Phylogeny of Saururaceae Inferred from matR Sequence Data

基于线粒体matR 基因序列初步探讨三白草科的系统发育 孟少武¹ 陈之端²李德铢¹梁汉兴¹      

Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence Data

Abstract: The nuclear LSU rRNA gene was examined in order to evaluate the current phylogeny of ascomycetes, which is mainly based on nuclear SSU rRNA data. Partial LSU rRNA gene sequences of 19 ascomycetes were determined and aligned with the corresponding sequences of 13 other ascomycetes retrieved from Genbank, including all classes traditionally distinguished and most of the recently accepted classes. The classification based on SSU rDNA data and morphological characters is supported, while the traditional classification and classifications based on the ascus type are rejected. Ascomycetes with perithecia and cleistothecia form monophyletic groups, while the discomycetes are a paraphyletic assemblage. The Pezizales are basal to all other filamentous ascomycetes. The monophyly of Loculoascomycetes is uncertain. The results of the LSU rDNA analysis agree with those of the SSU rDNA and RPB2 gene analyses, suggesting that most classes circumscribed in the filamentous ascomycetes are monophyletic. The branching order and relationships among these classes, however, cannot be elucidated with any of these data sets.     

基于matR基因序列分析的山茶科系统关系

通过线粒体matR基因序列分析探讨了山茶科的分类学范围和系统演化关系。结果显示,传统山茶科的两个核心——山茶亚科（Theoideae或Camellioideae）和厚皮香亚科（Ternstroemioideae）不构成姐妹群关系,山茶亚科是一个支持率很高的单系类群,厚皮香亚科没有形成单系;山茶亚科下可区分出3个明显的分支,基部的分支由紫茎属（Stewartia）和舟柄茶属（Hartia）组成,木荷属（Schima）、美洲荷属（Franklirda）和美国大头茶属（Gordonia）构成第2个分支,该分支与由山茶属（Camellia）、核果茶属（Pyrenaria）、多瓣核果茶属（Parapyrenaria）、石笔木属（Tutcheria）、大头荣属（Polyspora）和圆籽荷属（Aptersperma）组成的第3个分支互为姐妹群。研究结果很好地支持了Prince和Parks等学者提出的的狭义山茶科（仅含山茶亚科）和狭义大头茶属的概念以及科下3个族（紫茎族Stewartieae、大头茶族Gordonieae和山茶族Theeae）的划分。但本研究更为清晰地揭示了科下3个族间的系统关系,即紫茎族是最基部的分支,山茶族与大头茶族间有更近的亲缘关系。同时,本文认为,厚皮香（亚）科是否为单系类群值得进一步研究。     

Evolution of the Gibbon Subgenera Inferred from CytochromebDNA Sequence Data

DNA sequences for the mitochondrial cytochromebgene from the four extant gibbon subgenera are described. The data confirm that the gibbon subgenera evolved from a common hylobatid ancestor and suggest that they diverged from each other after the divergence of the extant African great ape species. The cytochromebgene does not resolve the evolutionary relationships between the gibbon subgenera themselves.     

中国柽柳属和水柏枝属的分子系统学研究

对中国柽柳科 3属 2 1种植物的核糖体DNA中的内转录间隔区 (ITS)序列及 5 8SrRNA基因的 3′端序列进行测定。结果表明 ,ITS - 1片段的长度范围在 2 5 4bp～ 2 6 9bp之间 ,ITS - 2片段的长度范围在 2 2 5bp～ 2 5 3bp之间。以Reaumuriasongarica作为功能性外类群 ,运用PAUP软件分析仅得到一个最简约树。简约树步长为 4 6 6步 ,一致性指数CI =0 85 84 ,保持性指数RI=0 86 2 2。系统发育分析表明 :秀丽水柏枝不应从水柏枝属中分出。另外 ,研究分析为目前分类上存有争议的白花柽柳、短毛柽柳及甘蒙柽柳的划分提供了分子生物学证据     

应用ITS序列分析新疆濒危植物盐桦的系统发育

目的:依据ITS序列分析新疆濒危植物盐桦的系统发育.方法:运用PCR直接测序法,对珍稀濒危植物盐桦(Betulahalophila)的nrDNA的ITS区(包括ITS-1,5.8SrDNA和ITS-2)进行序列测定,并与GenBank中提取的17种桦木科桦木属植物的ITS区序列进行了组合分析.结果:盐桦的ITS序列和已公布的17种桦木科桦木属植物的ITS区序列差别不大,同源性在99.67%～99.01%之间.采用clustalx软件对盐桦和17种桦木属植物的ITS区序列进行系统发育分析,构建了桦木属植物的ITS分子系统树,18种桦木科桦木属植物形成三个分支,盐桦与Betula alnoides、Betula populifolia、Betula pubescens同为一支.结论:盐桦在桦木科桦木属内有独特的分类地位.     

Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts

Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic data sets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study.     

Phylogenetic Relations among Percid Fishes as Inferred from Mitochondrial CytochromebDNA Sequence Data

Hypotheses of relationship among genera of Percidae have been conflicting. Based on different phylogenetic premises, the evolution of small benthic forms in Percidae has been interpreted as resulting from either convergence or common ancestry. In order to assess various phylogenetic hypotheses of Percidae we collected complete sequences (1140 bp) of mitochondrially encoded cytochromebfor 21 species of percids. Seven species representing four additional families of Perciformes were used as outgroups. Maximum parsimony and minimum evolution analyses both recovered single shortest trees, and the results of these analyses were generally congruent with one another. All analyses consistently recovered three monophyletic groups in Percidae: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma,andPercina), Percinae (PercaandGymnocephalus), and Luciopercinae (Stizostedion, Zingel,andRomanichthys). As a result of this analysis we present a revised classification of Percidae and discuss the phylogenetic evidence for the independent evolution of small benthic species within Etheostomatinae and Luciopercinae.     

Polymorphism Data Can Reveal the Origin of Species Abundance Statistics

What is the underlying mechanism behind the fat-tailed statistics observed for species abundance distributions? The two main hypotheses in the field are the adaptive (niche) theories, where species abundance reflects its fitness, and the neutral theory that assumes demographic stochasticity as the main factor determining community structure. Both explanations suggest quite similar species-abundance distributions, but very different histories: niche scenarios assume that a species population in the past was similar to the observed one, while neutral scenarios are characterized by strongly fluctuating populations. Since the genetic variations within a population depend on its abundance in the past, we present here a way to discriminate between the theories using the genetic diversity of noncoding DNA. A statistical test, based on the Fu-Li method, has been developed and enables such a differentiation. We have analyzed the results gathered from individual-based simulation of both types of histories and obtained clear distinction between the Fu-Li statistics of the neutral scenario and that of the niche scenario. Our results suggest that data for 10–50 species, with approximately 30 sequenced individuals for each species, may allow one to distinguish between these two theories.     

Assessing SSU rDNA Barcodes in Foraminifera: A Case Study using Bolivina quadrata

The Small Subunit Ribosomal RNA gene (SSU rDNA) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina, with particular emphasis on Bolivina quadrata for which ten new sequences ( KY468817 – KY468826 ) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e. genus).     

Gravel Bars Can Be Critical for Biodiversity Conservation: A Case Study on Scaly-Sided Merganser in South China

Gravel bars are characteristic components of river landscapes and are increasingly recognized as key sites for many waterbirds, though detailed studies on the ecological function of gravel bars for waterbirds are rare. In this study, we surveyed the endangered Scaly-sided Merganser Mergus squamatus along a 40 km river section of Yuan River, in Central China, for three consecutive winters. We derived the landscape metrics of river gravel bars from geo-rectified fine resolution (0.6 m) aerial image data. We then built habitat suitability models (Generalized Linear Models—GLMs) to study the effects of landscape metrics and human disturbance on Scaly-sided Merganser presence probability. We found that 1) the Scaly-sided Merganser tended to congregate at river segments with more gravel patches; 2) the Scaly-sided Merganser preferred areas with larger and more contiguous gravel patches; and 3) the number of houses along the river bank (a proxy for anthropogenic disturbance) had significantly negative impacts on the occurrence of the Scaly-sided Merganser. Our results suggest that gravel bars are vital to the Scaly-sided Merganser as shelters from disturbance, as well as sites for feeding and roosting. Therefore, maintaining the exposure of gravel bars in regulated rivers during the low water period in winter might be the key for the conservation of the endangered species. These findings have important implications for understanding behavioral evolution and distribution of the species and for delineating between habitats of different quality for conservation and management.     

