Three-taxon Analysis Research Articles

Comparative biogeography of North American turtle faunas: Neogene regionalization

North America harbors substantial species diversity in nonmarineturtles (includes tortoises and terrapins), much of which arose in the Neogene Period (Miocene and Pliocene epochs) within Kinosternon, Emydinae, Trachemys, Pseudemys, Graptemys, and Gopherus. This diversity is distributed among 16 biogeographical provinces, but natural, hierarchical relations among provinces are unresolved. We used three-item analysis to identify such relations among provinces for these clades, following a recent, relatively complete phylogenetic reconstruction. The final three-item analysis identified 53,353 taxon‐area cladograms — free of paralogy and multiple areas on a single branch. The final intersection tree has a retention index of 73.6% and a completeness index of 75.4%, both indicating moderately strong congruence in patterns among turtle clades. All six turtle clades support some nodes on the intersection tree, which is divided into eastern and western forks. The crown group on the eastern fork includes four provinces almost entirely east of the Mississippi River drainage, whereas the western fork is split into wet tropics and aridlands sub-forks. The east-west transition zone spans the Mississippi River drainage and Great Plains. Our summary of divergence estimates and geological history suggests that although phylogenetic synchrony existed between select taxa, there was general asynchrony because provincial turtle faunas developed over an extended period (Neogene). Temperature-sensitive distributions of various taxa responded to climatic cycles by expanding during periods of warming, but contracting during periods of cooling. Grassland expansion and geomorphic change in the Neogene created provincial boundaries that, although sometimes crossed under favorable climates, more commonly acted as dispersal barriers. Despite asynchrony in faunal assembly, existence of shared patterns reveals natural relations among provinces, producing a regionalization for North American turtles, useful for understanding their evolution as well as the biogeography of North America.

Revealing Evolutionary Patterns Behind Homogeneity: the Case of the Palaeolithic Assemblages from Notarchirico (Southern Italy)

Notarchirico is at a nodal point in time and space for understanding the settlement of Europe in terms of migration or in situ evolution. Former technological analyses have not shown significant differences between the different lithic assemblages at Notarchirico. Our approach here is to produce a phylogenetic analysis of the lithic assemblages taken as the terminal of the analysis and interpreted as cultural units. In the cladistic framework, characters are hypotheses of relationships between lithic assemblages, and homologies are hypotheses of relationships between lithic objects: cores, flakes, nodules. To effectively grasp informative lithic innovations in the assemblages, we formalise cladistic hypotheses as hierarchical characters in the framework of three-item analysis and propose a new algorithm to remove the high number of repeated terminals among trees inherent to a cladistic analysis of assemblages. Beyond the classic distinction of the presence or absence of bifaces, our analysis of the five Notarchirico layers, dated between 670 and 700 ka, highlights a well-supported cladogram grounded on complex hierarchical characters on lithic artefacts. This cladogram shows a paralogy event between the flake-free layer H, representing short-term occupancy, and the other layers representing long-term settlements. The resulting cladogram shows that relationships between lithic assemblages at Notarchirico do not follow the stratigraphy. Moreover, the Notarchirico lithic assemblages cannot be explained in an entirely local way, but seem to be part of a more complex European history.

Revision of the Cretaceous rudist genus Sellaea (Bivalvia, Hippuritida) with new insights on American forms: Phylogenetic and biogeographic implications

Sellaea is a key genus for understanding the expansion of rudists in the middle Cretaceous. Its incursion into the Americas in the Albian is open to taxonomic debate, as several researchers have hypothesised that the American Sellaea belongs to a new genus. A taxonomic revision with analysis of new material from the Edwards Formation (Texas, USA) coupled with a cladistic analysis using three-taxon analysis allows us to redefine the genus Sellaea. The phylogeny reveals two distinct endemic groups, one belonging to the Mediterranean province, and one to the Caribbean province. However, the involved synapomorphies, related to the left valve posterior cavity, the shell margin, and the outline, are not sufficient to create a new genus. The character related to pallial canals is the only one to be homoplastic in the phylogeny of Sellaea. The presence of canals is therefore a variable character state within the genus. The genus is redefined accordingly, allowing the relocation of several species originally assigned to Caprotina, including species that lack pallial canals and species with unknown right valves. Sellaea minuta is the only species retained over the four Sellaea described from the Americas. The redefined genus Sellaea is Albian-Cenomanian in extent, with the incursion of a single species into North America in the Albian.

