Structural rRNA characters support monophyly of raptorial limbs and paraphyly of limb specialization in water fleas

The evolutionary success of arthropods has been attributed partly to the diversity of their limb morphologies. Large morphological diversity and increased specialization are observed in water flea (Cladocera) limbs, but it is unclear whether the increased limb specialization in different cladoceran orders is the result of shared ancestry or parallel evolution. We inferred a robust among-order cladoceran phylogeny using small-subunit and large-subunit rRNA nuclear gene sequences, signature sequence regions, novel stem-loops and secondary structure morphometrics to assess the phylogenetic distribution of limb specialization. The sequence-based and structural rRNA morphometric phylogenies were congruent and suggested monophyly of orders with raptorial limbs, but paraphyly of orders with reduced numbers of specialized limbs. These results highlight the utility of complex molecular structural characters in resolving ancient rapid radiations.     

Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus)

The squirrel family, Sciuridae, is one of the largest and most widely dispersed families of mammals. In spite of the wide distribution and conspicuousness of this group, phylogenetic relationships remain poorly understood. We used DNA sequence data from the mitochondrial cytochrome b gene of 114 species in 21 genera to infer phylogenetic relationships among sciurids based on maximum parsimony and Bayesian phylogenetic methods. Although we evaluated more complex alternative models of nucleotide substitution to reconstruct Bayesian phylogenies, none provided a better fit to the data than the GTR+G+I model. We used the reconstructed phylogenies to evaluate the current taxonomy of the Sciuridae. At essentially all levels of relationships, we found the phylogeny of squirrels to be in substantial conflict with the current taxonomy. At the highest level, the flying squirrels do not represent a basal divergence, and the current division of Sciuridae into two subfamilies is therefore not phylogenetically informative. At the tribal level, the Neotropical pygmy squirrel, Sciurillus, represents a basal divergence and is not closely related to the other members of the tribe Sciurini. At the genus level, the sciurine genus Sciurus is paraphyletic with respect to the dwarf squirrels (Microsciurus), and the Holarctic ground squirrels (Spermophilus) are paraphyletic with respect to antelope squirrels (Ammospermophilus), prairie dogs (Cynomys), and marmots (Marmota). Finally, several species of chipmunks and Holarctic ground squirrels do not appear monophyletic, indicating a need for reevaluation of alpha taxonomy.     

Culture and Co-Culture of Mouse Ovaries and Ovarian Follicles

The mammalian ovary is composed of ovarian follicles, each follicle consisting of a single oocyte surrounded by somatic granulosa cells, enclosed together within a basement membrane. A finite pool of follicles is laid down during embryonic development, when oocytes in meiotic arrest form a close association with flattened granulosa cells, forming primordial follicles. By or shortly after birth, mammalian ovaries contain their lifetime’s supply of primordial follicles, from which point onwards there is a steady release of follicles into the growing follicular pool.The ovary is particularly amenable to development in vitro, with follicles growing in a highly physiological manner in culture. This work describes the culture of whole neonatal ovaries containing primordial follicles, and the culture of individual ovarian follicles, a method which can support the development of follicles from an immature through to the preovulatory stage, after which their oocytes are able to undergo fertilization in vitro. The work outlined here uses culture systems to determine how the ovary is affected by exposure to external compounds. We also describe a co-culture system, which allows investigation of the interactions that occur between growing follicles and the non-growing pool of primordial follicles.     

Two misconceptions of phylogeny and classification

A recent contribution embodies the assumptions that organisms may be excluded from relationship with others on the basis of autopomorphy, and that its position in a classification is an inherent characteristic of an organism. Both of these assumptions are fallacious.     

