Bayesian Research Articles

Description and Phylogenetic Relationships of a New Genus and Species of Lizard (Squamata, Gymnophthalmidae) from the Amazonian Rainforest of Northern Brazil

Marinussaurus curupira, a new genus and species of Gymnophthalmidae lizard is described from Iranduba, state of Amazonas, Brazil. The genus is characterized by an elongate body; short and stout pentadactyl limbs; all digits clawed; single frontonasal; two prefrontals; absence of frontoparietals; interparietal and parietals forming a straight posterior margin, with interparietal shorter than parietals; distinctive ear opening and eyelid; few temporals; three pairs of chin shields; nasal divided; a distinct collar; smooth, mainly hexagonal, dorsal scales; smooth quadrangular ventral scales; two precloacal and three femoral pores on each side in males; pores between three or four scales. Parsimony (PAR) and partitioned Bayesian (BA) phylogenetic analyses with morphological and molecular data recovered the new genus as a member of the Ecpleopodini radiation of the Cercosaurinae. A close relationship of the new genus with Arthrosaura is postulated.

The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within canidae

The dhole (Cuon alpinus) is the only existent species in the genus Cuon (Carnivora: Canidae). In the present study, the complete mitochondrial genome of the dhole was sequenced. The total length is 16672 base pairs which is the shortest in Canidae. Sequence analysis revealed that most mitochondrial genomic functional regions were highly consistent among canid animals except the CSB domain of the control region. The difference in length among the Canidae mitochondrial genome sequences is mainly due to the number of short segments of tandem repeated in the CSB domain. Phylogenetic analysis was progressed based on the concatenated data set of 14 mitochondrial genes of 8 canid animals by using maximum parsimony (MP), maximum likelihood (ML) and Bayesian (BI) inference methods. The genera Vulpes and Nyctereutes formed a sister group and split first within Canidae, followed by that in the Cuon. The divergence in the genus Canis was the latest. The divarication of domestic dogs after that of the Canis lupus laniger is completely supported by all the three topologies. Pairwise sequence divergence data of different mitochondrial genes among canid animals were also determined. Except for the synonymous substitutions in protein-coding genes, the control region exhibits the highest sequence divergences. The synonymous rates are approximately two to six times higher than those of the non-synonymous sites except for a slightly higher rate in the non-synonymous substitution between Cuon alpinus and Vulpes vulpes. 16S rRNA genes have a slightly faster sequence divergence than 12S rRNA and tRNA genes. Based on nucleotide substitutions of tRNA genes and rRNA genes, the times since divergence between dhole and other canid animals, and between domestic dogs and three subspecies of wolves were evaluated. The result indicates that Vulpes and Nyctereutes have a close phylogenetic relationship and the divergence of Nyctereutes is a little earlier. The Tibetan wolf may be an archaic pedigree within wolf subspecies. The genetic distance between wolves and domestic dogs is less than that among different subspecies of wolves. The domestication of dogs was about 1.56-1.92 million years ago or even earlier.

The classification of oximetry signals using Bayesian neural networks to assist in the detection of obstructive sleep apnoea syndrome

In the present study, multilayer perceptron (MLP) neural networks were applied to help in the diagnosis of obstructive sleep apnoea syndrome (OSAS). Oxygen saturation (SaO2) recordings from nocturnal pulse oximetry were used for this purpose. We performed time and spectral analysis of these signals to extract 14 features related to OSAS. The performance of two different MLP classifiers was compared: maximum likelihood (ML) and Bayesian (BY) MLP networks. A total of 187 subjects suspected of suffering from OSAS took part in the study. Their SaO2 signals were divided into a training set with 74 recordings and a test set with 113 recordings. BY-MLP networks achieved the best performance on the test set with 85.58% accuracy (87.76% sensitivity and 82.39% specificity). These results were substantially better than those provided by ML-MLP networks, which were affected by overfitting and achieved an accuracy of 76.81% (86.42% sensitivity and 62.83% specificity). Our results suggest that the Bayesian framework is preferred to implement our MLP classifiers. The proposed BY-MLP networks could be used for early OSAS detection. They could contribute to overcome the difficulties of nocturnal polysomnography (PSG) and thus reduce the demand for these studies.

