The guinea-pig is not a rodent

Somatostatin receptor subtypes: basic pharmacology and tissue distribution

The heptahelical receptor superfamily constitutes the largest single family of transmembrane-signalling molecules that regulate a wide range of physiological processes. The five somatostatin receptors represent a distinct subgroup of this seven transmembrane receptor superfamily. They range in size from 356 to 391 amino acids with 39-57% protein identity between the subtypes with 100 residues strictly conserved among the somatostatin receptor sequences. A high grade of mRNA homology exists in somatostatin receptor subtypes cloned from different species. Following somatostatin receptor binding and functional activity studies, two alternative models of ligand-binding interaction have been hypothesised. One relies on the presence of a binding pocket within the receptor structure constituted by specific amino acids residues, the other denies the presence of such binding structures and suggests that it is the interaction of agonists with specific extracellular and/or transmembrane domains that determine stable receptor structure conformation. Somatostatin receptors, as, indeed, all G-protein-coupled receptors are able to regulate their responsiveness to agonist exposure. This agonist-specific regulation includes three main events, namely, desensitisation, receptor internalisation and receptor degradation. The cell expression of somatostatin receptor subtypes, at the mRNA level, has been characterised in rodent and in human organs with multiple subtype expression in brain and peripheral tissues.

A memetic-aided approach to hierarchical clustering from distance matrices: application to gene expression clustering and phylogeny

We propose a heuristic approach to hierarchical clustering from distance matrices based on the use of memetic algorithms (MAs). By using MAs to solve some variants of the Minimum Weight Hamiltonian Path Problem on the input matrix, a sequence of the individual elements to be clustered (referred to as patterns) is first obtained. While this problem is also NP-hard, a probably optimal sequence is easy to find with the current advances for this problem and helps to prune the space of possible solutions and/or to guide the search performed by an actual clustering algorithm. This technique has been successfully applied to both a Branch-and-Bound algorithm, and to evolutionary algorithms and MAs. Experimental results are given in the context of phylogenetic inference and in the hierarchical clustering of gene expression data.

Asoprisnil (J867): a selective progesterone receptor modulator for gynecological therapy

Asoprisnil is a novel selective steroid receptor modulator that shows unique pharmacodynamic effects in animal models and humans. Asoprisnil, its major metabolite J912, and structurally related compounds represent a new class of progesterone receptor (PR) ligands that exhibit partial agonist and antagonist activities in vivo. Asoprisnil demonstrates a high degree of receptor and tissue selectivity, with high-binding affinity for PR, moderate affinity for glucocorticoid receptor (GR), low affinity for androgen receptor (AR), and no binding affinity for estrogen or mineralocorticoid receptors. In the rabbit endometrium, both asoprisnil and J912 induce partial agonist and antagonist effects. Asoprisnil induces mucification of the guinea pig vagina and has pronounced anti-uterotrophic effects in normal and ovariectomized guinea pigs. Unlike antiprogestins, asoprisnil shows only marginal labor-inducing activity during mid-pregnancy and is completely ineffective in inducing preterm parturition in the guinea pig. Asoprisnil exhibits only marginal antiglucocorticoid activity in transactivation in vitro assays and animal models. In male rats, asoprisnil showed weak androgenic and anti-androgenic properties. In toxicological studies in female cynomolgus monkeys, asoprisnil treatment abolished menstrual cyclicity and endometrial atrophy. Early clinical studies of asoprisnil in normal volunteers demonstrated a dose-dependent suppression of menstruation irrespective of the effects on ovulation, with no change in basal estrogen concentrations and no antiglucocorticoid effects. Unlike progestins, asoprisnil does not induce breakthrough bleeding. With favorable safety and tolerability profiles thus far, asoprisnil appears promising as a novel treatment of gynecological disorders, such as uterine fibroids and endometriosis.

Agonists for neuropeptide Y receptors Y1 and Y5 stimulate different phases of feeding in guinea pigs

1. The stimulatory effect of neuropeptide Y (NPY) on food intake is well established but the roles of the receptor subtypes Y(1) and Y(5) have been difficult to define. We have studied the effects of two novel Y(1)-preferring and two Y(5)-preferring agonists on feeding in guinea pigs. 2. The Y(1)-preferring receptor agonists [Arg(6),Pro(34)]pNPY and [Phe(7),Pro(34)]pNPY had high affinity for the Y(1) receptor (K(i) values 0.07 and 0.04 nM, respectively) and nanomolar affinity for the Y(5) receptor. Administration of either compound into the third brain ventricle increased food intake equally to NPY. 3. The Y(5) agonist [Ala(31),Aib(32)]pNPY displayed a moderate affinity for the Y(5) receptor (K(i) 7.42 nM) and a low affinity for Y(1) (K(i) 1.7 micro M). This compound had only a modest effect on feeding. 4. The other Y(5)-preferring peptide [cPP(1-7),NPY(19-23),Ala(31),Aib(32),Gln(34)]hPP had a higher affinity at the Y(5) receptor (K(i) 1.32 nM) and also at the Y(1) receptor (K(i) 85 nM). It potently stimulated feeding: the food consumption after administration of this peptide was two-fold compared to NPY. 5. Our results support the view that both the receptor subtypes Y(1) and Y(5) are involved in the stimulation of feeding. As the action profiles of the Y(1) and Y(5) agonists on feeding parameters were different, it seems that they influence different phases of eating.

RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences

The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs via compensatory substitutions, hence changes on either side of a pair are correlated. Accounting for this correlation is important for phylogenetic inference because it affects the likelihood calculation. In the present study we use the complete set of tRNA and rRNA sequences from 69 complete mammalian mitochondrial genomes. The likelihood calculation uses two evolutionary models simultaneously for different parts of the sequence: a paired-site model for the paired sites and a single-site model for the unpaired sites. We use Bayesian phylogenetic methods and a Markov chain Monte Carlo algorithm is used to obtain the most probable trees and posterior probabilities of clades. The results are well resolved for almost all the important branches on the mammalian tree. They support the arrangement of mammalian orders within the four supra-ordinal clades that have been identified by studies of much larger data sets mainly comprising nuclear genes. Groups such as the hedgehogs and the murid rodents, which have been problematic in previous studies with mitochondrial proteins, appear in their expected position with the other members of their order. Our choice of genes and evolutionary model appears to be more reliable and less subject to biases caused by variation in base composition than previous studies with mitochondrial genomes.

