An Analysis of Marsupial Interordinal Relationships Based on 12S rRNA, tRNA Valine, 16S rRNA, and Cytochrome b Sequences

The basal split among living marsupials is traditionally placed between the cohorts Ameridelphiaand Australidelphia. Ameridelphia includes all American forms excepting the South AmericanDramicuipx gliroidex (Order Microbiotheria). Australidelphia includes all Australasian taxaplus Dromiciops glinmles. DNA data support Eometatheria Dromiciaps + Diprotodontia +Dasyuromorphia + Notoryctemorphia) but do not resolve the position of bandicoots, whetherwith other australidelphians or with ameridelphians. Also, the most robust molecular trees (DNAhybridization, multigene studies) exhibit minimal branch subdivision and raise the possibility ofartit'actual associations owing to long branch attraction. We analyzed data sets that consistedof complete sequences tor four niitochondrial genes (cytochrome b, 12S rRNA, tRNA valine,16S rRNA). One data set included 14 marsupial taxa. A second data set included 14 marsupialsas well as outgroup sequences (one monolreme; 20 placentals). Phylogenetic analyses includedparsimony, minimum evolution, maximum likelihood, and quartet puzzling. When phylogeneticanalyses were restricted to just the marsupial sequences, there was 75 to 96% boostrap supportfor the separation of Ameridelphia versus Australidelphia. This suggests that either one orboth of these groups are monophyletic. Also, there was 71 to 98% bootstrap support for theseparation of Eometatheria versus Ameridelphia + Peramelina. Nonmonophyly of several a prioriclades was accepted by at least some statistical tests including the following: Diprotodontia+ Peramelina, Notoryctemorphia + Peramelina, Diprotodonlia + Notoryctemorphia, and themonophyly of Australasian marsupials. With the inclusion of outgroup sequences, there wasreduced bootstrap support for associations among marsupial orders and statistical tests failed toreject all interordinal associations that were tested.     

Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology

The intra-phyletic relationships of sipunculan worms were analyzed based on DNA sequence data from four gene regions and 58 morphological characters. Initially we analyzed the data under direct optimization using parsimony as optimality criterion. An implied alignment resulting from the direct optimization analysis was subsequently utilized to perform a Bayesian analysis with mixed models for the different data partitions. For this we applied a doublet model for the stem regions of the 18S rRNA. Both analyses support monophyly of Sipuncula and most of the same clades within the phylum. The analyses differ with respect to the relationships among the major groups but whereas the deep nodes in the direct optimization analysis generally show low jackknife support, they are supported by 100% posterior probability in the Bayesian analysis. Direct optimization has been useful for handling sequences of unequal length and generating conservative phylogenetic hypotheses whereas the Bayesian analysis under mixed models provided high resolution in the basal nodes of the tree.     

Multilocus ribosomal RNA phylogeny of the leaf beetles (Chrysomelidae)

Basal relationships in the Chrysomelidae (leaf beetles) were investigated using two nuclear (small and partial large subunits) and mitochondrial (partial large subunit) rRNA (≈ 3000 bp total) for 167 taxa covering most major lineages and relevant outgroups. Separate and combined data analyses were performed under parsimony and model‐based tree building algorithms from dynamic (direct optimization) and static (Clustal and BLAST) sequence alignments. The performance of methods differed widely and recovery of well established nodes was erratic, in particular when using single gene partitions, but showed a slight advantage for Bayesian inferences and one of the fast likelihood algorithms (PHYML) over others. Direct optimization greatly gained from simultaneous analysis and provided a valuable hypothesis of chrysomelid relationships. The BLAST‐based alignment, which removes poorly aligned sequence segments, in combination with likelihood and Bayesian analyses, resulted in highly defensible trees obtained in much shorter time than direct optimization, and hence is a viable alternative when data sets grow. The main taxonomic findings include the recognition of three major lineages of Chrysomelidae, including a basal “sagrine” clade (Criocerinae, Donaciinae, Bruchinae), which was sister to the “eumolpine” (Spilopyrinae, Eumolpinae, Cryptocephalinae, Cassidinae) plus “chrysomeline” (Chrysomelinae, Galerucinae) clades. The analyses support a broad definition of subfamilies (i.e., merging previously separated subfamilies) in the case of Cassidinae (cassidines + hispines) and Cryptocephalinae (chlamisines + cryptocephalines + clytrines), whereas two subfamilies, Chrysomelinae and Eumolpinae, were paraphyletic. The surprising separation of monocot feeding Cassidinae (associated with the eumolpine clade) from the other major monocot feeding groups in the sagrine clade was well supported. The study highlights the need for thorough taxon sampling, and reveals that morphological data affected by convergence had a great impact when combined with molecular data in previous phylogenetic analyses of Chrysomelidae. © The Willi Hennig Society 2007.     

Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci

This study represents the first phylogenetic analysis of the molluscan class Polyplacophora using DNA sequence data. We employed DNA from a nuclear protein-coding gene (histone H3), two nuclear ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), one mitochondrial protein-coding gene (cytochrome c oxidase subunit I), and one mitochondrial ribosomal gene (16S rRNA). A series of analyses were performed on independent and combined data sets. All these analyses were executed using direct optimization with parsimony as the optimality criterion, and analyses were repeated for nine combinations of parameters affecting indel and transversion/transition cost ratios. Maximum likelihood was also explored for the combined molecular data set, also using the direct optimization method, with a model equivalent to GTR + I + Γ that accommodates gaps. The results of all nine parameter sets for the combined parsimony analysis of all molecular data (as well as ribosomal data) and the maximum-likelihood analysis of all molecular data support monophyly of Polyplacophora. The resulting topologies mostly agree with a division of Polyplacophora into two major lineages: Lepidopleuridae and Chitonida (sensu Sirenko 1993). In our analyses the genus Callochiton is positioned as the sister group to Lepidopleuridae, and not as sister group to the remaining Chitonida (sensu Buckland-Nicks & Hodgson 2000), nor as the sister group to the remaining Chitonina (sensu Buckland-Nicks 1995). Chitonida (excluding Callochiton) is monophyletic, but conventional subgroupings of Chitonida are not supported. Acanthochitonina (sensu Sirenko 1993) is paraphyletic, or alternatively monophyletic, and is split into two clades, both with abanal gills only and cupules in the egg hull, but one has simple cupules whereas the other has more strongly hexagonal cupules. Sister to the Acanthochitonina clades is Chitonina, including taxa with adanal gills and a spiny egg hull. Schizochiton, the only genus with adanal gills that has an egg hull with cupules, is the sister-taxon to one of the Acanthochitonina clades plus Chitonina, or alternatively basal to Chitonina. Support values for either position are low, leaving this relationship unsettled. Our results refute several aspects of conventional classifications of chitons that are based primarily on shell characters, reinforcing the idea that chiton classification should be revised using additional characters.     

The relative sensitivity of different alignment methods and character codings in sensitivity analysis

Sensitivity analysis provides a way to measure robustness of clades in sequence‐based phylogenetic analyses to variation in alignment parameters rather than measuring their branch support. We compared three different approaches to multiple sequence alignment in the context of sensitivity analysis: progressive pairwise alignment, as implemented in MUSCLE; simultaneous multiple alignment of sequence fragments, as implemented in DCA; and direct optimization followed by generation of the implied alignment(s), as implemented in POY. We set out to determine the relative sensitivity of these three alignment methods using rDNA sequences and randomly generated sequences. A total of 36 parameter sets were used to create the alignments, varying the transition, transversion, and gap costs. Tree searches were performed using four different character‐coding and weighting approaches: the cost function used for alignment or equally weighted parsimony with gap positions treated as missing data, separate characters, or as fifth states. POY was found to be as sensitive, or more sensitive, to variation in alignment parameters than DCA and MUSCLE for the three empirical datasets, and POY was found to be more sensitive than MUSCLE, which in turn was found to be as sensitive, or more sensitive, than DCA when applied to the randomly generated sequences when sensitivity was measured using the averaged jackknife values. When significant differences in relative sensitivity were found between the different ways of weighting character‐state changes, equally weighted parsimony, for all three ways of treating gapped positions, was less sensitive than applying the same cost function used in alignment for phylogenetic analysis. When branch support is incorporated into the sensitivity criterion, our results favour the use of simultaneous alignment and progressive pairwise alignment using the similarity criterion over direct optimization followed by using the implied alignment(s) to calculate branch support.     

