Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences

India has a diverse caecilian fauna, including representatives of three of the six currently recognized families, the Caeciliidae, Ichthyophiidae, the endemic Uraeotyphlidae, but previous molecular phylogenetic studies of caecilians have not included sequences for any Indian caecilians. Partial 12S and 16S mitochondrial gene sequences were obtained for a single representative of each of the caecilian families found in India and aligned against previously reported sequences for 13 caecilian species. The resulting alignment (16 taxa, 1200 sites, of which 288 cannot be aligned unambiguously) was analyzed using parsimony, maximum-likelihood, and distance methods. As judged by bootstrap proportions, decay indices, and leaf stabilities, well-supported relationships of the Indian caecilians are recovered from the alignment. The data (1) corroborate the hypothesis, based on morphology, that the Uraeotyphlidae and Ichthyophiidae are sister taxa, (2) recover a monophyletic Ichthyophiidae, including Indian and South East Asian representatives, and (3) place the Indian caeciliid Gegeneophis ramaswamii as the sister group of the caeciliid caecilians of the Seychelles. Rough estimates of divergence times suggest an origin of the Uraeotyphlidae and Ichthyophiidae while India was isolated from Laurasia and Africa and are most consistent with an Indian origin of these families and subsequent dispersal of ichthyophiids into South East Asia.     

Molecular systematics of caeciliid caecilians (Amphibia: Gymnophiona) of the Western Ghats, India

Together, Indian plus Seychelles caeciliid caecilian amphibians (Gymnophiona) constitute approximately 10% of the extant species of this order. A molecular phylogenetic analysis of all but one (or two) nominal species (16, in five genera) is presented based on mitochondrial (12S, 16S, cytb, cox1) and nuclear (RAG1) sequence data. Results strongly support monophyly of both Seychelles and peninsular Indian caeciliids, and their sister-group status. Within the Indian caeciliids, Indotyphlus and Gegeneophis are monophyletic sister genera. The phylogenetic position of Gegeneophis ramaswamii, Gegeneophis seshachari, and Gegeneophis carnosus are not well resolved, but all lie outside a well-supported clade of most northern Western Ghats Gegeneophis (madhavai, mhadeiensis, goaensis, danieli/nadkarnii). Most nominal species of Indian caeciliid are diagnosed by robust haplotype clades, though the systematics of G. carnosus-like forms in northern Kerala and southern Karnataka requires substantial further investigation. For the most part, Indian caeciliid species comprise narrowly distributed, allopatric taxa with low genetic diversity. Much greater geographic genetic diversity exists among populations referred to G. seshachari, such that some populations likely represent undescribed species. This, the first phylogenetic analysis of Indian caeciliids, generally provides additional support for recent increases in described species (eight since 1999), and a framework for ongoing taxonomic revision.     

Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of five individual caecilians (Amphibia: Gymnophiona) representing five of the six recognized families: Rhinatrema bivittatum (Rhinatrematidae), Ichthyophis glutinosus (Ichthyophiidae), Uraeotyphlus cf. oxyurus (Uraeotyphlidae), Scolecomorphus vittatus (Scolecomorphidae), and Gegeneophis ramaswamii (Caeciliidae). The organization and size of these newly determined mitogenomes are similar to those previously reported for the caecilian Typhlonectes natans (Typhlonectidae), and for other vertebrates. Nucleotide sequences of the nuclear RAG1 gene were also determined for these six species of caecilians, and the salamander Mertensiella luschani atifi. RAG1 (both at the amino acid and nucleotide level) shows slower rates of evolution than almost all mt protein-coding genes (at the amino acid level). The new mt and nuclear sequences were compared with data for other amphibians and subjected to separate and combined phylogenetic analyses (Maximum Parsimony, Minimum Evolution, Maximum Likelihood, and Bayesian Inference). All analyses strongly support the monophyly of the three amphibian Orders. The Batrachia hypothesis (Gymnophiona, (Anura, Caudata) receives moderate or good support depending on the method of analysis. Within Gymnophiona, the optimal tree (Rhinatrema, (Ichthyophis, Uraeotyphlus), (Scolecomorphus, (Gegeneophis Typhlonectes) agrees with the most recent morphological and molecular studies. The sister group relationship between Rhinatrematidae and all other caecilians, that between Ichthyophiidae and Uraeotyphlidae, and the monophyly of the higher caecilians Scolecomorphidae+Caeciliidae+Typhlonectidae, are strongly supported, whereas the relationships among the higher caecilians are less unambiguously resolved. Analysis of RAG1 is affected by a spurious local rooting problem and associated low support that is ameliorated when outgroups are excluded. Comparisons of trees using the non-parametric Templeton, Kishino-Hasegawa, Approximately Unbiased, and Shimodaira-Hasegawa tests suggest that the latter may be too conservative.     