Revisiting the Glires concept--phylogenetic analysis of nuclear sequences

The so-called Glires hypothesis postulates a sister-group relationship between Rodentia (e.g., rat and mouse) and Lagomorpha (e.g., rabbit). Recent molecular phylogenetic analyses have yielded incongruent results, and either supported or refuted the Glires grouping. In order to study this inconsistency we have reconstructed phylogenetic trees based on data sets of 20 orthologous nuclear protein coding genes (6441 aa, sites) and 12 mitochondrial protein coding genes (3559 aa sites). The size of the nuclear data set is considerably larger than any comparable data set hitherto used to study the Glires concept. Analysis of the nuclear data strongly supported the phylogenetic tree (frog, chicken, ((rat, mouse), (rabbit, (human, (cattle, dog))))), while the mt data could not conclusively resolve the position of rabbit relative to that of human. This result was supported by all methods. Thus, the Glires hypothesis was rejected by this study.

Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models

It is essential to test a priori scientific hypotheses with independent data, not least to partly negate factors such as gene-specific base composition biases misleading our models. Seven new gene segments and sequences plus Bayesian likelihood phylogenetic methods were used to compare and test five recent placental phylogenies. These five phylogenies are similar to each other, yet quite different from Fthose of previously proposed trees, and span Waddell et al. [Syst. Biol. 48 (1999) 1] to Murphy et al. [Science 294 (2001b) 2348]. Trees for RAG1, gamma-fibrinogen, ND6, mt-tRNA, mt-RNA, c-MYC, epsilon -globin, and GHR are significantly congruent with the four main groups of mammals common to the five phylogenies, i.e., Afrotheria, Laurasiatheria, Euarchontoglires, Xenarthra plus Boreoeutheria (Laurasiatheria plus Euarchontoglires). Where these five a priori phylogenies differ, remain areas generally hard to resolve with the new sequences. The root remains ambiguous and does not reject a basal Afrotheria (the Exafroplacentalia hypothesis), Afrotheria plus Xenarthra together with basal (Atlantogenata), or Epitheria (Xenarthra basal) convincingly. Good evidence is found that Eulipotyphla is monophyletic and is located at the base of Laurasiatheria. The shrew mole, Uropsilus, is found to cluster consistently with other moles, while Solenodon may be the sister taxa to all other eulipotyphlans. Support is found for a probable sister pairing of just hedgehogs/gymnures and shrews. Relationships within Afrotheria, except the Paenungulata clade, remain hard to resolve, although there is congruent support for Afroinsectiphillia (aardvark, elephant shrews, golden moles, and tenrecs). A first-time use is made of MCMC enacted general time-reversible (GTR) amino acid and codon-based models for general tree selection. Even with ND6, a GTR amino acid model provided resolution of fine features, such as the sister group relationship of walrus to Otatriidae, and with BRCA a more reasonable rooting. An extensive analysis of GHR sequences reveals strong congruence with prior phylogenies, including strong support for Eulipotyphla, and good resolution within Rodentia. A codon model gives a worse likelihood than a nucleotide model and sometimes switches support, e.g., with RAG1+gamma-fibrinogen from a hyrax-sirenian association to support for Tethytheria. An analysis of the concatenated data is in accordance with well-resolved features of the gene trees. Taken all together, this work suggests that we are on the right path finding strong confirmation of prior phylogenies. However, with the use of robust criteria for assessing trees (i.e., not Bayesian posteriors), it is apparent parts of the tree remain hard to resolve. Since our current models are far from fitting the sequence data, we should continue with our exploratory analyses to arrive at a refined set of hypotheses for future testing using more model independent characters (e.g., rare indels, gene rearrangement, and SINE data).

Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla

We sequenced the complete mitochondrial (mt) genomes of three insectivores: the long-eared hedgehog Hemiechinus auritus, the Japanese mole Mogera wogura, and the greater Japanese shrew-mole Urotrichus talpoides. These mtDNA data together with other previously sequenced mtDNAs were analyzed using a maximum likelihood method to infer their phylogenetic relationships among eutherians. Previous mitochondrial protein analyses used a simple model that did not consider site-heterogeneity, and Erinaceoidea (hedgehogs and moonrats) was placed at the basal eutherian position that is separated from Soricoidea (shrews) and Talpoidea (moles), suggesting the exclusion of the Erinaceoidea-Eulipotyphla tree. By including the new mtDNA sequences and introducing site-heterogeneity into the model, the Erinaceoidea-Eulipotyphla tree emerges as the best tree or as a tree with a log-likelihood score indistinguishable from that of the best tree. However, this conclusion depends on species sampling in Erinaceoidea, demonstrating the importance of both species sampling and use of an appropriate substitution model when inferring phylogenetic relationships.

Electrical activity in endocrine pituitary cells in situ: a support for a multiple-function coding

The anterior pituitary is an endocrine gland that controls basic body functions. Pituitary cell functioning depends on membrane excitability, which induces cytosolic calcium rises. Here, we reported the first identification of small-amplitude voltage fluctuations that controlled spike firing in endocrine cells recorded in situ. Three patterns of voltage fluctuations were distinguishable by their durations (1-100 s). These patterns could be ordered on top of each other, namely in response to secretagogues. Thus, pituitary endocrine cells express in situ a cell code in which small-amplitude voltage fluctuations lead to a multimodal arrangement of spike firing, which may finely tune calcium-dependent functions.

Nucleotide sequences of putative cDNAs for guinea-pig monoamine oxidase

To study the molecular structure of guinea pig monoamine oxidase (MAO) and its phylogenetic relationship with other mammalian MAOs, we determined nucleotide sequences of putative MAO cDNAs isolated from guinea pig tissues. Both the 5'- and 3'-ends of the cDNAs were amplified using the RACE (rapid amplification of cDNA ends) method. The sequence (1924 bp) of a putative guinea-pig MAO-B cDNA covers a complete coding region that corresponds to 521 amino acids. We also analyzed a partial sequence of a putative guinea-pig MAO-A cDNA, which corresponds to 506 amino acids, but have left the region of 66 bp at the 3'-end undetermined. The nucleotide and deduced amino-acid sequences of the putative guinea-pig MAO cDNAs showed the highest homology with that of human MAO cDNAs among the known mammalian MAO sequences. These results suggest that guinea-pig MAOs are structurally similar to human MAOs. Our molecular phylogenetic data support the idea that guinea pigs and rodents diverged before the separation between rodents and other lineage leading to Primates and Artiodactyla.

Enduring maternal influences in a precocial rodent

The guinea pig is highly developed at birth and requires little active maternal care. Yet the mother and other social figures markedly influence biobehavioral processes of the offspring. Here, responses of guinea pigs and nonhuman primates to maternal and other social separation procedures are compared, and influences of social partners on endocrine responses and behavior in periadolescent guinea pigs are described.

Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires

Complete mitochondrial genomes are reported for a pika (Ochotona collaris) and a vole (Volemys kikuchii) then analysed together with 35 other mitochondrial genomes from mammals. With standard phylogenetic methods the pika joins with the other lagomorph (rabbit) and the vole with the other murid rodents (rat and mouse). In addition, with hedgehog excluded, the seven rodent genomes consistently form a homogeneous group in the unrooted placental tree. Except for uncertainty of the position of tree shrew, the clade Glires (monophyletic rodents plus lagomorphs) is consistently found. The unrooted tree obtained by ProtML (Protein Maximum Likelihood, a program in MOLPHY) is compatible with a reclassification of mammals [Syst. Biol. 48, 1-5 (1999)] which is also supported by other recent studies. However, when this tree is rooted with marsupials plus platypus, the outgroup often joins the lineage leading to the three murid rodents, so the rodents are no longer monophyletic. Apart from misplacing the root, the presence of the outgroups also distorts other parts of the unrooted tree. Either constraining the tree to maintain rodents monophyletic, or omitting murids, maintains the ingroup tree and sees the outgroup join on the edge to Xenarthra, to Afrotheria, or to these two groups together. This emphasises the importance of carrying out both an unrooted and a rooted analysis. It is known from cancer research that murid rodents have reduced activity in some DNA repair mechanisms and this alters their substitution pattern - this may be the case for mitochnodrial DNA as well. Comparing nucleotide compositions may identify taxa that differ in aspects of their DNA repair mechanisms.

Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes

Rodentia is the largest order of placental mammals, with approximately 2,050 species divided into 28 families. It is also one of the most controversial with respect to its monophyly, relationships between families, and divergence dates. Here, we have analyzed and compared the performance of three nuclear genes (von Willebrand Factor, interphotoreceptor retinoid-binding protein, and Alpha 2B adrenergic receptor) for a large taxonomic sampling, covering the whole rodent and placental diversity. The phylogenetic results significantly support rodent monophyly, the association of Rodentia with Lagomorpha (the Glires clade), and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade. The resolution of relationships among rodents is also greatly improved. The currently recognized families are divided here into seven well-defined clades (Anomaluromorpha, Castoridae, Ctenohystrica, Geomyoidea, Gliridae, Myodonta, and Sciuroidea) that can be grouped into three major clades: Ctenohystrica, Gliridae + Sciuroidea, and a mouse-related clade (Anomaluromorpha, Castoridae + Geomyoidea, and Myodonta). Molecular datings based on these three genes suggest that the rodent radiation took place at the transition between Paleocene and Eocene. The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights.

Mammalian mitogenomic relationships and the root of the eutherian tree

The strict orthology of mitochondrial (mt) coding sequences has promoted their use in phylogenetic analyses at different levels. Here we present the results of a mitogenomic study (i.e., analysis based on the set of protein-coding genes from complete mt genomes) of 60 mammalian species. This number includes 11 new mt genomes. The sampling comprises all but one of the traditional eutherian orders. The previously unrepresented order Dermoptera (flying lemurs) fell within Primates as the sister group of Anthropoidea, making Primates paraphyletic. This relationship was strongly supported. Lipotyphla ("insectivores") split into three distinct lineages: Erinaceomorpha, Tenrecomorpha, and Soricomorpha. Erinaceomorpha was the basal eutherian lineage. Sirenia (dugong) and Macroscelidea (elephant shrew) fell within the African clade. Pholidota (pangolin) joined the Cetferungulata as the sister group of Carnivora. The analyses identified monophyletic Pinnipedia with Otariidae (sea lions, fur seals) and Odobenidae (walruses) as sister groups to the exclusion of Phocidae (true seals).

Phylogeny of Thogoto virus

Thogoto virus is a tick-borne member of the family Orthomyxoviridae. Previously, based on the similarity in antigenic relationship by cross-neutralization test, all virus strains were concluded to have derived from the same origin. In this study, we obtained partial gene sequences of 4 genes (PB1-like protein, PA-like protein, glycoprotein, and nucleoprotein) of 8 Thogoto virus strains isolated in Africa, Asia, and Europe and studied the genetic variation and phylogeny. Unrooted phylogenetic trees created by both neighbor-joining and maximum likelihood methods based on nucleotide and amino acid sequences for 4 genes were mostly similar and revealed two lineages, Euro-Asian and African. Intra-lineage nucleotide sequence variation was greater in the Euro-Asian lineage than in the African lineage for all 4 genes. Furthermore, for the strains of Euro-Asian lineage, variations for two genes associated with RNA-dependent RNA polymerase activities were greater than those for glycoprotein or nucleoprotein gene, based on both nucleotide and amino acid sequence differences as well as on synonymous and nonsynonymous differences, indicating greater mutation rates for the polymerase activity genes in these strains.

Receptor subtypes Y1 and Y5 mediate neuropeptide Y induced feeding in the guinea-pig

1. Neuropeptide Y (NPY) is one of the most potent stimulants of food intake. It has been debated which receptor subtype mediates this response. Initially Y(1) was proposed, but later Y(5) was announced as a 'feeding' receptor in rats and mice. Very little is known regarding other mammals. The present study attempts to characterize the role of NPY in feeding behaviour in the distantly related guinea-pig. When infused intracerebroventricularly, NPY dose-dependently increased food intake. 2. PYY, (Leu(31),Pro(34))NPY and NPY(2 - 36) stimulated feeding, whereas NPY(13 - 36) had no effect. These data suggest that either Y(1) or Y(5) receptors or both may mediate NPY induced food intake in guinea-pigs. 3. The Y(1) receptor antagonists, BIBO 3304 and H 409/22 displayed nanomolar affinity for the Y(1) receptor (K(i) values 1.1+/-0.2 nM and 5.6+/-0.9 nM, respectively), but low affinity for the Y(2) or Y(5) receptors. When guinea-pigs were pretreated with BIBO 3304 and H 409/22, the response to NPY was inhibited. 4. The Y(5) antagonist, CGP 71683A had high affinity for the Y(5) receptor (K(i) 1.3+/-0.05 nM) without having any significant activities at the Y(1) and Y(2) receptors. When CGP 71683A was infused into brain ventricles, the feeding response to NPY was attenuated. 5. The present study shows that NPY stimulates feeding in guinea-pigs through Y(1) and Y(5) receptors. As the guinea-pig is very distantly related to the rat and mouse, this suggests that both Y(1) and Y(5) receptors may mediate NPY-induced hyperphagia also in other orders of mammals.

