Cladistics
0748-3007
Cơ quản chủ quản: WILEY , Wiley-Blackwell Publishing Ltd
Lĩnh vực:
Ecology, Evolution, Behavior and Systematics
Các bài báo tiêu biểu
COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE?: ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE Abstract Absolute criteria for evaluating cladistic analyses are useful, not only because cladistic algorithms impose structure, but also because applications of cladistic results demand some assessment of the degree of corroboration of the cladogram. Here, a means of quantitative evaluation is presented based on tree length. The length of the most‐parsimonious tree reflects the degree to which the observed characters co‐vary such that a single tree topology can explain shared character states among the taxa. This “cladistic covariation” can be quantified by comparing the length of the most parsimonious tree for the observed data set to that found for data sets with random covariation of characters. A random data set is defined as one in which the original number of characters and their character states are maintained, but for each character, the states are randomly reassigned to the taxa. The cladistic permutation tail probability, PTP, is defined as the estimate of the proportion of times that a tree can be found as short or shorter than the original tree. Significant cladistic covariation exists if the PTP is less than a prescribed value, for example, 0.05. In case studies based on molecular and morphological data sets, application of the PTP shows that:
In the comparison of four different molecular data sets for orders of mammals, the sequence data set for alpha hemoglobin does not have significant cladistic covariation, while that for alpha crystallin is highly significant. However, when each data set was reduced to the 11 common taxa in order to standardize comparison, reduced levels of cladistic covariation, with no clear superiority of the alpha crystallin data, were found. Morphological data for these 11 taxa had a highly significant PTP, producing a tree roughly congruent with those for the three molecular sets with marginal or significant PTP values. Merging of all data sets, with the exclusion of the poorly structured alpha hemoglobin data, produced a data set with a significant PTP, and provides an estimate of the phylogenetic relationships among these 11 orders of mammals. In an analysis of lactalbumin and lysozyme DNA sequence data for four taxa, purine‐pyrimidine coding yields a data set with significant cladistic covariation, while other codings fail. The data for codon position 3 taken alone exhibit the strongest cladistic covariation. A data set based on flavonoids in taxa of Polygonum initially yields a significant PTP; however, deletion of identically scored taxa leaves no significant cladistic covariation. For mitochondrial DNA data on population genome types for four species of the crested newt, there is significant cladistic covariation for the set of all genome types, and among the five mtDNA genome types within one of the species. However, a conditional PTP test that assumes species monophyly shows that no significant cladistic covariation exists among the fur species for these data. In an application of the test to a group of freshwater insects, as preliminary to biological monitoring, individual subsets of the taxonomic data representing larval, pupal, and adult stages had non‐significant PTPs, while the complete data set showed significant cladistic structure.
Tập 7 Số 1 - Trang 1-28 - 1991
HOMOPLASY AS PATTERN: MULTIVARIATE ANALYSIS OF MORPHOLOGICAL CONVERGENCE IN ANSERIFORMES Abstract— A multivariatc model for taxa and characters is presented that represents taxa as points in an ordination space such that shared derived character states define groups of taxa or regions in this space. This model is compared, in terms of concepts of information content and explanatory power, to the eladistie model that relates characters and taxa to a hierarchical pattern. While a cladogram may be identified with a phylogenetic hypothesis, the ordination pattern may be equated with hypotheses about similarities among the taxa in habitat, feeding mode, or other ecological factors.This basic data‐pattern model is appropriate for the explanation of the character convergences implied by a particular phylogenetic hypothesis. Under the assumptions of the model, the underlying ordination pattern may be inferred from the observed character data using robust ordination procedures recently developed in community ecology. As an illustration of the method, the morphological convergences derived from a recent phylogenetic hypothesis for genera of Anseriformes are analysed. In the resulting two‐dimensional ordination, the genera are arranged such that the convergenlly derived states form regions in the space. While this pattern implies that some of the taxa that are close together in the space are phylogcnetically dissimilar , taxa that are close together in the space are found to be similar in their mode of feeding. Thus, the ordination demonstrates that taxa sharing these morphological convergences tend to utilize habitat in the same way in terms of mode of feeding. The explanatory power of the pattern and the degree of recovery of habitat information are tested against null hypotheses using Monte Carlo simulations. Extensions of the method are discussed, including applications to studies of parasite—host relationships and to biogeography.
Tập 5 Số 3 - Trang 235-258 - 1989
Majority Does Not Rule: The Trouble with Majority-Rule Consensus Trees
Tập 17 - Trang 282-284 - 2001
Can Extensive Reticulation and Concerted Evolution Result in a Cladistically Structured Molecular Data Set?
Tập 17 Số 4 - Trang 301-312 - 2001
Plastid phylogenomics and molecular evolution of Alismatales Abstract Past phylogenetic studies of the monocot order Alismatales left several higher‐order relationships unresolved. We addressed these uncertainties using a nearly complete genus‐level sampling of whole plastid genomes (gene sets representing 83 protein‐coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter‐ and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister‐group of the rest of the order, one likelihood analysis indicated a contrasting Araceae‐sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral‐state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae.
Tập 32 Số 2 - Trang 160-178 - 2016
A large‐scale phylogeny of the lycophyte genus<i>Selaginella</i>(Selaginellaceae: Lycopodiopsida) based on plastid and nuclear loci Abstract The lycophyte genusSelaginella alone constitutes the family Selaginellaceae, the largest of the lycophyte families. The genus is estimated to contain 700–800 species distributed on all continents except Antarctica, with highest species diversity in tropical and subtropical regions. The monophyly ofSelaginella in this broad sense has rarely been doubted, whereas its intrageneric classification has been notoriously contentious. Previous molecular studies were based on very sparse sampling ofSelaginella (up to 62 species) and often usedDNA sequence data from one genome. In the present study,DNA sequences of one plastid (rbcL ) and one nuclear (ITS ) locus from 394 accessions representing approximately 200 species ofSelaginella worldwide were used to infer a phylogeny using maximum likelihood, Bayesian inference and maximum parsimony methods. The study identifies strongly supported major clades and well resolves relationships among them. Major results include: (i) six deep‐level clades are discovered representing the deep splits ofSelaginella ; and (ii) 20 major clades representing 20 major evolutionary lineages are identified, which differ from one another in molecular, macro‐morphological, ecological and spore features, and/or geographical distribution.
Tập 32 Số 4 - Trang 360-389 - 2016
<scp>TNT</scp> version 1.5, including a full implementation of phylogenetic morphometrics Abstract Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT ). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.
Tập 32 Số 3 - Trang 221-238 - 2016