Syst. Biol. 48(3):413--435, 1999

More characters or more taxa for a robust phylogeny--case study from the coffee family (Rubiaceae)

Birgitta Bremer 1,4, Robert K. Jansen 2, Bengt Oxelman 1, Maria Backlund 1, Henrik Lantz 1, and Ki-Joong Kim 2,3

1 Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyv, 18D,
SE-75236 Uppsala, Sweden.

2 Section of Integrative Biology and Institute of Cellular and Molecular Biology,
University of Texas, Austin, Texas 78713, USA.

3 Department of Biology, Yeungnam University, Keongsan, Keonbuk, Korea 712-749.

4 Authors listed in order of contribution. Address correspondence to Birgitta Bremer. Email: birgitta.bremer@systbot.uu.se.

Abstract.---Using different data sets mainly from the plant family Rubiaceae, but in parts also from the Apocynaceae, Asteraceae, Lardizabalaceae, Saxifragaceae, and Solanaceae, we have investigated the effect of number of characters, number of taxa, and kind of data on bootstrap values within phylogenetic trees. The percentage of supported nodes within a tree is positively correlated with the number of characters, and negatively correlated with the number of taxa. The morphological analyses are based on few characters and weakly supported trees are expected. The percentage of supported nodes is also dependent on the kind of data analyzed. In analyses of Rubiaceae based on the same number of characters, RFLP data give trees with higher percentage of supported nodes than rbcL and morphological data. We also discuss the support values for particular nodes at the familial and subfamilial levels. Two new data sets of ndhF and rbcL sequences of Rubiaceae are analyzed and together with earlier studies of the family we can conclude that the monophyly of the Rubiaceae is supported and within the family there are three well supported, but not easily characterized, large subfamilies, Rubioideae, Cinchonoideae s.s. and Ixoroideae s.l. There are also a few genera (Luculia and Coptosapelta) unclassified to subfamily.
[Rubiaceae; phylogeny, subfamilies, bootstrap, support, morphology; rbcL, ndhF, RFLP.]


Syst. Biol. 48(3):436--454, 1999

Incongruence between morphological data sets: an example from the evolution of endoparasitism among parasitic wasps (Hymenoptera: Braconidae)

Donald L. J. Quicke 1-3 and Robert Belshaw 1

1 Unit of Parasitoid Systematics, CABI Bioscience Centre (UK), Department of Biology,
Imperial College at Silwood Park, Ascot, Berkshire SL5 7PY, England; Email: d.quicke@ic.ac.uk.

2 Deparment of Entomology, The Natural History Museum, London SW7 5BD, England.

3 Address correspondence to this author, at the Imperial College at Silwood Park.

Abstract.---Phylogenetic analyses of molecular and morphological data sets for a group of parasitic wasps (Hymenoptera: Braconidae) give strikingly different results. The molecular data indicate that the major life history transition from ectoparasitism to endoparasitism has occurred independently several times within the family while the morphological data indicate a single origin. Similar incongruent topologies are obtained if the morphological data are partitioned by either of two methods: distinguishing (1) characters of the larval stage and female reproductive system, or (2) characters selected individually by the authors prior to the analysis as likely to be mechanistically associated with endo/ectoparasitism. This result is supported by significant differences in tests of incongruence, and we propose that it is caused by convergence among morphological characters resulting from a shared life history strategy.
[Conflict; convergence; homoplasy; Hymenoptera; incongruence; parasitoid.


Syst. Biol. 48(3):455--490, 1999

The position of Cetacea within Mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Maureen A. O'Leary 1,3 and Jonathan H. Geisler 2

1 Department of Anotomical Sciences, State University of New York, Stony Brook, New York 11794-8081, USA;
E-mail: moleary@mail.som.sunysb.edu

2 Department of Vertebrate Paleontology, American Museum of Natural History, New York, New York 10024-5192, USA;
Email: geisler@amnh.org

3 Address correspondence to Dr. Maureen A. O'Leary, Department of Anatomical Sciences, HSC T-8 (040),
SUNY at Stony Brook, Stony Brook, New York 11794-8081, USA.