Horned lizard (Phrynosoma) phylogeny inferred from mitochondrial genes and morphological characters: understanding conflicts using multiple approaches

The genus Phrynosoma includes 13 species of North American lizards characterized by unique and highly derived morphologies and ecologies. Understanding interspecific relationships within this genus is essential for testing hypotheses about character evolution in this group. We analyzed mitochondrial ND4 and cytochrome b gene sequence data from all species of Phrynosoma in conjunction with a previously published dataset including 12S and 16S rRNA gene sequences and morphological characters. We used multiple phylogenetic methods and diagnostic tests for data combinability and taxonomic congruence to investigate the data in separate and combined analyses. Separate data partitions resulted in several well-supported lineages, but taxonomic congruence was lacking between topologies from separate and combined analyses. Partitioned Bremer support analyses also reveals conflict between data partitions in certain tree regions. When taxa associated with well-supported clades were removed from analyses, phylogenetic signal was lost. Combined, our results initially suggest conflict between data partitions, but further tests show the data are only appropriate for phylogenetic reconstruction of those parts of the topology that were well resolved. Nonetheless, our data analyses reveal five well-supported clades: (1) Phrynosoma ditmarsi and Phrynosoma hernandesi, (2) P. ditmarsi, P. hernandesi, and Phrynosoma douglasii, (3) P. ditmarsi, P. hernandesi, P. douglasii, and Phrynosoma orbiculare, (4) Phrynosoma mcallii and Phrynosoma platyrhinos, and (5) Phrynosoma braconnieri and Phrynosoma taurus.     

Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: Preliminary report

We analyzed the 896 base-pair (bp) mitochondrial DNA (mtDNA) sequences for seven gibbons, representative of three out of four subgenera. The result from our molecular analysis is consistent with previous studies as to the monophyly of subgenus Hylobates species, yet the relationship among subgenera remains slightly ambiguous. A striking result of the analysis is the phylogenetic location of Kloss's gibbon (H. klossii). Kloss's gibbon has been considered to be an initial off-shoot of the subgenus Hylobates because of its morphological primitiveness. However, our molecular data strongly suggest that Kloss's gibbon speciated most recently within the subgenus Hylobates. Correspondence to: S. Horai     

MLGO: phylogeny reconstruction and ancestral inference from gene-order data

Background

The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements.

Results

MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO is based on likelihood computation and shows advantages over existing methods in terms of accuracy, scalability and flexibility.

Conclusions

To the best of our knowledge, it is the first web tool for analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions and duplications. The web tool is available from http://www.geneorder.org/server.php.     

An improved phylogeny of the Andean tit-tyrants (Aves, Tyrannidae): more characters trump sophisticated analyses

The phylogeny of the flycatcher genus Anairetes was previously inferred using short fragments of mitochondrial DNA and parsimony and distance-based methods. The resulting topology spurred taxonomic revision and influenced understanding of Andean biogeography. More than a decade later, we revisit the phylogeny of Anairetes tit-tyrants using more mtDNA characters, seven unlinked loci (three mitochondrial genes, six nuclear loci), more closely related outgroup taxa, partitioned Bayesian analyses, and two coalescent species-tree approaches (Bayesian estimation of species trees, BEST; Bayesian evolutionary analysis by sampling trees, (*)BEAST). Of these improvements in data and analyses, the fourfold increase in mtDNA characters was both necessary and sufficient to incur a major shift in the topology and near-complete resolution. The species-tree analyses, while theoretically preferable to concatenation or single gene approaches, yielded topologies that were compatible with mtDNA but with weaker statistical resolution at nodes. The previous results that had led to taxonomic and biogeographic reappraisal were refuted, and the current results support the resurrection of the genus Uromyias as the sister clade to Anairetes. The sister relationship between these two genera corresponds to an ecological dichotomy between a depauperate humid cloud forest clade and a diverse dry-tolerant clade that has diversified along the latitudinal axis of the Andes. The species-tree results and the concatenation results each reaffirm the primacy of mtDNA to provide phylogenetic signal for avian phylogenies at the species and subspecies level. This is due in part to the abundance of informative characters in mtDNA, and in part to its lower effective population size that causes it to more faithfully track the species tree.     