Rosin Surfactant QRMAE Can Be Utilized as an Amorphous Aggregate Inducer: A Case Study of Mammalian Serum Albumin

Quaternary amine of diethylaminoethyl rosin ester (QRMAE), chemically synthesized biocompatible rosin based cationic surfactant, has various biological applications including its use as a food product additive. In this study, we examined the amorphous aggregation behavior of mammalian serum albumins at pH 7.5, i.e., two units above their isoelectric points (pI ~5.5), and the roles played by positive charge and hydrophobicity of exogenously added rosin surfactant QRMAE. The study was carried out on five mammalian serum albumins, using various spectroscopic methods, dye binding assay, circular dichroism and electron microscopy. The thermodynamics of the binding of mammalian serum albumins to cationic rosin modified surfactant were established using isothermal titration calorimetry (ITC). It was observed that a suitable molar ratio of protein to QRMAE surfactant enthusiastically induces amorphous aggregate formation at a pH above two units of pI. Rosin surfactant QRMAE-albumins interactions revealed a unique interplay between the initial electrostatic and the subsequent hydrophobic interactions that play an important role towards the formation of hydrophobic interactions-driven amorphous aggregate. Amorphous aggregation of proteins is associated with varying diseases, from the formation of protein wine haze to the expansion of the eye lenses in cataract, during the expression and purification of recombinant proteins. This study can be used for the design of novel biomolecules or drugs with the ability to neutralize factor(s) responsible for the aggregate formation, in addition to various other industrial applications.     

Estimating Allee Dynamics before They Can Be Observed: Polar Bears as a Case Study

Allee effects are an important component in the population dynamics of numerous species. Accounting for these Allee effects in population viability analyses generally requires estimates of low-density population growth rates, but such data are unavailable for most species and particularly difficult to obtain for large mammals. Here, we present a mechanistic modeling framework that allows estimating the expected low-density growth rates under a mate-finding Allee effect before the Allee effect occurs or can be observed. The approach relies on representing the mechanisms causing the Allee effect in a process-based model, which can be parameterized and validated from data on the mechanisms rather than data on population growth. We illustrate the approach using polar bears (Ursus maritimus), and estimate their expected low-density growth by linking a mating dynamics model to a matrix projection model. The Allee threshold, defined as the population density below which growth becomes negative, is shown to depend on age-structure, sex ratio, and the life history parameters determining reproduction and survival. The Allee threshold is thus both density- and frequency-dependent. Sensitivity analyses of the Allee threshold show that different combinations of the parameters determining reproduction and survival can lead to differing Allee thresholds, even if these differing combinations imply the same stable-stage population growth rate. The approach further shows how mate-limitation can induce long transient dynamics, even in populations that eventually grow to carrying capacity. Applying the models to the overharvested low-density polar bear population of Viscount Melville Sound, Canada, shows that a mate-finding Allee effect is a plausible mechanism for slow recovery of this population. Our approach is generalizable to any mating system and life cycle, and could aid proactive management and conservation strategies, for example, by providing a priori estimates of minimum conservation targets for rare species or minimum eradication targets for pests and invasive species.     

Molecular Phylogeny of the Suborder Leucodontineae (Musci; Leucodontales) Inferred from rbcL Sequence Data

