Syst. Biol. 48(4):683--714, 1999

Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks

Kevin G. McCracken 1,4,5, John Harshman 2, David A. McClellan 3, and Alan D. Afton 4

1 School of Forestry, Wildlife, and Fisheries, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

2 4869 Pepperwood Way, San Jose, California 95124, USA.

3 Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

4 U.S. Geological Survey, Louisiana Cooperative Fish and Wildlife Research Unit, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

5 Present address and address for correspondence: Department of Biological Sciences, 107 Galvin Life Science Center, University of Notre Dame, Notre Dame, Indiana 46556, USA

Abstract.---The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group of characters tracks phylogeny and another set tracks adaptive history. In such cases, convergent characters may be correlated with one or a few functional anatomical units and readily identifiable using comparative methods. Stifftail ducks (Oxyurinae) offer one such opportunity to study correlated character evolution and function in the context of phylogenetic reconstruction. Morphological analyses place stifftail ducks as part of a large clade of diving ducks that includes the sea ducks (Mergini), Hymenolaimus, Merganetta, and Tachyeres, and possibly the pochards (Aythyini). Molecular analyses, on the other hand, place stifftails far from other diving ducks and suggest, moreover, that stifftails are polyphyletic. Mitochondrial cytochrome b gene sequences of eight stifftail species traditionally supposed to form a clade were compared with each other and with sequences from 50 other anseriform and galliform species. Stifftail ducks are not the sister group of sea ducks, but lie outside the typical ducks (Anatinae). Of the four traditional stifftail genera, monophyly of Oxyura and its sister group relationship with Nomonyx are strongly supported. Heteronetta probably is the sister group of that clade, but support is weak. Biziura is not a true stifftail. Within Oxyura, Old World species (O. australis, O. leucocephala, O. maccoa) appear to form a clade, with New World species (O. jamaicensis, O. vittata) branching basally. Incongruence between molecules and morphology is interpreted to be the result of adaptive specialization and functional convergence in the hind limbs of Biziura and true stifftails. When morphological characters are divided into classes, only hind-limb characters are significantly in conflict with the molecular tree. Null models of synonomous and nonsynonomous substitution based on patterns of codon-degeneracy and chemical dissimilarity, likewise, indicate that the nucleotide and amino acid changes postulated by the molecular tree are more plausible than those postulated by the morphological tree. These findings teach general lessons about the utility of highly adaptive characters (in particular those related to foraging ecology) and underscore the problems that convergence can pose for attempts to recover phylogeny. They also demonstrate how the concept of natural data partitions and simple models of evolution (e.g., parsimony, likelihood, neutrality) can be used to test the accuracy of independent phylogenetic estimates and provide arguments in favor of one tree topology over another.
[Anseriformes; Anatidae; Oxyurinae; cytochrome b; congruence analysis; functional morphology; behavior, diving, foraging ecology.]

Syst. Biol. 48(4):715--734, 1999

Molecular phylogeny of the marmots (Rodentia: Sciuridae): tests of evolutionary and biogeographic hypotheses

Scott J. Steppan 1,2,5, Mikhail R. Akhverdyan 3,4, Elena A. Lyapunova 3, Darrilyn G. Fraser 1,6, Nikolai N. Vorontsov 3, Robert S. Hoffmann 2, and Michael J. Braun 1,2

1 Laboratory of Molecular Systematics, Smithsonian Institution, 4210 Silver Hill Road, Suitland, Maryland 20746, USA.

2 Deparment of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA.

3 Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.

4 Institute of Zoology, National Academy of Sciences, Republic of Armenia, 375 014 Yerevan, Armenia.

5 Present address and address for correspondence: Department of Biological Sciences, Florida State University, Tallahassee, Florida 32306-1100. USA, E-mail:

6 Present address: Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington 40456, USA.

Abstract.---There are 14 species of marmots distributed across the Holarctic, and despite extensive systematic study, their phylogenetic relationships remain largely unresolved. In particular, comprehensive studies have been lacking. A well-supported phylogeny is needed to place the numerous ecological and behavioral studies on marmots in an evolutionary context. To address this situation, we obtained complete cytochrome (cyt) b sequences for 13 of the species and partial sequence for the 14th. We employed a statistical approach to both phylogeny estimation and hypothesis testing using parsimony and maximum likelihood based methods. We conducted statistical tests on a suite of previously proposed hypotheses of phylogenetic relationships and biogeographic histories. The cyt b data strongly support the monophyly of Marmota and a western montane clade in the Nearctic. The results are consistent with an initial diversification in North America followed by an invasion and subsequent rapid diversification in the Palearctic. These analyses reject the two major competing hypotheses of M. broweri’s phylogenetic relationships: namely, that it is the sister species to camtschatica of eastern Siberia and that it is related closely to caligata of the Nearctic. The Alaskan distribution of M. broweri is best explained as a reinvasion from the Palearctic but a Nearctic origin can not be rejected. Several other conventionally recognized species groups can also be rejected. Social evolution has been homoplastic, with large colonial systems evolving in two groups convergently. The cyt b data do not provide unambiguous resolution of several basal nodes in the Palearctic radiation, leaving some aspects of pelage and karyotypic evolution equivocal.
[Marmota; cyt b; phylogenetics; Holarctic; Beringia; hypothesis testing]