A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores

The internal phylogeny of the arachnid order Opiliones is investigated by including molecular data from five molecular markers for ca. 140 species totalling 43 families of Opiliones. The phylogenetic analyses consisted of a direct optimization (DO) approach using POY v. 4 and sophisticated tree search algorithms as well as a static alignment analysed under maximum likelihood. The four Opiliones suborders were well‐supported clades, but subordinal relationships did not receive support in the DO analysis, with the exception of the monophyly of Palpatores (=Eupnoi + Dyspnoi). Maximum‐likelihood analysis strongly supported the traditional relationship of Phalangida and Palpatores: (Cyphophthalmi ((Eupnoi + Dyspnoi) Laniatores)). Relationships within each suborder are well resolved and largely congruent between direct optimization and maximum‐likelihood approaches. Age estimates for the main Opiliones lineages suggest a Carboniferous diversification of Cyphophthalmi, while its sister group, Phalangida, diversified in the Early Devonian. Diversification of all suborders predates the Triassic, and most major lineages predate the Cretaceous. The following taxonomic changes are proposed. Dyspnoi: Hesperonemastoma is transferred to Sabaconidae. Insidiatores: Sclerobunidae stat. nov. is erected as a family for Zuma acuta. © The Willi Hennig Society 2009.     

Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes

Many phylogenetic analyses that include numerous terminals but few genes show high resolution and branch support for relatively recently diverged clades, but lack of resolution and/or support for "basal" clades of the tree. The various benefits of increased taxon and character sampling have been widely discussed in the literature, albeit primarily based on simulations rather than empirical data. In this study, we used a well-sampled gene-tree analysis (based on 100 mitochondrial genomes of higher teleost fishes) to test empirically the efficiency of different methods of data sampling and phylogenetic inference to "correctly" resolve the basal clades of a tree (based on congruence with the reference tree constructed using all 100 taxa and 7990 characters). By itself, increased character sampling was an inefficient method by which to decrease the likelihood of "incorrect" resolution (i.e., incongruence with the reference tree) for parsimony analyses. Although increased taxon sampling was a powerful approach to alleviate "incorrect" resolution for parsimony analyses, it had the general effect of increasing the number of, and support for, "incorrectly" resolved clades in the Bayesian analyses. For both the parsimony and Bayesian analyses, increased taxon sampling, by itself, was insufficient to help resolve the basal clades, making this sampling strategy ineffective for that purpose. For this empirical study, the most efficient of the six approaches considered to resolve the basal clades when adding nucleotides to a dataset that consists of a single gene sampled for a small, but representative, number of taxa, is to increase character sampling and analyze the characters using the Bayesian method.     