Abstract.---Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also, that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate amounts to 89% of the ingroup. Addition of data from recently described cetacean astragali attributed to cetaceans does not overturn artiodactyl monophyly.
[Artiodactyla; astragalus; Cetacea; fossils; homoplasy; Mesonychia; morphology; phylogeny.]


Syst. Biol. 48(3):491--522, 1999

Ontogeny and phylogeny in the northern swordtail clade of Xiphophorus

Jeffrey M. Marcus 1 and Amy R. McCune

Section of Ecology and Systematic, Division of Biological Sciences, Cornell University, Ithaca, New York 14853, USA.

1 Present address and address for correspondence: Department of Zoology, Box 90325,
Duke University, Durham, North Carolina 27708-0325, USA;
Email: jmm12@acpub.duke.edu.

Abstract.---It has been hypothesized than morphological diversity within clades can be generated by simple alterations of shared developmental programs. However, few studies have examined changes in heterochrony, the rate and timing of developmental events, in an explicitly phylogenetic context. We studied how developmental patterns have changed phylogenetically in the northern swordtail clade of Xiphophorus. We reared individuals of an outgroup and seven of nine species in the clade and followed their development for ~300 days. For each individual, we used nonlinear regression to estimate three growth parameters: growth rate, adult body size, and age of cessation of growth. We estimated sword growth rates in males by linear regression. We then used the means of these growth parameters to construct standard growth curves for each species and to study growth patterns in a phylogenetic context. A combined phylogeny was constructed from both phenotypic and DNA sequence data. The phenotypic data set, compiled from the literature, consisted of 86 morphological, pigmentation, behavioral, and random amplified polymorphic DNA characters, many of which had not been used before for phylogenetic analysis. DNA sequence data from three genes for a total of 1284 bases were also obtained from the literature and included in the analysis. Relationships between growth parameters were examined by phylogenetically independent contrasts in relation to seven different phylogenies based on the most-parsimonious trees generated from the phenotypic, DNA sequence, and combined data sets; this allowed us to identify relationships between variables that were not sensitive to ambiguities in Xiphophorus phylogeny. Our analysis revealed statistically significant correlations between female body size and male body size, and between female growth rate and male sword growth rate, for all seven phylogenies. Marginally statistically significant relationships were also identified between female body size and female growth rate, and between female growth rate and male body size. We relate these relationships to what is known about the ecology, genetics, and behavior of Xiphophorus to better understand the evolution of growth patterns of both the body as a whole and the sword in particular. The relationship of these data to the evolution of swords is discussed.
[Development; evolution; growth; heterochrony; independent contrasts; swords; Xiphophorus,]


Syst. Biol. 48(3):523--546, 1999

Primates and their pinworm parasites: the Cameron hypothesis revisited

J. P. Hugot

Museum National d'Histoire Naturelle, Institut de Systematiquie, FR 1541 du CNRS,
Laboratoire de Zoologie des Mammiferes et Oiseaux
(Biosystematique et Coevolution chez les Nematodes Parasites),
55, rue Buffon, 75231 Paris cedex 05, France;
Email: hugot@cimrs1.mnhn.fr

Abstract.---A morphologically based cladistic analysis of the Enterobiinae, which includes most of the Oxyuridae parasitic in Primates, allows a re-evaluation of the Cameron's hypothesis of close coevolution between hosts and parasites. Each of the three genera separated in the Enterobiinae fit with one of the suborders defined in Primates: Lemuricola with the Strepsirhini, Trypanoxyuris with the Platyrrhini, and Enterobius with the Catarrhini. Inside each of the three main groups, the subdivisions observed in the parasite tree also fit with many of the subdivisions generally accepted within the Primate order. These results confirm the subgroups previously described in the subfamily and support Cameron's hypothesis in its aspect of association by descent. Although the classification of the Enterobiinae generally closely underlines the classification of Primates, several discordances are also observed. These are discussed case by case, with use of computed reconstruction scenarios. Given that the occurrences of the same pinworm species as a parasite for several congeneric host species is not the generalised pattern, and given that several occurrences also are observed in which the speciations of the parasites describe a more complex network, Cameron's hypothesis of a slower rhythm of speciation in the parasites can be considered partly refuted. The presence of two genera parasitic on squirrels in a family which contains primarily primate parasites is also discussed. The cladistic analysis does not support close relationships between the squirrel parasites and suggests an early separation from the Enterobiinae for the first one (Xeroxyuris), and a tardy hostswitching from the Platyrrhini to the squirrels for the second. (Rodentoxyuris).
[Cameron's hypothesis; cospeciation, Enterobiinae; host/parasite coevolution; Nematoda; Oxyurid; pinworm; Primate.]


