No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Why Morphometrics Is Not Special: Coding Quantitative Data for Phylogenetic Analysis
Abstract
Thorpe (1984) and Chappill (1989) argued that selection of a coding method should be [figure: see text] based on the purpose of coding. In our view, the purpose of coding is dictated by the principles of phylogenetic systematics. The foundation of phylogenetic systematics is the observation that monophyletic groups can be recognized if homologous character states, shared evolutionary novelties, can be identified (Hennig, 1966). Unfortunately, characters do not have labels indicating their homology. Instead, a systematist must propose a hypothesis of homology and evaluate its congruence with independent hypotheses based on other traits. In this context, the purpose of coding is to represent those hypotheses. The major obstacle to coding is that the a priori groups under analysis (i.e., taxa) often have ranges of variation that overlap to some degree. This is true whether traits are described qualitatively or quantitatively. One advantage of quantitative description is that it permits a more detailed analysis of how much the ranges of variation overlap. It may seem appropriate to use statistical methods to summarize the amount of overlap and even to decide objectively (on a priori grounds) whether taxa are similar or different. Above, we demonstrated some of the problems resulting from these uses of statistical analysis. In our view, the most important problem is the implication that similarity of the feature across taxa is the basis for inferring homology. The similarity that is relevant to phylogenetic analysis is not proximity in morphospace, but shared novelty. Statistical methods can describe proximity, but they cannot recognize novelty. The method of coding we recommend uses graphical displays of individual values. Coding decisions are based on all of the individuals in each taxon, not on summaries derived from models of expected distributions. Then, the evidence for inferring divergence is independently evaluated for each pair of overlapping taxa. Coding decisions are not based on a priori rules that have no bearing on recognition of evolutionary novelty. This is the same approach that is used to code qualitatively described traits.
... In practice, however, things are a bit more complicated. Many authors have pointed out that it is a common practice for phylogenetic systematic analyses to be performed on data matrices containing quantitative, ratio-scale variables that have been semantically 'discretized' into nominal variables (= characters, see Simon 1983;Almeida and Bisby 1984;Thorpe 1984;Archie 1985;Baum 1988;Goldman 1988;Chappill 1989;Stussey 1990;Stevens 1991;Theile 1993;Rae 1998;Strait et al. 1996;Swiderski et al. 1998). Moreover, even many standard examples of 'good' cladistic (= nominal) variables fail to stand up to even casual scrutiny. ...
... Once the presence of such discontinuities within the sample has been made obvious by the morphometric analysis, they can be readily understood and utilized by more traditional qualitative inspection. Similar conclusions have been reached by a number of other systematists (Theile and Ladiges 1988;Theile 1993;Fink and Zelditch 1995;Rohlf 1998;Swiderski et al. 1998;Rae 1998), though none has provided a simple example of this process. [Note: see also Chappill 1989 and Theile 1993 for discussions of semantic confusion between the notions of continuous variables and discontinuous patterns of variation that often occur in the systematic literature.] ...
... However, continuously-distributed ratio-scale or interval-scale variables cannot be transformed into the nominal or sometimes ordinal variables used by most phylogenetic inference algorithms except through the application of ad hoc rules. Gap coding (Mickevich and Johnson 1976;Archie 1985), segment coding (Colless 1980;Thorpe 1984;Chappill 1989) statistical 'difference between means' tests (e.g., homogeneous subset coding , Farris 1990;Theile 1993;Rae 1998); and statistical 'overlap analysis' (Almedia and Bisby 1984;Swiderski et al. 1998) all represent attempts to devise rule-based systems for subdividing continuous patterns of variation in morphological variables based on a consideration of frequency and/or a priori group membership. ...
Although many of the goals and concepts of qualitative morphological analysis and morphometrics are similar, systematists have largely rejected the use of morphometric methods in phylogenetic analysis on a variety of grounds. This review finds that (1) the concepts of a cladistic character and a morphometric vari- able are essentially identical, (2) morphometric methods can be instrumental in discovering and document- ing new morphological character and character states, (3) prior objections to the use of morphometric vari- ables because of their continuous nature confuse the issues of variable type with those surrounding the dis- tributions of sets of observations, (4) morphometrics offers the best method of determining whether mor- phological observations are discontinuous (= can be coded as discrete character states) or continuous (= can- not be coded as discrete character states), (5) constellations of landmark-based morphometric variables repre- sent adequate summaries of putative structure-level homologues for use in phylogenetic analyses, (6) partial warp analyses do not perform well in either simulated or actual phylogenetic systematic analyses because of their inherent instability and lack of adequate spatial localization, and (7) a new method of subdivided rela- tive warp analysis (described herein) performs very well at recognizing simulated morphological character states and recovering a simulated morphological phylogenetic hierarchy. Based on these results it is con- cluded that the potential of morphometric data analysis methods (especially relative warp-based methods) to contribute to phylogenetic-systematic investigations should be explored further.
... However, the need for a theoretical basis as mentioned by Pimentel and Riggins (1987) is not really necessary, because the characters are used unordered (Fitch parsimony) and the cladogram will provide the knowledge base for the state changes and not a theory. Therefore, Thiele (1993) and Swiderski et al. (1998) are followed in the present analysis; continuous characters are used if states do not overlap (Thiele 1993) or if only very few species show overlap in a minor number of collections (Swiderski et al. 1998). ...
... However, the need for a theoretical basis as mentioned by Pimentel and Riggins (1987) is not really necessary, because the characters are used unordered (Fitch parsimony) and the cladogram will provide the knowledge base for the state changes and not a theory. Therefore, Thiele (1993) and Swiderski et al. (1998) are followed in the present analysis; continuous characters are used if states do not overlap (Thiele 1993) or if only very few species show overlap in a minor number of collections (Swiderski et al. 1998). ...
A phylogenetic analysis of Harpullia (two incompletely-known species excluded, Conchopetalum and Majidea as outgroups) based on morphological characters resulted in five most parsimonious cladograms. These cladograms and the strict consensus cladogram show a few polytomies. Only a few branches have relatively high Decay Indices. The strict consensus cladogram indicates that Harpullia is monophyletic (five synapomorphies) and does not support the existing subgeneric classification. Thus, it is advisable to refrain from any subgeneric classification. The historical biogeographic pattern confirms the one already found for eight other genera of Sapindaceae. Harpullia originated on the New Guinean—Australian plate and from there dispersal and speciation occurred towards New Caledonia and Southeast Asia main land. Communicating Editor: Matt Lavin
... As many morphological characters can be quantified with continuous data, their treatment in cladistics has been the subject of numerous papers (Kluge & Farris 1969;Mickevich & Johnson 1976;Mickevich & Far-ris 1981;Simon 1983;Rogers 1984;Archie 1985;Pimentel & Riggins 1987;Cranston & Humphries 1988;Goldman 1988;Chappill 1989;Thiele & Ladiges 1988;Farris 1990;Pogue & Mickevich 1990;Maddison 1991;Stevens 1991;Thiele 1993;Pleijel 1995;Wiens 1995;Strait et al. 1996;Rae 1998;Swiderski et al. 1998;Zar 1999;Poe & Wiens 2000;Smith & Gutberlet 2001;Wiens 2001;Garcia-Cruz & Sosa 2006;Lens et al. 2007;Lawing et al. 2008;De Bivort et al. 2010). Typically, continuous morphological data (such as measured lengths and angles of aspects of organisms' anatomy) are divided up or discretized into 2 or more discrete character states. ...
... Different states are defined based on gaps in the range of values observed in operational taxonomic units (OTUs), with each character state assigned a defined range of values (e.g. Mickevich & Johnson 1976;Colless 1980;Simon 1983;Almeida & Brisby 1984;Thorpe 1984;Archie 1985;Baum 1988;Goldman 1988;Thiele 1993;Strait et al. 1996;Swiderski et al. 1998;Wiens 2001). Numerous methods for identifying significant gaps within continuous distributions of data have been proposed. ...
Since the introduction of the cladistic method in systematics, continuous characters have been integrated into analyses but no methods for their treatment have received unanimous support. Some methods require a large number of character states to discretise continuous characters in order to keep the maximum level of information about taxa differences within the coding scheme. Our objective was to assess the impact of increasing character state number on the outcomes of phylogenetic analyses. Analysis of a variety of simulated data sets shows that these methods for coding continuous characters can lead to the generation of well-resolved trees that do not reflect phylogenetic signal. We call this phenomenon the flattening of the tree-length distribution; it is influenced by both the relative quantity of continuous characters in relation to discrete characters, and the number of characters in relation to the number of taxa. Bootstrap tests provide one method to avoid this potential bias.
... A number of methods for coding continuous characters have been proposed; the gap-coding method utilizes descriptive statistics such as standard deviation or standard error, which are then taken into consideration to establish the amount of overlap allowed in the patterns of variability (Mickevich and Johnson 1976;Almeida and Bisby 1984;Swiderski et al. 1998). The segment coding method divides the range of variation into segments of equal size and assigns each species to one of these segments (Colless 1980;Thorpe 1984;Baum 1988;Chappill 1989). ...
... Two methods, gapweighting (Thiele 1993), and step-matrix gap-weight-ing (Wiens 2001) are similar to segment coding in that they divide the observed variation into a large number of segments of equal size and treat these segments as ordered character states, giving large weights to large differences in species means and small weights to small differences (Thiele 1993;Wiens 2001). Many of these methods seek to place boundaries between states where quantitative gaps between the taxa are found (Archie 1985;Strait et al. 1996;Rae 1998;Swiderski et al. 1998). ...
Five character construction methods were compared for a data set of 25 quantitative morphological characters sampled from the Govenia superba complex. The methods were simple-gap, gap coding, gap-weighting, analysis of variance followed by a multiple range test, and an "arbitrary" coding method. Three indices, data decisiveness, consistency index, and skewness (g1), were used as estimators of phylogenetic signal. Performance of coding methods was evaluated by the following criteria: (1) number of informative characters, (2) number of equally parsimonious trees, (3) clade support measured by bootstrapping, and (4) phylogenetic signal, compared using randomization tests that established critical values for the three indices and allowed them to be compared between coding methods. This study demonstrates that a large number of characters are accessible for phylogenetic analysis when continuous characters are included. The quantitative character data for the Govenia complex contain significant phylogenetic information when the gap-weighting method is used to construct character states. This indicates that methods that divide variation into small segments and allow overlapping of measurements recover a strong phylogenetic signal, and yield small number of well-resolved trees with strong bootstrap support and statistically significant phylogenetic signal. In contrast, methods such as gap coding or analysis of variance-multiple range test lead to data matrices with few informative characters and many equally parsimonious trees and weak phylogenetic signal. Moreover, the simple-gap coding method data matrix failed to recover significant phylogenetic signal.
