Abstract. Fruit type in the genus Lithocarpus (Fagaceae) includes both classic oak acorns and novel modifications. Bornean taxa with modified fruits can be separated into two sections (Synaedrys and Lithocarpus) based on subtle shape differences. Following strict criteria for homology and representation, this variation in shape can be captured and the sections distinguished using elliptic Fourier or eigenshape analysis. Phenograms of fruit shape, constructed using restricted maximum likelihood techniques and these morphometric descriptors, were incorporated into combined and comparative analyses with molecular sequence data from the internal transcribed spacer (ITS) region of the nuclear rDNA using branch-weighted matrix representation. The combined analysis strongly suggested independent derivation of the novel fruit type in the two sections from different acorn-like ancestors, while the comparative analysis indicated frequent decoupling between the molecular and morphological change as inferred at well-supported nodes. The acorn fruit type has undergone little modification between ingroup and outgroup, despite large molecular distance. Greater morphological than molecular change was inferred at critical transitions between acorn and novel fruit types, particularly for section Lithocarpus. The combination of these two different types of data improved our understanding of the macroevolution of fruit type in this difficult group and the comparative analysis highlighted the significant incongruities in evolutionary pattern between the two datasets. [Fourier, eigenshape, matrix representation, enclosed receptacle, continuous characters, branch length estimates]
Cognato and Vogler
Abstract. The possibility of gene tree incongruence in a species-level phylogenetic analysis of the genus Ips (Coleoptera: Scolytidae) was investigated based on mitochondrial 16S rRNA and nuclear Elongation factor -1_ sequences, and existing Cytochrome Oxidase I and non-molecular data sets. Separate cladistic analyses of the data partitions resulted in partially discordant most-parsimonious trees but revealed only low conflict of the phylogenetic signal. Interactions among data partitions, which differed in the level of sequence divergence (COI> 16S > EF-1_), base composition, and homoplasy, revealed that much of the branch support only emerges in the simultaneous analysis, in particular for deeper nodes in the tree which are almost entirely supported due to "hidden support" (sensu Gatesy et al., 1999). Apparent incongruence between data partitions is in part due to suboptimal alignments and bias of character transformations, but there is little evidence to invoke incongruent phylogenetic histories of genetic loci. There is also no justification for eliminating or downweighting gene partitions based on their level of homoplasy or apparent incongruence with other partitions, as the signal only emerges in the interaction of all data. In comparison to the traditional taxonomy, the pini, plastographus and perturbatus groups are polyphyletic, whereas the grandicollis group is monophyletic except for the inclusion of the (monophyletic) calligraphus group. The latidens group and some European species are distantly related and closer to other genera within Ipini. Our robust cladogram was used to revise the classification of Ips. We provide new diagnoses for Ips and four subgeneric taxa. [bark beetle systematics, phylogenetic congruence, mitochondrial 16S rRNA, Elongation factor, DNA sequence alignment, phylogenetic information content, saturation]
Abstract. Although the phylogenetic position of brachiopods has always been subject to debate, many authors place them as a sister group to deuterostomes on the basis of morphological and developmental characters. However, molecular phylogeny consistently places them among protostomes. More precisely, brachiopods branch inside the lophotrochozoan assemblage, together with annelids, molluscs, nemerteans, flatworms and others. That result was criticized on the basis of i) the prior knowledge of brachiopod morphology and ii) the known limitations of molecular phylogenies. Here we review recent data of molecular origin, particularly those displaying qualitative properties close to those of morphological characters. The complement of Hox genes present in all metazoa tested to date has proved to be a powerful tool for broad phylogenetic reconstruction. The mitochondrial genome also provides qualitative characters, since it shows discrete events of gene rearrangements. We discuss the data, and the way they should be interpreted in the perspective of several hypotheses for metazoan phylogeny. We conclude that they strongly argue in favor of the protostome (and lophotrochozoan) affinity of the brachiopods. There is therefore a need for a reinterpretation of brachiopod morphological and developmental characters. We identify some research axes on brachiopod morphology. [Brachiopod, Phylogeny, Mitochondrial gene order, Hox genes, Rare genomic changes]
Fishbein et al.
