Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals

Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years.     

Characterization and phylogenetic utility of the mammalian protamine p1 gene

We sequenced the protamine P1 gene (ca. 450 bp) from 20 bats (order Chiroptera) and the flying lemur (order Dermoptera). We compared these sequences with published sequences from 19 other mammals representing seven orders (Artiodactyla, Carnivora, Cetacea, Perissodactyla, Primates, Proboscidea, and Rodentia) to assess structure, base compositional bias, and phylogenetic utility. Approximately 80% of second codon positions were guanine, resulting in protamine proteins containing a high frequency of arginine residues. Our data indicate that codon usage for arginine differs among higher mammalian taxa. Parsimony analysis of 40 species representing nine orders produced a well-resolved tree in which most nodes were supported strongly, except at the lowest taxonomic levels (e.g., within Artiodactyla and Vespertilionidae). These data support monophyly of several taxa proposed by morphologic and molecular studies (all nine orders: Laurasiatheria, Cetartiodactytla, Yangochiroptera, Noctilionoidea, Rhinolophoidea, Vespertilionoidea, Phyllostomidae, Natalidae, and Vespertilionidae) and, in agreement with recent molecular studies, reject monophyly of Archonta, Volitantia, and Microchiroptera. Bats were sister to a clade containing Perissodactyla, Carnivora, and Cetartiodactyla, and, although not unequivocally, rhinolophoid bats (traditional microchiropterans) were sister to megachiropterans. Sequences of the protamine P1 gene are useful for resolving relationships at and above the familial level in bats, and generally within and among mammalian orders, but with some drawbacks. The coding and intervening sequences are small, producing few phylogenetically informative characters, and aligning the intron is difficult, even among closely related families. Given these caveats, the protamine P1 gene may be important to future systematic studies because its functional and evolutionary constraints differ from other genes currently used in systematic studies.     

A new phylogenetic marker,apolipoprotein B,provides compelling evidence for eutherian relationships

Higher-level relationships within, and the root of Placentalia, remain contentious issues. Resolution of the placental tree is important to the choice of mammalian genome projects and model organisms, as well as for understanding the biogeography of the eutherian radiation. We present phylogenetic analyses of 63 species representing all extant eutherian mammal orders for a new molecular phylogenetic marker, a 1.3kb portion of exon 26 of the apolipoprotein B (APOB) gene. In addition, we analyzed a multigene concatenation that included APOB sequences and a previously published data set (Murphy et al., 2001b) of three mitochondrial and 19 nuclear genes, resulting in an alignment of over 17kb for 42 placentals and two marsupials. Due to computational difficulties, previous maximum likelihood analyses of large, multigene concatenations for placental mammals have used quartet puzzling, less complex models of sequence evolution, or phylogenetic constraints to approximate a full maximum likelihood bootstrap. Here, we utilize a Unix load sharing facility to perform maximum likelihood bootstrap analyses for both the APOB and concatenated data sets with a GTR+Gamma+I model of sequence evolution, tree-bisection and reconnection branch-swapping, and no phylogenetic constraints. Maximum likelihood and Bayesian analyses of both data sets provide support for the superordinal clades Boreoeutheria, Euarchontoglires, Laurasiatheria, Xenarthra, Afrotheria, and Ostentoria (pangolins+carnivores), as well as for the monophyly of the orders Eulipotyphla, Primates, and Rodentia, all of which have recently been questioned. Both data sets recovered an association of Hippopotamidae and Cetacea within Cetartiodactyla, as well as hedgehog and shrew within Eulipotyphla. APOB showed strong support for an association of tarsier and Anthropoidea within Primates. Parsimony, maximum likelihood and Bayesian analyses with both data sets placed Afrotheria at the base of the placental radiation. Statistical tests that employed APOB to examine a priori hypotheses for the root of the placental tree rejected rooting on myomorphs and hedgehog, but did not discriminate between rooting at the base of Afrotheria, at the base of Xenarthra, or between Atlantogenata (Xenarthra+Afrotheria) and Boreoeutheria. An orthologous deletion of 363bp in the aligned APOB sequences proved phylogenetically informative for the grouping of the order Carnivora with the order Pholidota into the superordinal clade Ostentoria. A smaller deletion of 237-246bp was diagnostic of the superordinal clade Afrotheria.     

Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.     

Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’

The beetle suborder Adephaga has been the subject of many phylogenetic reconstructions utilizing a variety of data sources and inference methods. However, no strong consensus has yet emerged on the relationships among major adephagan lineages. Ultraconserved elements (UCEs) have proved useful for inferring difficult or unresolved phylogenies at varying timescales in vertebrates, arachnids and Hymenoptera. Recently, a UCE bait set was developed for Coleoptera using polyphagan genomes and a member of the order Strepsiptera as an outgroup. Here, we examine the utility of UCEs for reconstructing the phylogeny of adephagan families, in the first in vitro application a UCE bait set in Coleoptera. Our final dataset included 305 UCE loci for 18 representatives of all adephagan families except Aspidytidae, and two polyphagan outgroups, with a total concatenated length of 83 547 bp. We inferred trees using maximum likelihood analyses of the concatenated UCE alignment and coalescent species tree methods (astral ii , ASTRID, svdquartets ). Although the coalescent species tree methods had poor resolution and weak support, concatenated analyses produced well‐resolved, highly supported trees. Hydradephaga was recovered as paraphyletic, with Gyrinidae sister to Geadephaga and all other adephagans. Haliplidae was recovered as sister to Dytiscoidea, with Hygrobiidae and Amphizoidae successive sisters to Dytiscidae. Finally, Noteridae was recovered as monophyletic and sister to Meruidae. Given the success of UCE data for resolving phylogenetic relationships within Adephaga, we suggest the potential for further resolution of relationships within Adephaga using UCEs with improved taxon sampling, and by developing Adephaga‐specific probes.     

A genomic approach to examine the complex evolution of laurasiatherian mammals

Recent phylogenomic studies have failed to conclusively resolve certain branches of the placental mammalian tree, despite the evolutionary analysis of genomic data from 32 species. Previous analyses of single genes and retroposon insertion data yielded support for different phylogenetic scenarios for the most basal divergences. The results indicated that some mammalian divergences were best interpreted not as a single bifurcating tree, but as an evolutionary network. In these studies the relationships among some orders of the super-clade Laurasiatheria were poorly supported, albeit not studied in detail. Therefore, 4775 protein-coding genes (6,196,263 nucleotides) were collected and aligned in order to analyze the evolution of this clade. Additionally, over 200,000 introns were screened in silico, resulting in 32 phylogenetically informative long interspersed nuclear elements (LINE) insertion events. The present study shows that the genome evolution of Laurasiatheria may best be understood as an evolutionary network. Thus, contrary to the common expectation to resolve major evolutionary events as a bifurcating tree, genome analyses unveil complex speciation processes even in deep mammalian divergences. We exemplify this on a subset of 1159 suitable genes that have individual histories, most likely due to incomplete lineage sorting or introgression, processes that can make the genealogy of mammalian genomes complex. These unexpected results have major implications for the understanding of evolution in general, because the evolution of even some higher level taxa such as mammalian orders may sometimes not be interpreted as a simple bifurcating pattern.     