... In the middle, other systematists (with whom we agree) have suggested to disregard only those characters in which variation is overlapping. They have concluded that arguments against the use of quantitative data are not supported by systematic theory, and that problems to use them as characters reside basically in the methods by which states and codes are derived from quantitative variation (Thiele, 1993;Rae, 1998;Swiderski, Zelditch & Fink, 1998). ...
... Observations of each taxon are summarized in estimated parameters of distribution and central tendency (in a statistical sense). The decisions of which distributions (and associated central tendencies) are different or not should be made by evaluating variation levels within and between taxa included in the analysis (Rae, 1998;Swiderski et al., 1998). A character can be considered as potentially useful if it shows greater variance between groups than within (De Luna & Mishler, 1996). ...
The recognition of transformed homologues entails an evaluation of similarity of features among taxa and then an assessment of homology by character congruence. We approached the similarity test of character state identity with morphometric analyses of character variation to judge whether all variants from a taxonomic sample belong to the same phylogenetic state (taxic homology) or whether some variants are sufficiently different to recognize them as different states (transformational homology). This method seeks to recognize as many character states as the groups of taxon means that are revealed by an analysis of variance followed by a multiple range test. We exemplify this quantitative approach with an analysis of character variation for a phylogenetic study of eight Artibeus species and two outgroups. All 23 features analysed are taxonomically useful because at least two states could be defined. We argue that statistical tests are a consistent and non-arbitrary procedure for the similarity test in the assessment of character states when hypothesizing primary homologies. Cladistic analyses and descriptive indices of historical signals of previous molecular and morphological data, combined with our morphometric data, showed that morphometric characters contain cladistic structure and they are phylogeneticaly useful. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 45–55.
... Besides the problems already mentioned, many of S&F's (2003a) characters demonstrate either a lack of understanding of, or disregard for, established methods and standards for morphological character coding in systematics. Fifteen (9%) of their characters contain states with grossly overlapping variation (Table 7), despite well-known methods for coding continuous variation, one cited by Soleglad et al. (2005, p. 5), which stipulate that gaps in the variation must be evident in order to code states discretely or that quantitative data should be analyzed as such if, indeed, they should be included at all (Pimentel and Riggins, 1987;Cranston and Humphries, 1988;Felsenstein, 1988;Chappill, 1989;Stevens, 1991;Thiele, 1993;Gift and Stevens, 1997;Rae, 1998;Swiderski et al., 1998;Schuh, 2000;Wiens, 2001;Goloboff et al., 2004). ...
... Such examples suggest that S&F (2003a) are unaware of more than 20 years of literature on strategies for coding and analyzing polymorphic data (Mickevich and Mitter, 1981;Archie, 1985;Pimentel and Riggins, 1987;Nixon and Davis, 1991;Platnick et al., 1991;Mabee and Humphries, 1993;Thiele, 1993;Wiens, 1995Wiens, , 1998aWiens, , 1998cWiens, , 1999Wiens, , 2000Wiens, , 2001Nixon and Carpenter, 1996;Kron and Judd, 1997;Rice et al., 1997;Servedio, 1997, 1998;Swiderski et al., 1998;Kornet and Turner, 1999;Prendini, 2001a;Simmons, 2001;Smith and Gutberlet, 2001). ...
Soleglad and Fet's (2003a) attempt to reconstruct the phylogeny of Recent (including extant) scorpions, the revised classification derived from it, and recent emendations, mostly published in their self-edited online journal, Euscorpius, are deficient. Separate analyses of three independent matrices (morphology, 16S rDNA, 18S rDNA) were presented. In the morphological matrix, 52 binary and 10 tristate trichobothrial characters were replaced with one character comprising six ordered states representing trichobothrial “types”. The remaining matrix of 105 characters was further reduced to 33 “fundamental” characters (20% of the morphological dataset), the analysis of which appears to be the basis for the revised classification presented. The taxon sample for the morphological analysis included 14 supraspecific terminal taxa representing genera, the monophyly of only 7 (12.5%) of which has been confirmed. A composite terminal, assembled from the fragments of fossils that may not be confamilial let alone monophyletic, was created for the Palaeopisthacanthidae, employed as the primary outgroup for the analysis. Other important outgroup taxa, notably eurypterids, xiphosurans and other arachnids, were omitted entirely. The morphological characters presented contained numerous unjustifiable assumptions of character polarity and phylogenetic relationship. An approach to character coding, deliberately adopted to reduce “homoplasy”, biased the analysis towards a preconceived result. Structurally and topographically similar features in different taxa were explicitly assigned separate (often autapomorphic) states according to presumed phylogenetic relationships among the taxa in which they were observed. Putative “reversals” were coded as separate characters or states. Character transformation was forced by ordering, additive coding or Sankoff optimization through allegedly intermediate states for which there is no empirical evidence. Many characters were defined in a manner that demonstrates either a lack of understanding of, or disregard for, established methods and standards of morphological character coding. Some states display overlapping variation whereas others subsume variation that is not structurally or topographically similar. Polymorphic “states” were created for terminals with interspecific variation and unknown “states” for terminals that should have been scored unknown. Many characters were not evaluated for particular terminal taxa, but merely scored inapplicable although the structures and, consequently, the characters in question are present and therefore applicable to them. In view of the significant theoretical and empirical problems with the approach to cladistics taken by Soleglad and Fet, we find no justification for accepting either the results of their analyses or the revised classification derived from them. Pending the outcome of a rigorous phylogenetic analysis, published according to acceptable standards of scholarship in a peer-reviewed journal, we revert to the suprageneric classification of Scorpiones reflected by the most recent peer-reviewed, published treatments and reject all changes to the classification proposed by Soleglad, Fet and colleagues since 2001. We argue that an analysis and revised classification of the kind presented in various papers by these authors could not survive the peer-review process of a mainstream scientific journal. The poor scholarship exemplified by these and other papers published in Euscorpius emphasize the importance of quality control associated with the emergent infrastructure of online publishing. A centralized register of taxa may be the only solution for ensuring quality control in the taxonomy of the future.© The Willi Hennig Society 2005.
... Phylogenetic analyses infer potential evolutionary relationships based on similarities implying common descent from shared ancestry and are performed on data sets consisting of PrePrints physical, functional, or molecular representations (Swiderski et al., 1998). Genomic analyses typically construct the analytic matrix using nucleotide or amino-acid sequences from different individuals or species (termed "taxa"; singular "taxon"). ...
The characterization of complex diseases remains a great challenge for biomedical researchers due to the myriad interactions of genetic and environmental factors. Adaptation of phylogenomic techniques to increasingly available genomic data provides an evolutionary perspective that may elucidate important unknown features of complex diseases. Here an automated method is presented that leverages publicly available genomic data and phylogenomic techniques. The approach is tested with nine genes implicated in the development of Alzheimer Disease, a complex neurodegenerative syndrome. The developed technique, implemented through a suite of Ruby scripts entitled “ASAP2,” first compiles a list of sequence-similarity based orthologues using PSI-BLAST and a recursive NCBI BLAST+ search strategy, then constructs maximum parsimony phylogenetic trees for each set of nucleotide and protein sequences, and calculates phylogenetic metrics (partitioned Bremer support values, combined branch scores, and Robinson-Foulds distance) to provide an empirical assessment of evolutionary conservation within a given genetic network. This study demonstrates the potential for using automated simultaneous phylogenetic analysis to uncover previously unknown relationships among disease-associated genes that may not have been apparent using traditional, single-gene methods. Furthermore, the results provide the first integrated evolutionary history of an Alzheimer Disease gene network and identify potentially important co-evolutionary clustering around components of oxidative stress pathways.
... For years experts were in search of a silver bullet for accurate taxonomic identification that would be helpful even in the recognition of exotic pests of agriculture importance [7] . Morphological phylogenetics has confronted with so many practical problems including discovering the most befitting representation of constantly deviating phylogenetic dimensions determining the appropriate trait as a measure to catalogue organisms, requirement of expertised minds to assume hypotheses based on evolutionary relevant phenotypic traits and the herculean task of amassing data on morphological characters from field observation or literature [8,9,10] .These practical difficulties of morphological phylogenetics are easily overcome with the advent of molecular phylogenetics which has thrown light on solving this complicated issue by the introduction a new versatile technique namely DNA barcoding is the utilization of short DNA sequences to discriminate among species [11] . Hebert et al (2003a detailed that the Folmer region of mitochondrial COI gene could attorney for the genetic barcoding for all animal life. ...
Grey weevil, Myllocerus viridanus (Fabricius) is a polyphagous pest with a wide range of host plants. The pest is reported to cause damage to plants of agriculture and horticulture importance. Taxonomic identification plays a crucial role in designing the accurate management procedures against insect pests. Inaccurate identification often may form a hurdle in implementation of proper management strategies. This work utilizes the advancement in the field of molecular systematics such as DNA barcoding for tracing the phylogeny of the weevil pest by the partial sequencing of mitochondrial cytochrome oxidase I (CO I). The species discrimination studies based on DNA barcoding involved steps like DNA isolation and PCR amplification. Evolutionary analysis was carried out in Mega 7 software. GenBank deposition indicated the novel and first time records of M.viridanus and was provided with accession numbers KU871376&MG021103 Further analysis showed that M.viridanus has 96% similarity with M.undecimpustulatus (KX778624) and 85%. The translational product of aligned data showed a difference in two amino acid sequences between M.viridanus and M.undecimpustulatus. The nucleotide sequences with 96-84% similarity were retrieved from NCBI and included in the study. The protein translation yielded a short chain of 219 amino acids. This approach was very informative and it helped in the better understanding of genetic variation among closely related species
... During the last two decades, several proposals for estimating phylogenies from morphometric data have been discussed contentiously. Some authors have suggested phylogenetic analyses based on cladistic characters derived from partial warp scores Zelditch et al. 1995Zelditch et al. , 1998Swiderski et al. 1998;Bogdanowicz et al. 2005;Clouse et al. 2011) or principal component (PC) scores (MacLeod 2002;González-José et al. 2008Aguilar-Medrano et al. 2011;Brocklehurst et al. 2016). These proposals, however, have been criticized for various reasons, especially the decomposition of phenotypic spaces into distinct characters (Bookstein 1994;Naylor 1996;Adams and Rosenberg 1998;Rohlf 1998;Monteiro 2000;Adams et al. 2011;Zelditch et al. 2012). ...