A new cladistic insight on comparative anatomy and phylogeny of rudists (Bivalvia, Hippuritida)

The phylogenetic history of rudist bivalves is reviewed using a cladistic analysis based on 41 morphological shell characters and a new topology is proposed. A novel approach to rudist comparative anatomy has enabled the mapping of homologous zones. We highlight that ‘pallial canals’ can be homologous to four specific cavities that have merged during rudist evolution. The characters of the myophores and muscle insertions have also been reappraised using a hierarchical scheme. We formalize, for the first time, the complex diversification of rudist myophores by constructing tree-like characters that can contain up to six informative states for each of the four myophores. All characters have been coded as independent features. This has enabled the identification of different evolutionary rates of change between left and right valves and allows the recognition of the various morphoanatomic responses of one valve to the structural changes of the other. All characters have been coded in hierarchies and analysed in three-taxon analysis. Taxonomic sampling composed of two species per family allows an exhaustive monophyly test of all families of the suborder Hippuritidina. Only the families Polyconitidae, Plagioptychidae, Radiolitidae and Hippuritidae are found to be monophyletic. The two superfamilies are both found to be polyphyletic. The Hippuritidae is found to be the sister group of the Radiolitidae. Pachytraga is found as the sister group of all the rudists with pallial canals except Sellaea. Two evolutionary radiations in rudists are dated, using the cladistic concept of temporal hierarchy, to the Hauterivian + and the Albian+.

RNA consensus structures for inferring green algal phylogeny: A three-taxon analysis for Golenkinia/Jenufa, Sphaeropleales and Volvocales (Chlorophyta, Chlorophyceae)

Background and Aims: Order please! was a recently published, very nice and apt title for a persistent problem in green algae phylogenetics. The green algal class Chlorophyceae comprises two clades (SV and OCC) made up of five orders (Sphaeropleales, Volvocales, Oedogoniales, Chaetopeltidales and Chaetophorales). A variety of data and methods have shown that one further group (Golenkinia+Jenufa) cannot be unambiguously placed among the five orders. In addition, concerning Sphaeropleaceae and/or Treubarinia the monophyly of Sphaeropleales and Volvocales remain unresolved. Methods: IUPAC (International Union of Pure and Applied Chemistry) encoded consensus sequences for different 18S rDNA data sets as well as corresponding 18S rDNA consensus structures were assembled for Sphaeropleales, Volvocales (with or without Treubarinia) and a Golenkinia+Jenufa assemblage to independently infer phylogenetic relationships in a three-taxon analysis. Using a known template structure, individual 18S rDNA secondary structures were predicted by homology modelling. Sequences and their individual secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, or unpaired), were simultaneously aligned; consensus structures and IUPAC encoded consensus sequences were read out from the different sequence-structure alignments. Key Results: In contrast to previous studies using 18S rDNA data, results of this study corroborate chloroplast data and strongly support a sister group relationship between Golenkinia+Jenufa and the Sphaeropleales. The Golenkinia+Jenufa assemblage shows 330 matches to the Sphaeropleales (sequence-structure consensus) but only 214 matches to the Volvocales (sequence-structure consensus). Phylogenetically informative nucleotides are highlighted and visualized in their structural context taking into account structural domains (I-IV) and hypervariable regions (V2-V9). Rooting the three-taxon scenario remains difficult because the extremely long branches of Golenkinia and Jenufa are attracted to a chosen outgroup, reducing bootstrap support in any conceivable four-taxon tree obtained by parsimony or profile-neighbor-joining analysis. Conclusions: This algal case study of 18S rDNA consensus data (IUPAC encoded sequences and consensus structures) coupled with profile distances between groups of sequences, demonstrated that a phylogenetic problem can be reduced to a three-taxon analysis.

Phylogenetic position of the fish genera Lobotes, Datnioides and Hapalogenys, with a reappraisal of acanthuriform composition and relationships based on adult and larval morphology.

