Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach

Recent trends in molecular phylogenetic analysis: where to next?

The acquisition of large multilocus sequence data is providing researchers with an unprecedented amount of information to resolve difficult phylogenetic problems. With these large quantities of data comes the increasing challenge regarding the best methods of analysis. We review the current trends in molecular phylogenetic analysis, focusing specifically on the topics of multiple sequence alignment and methods of tree reconstruction. We suggest that traditional methods are inadequate for these highly heterogeneous data sets and that researchers employ newer more sophisticated search algorithms in their analyses. If we are to best extract the information present in these data sets, a sound understanding of basic phylogenetic principles combined with modern methodological techniques are necessary.

Jaw morphology and ontogeny in five species of Ophryotrocha

Detailed scanning electron microscopy of jaws within the genus Ophryotrocha (Dorvilleidae, Annelida) was performed on 871 jaw parts. The investigations resulted in new understandings of the ontogeny and jaw morphology and have systematic implications for the family. Five species in the genus (Ophryotrocha alborana, O. diadema, O. gracilis, O. hartmanni, and O. labronica pacifica) were kept in culture, and the development of the jaws was studied by sampling throughout their life history. Ophryotrocha species have mandibular plates that remain the same throughout ontogeny, whereas the posterior shafts elongate. Both mandibular plate morphology and shaft ontogeny have species-specific distinctions. In Ophryotrocha, the maxillae can be assigned to three to four distinct types, which are replaced by moulting. The maxillary morphology and developmental stages at which moults occur are species specific, although with broad intervals. A redefinition is given for some of the basic jaw elements, and new homologies are proposed for structures that are also present across other dorvilleid taxa.

Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes

BACKGROUND

Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. SThe "total-evidence" analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole.

RESULTS

Phylogenetic relationships within Annelida were analysed on the basis of 93 morphological characters and sequences of six genes (18S, 28S, and 16S rRNA, EF1alpha, H3, COI), altogether, 87 terminals of all annelid "families" and 3,903 informative characters, by Bayesian and maximum-parsimony methods. The analysis of the combined dataset yields the following scheme of relationships: Phyllodocida and Eunicida are monophyletic groups, together probably forming monophyletic Aciculata (incl. Orbiniidae and Parergodrilidae that form a sister group of the Eunicida). The traditional "Scolecida" and "Canalipalpata" are both polyphyletic, forming instead two clades: one including Cirratuliformia and the "sabelloid-spionoid clade" (incl. Sternaspis, Sabellidae-Serpulidae, Sabellariidae, Spionida s.str.), the other ("terebelloid-capitelloid clade") including Terebelliformia, Arenicolidae-Maldanidae, and Capitellidae-Echiurida. The Clitellata and "clitellate-like polychaetes" (Aeolosomatidae, Potamodrilidae, Hrabeiella) form a monophyletic group. The position of the remaining annelid groups is uncertain--the most problematic taxa are the Opheliidae-Scalibregmatidae clade, the Amphinomida-Aberranta clade, Apistobranchus, Chaetopteridae, Myzostomida, the Sipunculida-Dinophilidae clade, and the "core Archiannelida" (= Protodrilidae, Nerillidae, Polygordiidae, Saccocirridae).

CONCLUSION

The combined ("total-evidence") phylogenetic analysis provides a modified view of annelid evolution, with several higher-level taxa, i.e. Phyllodocida, Eunicida, orbinioid-parergodrilid clade (OPC), Cirratuliformia, sabelloid-spionoid clade (SSC), terebelloid-capitelloid clade (TCC), and "Clitellatomorpha". Two unorthodox clades, the "core Archiannelida" and Sipunculida-Dinophilidae, are proposed. Although the deep-level evolutionary relationships of Annelida remain poorly understood, we propose the monophyly of the Aciculata, sister-group relationships between the Eunicida and OPC, between the Cirratuliformia and SSC, and possibly also between the "Clitellatomorpha" and Oweniidae-Pogonophora clades.

Phylogeny and biogeography of hawkmoths (Lepidoptera: Sphingidae): evidence from five nuclear genes

BACKGROUND

The 1400 species of hawkmoths (Lepidoptera: Sphingidae) comprise one of most conspicuous and well-studied groups of insects, and provide model systems for diverse biological disciplines. However, a robust phylogenetic framework for the family is currently lacking. Morphology is unable to confidently determine relationships among most groups. As a major step toward understanding relationships of this model group, we have undertaken the first large-scale molecular phylogenetic analysis of hawkmoths representing all subfamilies, tribes and subtribes.