Reconstructing the phylogeny of the Sipuncula

Sipunculans are marine spiralian worms with possible close affinities to the Mollusca or Annelida. Currently 147 species, 17 genera, 6 families, 4 orders and 2 classes are recognized. In this paper we review sipunculan morphology, anatomy, paleontological data and historical affiliations. We have conducted cladistic analyses for two data sets to elucidate the phylogenetic relationships among sipunculan species. We first analyzed the relationships among the 45 species of Phascolosomatidea with representatives of the Sipunculidea as outgroups, using 35 morphological characters. The resulting consensus tree has low resolution and branch support is low for most branches. The second analysis was based on DNA sequence data from two nuclear ribosomal genes (18S rRNA and 28S rRNA) and one nuclear protein-coding gene, histone H3. Outgroups were chosen among representative spiralians. In a third analysis, the molecular data were combined with the morphological data. Data were analyzed using parsimony as the optimality criterion and branch support evaluated with jackknifing and Bremer support values. Branch support for outgroup relationships is low but the monophyly of the Sipuncula is well supported. Within Sipuncula, the monophyly of the two major groups, Phascolosomatidea and Sipunculidea is not confirmed. Of the currently recognized families, only Themistidae appears monophyletic. The Aspidosiphonidae, Phascolosomatidae and Golfingiidae would be monophyletic with some adjustments in their definition. The Sipunculidae is clearly polyphyletic, with Sipunculus nudus as the sister group to the remaining Sipuncula, Siphonosoma cumanense the sister group to a clade containing Siphonosoma vastumand the Phascolosomatidea, and Phascolopsis gouldi grouping within the Golfingiiformes, as suggested previously by some authors. Of the genera with multiple representatives, only Phascolosoma and Themiste are monophyletic as currently defined. We are aiming to expand our current dataset with more species in our molecular database and more detailed morphological studies.     

Confirming the phylogeny of mammals by use of large comparative sequence data sets

The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence data sets not only allow smaller and more difficult branches to be resolved but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large data set of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large data set, we partitioned the sequence data in several ways and utilized maximum likelihood, maximum parsimony, and Neighbor-Joining algorithms, implemented in parallel on Linux clusters. These studies yielded well-supported phylogenetic trees, largely confirming other recent molecular phylogenetic analyses. Our results provide support for rooting the placental mammal tree between Atlantogenata (Xenarthra and Afrotheria) and Boreoeutheria (Euarchontoglires and Laurasiatheria), illustrate the difficulty in resolving some branches even with large amounts of data (e.g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence data sets can play in refining our understanding of the evolutionary relationships of vertebrates.     

Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

Phylogenetic relationships among Lemuridae (Primates): evidence from mtDNA

The family Lemuridae includes four genera: Eulemur, Hapalemur, Lemur,Varecia. Taxonomy and phylogenetic relationships between L. catta, Eulemur and Hapalemur, and of Varecia to these other lemurids, continue to be hotly debated. Nodal relationships among the five Eulemur species also remain contentious. A mitochondrial DNA sequence dataset from the ND 3, ND 4 L, ND 4 genes and five tRNAs (Gly, Arg, His, Ser, Leu) was generated to try to clarify phylogenetic relationships w ithin the Lemuridae. Samples (n=39) from all ten lemurid species were collected and analysed. Three Daubentonia madagascariensis were included as outgroup taxa. The approximately 2400 bp sequences were analysed using maximum parsimony, neighbor-joining and maximum likelihood methods. The results support monophyly of Eulemur, a basal divergence of Varecia, and a sister-group relationship for Lemur/Hapalemur. Based on tree topology, bootstrap values, and pairwise distance comparisons, we conclude thatVarecia and Eulemur both represent distinct genera separate from L. catta. H. griseus andH. aureus form a clade with strong support, but the sequence data do not permit robust resolution of the trichotomy involving H. simus, H. aureus/H. griseus and L. catta. Within Eulemur there is strong support for a clade containing E. fulvus, E. mongoz and E. rubriventer. However, analyses failed to clearly resolve relationships among those three species or with the more distantly related E. coronatus and E. macaco. Our sequencing data support the current subspecific status of E.m. macaco and E.m. flavifrons, and that of V.v. variegata and V.v. rubra. However, tree topology and relatively large genetic distances among individual V.v. variegata indicate that there may be more phylogenetic structure within this taxon than is indicated by current taxonomy.     

Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers

Abstract.  In this study, we assessed the ability of mitochondrial genome sequences to recover a test phylogeny of five hymenopteran taxa from which phylogenetic relationships are well accepted. Our analyses indicated that the test phylogeny was well recovered in all nucleotide Bayesian analyses when all the available holometabolan (i.e. outgroup) taxa were included, but only in Bayesian analyses excluding third codon positions when only the hymenopteran representatives and a single outgroup were included. This result suggests that taxon sampling of the outgroup might be as important as taxon sampling of the ingroup when recovering hymenopteran phylogenetic relationships using whole mitochondrial genomes. Parsimony analyses were more sensitive to both taxon sampling and the analytical model than Bayesian analyses, and analyses using the protein dataset did not recover the test phylogeny. In general, mitochondrial genomes did not resolve the position of the Hymenoptera within the Holometabola with confidence, suggesting that an increased taxon sampling, both within the Holometabola and among outgroups, is necessary.     

Phylogenetic relationships of Pelobatoidea re-examined using mtDNA

Pelobatoidea is a clade of ancient anurans with obscure relationships to the remaining clades of frogs. We used partial sequences of two mitochondrial genes (cytochrome b and 16S RNA) from all Pelobatoidea subclades, including all species of Pelobatidae and Pelodytidae and four outgroup taxa (Xenopus, Ascaphus, Discoglossus, and Rana), to propose a phylogenetic hypothesis for relationships within Pelobatoidea. Maximum likelihood and Bayesian analyses support the monophyly of Pelobatoidea, but our hypothesis of internal relationships differs substantially from all previous hypotheses. Megophryidae is sister to Pelobates, and this clade is sister to Pelodytes. The most basal clade within Pelobatoidea is formed by Scaphiopus and Spea. The family Pelobatidae, as previously defined is not monophyletic, and it is split into Eurasian spadefoot toads Pelobates which retain the name Pelobatidae and North American spadefoot toads Scaphiopus and Spea which comprise the revived taxon Scaphiopodidae. Our analysis uncovers the existence of morphologically cryptic taxa within previously recognized species of the genus Spea and reveals marked genetic differentiation within Iberian Pelodytes. We discuss biogeographic implications and the evolution of fossoriality in the light of the new phylogenetic hypothesis.     

Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data

Great progress has been made toward resolving the evolutionary relationships among extant mammals, yet there are still areas of disagreement. The relationships among ferungulates that have high quality draft genome sequences available (i.e. dog, cow, horse) are unresolved, and thus we examined their phylogeny using currently known mammalian 1:1 orthologs. This dataset consists of 40 million base pairs from 2705 protein-coding genes. Maximum likelihood and Bayesian analyses of the combined and individual gene phylogenies strongly support a sister grouping of cow and horse to the exclusion of dog although topology tests could not rule out a horse and dog sister group relationship.     

Phylogenetic relationships of the carabid subfamily Harpalinae (Coleoptera) based on molecular sequence data

The carabid subfamily Harpalinae contains most of the species of carabid beetles. This subfamily, with over 19,000 species, radiated in the Cretaceous to yield a large clade that is diverse in morphological form and ecological habit. While there are several morphological, cytological, and chemical characters that unite most harpalines, the placement of some tribes within the subfamily remains controversial, as does the sister group relationships to this large group. In this study, DNA sequences from the 28S rDNA gene and the wingless nuclear protein-coding gene were collected from 52 carabid genera representing 31 harpaline tribes in addition to more than 21 carabid outgroup taxa to reconstruct the phylogeny of this group. Molecular sequence data from these genes, along with additional data from the 18S rDNA gene, were analyzed with a variety of phylogenetic analysis methods, separately for each gene and in a combined data approach. Results indicated that the subfamily Harpalinae is monophyletic with the enigmatic tribes of Morionini, Peleciini, and Pseudomorphini included within it. Brachinine bombardier beetles are closely related to Harpalinae as they form the sister group to harpalines or, in some analyses, are included within it or with austral psydrines. The austral psydrines are the sister group to Harpalinae+Brachinini clade in most analyses and austral psydrines+Brachinini+Harpalinae clade is strongly supported.     

