Razafimandimbison et al.
Abstract.—The internal transcribed spacer (ITS) of nrDNA has been widely used by systematists for reconstructing phylogenies of closely related taxa. While the occurrence of ITS putative pseudogenes is well documented for many groups of animals and plants, their potential utility in phylogenetic analyses has often been underestimated or even ignored in part because of deletions that make them difficult to align unambiguously. In addition, their long branches often can lead to spurious relationships, particularly in parsimony analyses. We have discovered unusually high levels of ITS polymorphism (up to 30%, 40%, and 14%, respectively) in three tropical tree species of the coffee family (Rubiaceae), Adinauclea fagifolia, Haldina cordifolia, and Mitragyna rubrostipulata. Both secondary structure stability and patterns of nucleotide substitutions in a highly conserved region (5.8S gene) are used for distinguishing presumed functional sequences from putative pseudogenes. We find that the combination of both criteria is the most powerful approach. The sequences from A. fagifoliaappear to be a mix of functional genes and highly distinct putative pseudogenes, whereas those from H. cordifolia and M. rubrostipulata are identified as putative pseudogenes. We explore the potential utility of the identified putative pseudogenes in the phylogenetic analyses of Naucleeae sensu lato. Both Bayesian and parsimony trees identify the same monophyletic groups and show that the polymorphisms do not transcend species boundaries, implying that they do not predate the divergence of these three species. Furthermore, the resulting trees are similar to those produced in previous studies by analysis of chloroplast genes. In contrast to previous studies, therefore, divergent putative pseudogenes can be useful for phylogenetic analyses, especially, when no sequences of their functional counterparts are available. Our studies clearly show that ITS polymorphism may not necessarily mislead phylogenetic inference. Despite using many different PCR conditions (different primers, higher denaturing temperatures, and absence or presence of DMSO and BSA-TMACl), we recovered only a few functional ITS copies from A. fagifolia and none from H. cordifolia and M. rubrostipulata. We conclude that PCR selection may be occurring and/or the presumed functional alleles are located in minor loci (with few rDNA copies).

Zakharov et al.
Abstract.—Swallowtail butterflies are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology, but present numerous unresolved phylogenetic problems. We inferred phylogenetic relationships for 51 of about 205 species of the genus Papilio (sensu lato), from 3.3 kb sequences of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidase I and II and 1.0 kb of elongation factor-1a). Congruent phylogenetic trees were recovered within Papilio from analyses of combined data, using maximum likelihood, Bayesian analysis, and maximum parsimony bootstrap consensus. Several disagreements with the traditional classification of Papilio were found. Five major previously hypothesized subdivisions within Papilio were well supported: Heraclides, Pterourus, Chilasa, Papilio (sensu stricto), and Eleppone. Further studies are required to clarify relationships within traditional “Princeps”, which was found to be paraphyletic. Several biologically interesting characteristics of Papilio appear to have polyphyletic origins, including mimetic adults, larval host associations, and larval morphology. Early diversification within Papilio is estimated at 55-65 million years ago, based on a combination of biogeographic time constraints rather than fossils. This divergence time suggests that Papilio has slower apparent substitution rates than in Drosophila and fig-pollinating wasps, and/or divergences corrected using best fitting substitution models are still being consistently underestimated. The amount of sequence divergence between Papilio subdivisions is equivalent to divergences between genera in other tribes of the Papilionidae, as well as to genera of moths of the noctuid subfamily Heliothinae.

Sanmartín and Ronquist
Abstract.—The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions for taxa presumed to have originated in the Mesozoic are explained by the sequential break-up of the supercontinent Gondwana during the last 165 Myr, causing successive division of an ancestral biota. However, recent biogeographic studies, based on molecular estimates and more accurate paleogeographic reconstructions, indicate that dispersal may have been more important than traditionally assumed. Here, we examine the relative role played by vicariance and dispersal in shaping Southern Hemisphere biotas by analyzing a large data set of 54 animal and 19 plant phylogenies, including marsupials, ratites, and southern beeches (1393 terminals in all). Parsimony-based tree fitting in conjunction with permutation tests were used to examine to what extent Southern Hemisphere biogeographic patterns fit the break-up sequence of Gondwana, and to identify concordant dispersal patterns. Consistent with other studies, the animal data are congruent with the geological sequence of Gondwana break-up (Africa, (New Zealand, (southern South America, Australia))). Trans-Antarctic dispersal (Australia « S. South America) is also significantly more frequent than any other dispersal event in animals, which may be explained by the long period of geological contact between Australia and South America via Antarctica. In contrast, the dominant pattern in plants, (S. South America, (Australia, New Zealand)), is better explained by dispersal, particularly the prevalence of trans-Tasman dispersal between New Zealand and Australia. Finally, our results confirm the “hybrid” origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially in animals.

