Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants

We have estimated the time for the last common ancestor of extant seed plants by using molecular clocks constructed from the sequences of the chloroplastic gene coding for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and the nuclear gene coding for the small subunit of rRNA (Rrn18). Phylogenetic analyses of nucleotide sequences indicated that the earliest divergence of extant seed plants is likely represented by a split between conifer-cycad and angiosperm lineages. Relative-rate tests were used to assess homogeneity of substitution rates among lineages, and annual angiosperms were found to evolve at a faster rate than other taxa for rbcL and, thus, these sequences were excluded from construction of molecular clocks. Five distinct molecular clocks were calibrated using substitution rates for the two genes and four divergence times based on fossil and published molecular clock estimates. The five estimated times for the last common ancestor of extant seed plants were in agreement with one another, with an average of 285 million years and a range of 275-290 million years. This implies a substantially more recent ancestor of all extant seed plants than suggested by some theories of plant evolution.     

Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data

Until a few decades ago, phylogenetic relationships among placental orders were ambiguous and usually depicted to radiate as an unresolved "bush." Resolution of this bush by various workers has been progressing slowly, but with promising results corroborated by nondental, dental, and molecular characters. In this study we continue to seek resolution. A total of 258 nondental and 2 dental characters was analyzed by PAUP and MacClade on 39 vertebrate taxa (3 reptiles, 1 nonmammalian therapsid, and 35 mammals; 20 of the mammals are extant and 15 are extinct) to study higher taxonomic relationships with emphasis on Placentalia (Eutheria). About two-thirds of the characters are osteological, the rest concern soft tissues, including myological but excluding molecular characters (most are our data, the rest are from the literature). Cladistic analysis included all 39 taxa (fossil taxa help to evaluate polarities of characters) and all characters were given equal weight. Extant Mammalia are divided into Prototheria and Theria, the latter into Marsupialia and Placentalia. Placentalia comprises Xenarthra and Epitheria. Within Epitheria, Lipotyphla and Preptotheria (emended) are sister-taxa. Preptotherian taxa group into: ungulate-related taxa and various nonungulates. The former include Carnivora, Pholidota, Tubulidentata, Artiodactyla, Cetacea, Perissodactyla, Hyracoidea, Proboscidea, and Sirenia. A possible association to embrace Lagomorpha, Rodentia, Macroscelidea, Scandentia, Primates, Chiroptera, and Dermoptera is suggested. Significant differences between our findings and those of recent investigators include the dissociation of Pholidota from Xenarthra and the plesiomorphous position of Lipotyphla within Epitheria. Congruence between morphological and molecular results is closer than previously reported.     

Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes

We have sequenced the mitochondrial cytochrome b gene from the guinea pig, the African porcupine, and a South American opossum. A phylogenetic analysis, which includes 22 eutherian and four other vertebrate cytochrome b sequences, indicates that the guinea pig and the porcupine constitute a natural clade (Hystricomorpha) that is not a sister group to the clade of mice and rats (Myomorpha). Therefore, the hypothesis that the Rodentia is paraphyletic receives additional support. The artiodactyls, the perissodactyls, and the cetaceans form a group that is separated from the primates and the rodents. The 26 sequences are used to study the structure/function relationships in cytochrome b, whose function is electron transport. Most of the amino acid residues involved in the two reaction centers are well conserved in evolution. The four histidines that are believed to ligate the two hemes are invariant among the 26 sequences, but their nearby residues are not well conserved in evolution. The eight transmembrane domains represent some of the most divergent regions in the cytochrome b sequence. The rate of nonsynonymous substitution is considerably faster in the human and elephant lineages than in other eutherian lineages; the faster rate might be due to coevolution between cytochrome b and cytochrome c.     

Clinical trial of an oral vestibular shield for the control of snoring

1. Comparative aspects of iodine conservation in mammals were studied on the basis of published data on kidney and thyroid weights and function. 2. Very small mammals possessed an efficient reabsorption of iodide to compensate for the high glomerular filtration rate (GFR). 3. Humans and mammals of a similar and larger size had "lost" the ability to reabsorb iodide efficiently. 4. Very large mammals are protected against renal loss of iodide due to the relatively low GFR. 5. Thyroid weights in relation to body weight were highest in humans suggesting that humans and other mammals of a similar size are especially susceptible to iodine deficiency.     

