scholarly journals Character correlation and its use for identification

Zootaxa ◽  
2021 ◽  
Vol 5071 (1) ◽  
pp. 131-142
Author(s):  
JAMES E. HAYDEN
Keyword(s):  
Multiple Regression ◽  
Cladistic Analysis ◽  
Worked Examples ◽  
State Transitions ◽  
Character State ◽  
Correlation Index ◽  
Analytical Error ◽  
Character Correlation

A method is presented for correlating phylogenetic characters through cladistic analysis. It extends the use of phylogenetic datasets for diagnostic purposes. It improves matrix-based identification tools by predicting novel character-state combinations that were not observed when the key was constructed. By interpreting homoplasy as analytical error, hypothetical character-state combinations are tested for the homoplasy that they would add to the shortest tree(s). The correlation is equal to the homoplasy summed across all state combinations, divided by a maximum possible value. The results depend on uncertainty about the sequence of state transitions and their overlap among characters. A correlation index r is proposed for sets of non-additive characters; it is a kind of multiple-regression value, and its ensemble value R is a statistic of a whole matrix. This approach can be used to select sets of the best "proxy" characters to substitute for unobservable characters of interest. The concept can be extended to continuous characters. Worked examples are given with datasets of various insect orders.  

Evolution of Angiosperm Pollen: 8. Lamiids

2020 ◽  
Vol 105 (3) ◽  
pp. 323-376
Author(s):  
Li-E Yang ◽  
Lu Lu ◽  
Kevin S. Burgess ◽  
Hong Wang ◽  
De-Zhu Li
Keyword(s):  
Maximum Likelihood ◽  
Pollen Morphology ◽  
Pollen Size ◽  
State Transitions ◽  
Character State ◽  
Evolutionary Mechanisms ◽  
Pollen Characters ◽  
Exine Ornamentation ◽  
Shape Class ◽  
Pollen Character

Lamiids, a clade composed of approximately 15% of all flowering plants, contains more than 50,000 species dispersed across 49 families and eight orders (APG IV, 2016). This paper is the eighth in a series that analyzes pollen characters across angiosperms. We reconstructed a maximum likelihood tree based on the most recent phylogenetic studies for the Lamiids, comprising 150 terminal genera (including six outgroups) and covering all eight orders and 49 families within the clade. To illustrate pollen diversity across the Lamiids, pollen grains from 22 species (22 genera in 14 families) were imaged under light, scanning, and transmission electron microscopy. Eighteen pollen characters that were documented from previous publications, websites, and our new observations were coded and optimized onto the reconstructed phylogenetic tree using Fitch parsimony, maximum likelihood, and hierarchical Bayesian analysis. Pollen morphology of the Lamiids is highly diverse, particularly in shape class, pollen size, aperture number, endoaperture shape, supratectal element shape, and tectum sculpture. In addition, some genera show relatively high infrageneric pollen variation within the Lamiids: i.e., Coffea L., Jacquemontia Choisy, Justicia L., Pedicularis L., Psychotria L. nom. cons., Sesamum L., Stachytarpheta Vahl, and Veronica L. The plesiomorphic states for 16 pollen characters were inferred unambiguously, and 10 of them displayed consistent plesiomorphic states under all optimization methods. Seventy-one lineages at or above the family level are characterized by pollen character state transitions. We identified diagnostic character states for monophyletic clades and explored palynological evidence to shed light on unresolved relationships. For example, palynological evidence supports the monophyly of Garryales and Metteniusaceae, and sister relationships between Icacinaceae and Oncothecaceae, as well as between Vahliales and Solanales. The evolutionary patterns of pollen morphology found in this study reconfirm several previously postulated evolutionary trends, which include an increase in aperture number, a transition from equatorially arranged apertures to globally distributed ones, and an increase in exine ornamentation complexity. Furthermore, there is a significant correlation between pollen characters and a number of ecological factors, e.g., pollen size and pollination type, pollen ornamentation and pollination type, and shape class and plant growth form. Our results provide insight into the ecological, environmental, and evolutionary mechanisms driving pollen character state changes in the Lamiids.

