Arenavirus Coinfections Are Common in Snakes with Boid Inclusion Body Disease

Recently, novel arenaviruses were found in snakes with boid inclusion body disease (BIBD); these form the new genus Reptarenavirus within the family Arenaviridae. We used next-generation sequencing and de novo sequence assembly to investigate reptarenavirus isolates from our previous study. Four of the six isolates and all of the samples from snakes with BIBD contained at least two reptarenavirus species. The viruses sequenced comprise four novel reptarenavirus species and a representative of a new arenavirus genus.     

Phylogenetic Analysis of theArenaviridae:Patterns of Virus Evolution and Evidence for Cospeciation between Arenaviruses and Their Rodent Hosts

Viruses of theArenaviridaecause hemorrhagic fevers and neurologic disease in humans. Historically, the arenaviruses have been divided into two complexes (LASV-LCMV, Tacaribe) through the use of antigenic typing. The phylogeny of theArenaviridaeas a whole has not been estimated previously due to a lack of sequence data for all members of the family. In this study, nucleocapsid protein gene sequence data were obtained for all currently known arenaviruses and used to estimate, for the first time, a phylogeny of the entire virus family. The LCMV-LASV complex arenaviruses are monophyletic and comprise three distinct lineages. The Tacaribe complex viruses also are monophyletic and occupy three distinct lineages. Comparisons of arenavirus phylogeny with rodent host phylogeny and taxonomic relationships provide several examples in which virus–host cospeciation is potentially occurring. The pathogenic arenaviruses do not appear to be monophyletic, suggesting that the pathogenic phenotype has arisen in multiple independent events during virus evolution.     

Foraging Behavior in the Arboreal Boid Corallus grenadensis

Corallus grenadensis is an arboreal boa endemic to the Grenada Bank. Thirty-five encounters with boas resulted in 17.65 hours of observations, including 6.3 hours of video-tape (which included two acts of predation). Boas under 100 cm are largely active foragers that move slowly through bushes and trees and tongue-flick leaf and branch surfaces apparently seeking chemosensory evidence of nocturnally quiescent lizard (Anolis) prey. Significantly more search time was directed to branches below the snake rather than to either the branches supporting the snake or to those above the snake, and tongue-flick rates were significantly higher for moving snakes than for those that were stationary. Smaller snakes prey on nocturnally quiescent lizards and they spent more time moving than did large snakes that feed on nocturnally active rodents and often employ an ambush foraging strategy. Once visual and, presumably, thermal information was received from a sleeping anole, C. grenadensis adopted a lengthy stalking process devoid of tongue-flicks. Snakes approached inactive lizards from adjacent branches with great stealth, moving at a rate of about 1 cm/min. The strike was made from close range (within 3 cm), and the prey was never released once contact was made. We conclude that, if chemosensory cues successfully lead a treeboa to a visual encounter with a sleeping lizard, subsequent behavior ensures a high rate of predation success.     

Different Relationships between Temporal Phylogenetic Turnover and Phylogenetic Similarity and in Two Forests Were Detected by a New Null Model

Background

Ecologists have been monitoring community dynamics with the purpose of understanding the rates and causes of community change. However, there is a lack of monitoring of community dynamics from the perspective of phylogeny.

Methods/Principle Findings

We attempted to understand temporal phylogenetic turnover in a 50 ha tropical forest (Barro Colorado Island, BCI) and a 20 ha subtropical forest (Dinghushan in southern China, DHS). To obtain temporal phylogenetic turnover under random conditions, two null models were used. The first shuffled names of species that are widely used in community phylogenetic analyses. The second simulated demographic processes with careful consideration on the variation in dispersal ability among species and the variations in mortality both among species and among size classes. With the two models, we tested the relationships between temporal phylogenetic turnover and phylogenetic similarity at different spatial scales in the two forests. Results were more consistent with previous findings using the second null model suggesting that the second null model is more appropriate for our purposes. With the second null model, a significantly positive relationship was detected between phylogenetic turnover and phylogenetic similarity in BCI at a 10 m×10 m scale, potentially indicating phylogenetic density dependence. This relationship in DHS was significantly negative at three of five spatial scales. This could indicate abiotic filtering processes for community assembly. Using variation partitioning, we found phylogenetic similarity contributed to variation in temporal phylogenetic turnover in the DHS plot but not in BCI plot.