The mitochondrial genome complete sequence and organization of the Pig-nosed Turtle Carettochelys insculpta (Testudines, Carettochelyidae) and its phylogeny position in Testudines

AbstractThe Pig-nosed Turtle Carettochelys insculpta (Testudines; Cryptodira; Carettochelyidae) is the sole living representative of the Carettochelyidae. The phylogenetic position of C. insculpta within Testudines has not yet been determined unequivocally. To address this issue, we sequenced the whole mitochondrial DNA (mtDNA) of C. insculpta using the long-and-accurate PCR (LA-PCR) method. The results show that the length of C. insculpta mtDNA is 16 439 bp and its structure is conserved compared to those of other turtles and other vertebrates except the NADH4 gene beginning with an ATC start codon. The 3′-side of the control region in mtDNA has two tandem repeat motifs, each consisting of nine 5′-CA-3′ units and sixteen 5′-AT-3′ units. To assess the phylogenetic position of C. insculpta, Maximum parsimony (MP), Maximum likelihood (ML) and Bayesian (BI) analyses were conducted based on complete mtDNA from 22 taxa. MP analyses robustly supported that the earliest phylogenetic tree splits separated into three basal branches: the Pelomedusidae (Pelomedusa subrufa), the Carettochelyidae (C. insculpta) and an assemblage of 18 cryptodiran turtle species; while ML and BI analyses suggested that Carettochelyidae and Trionychidae formed a clade, and that this clade was the sister taxon to all other cryptodiran turtles.

Estimation of Bayes Factors in a Class of Hierarchical Random Effects Models Using a Geometrically Ergodic MCMC Algorithm

We consider a Ba yesian random effects model that is commonly used in meta-analysis, in which the random effects have a t distribution, with degrees of freedom parameter to be estimated. We develop a Markov chain Monte Carlo algorithm for estimating the posterior distribution in this model, and establish geometric convergence of the algorithm. The geometric convergence rate has important theoretical and practical ramifications. Indeed, it implies that, under standard moment conditions, the ergodic averages used to estimate posterior quantities of interest satisfy central limit theorems. Moreover, it guarantees the consistency of a batch means estimate of the asymptotic variance in the CLT, which in turn allows for the construction of asymptotically valid standard errors. We show how our Markov chain can be used, in conjunction with an importance sampling method, to carry out an empirical Bayes approach for estimating the degrees of freedom parameter. To illustrate our methodology we consider a meta-analysis of studies that link intake of nonsteroidal anti-inflammatory drugs to a reduction in colon cancer risk, in which some of the studies are outliers. To model the distribution of the study effects we consider the family of t distributions, as well as a family of mixtures of Dirichlet process priors centered at the t distributions, and show how our methodology can be used to make a choice of model. Supplemental materials are available online.

Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Mitochondrial DNA of the Co-1 gene region was sequenced for 8 fish species (in total 17 sequences of at least 532 bp) from the far east of Russia and compared to 3 other perciform sequences, altogether comprising 20 perch-like fish sequences and 2 outgroup sequences (Cypriniformes). The analysis of the protein-coding Co-1 gene revealed a statistically substantiated bias in the (T+C):(A+G) content, confirming the basic findings on the pyrimidines-prunes ratio. The average scores of p-distances for different scales of the evolutionary history of the Co-1 gene revealed a pat- tern of increased nucleotide diversity at 4 different levels: (1) intraspecies, (2) intragenus, (3) intrafamily and (4) intraorder. The scores of the average p-distances of the 4 categories of compari- son were: (1) 0.11 ± 0.04%, (2) 1.87 ± 0.68%, (3) 12.67 ± 0.28%, and (4) 16.52 ± 0.10%, respectively (mean ± SE). These data support the concept that speciation in the order Perciformes in most cases follows a geographic mode through accumulation of numerous small genetic changes over a long time. The phylogenetic trees for 18 and 21 sequences of perch-like fishes together with 2 other fishes belonging to the ray-finned fishes (Actinopterygii) were developed using the Co-1 gene and 4 differ- ent analytical approaches: neighbour-joining (NJ), maximum likelihood (ML), Bayesian (BA) and maximum parsimony (MP). The analysis revealed a monophyletic origin for the representatives of the Stichaeidae, which was the principal percoid family investigated (86, 96 and 100% support in our NJ, ML and BA analyses, respectively). Species identification on a per individual basis or Co-1-based DNA barcoding was high.