Extended phylogeny of the Craspedida (Choanomonada)

Currently choanoflagellates are classified into two distinct orders: loricate Acanthoecida and non-loricate Craspedida. The morphologically based taxonomy of the order Craspedida is in need of a revision due to its controversial, paraphyletic and inconsistent systematics and nomenclature. In this study, we add molecular data (SSU and parts of the LSU rDNA) of six new Craspedida species isolated from saline, brackish and freshwater habitats to the existing knowledge. Four of these six organisms could be described as new species: Paramonosiga thecata, “Salpingoeca” euryoecia, “Salpingoeca” ventriosa, “Sphaeroeca” leprechaunica, whereas two are assigned to previous morphologically described species: “Salpingoeca” fusiformis Saville Kent, 1880 and “Salpingoeca” longipes Saville Kent, 1880. Paramonosiga is established as a new genus of the Craspedida based on its phylogenetic position. Extending the dataset by six additional sequences shows that the craspedid taxonomy is still unsolved as the type specimen Salpingoeca gracilis has not yet been sequenced and hence a clear assignment to the genus Salpingoeca is not possible. Trying to assign morphological and ecological data to phylogenetic clades is not successful. We give an improved/emended morphological diagnosis for the two redescribed species and add molecular data for all six species, shedding light on their phylogenetic position.     

A molecular phylogeny of warbling-finches (Poospiza): paraphyly in a neotropical Emberizid genus

We investigated the phylogenetic relationships of 12 species within a single genus of neotropical passerine (Poospiza) using 849 bp (283 codons) of the cytochrome b mitochondrial gene. We further explored evolutionary affinities of these taxa using sequence from an additional 47 thraupine (tanagers) and 7 emberizine (sparrows and buntings) genera, members of the predominantly New World family Emberizidae. Poospiza have traditionally been considered part of the emberizine radiation. However, our analyses suggest that members of this genus are more closely related to some thraupine lineages than they are to the other neotropical emberizine genera included in our study (Atlapetes, Embernagra, Melopyrrha, Phrygilus, Saltatricula, Tiaris). Although member taxa are closely related, the genus Poospiza appears to be paraphyletic with representatives of 6 thraupine genera (Cnemoscopus, Cypsnagra, Hemispingus, Nephelornis, Pyrrhocoma, Thylpopsis) interspersed among four well-supported Poospiza clades. The majority of species within this Poospiza-thraupine clade have geographic ranges that are exclusive to, or partially overlap with, the Andes Mountains. It is probable that these mountains have played an important role in driving cladogenesis within this group. Sequence divergence (transversions only; mean 4.7+/-1.3%) within the clade suggests that much of this diversification occurred within the late Miocene and Pliocene, a period coincident with major orogenic activity in central-western South America.     

Ovoviviparity and genital evolution: a lesson from an earwig species with coercive traumatic mating and accidental breakage of elongated intromittent organs

Ovoviviparity or viviparity has evolved independently in animals and involves adaptations in females to accommodate developing embryos for a prolonged duration in their bodies, a condition which has likely to have influenced the evolution of the male genitalia. We aimed to ascertain whether the elongated male genitalia of the ovoviviparous free‐living earwig species Marava arachidis (Dermaptera: Spongiphoridae) delivers sperm directly to the female ovaries where fertilization occurs. Males mated coercively with females by grabbing the female antenna with their mouth parts. Although females resisted the mating attempts, pairs mated 3.3 times on average over 15 h. The elongated intromittent organ, known as a virga, was inserted into the long‐tubed spermatheca during insemination. Surgical ectomy of the spermatheca confirmed that sperm migrated from here to the ovaries with a variable delay. A pair of sclerites in the male genitalia frequently inflicted wounds near the spermathecal opening, while the single, thin virga sometimes broke off during mating. However, unlike earwigs bearing a ‘spare’ virga, damage was restricted to the tip of the virga, without which the males could still inseminate the females. We discuss the evolution of the genitalia in this insect in the light of sexual selection and sexual conflict over mating and fertilization.     