Lobotes,DatnioidesandHapalogenysare assigned to a newly defined Acanthuriformes on the basis of their pattern of tooth replacement (termed posterolateral tooth replacement), where new teeth form at the posterolateral ends of series. Posterolateral tooth replacement is shown to be a synamorphy of the order. The order is expanded to include Chaetodontidae, Pomacanthidae, Drepaneidae, Ephippidae, Leiognathidae,Antigonia, Scatophagidae andCapros, along with the more traditional members, Siganidae, Luvaridae, Zanclidae and Acanthuridae. Three-item analysis of 63 adult and larval morphological characters yields two optimal trees that differ only in the relative positions of Capros and Siganidae. The intersection tree of the two optimal trees is: (((Hapalogenys (Datnioides, Lobotidae)) (Pomacanthidae (Drepaneidae (Chaetodontidae (Ephippidae (Leiognathidae (Scatophagidae (Antigonia(Siganidae, Capros(Luvaridae (Zanclidae, Acanthuridae)))))))))))). This cladogram is compared with recent phylogenies based on analyses of sequence data, and few differences are found once the weakly-supported interior nodes of the latter are collapsed. Aside from expansion of the Acanthuriformes, the following classification changes are proposed in order to reflect the phylogenetic relationships: redefinition of the Lobotidae to include Lobotes, Datnioides and Hapalogenys; separate families forAntigoniaandCapros (Antigoniidae and Caproidae, respectively); continued recognition of Drepaneidae (often considered a synonym of Ephippidae). The larvae ofCapros aperare illustrated to show features overlooked in earlier descriptions.

Impact of errors on cladistic inference: simulation-based comparison between parsimony and three-taxon analysis

Simulation-based and experimental studies are crucial to produce factual arguments to solve theoretical and methodological debates in phylogenetics. However, despite the large number of works that tested the relative efficiency of phylogenetic methods with various evolutionary models, the capacity of methods to manage various sources of error and homoplasy has almost never been studied. By applying ordered and unordered methods to datasets with iterative addition of errors in the ordering scheme, we show that unordered coding in parsimony is not a more cautious option. A second debate concerns how to handle reversals, especially when they are regarded as possible synapomorphies. By comparing analyses of reversible and irreversible characters, we show empirically that three-taxon analysis (3ta) manages reversals better than parsimony. For Brownian motion data, we highlight that 3ta is also more efficient than parsimony in managing random errors, which might result from taphonomic problems or any homoplasy generating events that do not follow the dichotomy reversal/ convergence, such as lateral gene transfer. We show parsimony to be more efficient with numerous character states (more than four), and 3ta to be more efficient with binary characters, both methods being equally efficient with four states per character. We finally compare methods using two empirical cases of known evolution.

Dealing with propositions, not with the characters: the ability of three-taxon statement analysis to recognise groups based solely on ‘reversals’, under the maximum-likelihood criteria

Three-taxon statement matrices can be analysed using the maximum-likelihood method. In the present paper, it is demonstrated that groups based solely on putative reversals are always recognisable after maximum-likelihood analysis of three-taxon statement matrices, even without a priori recoding of the putative reversals as new character states or fractional weighting of three-taxon statements. Parametric implementations of three-taxon statement analysis still require more investigation. However, it must be highlighted that a focus on the set of hypotheses, rather than on the ‘actual data’, is required.

Comparative biogeography of Southeast Asia and the West Pacific region

The relationship between the areas of Southeast Asia and the West Pacific region is still debated because of their complex historical geology and the enormous diversity of taxa. Cladistic methods have previously been used to reconstruct the relationships between areas in the region but never with such a high number of unrelated taxa (35). We use a compilation of phylogenies to investigate area relationships among Southeast Asia and the West Pacific region, run the comparative analysis with LisBeth [based on three-item analyses (3ia)] and compare the results with recently published geological reconstructions of the region. We discuss the relevance of such an approach to the interpretation of general pattern. The two questions addressed are: (1) is there an emerging common pattern; and (2) how to explain actual distributions of taxa in Southeast Asia and the West Pacific region. Three-item analysis found 27 optimal trees. An intersection tree reconstructed from the common three-area statements had an overall retention index of 84.8% and retrieved 13 nodes with two major branches compatible with a separation between Southeast Asia and the West Pacific region (i.e. congruent with some geological reconstructions). Any congruent patterns revealed by the combination of unrelated taxa should reflect a common cause. The extraction of information on area relationships contained in phylogenetic analyses of taxa consists of testing for area homologues. We obtained the tree from this region based on an empirical dataset which we hope will contribute to new insights into area classification in the region.