Frequency of independent origins of viviparity among caecilians (Gymnophiona): evidence from the first 'live-bearing' Asian amphibian

Viviparity is reported for Gegeneophis seshachari (Gymnophiona: Caeciliidae) from a gravid female containing four oviductal foetuses. The oviducts are highly vascularized and contain patches of thickened, layered tissue similar to foetal gut contents. Gegeneophis seshachari probably resemble other viviparous caecilians in having foetuses that ingest thickened oviduct lining using specialized deciduous teeth. This is the first report of viviparity in Asian amphibians and Indo-Seychellean caeciliids. Gegeneophis is the only caecilian genus known to include oviparous and viviparous species, and G. seshachari is the smallest known viviparous caecilian. Phylogenetic analysis of mitochondrial DNA sequences supports assignment of G. seshachari to a monophyletic Gegeneophis. Character optimization indicates that viviparity has evolved independently at least four times within Gymnophiona--a rate of incidence relative to the number of extant species that is higher than for other vertebrate groups except squamate reptiles. Our findings strengthen the proposal that caecilian reproduction demands further attention.     

The Braincase of Eocaecilia micropodia (Lissamphibia,Gymnophiona) and the Origin of Caecilians

The scant fossil record of caecilians has obscured the origin and evolution of this lissamphibian group. Eocaecilia micropodia from the Lower Jurassic of North America remains the only stem-group caecilian with an almost complete skull preserved. However, this taxon has been controversial, engendering re-evaluation of traits considered to be plesiomorphic for extant caecilians. Both the validity of the placement of E. micropodia as a stem caecilian and estimates of the plesiomorphic condition of extant caecilians have been questioned. In order to address these issues, the braincase of E. micropodia was examined via micro-computed tomography. The braincase is considered to be a more reliable phylogenetic indicator than peripheral regions of the skull. These data reveal significant new information, including the possession of an ossified nasal septum, ossified anterior wall of the sphenethmoid, long anterolateral processes on the sphenethmoid, and paired olfactory nerve foramina, which are known only to occur in extant caecilians; the latter are possibly related to the evolution of the tentacle, a caecilian autapomorphy. A phylogenetic analysis that included 64 non-amniote taxa and 308 characters represents the first extensive test of the phylogenetic affinities of E. micropodia. The results place E. micropodia securely on the stem of extant caecilians, representing a clade within Temnospondyli that is the sister taxon to batrachians plus Gerobatrachus. Ancestral character state reconstruction confirms the braincase of E. micropodia to be largely representative of the plesiomorphic condition of extant caecilians. Additionally, the results refine the context within which the evolution of the caecilian form can be evaluated. The robust construction and pattern of the dermal skull of E. micropodia is interpreted as symplesiomorphic with advanced dissorophoid temnospondyls, rather than being autapomorphic in its robust construction. Together these data increase confidence in incorporating E. micropodia into discussions of caecilian evolution.     

