Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living bony-tongue fishes (Osteoglossomorpha: Teleostei)

Fishes of the Superorder Osteoglossomorpha (the "bonytongues") constitute a morphologically heterogeneous group of basal teleosts, including highly derived subgroups such as African electric fishes, the African butterfly fish, and Old World knifefishes. Lack of consensus among hypotheses of osteoglossomorph relationships advanced during the past 30 years may be due in part to the difficulty of identifying shared derived characters among the morphologically differentiated extant families of this group. In this study, we present a novel phylogenetic hypothesis for this group, based on the analysis of more than 4000 characters from five molecular markers (the mitochondrial cytochrome b, 12S and 16S rRNA genes, and the nuclear genes RAG2 and MLL). Our taxonomic sampling includes one representative of each extant non-mormyrid osteoglossomorph genus, one representative for the monophyletic family Mormyridae, and four outgroup taxa within the basal Teleostei. Maximum parsimony analysis of combined and equally weighted characters from the five molecular markers and Bayesian analysis provide a single, well-supported, hypothesis of osteoglossomorph interrelationships and show the group to be monophyletic. The tree topology is the following: (Hiodon alosoides, (Pantodon buchholzi, (((Osteoglossum bicirrhosum, Scleropages sp.), (Arapaima gigas, Heterotis niloticus)), ((Gymnarchus niloticus, Ivindomyrus opdenboschi), ((Notopterus notopterus, Chitala ornata), (Xenomystus nigri, Papyrocranus afer)))))). We compare our results with previously published phylogenetic hypotheses based on morpho-anatomical data. Additionally, we explore the consequences of the long terminal branch length for the taxon Pantodon buchholzi in our phylogenetic reconstruction and we use the obtained phylogenetic tree to reconstruct the evolutionary history of electroreception in the Notopteroidei.     

Evolutionary relationships among parvoviruses: virus-host coevolution among autonomous primate parvoviruses and links between adeno-associated and avian parvoviruses

The current classification of parvoviruses is based on virus host range and helper virus dependence, while little data on evolutionary relationships among viruses are available. We identified and analyzed 472 sequences of parvoviruses, among which there were (virtually) full-length genomes of all 41 viruses currently recognized as individual species within the family Parvoviridae. Our phylogenetic analysis of full-length genomes as well as open reading frames distinguished three evolutionary groups of parvoviruses from vertebrates: (i) the human helper-dependent adeno-associated virus (AAV) serotypes 1 to 6 and the autonomous avian parvoviruses; (ii) the bovine, chipmunk, and autonomous primate parvoviruses, including human viruses B19 and V9; and (iii) the parvoviruses from rodents (except for chipmunks), carnivores, and pigs. Each of these three evolutionary groups could be further subdivided, reflecting both virus-host coevolution and multiple cross-species transmissions in the evolutionary history of parvoviruses. No parvoviruses from invertebrates clustered with vertebrate parvoviruses. Our analysis provided evidence for negative selection among parvoviruses, the independent evolution of their genes, and recombination among parvoviruses from rodents. The topology of the phylogenetic tree of autonomous human and simian parvoviruses matched exactly the topology of the primate family tree, as based on the analysis of primate mitochondrial DNA. Viruses belonging to the AAV group were not evolutionarily linked to other primate parvoviruses but were linked to the parvoviruses of birds. The two lineages of human parvoviruses may have resulted from independent ancient zoonotic infections. Our results provide an argument for reclassification of Parvovirinae based on evolutionary relationships among viruses.     

