Evolutionary relationships among the Pulmonate land snails and slugs (Pulmonata, Stylommatophora)

We have incorporated an additional 56 species of land snails and slugs in our ribosomal (r) RNA molecular phylogeny. The new taxa include representatives of several important groups. The molecular tree now includes 160 species of stylommatophoran land snails and slugs in 144 genera in 61 families. In the rDNA tree, the Stylommatophora are principally divided into an 'achatinoid' and a 'non-achatinoid' clade. Within these clades, several major land snail groups, including the Orthurethra, Elasmognatha, Limacoidea, and Helicoidea, are supported. Overall, the rDNA molecular phylogeny has remained stable following the incorporation of the additional taxa, with these additions having little impact on the major evolutionary patterns in the tree. Taxonomic coverage of the Orthurethra, Orthalicidae, Camaenidae, and Bradybaenidae is increased significantly. The camaenids and bradybaenids form a complex, and both appear to be paraphyletic. Several families of uncertain affinity, such as the Sagdidae and Thyrophorellidae, are included for the first time. The Sagdidae are shown to belong to the Helicoidea, and the Thyrophorellidae to the Achatinoidea.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 593–610.     

A comparative study of the ultrastructure and mineralogy of calcified land snail eggs (Pulmonata: Stylommatophora)

This study indicates that eggs containing calcium carbonate crystals occur in at least 36 of the 65 known families of the land snails (class Gastropoda: order Stylommatophora). Eggs from 22 of these families were available for examination. The x-ray diffraction data, available for the first time for 21 of these families, shows that these egg shells are all made of calcite only, or of a combination of calcite with smaller amounts of aragonite. All of the snail (body) shells examined were made of aragonite only. This is the first ultrastructural investigation of these egg shells, and it indicates that the eggs exhibit enough structural diversity to allow identification of parental animals to genus, and often to species level solely on the basis of egg shell ultrastructure. All of the calcified eggs may be divided into two groups: (1) partly calcified, with discrete crystals of CaCo₃ dispersed in the jelly layer, and (2) heavily calcified, with a hard, brittle egg shell made of fused crystals of CaCO₃ much like an avian egg. Both types of calcified eggs occur in oviparous as well as in ovoviviparous snails. Because of the wide distribution of calcified eggs in the Stylommatophora, and because of the occurrence of heavily calcified eggs in ancient families such as Partulidae, Endodontidae, and Zonitidae, the calcified egg is viewed as a primitive land snail trait associated with terrestrial adaptation. The function of the calcified egg shell, in addition to mechanical support of egg contents, is to supply the developing embryo with enough calcium to form the embryonic shell by the time of hatching.     

New clades of euthyneuran gastropods (Mollusca) from 28S rRNA sequences

Recent morphological and molecular results on phylogeny of euthyneuran gastropods, which include opisthobranchs and pulmonates, have greatly diminished previous supposed resolution of their phylogenetic relationships. In addition to recent morphological results, sequences of the D1 and D2 domains of the 28S rRNA are here analyzed by parsimony for 31 euthyneuran species. The molecular and previous morphological data sets were not congruent according to an ILD test, and morphological and molecular data could not be analyzed simultaneously. Consequently Bremer's Combinable Component Consensus was used to obtain a new tree, with the following supported molecular results: monophyly of a new clade of opisthobranchs including actively swimming Euthyneura, i.e., pelagic Gymnosomata and Thecosomata plus benthic Anaspidea; first molecular confirmation of monophylies of Hygrophila, including Chilina, Acteonoidea, and Sacoglossa, which include both shell-bearing species and slugs; and new confirmation of the monophyly of Stylommatophora. Morphological characters which support the new clades obtained here are discussed.     