Sequence and expression analysis of deer mouse interferon-gamma, interleukin-10, tumor necrosis factor, and lymphotoxin-alpha

Deer mice (Peromyscus maniculatus) are the principal host species of Sin Nombre (SN) virus, the primary etiologic agent of hantavirus cardiopulmonary syndrome in North America. The disease is a cytokine-mediated immunopathology characterized by pulmonary mononuclear infiltrates without discernible viral pathology. Infected deer mice remain life-long carriers and virus is found in many organs, including the lungs, but without pathology. It is unclear how deer mice respond to SN virus because no tools exist to examine the immune response in infected animals. As an initial step in examining host responses to SN virus, we have cloned partial cDNAs of deer mouse interferon-gamma (IFN-gamma), interleukin-10 (IL-10), tumor necrosis factor (TNF) and lymphotoxin-alpha (LTalpha). IL-10, TNF and LTalpha sequences are highly conserved compared to orthologs of other mammalian species, while IFN-gamma is substantially less conserved. Phylogenetic analyses indicate that the amino acid sequences of IFN-gamma and TNF may be useful in resolving relationships at the subfamily level within the rodent family Muridae. While all four sets of analyses were able to reconstruct clade Rodentia, they were not able to resolve the relationships among the mammalian orders represented in this study. Reverse transcriptase polymerase chain reaction (RT-PCR) analysis of concanavalin A-stimulated splenocytes determined that maximal IFN-gamma and TNF expression occurred rapidly while IL-10 and LTalpha expression was maximal at 24 h.

Molecular systematics of sciurognathi (rodentia): the mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae)

Nucleotide sequence data from the mitochondrial 12S rRNA and cytochrome b genes were used to analyze phylogenetic relationships among sciurognath rodents. Our sample taxa included representatives of 11 sciurognath and 3 hystricognath families with two marsupial species, Didelphis virginiana and Macropus robustus, as outgroups. The dataset was analyzed using both maximum-parsimony (weighted and unweighted) and likelihood methods. Three suprafamilial groupings are strongly supported: Geomyidae + Heteromyidae (Geomyoidea), Sciuridae + Aplodontidae (Sciuroidea), and Pedetidae + Anomaluridae (Anomaluroidea). Although moderately supported, two sister group relationships were identified between Gliridae and Sciuroidea and between Castor and Geomyoidea. In contrast to previous nuclear DNA evidence, the evolutionary affinities between Ctenodactylidae and Hystricognathi (Ctenohystrica) and between Muridae and Dipodidae (Myodonta) are not supported by the mitochondrial data. Molecular divergence dates based on the combined data were estimated for suprafamilial groupings and are discussed in the light of current morphological and paleontological interpretations of rodent phylogeny.

Physiological properties of central amygdala neurons: species differences

The connections of limbic structures are remarkably constant across species. However, different species express fear in distinct ways. Because the central amygdaloid nucleus is considered an important mediator of fear responses, we compared the physiological properties of central amygdala neurons in guinea pigs, rats and cats using whole-cell recordings in coronal slices in vitro. In guinea pigs, most central medial and lateral neurons displayed an outward rectification that delayed firing onset in response to depolarizing current pulses (hence the designation late-firing neurons). Late-firing neurons were also prevalent in the lateral sector of the cat central nucleus. In contrast, late-firing neurons were rare in the rat central nucleus and the cat central medial nucleus. There, most neurons generated Ni2+-sensitive low-threshold bursts of Na+ spikes and/or displayed pronounced inward rectification in the hyperpolarizing direction. Species differences in passive properties were also observed, but they were mainly related to the relative prevalence of late-firing cells. Indeed, late-firing cells had a significantly lower input resistance and more negative membrane potential than other types of central neurons. Thus, there are marked species differences in the physiological properties of central neurons. Because the synaptic responsiveness of neurons is constrained by their physiological properties, our findings raise the possibility that the contrasting behavioural responsiveness observed across species is partly dependent on the species-specific physiological properties of central neurons.

Phylogenetic position of Eulipotyphla inferred from the cDNA sequences of pepsinogens A and C

Although to date the phylogenetic position of the provisional order Eulipotyphla has been assessed by various molecular markers, it has not been conclusively clarified due to low statistical supporting values and inconsistent results. To clarify the phylogenetic position of Eulipotyphla, we cloned cDNAs for pepsinogens A and C from five mammalian species belonging to four different orders and determined their nucleotide sequences. Molecular phylogenetic analysis based on the 1st and 2nd codon positions of the protein-coding region of cDNA sequences strongly supported the close relationship between Eulipotyphla and Chiroptera. Carnivora was found to be a sister group to these two orders. The monophyly of the order Rodentia and that of the cohort Glires (Rodentia and Lagomorpha) was also shown by the present phylogenetic trees of pepsinogens.

Sources of incongruence among mammalian mitochondrial sequences: COII, COIII, and ND6 genes are main contributors

To investigate the origins of incongruence among mammalian mitochondrial protein-coding genes, we compiled a matrix that included 13 protein-coding-genes for 41 mammals from 14 different orders. This matrix was examined for congruence using different partitioning strategies. The incongruence length difference test showed significant incongruence among the 13 gene partitions used simultaneously, and the result was not affected by third codon or transversion weighting. In the pair-wise comparisons, significant incongruence was detected between NADH:ubiquinone oxidoreductase subunit 6 gene (ND6), cytochrome oxidase subunit II (COII), or cytochrome oxidase subunit III (COIII) gene partitioned individually against the rest of the genes. Omission of any of the 14 mammalian orders alone or in combinations from the matrix did not result in a statistically significant improvement of congruence, suggesting that taxonomic sampling will not improve congruence among the data sets. However, omission of the ND6, COII, and COIII significantly improved congruence in our data matrix. Possible origins of unusual phylogenetic properties of the three genes are discussed.

Molecular cloning and functional characterization of guinea pig IL-12

IL-12 is a heterodimeric cytokine that plays a central role in cell-mediated immunity. We cloned complete cDNAs of guinea pig homologues of IL-12 p35 and p40 subunits, and compared their functional properties with human IL-12. Both p35 and p40 mRNA were constitutively expressed in the testis and peritoneal macrophages. On immunoblotting, anti-guinea pig p40 antibody detected the constitutive expression of p40 protein in the testis, while in macrophages it was induced in response to lipopolysaccharide. An unidentified 200-kDa macromolecule was also expressed in the testis. All recombinant hybrid heterodimer p70 (guinea pig p70, human p70 and two interspecies heterodimers) exerted proliferative activity toward concanavalin A-primed guinea pig and human lymphoblasts in a dose-dependent manner. A similar tendency was observed in IFN-gamma production in IL-2-treated human lymphocytes. All hybrid heterodimers also induced IFN-gamma mRNA from IL-2-treated guinea pig splenocytes. Thus, unlike the current concept that the p35 subunit determines the species incompatibility of IL-12 in humans and mice, p35 has marginal ability to define its species-specific functional expression between humans and guinea pigs. In addition, constitutive expression of IL-12 or related molecules in the testis indicated a potential role of this molecule in regulation of physiological or pathophysiological conditions in the reproductive system.