石山苣苔属(苦苣苔科)花形态演化及分类学意义

石山苣苔属(苦苣苔科)约30种,主要分布于我国南部的石灰岩地区.目前该属已知物种数虽少但花形态极其多样,是该科中分类最为困难的类群之一.基于分子证据,其它8个属中花形态迥异的一些物种被并入石山苣苔属.然而,该属花形态的演化趋势缺乏系统性的研究,传统分类对属的界定与分子系统学研究结果相矛盾的原因,以及是否有形态特征支持新界定的石山苣苔属还不清楚.该研究中,总共编码了19种石山苣苔属植物和9种报春苣苔属植物的35个形态特征,其中包括26个花部形态特征,在分子系统树上追踪了它们的演化路径.结果表明:无论属内还是属间,多数花部形态特征,尤其以往属的分类界定特征,在演化过程中变化频繁且发生了高度同塑性演化,这是导致传统形态分类不自然的关键因素.此外,在观察研究的所有特征中,花丝和柱头的差异可能在石山苣苔属植物共同祖先中经历了演变,或可用于区分石山苣苔属与其姐妹报春苣苔属的大多数种类.因此,在苦苣苔科植物的分类学研究中应当慎用这些花部性状作为分类依据,而且应对形态特征进行广泛地观察研究,在密集的取样和分辨率更高、更可靠的系统树上追踪它们的演化规律.更为重要的是,需要进一步研究导致复杂形态性状演化的内在分子调控机理和外在的自然选择动力,最终更加深入地理解石山苣苔属等典型喀斯特植物的演化过程和机理.     

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account nonindependence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty, but approaches accounting for all of them are less common. Here, we show how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well-known phylogenetic generalized least squares (PGLS) framework. This Bayesian formulation allows uncertainty about phylogeny, evolutionary regimes, or other statistical parameters to be taken into account for studies as simple as testing for coevolution in two traits or as complex as testing whether bursts of phenotypic change are associated with evolutionary shifts in intertrait correlations. A mixture of validation approaches indicates that the approach has good inferential properties and predictive performance. We provide suggestions for implementation and show its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.     

Is morphology telling the truth about the evolution of the species rich genus Peperomia (Piperaceae)?

Peperomia is with approximately 1,600 species one of the species rich angiosperm genera. Several characters on which current infrageneric classifications are based are influenced by parallel evolution. A well-resolved molecular backbone phylogeny of the genus is needed to address evolutionary questions about morphological traits. Based on separate and combined analyses of a morphological data set and three molecular data sets, phylogenetic relationships within Peperomia are investigated with respect to character evolution. The resulting trees from different datasets are highly congruent. Morphological characters are mapped on a combined molecular tree, visualizing the contrast between previously used homoplastic characters and some newly observed characters, that can be used to delimit monophyletic groups. Length mutational events of the chloroplast dataset are coded and plotted on the respective tree, to test if indels support alternative hypothesis of relationships found in the nuclear datasets as well as the overall performance of indels compared with substitutional mutations. Our findings indicate that length distribution of indels is highest among five and six bp events. Autapomorphic and synapomorphic length mutations are most frequent in both insertions and deletions and are also more frequent independent of the length of the mutation. Concluding, independent of the length, mutations are of phylogenetic importance and should not be disregarded. None of the homoplastic indels turn into synapomorphic indels, supporting the different topology of the nrDNA tree but indicate areas of molecular evolution in favour of length mutations resulting in independent events.     

Strongest Evidence: Maximum Apparent Phylogenetic Signal as a New Cladistic Optimality Criterion

A new method for phylogenetic inference, Strongest Evidence (SE), is described. In this method, a character's support for a phylogenetic hypothesis, its apparent phylogenetic signal, is greatest when the amount of implied homoplasy is most remarkably small given background knowledge alone. Because evolutionary rates are not assumed to be slow, background expectations for character length can be derived through modeling complete dissociation between branching pattern and character state assignments. As in unweighted parsimony, SE holds that fewer required evolutionary steps in a character indicates stronger support for a tree. However, in SE, the relationship between steps and support differs by unlabeled tree topology and character state distribution. Strongest evidence is contrasted in detail with both unweighted parsimony and Goloboff's method of implied weights. An iterative process is suggested for incrementally resolving a phylogenetic hypothesis while conducting cladistic analyses at increasingly local levels.     

Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes

Butterflies in the nymphalid subfamily Ithomiinae are brightly colored and involved in mimicry. Here we present a phylogenetic hypothesis for 23 of the 24 species in the genus Ithomia, based on seven different gene regions, representing 5 linkage groups and 4469 bp. We sequenced varying length regions of the following genes: (1) elongation factor 1alpha (Ef1alpha; 1028 bp); (2) tektin (tektin; 715 bp); (3) wingless (wg; 405 bp); (4) ribosomal protein L5 (RpL5; 722 bp, exons 1, 2, 3, and introns 1 and 2); and (5) mitochondrial cytochrome oxidase I, II (Co1 and Co2 and intervening leucine tRNA; 1599 bp). The results show incongruence between some genetic loci, although when alternate topologies are compared statistically it was generally true that one topology was supported by a majority of loci sampled. This highlights the need to sample widely across the genome in order to obtain a well-supported phylogenetic hypothesis. A combined evidence topology is presented based on a Bayesian analysis of all the gene regions, except the fast-evolving RpL5. The resulting hypothesis is concordant with the most probable relationships determined from our topological comparisons, although in some parts of the tree relationships remain weakly supported. The tree suggests diversification has largely occurred within biogeographic regions such as Central America, the Amazon, the southern and northern Andes, with only occasional dispersal (or vicariance) between such regions. This phylogenetic hypothesis can now be used to investigate patterns of diversification across the genus, such as the potential role of color pattern changes in speciation.     

Evolution of Picornaviridae: An examination of phylogenetic relationships and cophylogeny

Picornaviruses are responsible for some of the most common and debilitating illnesses affecting humans and animals worldwide. To extend our knowledge of the evolution of picornaviruses and their molecular epidemiology, phylogenetic relationships among 11 genera and the unassigned seal picornavirus type 1 were estimated from the conserved proteins 2C, 3C^pro, and 3D^pol. Each gene was analyzed separately and as a combined dataset. Different tree topologies were recovered from each gene. However, their sequences were determined to be combinable based on our finding of no recombination among genera and failing to reject the hypothesis of homogeneity among datasets using ILD tests. The combined data tree topology was identical to the 3D^pol gene tree; a topology largely consistent with previous phylogenetic hypotheses based on 3D^pol and the coding genome. Phylogenetic trees estimated from six phenotypic characters were not congruent with those recovered from molecular datasets; further supporting the hypothesis that viral phenotypes are highly plastic. Finally, we tested the hypothesis of host–virus cophylogeny. Both global and individual tests of the relationships between host and virus trees failed to detect a significant association. These results emphasize the importance of horizontal transmission among host species for picornavirus diversification rather than vertical transmission accompanying speciation.     

Nuclear and Nucleomorph SSU rDNA Phylogeny in the Cryptophyta and the Evolution of Cryptophyte Diversity

The plastid-bearing members of the Cryptophyta contain two functional eukaryotic genomes of different phylogenetic origin, residing in the nucleus and in the nucleomorph, respectively. These widespread and diverse protists thus offer a unique opportunity to study the coevolution of two different eukaryotic genomes within one group of organisms. In this study, the SSU rRNA genes of both genomes were PCR-amplified with specific primers and phylogenetic analyses were performed on different data sets using different evolutionary models. The results show that the composition of the principal clades obtained from the phylogenetic analyses of both genes was largely congruent, but striking differences in evolutionary rates were observed. These affected the topologies of the nuclear and nucleomorph phylogenies differently, resulting in long-branch attraction artifacts when simple evolutionary models were applied. Deletion of long-branch taxa stabilized the internal branching order in both phylogenies and resulted in a completely resolved topology in the nucleomorph phylogeny. A comparison of the tree topologies derived from SSU rDNA sequences with characters previously used in cryptophyte systematics revealed that the biliprotein type was congruent, but the type of inner periplast component incongruent, with the molecular trees. The latter is indicative of a hidden cellular dimorphism (cells with two periplast types present in a single clonal strain) of presumably widespread occurrence throughout cryptophyte diversity, which, in consequence, has far-reaching implications for cryptophyte systematics as it is practiced today.     

The phylogeny of early eureptiles: comparing parsimony and Bayesian approaches in the investigation of a basal fossil clade