Phylogenetic and morphometric analyses of Eastern fluted-point forms

2015 ◽  
Author(s):  
◽  
Matthew T. Boulanger
Keyword(s):  
Material Culture ◽  
Selective Pressure ◽  
Cladistic Analysis ◽  
Eastern North America ◽  
Character State ◽  
State Change ◽  
University Of Missouri ◽  
Projectile Points ◽  
Morphometric Analyses ◽  
The University

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] This dissertation constitutes two mutually complementary approaches to the study of Paleoindian material culture in eastern North America, ca. 13,500-10,500 calendar years before present. Archaeologists have long held that the East contains a substantially greater degree of morphological variation in Paleoindian point forms, though precisely why this is the case has rarely been explained. It is also unclear how many of the various point forms relate to each other in an evolutionary sense--which forms are derived from which, and why? Morphological analyses are conducted on a large sample of intact Paleoindian projectile points from across the East. I use paradigmatic classification to establish classes for use in a cladistic analysis to evaluate heritable continuity within the sample. Results of this analysis suggest that shape and form of Paleoindian projectile points changed in a more-or-less stochastic fashion across space, and evidence for strong selective pressure is limited. Findings concerning the process of character-state change suggest that some characters become fixed early in the evolution of points, whereas others appear to change frequently. The results of this study demonstrate that changes in Paleoindian projectile points can be explained within a cultural-evolution framework.

scholarly journals Boolean logic and character state identity: pitfalls of character coding in metazoan cladistics

2002 ◽  
Vol 71 (1-3) ◽  
pp. 67-91 ◽  
Author(s):  
Ronald A. Jenner
Keyword(s):  
Cladistic Analysis ◽  
Comparative Morphology ◽  
Boolean Logic ◽  
Morphological Data ◽  
Critical Study ◽  
Published Data ◽  
Character State ◽  
Data Sets ◽  
State Identity ◽  
Character Coding

A critical study of the morphological data sets used for the most recent analyses of metazoan cladistics exposes a rather cavalier attitude towards character coding. Binary absence/presence coding is ubiquitous, but without any explicit justification. This uncompromising application of Boolean logic in character coding is remarkable since several recent investigations have nominated absence/presence coding as the most problematic coding method available for standard cladistic analysis. Moreover, the prevalence of unspecified “absence” character states in the published data sets introduces a discrepancy between the theoretical foundations of phylogenetic parsimony and current practices in metazoan cladistics. Because phylogenetic parsimony assumes transformation of character states, its effective operation breaks down when not all character states are carefully delimited. Examples of resulting meaningless character state transformations are discussed in two categories: 1) when unspecified “absence” states are plesiomorphic; and 2) when unspecified “absence” states are apomorphic (character reversals). To facilitate future progress in metazoan cladistics, the mandatory link between comparative morphology and character coding needs to be reestablished through a more explicit study of morphological variation prior to character coding, and through a more explicitly experimental approach to character coding.

La répartition des caractères dans la classification des Hamamelididae (Angiospermae)

1987 ◽  
Vol 65 (8) ◽  
pp. 1756-1767 ◽  
Author(s):  
Denis Barabé ◽  
Yves Bergeron ◽  
Gilles Vincent
Keyword(s):  
Numerical Methods ◽  
Correlation Coefficient ◽  
Cladistic Analysis ◽  
Structural Level ◽  
Cophenetic Correlation ◽  
Cluster Membership ◽  
Cophenetic Correlation Coefficient ◽  
Character Correlation ◽  
Floral Characters

By using numerical methods, the authors have analyzed correlations between vegetative and floral characters within the Hamamelididae subclass to determine which characters prevail in the characterization of each group of families. The cophenetic correlation coefficient, topological difference, cluster membership divergence, subtree membership divergence, and partition membership divergence show very little congruence between the vegetative and floral characters; this is explained by the heterobathmic evolution of the characters. In Hamamelididae, characters that best delimit groups are also those which play an important role in phylogeny. When both vegetative and floral characters indicate the same delimitations, the classification can be considered natural. The best discriminating characters at the structural level are generally the most important in a cladistic analysis because of their variability. If the character correlation principle is considered, an exhaustive analysis of the classification can help to solve phylogenetic problems.

scholarly journals Convergent? Minds? Some questions about mental evolution

2017 ◽  
Vol 7 (3) ◽  
pp. 20160125 ◽  
Author(s):  
Matt Cartmill
Keyword(s):  
Phylogenetic Tree ◽  
Error Detection ◽  
Experimental Techniques ◽  
State Transitions ◽  
Character State ◽  
Detection Mechanism ◽  
Cognitive Capacities ◽  
Primitive State ◽  
Mental Events ◽  
Shared Character

In investigating convergent minds, we need to be sure that the things we are looking at are both minds and convergent. In determining whether a shared character state represents a convergence between two organisms, we must know the wider distribution and primitive state of that character so that we can map that character and its state transitions onto a phylogenetic tree. When we do this, some apparently primitive shared traits may prove to represent convergent losses of cognitive capacities. To avoid having to talk about the minds of plants and paramecia, we need to go beyond assessments of behaviourally defined cognition to ask questions about mind in the primary sense of the word, defined by the presence of mental events and consciousness. These phenomena depend upon the possession of brains of adequate size and centralized ontogeny and organization. They are probably limited to vertebrates. Recent discoveries suggest that consciousness is adaptively valuable as a late error-detection mechanism in the initiation of action, and point to experimental techniques for assessing its presence or absence in non-human mammals.

scholarly journals A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination.