Phylogenetic relationships of the genus Cheilosia and the tribe Rhingiini (Diptera, Syrphidae) based on morphological and molecular characters

The phylogenetic relationships of the tribe Rhingiini and the genus Cheilosia (Diptera, Syrphidae) were investigated using morphological and molecular characters. The genus Cheilosia is one of the most diverse lineages of hoverflies (Syrphidae). The mitochondrial protein coding gene cytochrome c oxidase subunit I (COI), and the D2‐3 region of the nuclear 28S rRNA gene were chosen for sequencing, and morphological characters were scored for both adults and immature stages. The combined dataset included 56 ingroup taxa. The datasets were analyzed separately and in conjunction, using both static and dynamic alignment under the parsimony criterion. The aim of the study was to assess the phylogenetic relationships of the tribe Rhingiini, and to explore if the subgenera of Cheilosia were supported as monophyletic clades. Results showed that the monophyly of subtribes of Rhingiini remained ambiguous, especially due to unstable phylogenetic placements of the genera Portevinia and Rhingia. We recovered most subgenera of Cheilosia as monophyletic clades. Dynamic alignment, using the optimization alignment program POY, always recovered more parsimonious topologies under all parameter weighting schemes, than did parsimony analyses using static alignment and analyzed with NONA.     

Diversification Times and Biogeographic Patterns in Apiales

This study provides an overview of the historical biogeography of the major clades of Apiales based on extensive taxon sampling from all major lineages of the order, and character sampling of sequence data from the plastid rpl16 intron and trnD-trnY-trnE-trnT intergenic spacers. Divergence times were estimated in BEAST using relaxed molecular clocks and six calibration points from three families. Biogeographic reconstructions were estimated in DIVA and Lagrange using stratified and non-stratified models, addressing alternative scenarios for taxa with conflicting or poorly supported placements. Our analyses in BEAST estimated the origin of Apiales to Australasia in the Early Cretaceous (c.117 Ma). Most major clades also appear to have originated in Australasia, with the youngest family (Apiaceae) originating in the Late Cretaceous, c. 87 Ma. Diversification of the early lineages appears to be influenced by vicariance events related to the break up of Africa and Australasia (Torricelliaceae from Griseliniaceae and Apiineae), Australasia from Zealandia (e.g., Myodocarpaceae and Araliaceae), and Antarctica from South America, Australia, and possibly Africa (main lineages of Apiaceae). Long-distance dispersal appears as the likely explanation for many younger lineages within major clades, including Subantarctic pathways (e.g., Griseliniaceae and Azorelloideae), across the Pacific and Indian Ocean Basins (e.g., Pittosporaceae and Araliaceae), from Asia across Europe into the Americas (Araliaceae).     

Phylogenetic relationships of Rhododendroideae (Ericaceae)

The Rhododendroideae are usually recognized as a subfamily within Ericaceae. This group has been considered primitive (i.e., occupying the ancestral or basal position relative to all other Ericaceae) due to the occurrence of separate petals in several taxa, deciduous corollas, and septicidally dehiscent capsules. Previous molecular studies using rbcL and nr18s sequences have indicated that Rhododendroideae may be paraphyletic and cladistically derived (i.e., the relative position in the geneology of Ericaceae is not basal). The matK sequences of 42 taxa from traditional Rhododendroideae and potentially related clades were obtained via standard gene amplication and double-stranded dideoxy sequencing. Phylogenetic analyses of these sequences using Actinidia chinensis as the outgroup indicate that the Rhododendroideae are paraphyletic. Trees obtained in the analyses indicate an expanded rhododendroid clade that includes four major subclades - empetroid, rhodo, ericoid, and phyllodocoid. The ericoid clade is sister to the phyllodocoid clade and the empetroid clade is sister to the rhodo clade. Relationships within the clades are generally well resolved except within the rhodo clade where matK data indicate that Rhododendron is probably paraphyletic. Daboecia and Calluna are included within the ericoid clade; Erica is paraphyletic. Cassiope lies outside the rhododendroid clade. The relationships indicated by the matK data suggest that sympetalous flowers are likely plesiomorphic within rhododendroids.     

Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis

The first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000–2700 bp for each taxon) from the nuclear genes 18S and 28S and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae +Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))).     