In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared-change parsimony performed similarly well as maximum likelihood, and both methods outperformed Wagner and Euclidean parsimony, neighbor-joining and UPGMA. Under an evolutionary model of isotropic Brownian motion, phylogeny can be estimated reliably if dimensionality is high, even with relatively unfavorable combinations of branch lengths. By contrast, if there is phenotypic integration such that most variation is concentrated in one or a few dimensions, the reliability of phylogenetic estimates is severely reduced. Evolutionary models with stabilizing selection also produce highly unreliable estimates, which are little better than picking a phylogenetic tree at random. To examine how these results apply to phylogenies with more than four taxa, we conducted further simulations with up to eight taxa, which indicated that the effects of dimensionality and phenotypic integration extend to more than four taxa, and that convergence among internal nodes may produce additional complications specifically for greater numbers of taxa. Overall, the simulations suggest that multidimensional data, under evolutionary models that are plausible for biological data, do not produce reliable estimates of phylogeny.
... The continuously scaled nature of many variables does not, however, preclude the discovery of discrete states of expression within them. Systematists who argue that continuous variables can only be delimited into discrete states by some arbitrary rule or coding algorithm conflate two different levels of variation: that of the variable itself (i.e., its theoretical distribution in morphospace), which is continuous, and that of the variable observations (i.e., the data, or individual attributes), which may be either continuously or discontinuously distributed [Thiele, 1993;Swiderski et al., 1998;MacLeod, 2002;Sereno, 2007]. Character coding is therefore not absolutely necessary for phylogenetic analysis, nor perhaps even desirable [Felsenstein, 1988[Felsenstein, , 2002. ...
The early stages of phylogenetic inference from morphological data involve a sequence of choices about which analytical methods to employ. At each stage, the selection of one method over another can dramatically impact tree inference. Phylogenetic hypotheses are sensitive to decisions relating to which taxa and characters to select for analysis, whether and how to delimit character states, which taxa to use as outgroups, and how to account for character dependence. Using extant hominoids as a test case, I quantify the degree to which phylogenetic inferences are sensitive to the choice of method used to transform continuously scaled variables into categorical traits. I demonstrate that the character coding strategy significantly impacts hypotheses of character state identity and phylogenetic branching patterns. To avoid biasing evolutionary hypotheses, I recommend that continuously scaled characters be analyzed without prior discretization.
... Chappill (1989), Stevens (1991), and Thiele (1993) provided very useful discussions disputing this notion. An important point is that most "discrete, xed, qualitative" characters considered acceptable for phylogenetic analysis are actually quantitative characters being described qualitatively and thus fundamentally not different from the characters that Pimentel and Riggins (1987) and Cranston and Humphries (1988) would exclude (Stevens, 1991;Thiele, 1993;Swiderski et al., 1998). Also, as Thiele (1993) and Chappill (1989) pointed out, if the variation observed in polymorphic multistate characters has a genetic basis, then those characters should be considered a potential source of phylogenetic information. ...
A new method of coding polymorphic multistate characters for phylogenetic analysis is presented. By dividing such characters into subcharacters, their frequency distributions can be represented with discrete states. Differential weighting is used to counter the effect of representing one character with multiple characters. The new method, generalized frequency coding (GFC), is potentially superior to previously used methods in that it incorporates more information and is applicable to both qualitative and quantitative characters. When applied to a previously published data set that includes both types of polymorphic multistate characters, the method performed well, as assessed with g1 and nonparametric bootstrap statistics and giving results congruent with those of other studies. The data set was also used to compare GFC with both gap-weighting and Manhattan distance step matrix coding. On these grounds and for philosophical reasons, we consider GFC to be a better estimator of phylogeny.
... Continuous measurements were unordered and plotted to determine natural breaks (e.g., change in slope or discontinuities) of variation. The natural breaks in the data were utilized to create bins of discrete states via gap coding (see Mickevich and Johnson, 1976;Archie, 1985;Thiele, 1993;Swiderski et al., 1998). The mean and standard deviation values were calculated for each bin and used to define character state ranges following Morton and Kincaid (1995) and Stigall (2013, 2014). ...
Systematic revision of the Late Ordovician brachiopod genera Eochonetes Reed, 1917 and Thaerodonta Wang, 1949 was conducted utilizing specimen-based morphometric and species-level phylogenetic analyses. Previous studies had recognized Thaerodonta and Eochonetes as either distinct taxonomic entities or synonyms. New multivariate and phylogenetic analyses confirm the synonymy of Thaerodonta with Eochonetes and provide a framework to assess evolutionary and ecological patterns within the clade. Multivariate analyses were employed to delineate species in morphospace and provided information on potential species relationships. Phylogenetic analysis was used to produce an evolutionary framework for taxonomic revision and identify character evolution within the clade. Most species previously assigned to Thaerodonta are transferred to Eochonetes , and three others are excluded from Eochonetes and provisionally referred to other sowerbyellid genera. Three new species ( Eochonetes maearum new species, E. voldemortus new species, E. minerva new species) are described, one species ( Leptaena saxea Sardeson, 1892) is synonymized with E. recedens Sardeson, 1892, and one subspecies ( Thaerodonta mucronata scabra Howe, 1965) is rejected. This study demonstrates that a combination of complementary approaches and data types has the potential to advance interpretations beyond analyses confined to single analytical tools. Specifically, multivariate analyses provide constraints on species boundaries, whereas species-level phylogenetic analyses provide frameworks to examine morphological, ecological, and biogeographic evolution within a clade.
... In skeletal morphology, geometric morphometric methods offer an approach complementary to qualitative studies, and combined with several statistical multivariate tests, allow for quantitative study of shape variation. In zoology, these methods have been employed to describe shape change associated to ontogeny and allometry (e.g., Monteiro & Abe 1997;Larson 2002Larson , 2005, variation among populations, sexes, species (e.g., Rohlf 1993;Fink & Zelditch 1995;Swiderski et al. 1998;Corti et al. 2000;Marcus et al. 2000;Baylac et al. 2003;Frieß 2003;Giri & Collins 2004;Zelditch et al. 2004;Anderson & Roopnarine 2005;Beszteri et al. 2005;Stayton 2005;Vera Candioti et al. 2007), and morphological variation related to ecological features (e.g., Adams and Rohlf 2000;Claude et al. 2004;Dayton et al. 2005). On the other hand, in several studies that analyze the morphology-ecology relation, although morphology is exhaustively examined, ecological variables are described qualitatively or inferred from morpho-functional aspects. ...
I studied anatomy, gut content, and the relationship among these traits in a set of anuran tadpoles. Larval stages (mainly Gosner stages 31-36) of nineteen species from various lentic environments were selected. Morphological characters from the skeleton, musculature, oral apparatus and buccopharyngeal cavity were recorded, and a gut content analysis was performed, with emphasis on food size distribution. Ordination techniques were applied in order to find patterns of similarity in morphology and gut content. Canonical ordination methods were used to investigate the relationship among gut content, morphology, and phylogeny in the species considered. The results show that several skeletal, muscular, and buccal characters are relatively maintained within genera. Other features, which have appeared independently in different lineages, reflect convergence phenomena in some cases related to ecological aspects. The configuration of the hyobranchial skeleton, the development of the buccal floor depressor and levator muscles, and mouth gape width correlate with prey size. In some species, morphology is clearly related with feeding. Tadpoles that ingest large food particles relative to their body length present morphological traits attributable to macrophagy. Taxonomically unrelated tadpoles of Dendropsophus nanus, D. microcephalus and Ceratophrys cranwelli possess hyobranchial skeletons with robust, rostrocaudally long ceratohyals and reduced branchial baskets with short ceratobranchials devoid of lateral projections and spicules. Lepidobatrachus llanensis tadpoles have laterally extended ceratohyals which, along with the lateral extension of the jaws, result in a very wide oral apparatus and an ample buccopharyngeal cavity that allows the tadpole to ingest large and whole prey; the branchial basket, although its ceratobranchials lack lateral projections and spicules, is slightly reduced in area. The four species mentioned have a noticeable development of the buccal floor depressor muscles, and buccal cavities with scarce filtering and entrapping structures. In Elachistocleis bicolor, Dermatonotus muelleri, Chiasmocleis panamensis, and Xenopus laevis tadpoles, the branchial basket occupies >70% of the total hyobranchial skeleton area, and the hypobranchial plates are highly reduced; the buccal floor levator muscles are well-developed, with an increased site of attachment on the ventral expansion of the lateral process of the ceratohyal; the scarcity of the filtering structures in the buccopharyngeal cavity are balanced with the great development of the branchial filters and secretory zones; all these features relate to a diet based on small particles not significantly different from those of most other species; however, experimental studies show that species with similar hyobranchial apparatus and muscles are the most efficient when retaining minute particles. Finally, a large group of species present generalized morphological characters, such as a branchial basket occupying about 50% of the total hyobranchial apparatus, intermediate values of mouth gape width and buccal floor levator / depressor muscles ratio, and abundant filtering structures in the buccopharyngeal cavity; these species feed frequently on food particles between 1-30% of the tadpole body length; however, in some of the species, macrophagous diets are also reported in the literature, indicating that this morphology is flexible in more ample prey size ranges.
... The results obtained from geometric morphometrics show consistency when compared with works of functional morphology (Wainwright, 1988; Wainwright et al., 2004) because they indicate that the variations seen in the labrids occur mainly in the area of the skull. despite the rejection related to the use of data generated by geometric morphometrics for phylogenetic purposes (Fink and zelditch, 1995; Swiderski et al., 1998 Swiderski et al., , 2000 Acero et al., 2005), the results are satisfactory in this and other previous studies. However, caution is suggested in inferring phylogenetic relationships, since the results of morphometric similarities may be reflecting non-homologous and convergent characters due to ecological roles, without representing kinships. ...
A study of geometric morphometries was carried out based on 109 specimens of four Labridae species captured in north-eastern Brazil. The canonical variable analysis applied on the W Matrix discriminated the species, and the partial warps analysis located the morphological variations. According to analysis, the Halichoeres species constitute a monophyletic group, with H. poeyi as the sister-group of the clade H. brasiliensis + H. dimidiatus. The cladogram of these species was estimated using Bodianus rufiis as outgroup. The Halichoeres species share shorter head lengths and deeper heads in relation to the outgroup. Within Halichoeres , the more basal taxon (H. poeyi) can be characterized by autapomor-phies such as short snout and deeper head. In the clade H. brasiliensis + H. dimidiatus , the snout is longer and the caudal peduncle is deeper than in H. poeyi. The results obtained from the geometric morphometry are consistent with works of functional morphology and their applications for the testing of phylogenetic hypotheses are equally satisfactory. However, caution is necessary because the similarities in morphometric data can reflect non-homologous and convergent features due to ecological roles, without representing kinships.