A cladistic re-analysis of the Gadiformes (Teleostei, Paracanthopterygii) using three-item analysis

In the present paper, we describe LisBeth, a newly published phylogenetic program. LisBeth implements the cladistic three-item analysis for systematics and biogeography. We show how LisBeth handles character representation, character analysis, exact search functions, reconstruction of the intersection tree and other features, such as retention index, completeness index, character history and link with other programs such as PAUP*, version 4.0b10, TNT and Xper2. Using LisBeth, we reanalyze the phylogeny based on morphological characters of the order Gadiformes (Teleostei, Paracanthopterygii) published by Endo (2002) and compare our results. We also describe the generation of hypotheses of homology following Endo's guidelines versus 3ia representation schemes. We compare the topologies of all results and show the implications of the interpretation of character history.

Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three-item statements

The cladistic literature does not always specify the kind of multistate character treatment that is applied for an analysis. Characters can be treated either as unordered transformation series or as rooted [three-item analysis (3ia)] or unrooted state trees (ordered characters). We aimed to measure the impact of these character treatments on phylogenetic inference. Discrete characters can be represented either as rows or columns in matrices (e.g. for parsimony) or as hierarchies for 3ia. In the present study, we use simulated and empirical examples to assess the relative merits of each method considering both the character treatment and representation. We measure two parameters (resolving power and artefactual resolution) using a new tree comparison metric, ITRI (inter-tree retention index). Our results suggest that the hierarchical character representation not only results (with our simulation settings) in the greatest resolving power, but also in the highest artefactual resolution. Our empirical examples provide equivocal results. Parsimony unordered states yield less resolving power and more artefactual resolutions than parsimony ordered states, both with our simulated and empirical data. Relationships between three operational taxonomic units (OTUs), irrespective of their relationships with other OTUs, are called three-item statements (3is). We compare the intersection tree (which reconstructs a single tree from all of the common 3is of source trees) with the traditional strict consensus and show that the intersection tree retains more of the information contained in the source trees.

LisBeth: New cladistics for phylogenetics and biogeography

Within phylogenetics, two methods are known to implement cladistics: parsimony or maximum parsimony (MP) and three-item analysis (3ia). Despite the lack of suitable software, 3ia is occasionally used in systematic, and more regularly, in historical biogeography. Here, we present LisBeth, the first and only phylogenetic/biogeographic program freely available that uses the 3ia approach and offer some insights into its theoretical propositions. LisBeth does not rely on the conventional taxon/character matrix. Instead, characters are represented as rooted trees. LisBeth performs 3ia analyses based on maximum congruence of three-item statements and calculates the intersection tree (which differs from usual consensus). In biogeography, it applies the transparent method to handle widespread taxa and implements paralogy-free subtree analysis to remove redundant distributions. For the sake of interoperability, LisBeth may import/export characters from/to matrix in NEXUS format, allowing comparison with other cladistic programs. LisBeth also imports phylogenetic characters from Xper2 knowledge bases.

A Response to Mooi, Williams and Gill

Mooi et al. again suggest that finding trees under various universally-used optimality criteria is “authority.” We reject this argument. Their alternative of picking “good” characters that happen to evolve at a certain rate is equally authoritarian (indeed, it is easy to characterize just about any method as “authoritarian” because, well, it’s a method; the only thing fully immune from the charge of “authoritarianism” is doing nothing). To explain: the usual manner in which characters are selected for morphological analysis follows three basic steps. (1) Characters that display random variation or as much variation within taxa as between taxa in an analysis are typically discarded. (2) Characters that show no variation between taxa in the study are discarded. (3) Characters that do not meet the above criteria but which are shared between two to N-1 taxa in the study are analyzed. This amounts to a rate model of evolution. We don’t see any particular problem with adopting such models, but investigators should rec­ognize them as models with their own optimality criteria. We might term it the “screen data for usefulness model.” Mooi et al. argue in favor of a particular brand of this model, Three-Taxon Analysis (3ta), in which characters that change only once (i.e., without reversals) are chosen. We explain below why taking this course would be restric­tive and misguided.

Systemic foundering

Systemic foundering

Three-item analysis and parsimony, intersection tree and strict consensus: a biogeographical example

Abstract Using a biogeographical example, we show that the strict consensus of parsimony programs fails to summarize the information present in the initial hypotheses of homology. The intersection tree used in the three-item analysis program Nelson05 maximizes the compatibility of the three-item statements deduced from the source trees. The 3ia solution is more precise than the parsimony one because it accurately summarizes the initial information.