Molecular cloning of CYP1A from the estuarine fish Fundulus heteroclitus and phylogenetic analysis of CYP1 genes: update with new sequences

Since we published a phylogenetic analysis of the CYP1A subfamily in 1995, several additional full-length sequences have been reported, including three members of an entirely new subfamily, CYP1B. Two avian sequences were recently published, so that CYP1A sequence data are now available from three of the five major vertebrate lineages. The two new branches that have been added to the CYP1 family tree significantly add to our understanding of P450 evolution. The inclusion of the CYP1Bs to the phylogenetic analysis allows us to root inferred trees. Addition of the avian CYP1As indicates that the CYP1A1/CYP1A2 duplication present in the mammalian lineage may have occurred after the divergence of birds and mammals. The number of fish species from which full-length coding regions of CYP1A genes have been sequenced has increased from four (trout, plaice, toadfish, and scup) to nine. These include CYP1A sequences from tomcod, butterflyfish, sea bream, sea bass, and the full-length sequence of CYP1A from the killifish Fundulus heteroclitus that is reported here. Phylogenetic analyses incorporating the new fish CYP1A sequences support our original conclusion that the fish CYP1As are monophyletic and indicate that the genes are evolving at very different rates in different species.     

B-50, the growth associated protein-43: modulation of cell morphology and communication in the nervous system

The growth-associated protein B-50 (GAP-43) is a presynaptic protein. Its expression is largely restricted to the nervous system. B-50 is frequently used as a marker for sprouting, because it is located in growth cones, maximally expressed during nervous system development and re-induced in injured and regenerating neural tissues. The B-50 gene is highly conserved during evolution. The B-50 gene contains two promoters and three exons which specify functional domains of the protein. The first exon encoding the 1-10 sequence, harbors the palmitoylation site for attachment to the axolemma and the minimal domain for interaction with G0 protein. The second exon contains the "GAP module", including the calmodulin binding and the protein kinase C phosphorylation domain which is shared by the family of IQ proteins. Downstream sequences of the second and non-coding sequences in the third exon encode species variability. The third exon also contains a conserved domain for phosphorylation by casein kinase II. Functional interference experiments using antisense oligonucleotides or antibodies, have shown inhibition of neurite outgrowth and neurotransmitter release. Overexpression of B-50 in cells or transgenic mice results in excessive sprouting. The various interactions, specified by the structural domains, are thought to underlie the role of B-50 in synaptic plasticity, participating in membrane extension during neuritogenesis, in neurotransmitter release and long-term potentiation. Apparently, B-50 null-mutant mice do not display gross phenotypic changes of the nervous system, although the B-50 deletion affects neuronal pathfinding and reduces postnatal survival. The experimental evidence suggests that neuronal morphology and communication are critically modulated by, but not absolutely dependent on, (enhanced) B-50 presence.     

Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments

We report several novel environmental sequences of archaea from the kingdom Crenarchaeota, recovered from anaerobic freshwater-lake sediments in Michigan. A nested PCR approach with Archaea- and Crenar-chaeota-specific primers was used to amplify partial Small-subunit ribosomal DNAs. Phylogenetic analysis of seven sequences shows that these DNAs represent a monophyletic lineage diverging prior to all recently identified crenarchaeotal phylotypes isolated from temperate environments. Including our lineage, all uncultured crenarchaeotal sequences recovered from moderate or cold environments form a distinct, monophyletic group separate from the "genuine" thermophilic crenarchaeota. Our finding extends the emerging picture that crenarchaeota, thought until recently to be solely extreme thermophiles, have radiated into an unexpectedly large variety of ecologically important, temperate environments.     

Biogeographic origins of goannas (Varanidae): a molecular perspective

This project aims to clarify the phylogenetic relationships among the extant species of Varanus in order to elucidate the origins of Varanidae, using DNA sequences. Results obtained for a minimum of 662 nucleotides of 12S rRNA sequence data from each of 21 extant species of Varanus indicate that the Australian varanids form a single monophyletic clade and also suggest that within the Australian varanids, members of the subgenus Odatria (pygmy monitors) may from a clade separate from those in the subgenus Varanus (large monitors). The Asian species appear to be sister taxa to the Australian species, while the two African species investigated were most divergent, suggesting that the Varanidae are not Gondwanic in origin. Hypothesis testing analyses were performed and involved constraining the 12S sequence data according to previously described topologies and testing the difference using parametric and nonparametric statistics. The phylogeny generated using 12S sequence data was statistically different from previously described morphological trees, while there was some support for topologies based on chomosomal and immunological datasets. Overall, our results suggest that the Australian species may be derived from an Asian source and are, therefore, in agreement with the hypothesis based on the fossil record suggesting that Varanidae may be Asian in origin.     