Evolutionary relationships of the lungless caecilian Atretochoana eiselti (Amphibia: Gymnophiona: Typhlonectidae)

Appreciation of the diversity of caecilian amphibians has recently been enhanced by the discovery of a radically divergent aquatic caecilian of the Neotropical Typhlonectidae. Atretochoana eiselti is the largest lungless tetrapod and the only lungless caecilian, and it possesses a suite of remarkable cranial modifications that set it apart from all other caecilians. Numerical phylogenetic analyses, using 141 morphological characters, were performed in order to resolve the evolutionary relationships of Atretochoana and representatives of all other typhlonectid genera. These analyses yield a single most parsimonious tree, (Chthonerpeton (Nectocaecilia (Typhlonectes natans, Typhlonectes compressicauda) (Potomotyphlus, Atretochoana)))) , that is both well resolved and, as judged by Bremer support and by bootstrapping, is well supported. This tree is used as a basis for interpreting ecological shifts and associated morphological evolution within the Typhlonectidae. The available data suggest that the rate of morphological evolution in the Atretochoana lineage is significandy greater than that in other typhlonectid lineages.     

Discovery of a new family of amphibians from northeast India with ancient links to Africa

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India-an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.     

Ultrastructure of the mature spermatozoa of caecilians (Amphibia: Gymnophiona)

The spermatozoa of Gymnophiona show the following autapomorphies: 1) penetration of the distal centriole by the axial fiber; 2) presence of an acrosomal baseplate; 3) presence of an acrosome seat (flattened apical end of nucleus); and 4) absence of juxta-axonemal fibers. The wide separation of the plasma membrane bounding the undulating membrane is here also considered to be apomorphic. Three plesiomorphic spermatozoal characters are recognized that are not seen in other Amphibia but occur in basal amniotes: 1) presence of mitochondria with a delicate array of concentric cristae (concentric cristae of salamander spermatozoa differ in lacking the delicate array); 2) presence of peripheral dense fibers associated with the triplets of the distal centriole; and 3) presence of a simple annulus (a highly modified, elongate annulus is present in salamander sperm). The presence of an endonuclear canal containing a perforatorium is a plesiomorphic feature of caecilian spermatozoa that is shared with urodeles, some basal anurans, sarcopterygian fish, and some amniotes. Spermatozoal synapomorphies are identified for 1) the Uraeotyphlidae and Ichthyophiidae, and 2) the Caeciliidae and Typhlonectidae, suggesting that the members of each pair of families are more closely related to each other than to other caecilians. Although caecilian spermatozoa exhibit the clear amphibian synapomorphy of the unilateral location of the undulating membrane and its axial fiber, they have no apomorphic characters that suggest a closer relationship to either the Urodela or Anura.     

Late Neogene planktonic foraminifera of the Cibao Valley (northern Dominican Republic): Biostratigraphy and paleoceanography

An assemblage of planktonic foraminifera is described from 125 samples taken from the Cercado, Gurabo, and Mao Formations in the Cibao Valley, northern Dominican Republic. The primary objectives of this study are to establish a biochronologic model for the late Neogene of the Dominican Republic and to examine sea surface conditions within the Cibao Basin during this interval. The Cercado Formation is loosely confined to Zones N17 and N18 ( 7.0–5.9 Ma). The Gurabo Formation spans Zones N18 and N19 ( 5.9–4.5 Ma). The Mao Formation is placed in Zone N19 ( 4.5–3.6 Ma). Changes in the relative abundances of indicator species are used to reconstruct sea surface conditions within the basin. Increasing relative abundances of Globigerinoides sacculifer and Globigerinoides ruber, in conjunction with a decreasing relative abundance of Globigerina bulloides, suggests the onset of increasing sea surface temperature and salinity in conjunction with diminishing primary productivity at 6.0 Ma. Abrupt increases in the relative abundances of G. sacculifer and G. ruber at 4.8 Ma suggest a major increase in sea surface temperature and salinity in the early Pliocene. The most likely mechanism for these changes is isolation of the Caribbean Ocean through progressive restriction of Pacific–Caribbean transfer via the Central American Seaway. Periods of high productivity associated with upwelling events are recorded in the upper Cercado Formation ( 6.1 Ma) and in the middle Mao Formation ( 4.2 Ma) by spikes in G. bulloides and Neogloboquadrina spp. respectively. The timing of major increases in sea surface salinity and temperature as well as decreasing productivity ( 4.8 Ma) and periods of upwelling ( 6.1and 4.2 Ma) in the Cibao Basin generally corroborate previously suggested Caribbean oceanographic changes related to the uplift of Panama. Changes in sea surface conditions depicted by paleobiogeographic distributions in the Cibao Basin suggest that shoaling along the Isthmus of Panama had implications in a shallow Caribbean basin as early as 6.0 Ma. Major paleobiologic changes between 4.8 and 4.2 Ma likely represent the period of final closure of the CAS and a nearly complete disconnection between Pacific and Caribbean water masses. This study illustrates the use of planktonic foraminifera in establishing some paleoceanographic conditions (salinity, temperature, productivity, and upwelling) within a shallow water basin, outlining the connection between regional and localized oceanographic changes.     