Molecular phylogeny of hyperoliid treefrogs: biogeographic origin of Malagasy and Seychellean taxa and re-analysis of familial paraphyly

Treefrogs of the family Hyperoliidae are distributed in Africa, Madagascar and the Seychelles. In this study, their phylogeny was studied using sequences of fragments of the mitochondrial 16S and 12S rRNA and cytochrome b genes. The molecular data strongly confirmed monophyly of the subfamily Hyperoliinae but indicated that the genus Leptopelis (subfamily Leptopelinae) is more closely related to species of the African family Astylosternidae. The Seychellean genus Tachycnemis was the sister group of the Malagasy Heterixalus in all molecular analyses; this clade was deeply nested within the Hyperoliinae. A re-evaluation of the morphological data did not contradict the sister group relationships of these two genera. The subfamily Tachycneminae is therefore considered as junior synonym of the Hyperoliinae. In addition, the molecular analysis did not reveal justification for a subfamily Kassininae. Biogeographically, the origin of Malagasy hyperoliids may not be well explained by Mesozoic vicariance in the context of Gondwana breakup, as indicated by the low differentiation of Malagasy hyperoliids to their African and Seychellean relatives and by analysis of current distribution patterns.     

The mitogenomes of three beetles (Coleoptera: Polyphaga: Cucujiformia): New gene rearrangement and phylogeny

The mitochondrial genome (mitogenome) has been extensively used for studying phylogenetic relationships at different taxonomic levels. Several molecular analyses have been performed, but the phylogenetic relationships among infraorders in Polyphaga have not been well resolved. In this work, three nearly complete mitogenomes of Coleoptera, Sitophilus oryzae, Oryzaephilus surinamensis and Callosobruchus chinensis, were determined. The O. surinamensis and S. oryzae mitogenomes harbor gene content typical of other Polyphaga mitogenomes, while a gene rearrangement (trnQ) was found in the C. chinensis mitogenome. The mitogenomes of these three Coleoptera species each consist of approximately 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one A + T-rich region. Phylogenetic analysis within Polyphaga was carried out based on mitochondrial data. The phylogenetic results within Polyphaga support the basal position of Cyphon sp., which belonged to Scirtoidea, Elateriformia. Within Cucujiformia, monophyletic Curculionoidea, Chrysomeloidea and Tenebrionoidea were confirmed.     

The phylogeny of varanoid lizards and the affinities of snakes

Evidence that platynotan squamates (living varanoid lizards, snakes and their fossil relatives) are monophyletic is presented. Evolutionary relationships within this group are then ascertained through a cladistic analysis of 144 osteological characters. Mosasauroids (aigialosaurs and mosasaurs), a group of large marine lizards, are identified as the nearest relatives of snakes, thus resolving the long-standing problem of snake affinities. The mosasauroid–snake clade (Pythonomorpha) is corroborated by 40 derived characters, including recumbent replacement teeth, thecodonty, four or fewer premaxillary teeth, supratemporal–prootic contact, free mandibular tips, crista circumfenestralis, straight vertical splenio-angular joint, loss of posterior ramus of the coronoid, reduced basipterygoid processes, reduced interpterygoid vacuity, zygosphene–zygantral articulations, and absence of epiphyses on the axial skeleton and skull. After mosasauroids, the next closest relatives of snakes are varanids (Varanus, Saniwa and Saniwides) and lanthanotids (Lanthanotus and Cherminotus). Derived features uniting varanids and lanthanotids include nine cervical vertebrae and three or fewer pairs of sternal ribs. The varanid–lanthanotid–pythonomorph clade, here termed Thecoglossa, is supported by features such as the anteriorly positioned basal tubera, and the loss of the second epibranchial. Successive outgroups to thecoglossans are Telmasaurus, an unresolved polytomy (Estesia, Gobidermatidae and Helodermatidae), Paravaranus and Proplatynota. The ''necrosaurs'' are demonstrated to be an artificial (polyphyletic) assemblage of primitive platynotans that are not particularly closely related to each other.Snakes are presumed to have evolved from small, limbless, burrowing lizards and the inability of previous analyses to resolve the affinities of snakes has been attributed to extensive convergence among the numerous lineages of such lizards. The present study contradicts this claim, demonstrating that the problem is due instead to omission of critical fossil taxa. No modern phylogenetic analysis of squamate relationships has simultaneously included both mosasauroids and snakes: previous studies have therefore failed to identify the mosasauroid–snake association and the suite of derived characters supporting it. Mosasauroids are large aquatic animals with well-developed appendages, and none of the derived characters uniting mosasauroids and snakes is obviously correlated with miniaturization, limb reduction or fossoriality. Recognition that mosasauroids, followed by varanids and lanthanotids, are the nearest relatives of snakes will also facilitate studies of relationships within snakes, which until now have been hampered by uncertainty over the most appropriate (closely-related) lizard outgroups.     

