Outgroup Choice Research Articles

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

BackgroundThe scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments.ResultsIn this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis), and the threatened Javan (Rhinoceros sondaicus), Sumatran (Dicerorhinus sumatrensis), and black (Diceros bicornis) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum) and Indian (Rhinoceros unicornis) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse vs tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths.ConclusionSatisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete mitochondrial genomes becomes commonplace in evolutionary studies."The human factor in classification is nowhere more evident than in dealing with this superfamily (Rhinocerotoidea)." G. G. Simpson (1945)

Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?

Did the mammal radiation arise through initial divergence of prototherians from a common ancestor of metatherians and eutherians, the Theria hypothesis, or of eutherians from a common ancestor of metatherians and prototherians, the Marsupionta hypothesis? Molecular phylogenetic analyses of point substitutions applied to this problem have been contradictory – mtDNA-encoded sequences supported Marsupionta, nuclear-encoded sequences and RY (purine–pyrimidine)-recoded mtDNA supported Theria. The consistency property of maximum likelihood guarantees convergence on the true tree only with longer alignments. Results from analyses of genome datasets should therefore be impervious to choice of outgroup. We assessed whether important hypotheses concerning mammal evolution, including Theria/Marsupionta and the branching order of rodents, carnivorans and primates, are resolved by phylogenetic analyses using ~2.3 megabases of protein-coding sequence from genome projects. In each case, only two tree topologies were being compared and thus inconsistency in resolved topologies can only derive from flawed models of sequence divergence. The results from all substitution models strongly supported Theria. For the eutherian lineages, all models were sensitive to the outgroup. We argue that phylogenetic inference from point substitutions will remain unreliable until substitution models that better match biological mechanisms of sequence divergence have been developed.

Are Victoria West cores “proto-Levallois”? A phylogenetic assessment

Cores from South Africa assigned to the “Victoria West” industry have long been purported as a “proto-Levallois” core form, and thus regarded as ancestral to the Levallois prepared core technologies of the Middle Paleolithic and African Middle Stone Age. Similarities in form between Victoria West cores, in terms of surface morphology and the removal of large flakes from a prepared surface, led to hypothesized schemes of technological evolution from Victoria West cores through to fully developed Levallois cores. However, the phylogenetic basis of this Victoria West “proto-Levallois” hypothesis, and the assumptions of phylogenetic homology upon which it rests, have never been tested formally. In recent years, archaeologists have begun to use phylogenetic methods drawn from biology to test hypotheses of technological and cultural evolution. Here, the phylogenetic assumptions of the Victoria West “proto-Levallois” hypothesis are tested directly using a cladistic (maximum parsimony) protocol. The cladistic analyses indicate that Victoria West cores are not the basal sister taxon of a Levallois clade, as predicted by the proto-Levallois hypothesis. Moreover, character analyses demonstrate that several characters relating to core surfaces and flake scar morphology are not phylogenetically homologous, but result from convergent technological evolution within the Acheulean techno-complex. Post hoc analyses further determine that these results are not confounded by choice of outgroup or raw material factors. The results were also shown to be robust on the basis of the ensemble retention index statistic, bootstrap analyses, and permutation tests. Hence, it is concluded that Victoria West cores do not represent a “proto-Levallois” core form, and that the term “para-Levallois” should more correctly be applied on phylogenetic grounds. It is further argued that even in cases where different technologies are found to share phylogenetically homologous features, use of the term “proto” is questionable on theoretical grounds.

The historical biogeography of Pteroglossus aracaris (Aves, Piciformes, Ramphastidae) based on Bayesian analysis of mitochondrial DNA sequences

Most Neotropical birds, including Pteroglossus aracaris, do not have an adequate fossil record to be used as time constraints in molecular dating. Hence, the evolutionary timeframe of the avian biota can only be inferred using alternative time constraints. We applied a Bayesian relaxed clock approach to propose an alternative interpretation for the historical biogeography of Pteroglossus based on mitochondrial DNA sequences, using different combinations of outgroups and time constraints obtained from outgroup fossils, vicariant barriers and molecular time estimates. The results indicated that outgroup choice has little effect on the Bayesian posterior distribution of divergence times within Pteroglossus, that geological and molecular time constraints seem equally suitable to estimate the Bayesian posterior distribution of divergence times for Pteroglossus, and that the fossil record alone overestimates divergence times within the fossil-lacking ingroup. The Bayesian estimates of divergence times suggest that the radiation of Pteroglossus occurred from the Late Miocene to the Pliocene (three times older than estimated by the “standard” mitochondrial rate of 2% sequence divergence per million years), likely triggered by Andean uplift, multiple episodes of marine transgressions in South America, and formation of present-day river basins. The time estimates are in agreement with other Neotropical taxa with similar geographic distributions.