New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i)

To date, there is little consensus concerning the phylogenetic relationships among neognath orders, which include all extant birds except ratites and tinamous. Different data sets, both molecular and morphologic, have yielded radically different and often unresolved ordinal topologies, especially within the neoaves clade. This lack of resolution and ongoing conflict indicates a need for additional phylogenetic characters to be applied to the question of higher-level avian phylogeny. In this study, sequences of a single-copy nuclear gene, ZENK, were used to reconstruct an ordinal-level phylogeny of neognath birds. Strong support was indicated for the oldest divergence within Neognathae; the chicken- and duck-like birds formed a clade that was sister to all other modern birds. In addition, many families of traditional taxonomic orders clustered together in the ZENK tree, indicating the gene's general phylogenetic reliability. However, within the neoaves clade, there was little support for relationships among orders, which is a result similar to all other recent molecular studies of higher-level avian phylogeny. This similarity among studies suggests the possibility of a rapid radiation of the major neoaves lineages. Despite the ongoing lack of neoaves resolution, ZENK's sequence divergence and base composition patterns indicate its general utility as a new phylogenetic marker for higher-level avian systematics.     

Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology

In this study, we constructed the first molecular phylogeny of the diverse crab superfamily Majoidea (Decapoda: Pleocyemata: Brachyura), using three loci (16S, COI, and 28S) from 37 majoid species. We used this molecular phylogeny to evaluate evidence for phylogenetic hypotheses based on larval and adult morphology. Our study supports several relationships predicted from larval morphology. These include a monophyletic Oregoniidae family branching close to the base of the tree; a close phylogenetic association among the Epialtidae, Pisidae, Tychidae, and Mithracidae families; and some support for the monophyly of the Inachidae and Majidae families. However, not all majoid families were monophyletic in our molecular tree, providing weaker support for phylogenetic hypotheses inferred strictly from adult morphology (i.e., monophyly of individual families). This suggests the adult morphological characters traditionally used to classify majoids into different families may be subject to convergence. Furthermore, trees constructed with data from any single locus were more poorly resolved than trees constructed from the combined dataset, suggesting that utilization of multiple loci are necessary to reconstruct relationships in this group.     

New approaches to phylogenetic tree search and their application to large numbers of protein alignments

Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies, including molecular systematics, phylogenetics, and comparative genomics. Finding the optimal tree relating a set of sequences using score-based (optimality criterion) methods, such as maximum likelihood and maximum parsimony, may require all possible trees to be considered, which is not feasible even for modest numbers of sequences. In practice, trees are estimated using heuristics that represent a trade-off between topological accuracy and speed. I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds. The heuristics function by allowing the efficient exploration of large numbers of trees through novel hill-climbing and resampling strategies. These heuristics, and other computational approximations, are implemented for maximum likelihood estimation of trees in the program Leaphy, and its performance is compared to other popular phylogenetic programs. Trees are estimated from 4059 different protein alignments using a selection of phylogenetic programs and the likelihoods of the tree estimates are compared. Trees estimated using Leaphy are found to have equal to or better likelihoods than trees estimated using other phylogenetic programs in 4004 (98.6%) families and provide a unique best tree that no other program found in 1102 (27.1%) families. The improvement is particularly marked for larger families (80 to 100 sequences), where Leaphy finds a unique best tree in 81.7% of families.     

Molecular evolution inDrosophila and higher diptera

Summary LHP is a suitable protein for studying evolution in flies (Diptera). This blood protein, which occurs at high concentration late in larval development, was purified to homogeneity from 5 species of Drosophilidae and one species each of Tephritidae and Calliphoridae. Rabbit antisera to the purified LHPs allowed immunological comparisons to be made with the micro-complement fixation technique. Various indirect tests indicated that immunological distance is a reliable estimator of the degree of amino acid sequence difference between LHPs from different species. An evolutionary tree for the 7 LHPs was constructed from the immunological distances with the method of Fitch and Margoliash (1967) to provide the branching order and the method of Chakraborty (1977) to provide the branch lengths. A modified method of tree construction allowed LHPs from 10 additional species to be attached to this tree. The resulting LHP tree for 17 species agrees approximately in branching order with that based on Throckmorton's study of 60 anatomical traits. However, the ratio of anatomical change to LHP change along branches within the tree varies widely, confirming the independence of organismal and molecular evolution. The LHP tree thus provides a new perspective on evolution within and among the families of higher Diptera.     