... Despite the antiquity and generally narrow context of the concept, the issue of homology and its practical application remain the subject of substantial controversy (Rieppel, 1980(Rieppel, , 1992(Rieppel, , 1994Roth, 1984Roth, , 1988Roth, , 1991Sattler, 1984). Subsequently, however, the concept and criteria for the diagnosis of homology have been recognized as equally vital and challenging for phylogenetic interpretation of characters as diverse as DNA sequences (Patterson, 1988;Mindell, 1991;Hillis, 1994;Brower and Schawaroch, 1996), proteins (Fitch, 1970), metric abstractions (Bookstein, 1994;Fink and Zelditch, 1995;Zelditch et al., 1995Adams and Rosenberg, 1998;Rohlf, 1998;Swiderski et al., 1998;, and behavioral repertoires (Wenzel, 1992;Greene, 1994). In that Owen (1843) originally contrasted "analogues" --phylogenetically independent structures having common functions in different taxa^ -from "homologues," it is not surprising that an emphasis on function persists in the diagnosis of homology and the utility of characters for phylogenetic reconstruction (Bock, 1967(Bock, , 1977(Bock, , 1979(Bock, , 1989; but see Cracraft, 1981Z?). ...
Two landmarks of the temporal region of the skull in most birds are the zygomatic process (processus zygomaticus) and the postorbital process (processus postorbitalis). The morphology and homology of these processes in gallinaceous birds (Galliformes) and waterfowl (Anseriformes), however, are not clear. Anseriformes usually are said to lack a processus zygomaticus. By contrast, the processus zygomaticus of many Galliformes often is described as connected to the tip of the processus postorbitalis, forming a temporal arch. Olson and Feduccia (1980a) cited these cranial differences as evidence opposing a hypothesis of sister relationship between the two orders, an hypothesis having a substantial history of advocacy (Seebohm, 1889; Shufeldt, 1901; Delacour, 1954; Johnsgard, 1965; Cracraft, 1981a, 1986; Schulin, 1987). Dzerzhinsky (1982, 1995) contradicted the proposal by Olson and Feduccia (1980a), interpreting the two processes as completely fused in Anseriformes, forming a unique 'sphenotemporal process,' which he averred to have been derived evolutionarily from the condition found in the Galliformes. In the present study, we examined skulls and jaw muscles of juvenile and adult specimens of selected taxa from both orders to test these opposing hypotheses, and found that: (a) the processus zygomaticus is small or lacking in adult Galliformes, and absent in all Anseriformes; (b) the processus zygomaticus is connected to the tip of the processus postorbitalis by an ossified aponeurosis of m. adductor mandibulae externus (aponeurosis zygomatica) in adults of most galliforms, whereas the aponeurosis zygomatica of anseriforms has a linear origin along the os squamosum as far as the processus postorbitalis; the aponeurosis zygomatica is ossified in Anhimidae and unossified in Anatidae; (c) a laterally exposed fossa of the temporal region (fossa musculorum temporalium) is reduced in Galliformes and absent in Anseriformes; (d) pars superficialis and pars zygomatica of m. adductor mandibulae externus are shifted rostrad in Galliformes and Anseriformes, and (e) pars articularis of m. adductor mandibulae externus is much enlarged in both orders. Based on these observations, we conclude that the parts of musculus adductor mandibulae externus of Anseriformes have been misinterpreted in a number of previous studies, perhaps reflecting confusion about associated processes and fossae. These findings are interpreted with respect to the homology of the osteological features and their associated muscles. The distribution of the included states supports the growing consensus for a sister relationship between the Galliformes and Anseriformes.
... In the use of morphometric data as discretized characters, it is very important to choose the coding method. To decide the most appropriate method we were guided by the results of other authors who had used different approaches: gap-coding (Swiderski et al. 1998), coding segment (Chappill 1989), gap-weighting (Thiele 1993), step-matrix gap-weighting (Wiens 2001), analyses of variance (Guerrero et al. 2003) and phylogenetic PCA (Polly et al. 2013). Proposed by Thiele (1993) gapweighting method proved to be well supported both theoretically and practically Garcia-Cruz & Sosa 2006;. ...
Architectonics of the leech body constitute a source of promorphological characters which have been used for modeling. A geometric model of the leech body form was applied in a phylogenetic analysis for the estimation of the utility of morphometric data in the reconstruction of the history of Hirudinida. A cladistic analysis included species representing all main ecological groups of leeches. In the analysis the morphometric data were used as non-discretized mean values and as mean values coded with the gap-weighting method. Obtained phylogenetic trees were compared with cladograms generated based on combined data sets including discrete qualitative morphological characters as well as known molecular phylogenies of leeches. The study demonstrates that the morphometric characters provide additional evidence for the confirmation of monophyletic groups within Hirudinida. Thus, the morphometric data resulting from the geometric model of the leech body form appeared to be applicable for the reconstruction of leech phylogeny
... Only discrete (qualitative) morphological characters have been, for a long time, applied in most phylogenetic analyses, because continuous (quantitative) characters were considered inappropriate (Pimentel and Riggins, 1987). However, as the phylogenetic utility of quantitative morphological data has been demonstrated (Chappill, 1989;Stevens, 1991;Thiele, 1993;Swiderski et al., 1998) with the development of various methods for the discretization (Mickevich and Johnson, 1976;Colless, 1980;Thorpe, 1984;Archie, 1985;Baum, 1988;Thiele, 1993;Strait et al., 1996;Wiens, 2001;Goloboff et al., 2006), the use of continuous characters in phylogenetic analysis has considerably increased even in the study of invertebrate fossils (e.g., Hopkins, 2011;Bert and Bersac, 2013;Pachut and Horowitz, 2013;Stigall, 2013, 2014). In the present study, we deployed two different methods to treat continuous characters, producing three character-taxon matrices for these characters (Tables 4 and 5). ...
The brachiopod Superfamily Spiriferoidea diversified greatly and was widely distributed in the late Palaeozoic (Carboniferous–Permian), and yet its phylogeny has been seldom investigated with analytical methods. This is reflected in the current flux of very different classification schemes for this superfamily. This paper provides the first attempt to investigate the phylogenetic relationships of spiriferoid brachiopods through both cladistic and Bayesian analyses involving 24 discrete and continuous characters. The continuous characters, from morphometric data, have been separately discretized using the gap weighting method, and the ‘as such’ option in TNT. Our results highlight the potential significance of continuous characters in reconstructing and elucidating phylogenies, as much as qualitative characters. Building on the outcomes of the analyses, we also briefly evaluate existing classification schemes of Spiriferoidea. We found that none of the existing classifications fully reflect the phylogeny properly; major families within the superfamily, such as Spiriferidae, Choristitidae, and Trigonotretidae, turned out to be polyphyletic. Although this study is considered preliminary, due to the selection of and restriction to certain taxa, combined with the use of a relatively small number of characters, it nevertheless demonstrates that potentially the true phylogenetic relationships of spiriferoid taxa sharply contrast with any of the existing classification schemes. This highlights the need to develop an alternative scheme that takes into account a more comprehensive range of phylogenetic variables.
... Continuous characters were coded based on the total range of morphometric values measured for each species presented in Tables 5 and 6. Measurements of continuous characters were separated into discrete states using a procedure similar to those suggested by Morton and Kincaid (1995) and Swiderski et al. (1998). Morphometric measurements were visually inspected by examining univariate frequency distributions and box plots. ...
The orthidine brachiopod genera Plaesiomys and Hebertella are significant constituents of Late Ordovician benthic marine communities throughout Laurentia. Species-level phylogenetic analyses were conducted on both genera to inform systematic revisions and document evolutionary relationships. Phylogenetic analyses combined discrete and continuous characters, from which character states were determined using a statistical approach, and utilized both cladistic and Bayesian methodologies. Plaesiomys cutterensis , P. idahoensis , and P. occidentalis are herein recognized as distinct species rather than subspecies of P. subquadratus . Similarly, Hebertella montoyensis and H. prestonensis are recognized as distinct species separate from H. occidentalis , and H. richmondensis is recognized as a distinct species rather than a geographical variant of H. alveata . Hebertella subjugata is removed from its tentative synonymy with H. occidentalis and revalidated.
The development of species-level evolutionary hypotheses for Plaesiomys and Hebertella provides a detailed framework for assessing evolutionary and paleobiogeographic patterns of Late Ordovician brachiopods from Laurentia. The geographic range of Hebertella expanded throughout Laurentia during the Richmondian into both intracratonic and marginal basins. Plaesiomys subquadratus participated in the Late Ordovician Richmondian Invasion. The recovered phylogenetic topology for Plaesiomys suggests that P. subquadratus may have migrated into the Cincinnati region from a basin situated to the paleo-northeast.
... In HSC, this is implemented via the coding of intermediates: if the means of taxa A and C are significantly different for a trait, but taxon B has a mean that lies between those of A and C, but is not significantly different from either, taxon B is coded as intermediate. As pointed out previously (Swiderski et al., 1998), this is exactly the distribution that would be expected in a trait changing via gradualism; to argue that this "creates non-existent differences" is to ignore the obvious power of selection on populations. ...
A consensus is emerging that continuous (or metric) measures can be useful in
phylogenetic systematics. Many of the methods for coding such characters, how-
ever, employ elements that are arbitrary and therefore should be excluded from
use in cladistic analysis. The continued use of such potentially inappropriate
methods can be attributed to either their simplicity or the availability of
computer programs specifically designed to produce data matrices using these
methods. Conversely, one of the most suitable methods, homogeneous subset
coding (HSC), is underused, probably due to the lack of a suitable software
implementation for this somewhat complex procedure.
This paper describes TaxMan, a Web-based facility for the coding of
continuous data using HSC. Data are entered using a form accessible via any
internet browser and are automatically converted to a matrix suitable for input
into tree-searching software. This implementation of the HSC technique provides
an uncomplicated procedure for the incorporation of metric data in phylogenetic
systematics. The algorithmic implementation of the HSC procedure, and
interpolation of the Studentised range and maximum modulus distributions
required by it, is described in detail in appendices.
... Maximum lengths were determined from the literature (Bayer, 1961;Sánchez, 1998;. Only continuous characters that could be coded according to gap coding were considered informative (Mickevich and Johnson, 1976, see also Swiderski et al., 1998). The type of branching (pinnate, alternate, and reticulate: Fig. 3.1) of every species was qualitatively examined from digital images taking in the Exuma Cays, Bahamas (2000). ...