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 MrBayes, 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.

Taxon combinations, parsimony analysis (PAUP*), and the taxonomy of the yellow‐tailed woolly monkey,Lagothrix flavicauda

The classifications of primates, in general, and platyrrhine primates, in particular, have been greatly revised subsequent to the rationale for taxonomic decisions shifting from one rooted in the biological species concept to one rooted solely in phylogenetic affiliations. Given the phylogenetic justification provided for revised taxonomies, the scientific validity of taxonomic distinctions can be rightly judged by the robusticity of the phylogenetic results supporting them. In this study, we empirically investigated taxonomic-sampling effects on a cladogram previously inferred from craniodental data for the woolly monkeys (Lagothrix). We conducted the study primarily through much greater sampling of species-level taxa (OTUs) after improving some character codings and under a variety of outgroup choices. The results indicate that alternative selections of species subsets from within genera produce various tree topologies. These results stand even after adjusting the character set and considering the potential role of interobserver disagreement. We conclude that specific taxon combinations, in this case, generic or species pairings, of the primary study group has a biasing effect in parsimony analysis, and that the cladistic rationale for resurrecting the Oreonax generic distinction for the yellow-tailed woolly monkey (Lagothrix flavicauda) is based on an artifact of idiosyncratic sampling within the study group below the genus level. Some recommendations to minimize the problem, which is prevalent in all cladistic analyses, are proposed.

Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology

Evolutionary relationships of the Pectinidae were examined using two mitochondrial genes (12S rRNA, 16S rRNA) and one nuclear gene (Histone H3) for 46 species. Outgroup taxa from Propeamussidae, Spondylidae and Limidae were also sequenced to examine the impact of outgroup choice on pectinid topologies. Our phylogenetic analyses resolved the Pectinidae as monophyletic, but many of the subfamilies and tribes within the family do not form monophyletic clades. The paraphyletic Aequipectinini group is the most basal member of the Pectinidae, with the Chlamydinae and Palliolinae representing the most recently derived pectinid groups. These results are in contrast with the current morphological hypothesis of Pectinidae evolution, which suggests the Chlamydinae and Pallioline are basal groups within the Pectinidae. Ingroup topology was found to be sensitive to outgroup choice and increasing taxon sampling within the Pectinidae resulted in more robust phylogenies.

Phylogenetic analysis of 48 gene families revealing relationships between Hagfishes, Lampreys, and Gnathostomata

It has become clear that the extant vertebrates are divided into three major groups, that is, hagfishes, lampreys, and jawed vertebrates. Morphological and molecular studies, however, have resulted in conflicting views with regard to their interrelationships. To clarify the phylogenetic relationships between them, 48 orthologous protein-coding gene families were analyzed. Even as the analysis of 34 nuclear gene families supported the monophyly of cyclostomes, the analysis of 14 mitochondrial gene families suggested a closer relationship between lampreys and gnathostomes compared to hagfishes. Lampreys were sister group of gnathostomes. The results of this study supported the cyclostomes. Choice of outgroup, tree-making methods, and software may affect the phylogenetic prediction, which may have caused much debate over the subject. Development of new methods for tackling such problems is still necessary.