Three-item analysis: Hierarchical representation and treatment of missing and inapplicable data

Matrix-based methods, including parsimony programs, represent and treat missing data in the same way, such that every character-state is possible, and inapplicable data, such that every character state is impossible. This is because the hierarchical nature of homology assessments cannot be represented in taxon–character matrices. We show that the hierarchical representation of hypotheses of homology used in three-item analysis permits the accurate treatment of missing and inapplicable data.

A systematic revision of the family Harpetidae (Trilobita)

– The systematics of the ten valid harpetid trilobite genera are reviewed. Seven are revised, using standard parsimony and three-item analysis. The monophyly of the Harpetidae is confirmed, and all ingroup genera can be defended as monophyletic groups except for the nonmonophyletic Scotoharpes group.

Diagnostic Efficiency of Three-Taxon Analysis

Matrices of three-taxon statements (3ts) represent a transformation of original data in that they are calculated from normal data matrices. Normal matrices cannot be considered transformational (or 3ts matrices original) in that sense, because the 3ts transformation cannot be reversed. That the 3ts transformation cannot be reversed also means that the transformation discards information. Use of 3ts greatly reduces the efficiency with which data can be represented through the diagnoses of a classification. This happens because, unlike normal characters, 3ts provide no direct way of identifying a feature as the same in several different organisms. The ensemble retention index R does not have the same interpretation in three-taxon analysis (3ta) as it does with normal data matrices. In normal analyses R measures diagnostic efficiency, whereas 3ta always has minimal efficiency. Although usually interpreted phylogenetically, parsimony analysis can be applied descriptively without assuming any evolutionary process. This means that objecting to evolution as theoretical, unknown, or nonexistent would provide no grounds for rejecting parsimony in favor of 3ta, even if one did believe the objection.

Phylogeny of Melaleuca, Callistemon, and Related Genera of the Beaufortia Suballiance (Myrtaceae) Based on 5S and ITS-1 Spacer Regions of nrDNA

A phylogenetic analysis of genera within the informal suballiance Beaufortia (family Myrtaceae), largely endemic to Australia and New Caledonia, is presented based on separate and combined data sets for 5S and ITS-1 spacer regions of nuclear ribosomal DNA. The two sets were not in conflict but the 5S data set was more informative. Data were analysed using conventional parsimony, jackknife parsimony, and three-item parsimony analyses. Three-item analysis gave more resolved trees than conventional parsimony analysis. The Beaufortia suballiance includes two major clades, with all Australian representatives of Callistemon (shown to be monophyletic) and most Australian representatives of Melaleuca forming one of these. The sister clade comprises a well-defined group of endemic New Caledonian taxa (classified as Callistemon and Melaleuca), some Australian species of Melaleuca, a clade including the Western Australia/Northern Territory genera Beaufortia, Lamarchea, and Regelia, and a clade including the south-west Western Australian genera Calothamnus, Eremaea, Conothamnus, and Phymatocarpus. All molecular analyses sup port the monophyly of Conothamnus and of Regelia, genera for which a number of species were included. Three-item analysis of the combined data set supports the monophyly of Beaufortia. The findings have implications for both taxonomy and biogeography.

Phylogeny of Melaleuca, Callistemon, and Related Genera of the Beaufortia Suballiance (Myrtaceae) Based on 5S and ITS-1 Spacer Regions of nrDNA.

A phylogenetic analysis of genera within the informal suballiance Beaufortia (family Myrtaceae), largely endemic to Australia and New Caledonia, is presented based on separate and combined data sets for 5S and ITS-1 spacer regions of nuclear ribosomal DNA. The two sets were not in conflict but the 5S data set was more informative. Data were analysed using conventional parsimony, jackknife parsimony, and three-item parsimony analyses. Three-item analysis gave more resolved trees than conventional parsimony analysis. The Beaufortia suballiance includes two major clades, with all Australian representatives of Callistemon (shown to be monophyletic) and most Australian representatives of Melaleuca forming one of these. The sister clade comprises a well-defined group of endemic New Caledonian taxa (classified as Callistemon and Melaleuca), some Australian species of Melaleuca, a clade including the Western Australia/Northern Territory genera Beaufortia, Lamarchea, and Regelia, and a clade including the south-west Western Australian genera Calothamnus, Eremaea, Conothamnus, and Phymatocarpus. All molecular analyses sup port the monophyly of Conothamnus and of Regelia, genera for which a number of species were included. Three-item analysis of the combined data set supports the monophyly of Beaufortia. The findings have implications for both taxonomy and biogeography.