More taxa,more characters: the hoatzin problem is still unresolved

The apparently rapid and ancient diversification of many avian orders complicates the resolution of their relationships using molecular data. Recent studies based on complete mitochondrial DNA (mtDNA) sequences or shorter lengths of nuclear sequence have helped corroborate the basic structure of the avian tree (e.g., a basal split between Paleognathae and Neognathae) but have made relatively little progress in resolving relationships among the many orders within Neoaves. We explored the potential of a moderately sized mtDNA data set ( approximately 5000 bp for each of 41 taxa), supplemented with data from a nuclear intron ( approximately 700 bp per taxon), to resolve relationships among avian orders. Our sampling of taxa addresses two issues: (1). the sister relationship and monophyly, respectively, of Anseriformes and Galliformes and (2). relationships of the enigmatic hoatzin Opisthocomus hoazin. Our analyses support a basal split between Galloanserae and Neoaves within Neognathae and monophyly of both Galliformes and Anseriformes. Within Galliformes, megapodes and then cracids branch basally. Within Anseriformes, mitochondrial data support a screamer (Anhimidae) plus magpie goose (Anseranatidae) clade. This result, however, may be an artifact of divergent base composition in one of the two anatids we sampled. With deletion of the latter taxon, Anseranas is sister to anatids as in traditional arrangements and recent morphological studies. Although our data provide limited resolution of relationships within Neoaves, we find no support for a sister relationship between either cuckoos (Cuculiformes) or turacos (Musophagiformes) and hoatzin. Both mitochondrial and nuclear data are consistent with a relationship between hoatzin and doves (Columbiformes), although this result is weakly supported. We also show that mtDNA sequences reported in another recent study included pervasive errors that biased the analysis towards finding a sister relationship between hoatzin and turacos.     

Phylogeny of the bee genus Halictus (Hymenoptera: halictidae) based on parsimony and likelihood analyses of nuclear EF-1alpha sequence data

We investigated higher-level phylogenetic relationships within the genus Halictus based on parsimony and maximum likelihood (ML) analysis of elongation factor-1alpha DNA sequence data. Our data set includes 41 OTUs representing 35 species of halictine bees from a diverse sample of outgroup genera and from the three widely recognized subgenera of Halictus (Halictus s.s., Seladonia, and Vestitohalictus). We analyzed 1513 total aligned nucleotide sites spanning three exons and two introns. Equal-weights parsimony analysis of the overall data set yielded 144 equally parsimonious trees. Major conclusions supported in this analysis (and in all subsequent analyses) included the following: (1) Thrincohalictus is the sister group to Halictus s.l., (2) Halictus s.l. is monophyletic, (3) Vestitohalictus renders Seladonia paraphyletic but together Seladonia + Vestitohalictus is monophyletic, (4) Michener's Groups 1 and 3 are monophyletic, and (5) Michener's Group 1 renders Group 2 paraphyletic. In order to resolve basal relationships within Halictus we applied various weighting schemes under parsimony (successive approximations character weighting and implied weights) and employed ML under 17 models of sequence evolution. Weighted parsimony yielded conflicting results but, in general, supported the hypothesis that Seladonia + Vestitohalictus is sister to Michener's Group 3 and renders Halictus s.s. paraphyletic. ML analyses using the GTR model with site-specific rates supported an alternative hypothesis: Seladonia + Vestitohalictus is sister to Halictus s.s. We mapped social behavior onto trees obtained under ML and parsimony in order to reconstruct the likely historical pattern of social evolution. Our results are unambiguous: the ancestral state for the genus Halictus is eusociality. Reversal to solitary behavior has occurred at least four times among the species included in our analysis.     