The morphology of prehatching embryos of Caecilia orientalis (Amphibia: Gymnophiona: Caeciliidae)

The state of development of advanced embryos of the direct‐developing Ecuadorian caecilian Caecilia orientalis (Caeciliidae: Gymnophiona: Amphibia) was examined. Because it is established that development is correlated with reproductive modes in a number of features, we included comparison with taxa that represent the major reproductive modes and all of the modern normal tables and ossification sequences. The embryos of C. orientalis most closely resemble those of stage 47/48 Gegeneophis ramaswamii, an Indian caeciliid, and stage 47/48 Hypogeophis rostratus, a Seychellian caeciliid, both direct developers, in details of bone mineralization, chondrocranial degeneration, and vertebrogenesis. They are most like stage 45 H. rostratus in external features (gills, pigmentation, etc.). They are less similar to prehatchings of Ichthyophis kohtaoensis, an ichthyophiid with free‐living larvae, and to fetuses of the viviparous caeciliid Dermophis mexicanus and the viviparous typhlonectid Typhlonectes compressicauda at comparable total lengths in both skeletal development and external features. The similarity of developmental features among the direct‐developers suggests a correlation with mode of life history. A noteworthy feature is that C. orientalis has an armature of multiple rows of teeth on the lower jaw with tooth crowns that resemble the “fetal” teeth of viviparous taxa and that are covered with a layer of oral mucosal epithelium until full development and eruption, but the upper jaw bears a single row of widely spaced, elongate, slightly recurved teeth that resemble those of the adult. J. Morphol., 2009. © 2009 Wiley‐Liss, Inc.     

Eastward from Africa: palaeocurrent-mediated chameleon dispersal to the Seychelles islands

Madagascar and the Seychelles are Gondwanan remnants currently isolated in the Indian Ocean. In the Late Cretaceous, these islands were joined with India to form the Indigascar landmass, which itself then split into its three component parts around the start of the Tertiary. This history is reflected in the biota of the Seychelles, which appears to contain examples of both vicariance- and dispersal-mediated divergence from Malagasy or Indian sister taxa. One lineage for which this has been assumed but never thoroughly tested is the Seychellean tiger chameleon, a species assigned to the otherwise Madagascar-endemic genus Calumma. We present a multi-locus phylogenetic study of chameleons, and find that the Seychellean species is actually the sister taxon of a southern African clade and requires accomodation in its own genus as Archaius tigris. Divergence dating and biogeographic analyses indicate an origin by transoceanic dispersal from Africa to the Seychelles in the Eocene–Oligocene, providing, to our knowledge, the first such well-documented example and supporting novel palaeocurrent reconstructions.     

Molecular Evidence for the Early History of Living Amphibians

The evolutionary relationships of the three orders of living amphibians (lissamphibians) has been difficult to resolve, partly because of their specialized morphologies. Traditionally, frogs and salamanders are considered to be closest relatives, and all three orders are thought to have arisen in the Paleozoic (>250 myr). Here, we present evidence from the DNA sequences of four mitochondrial genes (2.7 kilobases) that challenges the conventional hypothesis and supports a salamander–caecilian relationship. This, in light of the fossil record and distribution of the families, suggests a more recent (Mesozoic) origin for salamanders and caecilians directly linked to the initial breakup of the supercontinent Pangaea. We propose that this single geologic event isolated salamanders and archaeobatrachian frogs on the northern continents (Laurasia) and the caecilians and neobatrachian frogs on the southern continents (Gondwana). Among the neobatrachian frog families, molecular evidence supports a South American clade and an African clade, inferred here to be the result of mid-Cretaceous vicariance.     