Phylogeny of Antarctic dragonfishes (Bathydraconidae,Notothenioidei, Teleostei) and related families based on their anatomy and two mitochondrial genes

Although Antarctic teleosts of the suborder Notothenioidei are well studied, the status of some families remains unclear because of limited taxonomic sampling and sometimes poor statistical support from molecular phylogenies. It is true for the Bathydraconidae, the sister-family of the famous haemoglobin-less icefishes, the Channichthyidae. The present study is aimed at clarifying bathydraconid phylogeny and the interrelationships of higher notothenioid families, taking nototheniids as the outgroup. For this purpose, about 300 positions in the mitochondrial control region, 750 positions in the cytochrome b, and a matrix of morphological characters were employed for separate and simultaneous phylogenetic analyses. We conclude that (1) molecular data strongly support the split of bathydraconids into three clades, here called the Bathydraconinae (Bathydraco, Prionodraco, Racovitzia), the Gymnodraconinae (Gymnodraco, Psilodraco, Acanthodraco), and the Cygnodraconinae (Cygnodraco, Gerlachea, Parachaenichthys). Interrelationships between these three and the Channichthyidae remain unclear. Molecular data support neither paraphyly nor monophyly of the bathydraconids, while morphology leads to the monophyly of the family based on the synapomorphic loss of the spinous dorsal fin; (2) The Channichthyidae, the Harpagiferidae, and the Artedidraconidae are monophyletic families; (3) the phylogeny of the haemoglobin-less channichthyids is completely resolved and congruent with the conclusions of based on anatomical characters; (4) The present molecular results as well as other molecular studies favour the hypothesis that harpagiferids are the sister-group of artedidraconids, though our morphological matrix puts harpagiferids as the sister-group of all other families on the basis of a single character. With regard to harpagiferid relationships, it is interesting to notice that, when analysed simultaneously, morphological characters are not automatically "swamped" within molecular ones: in the tree based on the simultaneous analysis of all available data, morphological characters impose their topology on molecules.     

The phylogenetic relationships of the suborder Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence

Fragments of 12S and 16S mitochondrial DNA genes were sequenced for 14 acanthuroid taxa (representing all six families) and seven outgroup taxa. The combined data set contained 1399 bp after removal of all ambiguously aligned positions. Examination of site saturation indicated that loop regions of both genes are saturated for transitions, which led to a weighted parsimony analysis of the data set. The resulting tree topology generally agreed with previous morphological hypotheses, most notably placing the Luvaridae within the Acanthuroidei, but it also differed in several areas. The putative sister group of Acanthuroidei, Drepane, was recovered within the suborder, and the sister group of the family Acanthuridae, Zanclus, was likewise recovered within the family. Morphological characters were included to produce a combined data set of 1585 characters for 14 acanthuroid taxa and a single outgroup taxon. An analysis of the same 15 taxa was performed with only the DNA data for comparison. The total-evidence analysis supports the monophyly of the Acanthuridae. A parametric bootstrap suggests the possibility that the paraphyly of Acanthuridae indicated by the molecular analyses is the result of long-branch attraction. The disagreement between molecular and morphological data on the relationships of the basal acanthuroids and its putative sister taxon is unresolved.     

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.     

