Showing papers by "Mark Wilkinson published in 1998"
TL;DR: Isolation of novel viruses from so many disparate hosts suggests that retroviruses are likely to be ubiquitous within all but the most basal vertebrate classes and, furthermore, gives a good indication of the overall retroviral diversity within vertebrates.
Abstract: We used the PCR to screen for the presence of endogenous retroviruses within the genomes of 18 vertebrate orders across eight classes, concentrating on reptilian, amphibian, and piscine hosts. Thirty novel retroviral sequences were isolated and characterized by sequencing approximately 1 kb of their encoded protease and reverse transcriptase genes. Isolation of novel viruses from so many disparate hosts suggests that retroviruses are likely to be ubiquitous within all but the most basal vertebrate classes and, furthermore, gives a good indication of the overall retroviral diversity within vertebrates. Phylogenetic analysis demonstrated that viruses clustering with (but not necessarily closely related to) the spumaviruses and murine leukemia viruses are widespread and abundant in vertebrate genomes. In contrast, we were unable to identify any viruses from hosts outside of mammals and birds which grouped with the other five currently recognized retroviral genera: the lentiviruses, human T-cell leukemia-related viruses, avian leukemia virus-related retroviruses, type D retroviruses, and mammalian type B retroviruses. There was also some indication that viruses isolated from individual vertebrate classes tended to cluster together in phylogenetic reconstructions. This implies that the horizontal transmission of at least some retroviruses, between some vertebrate classes, occurs relatively infrequently. It is likely that many of the retroviral sequences described here are distinct enough from those of previously characterized viruses to represent novel retroviral genera.
191 citations
TL;DR: A review of the available data indicates that the widespread view that a majority of caecilians are viviparous is mistaken, and the most parsimonious inference is that the ancestral amniotes did not practice extended embryo retention.
Abstract: A recent evaluation of alternative hypotheses for the origin of the amniotic egg, by mapping a single reproductive-mode character onto a phylogeny of tetrapods, concluded that the alternative hypotheses were equally parsimonious. However, this interpretation is dependent upon a mistaken coding of the caecilian amphibians as showing extended embryo retention. Although some caecilians are viviparous, phylogenetic analyses indicate that oviparity is ancestral for the group. With the coding of caecilians corrected, the most parsimonious inference is that the ancestral amniotes did not practice extended embryo retention. A review of the available data indicates that the widespread view that a majority of caecilians are viviparous is mistaken. Oviparity is the dominant reproductive mode in caecilians as it is in other living amphibians.
56 citations
01 Jan 1998
TL;DR: In this article, a class of measures of the information provided by consensus trees based on the number of permitted resolutions of the consensus is introduced, and a formula is derived and a proof given.
Abstract: Phylogenetic Information Content, a class of measures of the information provided by consensus trees based on the number of permitted resolutions of the consensus, is introduced. A formula for the number of permitted resolutions of Adams consensus trees is derived and a proof given. We argue that maximising PIC measures provides a sensible criterion for choosing among alternative consensus trees and we illustrate this for consensus trees of cladograms.
40 citations
TL;DR: Randomization tests of phylogenetic hypotheses based on the concepts of split support and split conflict are described here, as are tests where splits, rather than the data, are randomly permuted.
Abstract: Randomization tests allow the formulation and statistical testing of null hypotheses about the quality of entire data sets or the quality of fit between the data and particular phylogenetic hypotheses. Randomization tests of phylogenetic hypotheses based on the concepts of split support and split conflict are described here, as are tests where splits, rather than the data, are randomly permuted. These tree-independent randomization tests are explored through their application to phylogenetic data for caecilian amphibians. Of these tests, split support randomization tests appear to be the most promising tools for phylogeneticists. These tests seem quite conservative, are applicable to nonpolar data and unordered multistate characters, and do not have the problems of nonindependence that affect split conflict and hierarchy tests. Unlike split conflict tests, their power does not appear to be correlated with split size. However, all tests are sensitive to taxonomic scope. Split support tests may help discern data that are likely to be affected by the problems of long-branches effects. Comparison of test results for mutually incompatible splits may help identify the presence of strong misleading signals in phylogenetic data. Significant split support could be a prerequisite for considering phylogenetic hypotheses to be well supported by the data, and split support randomization tests might be usefully applied prior to or as part of tree construction.
23 citations
TL;DR: Although precise locality data are lacking for both the holotype and the second specimen, the latter specimen was almost certainly collected more recently and from within Brazil, justifying increased expectation that this remarkable species is still extant and tha...
