Syst. Biol. 46(2):235-268, 1997

Tests of turtle phylogeny: molecular, morphological, and paleontological approaches

H. Bradley Shaffer, 1 Peter Meylan, 2 and Mark L. McKnight 1

1 Section of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95616, USA;
E-mail: (H.B.S.)

2 Collegium of Natural Sciences, Eckerd College, 4200 54th Avenue South, St. Petersburg, Florida 33711, USA

Abstract.---We present phylogenetic analyses of both molecular and morphological data for the 23 major lineages of living turtles and seven key fossil taxa. Nearly 1 kilobase of cytochrome b sequence, 325 base pairs of 12S ribosomal DNA, and 115 morphological characters contained similar phylogenetic information, although each provided unique information on different nodes of chelonian history. A character-based combinability test (implemented in PAUP*) and a nonparametric test of taxonomic congruence indicated no strong evidence for heterogeneity among data sets, and we used a combined approach to estimate a final phylogeny of the major lineages of living turtles. This approach resulted in a very well-resolved tree, with only a few of the deep branches within the Cryptodira left as an unresolved polytomy. The addition of six relatively complete fossils chosen to help resolve this basal polytomy provided little added resolution to the tree and resulted in a sharp decline in bootstrap proportions for nodes near the fossils. Branch-length analysis and independent dates from the fossil record suggest that these unresolved nodes may represent a rapid radiation of the major cryptodiran lineages 90--120 million years ago.
[Combined molecular and morphological data; fossil and recent phylogeny; mitochondrial DNA; starburst phylogeny; Testudines; total evidence.]

Syst. Biol. 46(2):269-283, 1997

A new nuclear gene for insect phylogenetics: dopa decarboxylase is informative of relationships within heliothinae (Lepidoptera: Noctuidae)

Q. Q. Fang, 1, 2, 6 Soowon Cho, 2 Jerome C. Regier, 1 Charles Mitter, 2 Marcus Matthews, 3 Robert W. Poole, 4, 5 Timothy P. Friedlander, 1 and Suwei Zhao 1

1 Center for Agricultural Biotechnology, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA

2 Department of Entomology, University of Maryland at College Park, College Park, Maryland 20742, USA

3 Division of Entomology, CSIRO, GPO Box 1700, Canberra, ACT 26001, Australia

4 Systematic Entomology Laboratory, USDA, ARS, ;co National Museum of Natural History, Washington, D.C. 20560, USA

5 E.I.S., Inc., 722 Owens Street, Rockville, Maryland 20850, USA

6 Present address: Department of Biology, Georgia Southern University, Statesboro, Georgia 30460-8042, USA.

Abstract.---The lack of a readily accessible roster of nuclear genes informative at various taxonomic levels is a bottleneck for molecular systematics. In this report, we describe the first phylogenetic application of the sequence that encodes the enzyme dopa decarboxylase (DDC). For 14 test species within the noctuid moth subfamily Heliothinae that represent the previously best-supported groupings, a 690-bp fragment of DDC resolved relationships that are largely concordant with prior evidence from elongation factor-1;ga (EF-1;ga), morphology, and allozymes. Although both synonymous and nonsynonymous changes occur in DDC substantially more rapidly than they do in EF-1;ga, DDC divergences within Heliothinae are below saturation at all codon positions. Analysis of DDC and EF-1;ga in combination resulted in increased bootstrap support for several groupings. As a first estimate of previously unresolved relationships, DDC sequences were analyzed from 16 additional heliothines, for a total of 30 heliothine species plus outgroups. Previous relationships based on DDC were generally stable with increased taxon sampling, although a two- to eightfold downweighting of codon position 3 was required for complete concordance with the 140-species result. The weighted strict consensus trees were largely resolved and were congruent with most although not all previous hypotheses based on either morphology or EF-1;ga. The proposed phylogeny suggests that the major agricultural pest heliothines belong to a single clade, characterized by polyphagy and associated life history traits, within this largely host-specific moth subfamily. DDC holds much promise for phylogenetic analysis of Tertiary-age animal groups.
[Dopa decarboxyase; elongation factor-1;ga; Heliothinae; Insecta; Lepidoptera; Noctuidae; nuclear gene; phylogeny.]