Molecular phylogenies and nucleotide insertion-deletion

Molecular trees based on the analysis of sequence data can be obtained through parsimony procedures. Such approaches identify evolutionary events (homologies and homoplasies and their location in the tree). Nevertheless, it is not possible generally to analyze directly the information given by the aligned sequences. Noticeably, gaps ("indel") need special coding. Standard procedures for coding gaps offer alternatives which suffer of several weaknesses. In this article a new strategy of coding the sequences is defined in view to express the potential phylogenetic information contained in complex zones with internested insertion/deletion and substitutions, contrary to what is done up to the present. This strategy applies without loss or distortion of information to any case where gaps are present in aligned sequences. According to the hierarchy of internested states of characters (sites), this strategy introduces in the data matrix question marks, "?", which are optimized in fine in the cladogram based on all data. These "?" are not missing data, they are methodological codes, neutral to a priori phylogenetic hypotheses.     

Production of biologically active recombinant tilapia insulin-like growth factor-II polypeptides in Escherichia coli cells and characterization of the genomic structure of the coding region

Insulin-like growth factor-II (IGF-II) is a fetal growth factor in humans, but has not been clearly identified in fish up to now. For a detailed understanding of the physiological response of fish IGF-II, the first step was to clone tilapia IGF-II cDNA from the brain cDNA library, coding the region of genomic DNA, and also expressing tilapia IGF-II polypeptides from Escherichia coli. Tilapia cDNA sequences total 1,977 bp, and predicted nucleotide sequences and amino acid sequences of tilapia share 77.9% and 90.7% homology identity with rainbow trout IGF-II, respectively. The genomic structure of the tilapia prepro-IGF-II coding region is very difficult to sequence in mammals and birds. The cloned tilapia IGF-II gene coding region appears much more complex than in other vertebrates. In tilapia IGF-II, the first coding exon I encoding part of the signal peptide sequence is 25 amino acids shorter than the first coding exon of mammals and birds. The other 23 amino acids of the signal peptide, and the first amino acids of the B domain and C domain are encoded by tilapia coding exon 2. The C, A, and D domains, and the first 20 amino acids of the E peptide are encoded by tilapia coding exon 3. The other E peptides and the 3' untranslated region (UTR) region are encoded by tilapia coding exon 4. These data show that the IGF-II genes have significantly differing structures in vertebrate evolution, and there are differences of interrupting introns in the IGF-I genomic structure compared with mammals. To obtain recombinant biologically active polypeptides, tilapia IGF-II B-C-A-D domains were amplified using the polymerase chain reaction (PCR), then ligated with glutathione S-transferase (GST, pGEX-2T vector). Tilapia recombinant IGF-II protein was purified and characterized in E. coli. The fusion protein was also digested with thrombin and appeared as a recombinant IGF-II polypeptide single band with a molecular mass of 7 kD. The recombinant tilapia IGF-II protein biological function was measured by stimulation of [3H]thymidine incorporation. The assay concentration was set up from 0 to 120 nM to stimulate tilapia ovary cell line (TO-2) significantly to uptake thymidine. The results suggest that the recombinant IGF-II protein was dose dependent.     

Sensory capacities of marine mammals.

Examines the sensory capacities of aquatic and amphibious marine mammals and compares them with those of terrestrial primates. Auditory masking studies indicate comparable inner-ear functioning for aquatic, amphibious, and terrestrial mammals. Detection data from aquatic audiograms depict acute sensitivity to low intensities with extensive frequency ranges. Relative intensity sensitivity indicates that amphibious mammals have an aerial loss comparable to the aquatic loss for humans. Aquatic mammals have discrimination capacities for frequency, intensity, duration, and localization approximating those of humans. However, the differential sensitivity of amphibious mammals, though comparable to many terrestrial forms, is inferior to that of humans and aquatic forms. Visual detection data are almost nonexistent, and data on discrimination indicate relatively well-developed spatial acuity. Finally, the chemoreceptive modalities of olfaction and taste have degenerated considerably. (148 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Th1-like cytokine production profile and individual specific alterations in TCRBV-gene usage of T cells from newly diagnosed type 1 diabetes patients after stimulation with beta-cell antigens

Thirty complete coding sequences of human major histocompatibility complex (Mhc) class II DRB alleles, spanning 237 codons, were analyzed for phylogenetic information using distance, parsimony, and likelihood approaches. Allelic genealogies derived from different parts of the coding sequence (exon 2, the 5' and 3' ends of exon 2, respectively, and exons 3-6) were compared. Contrary to prior assertions, a rigorous analysis of allelic genealogies in this gene family cannot be used to justify the claim that the lineage leading to modern humans contained on average at least 100,000 individuals. Phylogenetic inferences based upon the exon 2 region of the DRB loci are complicated by selection and recombination, so this part of the gene does not provide a complete and accurate view of allelic relationships. Attempts to reconstruct human history from genetic data must use realistic models which consider the complicating factors of nonequilibrium populations, recombination, and different patterns of selection.     