METHODOLOGY/PRINCIPAL FINDINGS

The data set consisted of 131 sphingid species and 6793 bp of sequence from five protein-coding nuclear genes. Maximum likelihood and parsimony analyses provided strong support for more than two-thirds of all nodes, including strong signal for or against nearly all of the fifteen current subfamily, tribal and sub-tribal groupings. Monophyly was strongly supported for some of these, including Macroglossinae, Sphinginae, Acherontiini, Ambulycini, Philampelini, Choerocampina, and Hemarina. Other groupings proved para- or polyphyletic, and will need significant redefinition; these include Smerinthinae, Smerinthini, Sphingini, Sphingulini, Dilophonotini, Dilophonotina, Macroglossini, and Macroglossina. The basal divergence, strongly supported, is between Macroglossinae and Smerinthinae+Sphinginae. All genes contribute significantly to the signal from the combined data set, and there is little conflict between genes. Ancestral state reconstruction reveals multiple separate origins of New World and Old World radiations.

CONCLUSIONS/SIGNIFICANCE

Our study provides the first comprehensive phylogeny of one of the most conspicuous and well-studied insects. The molecular phylogeny challenges current concepts of Sphingidae based on morphology, and provides a foundation for a new classification. While there are multiple independent origins of New World and Old World radiations, we conclude that broad-scale geographic distribution in hawkmoths is more phylogenetically conserved than previously postulated.

Molecular cophylogenetic relationships between European bats and their ectoparasitic mites (Acari, Spinturnicidae)

Cospeciation between host-parasite species is generally thought to result in mirror-image congruent phylogenies. Incongruence can be explained by mechanisms such as host switching, duplication, failure to speciate and sorting events. To investigate the level of association in the host-parasite relationship between Spinturnicid mites and their bat hosts, we constructed the phylogenetic tree of the genus Spinturnix (Acari, Mesostigmata) and compared it to the host phylogeny. We sequenced 938bp of the mitochondrial 16S rDNA and Cytochrome Oxydase subunit I (COI) genes among eleven morphospecies of Spinturnix collected on 20 European Vespertilionid and Rhinolophid bat species. Phylogenetic reconstruction of hosts and parasites showed statistical evidence for cospeciation and suggested that their evolutionary history involved also failure to speciate events and host switches. The latter seem to be mainly promoted by similar roosting habits of the host. As currently understood, host associations of Spinturnicid mites likely results from a complex interaction between the phylogenetic history of the host and the behaviour and the ecology of both parasite and host.

Data congruence, paedomorphosis and salamanders

BACKGROUND

The retention of ancestral juvenile characters by adult stages of descendants is called paedomorphosis. However, this process can mislead phylogenetic analyses based on morphological data, even in combination with molecular data, because the assessment if a character is primary absent or secondary lost is difficult. Thus, the detection of incongruence between morphological and molecular data is necessary to investigate the reliability of simultaneous analyses. Different methods have been proposed to detect data congruence or incongruence. Five of them (PABA, PBS, NDI, LILD, DRI) are used herein to assess incongruence between morphological and molecular data in a case study addressing salamander phylogeny, which comprises several supposedly paedomorphic taxa. Therefore, previously published data sets were compiled herein. Furthermore, two strategies ameliorating effects of paedomorphosis on phylogenetic studies were tested herein using a statistical rigor. Additionally, efficiency of the different methods to assess incongruence was analyzed using this empirical data set. Finally, a test statistic is presented for all these methods except DRI.

RESULTS

The addition of morphological data to molecular data results in both different positions of three of the four paedomorphic taxa and strong incongruence, but treating the morphological data using different strategies ameliorating the negative impact of paedomorphosis revokes these changes and minimizes the conflict. Of these strategies the strategy to just exclude paedomorphic character traits seem to be most beneficial. Of the three molecular partitions analyzed herein the RAG1 partition seems to be the most suitable to resolve deep salamander phylogeny. The rRNA and mtDNA partition are either too conserved or too variable, respectively. Of the different methods to detect incongruence, the NDI and PABA approaches are more conservative in the indication of incongruence than LILD and PBS.

CONCLUSION

Paedomorphosis induces strong conflicts and can mislead the phylogenetic analyses even in combined analyses. However, different strategies are efficiently minimizing these problems. Though the exploration of different methods to detect incongruence is preferable NDI and PABA are more conservative than the others and NDI is computational less extensive than PABA.

MITONUCLEAR DISCORDANCE IS CAUSED BY RAMPANT MITOCHONDRIAL INTROGRESSION IN NEODIPRION (HYMENOPTERA: DIPRIONIDAE) SAWFLIES