Syst. Biol. 46(2):284-305, 1997

Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex

Kelly R. Zamudio, 1, 4 K. Bruce Jones, 2 and Ryk H. Ward 3

1 Department of Zoology, Box 351800, University of Washington, Seattle, Washington 98195, USA

2 Department of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154, USA

3 Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA

4 Present address: Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, California 94720, USA.

Abstract.---We surveyed mitochondrial DNA (mtDNA) sequence variation in short-horned lizards (Phrynosoma douglasi) from throughout western North America and used these data to estimate an intraspecific phylogeny and to assess biogeographic scenarios underlying the geographic structure of lineages in this species. We sequenced 783 base pairs from 38 populations of P. douglasi and three putative outgroups (P. ditmarsi, P. orbiculare, P. platyrhinos). We detected high levels of nucleotide variation among populations and a spatial distribution of mtDNA lineages compatible with major geographic regions. The phylogenetic hypotheses best supported by the data suggest that P. douglasi, as currently described, is paraphyletic with respect to P. ditmarsi. Populations of P. douglasi from the Pacific Northwest (ID, CA, OR, WA) form a monophyletic group that is sister to the subsequent radiation of P. ditmarsi and other P. douglasi clades. These results suggest that divergences within this widespread species are fairly old. We focused on the genetic structure of populations of P. douglasi from a geographic perspective and interpreted the intraspecific phylogeny in light of geologic and climatic changes in western North America during the last 20 million years. The generally high levels of genetic variation found in these population comparisons are in accord with high levels of morphological variation in this species group; however, only in the Pacific Northwest region is there spatial congruence between these phylogenetic results and subspecific ranges based on previous morphological studies. We compared the evolutionary units delineated in this study with previously described subspecies of P. douglasi and evaluated the support (from morphology and mtDNA) for each population lineage in the phylogeny and the implications for the taxonomy of this group.
[Biogeography; cytochrome b; geographic variation; mitochondrial DNA; ND4; paraphyly; Phrynosoma ditmarsi; Phrynosoma douglasi; phylogenetics; phylogeography; population structure.]

Syst. Biol. 46(2):306-312, 1997

The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa

Fran┘ois-Joseph Lapointe 1 and Guy Cucumel 2

1 D┌partement de sciences biologiques, Universit┌ de Montr┌al, C.P. 6128, Succursale centre-ville, Montr┌al, Qu┌bec H3C 3J7, Canada;
,br> 2 Ecole des sciences de la gestion, Universit┌ du Qu┌bec ;aga Montr┌al, C.P. 8888, Succursale centre-ville, Montr┌al, Qu┌bec H3C 3P8, Canada

Abstract.---The average consensus procedure, originally proposed to combine dendrograms (i.e., ultrametric trees), is extended here to apply to any type of tree with branch lengths (ultrametric or not) containing identical, inclusive, or overlapping sets of taxa. The method proceeds in two steps. First, the average of the path-length matrices corresponding to the trees to be combined is computed. Then, a least-squares algorithm is applied to this average matrix to obtain a consensus solution. The average consensus tree is a solution that minimizes the sum of squared distances between the consensus and the trees in the input profile. An application of the method to combine phylogenetic hypotheses for kangaroos is presented. [Consensus method; kangaroo; Macropodidae; phylogeny; supertree; weighted trees.]

Syst. Biol. 46(2):313-331, 1997

A comparison of phylogenetic nomenclature with the current system: a botanical case study

Philip D. Cantino, 1 Richard G. Olmstead, 2 and Steven J. Wagstaff 3 1 Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701-2979, USA

2 Department of Botany, Box 355325, University of Washington, Seattle, Washington 98195-5325, USA

3 Manaaki Whenua Landcare Research New Zealand, Ltd., Canterbury Agriculture and Science Centre, P.O. Box 69, Lincoln, Canterbury, New Zealand