Guilds of mycorrhizal fungi and their relation to trees,ericads, orchids and liverworts in a neotropical mountain rain forest

Mycorrhizas of vascular plants and mycorrhiza-like associations of liverworts and hornworts are integral parts of terrestrial ecosystems, but have rarely been studied in tropical mountain rain forests. The tropical mountain rain forest area of the Reserva Biológica San Francisco in South Ecuador situated on the eastern slope of the Cordillera El Consuelo is exceptionally rich in tree species, ericads and orchids, but also in liverworts. Previous light and electron microscopical studies revealed that tree roots are well colonized by structurally diverse Glomeromycota, and that epiphytic, pleurothallid orchids form mycorrhizas with members of the Tulasnellales and the Sebacinales (Basidiomycota). Sebacinales also occurred in mycorrhizas of hemiepiphytic ericads and Tulasnellales were found in liverworts belonging to the Aneuraceae. On the basis of these findings, we hypothesized that symbiotic fungi with a broad host range created shared guilds or even fungal networks between different plant species and plant families. To test this hypothesis, molecular phylogenetic studies of the fungi associated with roots and thalli were carried out using sequences of the nuclear rDNA coding for the small subunit rRNA (nucSSU) of Glomeromycota and the large subunit rRNA (nucLSU) of Basidiomycota. Sequence analyses showed that Sebacinales and Tulasnellales were only shared within but not between ericads and orchids or between liverworts and orchids, respectively. Regarding arbuscular-mycorrhiza-forming trees, however, 18 out of 33 Glomus sequence types were shared by two to four tree species belonging to distinct families. Nearly all investigated trees shared one sequence type with another tree individual. Host range and potential shared guilds appeared to be restricted to the plant family level for Basidiomycota, but were covering diverse plant families in case of Glomeromycota. Given that the sequence types as defined here correspond to fungal species, our findings indicate potential fungal networks between trees.     

贝叶斯推论及其在百合目分子系统学中的应用

贝叶斯推论作为进化生物学的最新进展,在适用复杂模型、大型数据集、计算速度和结果容易解释等方面明显优于其它算法。本文简要介绍了贝叶斯推论原理及其在分子进化和系统发育研究中的重要性,并使用该方法对百合目主要类群的系统发育关系进行了重建。结果显示,百合目rbcL基因最适合的DNA进化模型为GTR I G,贝叶斯法与距离法和最大简约法构建的系统发育树拓扑结构相似,没有显著差异,但是分辨率和支持率明显比后者高。贝叶斯分析结果显示,百合目内划分的7个科,除Smilacaceae科外,其余各科均为高后验概率(PP=1·0)支持的单系类群;文中作者还对各科间的系统关系进行了探讨。     

Phylogeny of the millipede order Spirobolida (Arthropoda: Diplopoda: Helminthomorpha)

This study examines relationships within the millipede order Spirobolida using an exemplar approach, sampling within families to maximize geographical and morphological diversity; due to lack of available material, Allopocockiidae and Hoffmanobolidae were not included in analyses. The focus of this study was to test monophyly of the order, the suborders, and the families of Spirobolida and to propose interfamilial relationships using morphological and molecular data in a total‐evidence approach. Both maximum‐parsimony analyses and Bayesian inference were employed to analyse two datasets consisting of combined morphological and molecular data, one aligned using progressive alignment methods and the second aligned by secondary structure models. Rhinocricidae was recovered sister to all remaining spirobolidan millipedes and is elevated to suborder status as suborder Rhinocricidea. Trigoniulidea was recovered as monophyletic as was Spirobolidea excluding Rhinocricidae; Spirobolidea is redefined to reflect this change. All previously recognized families were recovered, with the exception of Spirobolidae; in all instances, this family was paraphyletic or part of a polytomy that lacked sufficient resolution to assess its monophyly. The results reaffirm much of the existing taxonomic foundation within Spirobolida. This study provides the first phylogenetic test of higher‐level relationships within Spirobolida and will serve as a foundation for future work in this group at finer levels. © The Willi Hennig Society 2010.     

Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference

Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing five additional data sets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other data sets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.     