Conclusions/Significance

The mechanisms for community assembly in BCI and DHS vary from phylogenetic perspective. Only the second null model detected this difference indicating the importance of choosing a proper null model.     

Complete Mitochondrial DNA Sequences of Six Snakes: Phylogenetic Relationships and Molecular Evolution of Genomic Features

Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNA^Leu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.[Reviewing Editor: Dr. Bill Ballard]     

毒蛇咬伤的动态分析

目的探讨毒蛇咬伤不同时期的动态变化。方法根据３２年共收治各类型毒蛇咬伤患者６０６例的临床资料,分析不同时期毒蛇咬伤的动态变化。结果毒蛇的种类、毒蛇咬伤的多发季节、受伤人群的分布数量和死亡率都发生了变化,形成了新的动向和规律。结论毒蛇咬伤的种类和患者不断增多,多发季节明显改变,死亡率明显下降,受伤人群形成了新的动向。     

呼肠孤病毒科的系统发育分析

运用邻接法(neibor-joining,NJ)、最大似然法(maximum likehood,ML)对国际病毒分类委员会(Intemational Committee on Taxonomy of Viruses,ICTV)第八次报告中所有已报道的呼肠孤病毒科外层衣壳蛋白序列进行了系统发育分析.结果表明:两种方法构建的系统树拓扑结构基本一致,尽管部分分支略有差异,但都能够反映出科内各属的系统发育关系,分析结果支持了该科的分类地位.同时还比较两种建树方法的异同点,并对建树产生的差异原因作了探讨.     

Phylogenetic Analysis of Dioecy in Monocotyledons

Surveys of plant breeding systems in angiosperm families have shown a significant association between monoecy and dioecy, and researchers have proposed that dioecy has tended to evolve from monoecy. We evaluated this hypothesis in the context of a phylogeny of 918 monocotyledons assembled from 19 published trees. Binary and multistate breeding system characters were mapped onto a set of composite trees, and alternative models of character change were compared using maximum likelihood. Over a range of tree topologies and optimizations, we found three to eight times as many changes from hermaphroditism to dioecy as we did from monoecy to dioecy. Also, the rate at which monoecy gave rise to dioecy was not significantly higher than the rate at which hermaphroditism gave rise to dioecy. Our analysis implies that the correlation of monoecy and dioecy in angiosperm families does not reflect a preponderance of changes from monoecy to dioecy. Instead, we postulate that the family-level correlation results from the clustering of breeding system changes in the underlying phylogeny. Our results suggest renewed attention to modeling the transition from hermaphroditism to dioecy, possibly involving transient intermediates such as gynodioecy.     