A multi criterion approach for the selection of optimal outgroups in phylogeny: Recovering some support for Mandibulata over Myriochelata using mitogenomics

The choice of an appropriate outgroup is a fundamental prerequisite when the difference between two conflicting phylogenetic hypotheses depends on the position of the root. This is the case for the myriapods that may group either with Pancrustacea forming a clade called Mandibulata, in accordance with morphological characters, or with chelicerates to form Myriochelata (also called Paradoxopoda) as has recently been proposed by mitochondrial and ribosomal RNA gene phylogenies. In order to understand the impact that outgroup choice may have on phylogenetic reconstruction, we have investigated compositional heterogeneity and genetic distance in mtDNA sequences of several different outgroups to the arthropods, selected from deuterostomes, lophotrochozoans and ecdysozoans, and have used them to root a phylogenetically balanced and compositionarily homogeneous arthropod dataset. Results indicate that some outgroups, in particular from lophotrochozoans, nematodes and an onychophoran have G+C content and strand specific biases which are very different from those of arthropods, suggesting that the use of such outgroups may interfere with the stationarity of the model to create a random outgroup effect. We suggest a multi criterion approach for the selection of optimal outgroup species on the basis of (1) low substitution rate, (2) ingroup-like G+C composition, (3) a new strand bias estimator called the skew index, (4) the ability of the outgroup to avoid a “random branching effect” and (5) phylogenetic proximity to arthropods. Inference of phylogeny using various outgroups shows that use of phylogenetically distant and compositionally distinct lophotrochozoans as outgroups strongly supports Myriochelata and use of more closely related, but fast evolving nematodes supports Mandibulata. A dataset comprising multiple ecdysozoan outgroups also supports Mandibulata, unless the compositionally distant Onychophora are included. A group of the best outgroups selected according to our multi criteria selection, and including the most closely related, least genetically distant and most compositionally similar outgroup, a priapulid worm, supports Mandibulata. We conclude that support for the Myriochelata hypothesis from mitochondrial sequences may depend on the nature of the outgroup sequences rather than a true phylogenetic signal. Finally, we advocate a careful analysis and an objective choice of outgroup when dealing with derived sequences, such as mitochondrial genomes.

Rare Genomic Characters Do Not Support Coelomata: RGC_CAMs

Recently there has been a lively debate about a new class of rare genomic characters, RGC_CAMs, and their implications for deep bilaterian phylogeny. Most recently, nine bilaterian species were analyzed along with subsets of six outgroups (Rogozin et al. 2007b), and support for a coelomate clade reported. The authors suggested that our previously reported support for an ecdysozoan clade (Irimia et al. 2007) reflected (i) one outgroup, Nematostella vectensis, being too closely related to bilaterians and (ii) lack of "rigorous statistical analysis." Here, we report further studies of these characters. First, we discuss general issues of outgroup choice. Second, we point out that an argument used by Rogozin et al. against backmutation is not statistically significant. Third, we point out that the statistical method of Rogozin et al. fails to incorporate backmutations, leading to systematic placement of the long-branch taxon as the outgroup. A simple modification of the method yields very different results: 51 of 63 outgroup combinations favor Ecdysozoa, including 51 of 52 with at least eight phylogenetically informative characters, and all 19 with statistically significant signal. These results indicate that the Coelomata signal is a long-branch artifact.

Malagasy Primate Origins: Phylogenies, Fossils, and Biogeographic Reconstructions

The geographic origin of Malagasy primates is a rich source of debate, providing a useful context for understanding effects of differing phylogenetic interpretations upon area of origin reconstructions. This study has evaluated the biogeographic implications of competing primate phylogenies in order to reconstruct the area of origin of Malagasy strepsirhines. The robusticity of biogeographic inference is examined based on sensitivity to tree topology. The results demonstrate extreme vulnerability to both out-group choice and internal tree topology, suggesting caution for area of origin interpretations from phylogenies that exclude fossil taxa. Moreover, even a single taxon can have a powerful effect upon biogeographic interpretations. Perhaps not surprisingly, it is only with greater phylogenetic resolution that a clearer understanding of the biogeographic origins of Malagasy primates will emerge.