Phylogeny of Thylamys (Didelphimorphia, Didelphidae) species, with special reference to Thylamys karimii

The genus Thylamys Gray, 1843 lives in the central and southern portions of South America inhabiting open and shrub-like vegetation, from prairies to dry forest habitats in contrast to the preference of other Didelphidae genera for more mesic environments. Thylamys is a speciose genus including T. elegans (Waterhouse, 1839), T. macrurus (Olfers, 1818), T. pallidior (Thomas, 1902), T. pusillus (Desmarest, 1804), T. venustus (Thomas, 1902), T. sponsorius (Thomas, 1921), T. cinderella (Thomas, 1902), T. tatei (Handley, 1957), T. karimii (Petter, 1968), and T. velutinus (Wagner, 1842) species. Previous phylogenetic analyses in this genus did not include the Brazilian species T. karimii, which is widely distributed in this country. In this study, phylogenetic analyses were performed to establish the relationships among the Brazilian T. karimii and all other previously analyzed species. We used 402-bp fragments of the mitochondrial cytochrome b gene, and the phylogeny estimates were conducted employing maximum parsimony (MP), maximum likelihood (ML), Bayesian (BY), and neighbor-joining (NJ). The topologies of the trees obtained in the different analyses were all similar and pointed out that T. karimii is the sister taxon of a group constituted of taxa from dry and arid environments named the dryland species. The dryland species consists of T. pusillus, T. pallidior, T. tatei, and T. elegans. The results of this work suggest five species groups in Thylamys. In one of them, T. velutinus and T. kariimi could constitute a sister group forming one Thylamys clade that colonized Brazil.

Sequence diversity at cytochrome oxidase 1 (Co-1) gene among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish of Russia Far East with phylogenetic and taxonomic insights

Mitochondrial DNA (mtDNA) atCo-1 gene region was sequenced for 7 scorpion fish species (in total, 16 sequences of at least 552 bp) from the Far East of Russia and compared with 15 other sequences of Scorpaeniformes comprising altogether 29 scorpion-like fish sequences and two outgroup sequences (Cypriniformes). The analysis of the protein-codingCo-1 gene revealed statistically substantiated bias in the (T+C) ∶ (A+G) content, proving basic findings. The average scores ofp-distances for different scales of the evolutionary history atCo-1 gene revealed a clear pattern of increased nucleotide diversity at four different levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. The scores of averagep-distances for the compared fish groups were: (1) 1.00±0.20%, (2) 3.80±0.20%, (3) 12.40±1.20%, and (4) 18.00±0.38%, respectively (mean±SE). These data support the concept that speciation in the order Scorpaeniformes, in most cases, follows a geographic mode through accumulation of numerous small genetic changes over a long period of time. However, intraspecies diversity was surprisingly high among scorpionfish. Phylogenetic trees for 29 sequences of scorpionfish and 2 other fishes belonging to ray-finned fishes (Actinopterigii) were developed usingCo-1 gene and four different analytical approaches: Bayesian (BA), maximum likelihood (ML), neighbour-joining (NJ), and maximum parsimony (MP). The analysis revealed a monophyletic origin for the representatives of Cottidae, which is the principal scorpionfish family investigated (100, 96, 98% support level in our BA, MP, and NJ analyses). Similarly, the monophyletic origin of up to the three compared scorpion-like fish genera was supported by molecular phylogenetic data. Species identification on individual basis (barcoding tagging) was high. A few taxonomic complications arose during the analysis and they are discussed here in.

16S and 28S rDNA Sequences in Phylogenetic Analyses of Freshwater Prawns (Macrobrachium Bate, 1868) from Taiwan