A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3-ND4 gene sequences

The Hylobatidae (gibbons) are among the most endangered primates and their evolutionary history and systematics remain largely unresolved. We have investigated the species-level phylogenetic relationships among hylobatids using 1257 bases representing all species and an expanded data set of up to 2243 bases for select species from the mitochondrial ND3-ND4 region. Sequences were obtained from 34 individuals originating from all 12 recognized extant gibbon species. These data strongly support each of the four previously recognized clades or genera of gibbons, Nomascus, Bunopithecus, Symphalangus, and Hylobates, as monophyletic groups. Among these clades, there is some support for either Bunopithecus or Nomascus as the most basal, while in all analyses Hylobates appears to be the most recently derived. Within Nomascus, Nomascus sp. cf. nasutus is the most basal, followed by N. concolor, and then a clade of N. leucogenys and N. gabriellae. Within Hylobates, H. pileatus is the most basal, while H. moloch and H. klossii clearly, and H. agilis and H. muelleri likely form two more derived monophyletic clades. The segregation of H. klossii from other Hylobates species is not supported by this study. The present data are (1) consistent with the division of Hylobatidae into four distinct clades, (2) provide the first genetic evidence for all the species relationships within Nomascus, and (3) call for a revision of the current relationships among the species within Hylobates. We propose a phylogenetic tree as a working hypothesis against which intergeneric and interspecific relationships can be tested with additional genetic, morphological, and behavioral data.     

The deterministic effects of alignment bias in phylogenetic inference

Alignment of nucleotide and/or amino acid sequences is a fundamental component of sequence‐based molecular phylogenetic studies. Here we examined how different alignment methods affect the phylogenetic trees that are inferred from the alignments. We used simulations to determine how alignment errors can lead to systematic biases that affect phylogenetic inference from those sequences. We compared four approaches to sequence alignment: progressive pairwise alignment, simultaneous multiple alignment of sequence fragments, local pairwise alignment and direct optimization. When taking into account branch support, implied alignments produced by direct optimization were found to show the most extreme behaviour (based on the alignment programs for which nearly equivalent alignment parameters could be set) in that they provided the strongest support for the correct tree in the simulations in which it was easy to resolve the correct tree and the strongest support for the incorrect tree in our long‐branch‐attraction simulations. When applied to alignment‐sensitive process partitions with different histories, direct optimization showed the strongest mutual influence between the process partitions when they were aligned and phylogenetically analysed together, which makes detecting recombination more difficult. Simultaneous alignment performed well relative to direct optimization and progressive pairwise alignment across all simulations. Rather than relying upon methods that integrate alignment and tree search into a single step without accounting for alignment uncertainty, as with implied alignments, we suggest that simultaneous alignment using the similarity criterion, within the context of information available on biological processes and function, be applied whenever possible for sequence‐based phylogenetic analyses.     

A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach

Multi-gene phylogenetic analyses were conducted to address the evolution of Clavicipitaceae (Ascomycota). Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), beta-tubulin, elongation factor 1alpha (EF-1alpha), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), and mitochondrial ATP Synthase subunit 6 (mtATP6). These data were analyzed in a complete 66-taxon matrix and 91-taxon supermatrix that included some missing data. Separate phylogenetic analyses, with data partitioned according to genes, produced some conflicting results. The results of separate analyses from RPB1 and RPB2 are in agreement with the combined analyses that resolve a paraphyletic Clavicipitaceae comprising three well-supported clades (i.e., Clavicipitaceae clade A, B, and C), whereas the tree obtained from mtATP6 is in strong conflict with the monophyly of Clavicipitaceae clade B and the sister-group relationship of Hypocreaceae and Clavicipitaceae clade C. The distribution of relative contribution of nodal support for each gene partition was assessed using both partitioned Bremer support (PBS) values and combinational bootstrap (CB) analyses, the latter of which analyzed bootstrap proportions from all possible combinations of the seven gene partitions. These results suggest that CB analyses provide a more consistent estimate of nodal support than PBS and that combining heterogeneous gene partitions, which individually support a limited number of nodes, results in increased support for overall tree topology. Analyses of the 91-taxa supermatrix data sets revealed that some nodes were more strongly supported by increased taxon sampling. Identifying the localized incongruence of mtATP6 and analyses of complete and supermatrix data sets strengthen the evidence for rejecting the monophyly of Clavicipitaceae and much of the current subfamilial classification of the family. Although the monophyly of the grass-associated subfamily Clavicipitoideae (e.g., Claviceps, Balansia, and Epichlo?) is strongly supported, the subfamily Cordycipitoideae (e.g., Cordyceps and Torrubiella) is not monophyletic. In particular, species of the genus Cordyceps, which are pathogens of arthropods and truffles, are found in all three clavicipitaceous clades. These results imply that most characters used in the current familial classification of Clavicipitaceae are not diagnostic of monophyly.     