The AH receptor of the most dioxin-sensitive species, guinea pig, is highly homologous to the human AH receptor

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) brings about a wide spectrum of toxic and biochemical changes, most of which are mediated by the AH receptor (AHR). Recent cloning of the AHR from the two most TCDD-resistant laboratory animals, Han/Wistar (Kuopio) rats and hamsters, suggested a critical role for the C-terminal transactivation domain structure in TCDD sensitivity. Here we cloned the AHR from the most TCDD-susceptible species, guinea pig. The N-terminus of its AHR was highly similar to that in the resistant animals. However, the C-terminal Q-rich subdomain was only about half the size of this subunit in the hamster AHR. There was a distinct correlation across published mammalian species between the number of glutamine residues in the Q-rich subdomain and sensitivity to the acute lethality of TCDD. The closest homolog of the Guinea pig receptor turned out to be the human AHR, which may be relevant for dioxin risk assessment.

Evolution of the insulin molecule: insights into structure-activity and phylogenetic relationships

The conformation of insulin in the crystalline state has been known for more than 30 years but there remains uncertainty regarding the biologically active conformation and the structural features that constitute the receptor-binding domain. The primary structure of insulin has been determined for at least 100 vertebrate species. In addition to the invariant cysteines, only ten amino acids (GlyA1, IleA2, ValA3, TyrA19, LeuB6, GlyB8, LeuB11, ValB12, GlyB23 and PheB24) have been fully conserved during vertebrate evolution. This observation supports the hypothesis derived from alanine-scanning mutagenesis studies that five of these invariant residues (IleA2, ValA3, TyrA19, GlyB23, and Phe24) interact directly with the receptor and five additional conserved residues (LeuB6, GlyB8, LeuB11, GluB13 and PheB25) are important in maintaining the receptor-binding conformation. With the exception of the hagfish, only conservative substitutions are found at B13 (Glu --> Asp) and B25(Phe --> Tyr). In contrast, amino acid residues that were also considered to be important in receptor binding based upon the crystal structure of insulin (GluA4, GlnA5, AsnA21, TyrB16, TyrB26) have been much less well conserved and are probably not components of the receptor-binding domain. The hypothesis that LeuA13 and LeuB17 form part of a second receptor-binding site in the insulin molecule finds some support in terms of their conservation during vertebrate evolution, although the site is probably absent in some hystricomorph insulins. In general, the amino acid sequences of insulins are not useful in cladistic analyses especially when evolutionary distant taxa are compared but, among related species in a particular order or family, the presence of unusual structural features in the insulin molecule may permit a meaningful phylogenetic inference. For example, analysis of insulin sequences supports monophyletic status for Dipnoi, Elasmobranchii, Holocephali and Petromyzontiformes.

Birth of a gene: locus of neuronal BC200 snmRNA in three prosimians and human BC200 pseudogenes as archives of change in the Anthropoidea lineage

The gene encoding brain-specific dendritic BC200 small non-messenger RNA is limited to the primate order and arose from a monomeric Alu element. It is present and neuronally expressed in all Anthropoidea examined. By comparing the human sequence of about 13.2 kb with each of the prosimian (lemur 14.6 kb, galago 12 kb, and tarsier 13.8 kb) orthologous loci, we could establish that the BC200 RNA gene is absent from the prosimian lineages. In Strepsirhini (lemurs and lorises), a dimeric AluJ-like element integrated very close to the BC200 insertion point, while the corresponding tarsier region is devoid of any repetitive element. Consequently, insertion of the Alu monomer that gave rise to the BC200 RNA gene must have occurred after the anthropoid lineage diverged from the prosimian lineage(s). Shared insertions of other repetitive elements favor proximity of simians and tarsiers in support of their grouping into Haplorhini and the omomyid hypothesis. On the other hand, the nucleotide sequences in the segment that is available for comparison in all four species reveal less exchanges between Strepsirhini (lemur and galago) and human than between tarsier and human. Our data imply that the early activity of dimeric Alu sequences must have been concurrent with the activity of monomeric Alu elements that persisted longer than is usually thought. As BC200 RNA gave rise to more than 200 pseudogenes, we used their consensus sequence variations as a molecular archive recording the BC200 RNA sequence changes in the anthropoid lineage leading to Homo sapiens and timed these alterations over the past 35-55 million years.

Phylogeny of rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP

The order Rodentia includes nearly half of all living mammalian species. Phylogenetic relationships among 22 species of rodents were investigated by use of a 1.2-kb region from exon 1 of the single-copy nuclear gene IRBP. IRBP has been extensively used for study of interordinal phylogeny in mammals, which allowed inclusion of 50 outgroup species, representing every eutherian order plus seven marsupials. Several clades were strongly supported, regardless of analytical method or inclusion/exclusion of data. These include a monophyletic Muroidea, with a clade including Spalax and Rhizomys as the first divergence; a clade uniting Zapus with Dipus, but excluding Sicista; a monophyletic Myodonta (Muroidea plus Dipodidae); and a clade including Aplodontidae as sister to Sciuridae. One bipartition, separating Hystricognathi and Geomyoidea from the remaining rodents, is strongly supported in all analyses that include third-position sites but almost completely absent from analyses that exclude third-position sites. A combination of nonstationary nucleotide composition and branch length effects may be causing all methods examined (including those using the LogDet distance) to support an incorrect conclusion when third-position sites are analyzed together with first- and second-position sites.

Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes

The order Rodentia contains half of all extant mammal species, and from an evolutionary standpoint, there are persistent controversies surrounding the monophyly of the order, divergence dates for major lineages, and relationships among families. Exons of growth hormone receptor (GHR) and breast cancer susceptibility (BRCA1) genes were sequenced for a wide diversity of rodents and other mammals and combined with sequences of the mitochondrial 12S rRNA gene and previously published sequences of von Willebrand factor (vWF). Rodents exhibit rates of amino acid replacement twice those observed for nonrodents, and this rapid rate of evolution influences estimates of divergence dates. Based on GHR sequences, monophyly is supported, with the estimated divergence between hystricognaths and most sciurognaths dating to about 75 MYA. Most estimated dates of divergence are consistent with the fossil record, including a date of 23 MYA for Mus-Rattus divergence. These dates are considerably later than those derived from some other molecular studies. Among combined and separate analyses of the various gene sequences, moderate to strong support was found for several clades. GHR appears to have greater resolving power than do 12S or vWF. Despite its complete unresponsiveness to growth hormone, Cavia (and other hystricognaths) exhibits a conservative rate of change in the intracellular domain of GHR.