Using 15 species of freshwater prawns (Macrobrachium Bate, 1868) from Taiwan as the study material, characters of mitochondrial 16S rDNA sequences (16S) and nuclear 28S rDNA sequences (28S) were examined. Their phylogenetic analyses were conducted with Bayesian (BI), maximum likelihood (ML), maximum parsimony (MP), and minimum evolution and neighbor-joining (MENJ) methods. The 16S extracted was smaller in sequence length, rich in adenine, poor in cyctosine, and biased strongly to transitions in the nucleotide substitutions, whereas the 28S extracted was larger, rich in guanine, and biased to transversions. In the separate analyses of the two genes, the phylogenetic trees derived from the 28S had appreciably higher topological resolution with deeper branching (less polytomies) and higher topological confidence with stronger phylogenetic signals than the 16S trees. The poor resolution and confidence of the 16S trees were attributable primarily to its poor sequence divergences associated with high transition/transversion (ts/tv) ratios and low avalues of the gamma distributions. The result was a severe convergence of taxa within a narrow range of small genetic distances, so that their bifurcation could not be determined unambiguously. The 28S was highly diverged and had larger genetic distances with low ts/tv ratios and high a-values, resulting in much less convergence of the taxa. The 28S tree reconstructed with BI produced the best topological resolution and confidence in the separate analyses. The partition homogeneity test indicated that the 16S and 28S data sets were congruent. Their combined analyses with ML, MP, and MENJ showed no improvement in both topological resolution and confidence from the separate analyses of the 28S. With BI the combined analysis produced mixed results; improved the estimates of phylogenies for some of the taxa but confused or even obscured for the others.

PROC QTL—A SAS Procedure for Mapping Quantitative Trait Loci

Statistical analysis system (SAS) is the most comprehensive statistical analysis software package in the world. It offers data analysis for almost all experiments under various statistical models. Each analysis is performed using a particular subroutine, called a procedure (PROC). For example, PROC ANOVA performs analysis of variances. PROC QTL is a user-defined SAS procedure for mapping quantitative trait loci (QTL). It allows users to perform QTL mapping for continuous and discrete traits within the SAS platform. Users of PROC QTL are able to take advantage of all existing features offered by the general SAS software, for example, data management and graphical treatment. The current version of PROC QTL can perform QTL mapping for all line crossing experiments using maximum likelihood (ML), least square (LS), iteratively reweighted least square (IRLS), Fisher scoring (FISHER), Bayesian (BAYES), and empirical Bayes (EBAYES) methods.

Post Positivist Probability

Positivist philosophy provided the foundation for all social sciences as they were developed in the twentieth century. Now that p ositivism has been abandoned by philosophers, it is essential to replace methodolog y founded on positivist precepts. We show that the foundations of probability (both Baye sian and Frequentist) are wedded to positivist assumptions, which have been shown not t o be workable. We suggest an alternative non-positivist foundation for probabili ty theory, which avoids many of the problems faced by the current methodologies.

Molecular Phylogenetic Analysis of Some Fringillidae Species Based on Mitochondrial CoI Gene Sequences

Phylogenetic relationships of 36 Fringillidae species based on mitochondrial CoI gene sequences were reconstructed using the Bayesian (BI) maximum-likelihood (ML) and Neighbor-joining（NJ）methods. The results suggest that the relationship of Calcarius lapponicus and Emberiza is more closely related than other Fringillidae species.Our results support the view that Latoucheornis siemsseni is included in Genus Emberiza as E. siemsseni, and confirms that there is a close relationship between Mycerobas affinis and Eophona migratorius . This study also finds that Urocynchramus pylzowi is distantly related to Uragus sibiricus , but Uragus sibiricus and Carpodacus are closely related. The result also supports that fringillids and emberizids can be listed into two subfamilies under the family Fringillidae: Fringillinae and Emberizinae.

Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers

This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers.

Cytochrome oxidase 1 gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae) of Far East Russia with inferences in phylogeny and taxonomy

Mitochondrial DNA at the cytochrome oxidase 1 (Co-1) gene region was sequenced for six flatfish species (in total, 11 sequences of at least 539 base pairs) from the Far East of Russia and compared with other sequences of Pleuronectiformes, comprising altogether 26 flatfish sequences and two outgroup sequences (Perciformes). An analysis of the protein-coding Co-1 gene revealed a statistically substantiated bias in (T + C):(A + G) content, supporting earlier findings. Average scores of the p-distances for different scales of the evolutionary history at the Co-1 gene revealed a clear pattern of increased nucleotide diversity at four different levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intra-order. Scores of average p-distances of the four categories of comparison in flatfishes were (1) 0.17 +/- 0.09%, (2) 10.60 +/- 1.57%, (3) 12.40 +/- 0.27%, and (4) 19.93 +/- 0.05%, respectively (mean +/- standard error). These data jointly with current knowledge support the concept that speciation in the order Pleuronectiformes mostly follows a geographic mode through accumulation of numerous small genetic changes over a long period of time. A phylogenetic tree for 26 sequences of flatfishes and two other fishes belonging to ray-finned fishes (Actinopterigii) was developed using the Co-1 gene and four different analytical approaches: neighbour-joining, Bayesian (BA), maximum parsimony (MP), and maximum likelihood. The analysis revealed a monophyletic origin for the representatives of Pleuronectidae, which is the principal flatfish family investigated (73-100% support level in our MP and BA analyses). According to the current and literary data, the monophyletic origin for the six compared flatfish families was well supported. Species identification on a per-individual basis (barcoding tagging) was high.

