal' lineages of the Aleocharinae (Coleoptera: Staphylinidae) based on larval and adult characteristics

Abstract. This paper reports the conclusions of studies into the phylogeny of tachyporine group subfamilies and the ‘basal’ lineages of the subfamily Aleocharinae (Coleoptera: Staphylinidae) based on both larval and adult morphological data (133 adult characters, twenty-seven larval characters). Representatives of forty species of the tachyporine group were used in the analysis, including representatives of the Aleocharinae, Trichophyinae, Habrocerinae, Phloeocharinae, Olisthaerinae, and Tachyporinae. The Aleocharinae included representatives of the tribes Gymnusini, Deinopsini, Mesoporini, the ‘subfamily’ Trichopseniinae, and representatives of nine major tribes in the ‘higher’ Aleocharinae (Athetini, Hoplandriini, Falagriini, Lomechisini, Oxypodini, Aleocharini, Myllaenini, Homalotini, and Hypocyphtini). Analyses were performed first with adult characters alone and then with both larval and adult characters in a simultaneous analysis. The analysis based on adult characters produced eighty-five equally parsimonious trees (length = 499, consistency index = 42; retention index = 69). In the consensus tree, the Tachyporinae are not monophyletic, and the sister-group relationship between the Trichophyinae + Habrocerinae and the Aleocharinae is not resolved. The Aleocharinae are monophyletic, but, among the ‘basal’ Aleocharinae, the relationships of Gymnusini + Deinopsini, the Mesoporini, and the Trichopseniinae are unresolved. The combined adult and larval data, using Tachinus as the outgroup, produced six equally parsimonious trees (tree length = 588; consistency index = 43; retention index = 69). The strict consensus tree of the combined larval and adult data supports the following conclusions: (1) larval characters substantially stabilize the tree; (2) the subfamily Tachyporinae is not supported to be monophyletic; (3) the subfamilies Trichophyinae and Habrocerinae are sister groups, and together they are sister to the Aleocharinae; (4) the ‘basal’ Aleocharinae are not a monophyletic group, but the ‘higher’ Aleocharinae are monophyletic; (5) the sister group of the remaining Aleocharinae is a lineage made up of genera currently in the tribes Gymnusini and Deinopsini; (6) within the Gymnusini–Deinopsini lineage, the monophyly of the Gymnusini is weakly supported, but the monophyly of the Deinopsini is strongly supported; (7) the subfamily Trichopseniinae is strongly supported to be a member of the ‘basal’ Aleocharinae; (8) the Myllaenini are resolved well within the ‘higher’ Aleocharinae; (9) strong support for the monophyly of some tribes of ‘higher’ Aleocharinae suggests that morphological characters provide substantial phylogenetic signal for analysis of higher-level phylogeny of the Aleocharinae in spite of the preliminary nature of the analysis at this taxonomic level.     

POLYMORPHIC TAXA, MISSING VALUES AND CLADISTIC ANALYSIS

Abstract Missing values have been used in cladistic analyses when data are unavailable, inapplicable or sometimes when character states are variable within terminal taxa. The practice of scoring taxa as having "missing values" for polymorphic characters introduces errors into the calculation of cladogram lengths and consistency indices because some character change is hidden within terminals. Because these hidden character steps are not counted, the set of most parsimonious cladograms may differ from those that would be found if polymorphic taxa had been broken into monomorphic subunits. In some cases, the trees found when polymorphisms are scored as missing values may not include any of the most parsimonious trees found when the data are scored properly. Additionally, in some cases, polymorphic taxa may be found to be polyphyletic when broken into monomorphic subunits; this is undetected when polymorphisms are treated as missing. Because of these problems, terminal units in cladistic analysis should be based on unique, fixed combinations of characters. Polymorphic taxa should be subdivided into subunits that are monomorphic for each character used in the analysis. Disregarding errors in topology, the additional hidden steps in a cladogram in which polymorphisms are scored as missing can be calculated by a simple formula, based on the observation that if it is assumed that polymorphic terminals include all combinations of character states, 2 ^p − 1 additional steps are required for each taxon in which p polymorphic binary characters are scored as missing values. Thus, when several polymorphisms are scored as missing in the same taxon, very large errors can be introduced into the calculation of tree length.     

DOES IMBALANCE IN PHYLOGENIES REFLECT ONLY BIAS?

Phylogenetic tree imbalance was originally believed to indicate differences in evolutionary rates within trees, but other sources of imbalance have been identified, such as tree incompleteness and low quality of the data. To examine the effect of data quality, I calculated Colless's index for 69 recent complete phylogenies. On average, these phylogenies were more unbalanced than phylogenies generated by the equal rates Markov (ERM) model. I tried Mooers's (1995) method to correct for tree size, but his measure appeared to become dependent on tree size when there are large trees (i.e., > 14 tips) in a collection. Instead I corrected for tree size by taking the difference between Colless's index of observed trees and the ERM model expectation for a tree of the same size. The balance measure thus obtained did not correlate significantly to consistency and retention indices as indicators of data quality. It was also independent of the factors kingdom (plants and animals) and taxon level at the tips and type of data (molecular, morphological, and combined).     

THE PHYLOGENETIC RELATIONSHIPS AMONG REQUIEM AND HAMMERHEAD SHARKS: INFERRING PHYLOGENY WHEN THOUSANDS OF EQUALLY MOST PARSIMONIOUS TREES RESULT

Abstract— Protein variation among 37 species of carcharhiniform sharks was examined at 17 presumed loci. Evolutionary trees were inferred from these data using both cladistic character and a distance Wagner analysis. Initial cladistic character analysis resulted in more than 30 000 equally parsimonious tree arrangements. Randomization tests designed to evaluate the phylogenetic information content of the data suggest the data are highly significantly different from random in spite of the large number of parsimonious trees produced. Different starting seed trees were found to influence the kind of tree topologies discovered by the heuristic branch swapping algorithm used. The trees generated during the early phases of branch swapping on a single seed tree were found to be topologically similar to those generated throughout the course of branch swapping. Successive weighting increased the frequency and the consistency with which certain clades were found during the course of branch swapping, causing the semi-strict consensus to be more resolved. Successive weighting also appeared resilient to the bias associated with the choice of initial seed tree causing analyses seeded with different trees to converge on identical final character weights and the same semi-strict consensus tree.
The summary cladistic character analysis and the distance Wagner analysis both support the monophyly of two major clades, the genus Rhizoprionodon and the genus Sphyrna. . The distance Wagner analysis also supports the monophyly of the genus Carcharhinus . However, the cladistic analysis suggests that Carcharhinus is a paraphyletic group that includes the blue shark Prionace glauca .