Phylogeny of Mesocyclops (Copepoda: Cyclopidae) inferred from morphological characters

Evolutionary relationships were investigated in the genus Mesocyclops, a pantropical freshwater cyclopid group. In the phylogenetic analyses that involved all 71 known species, and used 81 morphological characters (265 character states) mainly of the adult females, two different approaches were applied: global parsimony, and a new distance method based upon the recognition of sister-groups on the basis of minimal distances iteratively corrected for unique character states (MICSEQ). In coding of the characters, half of which showed intraspecific variation, the ‘scaled’ method was employed, which assumes that any trait between its absence and fixed presence passes through a polymorphic stage. Impact of the reference points on topology of the trees generated by the parsimony method was tested in three ways where the outgroups comprised: (1) nine species representing six genera of two subfamilies; (2) three species from two genera supposedly not distant from Mesocyclops; and (3) one presumably close and one distant relative of Mesocyclops. The trees generated by the parsimony-based and corrected distance methods agreed as to the monophyly of the following groups: reidae-clade (M. reidae, M. chaci, M. yutsil); rarus-clade (Mesocyclops annae, M. pseudoannae, M. splendidus, M. rarus, M. paludosus, M. darwini, M. dayakorum); annulatus-clade (Mesocyclops intermedius, M. ellipticus, M. paranaensis, M. annulatus, M. tenuisaccus); meridianus-clade (Mesocyclops meridionalis, M. varius, M. venezolanus, M. brasilianus, M. pseudomeridianus, M. meridianus); major-clade (Mesocyclops major, M. pilosus, M. insulensis); dussarti-clade (M. dussarti, M. dadayi, M. isabellae, M. thermocyclopoides); pubiventris-clade (M. pubiventris, M. medialis, M. brooksi, M. notius). A majority of the analyses support a clade of the ‘true’Mesocyclops including all ingroup species except the reidae-group, and point to monophyly of the Old World species lacking medial spine on P1 basipodite. There were, however, some components for which the two procedures, regardless of the outgroup choice and/or character set, suggested different relationships. Basal relationships of Mesocyclops[between M. edax (North and Central America), the Neotropical species (M. longisetus, M. araucanus, M. evadomingoi, meridianus- and annulatus-clade), Old World group (P1 basipodite without medial spine) and the rarus-clade (Old World; P1 basipodite with medial spine)] remained unresolved. © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society, 2006, 147, 1–70.

The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences

The complete mitochondrial DNA sequence was determined for the mantid shrimp Harpiosquilla harpax. These data demonstrate that the H. harpax mitochondrial genome is a 15,714 bp circular molecule and encodes the typical 37 metazoan mitochondrial genes (13 protein-coding, 22 tRNA, and two rRNA genes). The gene arrangement of H. harpax is consistent with that of the putative arthropod ancestral gene order as depicted by Limulus polyphemus. H. harpax was employed as an outgroup taxon for a phylogenetic investigation of the Decapoda using sequences from complete mitochondrial genomes. Whilst our results are largely in agreement with current taxonomic treatments, the relationships indicated among the reptantian decapods are novel. Our results provide strong statistical support for a sister-group relationship between the Achelata and the Astacida. These findings not only refute previous phylogenetic hypotheses, but also have serious implications for the interpretation of morphological and developmental evolution in the Decapoda. In addition we also investigated the effects of outgroup selection on the resolution of ingroup relationships. We found outgroup choice to significantly influence tree topology thus reinforcing the importance of appropriate outgroup selection in phylogenetic studies.

Molecular analyses of the Apocrita (Insecta:Hymenoptera) suggest that the Chalcidoidea are sister to the diaprioid complex

Despite recent efforts, hypothesised phylogenetic relationships among apocritan wasps remain unresolved. In this study, molecular analyses were employed to analyse a dataset that included the 16S, the 28S and the COI genes of 87 apocritan representatives. Partial sequences of the 18S gene were also generated and added to this dataset. The topological effects of outgroup choice, method of phylogenetic analysis, and inclusion of the 18S data were systematically investigated, with particular focus on the relationship of the Chalcidoidea with other members of the Proctotrupomorpha (Platygastroidea, Proctotrupoidea, Cynipoidea). We report that ingroup topology was sensitive to the choice of outgroup, the method of phylogenetic analysis, and inclusion of 18S data. However, the Proctotrupomorpha were always monophyletic, and the Chalcidoidea were recovered, in every analysis except one, as the sister to the diaprioid complex (Diapriidae + Monomachidae + Maamingidae). The single exception, where the Chalcidoidea + Platygastroidea were recovered, utilised a more distant outgroup (Symphyta : Cephidae : Hartigia), maximum parsimony, and excluded the 18S data. Our results suggest the Chalcidoidea + (Diapriidae + Monomachidae + Maamingidae) relationship is more likely.