An error-correcting map for quartets can improve the signals for phylogenetic trees

From the DNA sequences for N taxa, the (generally unknown) phylogenetic tree T that gave rise to them is to be reconstructed. Various methods give rise, for each quartet J consisting of exactly four taxa, to a predicted tree L(J) based only on the sequences in J, and these are then used to reconstruct T. The author defines an "error-correcting map" (Ec), which replaces each L(J) with a new tree, Ec(L)(J), which has been corrected using other trees, L(K), in the list L. The "quartet distance" between two trees is defined as the number of quartets J on which the two trees differ, and two distinct trees are shown to always have quartet distance of at least N - 3. If L has quartet distance at most (N - 4)/2 from T, then Ec(L) will coincide with the correct list for T; and this result cannot be improved. In general, Ec can correct many more errors in L. Iteration of the map Ec may produce still more accurate lists. Simulations are reported which often show improvement even when the quartet distance considerably exceeds (N - 4)/2. Moreover, the Buneman tree for Ec(L) is shown to refine the Buneman tree for L, so that strongly supported edges for L remain strongly supported for Ec(L). Simulations show that if methods such as the C-tree or hypercleaning are applied to Ec(L), the resulting trees often have more resolution than when the methods are applied only to L.

Origins of the many NPY-family receptors in mammals

The NPY system has a multitude of effects and is particularly well known for its role in appetite regulation. We have found that the five presently known receptors in mammals arose very early in vertebrate evolution before the appearance of jawed vertebrates 400 million years ago. The genes Y(1), Y(2) and Y(5) arose by local duplications and are still present on the same chromosome in human and pig. Duplications of this chromosome led to the Y(1)-like genes Y(4) and y(6). We find evidence for two occasions where receptor subtypes probably arose before peptide genes were duplicated. These observations pertain to the discussion whether ligands or receptors tend to appear first in evolution. The roles of Y(1) and Y(5) in feeding may differ between species demonstrating the importance of performing functional studies in additional mammals to mouse and rat.

Studies of the human, rat, and guinea pig Y4 receptors using neuropeptide Y analogues and two distinct radioligands

The neuropeptide Y-family receptor Y4 differs extensively between human and rat in sequence, receptor binding, and anatomical distribution. We have investigated the differences in binding profile between the cloned human, rat, and guinea pig Y4 receptors using NPY analogues with single amino acid replacements or deletion of the central portion. The most striking result was the increase in affinity for the rat receptor, but not for human or guinea pig, when amino acid 34 was replaced with proline; [Ahx(8-20),Pro(34)]NPY bound to the rat Y4 receptor with 20-fold higher affinity than [Ahx(8-20)]NPY. Also, the rat Y4 tolerates alanine in position 34 since p[Ala(34)]NPY bound with similar affinity as pNPY while the affinity for hY4 and gpY4 decreased about 50-fold. Alanine substitutions in position 33, 35, and 36 as well as the large loop-deletion, [Ahx(5-24)]NPY, reduced the binding affinity to all three receptors more than 100-fold. NPY and PYY competed with (125)I-hPP at Y4 receptors expressed in CHO cells according to a two-site model. This was investigated for gpY4 by saturation with either radiolabeled hPP or pPYY. The number of high-affinity binding-sites for (125)I-pPYY was about 60% of the receptors recognized by (125)I-hPP. Porcine [Ala(34)]NPY and [Ahx(8-20)]NPY bound to rY4 (but not to hY4 or gpY4) according to a two-site model. These results suggest that different full agonists can distinguish between different active conformations of the gpY4 receptor and that Y4 may display functional differences in vivo between human, guinea pig, and rat.

Cloning and characterization of the guinea pig neuropeptide Y receptor Y5

The Y5 receptor has been postulated to be the main receptor mediating NPY-induced food intake in rats, based on its pharmacological profile and mRNA distribution. To further characterize this important receptor subtype, we isolated the Y5 gene in the guinea pig, a widely used laboratory animal in which all other known NPY receptors (Y1, Y2, Y4, y6) [2,13,33,37] have recently been cloned by our group. Our results show that the Y5 receptor is well conserved between species; guinea pig Y5 displays 96% overall amino acid sequence identity to human Y5, the highest identity reported for any non-primate NPY receptor orthologue, regardless of subtype. Thirteen of the twenty substitutions occur in the large third cytoplasmic loop. The identities between the guinea pig Y5 receptor and the dog, rat, and mouse Y5 receptors are 93%, 89%, and 89% respectively. When transiently expressed in EBNA cells, the guinea pig Y5 receptor showed a high binding affinity to iodinated porcine PYY with a dissociation constant of 0.41 nM. Competition experiments showed that the rank order of potency for NPY-analogues was PYY = NPY = NPY2-36 > gpPP > rPP >> NPY 22-36. Thus the pharmacological profile of the guinea pig Y5 receptor agrees well with that reported for the Y5 receptor from other cloned species.

Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction

Both mitochondrial and nuclear gene sequences have been employed in efforts to reconstruct deep-level phylogenetic relationships. A fundamental question in molecular systematics concerns the efficacy of different types of sequences in recovering clades at different taxonomic levels. We compared the performance of four mitochondrial data sets (cytochrome b, cytochrome oxidase II, NADH dehydrogenase subunit I, 12S rRNA-tRNA-16S rRNA) and eight nuclear data sets (exonic regions of alpha-2B adrenergic receptor, aquaporin, ss-casein, gamma-fibrinogen, interphotoreceptor retinoid binding protein, kappa-casein, protamine, von Willebrand Factor) in recovering deep-level mammalian clades. We employed parsimony and minimum-evolution with a variety of distance corrections for superimposed substitutions. In 32 different pairwise comparisons between these mitochondrial and nuclear data sets, we used the maximum set of overlapping taxa. In each case, the variable-length bootstrap was used to resample at the size of the smaller data set. The nuclear exons consistently performed better than mitochondrial protein and rRNA-tRNA coding genes on a per-residue basis in recovering benchmark clades. We also concatenated nuclear genes for overlapping taxa and made comparisons with concatenated mitochondrial protein-coding genes from complete mitochondrial genomes. The variable-length bootstrap was used to score the recovery of benchmark clades as a function of the number of resampled base pairs. In every case, the nuclear concatenations were more efficient than the mitochondrial concatenations in recovering benchmark clades. Among genes included in our study, the nuclear genes were much less affected by superimposed substitutions. Nuclear genes having appropriate rates of substitution should receive strong consideration in efforts to reconstruct deep-level phylogenetic relationships.