rbcL sequence data (1324 bp on average). Our analyses indicate (1) that Antitrichia is distantly related to the other members of Leucodontaceae and should be excluded from the family, (2) that Cryphaeaceae form a monophyletic clade, not with Anomodontaceae and Leptodontaceae, but with Leucodontaceae, refuting the placement of Leucodontaceae and Cryphaeaceae in different superfamilies, (3) that Forsstroemia, variously classified in Leucodontaceae, Cryphaeaceae or Leptodontaceae, forms a monophyletic clade with Neckera (Neckeraceae), and (4) that the presumed monophyly of Anomodon and that of Anomodontaceae are not supported. Received 18 September 1999/ Accepted in revised form 27 December 1999     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了15种杜鹃属(Rhododendron)植物、1种杜香属(Ledum)植物和Cassiope fastigiata的内转录间隔区(ITS) (包括5.8S)序列.加上从GenBank下载的13种杜鹃属植物和Bajiaria racemosa的ITS序列,以C. fastigiata和B. racemosa为外类群,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析.结果表明: 1)杜鹃属是一个单系类群,叶状苞亚属为杜鹃属的基部类群; 2)杜香属确应归并到杜鹃属中,且与有鳞杜鹃亚属有较近的亲缘关系; 3)有鳞杜鹃亚属和杜香构成一个单系分支,该分支是其余无鳞杜鹃花的姐妹群; 4)由无鳞杜鹃花组成的一个分支的内部支持率较低,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群,而羊踯躅亚属和马银花亚属均为多系类群; 5)在马银花亚属中,长蕊杜鹃组和马银花组均分别得到强烈支持,马银花组与异蕊杜鹃亚属可能构成姐妹群关系,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系.     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了 15种杜鹃属 (Rhododendron)植物、1种杜香属 (Ledum)植物和Cassiopefastigiata的内转录间隔区(ITS) (包括 5 .8S)序列。加上从GenBank下载的 13种杜鹃属植物和Bajiariaracemosa的ITS序列 ,以C .fastigiata和B .racemosa为外类群 ,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析。结果表明 :1)杜鹃属是一个单系类群 ,叶状苞亚属为杜鹃属的基部类群 ;2 )杜香属确应归并到杜鹃属中 ,且与有鳞杜鹃亚属有较近的亲缘关系 ;3)有鳞杜鹃亚属和杜香构成一个单系分支 ,该分支是其余无鳞杜鹃花的姐妹群 ;4 )由无鳞杜鹃花组成的一个分支的内部支持率较低 ,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群 ,而羊踯躅亚属和马银花亚属均为多系类群 ;5 )在马银花亚属中 ,长蕊杜鹃组和马银花组均分别得到强烈支持 ,马银花组与异蕊杜鹃亚属可能构成姐妹群关系 ,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系。     

Phylogenetic Analyses of Trichodinids (Ciliophora, Oligohymenophora) Inferred from 18S rRNA Gene Sequence Data

Partial 18S rRNA gene sequences of the three trichodinids, namely Trichodina modesta Lom, 1970, Trichodina paraheterodentata Tang and Zhao 2012. and Trichodinella epizootica (Raabe 1950) ?rámek-Hu?ek, 1953, were acquired and used to construct phylogenetic trees. The results revealed that Trichodinella epizootica clustered with Trichodinella sp.; Trichodina paraheterodentata Tang and Zhao 2012 was sister to the clade composed of Trichodina heterodentata Duncan, 1977 and Trichodina nobilis Chen, 1963; Trichodina modesta Lom, 1970 clustered with Trichodina reticulata Hirschman and Partsch, 1955. The branching order of species within the Mobilia clade was closely correlated with GC content. Furthermore, blade morphology was also found to be the primary morphological character in determining the phylogenetic relationships among members of the genus Trichodina. The present findings suggest that the genus Trichodina is paraphyletic when species of Trichodinella are included in the analyses.     

5S rRNA Gene Arrangements in Protists: A Case of Nonadaptive Evolution

Given their high copy number and high level of expression, one might expect that both the sequence and organization of eukaryotic ribosomal RNA genes would be conserved during evolution. Although the organization of 18S, 5.8S and 28S ribosomal RNA genes is indeed relatively well conserved, that of 5S rRNA genes is much more variable. Here, we review the different types of 5S rRNA gene arrangements which have been observed in protists. This includes linkages to the other ribosomal RNA genes as well as linkages to ubiquitin, splice-leader, snRNA and tRNA genes. Mapping these linkages to independently derived phylogenies shows that these diverse linkages have repeatedly been gained and lost during evolution. This argues against such linkages being the primitive condition not only in protists but also in other eukaryote species. Because the only characteristic the diverse genes with which 5S rRNA genes are found linked with is that they are tandemly repeated, these arrangements are unlikely to provide any selective advantage. Rather, the observed high variability in 5S rRNA genes arrangements is likely the result of the fact that 5S rRNA genes contain internal promoters, that these genes are often transposed by diverse recombination mechanisms and that these new gene arrangements are rapidly homogenized by unequal crossingovers and/or by gene conversions events in species with short generation times and frequent founder events.     

Worldwide Distribution Patterns of the Planktonic Shelled Protists Radiolaria (Polycystina) and Foraminifera: Similarities and Contrasts

Paleontological Journal - Planktonic Foraminifera and Polycystina (Radiolaria) depict roughly similar—but not identical—worldwide distribution patterns. Discrepancies affect both cold-...     

A Cladistic Analysis of Phenotypic Associations with Haplotypes Inferred from Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation

We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.