We investigate the pervasiveness of hybridization and mitochondrial introgression in Neodiprion Rohwer (Hymenoptera; Diprionidae), a Holarctic genus of conifer-feeding sawflies. A phylogenetic analysis of the lecontei species group revealed extensive discordance between a contiguous mitochondrial region spanning three genes (COI, tRNA-leucine, and COII) and three nuclear loci (EF1alpha, CAD, and an anonymous nuclear locus). Bayesian tests of monophyly and Shimodaira-Hasegawa (SH) tests of topological congruence were consistent with mitochondrial introgression; however, these patterns could also be explained by lineage sorting (i.e., deep coalescence). Therefore, to explicitly test the mitochondrial introgression hypothesis, we used a novel application of coalescent-based isolation with migration (IM) models to measure interspecific gene flow at each locus. In support of our hypothesis, mitochondrial gene flow was consistently higher than nuclear gene flow across 120 pairwise species comparisons (P < 1 x 10(-12)). We combine phylogenetic and coalescent evidence to identify likely cases of recent and ancient introgression in Neodiprion, and based on these observations, we hypothesize that shared hosts and/or pheromones facilitate hybridization, whereas disparate abundances between hybridizing species promote mitochondrial introgression. Our results carry implications for phylogenetic analysis, and we advocate the separation of high and low gene flow regions to inform analyses of hybridization and speciational history, respectively.

Annelid phylogeny and the status of Sipuncula and Echiura

BACKGROUND

Annelida comprises an ancient and ecologically important animal phylum with over 16,500 described species and members are the dominant macrofauna of the deep sea. Traditionally, two major groups are distinguished: Clitellata (including earthworms, leeches) and "Polychaeta" (mostly marine worms). Recent analyses of molecular data suggest that Annelida may include other taxa once considered separate phyla (i.e., Echiura, and Sipuncula) and that Clitellata are derived annelids, thus rendering "Polychaeta" paraphyletic; however, this contradicts classification schemes of annelids developed from recent analyses of morphological characters. Given that deep-level evolutionary relationships of Annelida are poorly understood, we have analyzed comprehensive datasets based on nuclear and mitochondrial genes, and have applied rigorous testing of alternative hypotheses so that we can move towards the robust reconstruction of annelid history needed to interpret animal body plan evolution.

RESULTS

Sipuncula, Echiura, Siboglinidae, and Clitellata are all nested within polychaete annelids according to phylogenetic analyses of three nuclear genes (18S rRNA, 28S rRNA, EF1alpha; 4552 nucleotide positions analyzed) for 81 taxa, and 11 nuclear and mitochondrial genes for 10 taxa (additional: 12S rRNA, 16S rRNA, ATP8, COX1-3, CYTB, NAD6; 11,454 nucleotide positions analyzed). For the first time, these findings are substantiated using approximately unbiased tests and non-scaled bootstrap probability tests that compare alternative hypotheses. For echiurans, the polychaete group Capitellidae is corroborated as the sister taxon; while the exact placement of Sipuncula within Annelida is still uncertain, our analyses suggest an affiliation with terebellimorphs. Siboglinids are in a clade with other sabellimorphs, and clitellates fall within a polychaete clade with aeolosomatids as their possible sister group. None of our analyses support the major polychaete clades reflected in the current classification scheme of annelids, and hypothesis testing significantly rejects monophyly of Scolecida, Palpata, Canalipalpata, and Aciculata.

CONCLUSION

Using multiple genes and explicit hypothesis testing, we show that Echiura, Siboglinidae, and Clitellata are derived annelids with polychaete sister taxa, and that Sipuncula should be included within annelids. The traditional composition of Annelida greatly underestimates the morphological diversity of this group, and inclusion of Sipuncula and Echiura implies that patterns of segmentation within annelids have been evolutionarily labile. Relationships within Annelida based on our analyses of multiple genes challenge the current classification scheme, and some alternative hypotheses are provided.

The phylogeny of the social Anelosimus spiders (Araneae: Theridiidae) inferred from six molecular loci and morphology

We use fragments of three nuclear genes (Histone 3, 18SrDNA, and 28SrDNA) and three mitochondrial genes (16SrDNA, ND1, and COI) totalling approximately 4.5kb, in addition to morphological data, to estimate the phylogenetic relationships among Anelosimus spiders, well known for their sociality. The analysis includes 67 individuals representing 23 of the 53 currently recognized Anelosimus species and all species groups previously recognized by morphological evidence. We analyse the data using Bayesian, maximum likelihood, and parsimony methods, considering the genes individually as well as combined (mitochondrial, nuclear, and both combined) in addition to a 'total evidence' analysis including morphology. Most of the data partitions are congruent in agreeing on several fundamental aspects of the phylogeny, and the combined molecular data yield a tree broadly similar to an existing morphological hypothesis. We argue that such congruence among data partitions is an important indicator of support that may go undetected by standard robustness estimators. Our results strongly support Anelosimus monophyly, and the monophyly of the recently revised American 'eximius lineage', although slightly altered by excluding A. pacificus. There was consistent support for the scattering of American Anelosimus species in three clades suggesting intercontinental dispersal. Several recently described species are reconstructed as monophyletic, supporting taxonomic decisions based on morphology and behaviour in this taxonomically difficult group. Corroborating previous results from morphology, the molecular data suggest that social species are scattered across the genus and thus that sociality has evolved multiple times, a significant finding for exploring the causes and consequences of social evolution in this group of organisms.