Abstract. Rapid, ancient radiations pose one of the most difficult challenges for phylogenetic estimation. We employed DNA sequence data comprising 9,006 aligned bp from five genes (chloroplast atpB, matK, rbcL, and 18S and 26S nrDNA) to elucidate relationships among major lineages of Saxifragales (angiosperms, eudicots). These relationships were poorly supported in prior studies, apparently because these lineages originated in rapid succession. Using an array of methods that explicitly incorporate assumptions about evolutionary process (weighted maximum parsimony, maximum likelihood, LogDet/paralinear transformed distances), we show that the initial diversification of Saxifragales was indeed rapid. We suggest that the poor resolution of our best phylogenetic estimate is not due to violations of assumptions or the combination of data partitions with conflicting histories or processes. We show that estimated branch lengths during the initial diversification are exceedingly short and we estimate that acquiring sufficient sequence data to resolve these relationships will require an extraordinary effort (~107 bp), assuming a linear increase in branch support with branch length. However, our simulation of much larger data sets containing a similar distribution of phylogenetic signal as the five sampled gene sequences suggests a limit to achievable branch support. We use statistical tests of differences in the likelihoods of topologies to evaluate whether the initial radiation of Saxifragales involved the simultaneous origin of major lineages. Our results are consist with predictions that resolving branching order of rapid, ancient radiations requires sampling characters that evolved rapidly at the time of the radiation, but have subsequently experienced a slower evolutionary rate. [Saxifragales; rapid radiation; data partition congruence; ribosomal DNA; chloroplast genes; phylogenetic resolution, maximum likelihood estimation and hypothesis testing]
Kjer et al.
Abstract. Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, comprise the Amphiesmenoptera. Despite extensive previous morphological work, there has been little phylogenetic agreement over the relationship among the three suborders: Annulipalpia, Spicipalpia, and Integripalpia, and conflict over the monophyly of Spicipalpia. In an effort to resolve this conflict, we sequenced fragments of the large and small subunit nuclear ribosomal RNAs (1078 nts; D1, D3, V4-5), the nuclear Elongation factor 1a gene (1098 nts), and a fragment of mitochondrial COI (411 nts). Seventy adult and larval morphological characters were re-analyzed and added to molecular data in a combined analysis. We evaluated signal and homoplasy in each of the molecular datasets, and attempted to rank the particular datasets according to how approriate they were for inferring relationhip among suborders. This evaluation included testing for conflict among datasets, comparing tree lengths among alternative hypotheses, measuring the left-skew of tree-length distributions from maximally divergent sets of taxa, evaluating the recovery of expected clades, visualizing whether or not substitutions were accumulating with time, and estimating nucleotide compositional bias. All these measures cast doubt on the reliability of the deep-level signal coming from the nucleotides of the COI and EF-1a genes, yet these data could still be included in combined analyses without overturning the results from the most conservative marker; the rRNA. The different datasets were found to be evolving under extremely different rates. A site-specific likelihood method for dealing with combined data when parameters are non-overlapping was proposed, and a similar weighting scheme under parsimony was evaluated. Among our phylogenetic conclusions, we found Annulipalpia to be the most basal of the three suborders, with Spicipalpia and Integripalpia forming a clade. Monophyly of Annulipalpia and Integripalpia was confirmed, while the relationships among spicipalpians remain equivocal. [Annulipalpia; Integripalpia; Spicipalpia; dataset combination; Bayesian inference; Pseudoreplicate reweighting; homoplasy]
Kress et al.
Abstract. The Zingiberales are a tropical group of monocotyledons that includes the bananas, gingers and their relatives. The phylogenetic relationships among the currently recognized eight families are investigated here using parsimony and maximum likelihood analyses of four character sets: 1) morphological features; and sequence data of the 2) chloroplast rbcL gene; 3) chloroplast atpB gene; and 4) nuclear 18S rDNA gene. Outgroups for the analyses include the closely related Commelinaceae + Philydraceae + Haemodoraceae + Pontederiaceae + Hanguanaceae as well as seven more distantly related monocots and paleoherbs. Only slightly different estimates of evolutionary relationships result from the analysis of each character set. The morphological data yield a single fully resolved most parsimonious tree. None of the molecular data sets alone completely resolves interfamilial relationships. The analyses of the combined molecular data set provide more resolution than individual genes and the addition of the morphological data provides a well-supported estimate of phylogenetic relationships: (Musaceae ((Strelitziaceae, Lowiaceae) (Heliconiaceae ((Zingiberaceae, Costaceae) (Cannaceae, Marantaceae))))). Evidence from branch lengths in the parsimony analyses and from the fossil record suggest that the Zingiberales originated in the early Cretaceous and underwent a rapid radiation in the mid-Cretaceous by which time most extant family lineages had diverged. [Zingiberales, monocots, phylogeny, rbcL, atpB, 18S, morphology, fossils, tropical.]
