Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers

The Nymphaeales (water-lilies and relatives) represent one of the earliest branching lineages of angiosperms and comprise about 70 aquatic species. Here, we present a comprehensive study of phylogenetic relationships within the Nymphaeales from a dataset containing 24 representatives of the order, including all currently recognized genera and all subgenera of the genus Nymphaea , plus 5 outgroup taxa. Nine different regions of the chloroplast genome − comprising spacers, group II introns, a group I intron, and a protein coding gene − were analysed. This resulted in a character matrix of 6597 positions and an additional 369 characters obtained from coded length mutations. Maximum parsimony and Bayesian analyses of the complete dataset yielded congruent, fully resolved and well-supported trees. Our data confirm the monophyly of the Cabombaceae but do not provide convincing support for the monophyly of Nymphaeaceae with respect to Nuphar . Moreover, the genus Nymphaea is inferred to be paraphyletic with respect to Ondinea , Victoria and Euryale . In fact, the Australian endemic Ondinea forms a highly supported clade with members of the Australian Nymphaea subgenus Anecphya . In addition, Victoria and Euryale are inferred to be closely related to a clade comprising all night-blooming water-lilies ( Nymphaea subgenera Hydrocallis and Lotos ). An experimental approach showed taxon sampling to be of influence on the nodes reconstructed in core Nymphaeaceae. The results underscore that more diverse genera, if not clearly known to be monophyletic, should be represented by all major lineages.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 141–163.     

Variation in the analysis of positively selected sites using nonsynonymous/synonymous rate ratios: an example using influenza virus

Sites in a gene showing the nonsynonymous/synonymous rate ratio (ω) >1 have been frequently identified to be under positive selection. To examine the performance of such analysis, sites of the ω ratio >1 in the HA1 gene of H3N2 subtype human influenza viruses were identified from seven overlapping sequence data sets in this study. Our results showed that the sites of the ω ratio >1 were of significant variation among the data sets even though they targeted similar clusters, indicating that the analysis is likely to be either of low sensitivity or of low specificity in identifying sites under positive selection. Most (43/45) of the sites showing ω >1 calculated from at least one data set are involved in B-cell epitopes which cover less than a half sites in the protein, suggesting that the analysis is likely to be of low sensitivity rather than of low specificity. It was further found that the analysis sensitivity could not be enhanced by including more sequences or covering longer time intervals. Previously some reports also likely identified only a portion of the sites under positive selection in the viral gene using the ω ratio. Low sensitivity of the analysis may result from that some sites under positive selection in the gene are also under negative (purifying) selection simultaneously for functional constrains, and so their ω ratios could be <1. Theoretically, the sites under the two opposite selection forces at the same time favor only certain nonsynonymous changes, e.g. those changing the antigenicity of the gene and maintaining the gene function. This study also suggested that sometimes we can identify more sites under positive selection using the ω ratio by integrating the positively selected sites estimated from multiple data sets.     

Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis

To identify fast-evolving genes in reef-building corals, we performed direct comparative sequence analysis with expressed sequence tag (EST) datasets from two acroporid species: Acropora palmata from the Caribbean Sea and A. millepora from the Great Barrier Reef in Australia. Comparison of 589 independent sequences from 1,421 A. palmata contigs, with 10,247 A. millepora contigs resulted in the identification of 196 putative homologues. Most of the homologous pairs demonstrated high amino acid similarities (over 90%). Comparisons of putative homologues showing low amino acid similarities (under 90%) among the Acropora species to the near complete datasets from two other cnidarians (Hydra magnipapillata and Nematostella vectensis) implied that some were non-orthologous. Within 86 homologous pairs, 39 exhibited dN/dS ratios significantly less than 1, suggesting that these genes are under purifying selection associated with functional constraints. Eight independent genes showed dN/dS ratios exceeding 1, while three deviated significantly from 1, suggesting that these genes may play important roles in the adaptive evolution of Acropora. Our results also indicated that CEL-III lectin was under positive selection, consistent with a possible role in immunity or symbiont recognition. Further studies are needed to clarify the possible functions of the genes under positive selection to provide insight into the evolutionary process of corals.     