Earliest known Old World monkey skull

Similarities of the skull are commonly used to support hypotheses of ancestor-descendant relationships between fossil and living ape genera, especially between the late Miocene apes Sivapithecus and Dryopithecus from Eurasia and the living orang-utan (Pongo) from Borneo and Sumatra. Yet determining whether craniofacial traits shared by extant and Miocene apes are primitive or derived is severely hampered by the rarity of well-preserved fossil crania, particularly of early members of their closest outgroup, the Old World monkeys (Cercopithecoidea). The discovery of a complete and undistorted skull of Victoriapithecus at middle Miocene deposits from Maboko Island, Kenya, provides evidence of intact cranial-vault and basicranial morphology, brain size and craniofacial hafting for a primate from between 32 and 7 million years ago. Victoriapithecus represents a branch of Old World monkey that is intermediate between extant cercopithecids (Colobinae and Cercopithecinae) and the common ancestor they shared with apes (Hominoidea). The skull preserves traits widely thought to be derived for extant and fossil members of a proposed Sivapithecus/Pongo clade, but which now appear to be primitive features of ancestral Old World higher primates in general.     

Bubble ring play of bottlenose dolphins (Tursiops truncatus): Implications for cognition.

Research on the cognitive capacities of dolphins and other cetaceans (whales and porpoises) has importance for the study of comparative cognition, particularly with other large-brained social mammals, such as primates. One of the areas in which cetaceans can be compared with primates is that of object manipulation and physical causality, for which there is an abundant body of literature in primates. The authors supplemented qualitative observations with statistical methods to examine playful bouts of underwater bubble ring production and manipulation in 4 juvenile male captive bottlenose dolphins (Tursiops truncatus). The results are consistent with the hypothesis that dolphins monitor the quality of their bubble rings and anticipate their actions during bubble ring play. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Morbillivirus infections in aquatic mammals

Morbillivirus infections which were not documented in aquatic mammals until 1988, have caused at least five epizootics in these species during the last 10 years. Affected populations include European harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) in 1998, Baikal seals (Phoca siberica) in Siberia from 1987-1988, striped dolphins (Stenella coeruleoalba) in the Mediterranean Sea from 1990-1992 and bottlenose dolphins (Tursiops truncatus) along the eastern coast of the United States from 1987-1988 and in the Gulf of Mexico from 1993-1994. Clinical signs and lesions in affected animals were similar to those of canine distemper. Lesions were mainly seen in lung, central nervous and lymphoid tissues and included formation of intranuclear and intracytoplasmic inclusion bodies. Syncytia were commonly found in lung and lymphoid tissues of cetaceans but not of pinnipeds. Antigenic and molecular biological studies indicate that a newly discovered morbillivirus, termed phocine distemper virus, and canine distemper virus were responsible for recent pinniped epizootics; cetacean die-offs were caused by strains of a second, newly recognized cetacean morbillivirus. Serological evidence of morbillivirus infection has been identified in a broad range of marine mammal populations and recent epizootics probably resulted from transfer of virus to immunologically-naive populations.     

Molecular characteristation of digenetic trematodes associated with Cyathura carinata (Crustacea: Isopoda) with a note on the utility of 18S ribosomal DNA for phylogenetic analysis in the Digenea (Platyhelminthes: Trematoda)

Analysis of 18S rDNA sequences isolated from Cyathura carinata (Crustacea: Isopoda) indicate that two different species of the Digenea (Platyhelminthes: Trematoda) parasitize this isopod species for which parasitic associations have previously been unknown. Phylogenetic analysis, based on the largest data set of digenetic 18S rDNA sequences published to date, also suggests that 18S rDNA is unsuitable for the reconstruction of phylogenetic relationships of the major digenetic lineages either due to rapid radiation of these lineages or the presence of homoplasy at this level.     

Progressive multiple alignment with constraints

A progressive alignment algorithm produces a multialignment of a set of sequences by repeatedly aligning pairs of sequences and/or previously generated alignments. We describe a method for guaranteeing that the alignment generated by a progressive alignment strategy satisfies a user-specified collection of constraints about where certain sequence positions should appear relative to others. Our main result is an algorithm to compute just the "prime" constraints that are implied by the user-given constraints; these are shown to be precisely the constraints that the alignment algorithm must obey. In practice, the time required to handle constraints is negligible and frequently much less than the time saved because the constraints permit searching a restricted region of the dynamic-programming grid. An alignment of the beta-like globin gene cluster of several mammals illustrates the practicality of the method.