Protein sequence signatures support the African clade of mammals

DNA sequence evidence supports a superordinal clade of mammals that comprises elephants, sea cows, hyraxes, aardvarks, elephant shrews, golden moles, and tenrecs, which all have their origins in Africa, and therefore are dubbed Afrotheria. Morphologically, this appears an unlikely assemblage, which challenges-by including golden moles and tenrecs-the monophyly of the order Lipotyphla (Insectivora). We here identify in three proteins unique combinations of apomorphous amino acid replacements that support this clade. The statistical support for such "sequence signatures" as unambiguous synapomorphic evidence for the naturalness of the Afrotherian clade is reported. Using likelihood, combinatorial, and Bayesian methods we show that the posterior probability of the mammalian tree containing the Afrotherian clade is effectively 1.0, based on conservative assumptions. Presenting sequence data for another African insectivore, the otter shrew Micropotamogale lamottei, we demonstrate that such signatures are diagnostic for including newly investigated species in the Afrotheria. Sequence signatures provide "protein-morphological" synapomorphies that may aid in visualizing monophyletic groupings.

Protein sequence signatures support the African clade of mammals

DNA sequence evidence supports a superordinal clade of mammals that comprises elephants, sea cows, hyraxes, aardvarks, elephant shrews, golden moles, and tenrecs, which all have their origins in Africa, and therefore are dubbed Afrotheria. Morphologically, this appears an unlikely assemblage, which challenges-by including golden moles and tenrecs-the monophyly of the order Lipotyphla (Insectivora). We here identify in three proteins unique combinations of apomorphous amino acid replacements that support this clade. The statistical support for such "sequence signatures" as unambiguous synapomorphic evidence for the naturalness of the Afrotherian clade is reported. Using likelihood, combinatorial, and Bayesian methods we show that the posterior probability of the mammalian tree containing the Afrotherian clade is effectively 1.0, based on conservative assumptions. Presenting sequence data for another African insectivore, the otter shrew Micropotamogale lamottei, we demonstrate that such signatures are diagnostic for including newly investigated species in the Afrotheria. Sequence signatures provide "protein-morphological" synapomorphies that may aid in visualizing monophyletic groupings.

Molecular evidence of an African Phiomorpha-South American Caviomorpha clade and support for Hystricognathi based on the complete mitochondrial genome of the cane rat (Thryonomys swinderianus)

The complete mitochondrial genome of an African cane rat, Thryonomys swinderianus (Rodentia, Hystricognathi), was included in a phylogenetic analysis along with 4 rodents, 14 additional eutherians, and 3 noneutherian outgroups. Monophyly of the suborder Hystricognathi, represented by the cane rat and the South American guinea pig, Cavia porcellus, was strongly supported by maximum-parsimony, neighbor-joining, and maximum-likelihood methods. The molecular-based estimate of the divergence time of Old and New World Hystricognathi (approximately 85 million years before present, MYBP) is consistent with an hypothesis of vicariance divergence due to the rifting of the African and South American continents 86-100 MYBP. Monophyly of Rodentia or the superordinal clade Glires (Rodentia and Lagomorpha) were not supported.

Sex- and tissue-specific expression of aspartic proteinases in Danio rerio (zebrafish)

Full-length zebrafish cDNAs encoding two aspartic proteinases were cloned and sequenced. One of the two cDNAs was a 1708 bp product with an open reading frame of 398 amino acid residues corresponding to a cathepsin D. The other was a 1383 bp product encoding a polypeptide chain of 416 amino acids homologous to nothepsin, an aspartic proteinase first identified by us in the liver of Antarctic Notothenioidei. Gene expression assessed by RT-PCR and northern blot hybridization of RNA from different tissues showed that the expression was tissue- and sex-specific. Whereas the cathepsin D gene was expressed in all the tissues examined independently of the sex, the nothepsin gene was expressed exclusively in female livers.

Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data

Extensive phylogenetic analyses of the updated sequence data of mammalian mitochondrial genomes were carried out using the maximum likelihood method in order to resolve deep branchings in eutherian evolution. The divergence times in the mammalian tree were estimated by a relaxed molecular clock of the mitochondrial proteins calibrated with multiple references. A Chiroptera/Eulipotyphla (i.e. bat/mole) clade and a close relationship of this clade to Fereuungulata (Carnivora+Perissodactyla+Cetartiodactyla) were reconfirmed with high statistical significance. However, a support for a monophyly of Fereuungulata relative to the Chiroptera/Eulipotyphla clade was fragile, and we suggest that the three branchings among Carnivora, Perissodactyla, Cetartiodactyla and Chiroptera/Eulipotyphla occurred successively in a short time period, estimated to be approximately 77Myr BP. The Chiroptera/Eulipotyphla divergence was estimated to roughly coincide with the Cretaceous-Tertiary boundary (65Myr BP). The monophyly of Rodentia, the Lagomorpha/Rodentia clade (traditionally called Glires), and the Afrotheria/Xenarthra clade were preferred over alternative relationships, but the supports of these clades were not strong enough to exclude other possibilities. Although several super-order taxa of eutherians were strongly supported by the analyses of the mitochondrial genome data, the branching order in the deepest part of the eutherian tree remained ambiguous from the data presently available.

Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny

The phylogenetic relationships among major lineages of rodents is one of the issues most debated by both paleontologists and molecular biologists. In the present study, we have analyzed all complete mammalian mitochondrial genomes available in the databases, including five rodent species (rat, mouse, dormouse, squirrel and guinea-pig). Phylogenetic analyses were performed on H-strand amino acid sequences by means of maximum-likelihood and on H-strand protein-coding and ribosomal genes by means of distance methods. Also, log-likelihood ratio tests were applied to different tree topologies under the assumption of rodent monophyly, paraphyly or polyphyly. The analyses significantly rejected rodent monophyly and showed the existence of two differentiated clades, one containing non-murids (dormouse, squirrel and guinea-pig) and the other containing murids (rat and mouse). Long-branch attraction between murids and the outgroups could not be responsible for the existence of two different rodent clades, as no significant differences in evolutionary rate have been observed, except in the case of the squirrel, which shows a lower rate. The impact of among-site rate variation models on the phylogeny of rodents has been evaluated using the gamma distribution model. Results have shown that relationships among rodents remained unchanged, and the general topology of the tree was not affected, even though some branches were not properly resolved, most likely due to a lack of fit between estimated and real rate heterogeneity parameters.