... Earlier work by Swiderski et al. (1998) used principal warps as characters, but as noted by Bookstein (2002) and Adams and Rosenberg (1998) these values are the result of a projection that is arbitrary from a biological perspective. González-José et al. (2008) also divided their data before the superimposition process and were able to avoid the problem of using arbitrary projections by treating the principal components for each module as additive for the parsimony part of their analysis, thus treating their data as continuous. ...
... Continuous patterns of variation among OTU s are problematic for simple parsimony-based phylogenetic inference methods (but see Felsenstein 1981;Maddison 1991). Continuous variables are not, so long as the patterns of OTU distribution along the continuously varying axis are discontinuous (e.g., Swiderski et al. 1998). In addition, examples of mean values, variances, and kurtoses of continuous biometric variables have been shown to be under direct genetic or epigenetic control (e.g., Falconer 1981), suggesting that, in principle, these types of variables may carry important phylogenetic signals. ...
The analysis of morphology is crucial to the study of phylogeny in many ancient and modern organismal groups. Recently a number of arguments have been made in favor of regarding certain kinds of morphometric variables as putatively homologous characters and allowing them to participate, along with other non-morphometric variables, in parsimony-based cladistic analyses. These arguments rest on the assumptions that geometric landmarks incorporate the concept of biological homology and that partial warp and principal warp morphometric variables uniquely incorporate and operationalize the concept of spatial localization, thus providing investigators with the ability to assess patterns and directions of geometrical variation in unmeasured regions of organic forms. Literature review, coupled with empirical investigations of similarities and differences among three different morphometric data analysis methods on two different datasets suggest that there is no support for these assertions. Geometric landmarks, which form the basis for all morphometric measurements and latent shape variables, have no necessary correspondence to biological homology. Partial warp variables, coordinate-point eigenshape variables, and inter-landmark distance-based singular vector shape-change variables all express localized (= regionally-weighted) geometric deformations. However, none of these deformation patterns are localized in the sense of being truly independent from globally-distributed aspects of shape change. All three of the morphometric
... Archie 1985;Goldman 1988;Strait et al. 1996;Guerrero et al. 2003;Hopkins 2011). In this analysis, measurements of continuous characters were normalized and separated into discrete states using a procedure similar to those suggested by Morton & Kincaid (1995) and Swiderski et al. (1998). Morphometric measurements were visually inspected by examining univariate frequency distributions and box plots and cut-offs were determined by the presence of discontinuities, disjunct clusters, or changes in slope within the distribution (Hunt 2007;Stigall Rode 2005). ...
Species of the orthide brachiopod genus Glyptorthis occur as common constituents of Late Ordovician benthic marine faunas, particularly in Laurentia. A phylogenetic analysis of 23 North American species of Glyptorthis was conducted to inform a systematic revision and ascertain evolutionary relationships amongst species. Both discrete and continuous characters, from which character states were determined using statistical methods, were utilized within a maximum parsimony approach. Glyptorthis maquoketensis is recognized as a distinct species of Glyptorthis rather than a subspecies of G. insculpta. Glyptorthis virginica is herein synonymized with G. uniformis. Several species of Glyptorthis became widely distributed via dispersal events during the evolution of the clade. The revised phylogenetic topology provides structure to interpret biogeographical patterns within the genus. For example, Glyptorthis insculpta participated in the Late Ordovician Richmondian Invasion into the Cincinnati Basin. The recovered phylogenetic topology suggests that G. insculpta may have invaded the Cincinnati Basin from a low latitude subtropical region of Laurentia, such as the American mid-Continent.
... where notation follows Shaw (1957) (Fig. 3). Despite debate over how continuous characters should be coded, they are demonstrably phylogenetically informative (Chappill, 1989;Stevens, 1991;Thiele, 1993;Rae, 1998;Swiderski et al., 1998). There are numerous methods for coding quantitative data into 'discrete' character states for inclusion in phylogenetic analysis, including various types of gap-coding (Michevich and Johnson, 1976;Colless, 1980;Almeida and Bisby, 1984;Thorpe, 1984;Archie, 1985;Baum, 1988;Goldman, 1988;Chappill, 1989;Guerrero et al., 2003), statistical methods (e.g., analysis of variance and multiple range test [ANOVA-MRT], Guerrero et al., 2003), and model fitting (e.g., finite mixture coding, Strait et al., 1996). ...
Considerable systematic work devoted to late Cambrian trilobites includes very little species-level phylogenetic analysis. This paper presents the phylogenetic analysis of 36 species representing eight genera assigned to the Family Pterocephaliidae that occur in the Great Basin of the western United States during the Steptoean stage (Furongian). Continuous characters are treated in four different ways: discretization using finite mixture coding, discretization using gap-weighting, "as such" using ranges of values as implemented in the phylogeny program TNT, and exclusion altogether. Results indicate that even the inclusion of only a few continuous characters dramatically increases the resolution of nodes. Despite the different treatments of continuous characters, major features of the trees are shared across all results. The subfamily Pterocephaliinae is restricted to genera which possess a concave anterior border. Relative stratigraphie placement was estimated using a composite section built in CONOP and used to scale the tree topologies and to assess stratigraphic consistency. Although previously hypothesized multispecies evolutionary series are not supported by the results, tree topology, stratigraphie distribution, and optimized character state transformation support the interpretation of several sister taxa as direct ancestor-descendent pairs.
... The consequence for phylogenetic analysis of incorporating a false hypothesis may be additional homoplasy in the analysis, or additional support provided for an incorrect conclusion. While morphometric data are not different in principle from data more traditionally coded as characters (Swiderski et al., 1998 ), they may be especially vulnerable to errors in homology assessment, and their evolution may more readily lend itself to modelling in a continuous framework (Felsenstein, 1988). The difficulty here, of course, is identifying an appropriate model. ...
SYNOPSIS. Morphometric approaches facilitate the analysis of quantitative vari- ation in form, typically becoming most useful for the study of organisms that have completed morphogenesis and are at differing stages of growth. Recent conceptual and technical refinements in the characterization and comparison of forms have joined methodological innovations in molecular biology, embryology, and phylog- eny reconstruction to advance the study of the evolution of development. Among the phenomena that have recently been examined morphometrically are develop- mental integration and heterochrony, discoveries that in turn raise deeper ques- tions about the connections among disciplines and among levels of description: the relationship between morphometric variables and characters, between phenome- nology and process, and the interplay (and evolutionary relevance) of genes and phenotypes. Morphometrics can continue to play a vital role in evolutionary studies of development as its results generate questions both for its practitioners and for other sorts of biologists to explore.
... At issue here is the inability of one author to interpret the character statements of another as the reason for character statement rejection. This does not concern perceived variability of specimens or taxa (criteria 1-5), disagreements over ''primary homology'' (criteria 6-9), logical shortcomings (criteria 10, 11), or even differing interpretations of the same morphology among specialists considering the same taxa (Hawkins et al., 1997;Swiderski et al., 1998;Hawkins, 2000;Stevens, 2000). ...
Systematists have questioned the distinction between characters and character states and their alignment with the traditional concept of homology. Previous definitions for character and character state show surprising variation. Here it is concluded that characters are simply features expressed as independent variables and character states the mutually exclusive conditions of a character. Together, characters and character states compose what are here termed character statements . Character statements are composed of only four fundamental functional components here identified as locator, variable, variable qualifier, and character state, and these components exist in only two patterns, neomorphic and transformational. Several controversies in character coding and the use of “absent” as a character state are understood here as a consequence of incomplete character statements and the inappropriate mixing of neomorphic and transformational character statements. Only a few logically complete patterns for morphological character data exist; their adoption promises to greatly reduce current variability in character data between analyses.
© The Willi Hennig Society 2007.
... The consequence for phylogenetic analysis of incorporating a false hypothesis may be additional homoplasy in the analysis, or additional support provided for an incorrect conclusion. While morphometric data are not different in principle from data more traditionally coded as characters (Swiderski et al., 1998 ), they may be especially vulnerable to errors in homology assessment, and their evolution may more readily lend itself to modelling in a continuous framework (Felsenstein, 1988). The difficulty here, of course, is identifying an appropriate model. ...
Morphometric approaches facilitate the analysis of quantitative variation in form, typically becoming most useful for the study of organisms that have completed morphogenesis and are at differing stages of growth. Recent conceptual and technical refinements in the characterization and comparison of forms have joined methodological innovations in molecular biology, embryology, and phylogeny reconstruction to advance the study of the evolution of development. Among the phenomena that have recently been examined morphometrically are developmental integration and heterochrony, discoveries that in turn raise deeper questions about the connections among disciplines and among levels of description: the relationship between morphometric variables and characters, between phenomenology and process, and the interplay (and evolutionary relevance) of genes and phenotypes. Morphometrics can continue to play a vital role in evolutionary studies of development as its results generate questions both for its practitioners and for other sorts of biologists to explore.
... The systematic utility of morphometric distances has been questioned also, even by proponents of this paradigm (e.g., Bookstein, 1994). But, in contrast to DNA-DNA hybridization scores and immunological distances, morphometric shape can be coded into discrete states using different procedures (Swiderski et al., 1998). Therefore, these data can be included in a supermatrix analysis as independent systematic evidence, so the ability to incorporate morphometric data does not necessarily distinguish supertree analysis from supermatrix analysis. ...
Strict and semi-strict supertree construction methods can be used to summarize groups that are consistent with all source phylogenies. Other procedures, such as Matrix Representation with Parsimony (MRP), arbitrate conflicts among incompatible source trees, and can provide more topological resolution than strict and semi-strict methods. MRP has been used to construct most of the large supertrees that have been published to date. We review some of the inherent problems with MRP and other supertree methods, point out specific difficulties in previously published MRP-supertree analyses, question some of the possible advantages of supertrees, and suggest that supermatrix analyses of character data should provide the primary framework for comparative biology in the 21st century.
... Recent studies have demonstrated that continuous data described by general morphometric methods are suitable for inclusion in phylogenetic analyses (e.g., Rae 1997Rae , 1998Swiderski et al. 1998;Zelditch et al. 2000Zelditch et al. , 2001Felsenstein 2002;Humphries 2002;Rae 2002;Jensen 2003). As Zelditch et al. (2001, p. 148) succinctly pointed out "some objections ostensibly directed at quantified shape data apply equally well to all shape data, or perhaps even to all data, not quantified size and shape data exclusively." ...