Tracking changing environments using stable carbon isotopes in fossil tooth enamel: an example from the South African hominin sites

The environmental contexts of the karstic hominin sites in South Africa have been established largely by means of faunal associations; taken together these data suggest a trend from relatively closed and more mesic to open, drier environments from about 3 to 1.5 Ma. Vrba argued for a major shift within this trend ca. 2.4-2.6 Ma, an influential proposal that posited links between bovid (and hominin) radiation in Africa and the intensification of Northern Hemisphere Glaciation. Yet faunal approaches often rely on habitat and feeding preferences of modern taxa that may differ from those of their extinct predecessors. Here we explore ways of extending ¹³C/¹²C data from fossil mammals beyond denoting “presence” or “absence” of C₄ grasses using the evolution of open environments in South Africa as a case study. To do so we calculated the relative proportions of C₃-, mixed-, and C₄-feeding herbivores for all the hominin sites for which we have sufficient data based on ¹³C/¹²C analyses of fossil tooth enamel. The results confirm a general trend towards more open environments since 3 Ma, but they also emphasize a marked change to open grassy habitats in the latest Pliocene/early Pleistocene. Mean ¹³C/¹²C for large felids also mirrored this trend.     

Identifying complementary areas for conservation in Thailand: an example using owls, hawkmoths and tiger beetles

Setting priorities in biodiversity conservation requires that explicit, efficient and appropriate methods are developed and made available to conservation managers. The principle of complementarity is fundamental to the most efficient of these methods. Given a goal of only a single representation of each taxon, complementarity analysis of data sets of owls, hawkmoths and tiger beetles in Thailand yields near-minimum sets of 6, 14 and 34 areas, respectively. The consensus of these sets comprises 48 areas. However, when the data are combined into a single data set, complementarity analysis gives a more efficient solution of 46 areas. Over 90% of the owls, hawkmoths and tiger beetles are already represented as a minimum of one population within the current protected areas network of Thailand. However, an additional 18 areas are still required for complete representation. Several of these additional areas are discussed and their potential contribution to biodiversity conservation in Thailand examined. Khao Pok Yo and Doi Pa Hom Pok are noted as being of particular importance. The case of Sanpatong emphasizes the need to remain aware of the biology and ecology of the species under study.     

Identifying potential keystone species from field data – an example from temporary ponds

Identifying keystone species is essential for understanding community dynamics and preserving species richness. However, few studies have used quantitative, a priori methods to identify potential keystone species. Species known to act as keystones in North Carolina (NC) temporary ponds ( Notophthalmus viridescens , eastern newt, and Siren intermedia , lesser siren) were tested to see whether they played the same role in similar habitats in South Carolina (SC). Newts and sirens had no effect on anuran species richness in SC. Instead, another salamander ( Ambystoma talpoideum , mole salamander) absent from the NC ponds was identified as a strong keystone in SC. It functioned independently of environmental factors and the densities of other predators. Larval dragonflies ( Tramea carolina , Carolina saddlebag) were identified as weak, context-dependent keystones in SC, supporting anuran richness in isolated ponds with very low pH. The results suggest that the identity of keystone species varies, even in similar habitats within a physiographic region.     

iRNA-Methyl: Identifying N-methyladenosine sites using pseudo nucleotide composition

Occurring at adenine (A) with the consensus motif GAC, N⁶-methyladenosine (m⁶A) is one of the most abundant modifications in RNA, which plays very important roles in many biological processes. The nonuniform distribution of m⁶A sites across the genome implies that, for better understanding the regulatory mechanism of m⁶A, it is indispensable to characterize its sites in a genome-wide scope. Although a series of experimental technologies have been developed in this regard, they are both time-consuming and expensive. With the avalanche of RNA sequences generated in the postgenomic age, it is highly desired to develop computational methods to timely identify their m⁶A sites. In view of this, a predictor called “iRNA-Methyl” is proposed by formulating RNA sequences with the “pseudo dinucleotide composition” into which three RNA physiochemical properties were incorporated. Rigorous cross-validation tests have indicated that iRNA-Methyl holds very high potential to become a useful tool for genome analysis. For the convenience of most experimental scientists, a web-server for iRNA-Methyl has been established at http://lin.uestc.edu.cn/server/iRNA-Methyl by which users can easily get their desired results without needing to go through the mathematical details.     