Lung morphology in rodents (Mammalia, Rodentia) and its implications for systematics

A new nomenclature of the lung lobes and of the bronchial tree is presented, with which the lungs in 40 species of 11 rodent families are described. Whole, fixed lungs and silicone casts of the bronchial tree are tested for 23 characters, based on the distribution of lung lobes, the number and geometry of first order bronchi, the pulmonary blood supply, and lung symmetry. Ten lung morphotypes are recognized, seven of them representing one or more families: Castor type (Castoridae), Cryptomys type (Bathyergidae), Ctenodactylus type (Ctenodactylidae), Eliomys type (Gliridae), Myocastor type (Myocastoridae), Octodon type (Octodontidae and Echimyidae) and Rattus type (Sciuridae, Muridae pt. and Dipodidae). The Hydromys type is found only in Hydromys chrysogaster (Muridae), while Galea type A and B both appear in Galea musteloides (Caviidae). The data are phylogenetically analyzed by the program PAUP 4.0 using as outgroup Lagomorpha or Insectivora. On the species level, there are no well-resolved cladograms. On the family level, the cladograms do not contradict traditional rodent systematics with one exception: the Caviidae do not fall within Caviomorpha or even within the Hystricomorpha, but form a sister group to Dipodidae (Myomorpha). This appears to be a result of convergence. The lungs of Gliridae are more similar to those of Muridae than to those of Sciuridae. Included in the ingroup, Oryctolagus (Lagomorpha) forms a clade with Caviidae + Dipodidae. Thus, the "Glires hypothesis" is neither supported nor refuted.

Neuropeptide Y receptor gene y6: multiple deaths or resurrections?

The neuropeptide Y family of G-protein-coupled receptors consists of five cloned members in mammals. Four genes give rise to functional receptors in all mammals investigated. The y6 gene is a pseudogene in human and pig and is absent in rat, but generates a functional receptor in rabbit and mouse and probably in the collared peccary (Pecari tajacu), a distant relative of the pig family. We report here that the guinea pig y6 gene has a highly distorted nucleotide sequence with multiple frame-shift mutations. One evolutionary scenario may suggest that y6 was inactivated before the divergence of the mammalian orders and subsequently resurrected in some lineages. However, the pseudogene mutations seem to be distinct in human, pig, and guinea pig, arguing for separate inactivation events. In either case, the y6 gene has a quite unusual evolutionary history with multiple independent deaths or resurrections.

Age- and species-dependent maturation of synaptic transmission in the superficial superior colliculus

Both neonatal maturity and postnatal maturation are known to be species dependent. For instance, guinea pigs are born with their eyes open, while eye opening takes place 2 weeks after birth in rats. Moreover, several abnormalities have been observed in albino compared to pigmented species. The pigment melanin is proposed to play a protective role and its absence is thought to contribute to neuronal deficits. In the present study, we aimed to investigate functional differences in synaptic transmission in the visual, superficial layers of the superior colliculus (SC) of albino and pigmented rats and pigmented guinea pigs, at eye opening and 1 month after birth. This was achieved by analysing evoked field excitatory postsynaptic potentials (fEPSPs) in vitro, and by investigating the ability of these responses to express gamma-aminobutyric acid (GABA)-induced long-term potentiation (LTPG), an enduring increase in synaptic efficacy resulting from bath application of GABA. Guinea pigs did not show any obvious differences with respect to overall fEPSP characteristics and synaptic plasticity at both ages studied, indicating that maturation must have occurred prenatally. Rats, however, underwent synaptic maturation and refinement to produce stronger fEPSPs and a more robust level of synaptic plasticity 1 month after birth compared to the conditions at eye opening. The state of pigmentation was found to have a crucial influence, with albino rats showing less enhancement of the strength of synaptic transmission in the SC. It can therefore be concluded that profound developmental differences in pre- and postnatal maturation of the superficial SC exist between guinea pigs and rats, and that the state of pigmentation is a crucial factor in this process.

The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of scandentia to other eutherian orders

The complete mitochondrial genome of Tupaia belangeri, a representative of the eutherian order Scandentia, was determined and compared with full-length mitochondrial sequences of other eutherian orders described to date. The complete mitochondrial genome is 16, 754 nt in length, with no obvious deviation from the general organization of the mammalian mitochondrial genome. Thus, features such as start codon usage, incomplete stop codons, and overlapping coding regions, as well as the presence of tandem repeats in the control region, are within the range of mammalian mitochondrial (mt) DNA variation. To address the question of a possible close phylogenetic relationship between primates and Tupaia, the evolutionary affinities among primates, Tupaia and bats as representatives of the Archonta superorder, ferungulates, guinea pigs, armadillos, rats, mice, and hedgehogs were examined on the basis of the complete mitochondrial DNA sequences. The opossum sequence was used as an outgroup. The trees, estimated from 12 concatenated genes encoded on the mitochondrial H-strand, add further molecular evidence against an Archonta monophyly. With the new data described in this paper, most of both the mitochondrial and the nuclear data point away from Scandentia as the closest extant relatives to primates. Instead, the complete mitochondrial data support a clustering of Scandentia with Lagomorpha connecting to the branch leading to ferungulates. This closer phylogenetic relationship of Tupaia to rabbits than to primates first received support from several analyses of nuclear and partial mitochondrial DNA data sets. Given that short sequences are of limited use in determining deep mammalian relationships, the partial mitochondrial data available to date support this hypothesis only tentatively. Our complete mitochondrial genome data therefore add considerably more evidence in support of this hypothesis.

Guinea pig D-amino-acid oxidase cDNA and phylogenetic position

The nucleotide sequence of cDNA that encodes guinea pig D-amino-acid oxidase (DAO) was determined. The cDNA consisted of 1,399 nucleotides and a poly(A) tail. The cDNA encodes 347 amino acid residues. In contrast to the hamster, rat, and mouse DAOs, guinea pig DAO had the 25th amino acid residue. The homology in amino acid sequences between the guinea pig DAO and the rodent DAOs was not high in comparison to the homology in amino acid sequences between the guinea pig DAO and DAOs of humans, pigs and rabbits. The phylogenetic position of the guinea pig varied depending on the source of sequences (amino acids or nucleotides) and the methods of phylogenetic tree construction. These results suggest that the guinea pig is not a simple rodent.

Lineage-specific evolutionary rate in mammalian mtDNA

The existence of a lineage-specific nucleotide substitution rate in mammalian mtDNA has been investigated by analyzing the mtDNA of all available species, that is, 35 complete mitochondrial genomes from 14 mammalian orders. A detailed study of their evolutionary dynamics has been carried out on both ribosomal RNA and first and second codon positions (P12) of H-strand protein-coding genes by using two different types of relative-rate tests. Results are quite congruent between ribosomal and P12 sites. Significant rate variations have been observed among orders and among species of the same order. However, rate variation does not exceed 1.8-fold between the fastest (Proboscidea and Primates) and the slowest (Perissodactyla) evolving orders. Thus, the observed mitochondrial rate variations among taxa do not invalidate the suitability of mtDNA for drawing mammalian phylogeny. Dependence of evolutionary rate differences on variations in mutation and/or fixation rates was examined. Body size, generation time, and metabolic rate were tested, and no significant correlation was observed between them and the taxon-specific evolutionary rates, most likely because the latter might be influenced by multiple overlapping variable constraints.