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Multistate Characters (multistate + character)

Distribution by Scientific Domains

Life Sciences	100%

Selected Abstracts

Cladistic coding of genomic maps

CLADISTICS, Issue 5 2002
Cyril Gallut
A new method of genomic maps analysis is described. The purpose of the method is to reconstruct phylogenetic relationships from the genomic organization of taxa. Our approach is based on gene order coding. This coding allows the description of genome topology without a prior hypothesis about evolutionary events and phylogenetic relationships. Different characters are used for each gene: (1) presence/absence, (2) orientation, and (3) relative position. The relative position of a particular gene inside the genome is the pair of genes surrounding it. The relative position character represents all the positions of a gene in the sampled genomes. It is coded as a multistate character. Our coding method has a priori variable cost implications on operators such as inversion, transposition, and gene loss/gain, which we discuss. The overall approach best fits the "duplication, random loss" evolutionary model. The coding method allows the reconstitution of a possible hypothetical common ancestor genome at each node of the tree. This reconstitution is based on the character states' optimization; it comes down to choosing, among all possible optimizations, the optimization compatible with a complete genome topology at each internal node. The multistate coding of gene relative position, which is an undeniable advantage of this method, permits this reconstitution. [source]

Phenotypic plasticity, polymorphism and phylogeny within placoderms

ACTA ZOOLOGICA, Issue 2009
K. Trinajstic
Abstract Intraspecies variation, polymorphism and asymmetric traits are observed within two families of Arthrodira, the Incisoscutidae and Camuropiscidae, from the Gogo Formation in northern Western Australia. Individual plates of the head and trunk shield show considerable variation between individuals. Plates that show the greatest degree polymorphic traits are the rostral (R), marginal (M), submarginal (SM), preorbital (PrO), anterior dorsolateral, anterior median ventral (AMV) and posterior ventrolateral (PVL) plates. The paths of the sensory line canals are the most variable feature and the dermal plates of the cheek show the greatest asymmetry. It is apparent that if anatomical data in arthrodires are to be interpreted with greater precision, detailed knowledge of intraspecies variation, polymorphic and asymmetric traits is essential. How these variables are treated in cladistic analysis is also critical. Here multistate characters were coded differently in five discrete analyses, each analysis yielding a different number of trees and relationships. It was concluded that including and coding for multistate characters gave the most robust tree. In addition, further morphological characters from a new specimen of Gogosteus sarahae Long (1994) indicates many of the characters used to separate this genus from Incisoscutum are inconsistent and so it is here considered that the genus Gogosteus is a junior synonym of Incisoscutum. [source]

Snake phylogeny based on osteology, soft anatomy and ecology

BIOLOGICAL REVIEWS, Issue 3 2002
MICHAEL S. Y. LEE
ABSTRACT Relationships between the major lineages of snakes are assessed based on a phylogenetic analysis of the most extensive phenotypic data set to date (212 osteological, 48 soft anatomical, and three ecological characters). The marine, limbed Cretaceous snakes Pachyrhachis and Haasiophis emerge as the most primitive snakes: characters proposed to unite them with advanced snakes (macrostomatans) are based on unlikely interpretations of contentious elements or are highly variable within snakes. Other basal snakes include madtsoiids and Dinilysia, both large, presumably non-burrowing forms. The inferred relationships within extant snakes are broadly similar to currently accepted views, with scolecophidians (blindsnakes) being the most basal living forms, followed by anilioids (pipesnakes), booids and booid-like groups, acrochordids (filesnakes), and finally colubroids. Important new conclusions include strong support for the monophyly of large constricting snakes (erycines, boines, pythonines), and moderate support for the non-monophyly of the ,trophidophiids' (dwarf boas). These phylogenetic results are obtained whether varanoid lizards, or amphisbaenians and dibamids, are assumed to be the nearest relatives (outgroups) of snakes, and whether multistate characters are treated as ordered or unordered. Identification of large marine forms, and large surface-active terrestrial forms, as the most primitive snakes contradicts with the widespread view that snakes arose via minute, burrowing ancestors. Furthermore, these basal fossil snakes all have long flexible jaw elements adapted for ingesting large prey (,macrostomy'), suggesting that large gape was primitive for snakes and secondarily reduced in the most basal living foms (scolecophidians and anilioids) in connection with burrowing. This challenges the widespread view that snake evolution has involved progressive, directional elaboration of the jaw apparatus to feed on larger prey. [source]

A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology

BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2001
OLE SEBERG FLS
A cladistic analysis, primarily based on morphology, is presented from 40 diploid taxa representing the 24 monogenomic genera of the Triticeae. General problems related to the treatment of hybrids and supposedly allopolyploid heterogenomic taxa are highlighted. Special emphasis is given to taxa not traditionally included in Aegilops s.J. Most of the 33 characters used in the analysis are coded as binary. The only four multistate characters in the matrix are treated as unordered. Three diploid species of Bromus are used as outgroup. The number of equally parsimonious trees found is very large (approx. 170000; length = 107, ci = 0.36, ri = 0.75) and the strict consensus tree has an expectedly low level of resolution. However, most of the equally parsimonious trees owe their existence to an unresolved Aegilops clade. If this clade is replaced by its hypothetical ancestor, the number of equally parsimonious trees drops dramatically (48; length = 78, ci = 0.45, ri = 0.76). When trees for which more highly resolved compatible trees exist are excluded, only two trees remain. Bremer support is used as a measure of branch support. The trees based on morphology and on molecular data are largely incongruent. [source]