Abstract.---The family Lamiaceae was used as a case study to compare our current system of nomenclature with a phylogenetic alternative proposed by de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449--480), with emphasis on nomenclatural stability and efficiency. Comparison of published cladistic analyses revealed 19 suprageneric clades within Lamiaceae that are supported well enough to merit naming, but many genera could not be placed with confidence in any infrafamilial taxon. Two phylogenetic classifications were prepared, one following current nomenclatural rules and conventions and the other following the phylogenetic system of nomenclature. A comparison of the classifications revealed examples of unstable and ambiguous names that resulted from employing current rules and conventions to name clades. Old names based on nomenclatural types of uncertain phylogenetic relationship and infrafamilial taxon names based on the type of the family are particularly prone to instability. The phylogenetic system appears to have fewer problems but may also lead to nomenclatural confusion if taxon names are defined carelessly. The current system produces less efficient classifications because the principle of exhaustive subsidiary taxa leads to inclusion of redundant names (monotypic taxa) when the classification is based on an asymmetrical cladogram. In contrast, the phylogenetic system contains no redundant names. We endorse the recommendation that the principle of exhaustive subsidiary taxa be abandoned. Phylogenetic definitions should be provided for taxon names whenever phylogenies are translated into classifications. The definitions should be accompanied by a list of synapomorphies and a statement of clade membership to facilitate subsequent provisional referral of newly studied species to supraspecific taxa.
[Classification; Lamiaceae; nomenclature; phylogenetic systematics; phylogeny; taxonomy.]

Syst. Biol. 46(2):332-345, 1997

Accuracy of phylogenetic analysis including and excluding polymorphic characters

John J. Wiens 1 and Maria R. Servedio 2

1 Section of Amphibians and Reptiles, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania 15213-4080, USA;

2 Department of Zoology, University of Texas, Austin, Texas 78712-1064, USA;

Abstract.---Intraspecific variation is ubiquitous in systematic characters, yet systematists often do not deal with polymorphism explicity. For example, morphological systematists typically exclude characters in which any or "too much" polymorphism is observed, and molecular systematists often avoid intraspecific variation by sampling a single individual per species. Recent empirical studies have suggested that polymorphic characters contain significant phylogenetic information but are more homoplastic than fixed characters. Given these two observations, should including polymorphic characters increase or decrease accuracy? We addressed this question using simulated data sets that also show a strong relationship between homoplasy and intraspecific variability. Data sets were generated with eight species, two alleles per locus, and a variety of branch lengths, number of loci, and sample sizes (individuals sampled per species). The data sets were analyzed using eight parsimony coding methods (with and without a priori and successive weighting) and different variability thresholds for excluding polymorphic characters. Excluding polymorphic characters decreased accuracy under almost all conditions examined, even when only the more variable characters were excluded. Sampling a single individual per species also consistently decreased accuracy. Thus, two common approaches for dealing with intraspecific variation in morphological and molecular systematics can give relatively poor estimates of phylogeny. In contrast, the unweighted frequency method, including polymorphic characters and sampling a reasonable number of individuals per species (n ;me 5), can give accurate results under a variety of conditions.
[Accuracy; coding methods; computer simulations; parsimony; polymorphic characters; sample size; weighting.]

Syst. Biol. 46(2):346-353, 1997

Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA

Rasmus Nielsen

Department of Integrative Biology, University of California, Berkeley, California 94720, USA;

Abstract.---A maximum likelihood method for independently estimating the relative rate of substitution at different nucleotide sites is presented. With this method, the evolution of DNA sequences can be analyzed without assuming a specific distribution of rates among sites. To investigate the pattern of correlation of rates among sites, the method was applied to a data set consisting of the protein-coding regions of the mitochondrial genome from 10 vertebrate species. Rates appear to be strongly correlated at distances up to 40 codons apart. Furthermore, there appears to be some higher order correlation of sites approximately 75 codons apart. The method of site-by-site estimation of the rate of substitution may also be applied to examine other aspects of rate variation along a DNA sequence and to assess the difference in the support of a tree along the sequence.
[Correlation among sites; maximum likelihood; mtDNA; rate variation; site-by-site estimation.]