The significance of terminal duct structures and the role of neoteny in the evolution of the reproductive system of Pulmonata

A comparison of the adult morphology, in conjunction with the ontogenetical development, of the terminal reproductive system elements of Pulmonata yield the following information. Basom-matophora and Systellommatophora are, in the retention of embryonic ditremy in adult conditions, completely neotenous (paedogenetic). In Basommatophora a ditrematic semi-diaulie to ditrematie diaulic lineage is apparent; a sequential monotrematie monaulie (Glacidorbidae) to simultaneous monotrematic monaulic (Siphonariidae) lineage, as a divergent condition, is proposed. The Systellommatophora, in view of similarities in proximal pallial duct development, are considered to be more closely related to Stylommatophora. Embryonic Stylommatophora recapitulate a ditrematic condition, but later ontogenetic stages, as well as adult morphology, indicate the establishment of a (primarily) semi-diaulic monotrematic system. The posterior 'female' position and anterior 'male' position of the genital orifice indicate an inherent divergent development in Stylommatophora. A series depicting possible trends in terminal duct development of Stylommatophora with anterior 'male' position gonopore is reconstructed from an analysis of the various (gross) features present. The genital systems with female properties resulting from apomixis take a terminal position in this series. Pulmonate. reproductive systems are regarded as having developed from intermediate stages in the life cycle of a sequential protandrous prosobranch ancestor.     

Extensive paraphylies within sharks of the order Carcharhiniformes inferred from nuclear and mitochondrial genes

Using nuclear coding and mitochondrial ribosomal genes we try to clarify relationships within Carcharhiniformes with special focus on the two most problematic groups: scyliorhinids and triakids. The mitochondrial aligned sequences are 1542 bp long, and include principally portion of 16S rRNA gene. They are obtained for two outgroup species and 43 Carcharhiniformes species, covering 5 of the 8 families and 15 of the 48 genera of the order. The nuclear RAG1 sequences are 1454 bp long, and are obtained for 17 species representative of the diversity of all species sampled. We used Maximum Parsimony and Maximum Likelihood criteria for tree reconstruction. Paraphylies within the family Scyliorhinidae was proposed for the first time by Maisey [Zool. J. Linn. Soc. 82, 33, 1984] in a morphological cladistic analysis. This result has never been proposed again until recently from molecular phylogenies [Mol. Phylogenet. Evol. 31, 214, 2004]. Here, independent and simultaneous analyses of nuclear and mitochondrial data are congruent in supporting the paraphyly of scyliorhinids. Two groups of scyliorhinids are obtained, thoroughly in line with discrimination proposed by previous authors, based on presence/absence of supraorbital crests on the chondrocranium. The first group (Scyliorhinus+Cephaloscyllium) is basal within carcharhiniforms and the second group (Apristurus+Asymbolus+Cephalurus+Galeus+Parmaturus) is sister group of all the other families investigated (Carcharhinidae, Proscyllidae, Pseudotriakidae, and Triakidae). The paraphyly of triakids appeared probable but more investigations are needed. In conclusion several independent morphological and molecular phylogenetic studies support paraphyly within scyliorhinids. So we propose a new classification for the group, with the redefinition of the family Scyliorhinidae sensu stricto and the resurrection of the family Pentanchidae with a new definition.     

Tree of life for the genera of Chinese vascular plants

We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13?695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.     