Despite being the objects of numerous macroevolutionary studies, many of the best-represented constituents of the fossil record-including diverse examples such as foraminifera, brachiopods, and mollusks-have mineralized skeletons with limited discrete characteristics, making morphological phylogenies difficult to construct. In contrast to their paucity of phylogenetic characters, the mineralized structures (tests and shells) of these fossil groups frequently have distinctive shapes that have long proved useful for their classification. The recent introduction of methodologies for including continuous data directly in a phylogenetic analysis has increased the number of available characters, making it possible to produce phylogenies based in whole or part on continuous character data collected from such taxa. Geometric morphometric methods provide tools for accurately characterizing shape variation and can produce quantitative data that can therefore now be included in a phylogenetic matrix in a non-arbitrary manner. Here, the marine gastropod genus Conus is used to evaluate the ability of continuous characters-generated from a geometric morphometric analysis of shell shape-to contribute to a total evidence phylogenetic hypothesis constructed using molecular and morphological data. Furthermore, the ability of continuous characters derived from geometric morphometric analyses to place fossil taxa with limited discrete characters into a phylogeny with their extant relatives was tested by simulating the inclusion of fossil taxa. This was done by removing the molecular partition of individual extant species to produce a "cladistic pseudofossil" with only the geometric morphometric derived characters coded. The phylogenetic position of each cladistic pseudofossil taxon was then compared with its placement in the total evidence tree and a symmetric resampling tree to evaluate the degree to which morphometric characters alone can correctly place simulated fossil species. In 33-45% of the test cases (depending upon the approach used for measuring success), it was possible to place the pseudofossil taxon into the correct regions of the phylogeny using only the morphometric characters. This suggests that the incorporation of extinct Conus taxa into phylogenetic hypotheses will be possible, permitting a wide range of macroevolutionary questions to be addressed within this genus. This methodology also has potential to contribute to phylogenetic reconstructions for other major components of the fossil record that lack numerous discrete characters.
... The remaining 20 characters are continuous. The use of continuous characters in cladistic analysis has been much discussed (e.g., Crisp and Weston, 1987;Pimentel and Riggins, 1987;Cranston and Humphries, 1988;Felsenstein, 1988Felsenstein, , 2002Felsenstein, , 2004Farris, 1990;Stevens, 1991;Crowe, 1994;Disotell, 1994;Poe and Wiens, 2000;Goloboff et al., 2006;Hendrixson and Bond, 2009), and a number of methods for analyzing continuous characters have been proposed (e.g., Mickevich and Johnson, 1976;Colless, 1980;Almeida and Bisby, 1984;Thorpe, 1984;Archie, 1985;Baum, 1988;Felsenstein, 1988Felsenstein, , 2002Goldman, 1988;Chappill, 1989;Thiele, 1993;Miller and Coyle, 1996;Straight et al., 1996;Sosa and De Luna, 1998;Swiderski et al., 1998;Wiens, 2001;Guerrero et al., 2003;Garcia-Cruz and Sosa, 2006;Goloboff et al., 2006). Continuous characters have not played a major role in phylogenetic studies of anomodonts, although Angielczyk (2007) and Angielczyk and Rubidge (2010, in press) used continuous data that had been converted into discrete characters with Thiele's (1993) method in their analyses, and Cox and Li (1983) used measurement data as an important part of their classification of Triassic dicynodonts. ...
The dicynodont wastebasket genus Dicynodon is revised following a comprehensive review of nominal species. Most nominal species of Dicynodon pertain to other well-known dicynodont genera, especially Oudenodon and Diictodon. Of the Karoo Permian species that are referable to “Dicynodon” sensu lato, we recognize four common, valid morphospecies: Dicynodon lacerticeps, D. leoniceps, D. woodwardi, and Dinanomodon gilli, comb. nov. Eleven additional species of “Dicynodon” are recognized worldwide: D. alticeps, D. amalitzkii, D. bathyrhynchus, D. benjamini, D. bogdaensis, D. huenei, D. limbus, D. sinkianensis, D. traquairi, D. trautscholdi, and D. vanhoepeni. Morphometric analysis of D. lacerticeps and D. leoniceps specimens recovers statistically significant separation between these species in snout profile and squamosal shape, supporting their distinction. A new phylogenetic analysis of Anomodontia reveals that “Dicynodon” is polyphyletic, necessitating taxonomic revision at the generic level. D. benjamini and D. limbus are basal cryptodonts, whereas the other valid “Dicynodon” species are basal dicynodontoids. The genus Dicynodon is restricted to D. lacerticeps and D. huenei. We reinstate use of Daptocephalus, Sintocephalus, Turfanodon, Daqingshanodon, Jimusaria, and Gordonia for other species. We synonymize Vivaxosaurus permirus and Dicynodon trautscholdi (as V. trautscholdi, comb, nov.) We establish new generic names for several species formerly included in Dicynodon: Peramodon amalitzkii, comb, nov., Keyseria benjamini, comb, nov., Euptychognathus bathyrhynchus, comb, nov., Syops vanhoepeni, comb, nov., and Basilodon woodwardi, comb. nov. Of the main Karoo Permian taxa, Dicynodon, Basilodon, and Dinanomodon range throughout the Cistecephalus and Dicynodon assemblage zones, but Daptocephalus is restricted to the Dicynodon Assemblage Zone.
... Recently a number of arguments have been made in favor of regarding certain morphometric variables as putatively homologous characters and including them, sometimes along with other non-morphometric variables, in parsimonybased cladistic analyses. Zelditch et al. (1995; see also Fink andSwiderski et al., 1998;but cf. Adams and Rosenberg, 1995;Naylor, 1996;and Monteiro, 2000) have proposed the use of partial warp-based traits in phylogenetic analysis. ...
Traditionally, morphometric data have consisted of distances, angles, or ratios, and have been considered inappropriate for cladistic analyses. Recently, geometric morphometrics, based on homologous landmark point-coordinates, has provided a number of advantages over traditional morphometric data and methods, including the possibility that phylogenetically informative characters and character-states may be extracted and used in cladistic analyses. Using two data sets of 3-dimensional point coordinates collected from skulls of bats, we empirically evaluate this possibility. Partial warps were extracted from the point-coordinate matrix, and these were then re-coded by gap-coding, for use in the cladistic analyses. In the case of samples from Eidolon helvum populations (two mainland localities and four islands in the Gulf of Guinea), analyzing males and females separately, our analyses based on these data were unable to detect consistent phylogeographic patterns among the populations. In the case of samples from plecotine bat species, these analyses produced a consensus cladogram showing considerable concordance with an earlier cladistic analysis by us of this group. In both cases, our results reflect those of earlier studies (based on both morphologic and genetic data), suggesting that the data and analytic techniques described herein may have interesting utility in cladistic analyses.
... The use of quantitatively variable characters in phylogenetic analysis has been criticized, because coding quantitative characters into states may introduce artificial distinctions in cladistic analyses (Pimentel and Riggins, 1987;Farris, 1990). On the other hand, quantitative characters should be used when there is no overlap among their character states, and the arguments against their use are not supported by systematic theory (Zelditch et al., 1995;Swiderski et al., 1998). In the analysis presented here, morphometric data are useful because they represent autapomorphies that strongly support the Xylocopa and Oxaea clades. ...
Proventricular structure, analyzed by scanning electronic microscopy, is compared among 28 species of solitary bees representing four families. Observations on the shapes of proventricular folds and on hair-like cuticular projections are presented, discussed, and suggested as useful to future studies of bee systematics.
... Polymorphic coding is applied; inapplicable characters are treated as missing information ('?'). Quantitative data were coded according to the gap-coding method, modified to minimize character-state overlaps (for discussion see Swiderski et al. 1998) and to minimize the number of autapomorphic (unique) character states. Numbers of chromosomes are referred to the karyotype of Canis lupus (Wayne et al. 1987a,b). ...
Phylogenetic relationships within the Canidae are examined, based on three genes (cytb, COI, COII) and 188 morphological, developmental, behavioural and cytogenetic characters. Both separate and combined phylogenetic analyses were performed. To inspect the phylogenetic 'behaviour' of individual taxa, basic phylogenetic analysis was followed by experimental cladistic analyses based on different data-partition combinations and taxon-removal analyses. The following phylogeny of the Recent Canidae is preferred: (1) Urocyon is the most basal canid; (2) Vulpes is a monophyletic genus (including Fennecus and Alopex); (3) the doglike canids (DC) form a clade (= Dusicyon + Pseudalopex + Lycalopex + Cerdocyon + Atelocynus + Chrysocyon + Speothos + Lycaon + Cuon + Canis), split into two subclades, South American and Afro-Holarctic, with uncertain position of the Chrysocyon + Speothos subclade; (4) Canis is paraphyletic due to the position of Lycaon and Cuon. Otocyon and Nyctereutes are the most problematic canid genera, causing an unresolved branching pattern of Otocyon, Vulpes, Nyctereutes and DC clades. Reclassification of the two basal species of 'Canis' into separate genera is proposed (Schaeffia for 'C.' adustus, Lupulella for 'C'.' mesomelas). Although the morphological dataset ranked poorly in both separate and simultaneous analyses (measured by number of minimum-length topologies, relative number of resolved nodes in the strict consensus of all minimum-length topologies, consistency and retention indices, nodal dataset influence, and number of extra steps required by the data partition to reach the topology of the combined tree), the morphological synapomorphies represent nearly one quarter of all synapomorphies in the combined tree. Among the hidden morphological support of the combined tree the developmental and behavioural characters are conspicuously abundant.
... This method allows for transformation of the continuous variation of characters into multiple character states that ideally reflect the degree of quantitative variation of the characters sampled. These states are, however, sample-dependent, and the same character state is generally assigned to closely related taxa, which also results in partial loss of phylogenetic information ( Swiderski et al. 1998). A possible alternative is to code quantitative characters as continuous ( Thiele 1993). ...
Goicoechea, N., De La Riva, I. & Padial, J. M. (2010). Recovering phylogenetic signal from frog mating calls. —Zoologica Scripta, 39, 411–154.
