S171 Journal of Ichthyology, Vol. 45, Suppl. 1, 2005, pp. S171–S182. Original English Text Copyright © 2005 by Stankovic, Spalik, Golik, Balushkin, Borsuk, Koper, Rakusa-Suszczewski, Weglenski. 1 INTRODUCTION Notothenioids are a suborder of perciform fishes comprising 8 families, 48 genera, and 139 species (Bal- ushkin, 2000). While the majority of the species of six of the notothenoid families live within the Antarctic Region, one monotypic family, Pseudaphritidae, and most species of the family Bovichtidae have a non-Ant- arctic distribution. Notothenioidei is the most abundant suborder in number, biomass, and taxonomic diversity among the vertebrates of the southern regions of the Earth. The notothenioid ancestor was probably benthic, like the most primitive members of the group Hal- aphrithis platycephala (Bovichtidae) (Last et al., 2002). Many extant taxa are also benthic or demersal in habit. However, half of all living species have moved 1 This article was submitted by the authors in English. into non-benthic niches becoming epibenthic, pelagic, semipelagic or cryopelagic (Andriashev, 1970; East- man, 1993). The progressive loss of bone tissue, along with certain other morpho-physiological changes lead- ing to a decrease in body weight (these changes included the accumulation of fat in the subdermal layer, muscles, and special fat deposits) were the important morphological pre-adaptations which enabled notothe- nioids to colonize the pelagic biotopes (Balushkin, 2000). Notothenioids are characterized by a reduced haematocrit and haemoglobin concentration resulting from low metabolic demand and high oxygen solubility at low temperatures. In the family Channichthyidae (icefish), this trend has proceeded as far as the loss of functional erythrocytes. The synthesis of antifreeze glycopeptides is an evolutionary novelty of Antarctic notothenioids which has enabled them to successfully colonize ice-cold waters. The absence of these glyco- Polyphyly of Scorpaeniformes and Perciformes: New Evidence from the Study of Notothenioid’s Mitochondrial and Nuclear rDNA Sequence Data 1 A. Stankovic 1,4 *, K. Spalik 2 , P. Golik 3,4 , A. V. Balushkin 5 , P. Borsuk 3,4 , M. Koper 3 , S. Rakusa-Suszczewski 6 , and P. Weglenski 3,4 1 Novae Center for Archaeological Research, Warsaw University, Krakowskie Przedmiescie 32, 00–927 Warsaw, Poland 2 Department of Plant Systematics and Geography, Warsaw University, Aleje Ujazdowskie 4, 00–478 Warsaw, Poland 3 Department of Genetics, Warsaw University, Pawinskiego 5a, 02–106 Warsaw, Poland 4 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02–106 Warsaw, Poland 5 Laboratory of Ichthyology, Zoological Institute, Russian Academy of Sciences, Universitetskaia nab. 1, St. Petersburg, 199034 Russia 6 Department of Antarctic Biology, Polish Academy of Sciences, Ustrzycka 10/12, 02–141 Warsaw, Poland *E-mail: anams@poezta.ibb.waw.pl Received March 9, 2005 Abstract—Partial sequences of nuclear 18S and mitochondrial 12S and 16S rDNA genes from 21 species were analyzed using parsimony, maximum likelihood, and Bayesian inference in order to establish the phylogenetic position of notothenioids, a major group of Antarctic fishes. The outgroup included members of the orders Per- ciformes and Scorpaeniformes, which are both placed in the superorder Percomorpha. In all analyzes, the notothenioids containing Pseudaphritidae, Eleginopidae, Nototheniidae, Harpagiferidae, Artedidraconidae, and Channichthyidae were monophyletic and this result received very strong internal support from decay, bootstrap, and Bayesian analyzes. However, the orders Perciformes and Scorpaeniformes, as well as the perciform subor- der Trachinoidei and the scorpaeniform suborder Scorpaenoidei were shown to be polyphyletic. Among the species included in this study, the closest relatives of the monopyletic clade of notothenioids appeared to be two species of Sebastidae, Sebastes brevispinis and S. marinus. The sister relationship between notothenioids (with the exception of bovichtids) and S. brevispinis was also confirmed in a large analysis using 125 partial mito- chondrial 12S and 16S rDNA sequences. This phylogeny is in serious disagreement with current opinions on the timing of Sebastes and notothenioid radiations. The oldest separations in Sebastes are estimated at 18 mil- lion years ago, while the divergence of the Antarctic notothenioid lineage from its temperate pseudaphitid cous- ins is associated with the separation of Australia from Antarctica, which took place 45–55 million years ago. Molecular data suggest that the origin and diversification of notothenioids occurred much more recently than previously believed.