Genetics ◽  
1993 ◽  
Vol 134 (2) ◽  
pp. 659-669 ◽  
Author(s):  
A R Templeton ◽  
C F Sing
Keyword(s):  
Evolutionary History ◽  
Cladistic Analysis ◽  
Statistical Design ◽  
Worked Examples ◽  
Data Sets ◽  
Permutation Testing ◽  
Phenotypic Effect ◽  
Analytical Strategy ◽  
History Of ◽  
Endonuclease Mapping

Abstract We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, we presented an algorithm for estimating the set of likely claodgrams and recombination events. In this paper we present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper we also extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects.

scholarly journals Influence of different modes of morphological character correlation on phylogenetic tree inference

2018 ◽  
Author(s):  
Thomas Guillerme ◽  
Martin D. Brazeau
Keyword(s):  
Phylogenetic Analysis ◽  
A Priori ◽  
Probabilistic Methods ◽  
Morphological Data ◽  
Character State ◽  
Coding Schemes ◽  
Tree Inference ◽  
Character Correlation ◽  
Parsimony Trees ◽  
Character Correlations

AbstractPhylogenetic analysis algorithms require the assumption of character independence - a condition generally acknowledged to be violated by morphological data. Correlation between characters can originate from intra-organismal features, shared phylogenetic history or forced by particular character-state coding schemes. Although the two first sources can be investigated by biologists a posteriori and the third one can be avoided a priori with good practices, phylogenetic software do not distinguish between any of them.In this study, we propose a new metric of raw character difference as a proxy for character correlation. Using thorough simulations, we test the effect of increasing or decreasing character differences on tree topology. Overall, we found an expected positive effect of reducing character correlations on recovering the correct topology. However, this effect is less important for matrices with a small number of taxa (25 in our simulations) where reducing character correlation is not more effective than randomly drawing characters. Furthermore, in bigger matrices (350 characters), there is a strong effect of the inference method with Bayesian trees being consistently less affected by character correlation than maximum parsimony trees.These results suggest that ignoring the problem of character correlation or independence can often impact topology in phylogenetic analysis. However, encouragingly, they also suggest that, unless correlation is actively maximised or minimised, probabilistic methods can easily accommodate for a random correlation between characters.

scholarly journals A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations.

Genetics ◽  
1988 ◽  
Vol 120 (4) ◽  
pp. 1145-1154
Author(s):  
A R Templeton ◽  
C F Sing ◽  
A Kessling ◽  
S Humphries
Keyword(s):  
Genetic Variation ◽  
Restriction Endonuclease ◽  
Cladistic Analysis ◽  
Population Level ◽  
Worked Examples ◽  
Interindividual Variation ◽  
Phenotypic Effect ◽  
Candidate Locus ◽  
Restriction Endonuclease Mapping ◽  
Endonuclease Mapping

Abstract Genes that code for products involved in the physiology of a phenotype are logical candidates for explaining interindividual variation in that phenotype. We present a methodology for discovering associations between genetic variation at such candidate loci (assayed through restriction endonuclease mapping) with phenotypic variation at the population level. We confine our analyses to DNA regions in which recombination is very rare. In this case, the genetic variation at the candidate locus can be organized into a cladogram that represents the evolutionary relationships between the observed haplotypes. Any mutation causing a significant phenotypic effect should be imbedded within the same historical structure defined by the cladogram. We showed, in the first paper of this series, how to use the cladogram to define a nested analysis of variance (NANOVA) that was very efficient at detecting and localizing phenotypically important mutations. However, the NANOVA of haplotype effects could only be applied to populations of homozygous genotypes. In this paper, we apply the quantitative genetic concept of average excess to evaluate the phenotypic effect of a haplotype or group of haplotypes stratified and contrasted according to the nested design defined by the cladogram. We also show how a permutational procedure can be used to make statistical inferences about the nested average excess values in populations containing heterozygous as well as homozygous genotypes. We provide two worked examples that investigate associations between genetic variation at or near the Alcohol dehydrogenase (Adh) locus and Adh activity in Drosophila melanogaster, and associations between genetic variation at or near some apolipoprotein loci and various lipid phenotypes in a human population.

Character-State Weighting for Cladistic Analysis of Protein-Coding DNA Sequences

1993 ◽  
Vol 80 (3) ◽  
pp. 752 ◽  
Author(s):  
Victor A. Albert ◽  
Mark W. Chase ◽  
Brent D. Mishler
Keyword(s):  
Dna Sequences ◽  
Cladistic Analysis ◽  
Character State ◽  
Protein Coding
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