The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

The complete mitochondrial genome (16,837 bp) from the Keeled box turtle ( Pyxidea mouhotii) was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule: a large number of (ATTATATC) n direct tandem repeats followed by (TA) n microsatellite at the 3′ end of the control region (D-loop), which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood (ML) and Bayesian (BI) analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1) Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea- Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group (containing Pyxidea) may have originated from two ancestors; 2) the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.

Cytochrome b (Cyt-b) gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae), with phylogenetic and taxonomic insights

Mitochondrial DNA (mtDNA) at Cyt-b gene region was sequenced for six flatfish species (in total nine sequences of at least 1,117 bp) from the Far East of Russia and compared with other sequences of Pleuronectiformes comprising altogether 34 species and 3 outgroup species (Perciformes). Analysis of the protein-coding Cyt-b gene revealed a statistically substantiated bias in (T + C):(A + G) content, supporting earlier findings. Values of P-distances, as summarized for different scales of the evolutionary history at Cyt-b gene, revealed a clear pattern of increased nucleotide diversity at four different phylogenetic levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. Scores of average P-distances of the four categories of comparison in flatfishes were (1) 0.46 ± 0.19%, (2) 11.74 ± 2.26%, (3) 17.51 ± 3.13%, and (4) 25.60 ± 0.42%, respectively (mean ± SE). These data support the concept that speciation in the order Pleuronectiformes, in most cases, follows a geographic mode through the accumulation of numerous small genetic changes over a long period of time. A phylogenetic tree for 64 sequences of flatfishes and 3 other fishes belonging to ray-finned fishes (Actinopterigii) was developed using Cyt-b gene and four different analytical approaches: neighbour-joining (NJ), Bayesian (BA), maximum parsimony (MP), and maximum likelihood (ML). The analysis revealed a monophyletic origin for the representatives of Pleuronectidae, which is the principal flatfish family investigated (99% repetition level in our BA analysis). A well supported property of the phylogenetic tree was the monophyletic placement of all the five flatfish families and the order Pleuronectiformes among other representatives of ray-finned fishes of the class Actinopterigii. Species identification on per individual basis (barcoding tagging) was generally high. However, there were taxonomic complications that arose during analysis, and they are discussed. Major outcomes of this discussion are the necessity of synonymy acceptance for Hippoglossoides elassodon, and H. robustus, and for Pseudopleuronectes yokohamae and P. schrenki. Priority considerations suggest H. elassodon and P. yokohamae as valid species names.

Molecular systematics of Dolichopodidae (Diptera) inferred from COI and 12S rDNA gene sequences based on European exemplars