Abstract: The discovery is reported of a second specimen of the radically divergent lungless aquatic caecilian Atretochoana eiselti (Taylor), previously known only from the holotype. Aspects of the morphology of the second specimen are described and compared to the holotype, allowing a minimal evaluation of variation within this enigmatic species. With a total length of 805 mm, the second specimen is the largest known lungless tetrapod. Most of the distinctive morphological features reported for the holotype are true of the second specimen also indicating that the holotype is not a ‘hopeful monster’. An important exception, from the perspective of species identification, is variation in the form of the pattern of denticulations about the cloacal disk. Although precise locality data are lacking for both the holotype and the second specimen, the latter specimen was almost certainly collected more recently and from within Brazil. This justifies increased expectation that this remarkable species is still extant and tha...
13 citations
01 Jan 1998
11 citations
TL;DR: A phylogenetic analysis of four terminal taxa yielded a tree with Gargoyleosaurus as the sister taxon of the Ankylosauridae, but the authors' claim that their tree is robust is undermined when their data and their tree are evaluated using numerical techniques.
Abstract: The Ankylosauria comprises two families of armoured dinosaurs (Nodosauridae and Ankylosauridae) that are best known from well-preserved specimens from the Cretaceous period In their report on the skull of a new Jurassic ankylosaur, Gargoyleosaurus, Carpenter et al1 presented a phylogenetic analysis of four terminal taxa, which yielded a tree with Gargoyleosaurus as the sister taxon of the Ankylosauridae But the authors' claim that their tree is robust is undermined when their data and their tree are evaluated using numerical techniques
9 citations
7 citations
TL;DR: It is proposed that it should become standard practice in molecular phylogenetics for alignments, masks, and sup?
Abstract: Many researchers working on the phyloge? netic analysis of nucleotide or amino acid se? quences find it necessary, at some time, to build upon prior work. When this involves importing an alignment (and masks) that have been des? cribed and sometimes illustrated in a published paper but for which the sequences have not been deposited in a public database, there may be no alternative but to painstakingly retype the data, with all the possibilities that this offers for error. More commonly, the un? aligned sequences may be available from a se? quence database, but the awkward task of man? ual alignment reconstruction remains. Most conveniently, alignments may be available as computer files (1) on disk, by application to the corresponding author, (2) from an ftp or http site maintained by the corresponding author or his institution, or (3) from an alignment data? base. However, when received by these routes, an alignment (and masks) may well be in a file format that requires tedipus, error-prone wordprocessing adjustment to make it readable by a sequence alignment editor or phylogenetic analysis program. Moreover, of the three approaches, the first two are potentially eva? nescent and the third suffers from underuse and lack of file-format standardization (Stoesser, pers. comm.). Masks and weighting informa? tion, when presented PHYLIP-style (Felsen? stein, 1993) as a string of digits, offer a parti? cular difficulty; few alignment editors or phy? logenetic analysis programs that we have encountered can import them successfully. Given these difficulties, we propose that it should become standard practice in molecular phylogenetics for alignments, masks, and sup? plementary information to be made available in NEXUS file format by use of the EMBL align? ment database. NEXUS file format is an ASCII text-file for? mat that was "designed to make sharing of data b tween programs as easy and flexible as pos? sible" (Maddison and Maddison, 1992: p. 145; Maddison et al., 1997), Importantly, NEXUS file format provides unlimited flexibility, by the use of character partition and assumption blocks, for the identification of special cate? g ries of data such as masks, weights, second? ary structure features, etc., and comments can be freely added. NEXUS files are written auto? matically by some alignment editors, including GDE (Smith et al., 1994), MacClade (Maddison nd Maddison, 1992) and SeqApp (Gilbert, 1993), and most such programs also provide file-format interchange facilities. Alternative? ly, NEXUS files may readily be constructed hand from published descriptions (Swof? ford, 1993; Maddison et al., 1997). Many phylogeneticists already use or have access to pro? grams that read and write NEXUS files, and many more are likely to do so after publication of the new multicapable PAUP* (Swofford, pers. comm.). The existence of a sequence alignment data? base separate from the GenBank (Benson et al., 1998), EMBL (Stoesser et al, 1998), or other d tabases for individual sequences is little known, but would certainly be advantageous if were widely used and if its use were stan-
TL;DR: It is suggested higher-order homoplasy tests have potential uses analogous to the uses of the Le Quesne test, particularly with respect to data exploration.
Abstract: The Le Quesne test of character compatibility uses pairwise comparisons of characters to detect homoplasy in phylogenetic character data. If a pair of characters fails this test we can conclude that a minimum of a single extra step is required by the pair of characters. The rationale of the Le Quesne test is extended to comparisons of triplets of characters. The triplet homoplasy test can reveal that that there is a minimum of four extra steps across a triplet of characters and thus that there are at least two extra steps associated with one of the characters. The triplet homoplasy test can thus detect higher orders of homoplasy than can be detected by the pairwise Le Quesne test. The possibility of quartet and other higher-order homoplasy tests is discussed. The utility of higher-order homoplasy tests is discussed. It is suggested higher-order homoplasy tests have potential uses analogous to the uses of the Le Quesne test, particularly with respect to data exploration.