Evolutionary Patterns in Advanced Snakes

One prevalent view of phylogenetic events in advanced snakesholds that the fangs evolved along at least two pathways one(e.g. elapids) from ancestors with enlarged anterior and theother (e.g. viperids) from ancestors with enlarged posteriormaxillary teeth. Selective forces driving these changes arepresumed to arise from the increasing advantages of teeth andglands in venom injection. In this paper another plausible viewof these events is proposed. First fangs of both elapids and viperids likely evolved fromreal maxillary teeth. In non-venomous snakes, differences intooth morphology and function suggest that there may be somedivision of labor among anterior and posterior maxillary teeth.Anterior maxillary teeth, residing forward in the mouth likelyserve the biological role of snaring and impaling prey duringthe strike. They are also conical frequently recurved and lacka secretion groove. On the other hand posterior teeth becauseof their geometric position on the maxilla and mechanical advantages,tend to serve as aids in preingestion manipulation and swallowingof prey. They are often blade shaped and occasionally bear asecretion groove along their sides. Although both front andrear maxillary teeth of nonvenomous snakes may be elongatedthis is likely to serve these different functional roles andhence they evolved under different selective pressures. Whenfangs evolved they did so several times independently but fromrear maxillary teeth. In support one notes a) the similar positionpostorbital of venom and Duvernoy s glands b) similar embryonicdevelopment of fangs and rear maxillary teeth c) secretion groovewhen present, is found only on rear teeth and d) similar biologicalroles of some rear teeth and fangs. For ease in clearance ofthe prey during the strike the fangs are positioned forwardin the mouth accomplished in viperid snakes by forward rotationof the maxilla and elapids by rostral anatomical migration tothe front of the maxilla. Second, the adaptive advantage first favoring initial rear toothenlargement likely centered not on their role in venom injectionbut rather on their role in preingestion manipulation and swallowing.However once enlarged, teeth would be preadapted for later modificationinto fangs under selection pressures arising from advantagesof venom introduction. This has implications for the function and evolution of associatedstructures. Besides possibly subduring or even killing of preythe secretion of Duvernoy's gland may be involved in digestionor in neutralizing noxious or fouling products of the prey.The presence or absence of constriction need not be functionallytied to absence or presence of venom injection. The phylogeneticpathways outlined herein were likely traveled several timesindependently in advanced snakes.     

Scaling of Cardiovascular Physiology in Snakes

The elongate body form of snakes and the wide diversity of habitatsinto which they have radiated have affected the form and functionof the cardiovascular system. Heart position is strongly correlatedwith habitat. The heart is located 15–25% of the bodylength from the head in terrestrial and arboreal species, but25–45% in totally aquatic species. Semi-aquatic and fossorialspecies are intermediate. The viperids are exceptional, withgenerally more posterior hearts but arboreal species have heartscloser to the head. An anterior heartis favored when snakesclimb because it reduces the hydrostatic pressure of the bloodcolumn above the heart and tends to stabilize cephalic bloodpressure. In water, where hydrostatic bloodpressure is not aproblem, a more centrally located heart is favored because theheart does less work perfusing the body. In terrestrial species,head-heart distance increases linearly with body length andthe increased hydrostatic pressure is matched by higher restingarterial blood pressure in longer animals. Unlike mammals andbirds, snakes have blood pressures that increasewith body mass.The added stress on the ventricle wall in larger snakes is correlatedwith ventricles that are larger than predicted by other reptiles.Heart mass scales with body mass to the 0.95 power in snakesbut only 0.77–0.91 in other reptiles that are not as subjectto the hydrostatic effects of gravity. The spongy hearts ofreptiles do not conform well to the Principle of Laplace.     

Development of Antipredator Responses in Snakes

Individual and litter differences in the number of attacks directed by Mexican garter snakes (Thamnophis melanogaster) at a threatening stimulus were studied over the first year of life. Newborn snakes born to wildcaught females from the same population were tested the day after they were born and at 7, 16, 31, and 54 weeks of age on reactivity to a potent nonmoving and moving stimulus (a human finger). There were significant individual and interlitter differences in number of strikes directed at both stimuli but no significant effect of sex. Intercorrelations among the strike scores of individuals across test days averaged .54 for the nonmoving stimulus presentations and .63 for trials with the moving stimulus. Strike scores to the moving and nonmoving stimuli were significantly correlated at each age, however, attack responses to the moving stimulus declined over the year while those to the nonmoving stimulus remained constant. Measures of concordance showed that both individual strike scores and litter means were highly consistent, whereas consistency within litters was reduced. The results indicate that litter and individual differences among newborn snakes in the tendency to engage in antipredator behavior (“defensive temperament”) remain relatively stable from the first day after birth throughout the first year of life.     