Phylogeny of the Genus Cladonia s.lat. (Cladoniaceae, Ascomycetes) Inferred from Molecular, Morphological, and Chemical Data

Phylogenetic relationships within the genus Cladonia , including Cladina (Cladoniaceae, Lecanoromycetes), were reconstructed based upon simultaneous analyses of DNA sequences and morphological and chemical data. We used sequences from the internal transcribed spacer 1 (ITS1), the 5.8 rDNA gene, and the internal transcribed spacer 2 (ITS2) of the nuclear rDNA gene cluster, and partial sequences from the protein-coding β-tubulin gene. The analyses included 235 specimens of 168 taxa representing all currently recognized sections of Cladonia and Cladina and the outgroup genera Cladia, Pycnothelia , and Ramalea . Analyses were performed using optimization alignment with three different parameter values. The results of all analyses support the inclusion of Cladina in Cladonia . The current sectional division of Cladonia was not supported, and a new provisional classification for the genus is proposed.     

Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae

The nucleotide sequence for the nuclear-encoded small subunit ribosomal RNA gene (SSU rRNA) was determined for 24 species of the Chrysophyceae sensu stricto. These sequences were aligned, using primary and secondary structure, with nine previously published sequences for the Chrysophyceae, 14 for the Synurophyceae, and five for the Eustigmatophyceae (outgroup). Data analyses were the substitution rate calibration distance method using neighbor-joining (TREECON), Kimura 2-parameter neighbor-joining method (PAUP) and the maximum parsimony method (PAUP, PHYLIP). Trees from the analyses were largely congruent, but bootstrap support was weak at many nodes. The analyses recovered clades of uniflagellate and biflagellate organisms associated with current higher level taxonomy (e.g., subclass, order). The genus Ochromonas was polyphyletic, and O. tuberculata in particular was distantly related to the other Ochromonas species in the analysis. The family Paraphysomonadaceae occupied a basal position in three of four analyses. The class Synurophyceae appeared to be embedded within the Chrysophyceae, but bootstrap support was weak (< 50%) in all analyses except the PHYLIP parsimony analysis (= 81%). It was considered premature to place the Synurophyceae back into the Chrysophyceae based upon the analysis of one gene, especially given the ultrastructural and pigment differences between the two groups, but the relationship of these two groups deserves further study.     

The phylogeny of the Histeroidea (Coleoptera: Staphyliniformia)

For its size (ca. 4000 species) the Histeridae is one of the most ecologically and morphologically diverse families of beetles. Its mostly predaceous members occupy a wide variety of habitats for which their morphologies may be highly modified. Previous attempts to resolve the phylogeny of the family based on morphological data have left many difficult issues unresolved. This study is the first to utilize either larval or molecular (18S rDNA) data in combination with adult morphology in an attempt to resolve these issues. We compare the performance of optimization alignment with a fixed positional homology approach, over a range of parameter space. Optimizing alignment parameters for combined analyses of 18S and morphology for both approaches resulted in very similar topologies. Contrary to previous hypotheses which held the cylindrical, subcortical forms of the family (e.g., Niponius , Trypanaeus , Trypeticus ) to be the most primitive, our analyses find these to be highly specialized forms derived from within other more generalized taxa. Basal lineages within the family instead include Onthophilus , Anapleus , and Dendrophilus , all of which are ovoid, mainly generalist forms.     