Levasseur and Lapointe
Abstract. For more than ten years, systematists have been debating the superiority of character or taxonomic congruence in phylogenetic analysis. In this paper, we demonstrate that the competing approaches can converge to the same solution when a consensus method that accounts for branch lengths is selected. Thus, we propose to use both methods in combination, as a way to corroborate the results of combined and separate analyses. This so-called "global congruence" approach is tested with a wide variety of examples sampled from the literature, and the results are compared to standard consensus methods. Our analyses show that when the total evidence and consensus trees differ topologically, collapsing weakly supported nodes with low bootstrap support usually improves "global congruence". [average consensus, combined analysis, global congruence, separate analysis, total evidence]
Abstract. Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies using discrete morphological data, maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models for purposes of estimating phylogenies (including branch lengths) under the likelihood criterion. An important modifica-tion of standard Markov models involves making the likelihood conditional on characters being variable, because constant char-acters are absent in morphological data sets. Without this modification, branch lengths are often overestimated, resulting in potentially serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach to phylogenetic analysis of discrete morphological data, including combined-data likelihood analyses (morphology + sequence data), likelihood ratio tests, and Bayesian analyses. [maximum likelihood, phylogeny, discrete morphological character, Markov model.]
Abstract. Areas of endemism are central to cladistic biogeography. The concept has been much debated in the past, and from this the generally accepted definition as an area to which at least two species are endemic has emerged. Protocols for locating areas of endemism have been neglected, and there has been no attempt to date to develop optimality criteria against which to evaluate competing hypotheses of areas of endemism. Here various protocols for finding areas of endemism are evaluated: these are based on both phenetic and parsimony analyses, on unweighted data and data weighted by various criteria. The optimality criteria used to compare the performance of the methods include the number of species included in the areas of endemism, the number of areas delimited, and the degree of distributional congruency of the species restricted to each area of endemism. These methods are applied to the African Restionaceae in the Cape Floristic Region. Parsimony methods using weighted data are shown to perform best on the combination of all three optimality criteria. By varying the weighting parameters, the size of the areas of endemism can be varied. This provides a very useful tool for locating areas of endemism that satisfy prespecified scale criteria. [area of endemism; Parsimony Analysis of Endemism; biogeography; Restionaceae; Cape Floristic Region; centers of endemism]
Shull et al.
Abstract. Current hypotheses regarding family relationships in the suborder Adephaga (Coleoptera) are conflicting. Here we report full-length 18S ribosomal RNA sequences of 39 adephagans and 13 outgroup taxa. Data analysis focussed on the impact of sequence alignment on tree topology, using two principally different approaches. Tree alignments, which seek to minimize indels and substitutions on the tree in a single step, as implemented in an approximate procedure by the computer program POY, were contrasted with a more traditional procedure based on alignments followed by phylogenetic inference using parsimony, likelihood, and distance analyses. Despite the substantial differences between procedures, phylogenetic conclusions on basal relationships within Adephaga and relationships between the four suborders of Coleoptera were broadly similar. The analysis weakly supports monophyly of Adephaga, with Polyphaga usually as its sister, and the two small suborders Myxophaga and Archostemata basal to them. In some analyses, however, Polyphaga was reconstructed as having arisen from within Hydradephaga. Adephaga generally split into two monophyletic groups, corresponding to the terrestrial Geadephaga and the aquatic Hydradephaga, as initially proposed by Crowson (1955), consistent with a single colonization of the aquatic environment by adephagan ancestors and contradicting the recent proposition of three independent invasions. A monophyletic Hydradephaga is consistently, though not strongly, supported under most analyses, and a parametric bootstrapping test significantly rejects an hypothesis of non-monophyly. The enigmatic Trachypachidae, which exhibit many similarities to aquatic forms but whose species are entirely terrestrial, were usually recovered as a basal lineage within Geadephaga. There is strong evidence against the view that terrestrial trachypachids are related to the dytiscoid water beetles. [small subunit rRNA, sequence alignment, tree alignment, Adephaga, Coleoptera, aquatic beetles]