Pérez-Losada et al.
Abstract.—The Thoracica include the ordinary barnacles found along the sea shore and is the most diverse and well studied superorder of Cirripedia. However, while the literature abounds with scenarios explaining their evolution, very few studies have attempted to test these alternative hypotheses in a phylogenetic context. The few attempts at phylogenetic analyses have suffered from a lack of phylogenetic signal and small numbers of taxa. We collected DNA sequences from the nuclear 18S, 28S, and histone H3, and the mitochondrial 12S and 16S genes (4,871 bp total), and 37 adult and 53 larval morphological characters from 43 taxa representing all the extant thoracican suborders (except the monospecific Brachylepadomorpha). Moreover, four Rhizocephala (highly modified parasitic barnacles) taxa and a Rhizocephala + Acrothoracica (burrowing barnacles) hypothetical ancestor were used as the outgroup for the molecular and morphological analyses, respectively. We analyzed these data separately and combined using maximum likelihood (ML) under “hill climbing” and genetic algorithm heuristic searches, maximum parsimony procedures, and Bayesian inference coupled with Markov chain Monte Carlo techniques under mixed and homogeneous models of nucleotide substitution. The resulting phylogenetic trees answered the following key questions in barnacle evolution: 1) the four-plated Iblomorpha were shown as the most primitive thoracican and the plate-less Heteralepadomorpha as the sister group of the Lepadomorpha. This suggests, for the first time in an invertebrate, that exoskeleton biomineralization may have evolved from phosphatic to calcitic; 2) Sessilia (non-pedunculate) barnacles are monophyletic and have evolved from a stalked (pedunculate) multiplated (5+) scalpelloid-like ancestor rather than a 5-plated lepadomorphan-like one; 3) the Balanomorpha (symmetric sessile barnacles) have evolved as (Chthamaloidea (Coronuloidea (Tetraclitoidea, Balanoidea))).

Thoracican divergence times were estimated under ML-based local clock (Yoder and Yang, 2000), Bayesian (Kishino et al., 2001; Aris-Brosou and Yang, 2002), and penalized likelihood (Sanderson, 2002) approaches using an 18S data set and three calibration points [Heteralepadomorpha = 530 mya (C₁), Scalpellomorpha = 340 mya (C₂), Verrucomorpha = 120 mya (C₃)]. Estimated dates varied considerably within and between approaches depending on the calibration point. Highly parameterized local clock models that assume independent rates (r ≥ 15) for confamilial or congeneric species generated the most congruent estimates among calibrations and agreed better with the barnacle fossil record. Reasonable estimates were also obtained under the Bayesian procedure of Kishino et al. (2001) but using multiple calibrations. Most of the dates estimated under the Bayesian Aris-Brosou and Yang (2002) and penalized likelihood methods using single and/or multiple calibrations were inconsistent among calibrations and did not fit the fossil record.

Lemmon and Moriarty
Abstract.—We studied the importance of proper model assumption in the context of Bayesian phylogenetics, by examining more than 5000 Bayesian analyses and six nested models of nucleotide substitution.  We found that model misspecification can strongly bias bipartition posterior probability estimates.  These biases were most pronounced when rate heterogeneity was ignored.  Moreover, the type of bias seen at a particular bipartition appeared to be strongly influenced by the lengths of the branches surrounding that bipartition.  In the case of the Felsenstein zone, posterior probability estimates of bipartitions were biased when the assumed model was under-parameterized, but were unbiased when the assumed model was over-parameterized.  In the case of the inverse-Felsenstein zone, however, both under-parameterization and over-parameterization lead to biased bipartition posterior probabilities, though the bias caused by over-parameterization was less pronounced and disappeared with increased sequence length.  Model parameter estimates were also affected by model misspecification. Under-parameterization caused a bias in some parameter estimates, such as branch lengths and the gamma shape parameter, whereas over-parameterization caused a decrease in the precision of some parameter estimates.  We caution researchers to assure that the most appropriate model is assumed by employing both a priori model-choice methods and a posteriori model-adequacy tests.

Kandul et al.
Abstract.—Butterflies in the large Palearctic genus Agrodiaetus (Lepidoptera: Lycaenidae) are extremely uniform and exhibit few distinguishing morphological characters.  However, these insects are distinctive in one respect – as a group they possess amongst the greatest interspecific karyotype diversity in the animal kingdom, with chromosome numbers ranging from n = 10 to n = 125.  The monophyly of Agrodiaetus and its systematic position relative to other groups within the section Polyommatus have been controversial.  Characters from the mitochondrial genes COI and COII, and the nuclear gene EF1-a, were used to reconstruct the phylogeny of Agrodiaetus using maximum parsimony and Bayesian phylogenetic methods.  Ninety-one individuals, encompassing most of the taxonomic diversity of Agrodiaetus, and representatives of fourteen related genera were included in this analysis.  Our data indicate that Agrodiaetus is a monophyletic taxon.  Representatives of the genus Polyommatus (sensu stricto) are the closest relatives.  The sequences of the Agrodiaetus taxa in this analysis are tentatively arranged into twelve clades, only one of which corresponds to a species-group traditionally recognized in Agrodiaetus.  Heterogeneous substitution rates across a recovered topology were homogenized with a nonparametric rate smoothing algorithm before the application of a molecular clock.  Two published estimates of substitution rates dated the origin of Agrodiaetus between 2.51 and 3.85 MYA.  During this time, there was heterogeneity in the rate and direction of karyotype evolution among lineages within the genus.  Karyotype instability has evolved independently three times in the section Polyommatus, within the lineages Agrodiaetus, Lysandra and Plebicula.  Rapid karyotype diversification may have played a significant role in the radiation of the genus Agrodiaetus.