Advances in molecular systematics of the vetigastropod superfamily Trochoidea

Williams, S.T. (2012). Advances in molecular systematics of the vetigastropod superfamily Trochoidea. —Zoologica Scripta, 41, 571–595. The gastropod superfamily Trochoidea Rafinesque, 1815 is comprised of a diverse range of species, including large and charismatic species of commercial value as well as many small or enigmatic taxa that are only recently being represented in molecular studies. This study includes the first sequences for rarely collected species from the genera Gaza Watson, 1879, Callogaza Dall, 1881, Antimargarita Powell, 1951 and Kaiparathina Laws, 1941. There is also greater taxon sampling of genera that have proved difficult to place in previous phylogenetic analyses, like Tectus Montfort, 1810, Tegula Lesson, 1832, Margarites Gray, 1847, Margarella Thiele, 1893 and trochoid skeneimorphs. There is also greater sampling of poorly represented families Solariellidae and Liotiidae. Bayesian analysis of combined gene data sets based on four (28S, 12S, 16S and COI) or five genes (plus 18S) suggests that there are eight, possibly nine families in Trochoidea including the families Margaritidae and Tegulidae, which are recognized for the first time at familial rank. Other trochoidean families confirmed are Calliostomatidae, Liotiidae, Skeneidae, Solariellidae, Trochidae and Turbinidae. A clade including Cittarium and the commercially important genera Rochia and Tectus may represent a possible ninth family, but this is not formally recognized or described here and awaits confirmation from further studies. Relationships among families were not generally well supported except in the 5‐gene tree. In the 5‐gene tree, Turbinidae, Liotiidae, Tegulidae, Cittarium, Rochia and Tectus form a well‐supported clade consistent with the previous molecular and morphological studies linking these groups. This clade forms another well‐supported clade with Margaritidae and Solariellidae. Trochidae is sister to Calliostomatidae with strong support. Subfamilial relationships within Trochidae are consistent with recent molecular studies, with the addition of one new subfamily, Kaiparathininae Marshall 1993 (previously a tribe). Only two subfamilies are recognized within Turbinidae, both with calcareous opercula: Prisogasterinae and Turbininae. Calliostomatidae includes a new subfamily Margarellinae. Its assignment to Calliostomatidae, although well supported by molecular evidence, is surprising considering morphological evidence.     

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

Iguanian lizards form a diverse clade whose members have been the focus of many comparative studies of ecology, behavior, and evolution. Despite the importance of phylogeny to such studies, interrelationships among many iguanian clades remain uncertain. Within the Old World clade Acrodonta, Agamidae is sometimes found to be paraphyletic with respect to Chamaeleonidae, and recent molecular studies have produced conflicting results for many major clades. Within the largely New World clade Pleurodonta, relationships among the 12 currently recognized major subclades (mostly ranked as families) have been largely unresolved or poorly supported in previous studies. To clarify iguanian evolutionary history, we first infer phylogenies using concatenated maximum-likelihood (ML) and Bayesian analyses of DNA sequence data from 29 nuclear protein-coding genes for 47 iguanian and 29 outgroup taxa. We then estimate a relaxed-clock Bayesian chronogram for iguanians using BEAST. All three methods produce identical topologies. Within Acrodonta, we find strong support for monophyly of Agamidae with respect to Chamaeleonidae, and for almost all relationships within agamids. Within Pleurodonta, we find strong Bayesian support for almost all relationships, and strong ML support for some interfamilial relationships and for monophyly of almost all families (excepting Polychrotidae). Our phylogenetic results suggest a non-traditional biogeographic scenario in which pleurodonts originated in the Northern Hemisphere and subsequently spread southward into South America. The pleurodont portion of the tree is characterized by several very short, deep branches, raising the possibility of deep coalescences that may confound concatenated analyses. We therefore also use 27 of these genes to implement a coalescent-based species-tree approach for pleurodonts. Although this analysis strongly supports monophyly of the pleurodont families, interfamilial relationships are generally different from those in the concatenated tree, and support is uniformly poor. However, a species-tree analysis using only the seven most variable loci yields higher support and more congruence with the concatenated tree. This suggests that low support in the 27-gene species-tree analysis may be an artifact of the many loci that are uninformative for very short branches. This may be a general problem for the application of species-tree methods to rapid radiations, even with phylogenomic data sets. Finally, we correct the non-monophyly of Polychrotidae by recognizing the pleurodont genus Anolis (sensu lato) as a separate family (Dactyloidae), and we correct the non-monophyly of the agamid genus Physignathus by resurrection of the genus Istiurus for the former Physignathus lesueurii.