Nuclear DNA contents, rDNAs, and karyotype evolution in Vicia subgenus Vicia: II. Section Peregrinae

Nuclear DNA contents, automated karyotype analyses, and sequences of rDNA spacers have been determined for the species of Vicia belonging to sect. Peregrinae, as well as for V. mollis. The phylogenetic data generated from the comparison of rDNA sequences and karyomorphological results would both indicate that Vicia mollis is a sister group to sect. Peregrinae. The relationships among the species belonging to the Peregrinae section and species enclosed in sections Faba, Narbonensis, and Bithynicae have been also investigated: a clade including V. mollis and sect. Peregrinae is a sister group to a clade including V. bithynica and sect. Narbonensis. With our choice of outgroup, Vicia faba (including subsp. paucijuga) is external to the above mentioned inclusive group.

Molecular Phylogeny of the Carnivora (Mammalia): Assessing the Impact of Increased Sampling on Resolving Enigmatic Relationships

This study analyzed 76 species of Carnivora using a concatenated sequence of 6243 bp from six genes (nuclear TR-i-I, TBG, and IRBP; mitochondrial ND2, CYTB, and 12S rRNA), representing the most comprehensive sampling yet undertaken for reconstructing the phylogeny of this clade. Maximum parsimony and Bayesian methods were remarkably congruent in topologies observed and in nodal support measures. We recovered all of the higher level carnivoran clades that had been robustly supported in previous analyses (by analyses of morphological and molecular data), including the monophyly of Caniformia, Feliformia, Arctoidea, Pinnipedia, Musteloidea, Procyonidae + Mustelidae sensu stricto, and a clade of (Hyaenidae + (Herpestidae + Malagasy carnivorans)). All of the traditional "families," with the exception of Viverridae and Mustelidae, were robustly supported as monophyletic groups. We further have determined the relative positions of the major lineages within the Caniformia, which previous studies could not resolve, including the first robust support for the phylogenetic position of marine carnivorans (Pinnipedia) within the Arctoidea (as the sister-group to musteloids [sensu lato], with ursids as their sister group). Within the pinnipeds, Odobenidae (walrus) was more closely allied with otariids (sea lions/fur seals) than with phocids ("true" seals). In addition, we recovered a monophyletic clade of skunks and stink badgers (Mephitidae) and resolved the topology of musteloid interrelationships as: Ailurus (Mephitidae (Procyonidae, Mustelidae [sensu stricto])). This pattern of interrelationships of living caniforms suggests a novel inference that large body size may have been the primitive condition for Arctoidea, with secondary size reduction evolving later in some musteloids. Within Mustelidae, Bayesian analyses are unambiguous in supporting otter monophyly (Lutrinae), and in both MP and Bayesian analyses Martes is paraphyletic with respect to Gulo and Eira, as has been observed in some previous molecular studies. Within Feliformia, we have confirmed that Nandinia is the outgroup to all other extant feliforms, and that the Malagasy Carnivora are a monophyletic clade closely allied with the mongooses (Herpestidae [sensu stricto]). Although the monophyly of each of the three major feliform clades (Viverridae sensu stricto, Felidae, and the clade of Hyaenidae + (Herpestidae + Malagasy carnivorans)) is robust in all of our analyses, the relative phylogenetic positions of these three lineages is not resolvable at present. Our analyses document the monophyly of the "social mongooses," strengthening evidence for a single origin of eusociality within the Herpestidae. For a single caniform node, the position of pinnipeds relative to Ursidae and Musteloidea, parsimony analyses of data for the entire Carnivora did not replicate the robust support observed for both parsimony and Bayesian analyses of the caniform ingroup alone. More detailed analyses and these results demonstrate that outgroup choice can have a considerable effect on the strength of support for a particular topology. Therefore, the use of exemplar taxa as proxies for entire clades with diverse evolutionary histories should be approached with caution. The Bayesian analysis likelihood functions generally were better able to reconstruct phylogenetic relationships (increased resolution and more robust support for various nodes) than parsimony analyses when incompletely sampled taxa were included. Bayesian analyses were not immune, however, to the effects of missing data; lower resolution and support in those analyses likely arise from non-overlap of gene sequence data among less well-sampled taxa. These issues are a concern for similar studies, in which different gene sequences are concatenated in an effort to increase resolving power.