Evolution of the Monotremes: Phylogenetic Relationship to Marsupials and Eutherians, and Estimation of Divergence Dates Based on α-Lactalbumin Amino Acid Sequences

The amino acid sequences of the -lactalbumins of the echidna, Tachyglossus aculeatus, and the platypus, Ornithorhynchus anatinus, were compared with each other and with those of 13 eutherian and 3 marsupial species. Phylogenetic parsimony analyses, in which selected mammalian lysozymes were used as outgroups, yielded trees whose consensus indicated that the two monotremes are sister taxa to marsupials and eutherians and that the latter two clades are each other's closest relatives. The data do not support the notion of a Marsupionta (monotreme–marsupial) clade. Pairwise comparison between the -lactalbumins yielded maximum-likelihood distances from which divergence dates were estimated on the basis of three calibration points. The distance data support the view that the echidna and platypus lineages diverged from their last common ancestor at least 50 to 57 Ma (million years ago) and that monotremes diverged from marsupials and eutherian mammals about 163 to 186 Ma.     

Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes

Phylogenetic relationships among the salamander families have been difficult to resolve, largely because the window of time in which major lineages diverged was very short relative to the subsequently long evolutionary history of each family. We present seven new complete mitochondrial genomes representing five salamander families that have no or few mitogenome records in GenBank in order to assess the phylogenetic relationships of all salamander families from a mitogenomic perspective. Phylogenetic analyses of two data sets—one combining the entire mitogenome sequence except for the D-loop, and the other combining the deduced amino acid sequences of all 13 mitochondrial protein-coding genes—produce nearly identical well-resolved topologies. The monophyly of each family is supported, including the controversial Proteidae. The internally fertilizing salamanders are demonstrated to be a clade, concordant with recent results using nuclear genes. The internally fertilizing salamanders include two well-supported clades: one is composed of Ambystomatidae, Dicamptodontidae, and Salamandridae, the other Proteidae, Rhyacotritonidae, Amphiumidae, and Plethodontidae. In contrast to results from nuclear loci, our results support the conventional morphological hypothesis that Sirenidae is the sister-group to all other salamanders and they statistically reject the hypothesis from nuclear genes that the suborder Cryptobranchoidea (Cryptobranchidae + Hynobiidae) branched earlier than the Sirenidae. Using recently recommended fossil calibration points and a “soft bound” calibration strategy, we recalculated evolutionary timescales for tetrapods with an emphasis on living salamanders, under a Bayesian framework with and without a rate-autocorrelation assumption. Our dating results indicate: (i) the widely used rate-autocorrelation assumption in relaxed clock analyses is problematic and the accuracy of molecular dating for early lissamphibian evolution is questionable; (ii) the initial diversification of living amphibians occurred later than recent estimates would suggest, from the Late Carboniferous to the Early Permian (294 MYA); (iii) living salamanders originated during the Early Jurassic (183 MYA), and (iv) most salamander families had diverged from each other by Late Cretaceous. A likelihood-based ancestral area reconstruction analysis favors a distribution throughout Laurasia in the Early Jurassic for the common ancestor of all living salamanders.     

Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis

Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.     

Pleistocene climatic fluctuations explain the disjunct distribution and complex phylogeographic structure of the Southern Red-backed Salamander, <Emphasis Type="Italic">Plethodon serratus</Emphasis>