Few studies have tried to analyse the phylogenetic information contained in frog mating calls. While some of those studies suggest that sexual selection deletes any phylogenetic signal, others indicate that frog calls do retain phylogenetic informative characters. Discordant results can be the outcome of disparate rates of character evolution and evolutionary plasticity of call characters in different groups of frogs, but also the result of applying different coding methods. No study to date has compared the relative performance of different coding methods in detecting phylogenetic signal in calls, hampering thus potential consilience between previous results. In this study, we analyse the strength of phylogenetic signal in 10 mating call characters of 11 related species of frogs belonging to three genera of Andean and Amazonian frogs (Anura: Terrarana: Strabomantidae). We use six quantitative characters (number of notes per call, note length, call length, number of pulses per note, fundamental frequency and dominant frequency) and four qualitative ones (presence/absence of: pseudopulses, frequency modulation in notes, amplitude modulation in notes and amplitude modulation in pulses). We code quantitative characters using four different coding and scaling methods: (i) gap-coding, (ii) fixed-scale, (iii) step-matrix gap-weighting with between-characters scaling, and (iv) step-matrix gap-weighting with between-states scaling. All four coding methods indicate that frog calls contain phylogenetic information. These results suggest that divergent selection on frog mating calls may not always be strong enough to eliminate phylogenetic signal. However, coding methods strongly affect the amount of recoverable information. Step-matrix gap-weighting with between-characters scaling and gap-coding are suggested as the best methods available for coding quantitative characters of frog calls. Also, our results indicate that the arbitrariness in selecting character states and the method for scaling transitions weights, rather than the number of character states, is what potentially biases phylogenetic analyses with quantitative characters.
... Partial warps continue to be used (Bogdanowicz et al. 2005), relative warps have been argued to be more useful than partial warps (MacLeod 2002) and some hold that shapes are useful only as a first step in searching for phylogenetic characters (Rohlf 2002). Meanwhile, David and Laurin (1996) objected to shape data in cladistics because of shapeÕs epigenetic quality, Swiderski et al.Õs (1998) argument that morphometrics should be coded for cladistic analysis like any other data was answered with an argument that morphometrics can in fact create arbitrary characters (Monteiro 2000), Roth and Mercer (2000) rejected morphometric data as Ôintrinsically unsuitableÕ for phylogenetics based on non-homology, and Petersen and Seberg (2003) also disagreed with making homology statements on continuous data. Still, positions on these issues have been dynamic and proposed moratoriums on certain methods softened. ...
A phylogenetic estimation of the temperate Gondwanan mite harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi) was conducted using 143 morphological variables (59 raw and 84 scaled measurements) from 37 ingroup and 15 outgroup terminals. We used custom algorithms to do pairwise comparisons between characters and identify sets of dependent characters, which were collapsed using principal components analysis. We analysed the resulting data without discretization under the parsimony criterion. Monophyly or paraphyly of most groups suspected from previous molecular and morphological phylogenetic studies were recovered. Trees were optimized for monophyly of 20 different focus clades by varying character phylogenetic independence. This yielded a final tree with monophyly of 15 out of 20 focus clades, including the South African pettalids, which contains the troglomorphic species Speleosiro argasiformis Lawrence, 1931. Two of the remaining five clades were found paraphyletic, with the genera Aoraki, Rakaia, and Siro always being found polyphyeletic.
... Only measurements that could be separated by gap coding were considered informative characters (Mickevich and Johnson 1976; see also Swiderski et al. 1998). ...
Octocorals, especially gorgonians, are conspicuous on Caribbean coral reefs, but there is no consensus regarding species relationships. Mitochondrial protein-coding genes [NADH-dehydrogenase subunits 2 (ND2) and 6 (ND6), and mutS homolog (msh1), 1633 bp] from 28 shallow-water species were sequenced to develop the first molecular phylogeny for Caribbean octocorals. The specimens were collected primarily in the Caribbean or off Brazil in 1999-2001. Morphological characters (sclerites and axial ultrastructure) were also examined in order to map them onto the molecular phylogeny. Analyses of both nucleotide and amino acid substitutions using maximum parsimony and likelihood (including maximum-likelihood and Bayesian analysis) generated very similar results, with most nodes having high levels of support. These molecular results were significantly different from the generally accepted classification. Neither Plexauridae nor Gorgoniidae were monophyletic. Plexaurella spp., nominal plexaurids, were basal to the gorgoniids, sharing many morphological characters with them. This corroborates previous findings using secondary metabolites and biosynthetic pathways. The sea fans, Gorgonia spp. and Pacifigorgia spp., as well as the pinnate gorgonians, Muriceopsis flavida and Pseudopterogorgia spp., did not have sea fan or pinnate relatives, suggesting there has been convergent evolution of colony form. Caribbean plexaurids appeared more derived and/or recently evolved according to both morphological and molecular data (e.g. Eunicea spp. and Plexaura spp.). Molecular phylogenetics is a promising approach for reconstructing phylogenetic relationships among octocorals as well as to understand their complex morphology. Electronic Supplementary Material is available if you access this article at http://dx.doi.org/10.1007/s00227-003-1018-7. On that page (frame on the left side), a link takes you directly to the supplementary material.
... Multivariate and geometric methods offer sophisticated procedures for describing distance or landmark coordinate properties comparatively (Bookstein, 1991). Comparison of shape change expressed by deformation of projections on a coordinate system, has been suggested to provide characters that may be used for phylogenetic analysis (Zelditch et al., 1995;Swiderski et al., 1998), but the homology criterion still remains a problem (Rohlf, 1998;Zelditch et al., 1998). ...
It is argued, with selected examples from freshwaterfish systematics, that species should be viewed as anexpression of self-perpetuated clustered variation innature, conforming to the phylogenetic speciesconcept. The importance of species lies in thefunctional and structural significance of theirdiagnostic characters. Species can be nested by theircharacters into a tree diagram (phylogeny) orhierarchical alignment structure (classification) ofcharacter distribution, which may be taken to reflectevolution, the unifying theory of organismaldiversification. The phylogenetic species concept,which emphasizes recognition of a pattern ofvariation, describes better than any other proposedconcept the units called species by systematists.Other concepts are based on processes and normally donot permit recognition of particular taxa. Specieshave unique histories, and speciation may proceed bydifferent mechanisms. Whereas it may be postulatedthat speciation entails an irreversible change in thegenetic structure of taxa, recognized by phenotypicexpression and apparently also maintained to a largeextent by selection for a particular phenotype,species recognition must remain independent ofassumptions about species history and spatialdistribution. Species are monophyletic taxa and thespecies category does not differ significantly inphylogenetic regard from other systematic categories.Species as such are not necessarily evolutionaryunits. It is recommended to apply species names withreference to the diagnostic characters of the speciesand to abandon the type specimen described by theInternational Code of Zoological Nomenclature as anomenclatural reference unit.
The comparative morphology of the family Sparidae is described comprehensively for the first time and is used to formulate character data for phylogenetic analysis. The data is found to be particularly character rich in areas such as the braincase, jaws and gill arches. Phylogenetic analysis, using PAUP* was performed in order to resolve the evolutionary relationships for 29 sparid genera and representatives sparoid families: Centracanthidae; Lethrinidae; Nemipteridae. Parsimony analysis of this data yielded three equally parsimonious trees. The Sparidae constitute a monophyletic group, with the inclusion of Centracanthidae, which is embedded within cladistically derived sparids. A grouping of derived sparids are found to be reasonably well supported when judged by Bremer support and bootstrapping, while relationships amongest those taxa more basal are found to be weakly supported. Further analysis of the data is assessed from 1) character quality through application of Le Quesne probabilities; 2) data partitioning; 3) influence of outgroups; 4) effects of ordering and 5) recoding, using non-additive binary coding. These analyses also support a hypothesis of relationships amongest derived sparids that is both well supported and resolved. However, the relationships of basal sparids are sensitive to these analyses, suggesting that not much confidence may be placed in the revealed theories of their interrelationships. The conflict between alternative trees reflects the high levels of homoplasy, which is not uncommon for percoid data sets. The geographic distribution is explained using three methods of cladistic biogeography, based on irreversible and reversible methods of ancestral area analysis and dispersal-vicariance analysis. The Indo-Pacific is identified as the most likely ancestral area for the Sparidae. Reconstruction of the evolution of feeding strategies among sparids suggests that there is a progressive transition from generalist to specialized feeders with four assemblages recognized. The diversification of feeding strategies within the Sparidae may have had important consequences for the evolution of the group which is discussed. Fossil sparid material from the Early to Middle Eocene is redescribed and included in the Recent matrix for further phylogenetic analyses. Comparison of the fossil material warrants the erection of a new genus and species, Ellaserrata monksi and a new genus Abromasta microdon is erected for Pagellus microdon. A minimum age of origin for the group can be postulated at 55Ma.
The use of quantitative shape data in phylogenetic studies has been challenged on several grounds, the most important being that hypotheses of homology cannot apply to them. Two premises underlie that argument: (1) quantitative data comprise a single homogeneous class, and (2) qualitative and quantitative data are fundamentally different. The first premise is problematic because some morphometric variables are constrained to compare homologous features of organisms, whereas others are not. Those that are so constrained, including traditional measurement data, shape coordinates and partial warps, yield features that can be assessed for their similarities and differences, and the resulting hypotheses of homology can be tested for their congruence with the cladogram. Those variables that are not so constrained, including most outline-based variables as well as multivariate constructs such as principal components and canonical variates, may be useful tools discriminating and sorting taxa by overall similarities in shape, but not for dis-covering characters. The second premise is also problematic because the same logic and methods apply to both qualitative and quantitative data alike. Thus, if care is taken to ensure that morphometric comparisons are framed in terms of homology, there is no barrier to using quantitative variables in phylogenetic studies, especially those produced by geometric morphometrics. Not only are they tools for describing shape differences, they are also tools for understanding the evolutionary history of shape.
It has always been obvious that organisms have properties making them ‘different’ from each other. Historically, taxonomists have sought to register these differences and similarities by assigning species to subjectively-delimited groups within hierarchical classifications. Many current methods in sys-tematics still have a subjective component, and classifications often reflect biases inherent in their construction (Hull 1988).
The intra-populational and ontogenetic variation present in the skeletal structures of Compsothyris racovitzae (Joubin, 1901), the type species of the genus, was studied, described and illustrated in a series of specimens from Antarctic waters, including those recently dredged in the 'BENTART' oceanographic expeditions. Detailed SEM examinations have shown that dorsal internal structures such as the cardinalia display great variability and that the surface to which the posterior end of the lophophore was attached to the crura is composed of nonfibrous, roughly textured calcite, which has been described as the brachiotest in terebratulide loops. The need to include information on the range of intra-specific and ontogenetic variants in databases and in character state matrices for phylogenetic analyses is discussed, and it is suggested that databases could be used to standardize character states extracted from taxonomic descriptions into matrices for phylogenetic analyses.