Stromatolites and basin analysis: an example from the upper proterozoic of northwestern Canada

Stromatolites have been used for inter-basinal biostratigraphic correlation, rock-stratigraphic correlation within individual sedimentary basins and for palaeoecological studies of various kinds. In the northern part of Victoria Island stromatolites are abundant in the uppermost part of the Gelenelg Formation, which is the lowest unit of the upper Proterozoic Shaler Group. Measurable attributes of these stromatolites include elongate mounds, intermound channel fillings, ridges and grooves, elongate collumns and inclined columns. In a widespread stromatolitic bank that forms the upper part of the Glenelg Formation, and also in stromatolites of the overlying Reynolds Point Formation, several of these features show a preferred orientation in a northeasterly direction. Herringbone cross-beds in associated sandy oolitic limestones show a northeast—southwest bimodal-bipolar distribution that is probably related to tidal activity. This similarity of directional features suggests that the stromatolite orientations are also likely to have been tidally influenced. If each stromatolitic bank were deposited diachronously then the northeasterly preferred orientation may be explained as being due to tidal currents active at a migrating shoreline that trended in a northwest-southeast direction. Alternatively, if, in the absence of metazoan competitors, the stromatolite builders contemporaneously occupied a large part of the basin floor, their northeasterly orientation may reflect tidal currents parallel to the length of an elongate embayment of the Precambrian sea, analogous in many ways to the present-day Persian Gulf. Such an interpretation, involving parallelism between coastline and elongate stromatolites, would differ from those of most earlier reports, in which elongate stromatolites have generally been assumed to have been oriented normal to the ancient shoreline.     

Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial,exon and intron fragments

Background  

The number of rodent clades identified above the family level is contentious, and to date, no consensus has been reached on the basal evolutionary relationships among all rodent families. Rodent suprafamilial phylogenetic relationships are investigated in the present study using ~7600 nucleotide characters derived from two mitochondrial genes (Cytochrome b and 12S rRNA), two nuclear exons (IRBP and vWF) and four nuclear introns (MGF, PRKC, SPTBN, THY). Because increasing the number of nucleotides does not necessarily increase phylogenetic signal (especially if the data is saturated), we assess the potential impact of saturation for each dataset by removing the fastest-evolving positions that have been recognized as sources of inconsistencies in phylogenetics.     

Identifying chromosomal fragile sites from individuals: a multinomial statistical model

The inability to identify fragile sites from data for single individuals remains the major obstacle to determining whether these chromosomal loci are predisposed to cancer-causing and evolutionary rearrangements. We describe a novel statistical model that is amenable to data from single individuals and that establishes site-specific chromosomal breakage as nonrandom with respect to the distribution of total breakage. Our method tests incrementally smaller subsets of the data for homogeneity under a multinomial model that assigns equal probabilites to a maximal set of nonfragile sites and unrestricted probabilities to the remaining fragile sites with significantly higher numbers of breaks. We show how standardized Pearson's chi-square (X ²) and likelihood-ratio (G ²) statistics can be appropriately used to measure goodness-of-fit for sparse contingency (individual-based) data in this model. A sample application of this approach indicates extensive variation in fragile sites among individuals and marked differences in fragile-site inferences from pooled as opposed to per-individual data.     

Phylofloristics: an example from the Lesser Antilles

Aims The last decade has seen many plant ecologists integrating phylogenetic analysis into ecology to explain patterns of species co-occurrence and compositional similarity across assemblages. Despite the advances in this area, there are still some challenges that need to be addressed. One challenge is that most of the phylogenetic studies of plant assemblages have focused only on a small proportion of all of the vascular plants that co-occur (e.g. woody plants), while much of the remaining co-occurring flora has been ignored.Methods Here we introduce an analytical approach that we term phylofloristics that analyzes the compositional similarity of floras in relation to spatial and environmental gradients to understand their assembly. As an illustration, we assembled a large phylogenetic tree for the flora of the Lesser Antilles and evaluated the patterns of floristic and phylofloristic similarity among the island-specific floras. We analyzed the relationship of these similarities with spatial and environmental distance and compared the results for non-endemic and endemic lineages.Important findings The results show a major influence of environmental heterogeneity on the assembly of island floras and far less evidence for the importance of dispersal limitation of lineages and species. This study highlights the importance of incorporating broader taxonomic sampling to improve our understanding of assembly processes in ecology. We expect future phylofloristic studies will improve the approach we have taken by generating more refined phylogenetic trees and by incorporating phylogeographic information.     

Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles

Recently, as genome-scale data have become available for more organisms, the development of phylogenetic markers from nuclear protein-coding loci (NPCL) has become more tractable. However, new methods are needed to efficiently sort the large number of genes from genomic databases into more limited sets appropriate for particular phylogenetic questions, while avoiding introns and paralogs. Here we describe a general methodology for identifying candidate single-copy NPCL from genomic databases. Our method uses information from reference genomes to identify genes with relatively large continuous protein-coding regions (i.e., 700bp). BLAST comparisons are used to help avoid genes with paralogous copies or close relatives (i.e., gene families) that might confound phylogenetic analyses. Exon boundary information is used to identify appropriately spaced potential priming sites. Using this method, we have developed over 25 novel NPCL, which span a variety of desirable evolutionary rates for phylogenetic analyses. Although targeted for higher-level phylogenetics of squamate reptiles, many of these loci appear to be useful across and within other vertebrate clades (e.g., amphibians), and some are relatively rapidly evolving and may be useful for closely-related species (e.g., within genera). This general method can be used whenever large-scale genomic data are available for an appropriate reference species (not necessarily within the focal clade). The method is also well suited for the development of intron regions for lower-level phylogenetic and phylogeographic studies. We provide an online database of alignments and suggested primers for approximately 85 NPCL that should be useful across vertebrates.     