With ~7000 species in ~220 genera, the Dolichopodidae is one of the most speciose families of Diptera. Though the family as such is well defined, knowledge on the internal phylogenetic relationships is generally poor and although authors of successive monographs and catalogues indifferently listed most genera in specific subfamilies, their decisions were rarely based on sound phylogenetic analyses and never on molecular data. In a first attempt to unravel the phylogeny of Dolichopodidae, a combined COI + 12S rDNA dataset (1199 characters) of 119 samples of 101 European species was used in Bayesian (BAY), neighbour joining (NJ) and weighted/unweighted maximum parsimony analyses (MP). At the subfamily level, our study supports the monophyly of Dolichopodinae, Sympycninae, and Hydrophorinae (including Machaerium Haliday, 1832). Ten (Campsicnemus Haliday, 1851, Chrysotus Meigen, 1824, Dolichopus Latreille, 1796, Gymnopternus Loew, 1857, Medetera Fischer von Waldheim, 1819, Poecilobothrus Mik, 1878, Rhaphium Meigen, 1803, Teuchophorus Loew, 1857, Sciapus Zeller, 1842, Syntormon Loew, 1857) of the 14 multispecies genera formed monophyletic assemblages in all analyses and relationships among Argyra Macquart, 1834 species were supported in most analyses. At the subgeneric level, seven of the nine stable species-groups in Dolichopus as established during previous research were supported in most analyses. The validity of the recent transfer of Hercostomus chrysozygos Wiedemann, 1817 to Poecilobothrus was clearly supported in all analyses. Within Argyra and Rhaphium, interspecific relationships reflected previously used subgeneric classifications (Lasiargyra Mik, 1878, Leucostola Loew, 1857 and Argyra s.s. in Argyra; Porphyrops Meigen, 1824, Rhaphium s.s. and Xiphandrium Loew, 1857 in Rhaphium). Further, subclades within Medetera corresponded to species-groups defined by other authors featuring a different morphology and ecology. Anepsiomyia flaviventris (Meigen, 1824) most probably does not belong to Sympycninae but its current position within Peloropeodinae could not be confirmed.

A Re-analysis of the phylogeny of the genus Protobothrops (Reptilia: Viperidae), with particular reference to the systematic position of P. xiangchengensis

AbstractBased on three mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b), the phylogeny of Protobothrops is re-analyzed using Maximum-parsimony (MP), Maximum-likelihood (ML), and Bayesian (BI) approaches. All phylogenetic analyses indicate that all putative Protobothrops species examined formed a monophyletic group; however, the intrageneric relationships are still unresolved. The phylogenetic relationships further confirm that P. xiangchengensis is a valid species distinct from P. mucrosquamatus and that it is closely related to P. jerdonii.

Inferring the phylogenetic position of Boa constrictor among the Boinae

Snakes of the subfamily Boinae are found in Madagascar, the Papuan-Pacific Islands, and the Neotropics. It has been suggested that genera within each of these particular areas do not form monophyletic groups. Further, it was proposed that the New World Boa constrictor is more closely related to boine genera in Madagascar than to boines in the Neotropics. Along with inferring the relationship of all boine genera using data from the cytochrome b gene and morphology, the placement of Boa was also examined. Phylogenetic inferences using maximum likelihood and Bayesian (BI) methods for combined data analyses and separate analyses of DNA sequence and morphological data were conducted. Priors, parametric bootstraps, and the Shimodaira–Hasegawa test were used to examine the previously proposed placement of Boa with Madagascan taxa using these DNA data. DNA data and combined data analyses strongly reject the hypothesis that Boa is more closely related to Old World genera than to other New World genera. Additionally, strong tree support suggests that all species within Madagascar, the Papuan-Pacific Islands, and the Neotropics each form a monophyletic group with respect to their geographic region.

硫酸アルベカシンにおける投与設計に際しての留意点―Ｓａｗｃｈｕｋ‐Ｚａｓｋｅ法とＢａｙｅｓｉａｎ法を用いた場合の比較

Two methods are commonly used to analyze the pharmacokinetics of ABK : the Sawchuk-Zaske (SZ) method, which uses a one-compartment model, and the Bayesian (BS) method, which uses population parameters based on a two-compartment model. Since it seemed possible that serum ABK concentrations predicted from pharmacokinetic parameters calculated by these two methods might differ, we carried out a comparison. We performed TDM after administering ABK to 18 patients with pneumonia and evaluated the peak and trough concentrations predicted by the two methods. The predicted between peak concentrations for the SZ method and BS method were well correlated and so were the predicted between trough concentrations for both methods. However, the peak and trough concentrations predicted by the BS method were higher than those for the SZ method by 3.9± 1.5 and 1.1± 0.8μg/mL, respectively, which suggests that actual peak concentrations could be lower than the therapeutic range if the target peak levels are set between 7 and 11μg/ mL when designing the dosage regimen by the BS method. We also compared measured values with values predicted based on patients' pharmacokinetic parameters (population means) using the initial dosage design function of TDM software for Habekacin ® (Research Committee for Anti-MRSA Drugs). The relationship between the measured values (y) and the predicted values (x) was represented by the regression equation y=1.075x -0.309 (R2= 0.729, n= 36), demonstrating the usefulness of the initial dosage design.