The characterization of complex diseases remains a great challenge for biomedical researchers due to the myriad interactions of genetic and environmental factors. Network medicine approaches strive to accommodate these factors holistically. Phylogenomic techniques that can leverage available genomic data may provide an evolutionary perspective that may elucidate knowledge for gene networks of complex diseases and provide another source of information for network medicine approaches. Here, an automated method is presented that leverages publicly available genomic data and phylogenomic techniques, resulting in a gene network. The potential of approach is demonstrated based on a case study of nine genes associated with Alzheimer Disease, a complex neurodegenerative syndrome.
The developed technique, which is incorporated into an update to a previously described Perl script called “ASAP,” was implemented through a suite of Ruby scripts entitled “ASAP2,” first compiles a list of sequence-similarity based orthologues using PSI-BLAST and a recursive NCBI BLAST+ search strategy, then constructs maximum parsimony phylogenetic trees for each set of nucleotide and protein sequences, and calculates phylogenetic metrics (Incongruence Length Difference between orthologue sets, partitioned Bremer support values, combined branch scores, and Robinson–Foulds distance) to provide an empirical assessment of evolutionary conservation within a given genetic network. In addition to the individual phylogenetic metrics, ASAP2 provides results in a way that can be used to generate a gene network that represents evolutionary similarity based on topological similarity (the Robinson–Foulds distance).
The results of this study demonstrate the potential for using phylogenomic approaches that enable the study of multiple genes simultaneously to provide insights about potential gene relationships that can be studied within a network medicine framework that may not have been apparent using traditional, single-gene methods. Furthermore, the results provide an initial integrated evolutionary history of an Alzheimer Disease gene network and identify potentially important co-evolutionary clustering that may warrant further investigation.
The present study comprises an analysis of six different scoring schemes and eight different types of analytic methods aiming to investigate the evolution of a continuous character (i.e. corolla tube length) in Lithospermum L. (Boraginaceae). Corolla tube length in the genus is quite variable, ranging from 1 mm to 75 mm, and the length of the corolla tube has implications for pollination biology, such as longer corolla tubes (> 25 mm in length) being pollinated by hummingbirds or moths. In general, the various methods resolve similar ancestral character states; however, different states are reconstructed at nodes in which the descendants greatly differ in corolla tube length. Additionally, it is suggested that all of the variation of a continuous character should be included in analyses, and this may necessitate multiple analyses with different partitions of the data. The various analyses provide evidence that two maximum parsimony methods, linear parsimony and the TNT method, minimize the number of different rates of evolution. In Lithospermum, six origins of corolla tubes > 20 mm in length are resolved, and these origins occurred at two different times periods: (1) in the shadow of hummingbird diversification in North America (approximately 6–8 Mya) and (2) more recently (approximately 1–1.5 MyA). Four substantial decreases in corolla tube length also are reconstructed, and these may be associated with the origin of self‐pollination. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.
Sixty-three continuous osteological characters (18 skull continuous characters and the total length of neurocranium, 45 continuous characters of 15 elements of the viscerodermal skeleton) were analyzed and included in the reconstruction of phylogenetic relationships of the six Euro-Mediterranean mullet species from the South Adriatic Sea: Mugil cephalus Linnaeus, 1758; Liza saliens Risso, 1810; Liza aurata Risso, 1810; Liza ramada Risso, 1826; Chelon labrosus Risso, 1826 and Oedalechilus labeo Cuvier, 1829. The study reveals that Sphyraenidae was separated clearly from Mugilidae, C. labrosus and three Liza species form a common cluster (L. ramada and L. saliens being the closest), while O. labeo and M. cephalus cluster together.
We investigated the phylogenetic relationships of Campylorhamphus pucherani using DNA sequences from three mitochondrial genes and a nuclear intron, as well as morphological characters from the skeleton, the integument, and the musculature. The molecular phylogeny indicated that C. pucherani is not part of Campylorhamphus; instead, it is the sister species to Drymornis bridgesii, in a clade that also contains Lepidocolaptes. The morphological phylogeny also placed C. pucherani in a clade that contains Drymornis and Lepidocolaptes. Using a morphometric analysis of size and shape diversity, we demonstrated that the inclusion of C. pucherani in Drymornis would create an excessively heterogeneous genus compared with other dendrocolaptine genera. Because no generic name is available for C. pucherani, we describe the new genus Drymotoxeres for this species.
The first edition of Geometric Morphometrics for Biologists has been the primary resource for teaching modern geometric methods of shape analysis to biologists who have a stronger background in biology than in multivariate statistics and matrix algebra. These geometric methods are appealing to biologists who approach the study of shape from a variety of perspectives, from clinical to evolutionary, because they incorporate the geometry of organisms throughout the data analysis. The second edition of this book retains the emphasis on accessible explanations, and the copious illustrations and examples of the first, updating the treatment of both theory and practice. The second edition represents the current state-of-the-art and adds new examples and summarizes recent literature, as well as provides an overview of new software and step-by-step guidance through details of carrying out the analyses. Contains updated coverage of methods, especially for sampling complex curves and 3D forms and a new chapter on applications of geometric morphometrics to forensics Offers a reorganization of chapters to streamline learning basic concepts Presents detailed instructions for conducting analyses with freely available, easy to use software Provides numerous illustrations, including graphical presentations of important theoretical concepts and demonstrations of alternative approaches to presenting results.
Sorry not available as a full text download!
Gaylussacia includes 49 species of understory shrubs in the heath family (Ericaceae) with a disjunct distribution in North and South America. Little is known about evolutionary relationships among the species. To investigate phylogenetic and biogeographic relationships in Gaylussacia, three data sets were constructed and analyzed cladistically using parsimony: morphology, nuclear ribosomal internal transcribed spacer DNA sequences, and chloroplast trnL intron-trnF spacer DNA sequences. Molecular data sets were analyzed in two ways to determine the phylogenetic informativeness of insertion/deletion events. Comparison of results from separate analyses of each data set showed some incongruencies between the nuclear and chloroplast data sets, indicating possible past hybridization or lineage sorting. Combined analyses were conducted for ITS and morphology, and for trnL-trnF and morphology. The monophyly of the genus including G. brachycera was not strongly supported. In addition, the traditional sectional divisions of Gaylussacia were not supported in the morphological and nuclear DNA analyses. Finally, a broader perspective on the disjunct distribution of Gaylussacia includes the possibility of a North American origin for the genus, rather than a South American origin as previously hypothesized. Communicating Editor: Matt Lavin
In the 1990s Rubiaceae became a hot spot for systematists, mainly due to the comprehensive treatment of the family by Robbrecht in 1988. Next to the exploration of macromolecular characters to infer the phylogeny, the palynology of Rubiaceae finally received the attention it deserves. This article aims to present a state-of-the-art analysis of the systematic palynology of the family. The range of varíation in pollen morphology is wide, and some of the pollen features are not known from other angiosperm taxa; e.g., a looplike or spiral pattern for the position of apertures in pantoaperturate grains. We compiled an online database at the generic level for the major pollen characters and orbicule presence in Rubiaceae. An overview of the variation is presented here and illustrated per character: dispersal unit, pollen size and shape, aperture number, position and type, sexine ornamentation, nexine pattern, and stratification of the sporoderm. The presence/absence and morphological variation of orbicules at the generic level is provided as well. The systematic usefulness of pollen morphology in Rubiaceae is discussed at the (sub)family, tribal, generic, and infraspecific levels, using up-to-date evolutionary hypotheses for the different lineages in the family. The problems and opportunities of coding pollen characters for cladistic analyses are also treated.
Evolutionary shape changes in skull and mandibular anatomy was analysed in 223 specimens of pantherine felids (Neofelis nebulosa, Panthera leo, Panthera onca, Panthera pardus, Panthera tigris, Panthera uncia) compared to a small-felid outgroup, consisting of 86 specimens of nine different species, using digital surface morphometry on 25 (skull) and 17 (mandible) landmarks. Shape evolution in the pantherine species is complex and nonlinear, and involves both large-scale and small-scale shape changes. Shape changes frequently differ among the ingroup species, but the four large Panthera species (leo, onca, pardus, tigris) bear some resemblance to each other. The leopard and jaguar bear the closest resemblance to each other, and several shape changes are common to the lion and tiger, but have probably evolved convergently as a result of large size. The lion has undergone the largest and most numerous shape changes from a small-felid outgroup. Certain shape changes in the skull and, in some respects, the mandible of the clouded leopard bear resemblance to those in the four large Panthera species. The snow leopard is often regarded as the most primitive of the extant Panthera, and skull and mandibular shape changes often diverge markedly from those observed in the other five ingroup taxa; its overall skull shape is rather similar to the small-felid outgroup. This indicates that the shape changes in the clouded leopard are convergent with those of the four large Panthera species. Landmark integration showed no significant correlation with molecular phylogeny, chiefly owing to the snow leopard being placed among the four large Panthera species. A traditional phylogenetic topology with the snow leopard as the basal-most species of Panthera yielded a weak but nonsignificant phylogenetic signal. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 766–778.
The pollen morphology of 148 taxa (135 species and 13 varieties) of the parasitic plant genus Cuscuta (dodders, Convolvulaceae) was examined using scanning electron microscopy. Six quantitative characters were coded using the
gap-weighting method and optimized onto a consensus tree constructed from three large-scale molecular phylogenies of the genus
based on nuclear internal transcribed spacer (ITS) and plastid trn-LF sequences. The results indicate that 3-zonocolpate pollen is ancestral, while grains with more colpi (up to eight) have
evolved only in two major lineages of Cuscuta (subg. Monogynella and cladeO of subg. Grammica). Complex morphological intergradations occur between species when their tectum is described using the traditional qualitative
types—imperforate, perforate, and microreticulate. This continuous variation is better expressed quantitatively as “percent
perforation,” namely the proportion of perforated area (puncta or lumina) from the total tectum surface. Tectum imperforatum
is likely the ancestral condition, while pollen grains with increasingly larger perforation areas have evolved multiple times.
The reticulated tectum, unknown in other Convolvulaceae, has evolved in Cuscuta only in two lineages (subg. Monogynella, and cladeO of subg. Grammica). Overall, the morphology of pollen supports Cuscuta as a sister to either the “bifid-style” Convolvulaceae clade (Dicranostyloideae) or to one of the members of this clade.
Pollen characters alone are insufficient to reconstruct phylogenetic relationships; however, palynological information is
useful for the species-level taxonomy of Cuscuta.
KeywordsConvolvulaceae-
Cuscuta
-Dodders-Evolution-Phylogeny-Pollen morphology-Scanning electron microscopy-Taxonomy
ResearchGate has not been able to resolve any references for this publication.