Data decisiveness,data quality,and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences

We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.     

iProtGly‐SS: Identifying protein glycation sites using sequence and structure based features

Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly‐SS, a protein lysine glycation site identification method based on features extracted from sequence and secondary structural information. In the experiments, we found the best feature groups combination: Amino Acid Composition, Secondary Structure Motifs, and Polarity. We used support vector machine classifier to train our model and used an optimal set of features using a group based forward feature selection technique. On standard benchmark datasets, our method is able to significantly outperform existing methods for glycation prediction. A web server for iProtGly‐SS is implemented and publicly available to use: http://brl.uiu.ac.bd/iprotgly-ss/ .     

“山水林田湖草生命共同体”要素关联性分析——以长白山地区为例

对“山水林田湖草生命共同体”各要素相互关系的深入理解是对其实行保护、系统治理的重要基础。本研究以长白山地区为研究对象,利用空间叠置分析法定量分析该地区“山水林田湖草生命共同体”各要素间的关联性,解构各要素的关系以及相互影响程度,并量化其依存关系。研究结果显示：研究区内各市人口数量、城镇面积与耕地面积呈显著正相关关系（人口数量：R²=0.789,P < 0.05; 城镇面积：R²=0.863,P < 0.05）;耕地的分布与地表水体的分布具有较高的空间相关性（r=0.812）,两者的数量关系也呈显著正相关（R²=0.96,P < 0.01）;区内河流分布、土壤类型与地形、地貌密切相关;区内各市水土流失面积与其森林覆盖率呈显著线性负相关关系（R²=0.824,P < 0.05）。由此可见,6个要素之间存在很明显的依存关系。因此,长白山地区“山水林田湖草生命共同体”的保护与修复应该重视各要素之间的联系,针对其系统性和整体性特征实施相应的保护和治理。     

Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data

Understanding the evolution of gene function is a primary challenge of modern evolutionary biology. Despite an expanding database from genomic and developmental studies, we are lacking quantitative methods for analyzing the evolution of some important measures of gene function, such as gene-expression patterns. Here, we introduce phylogenetic comparative methods to compare different models of gene-expression evolution in a maximum-likelihood framework. We find that expression of duplicated genes has evolved according to a nonphylogenetic model, where closely related genes are no more likely than more distantly related genes to share common expression patterns. These results are consistent with previous studies that found rapid evolution of gene expression during the history of yeast. The comparative methods presented here are general enough to test a wide range of evolutionary hypotheses using genomic-scale data from any organism.     

Rooting phylogenies using gene duplications: an empirical example from the bees (Apoidea)

The placement of the root node in a phylogeny is fundamental to characterizing evolutionary relationships. The root node of bee phylogeny remains unclear despite considerable previous attention. In order to test alternative hypotheses for the location of the root node in bees, we used the F1 and F2 paralogs of elongation factor 1-alpha (EF-1α) to compare the tree topologies that result when using outgroup versus paralogous rooting. Fifty-two taxa representing each of the seven bee families were sequenced for both copies of EF-1α. Two datasets were analyzed. In the first (the "concatenated" dataset), the F1 and F2 copies for each species were concatenated and the tree was rooted using appropriate outgroups (sphecid and crabronid wasps). In the second dataset (the "duplicated" dataset), the F1 and F2 copies were aligned to each another and each copy for all taxa were treated as separate terminals. In this dataset, the root was placed between the F1 and F2 copies (e.g., paralog rooting). Bayesian analyses demonstrate that the outgroup rooting approach outperforms paralog rooting, recovering deeper clades and showing stronger support for groups well established by both morphological and other molecular data. Sequence characteristics of the two copies were compared at the amino acid level, but little evidence was found to suggest that one copy is more functionally conserved. Although neither approach yields an unambiguous root to the tree, both approaches strongly indicate that the root of bee phylogeny does not fall near Colletidae, as has been previously proposed. We discuss paralog rooting as a general strategy and why this approach performs relatively poorly with our particular dataset.