Eulenstein et al.
Abstract.—Supertree methods assemble separate phylogenetic trees with shared taxa into larger trees, or supertrees, in an effort to construct more comprehensive phylogenetic hypotheses.  In spite of much recent interest in supertrees, there are still few methods for supertree construction.  The flip supertree problem is an error correction approach that seeks to find a minimum number of changes, or "flips", to the matrix representation of the set of input trees to resolve their incompatibilities. A previous flip supertree algorithm was limited to finding exact solutions and was only feasible for small input trees.  Here we describe a heuristic algorithm for the flip supertree problem suitable for much larger input trees.  We report results from a series of 48 and 96-taxon simulations comparing supertrees constructed with the flip supertree heuristic algorithm to supertrees constructed using other approaches, including MinCut (MC), modified MinCut (MMC) and Matrix Representation with Parsimony (MRP).  Flip supertrees are generally far more accurate than supertrees constructed using MC or modified MMC algorithms and are at least as accurate as supertrees built with MRP.  Flip supertrees are therefore a viable alternative to other supertree methods when the number of taxa is large.

Danforth et al.
Abstract.—We analyzed the higher-level phylogeny of the bee family Halictidae based on the coding regions of three single-copy nuclear genes (long-wavelength [LW] opsin, wingless, and EF-1a). Our combined data set consisted of 2234 aligned nucleotide sites (702 bp for LW opsin, 405 bp for wingless, and 1127 bp for EF-1a), and a total of 779 parsimony informative sites. We included 58 species of halictid bees from 33 genera, representing all subfamilies and tribes, and rooted the trees using seven outgroups from other bee families, including Colletidae, Andrenidae, Melittidae, and Apidae. We analyzed the separate and combined data sets by a variety of methods, including equal weights parsimony, maximum likelihood, and Bayesian methods. The combined data set provides a strong phylogenetic signal with high bootstrap and Bremer support and high posterior probability well into the base of the tree. The phylogeny recovers monophyly of the Halictidae, monophyly of all four subfamilies and both tribes, recovers relationships among the subfamilies and tribes congruent with morphology, and provides robust support for the relationships among the numerous genera in the tribe Halictini (sensu Michener 2000). Using our combined nucleotide data set, several recently described halictid fossils from the Oligocene and Eocene, and recently developed Bayesian methods, we estimated the antiquity of major clades within the family. Our results indicate that each of the four subfamilies arose well before the Cretaceous/Tertiary boundary and suggest that the early radiation of halictid bees involved substantial African/South American interchange roughly coincident with the separation of these two continents in the late Cretaceous. This combination of single copy nuclear genes is capable of recovering Cretaceous-age divergences in bees with high levels of support. We propose that LW opsin, wingless, and EF-1a (F2 copy) may be useful in resolving relationships among the bee families and other Cretaceous-age insect lineages.

Huson and Steel
Abstract.—Given a collection of discrete characters (e.g. aligned DNA sites, gene adjacencies) a common measure of distance between taxa is to count the proportion of characters where the taxa have different character states. It is well known that tree-reconstruction based on these (uncorrected) distances can be statistically inconsistent and lead to different trees than character-based methods such as maximum likelihood, or maximum parsimony. However in these cases the distance data often reveal their unreliability by some deviation from additivity as evidenced by conflicting support for more than one tree. In this paper we describe two results that show how uncorrected (and mis-corrected) distance data can be simultaneously perfectly additive and misleading. Firstly we show that multi-state character data can be perfectly compatible and define one tree, and yet the uncorrected distances derived from these characters are perfectly tree-like (and obey a molecular clock) only for a completely different tree. Second we show that under a Markov model of character evolution a similar phenomenon can occur - not only is there statistical inconsistency using uncorrected distances, but there is no evidence of this inconsistency, since the distances 'look' perfectly tree-like (this does not occur in the classic 2- parameter Felsenstein zone). We characterize precisely when uncorrected distances are additive on the true (and on a false) tree for four taxa. We also extend this result to a more general setting that applies to distances corrected according to an incorrect model.