A phylogenetic evaluation of a biosystematic framework: Brodiaea and related petaloid monocots (Themidaceae)

Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl16 are presented separately and combined for 41 taxa from all 12 genera of the Themidaceae and for 20 taxa from nine related families in the higher Asparagales. The results from the combined analysis are the most resolved and provide a high level of support for the monophyly of Themidaceae. Within Themidaceae, the Milla complex of Mexico is supported as monophyletic within a paraphyletic Brodiaea complex of western North America. Four major clades are identified in each of the individual and combined analyses: (1) the Milla complex; (2) Brodiaea, Dichelostemma, and Triteleiopsis; (3) Triteleia, Bloomeria, and Muilla clevelandii; and (4) Androstephium and the other species of Muilla. These well-defined clades suggest that morphological characters (e.g., an extended perianth tube) that have been traditionally used to circumscribe the genera within the Brodiaea complex have evolved independently at least twice. In addition, common biogeographic distribution patterns (e.g., Brodiaea and Triteleia having centers of diversity in northern California and the Pacific Northwest) appear to be the result of separate evolutionary radiations.     

The information content of an ambiguously alignable region, a case study of the trnL intron from the Rhamnaceae

An earlier analysis of the trnL intron in the Colletieae (Rhamnaceae) showed polyphyly of the genus Discaria. Polyphyly of Discaria is supported only by an AT-rich region of ambiguous alignment within the trnL intron. Polyphyly of the genus relies on extracting the information of the AT-rich region correctly. Ambiguously aligned regions are commonly excluded from phylogenetic analysis. In the present study the question was raised whether random or noisy data could generate a pattern like the one found in the AT-rich region of ambiguous alignment. The original pattern was resistant to changes in alignment parameter cost when submitted to a sensitivity analysis using direct optimization. Artificially generated random or noisy data gave well-resolved trees but these were found to be extremely sensitive to changes in parameter costs. However, information from additional data, such as conserved regions, restricts the influence of random data. It is here suggested that the information in ambiguously aligned regions need not be dismissed, provided that an appropriate method that finds all possible optimal alignments is used to extract the information. In addition to commonly used support measures, some information of robustness to changes in alignment parameter costs is needed in order to make the most reliable conclusions.     

The origin of the Australasian marsupial fauna and the phylogenetic affinities of the enigmatic monito del monte and marsupial mole.

Alternative hypotheses in higher-level marsupial systematics have different implications for marsupial origins, character evolution, and biogeography. Resolving the position of the South American monito del monte (Order Microbiotheria) is of particular importance in that alternate hypotheses posit sister-group relationships between microbiotheres and taxa with disparate temporal and geographic distributions: pediomyids; didelphids; dasyuromorphians; diprotodontians; all other australidelphians; and all other marsupials. Among Australasian marsupials, the placement of bandicoots is critical; competing views associate bandicoots with particular Australasian taxa (diprotodontians, dasyuromorphians) or outside of a clade that includes all other Australasian forms and microbiotheres. Affinities of the marsupial mole are also unclear. The mole is placed in its own order (Notoryctemorphia) and sister-group relationships have been postulated between it and each of the other Australasian orders. We investigated relationships among marsupial orders by using a data set that included mitochondrial and nuclear genes. Phylogenetic analyses provide support for the association of microbiotheres with Australasian marsupials and an association of the marsupial mole with dasyuromorphs. Statistical tests reject the association of diprotodontians and bandicoots together as well as the monophyly of Australasian marsupials. The origin of the paraphyletic Australasian marsupial fauna may be accounted for by (i) multiple entries of australidelphians into Australia or (ii) bidirectional dispersal of australidelphians between Antarctica and Australia.