Syst. Biol. 48(4):735--754, 1999

Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae)

Javier Fuertes Aguilar 1, Josep Antoni Rosselo 2, and Gonzalo Nieto Feliner 1,3

1 Real Jardin Botanico, CSIC. Plaza de Murillo, 2, 28014 Madrid, Spain;
E-mail: (JFA), (GNF)

2 Departamento de Biologia Vegetal, Universitat de Valencia, Burjassot, 46100 Valencia, Spain;

3 Address correspondence to this author.

Abstract.---Cladistic analyses of the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences from 55 samples corresponding to 34 taxa in the genus Armeria reveal that ITS sequence diversity among and within species utterly conflicts with patterns of morphological similarity. Three facts are apparent from the results here reported: (1) different samples of a single subspecies, A. villosa subsp. longiaristata, appear in three of the five major clades; (2) samples of at least one of the six subspecies of A. villosa appear in four of the five major clades; and (3) composition of major clades shows greater congruence with the geographic origin of plants than with the traditional systematic arrangement based primarily on morphology. Specifically, the clades here termed Ia, II, III, and IV each encompass terminals restricted to geographically delimited areas. There are alternative explanations for the ITS pattern, but the most likely one is that nucleotide positions supporting the major clades are due, in some of the samples, to concerted evolution following horizontal transfer (gene flow) rather than to recency of common ancestry. This interpretation is consistent with previous systematic and experimental evidence and implies that reticulation in Armeria may be extensive. Harlan and de Wet (1963, Evolution 17:497-501) proposed the compilospecies concept to account for situations in which a genetically "aggressive" species captures portions of the genome of other sympatric species via extensive introgression. Evidence of extensive reticulation, ecological diversification, and geographic pattern indicates that A. villosa may fit the compilospecies concept, which is here supported on molecular grounds for the first time.
[Armeria; compilospecies; concerted evolution; hybridization; Plumbaginaceae; ribosomal DNA; reticulate evolution]

Syst. Biol. 48(4):755--789, 1999

Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida)

Fredrik Pleijel

Museum National d'Histoire Naturelle, 57 rue Cuvier, 75231 Paris Cedex 05, France;

Abstract.---Cladistic relationships between 7 parts of the hesionid polychaete group Heteropodarke are assessed in a parsimony analysis based on 34 morphological characters. Taxon names are defined by apomorphy-based phylogenetic definitions, without reference to Linnean ranks or types. Species entities are omitted and denied any role in taxonomy; taxon names refer to monophyletic groups only. Linnean binomial species names are not employed, and all taxa are assigned uninomials. Previously known parts of Heteropodarke (Africana Hartmann-Schršder, 1974; Formalis Perkins, 1984; Heteromorpha Hartmann-Schršder 1962; Lyonsi Perkins, 1984; Xiamenensis Ding, Wu, and Eestheide, 1997) are reexamined, and Bidentata, new taxon, and "Zmyrina" (informal name) are described from Papua New Guinea and Belize, respectively. The new taxon Crassichaetae is named for a subgroup of Heteropodarke, which is diagnosed by enlarged, anteriorly situated falcigers, and includes Africana, Heteromorpha, Lyonsi, and Xiamenensis. Within this group Africana and Heteromorpha are treated as taxa inquirendae.
[Apomorphy-based definitions; Linnean nomenclature; phylogenetic taxonomy; polychaetes; ranks; species concepts; species names; types.]

Syst. Biol. 48(4):790--807, 1999

Species names in phylogenetic nomenclature

Philip D. Cantino 1*, Harold N. Bryant 2, Kevin de Quieroz 3, Michael J. Donoghue 4, Torsten Eriksson 5, David M. Hillis 6, and Michael S. Y. Lee 7

1 Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701, USA;

2 Royal Saskatchewan Museum, 2340 Albert Street, Regina, Saskatchewan S4P 3V7, Canada;

3 Deparment of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA;

4 Harvard University Herbaria, 22 Divinity Ave., Cambridge, Massachusetts 02138, USA;

5 Bergius Foundation, Royal Swedich Academy of Sciences, Box 50017, 104 05 Stockholm, Sweden;

6 Section of Integrative Biology, School of Biological Sciences, University of Texas, Austin, Texas 78712, USA;

7 Department of Zoology, University of Queensland, Brisbane, Queensland 4072, Australia;

* All authors except the first are listed alphabetically. Address correspondence to this author.

Abstract.---Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480), because the former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Thirteen methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names, their capacity to convey phylogenetic information, and the distinguishability of species names governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.