Phylogenetic relationships among loliginid squids (Cephalopoda: Myopsida) based on analyses of multiple data sets

The phylogenetic relationships among the loliginid squids, a species-rich group of shallowwater muscular squids, have been investigated recently using several approaches, including allozyme electrophoresis and analyses of morphological and DNA sequence data, yet no consensus has been reached. This study examines the effects of combining multiple data sets (morphology, allozymes and DNA sequence data from two mitochondrial genes) on estimates of loliginid phylogeny. Various data combinations were analysed under three maximum parsimony weighting schemes: equal weights for all characters, successive approximations and implicit weights parsimony. When feasible, support for branches within trees was assessed with nonparametric bootstrapping and decay analysis. Some ingroup relationships were consistent across all analyses, but relationships among outgroup taxa and basal ingroup taxa varied. Combining data increased bootstrap support for several nodes. Methods that downweight highly variable characters (i.e. successive approximations and implicit weights parsimony) produced very similar trees which included two major clades: a clade consisting of all species sampled from American waters (except Sepioteuthis ), and a clade of several east Atlantic species ( Loligo forbesi Steenstrup, Loligo vulgaris Lamarck and Loligo reynaudi d'Orbigny) plus several Indo-West Pacific species in the genera Uroteuthis and Loliolus. The Sepioteuthis species occupied a basal position within Loliginidae, but Sepioteuthis itself was not always monophyletic. The position of a clade of a few Lolliguncula species and Loligo (Alloteuthis) also varied across analyses. A new loliginid classification is proposed based on these findings.     

Phylogeny of rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP

The order Rodentia includes nearly half of all living mammalian species. Phylogenetic relationships among 22 species of rodents were investigated by use of a 1.2-kb region from exon 1 of the single-copy nuclear gene IRBP. IRBP has been extensively used for study of interordinal phylogeny in mammals, which allowed inclusion of 50 outgroup species, representing every eutherian order plus seven marsupials. Several clades were strongly supported, regardless of analytical method or inclusion/exclusion of data. These include a monophyletic Muroidea, with a clade including Spalax and Rhizomys as the first divergence; a clade uniting Zapus with Dipus, but excluding Sicista; a monophyletic Myodonta (Muroidea plus Dipodidae); and a clade including Aplodontidae as sister to Sciuridae. One bipartition, separating Hystricognathi and Geomyoidea from the remaining rodents, is strongly supported in all analyses that include third-position sites but almost completely absent from analyses that exclude third-position sites. A combination of nonstationary nucleotide composition and branch length effects may be causing all methods examined (including those using the LogDet distance) to support an incorrect conclusion when third-position sites are analyzed together with first- and second-position sites.     

Molecular evolution of the mammalian alpha 2B adrenergic receptor

The alpha 2B adrenergic receptor (A2AB) is a heptahelical G protein-coupled receptor for catecholamines. We compared the almost complete coding region (about 1,175 bp) of the A2AB gene from 48 mammalian species, including eight newly determined sequences, representing all the 18 eutherian and two marsupial orders. Comparison of the encoded proteins reveals that residues thought to be involved in agonist binding are highly conserved, as are the regions playing a role in G protein-coupling. The three extracellular loops are generally more variable than the transmembrane domains and two of the intracellular loops, indicating a lower functional constraint. However, the greatest variation is observed in the very long, third intracellular loop, where only a few residues and a polyglutamyl tract are preserved. Although this polyglutamyl domain displays a great variation in length, its presence in all described A2ABs confirms its proposed role in agonist-dependent phosphorylation of the third intracellular loop. Phylogenetic analyses of the A2AB data set, including Bayesian methods, recognized the superordinal clades Afrotheria, Laurasiatheria, and Euarchontoglires, in agreement with recent molecular evidence, albeit with lower support. Within Afrotheria, A2AB strongly supports the paenungulate clade and the association of the continental African otter shrew with Malagasy tenrecs. Among Laurasiatheria, A2AB confirms the nesting of whales within the artiodactyls, as a sister group to hippopotamus. Within the Euarchontoglires, there is constant support for rodent monophyly.     

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. “Thaliacea” is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic “Ascidiacea”. Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.