The southeastern United States (U.S.) has experienced dynamic climatic changes over the past several million years that have impacted species distributions. In many cases, contiguous ranges were fragmented and a lack of gene flow between allopatric populations led to genetic divergence and speciation. The Southern Red-backed Salamander, Plethodon serratus, inhabits four widely disjunct regions of the southeastern U.S.: the southern Appalachian Mountains, the Ozark Plateau, the Ouachita Mountains, and the Southern Tertiary Uplands of central Louisiana. We integrated phylogenetic analysis of mitochondrial DNA sequences (1399 base pairs) with ecological niche modeling to test the hypothesis that climate fluctuations during the Pleistocene drove the isolation and divergence of disjunct populations of P. serratus. Appalachian, Ozark, and Louisiana populations each formed well-supported clades in our phylogeny. Ouachita Mountain populations sorted into two geographically distinct clades; one Ouachita clade was sister to the Louisiana clade whereas the other Ouachita clade grouped with the Appalachian and Ozark clades but relationships were unresolved. Plethodon serratus diverged from its sister taxon, P. sherando, ~5.4 million years ago (Ma), and lineage diversification within P. serratus occurred ~1.9–0.6 Ma (Pleistocene). Ecological niche models showed that the four geographic isolates of P. serratus are currently separated by unsuitable habitat, but the species was likely more continuously distributed during the colder climates of the Pleistocene. Our results support the hypothesis that climate-induced environmental changes during the Pleistocene played a dominant role in driving isolation and divergence of disjunct populations of P. serratus.     

High-resolution nannofossil biochronology of middle Paleocene to early Eocene at ODP Site 1262: Implications for calcareous nannoplankton evolution

Over the last several decades debates on the ‘tempo and mode’ of evolution have centered on the question whether morphological evolution preferentially occurs gradually or punctuated, i.e., with long periods of stasis alternating with short periods of rapid morphological change and generation of new species. Another major debate is focused on the question whether long-term evolution is driven by, or at least strongly influenced by changes in the environment, or by interaction with other life forms. Microfossils offer a unique opportunity to obtain the large datasets as well as the precision in dating of subsequent samples to study both these questions. We present high-resolution analyses of selected calcareous nannofossils from the deep-sea section recovered at ODP Site 1262 (Leg 208) in the South-eastern Atlantic. The studied section encompasses nannofossil Zones NP4–NP12 (equivalent to CP3–CP10) and Chrons C27r–C24n.We document more than 70 biohorizons occurring over an about 10 Myr time interval, ( 62.5 Ma to  52.5 Ma), and discuss their reliability and reproducibility with respect to previous data, thus providing an improved biostratigraphic framework, which we relate to magnetostratigraphic information, and present for two possible options of a new Paleocene stratigraphic framework based on cyclostratigraphy. This new framework enabled us to tentatively reconstruct steps in the evolution of early Paleogene calcareous nannoplankton through documentation of transitional morphotypes between genera and/or species and of the phylogenetic relations between the genera Fasciculithus, Heliolithus, Discoasteroides and Discoaster, as well as between Rhomboaster and Tribrachiatus. The exceptional record provided by the continuous, composite sequence recovered at Walvis Ridge allows us to describe the mode of evolution among calcareous nannoplankton: new genera and/or new species usually originated through branching of lineages via gradual, but relatively rapid, morphological transitions, as documented by the presence of intermediate forms between the end-member ancestral and descendant forms.Significant modifications in the calcareous nannofossil assemblages are often “related” to significant changes in environmental conditions, but the appearance of structural innovations and radiations within a single genus also occurred during “stable” environmental conditions. These lines of evidence suggest that nannoplankton evolution is not always directly triggered by stressed environmental conditions but could be also driven by endogenous biotic control.     

Incision of trivalent chromium [Cr(III)]-induced DNA damage by Bacillus caldotenax UvrABC endonuclease