For the first time the phylogenetic relationships of early eureptiles, consisting of captorhinids, diapsids, and protorothyridids, are investigated in a modern phylogenetic context using both parsimony and Bayesian approaches. Ninety parsimony-informative characters and 25 taxa were included in the analyses. The Bayesian analysis was run with and without a gamma-shape parameter allowing for variable rates across characters. In addition, we ran two more Bayesian analyses that included 42 autapomorphies and thus parsimony-uninformative characters in order to test the effect of variable branch lengths. The different analyses largely converged to the same topology, suggesting that the "protorothyridid" Coelostegus is the sister taxon of all other eureptiles and that the remaining "protorothyridids" are paraphyletic. Also, there is a close relationship between diapsids and Anthracodromeus, Cephalerpeton, and Protorothyris, a grouping of Thuringothyris with captorhinids, and a variable position of the "protorothyridids" Brouffia, Hylonomus, and Paleothyris. The lack of resolution in some parts of the tree might be due to "hard polytomies" and short divergence times between the respective taxa. The tree topology is consistent with the hypothesis that the temporal fenestrations of diapsid reptiles appear to be the consequence of a more lightly built skeleton, indicating a significant ecological shift in the early stages of diapsid evolution. Bayesian analysis is a very useful additional approach in studies of fossil taxa in which more traditional statistical support like the bootstrap is often weak. However, the exclusive use of the Mk model appears suitable only if autapomorphic characters are included, whereas the Mk+gamma model performed well with or without autapomorphies.     

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.     

Missing data,clade support and “reticulation”: the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re‐examined

Kozak et al. (2015, Syst. Biol., 64: 505) portrayed the inference of evolutionary history among Heliconius and allied butterfly genera as a particularly difficult problem for systematics due to prevalent gene conflict caused by interspecific reticulation. To control for this, Kozak et al. conducted a series of multispecies coalescent phylogenetic analyses that they claimed revealed pervasive conflict among markers, but ultimately chose as their preferred hypothesis a phylogenetic tree generated by the traditional supermatrix approach. Intrigued by this seemingly contradictory set of conclusions, we conducted further analyses focusing on two prevalent aspects of the data set: missing data and the uneven contribution of phylogenetic signal among markers. Here, we demonstrate that Kozak et al. overstated their findings of reticulation and that evidence of gene‐tree conflict is largely lacking. The distribution of intrinsic homoplasy and incongruence homoplasy in their data set does not follow the pattern expected if phylogenetic history had been obscured by pervasive horizontal gene flow; in fact, noise within individual gene partitions is ten times higher than the incongruence among gene partitions. We show that the patterns explained by Kozak et al. as a result of reticulation can be accounted for by missing data and homoplasy. We also find that although the preferred topology is resilient to missing data, measures of support are sensitive to, and strongly eroded by too many empty cells in the data matrix. Perhaps more importantly, we show that when some taxa are missing almost all characters, adding more genes to the data set provides little or no increase in support for the tree.     

Phylogenetic methodology for detecting protein interactions

Detecting protein-protein interactions and assigning proteins to functional complexes are key challenges of modern biology. The rise of genomics has lead to evidence that correlated patterns of presence/absence and/or fusing of proteins in any organism suggest these proteins interact. Unfortunately, methods based on such data work best with divergent genomes, whereas major sequencing efforts in vertebrates, for example, are yielding alignments of the same set of proteins sampled from the same set of taxa (species). Using vertebrate mitochondrial genomes to illustrate a novel method, we associate proteins based on vectors of their evolutionary tree edge (branch or internode) lengths. This approach is based on the expectation that molecular coevolution is greatest between proteins that interact in some way. Mitochondrial DNA-encoded proteins are associated into groups largely consistent with the complexes they come from. This association is apparently not due to the tree structure or mutation processes, leaving coevolution as the best explanation. We show that it is important that the tree used to derive the edge-length vector is estimated accurately in terms of both topology and edge lengths. Although more complex substitution models reduce systematic error, they also inflate stochastic error. This makes the use of less complex substitution models preferable in some circumstances. We describe a method to estimate correlations of pairwise evolutionary distances, which adjusts for non-independent correlations due to shared evolutionary history. Associations of proteins based on their edge-length vectors are visualized and assessed using a variety of hierarchical clustering and multidimensional scaling methods. New formula for estimating the fit of data to model, including the average percent standard deviation of distances on least squares trees, are presented. Use of edge-length vectors is compared and contrasted with correlated distance methods, correlated rates methods, and site-specific evidence of coevolution.     