Syst. Biol. 48(3):547--558, 1999

Polytomies and phylogenetically independent contrasts: examination of the bounded degrees of freedom approach

Theodore Garland, Jr. 1, and Ramon Diaz-Uriarte

Department of Zoology, 430 Lincoln Drive, University of Wisconsin, Madison, Wisonson 53706-1381, USA;
E-mail: tgarland@facstaff.wisc.edu

Abstract.---We examined the effect of soft polytomies on the performance (Type I error rate and bias) of FelsensteinŐs (1985; Am. Nat. 125:1-15) method of phylogenetically independent contrasts for estimating a bivariate correlation. We specifically tested the adequacy of bounding degrees of freedom, as suggested by Purvis and Garland (1993; Syst. Biol. 42:569-575). We simulated bivariate models on five phylogenetic trees. For non-Brownian motion simulations, the adequacy of branch-length standardization was checked with a simple diagnostic (Garland et al., 1992; Syst. Biol. 41:18-32), and transformations were applied as indicated. Surprisingly, soft polytomies tended to have negligible effects on Type I error rates when models other than Brownian motion were used. Overall, and irrespective of evolutionary model, degrees of freedom were appropriately bounded for hypothesis testing, and unbiased estimates of the correlation coefficient were obtained. Our results, along with those of previous simulation studies, suggest that independent contrasts can reliably be applied to real data, even with phylogenetic uncertainty.
[Comparative method; computer simulation; hypothesis teting; polytomies.]


Syst. Biol. 48(3):559--580, 1999

Congruence between phylogeny and stratigraphy: randomization tests and the gap excess ratio

Matthew A. Wills 1

Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, United Kingdom.

1 Present address: Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, United Kingdom;
Email: matthew.wills@university-museum.oxford.ac.uk.

Abstract.---Stratigraphic congruence indices (e.g., stratigraphic consistency index [SCI] of Huelsenbeck, 1994, Paleobiology 40:563-569; relative completeness index [RCI] of Benton, 1994, Trends Ecol. Evol. 9:181-185 [not to be confused with the rescaled consistency index of Farris, 1989, Cladistics 5:417-419]) are increasingly being quoted for cladograms containing fossil taxa. However, like the character consistency index (CI, summed over all characters), these values cannot be compared for trees derived from different data sets. Just as the number of characters and taxa in data matrices affects typical CI values, so tree balance and the distribution of stratigraphic ranges (and indirectly tree size) delimit the range of congruence indices that can be obtained. Because investigators often seek to compare the performance of cladograms from different sources (e.g., different taxa, habitats, periods in history), indices of fit insensitive to these factors are desirable. Two approaches are proposed here: (1) The gap excess ratio (GER) is a new metric that controls for the distribution of range data but is sensitive to differences in tree balance. The GER expresses the difference between the minimum implied gap (MIG; the total ghost range implied by a given set of stratigraphic ranges on a fiven tree) and Gmin (the minimum possible ghost range for those data on any tree) as a fraction of the range of values possible for those stratigraphic data on any tree. Rather than reflecting inferred completeness of the fossil record (as does the RCI, which is only partially determined by cladistic constraints), the GER indicates congruence alone. (2) Randomization tests hold most potentially conflated parameters constant and compare the observed RCI or GER index with the distribution of indices obtained by randomly reassigning range data over the tree. This enables us to deduce whether the MIG is significantly less (i.e., shows greater congruence) than for random permutations of the same range data. Stratigraphic congruence indices have been invoked as an ancillary criterion for assessing competing hypotheses of relationships derived from different sources or for choosing between equally parsimonious trees derived from the same character matrix. The first application is illustrated with comparisons fo actinopytrygian and eutherian phylogenies, and the second is illustrated with a study of trees for fossil and recent arthropods.
[Ghost ranges; homoplasy excess ratios; permutation tail probability; relative completeness index; retention index; stratigraphic consistency index.]