Phylogenetic Analysis of Antibiotic Glycosyltransferases

Catalyzed by a family of enzymes called glycosyltransferases, glycosylation reactions are essential for the bioactivities of secondary metabolites such as antibiotics. Due to the special characters of antibiotic glycosyltransferases (AGts), antibiotics can function by attaching some unusual deoxy-sugars to their aglycons. Comprehensive similarity searches on the amino acid sequences of AGts have been performed. We reconstructed the molecular phylogeny of AGts with neighbor-joining, maximum-likelihood, and Bayesian methods of phylogenetic inference. The phylogenetic trees show a distinct separation of polyene macrolide (PEM) AGts and other polyketide AGts. The former are more like eukaryotic glycosyltransferases and were deduced to be the results of horizontal gene transfer from eukaryotes. Protein tertiary structural comparison also indicated that some glycopeptide AGts (Gtf-proteins) have a close evolutionary relationship with MurGs, essential glycosyltransferases involved in maturation of bacterial cell walls. The evolutionary relationship of glycopeptide antibiotic biosynthetic gene clusters was speculated according to the phylogenetic analysis of Gtf-proteins. Considering the fact that polyketide AGts and Gtf-proteins are all GT Family 1 members and their aglycon acceptor biosynthetic patterns are very similar, we deduced that AGts and the synthases of their aglycon acceptors have some evolutionary relevance. Finally, the evolutionary origins of AGts that do not fall into GT Family 1 are discussed, suggesting that their ancestral proteins appear to be derived from various proteins responsible for primary metabolism. [Reviewing Editor: Dr. Niles Lehman]     

Phylogenetic Analysis of Metabolic Pathways

The information provided by completely sequenced genomes can yield insights into the multi-level organization of organisms and their evolution. At the lowest level of molecular organization individual enzymes are formed, often through assembly of multiple polypeptides. At a higher level, sets of enzymes group into metabolic networks. Much has been learned about the relationship of species from phylogenetic trees comparing individual enzymes. In this article we extend conventional phylogenetic analysis of individual enzymes in different organisms to the organisms' metabolic networks. For this purpose we suggest a method that combines sequence information with information about the underlying reaction networks. A distance between pathways is defined as incorporating distances between substrates and distances between corresponding enzymes. The new analysis is applied to electron-transfer and amino acid biosynthesis networks yielding a more comprehensive understanding of similarities and differences between organisms. Received: 14 August 2000 / Accepted: 4 January 2001     

雷州地区马尾藻系统进化分析

通过PCR扩增测序及种间比对,对获得的6种马尾藻18SrRNA、COI和ITS基因部分同源序列进行分析,结果显示:(1)18S rRNA基因同源序列长度为1 673 bp,其中保守位点1 668个,可变位点3个,简约信息位点1个,单变异多态位点2个;T、C、A、G的平均含量分别为26.4％、21.4％、24.4％、27.8％.(2)COI同源序列长度为643 bp,其中保守位点567个,可变位点76个,简约信息位点28个,单变异多态位点47个;T、C、A、G的平均含量分别为40.0％、17.6％、19.1％、23.3％.(3)ITS同源序列长度为1 539 bp,其中保守位点1 272个,可变位点193个,简约信息位点55个,单变异多态位点138个;T、C、A、G的平均含量分别为23.5％、26.5％、17.1％、32.9％.(4)基于Kimnra双参数模型计算遗传距离,选用褐藻纲部分物种为外源,构建18S rRNA,COI和ITS基因序列系统发育树.用COI和ITS基因构建的发育树与利用形态学进行的分类较为一致,真马尾藻亚属(Sargassum)的张氏马尾藻(Sargassum zhangii)、全缘马尾藻(Sargassum integerrimum)、匍枝马尾藻(Sargassum polycystum)、亨氏马尾藻(Sargassum henslowianum)、灰叶马尾藻(Sargassum cinereum)亲缘关系较近,先聚为一支,再与反曲叶亚属的半叶马尾藻(Sargassum hemiphyllum)聚为一支,然后与其他亚属的聚为一大支;而用18S rRNA基因构建的发育树中,亨氏马尾藻先与半叶马尾藻聚为一支,后与真马尾藻亚属的聚为一支,最后与其他亚属的聚为一大支.从序列的保守度分析,18SrRNA基因具有高度保守性,可用于属以上单元鉴别分类;COI和ITS基因多态性较高,可用于种间分类.