A molecular phylogenetic analysis of the “true thrushes” (Aves: Turdinae)

The true thrushes (Passeriformes: Muscicapidae, subfamily Turdinae) are a speciose and widespread avian lineage presumed to be of Old World origin. Phylogenetic relationships within this assemblage were investigated using mitochondrial DNA (mtDNA) sequence data that included the cytochrome b and ND2 genes. Our ingroup sampling included 54 species representing 17 of 20 putative turdine genera. Phylogenetic trees derived via maximum parsimony and maximum likelihood were largely congruent. Most of the Turdine taxa sampled can be placed into one of six well supported clades. Our data indicate a polyphyletic Zoothera which can be divided into at least two (Afro-Asian and Austral-Asian) main clades. The genus Turdus, as presently recognized, is paraphyletic but forms a well supported clade with the addition of three mostly monotypic genera ( Platycichla, Nesocichla, and Cichlherminia). We identify an exclusively New World clade that includes a monophyletic Catharus, Hylocichla, Cichlopsis, Entomodestes, Ridgwayia, and Ixoreus. Members of the morphologically and behaviorally distinct genera Sialia, Myadestes, and Neocossyphus unexpectedly form a basal clade. Using multiple outgroup choices, we show that this group is distantly related, but unequivocally the sister group to the remaining Turdines sampled. The Turdinae appear to be a relatively old songbird lineage, originating in the mid to late Miocene. If the Turdinae are indeed Old World in origin, our data indicate a minimum of three separate invasions of the New World.

Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)

AbstractAn analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an archaeognathan, Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds.© The Willi Hennig Society 2004.

PHYLOGENETIC RELATIONSHIPS AMONG RECENT CHIROPTERAN FAMILIES AND THE IMPORTANCE OF CHOOSING APPROPRIATE OUT-GROUP TAXA

Results of recent molecular studies cast doubt on the validity of the superorder Archonta, suborders Megachiroptera and Microchiroptera, and infraorder Yinochiroptera and has even led some to consider novel alternatives for the evolution of flight and echolocation in mammals. At present, higher-level relationships within Chiroptera still is without consensus, and much of this controversy is related to how bats are related to other mammals and also to relationships among family-level lineages within Chiroptera. Although this controversy superficially manifests itself as differences in the relative merits of morphologic versus molecular data, both classes of data are themselves conflicting. We contend that much of the discrepancy among these studies is due to improper choice of out-group, limited taxonomic sampling, or both. We examined approximately 3 kb of mitochondrial DNA from 104 bats representing the taxonomic, geographic, and morphologic diversity within all families (except the monotypic Craseonycteridae) and 58 additional taxa representing 12 other orders of mammals. Results of our analyses strongly support other recent work indicating that Archonta is not a natural assemblage and that the sister taxon to Chiroptera may include Cetartiodactyla, Perissodactyla, Carnivora, and possibly Pholidota. Using representatives of these taxa as out-groups to evaluate interfamilial relationships within Chiroptera, we detected strong support for recognition of the suborders Yinpterochiroptera and Yangochiroptera. Within Yangochiroptera, our analyses strongly support expansion of the superfamily Noctilionoidea to include the New World Thyropteridae and Furipteridae.

Phylogeny, Taxonomy, and Systematic Position of Clethra (Clethraceae, Ericales) with Notes on Biogeography: Evidence from Plastid and Nuclear DNA Sequences

The phylogenetic relationships of Clethra were investigated by cladistic analyses of DNA sequences from the plastid region trnL‐F and the nuclear region ITS. In accordance with the current taxonomy of the genus, section Clethra and section Cuellaria constitute two separate monophyletic groups, but the species Clethra arborea is to be moved to section Clethra from its former position in the monotypic subsection Pseudocuellaria of section Cuellaria. No support for any of the four series within subsection Cuellaria (section Cuellaria) was obtained. Most of the few morphological characters used as a basis for the current classification are homoplasious when optimized on the molecular phylogeny. An extended data set including various representatives of the ericoid clade was analyzed in order to test whether the choice of outgroup would influence the results, but no variation in the general topology of the tree was observed. The same analysis was used to explore the basal branching of the ericoid clade obtained...