Incisor-molar relationships in chimpanzees and other hominoids: implications for diet and phylogeny

In chimpanzees, the cutting edge of the incisor battery is longer in relation to the length of the molar row than in any other hominoid, extant or fossil, the only other lineage approaching it being the orangutan. Apart from their increased mesio-distal dimensions, the upper and lower incisors of chimpanzees differ in additional ways from those of almost all other hominoids. The I2/ is enlarged, so that the difference in size between it and the central upper incisor is less than it is in the heteromorphic upper incisors of other hominoids. The lower incisors are expanded mesio-distally, so much so that isolated I/2 crowns can resemble upper central incisors. In chimpanzees the lingual surface of the lower incisors is generally more procumbent than it is in other hominoids, which have more vertically oriented incisor crowns and there is a greater difference in enamel thickness between labial and lingual sides. The re-orientation of the lower incisor crown is reflected in the root, which in lateral view is anteriorly concave in chimpanzees whereas it is more orthogonal or convex in other hominoids. The molars of chimpanzees, especially the lowers, have extensive and relatively deep occlusal basins, and the main cusps are peripheralised and labio-lingually compressed, making them more trenchant than those of other hominoids. This paper examines the incisor-lower molar proportions in extinct and living hominoids and develops a new hypothesis about the evolution of the dentition of chimpanzees and links it to their diet. It also examines the incisor-molar proportions of hominids and African apes in order to throw light on the phylogenetic relationships between them. It is shown that chimpanzees are highly derived in this respect and that several recent ideas concerning the chimp-like appearance of the last common ancestor of hominids and African apes are likely to be incorrect.This revised version was published online in April 2005 with corrections to the cover date of the issue.     

Inferring the phylogeny of archaebacteria: The use of ribosomal sensitivity to protein-synthesis inhibitors

Summary The sensitivities to 37 protein-synthesis inhibitors were determined in cell-free translational systems for 13 Archaebacteria species. Multivariate factor analysis by principal components, cluster analysis by the unweighted pair-group clustering algorithm, and compatibility and parsimony methods of constructing phylogenetic trees were used both to infer the genealogical relationships within archaebacteria and to establish their relations with the eubacterial and eukaryotic kingdoms.     

Feeding behaviour and phylogeny: observations on early derivative Acari

Based on laboratory observations of three species of Allothyrus (Parasitiformes: Holothyrida: Allothyridae) from south east Queensland and gut content analysis of 62 individuals representing 11 species of Allothyrus from eastern Australia, we determined that Australian Allothyridae are scavengers that ingest fluids only. Living arthropods, nematodes, snails and annelids were ignored, but dead arthropods were readily fed upon and were sufficient to maintain adults and nymphs for many months. The adults were sluggish, timid animals that relied on armour, thanatosis and probably on noxious chemicals for protection: the juveniles produced secretions from idiosomal glands. In contrast, most early derivative Mesostigmata that we tested (Sejina, species of Sejus and Uropodella; Uropodina, Polyaspis sp. and Cercomegistina, an undescribed Asternoseiidae) were aggressive predators of small invertebrates and ingested fluids only; however, two species of Asternolaelaps (Sejina) had solid fungal and animal material in their guts. Similarly, the early derivative acariform (Palaeosomata, species of Stomacarus and Loftacarus) and opilioacariform mites (an undescribed Opilioacarida from Australia) that we examined all ingested particulate foods, including fungal and animal material. These observations are consistent with the hypothesis that the earliest mites were scavengers and opportunistic predators that ingested solid foods and that fluid feeding is a derived condition linking the three orders of Parasitiformes (Holothyrida, Ixodida and Mesostigmata).