Some hexavalent chromium [Cr(VI)]-containing compounds are lung carcinogens. Once within cells, Cr(VI) is reduced to trivalent chromium [Cr(III)] which displays an affinity for both DNA bases and the phosphate backbone. A diverse array of genetic lesions is produced by Cr including Cr–DNA monoadducts, DNA interstrand crosslinks (ICLs), DNA–Cr–protein crosslinks (DPCs), abasic sites, DNA strand breaks and oxidized bases. Despite the large amount of information available on the genotoxicity of Cr, little is known regarding the molecular mechanisms involved in the removal of these lesions from damaged DNA. Recent work indicates that nucleotide excision repair (NER) is involved in the processing of Cr–DNA adducts in human and rodent cells. In order to better understand this process at the molecular level and begin to identify the Cr–DNA adducts processed by NER, the incision of CrCl₃ [Cr(III)]-damaged plasmid DNA was studied using a thermal-resistant UvrABC NER endonuclease from Bacillus caldotenax (Bca). Treatment of plasmid DNA with Cr(III) (as CrCl₃) increased DNA binding as a function of dose. For example, at a Cr(III) concentration of 1 μM we observed 2 Cr(III)–DNA adducts per plasmid. At this same concentration of Cr(III) we found that 17% of the plasmid DNA contained ICLs (0.2 ICLs/plasmid). When plasmid DNA treated with Cr(III) (1 μM) was incubated with Bca UvrABC we observed 0.8 incisions/plasmid. The formation of endonuclease IV-sensitive abasic lesions or Fpg-sensitive oxidized DNA bases was not detected suggesting that the incision of Cr(III)-damaged plasmid DNA by UvrABC was not related to the generation of oxidized DNA damage. Taken together, our data suggest that a sub-fraction of Cr(III)–DNA adducts is recognized and processed by the prokaryotic NER machinery and that ICLs are not necessarily the sole lesions generated by Cr(III) that are substrates for NER.     

Aspects of the phylogeny of Platyhelminthes based on 18S ribosomal DNA and protonephridial ultrastructure

DNA studies of 23 taxa (20 platyhelminths, 1 nemertean, Homo and Artemia) and electron-microscopic studies of the protonephridia of many platyhelminths (supported by some additional ultrastructural data) have led to the following conclusions: the Neodermata are monophyletic; Temnocephalida and Dalyelliida form one clade and are not the primitive sister group of the Neodermata; Gyrocotylidea, Amphilinidea and Eucestoda form one monophylum; Pterastericolidae and Umagillidae are dalyelliids and not the sister group of the Neodermata; and Proseriata are unlikely to be closely related with the Tricladida. A large taxon consisting of the Proseriata and some other turbellarians may represent the sister group of the Neodermata.     

Early Neogene biochemostratigraphy of Pohang Basin: a paleoceanographic response to the early opening of the Sea of Japan (East Sea)

The location of the Pohang Basin near the Korea Strait in the southwest of the Sea of Japan (East Sea) makes this area appropriate for providing a record of paleoenvironmental/biotic changes associated with the early Neogene (16.5 Ma) opening of this gateway to the Pacific Ocean. Stable isotopic and planktonic foraminiferal records are presented that assist with the understanding of paleoenvironmental changes in the Sea of Japan resulting from the opening of the Korea Strait. The oldest sediments of early Neogene age of the Pohang Basin overlie Cretaceous basement and are Early Miocene (>16.5 Ma) shallow, estuarine facies containing a benthic foraminiferal assemblage dominated by Ammonia beccarii (L.). The oldest early Neogene planktonic foraminiferal assemblages in the basin are 16.5 Ma in age (latest Early Miocene foraminiferal zone N8). The migration of these planktonic assemblages to the Sea of Japan at that time appears to have resulted from the initial opening of the Korea Strait. The overlying early Neogene marine sequence of the Pohang Basin extends from 16.5 Ma (Zone N8) through 14 Ma (Zone N10). Change in the oxygen isotopic record of the Pohang Basin sequence suggests strong local paleoenvironmental control related to the early opening of the Korea Strait. Early Middle Miocene isotopic temperatures of planktonic foraminifera are relatively cool at 15 Ma at a time when global temperatures were high in the middle/low latitude regions. It was not until 14.8 Ma that isotopic temperatures of planktonic foraminifera increased markedly. This distinct warming is inferred to reflect the major intrusion of the Kuroshio Current into the Sea of Japan probably as a result of further critical opening and deepening of the Korea Strait. At this time planktonic foraminifera increased in abundance reflecting expanding oceanic influence. A cooling that followed at 14.5 Ma, when the strait was well open is unlikely to reflect local tectonic control on the paleoceanography, but global cooling during the early Middle Miocene associated with the expansion of the East Antarctic ice sheet.