Is Psammophily an Evolutionary Dead End? A Phylogenetic Test in the Genus Willemia (Collembola: Hypogastruridae)

The law of the unspecialized states that specialized taxa have evolved from more generalized ancestors. Moreover, it is usually assumed that ecological specialization is irreversible and hence leads to extinction. This study aims to test these assumptions using a phylogenetic framework in a case study within the springtail genus Willemia and its diverse life habits. This genus is represented mostly by loam-dwelling species (generalized condition), but some species are psammophilous, living in sandy habitats (specialized condition). Fifty-two morphological characters were examined in 34 of the 36 species of the genus and in three outgroups. The cladistic analysis yielded two most parsimonious trees (tree length 124 steps; consistency index 0.56; retention index 0.86). The evolution of psammophily versus loam-confined life is compared to the cladogram: unexpectedly, psammophily is not an evolutionary innovation that occurred once in a monophyletic group; the evolutionary scenario that parsimoniously fits the phylogeny suggests that psammophily is ancestral to the genus Willemia and reversed twice to loam-confined life. These results demonstrate that habitat generalists can evolve from habitat specialists and therefore that habitat specializations are not necessarily an evolutionary dead end. Many other seemingly specialized characters may be shown to be equally malleable.     

ACCURACY OF ESTIMATED PHYLOGENIES: EFFECTS OF TREE TOPOLOGY AND EVOLUTIONARY MODEL

A simulation study was carried out to investigate the relative importance of tree topology (both balance and stemminess), evolutionary rates (constant, varying among characters, and varying among lineages), and evolutionary models in determining the accuracy with which phylogenetic trees can be estimated. The three evolutionary context models were phyletic (characters can change at each simulated time step), speciational (changes are possible only at the time of speciation into two daughter lineages), and punctuational (changes occur at the time of speciation but only in one of the daughter lineages). UPGMA clustering and maximum parsimony (“Wagner trees”) methods for estimating phylogenies were compared. All trees were based on eight recent OTUs. The three evolutionary context models were found to have the largest influence on accuracy of estimates by both methods. The next most important effect was that of the stemminess × context interaction. Maximum parsimony and UPGMA performed worst under the punctuational models. Under the phyletic model, trees with high stemminess values could be estimated more accurately and balanced trees were slightly easier to estimate than unbalanced ones. Overall, maximum parsimony yielded more accurate trees than UPGMA—but that was expected for these simulations since many more characters than OTUs were used. Our results suggest that the great majority of estimated phylogenetic trees are likely to be quite inaccurate; they underscore the inappropriateness of characterizing current phylogenetic methods as being for reconstruction rather than for estimation.     

DOLLO'S LAW AND THE IRREVERSIBILITY OF DIGIT LOSS IN BACHIA

Several recent studies conclude that exceptions to Dollo's law are more common than used to be thought. If the claims are true this would change our view on the role of developmental constraints in the evolution of body plans. One study claims the reevolution of lost digits in the lizard genus Bachia ( Kohlsdorf and Wagner 2006 ). We evaluate this claim. We conclude that the proposed molecular phylogenetic tree is in conflict with evolutionary mechanisms concerning the biogeography of lizards and with morphology‐based phylogenies. A reanalysis of the molecular data does not support the topology of the published tree. Furthermore, two implicit assumptions, that digit numbers are fixed and that polydactyly evolves independently from other characters, are incorrect. We conclude that there is no convincing support for reevolution of digits in Bachia. We discuss our findings in the light of the current evidence for the reversal of losses of complex traits. We conclude that in metazoans, exceptions to Dollo's law are mainly found among meristic traits that originate relatively late during embryogenesis, when developmental systems are more compartmentalized. Finally, our study shows that phylogenetic analyses should incorporate evolutionary mechanisms including constraints, variation, and selection, not only for correct phylogenetic reconstruction, but also for correct evolutionary inference.     

Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration

Kluge's (2001, Syst. Biol. 50:322-330) continued arguments that phylogenetic methods based on the statistical principle of likelihood are incompatible with the philosophy of science described by Karl Popper are based on false premises related to Kluge's misrepresentations of Popper's philosophy. Contrary to Kluge's conjectures, likelihood methods are not inherently verificationist; they do not treat every instance of a hypothesis as confirmation of that hypothesis. The historical nature of phylogeny does not preclude phylogenetic hypotheses from being evaluated using the probability of evidence. The low absolute probabilities of hypotheses are irrelevant to the correct interpretation of Popper's concept termed degree of corroboration, which is defined entirely in terms of relative probabilities. Popper did not advocate minimizing background knowledge; in any case, the background knowledge of both parsimony and likelihood methods consists of the general assumption of descent with modification and additional assumptions that are deterministic, concerning which tree is considered most highly corroborated. Although parsimony methods do not assume (in the sense of entailing) that homoplasy is rare, they do assume (in the sense of requiring to obtain a correct phylogenetic inference) certain things about patterns of homoplasy. Both parsimony and likelihood methods assume (in the sense of implying by the manner in which they operate) various things about evolutionary processes, although violation of those assumptions does not always cause the methods to yield incorrect phylogenetic inferences. Test severity is increased by sampling additional relevant characters rather than by character reanalysis, although either interpretation is compatible with the use of phylogenetic likelihood methods. Neither parsimony nor likelihood methods assess test severity (critical evidence) when used to identify a most highly corroborated tree(s) based on a single method or model and a single body of data; however, both classes of methods can be used to perform severe tests. The assumption of descent with modification is insufficient background knowledge to justify cladistic parsimony as a method for assessing degree of corroboration. Invoking equivalency between parsimony methods and likelihood models that assume no common mechanism emphasizes the necessity of additional assumptions, at least some of which are probabilistic in nature. Incongruent characters do not qualify as falsifiers of phylogenetic hypotheses except under extremely unrealistic evolutionary models; therefore, justifications of parsimony methods as falsificationist based on the idea that they minimize the ad hoc dismissal of falsifiers are questionable. Probabilistic concepts such as degree of corroboration and likelihood provide a more appropriate framework for understanding how phylogenetics conforms with Popper's philosophy of science. Likelihood ratio tests do not assume what is at issue but instead are methods for testing hypotheses according to an accepted standard of statistical significance and for incorporating considerations about test severity. These tests are fundamentally similar to Popper's degree of corroboration in being based on the relationship between the probability of the evidence e in the presence versus absence of the hypothesis h, i.e., between p(e|hb) and p(e|b), where b is the background knowledge. Both parsimony and likelihood methods are inductive in that their inferences (particular trees) contain more information than (and therefore do not follow necessarily from) the observations upon which they are based; however, both are deductive in that their conclusions (tree lengths and likelihoods) follow necessarily from their premises (particular trees, observed character state distributions, and evolutionary models). For these and other reasons, phylogenetic likelihood methods are highly compatible with Karl Popper's philosophy of science and offer several advantages over parsimony methods in this context.     

EVOLUTIONARY CHARACTER ANALYSIS: TRACING CHARACTER CHANGE ON A CLADOGRAM

Abstract— There has been little formal discussion concerning character analysis in cladistics, even though characters and their character state trees are central to phylogenetic analyses. We refer to this field as Evolutionary Character Analysis. This paper defines the components of evolutionary character analysis: character state trees, transmodal characters, cladogram characters, attribute and character phylogenies; and the use of these components in phylogenetic inference and evolutionary studies. Character state trees and their effect on cladogram construction are discussed. A new method for numerically coding complex character state trees is described that further reduces the number of variables required to describe them. This method, ordinal coding, reduces the size of data matrices, and facilitates retrieval of state codes. This paper advocates the use of both biological evidence and evidence internal to the cladogram itself to construct character state trees (CSTs). We discuss general models of character evolution (morphocline analysis, Fitch minimum mutation model, etc.) and their role in forming CSTs. Character state trees formed with theories of character evolution are referred to as transmodal characters. These transmodal characters are contrasted with cladogram characters (Mickevich, 1982), and the place of each in a phylogenetic analysis is discussed. The method for determining cladogram characters is detailed with more complicated examples than found in previous publications. We advocate testing transmodal characters by comparing them with the resultant cladogram characters. This comparison involves transformation series analysis (TSA; Mickevich, 1982) which is viewed as an extension of reciprocal illumination. The TSA procedure and its place in hypothesis testing are reviewed. Tracing the evolution of characters interests both systematists and non-systematists alike. When character state trees (transmodal characters) are optimized on pre-existing phylogenies, character phylogenies and attribute phylogenies result. Attributes are defined as a feature that may or may not be homologous (i.e., ecological categories, plant hosts, etc.). We provide two illustrations of this approach, one involving the evolution of the anuran ear and another involving the coevolution of the butterfly Heliconius and its hostplants. Finally, the components of phylogenetic character analysis can be used to test more general evolutionary theories such as the biogenetic law and vicariance biogeography.