Choosing among alternative trees of multigene families

Estimation of gene trees is the first step in testing alternative hypotheses about the evolution of multigene families. The standard practice for inferring gene family history is to construct trees that meet some objective criteria based on the fit of the character state changes (nucleotide or amino acid changes) to the gene tree. Unfortunately, analysis of character state data can be misleading. In addition, this approach ignores information about the relationships of the species from which the genes have been sampled. In this paper I explore using statistics of fit between the character data and gene trees and the reconciliation of the gene and species trees for choosing among alternative evolutionary hypotheses of gene families. In particular, I advocate a two-pronged strategy for choosing among alternative gene trees. First, the character data are used to define a set of acceptable gene trees (i.e., trees that are not significantly different from the minimum length tree). Next, the set of acceptable gene trees is reconciled with a known species tree, and the gene tree requiring the fewest number of gene duplications and losses is adopted as the best estimate of evolutionary history. The approach is illustrated using three gene families: BMP, EGR, and LDH.     

phyloXML: XML for evolutionary biology and comparative genomics

Background  

Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types.     

Impact of Phyllocnistis citrella (Lepidoptera: Gracillariidae) on leaf area development and yield of mature citrus trees in the Mediterranean area

Seasonal population trends and damage to citrus trees by the leafminer Phyllocnistis citrella Stainton were studied in the Valencia area of eastern Spain from 1996 to 1999. The area-wide seasonal flushing pattern of citrus trees and leafminer population trends were determined in 10 mature citrus orchards. In the 10 orchards, the annual percentage of new shoots that developed in the spring ranged from 51 to 96% for individual orchards (mean of 80%). Phyllocnistis citrella populations damaged new leaves from July to November. During this period, approximately 45% of the new leaf area was lost due to leafminer mining. In addition, at three mature citrus orchards, two 'Navelina' sweet oranges from 1996 to 1999 and one 'Clementine' mandarin (variety 'Clemenules') in 1998 and 1999, the leaf area damage, spring flushing pattern, and crop yield were determined in trees sprayed one to three times a year with abamectin (Epimeck, 0.02%) to control P. citrella and compared with nonsprayed control trees. In these three orchards, damaged leaf area in summer-fall flushes was on average 52% in nonsprayed and 8% in sprayed trees. No significant differences were found between sprayed and nonsprayed trees in the spring flushing and flowering pattern, number of fruits or fruit diameter. In Mediterranean areas, P. citrella damaged only 5-15% of the annual new leaf area of mature trees and yield was usually not affected by the pest.     

A mast fruiting episode of the tropical tree Peltogyne purpurea (Caesalpinaceae) in the Osa Peninsula, Costa Rica

The existence of mast fruiting has not been well documented in the Neotropics. The occurrence of a mast fruiting episode in the population of the tree Peltogyne purpurea in the Osa Peninsula of Costa Rica is described. In February and March of 2000 most of the trees of this species produced a large fruit crop, compared with 1995-1999, when the number of fruit producing trees was very low or zero and those that did bear fruit, did so at a low intensity. In contrast, the fruit crop of 2000 was massive, all trees examined produced fruits and the intensity of fruiting was maximal. There is not enough information on the event for a hypothesis to be formed because the climatic or biological cues that triggered this sporadic flowering are unknown and there is no meteorological data available for this area. Populations with this mode of reproduction may experience local extinction bacause of logging operations.     

Groundwater Capture Using Hybrid Poplar Trees: Evaluation of a System in Ogden,Utah

A phytoremediation system was installed in 1996 in Ogden, Utah, with the objective of controlling groundwater containing petroleum hydrocarbons. Hybrid poplar trees were deeply and densely planted in rows oriented perpendicular to the direction of groundwater flow, and the stand was never irrigated. Piezometers were installed to measure water table elevation and contaminant levels upgradient, within, and down-gradient of the trees. In 1998, an analysis of the root structure of a representative tree indicated that roots had extended down to the saturated zone, approximately 6 ft below ground surface. The rate of water use by the stand during 1998 was estimated from reference evapotranspiration (ET_o), leaf area, and a water use multiplication factor ($tH) specific to poplar trees. Sap velocity data were collected to measure actual water use by the stand in late summer of 1998. Estimated and measured values compared favorably, with measured values averaging 2.8 gallons day^-1 tree^-1 (1.7 mm day^-1 tree^-1). Water use by the stand in 1999 averaged an estimated 445 gallons day^-1 (6.9 mm day^-1 for the stand). Although the trees transpired a volume of water equivalent to a 10-ft thickness of the saturated zone, water table elevation data collected in 1999 did not indicate a depression in the water table.     

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

The desire to infer the evolutionary history of a group of species should be more viable now that a considerable amount of multilocus molecular data is available. However, the current molecular phylogenetic paradigm still reconstructs gene trees to represent the species tree. Further, commonly used methods of combining data, such as the concatenation method, are known to be inconsistent in some circumstances. In this paper, we propose a Bayesian hierarchical model to estimate the phylogeny of a group of species using multiple estimated gene tree distributions, such as those that arise in a Bayesian analysis of DNA sequence data. Our model employs substitution models used in traditional phylogenetics but also uses coalescent theory to explain genealogical signals from species trees to gene trees and from gene trees to sequence data, thereby forming a complete stochastic model to estimate gene trees, species trees, ancestral population sizes, and species divergence times simultaneously. Our model is founded on the assumption that gene trees, even of unlinked loci, are correlated due to being derived from a single species tree and therefore should be estimated jointly. We apply the method to two multilocus data sets of DNA sequences. The estimates of the species tree topology and divergence times appear to be robust to the prior of the population size, whereas the estimates of effective population sizes are sensitive to the prior used in the analysis. These analyses also suggest that the model is superior to the concatenation method in fitting these data sets and thus provides a more realistic assessment of the variability in the distribution of the species tree that may have produced the molecular information at hand. Future improvements of our model and algorithm should include consideration of other factors that can cause discordance of gene trees and species trees, such as horizontal transfer or gene duplication.     

<Emphasis Type="Italic">Borrelia lusitaniae</Emphasis> OspA Gene Heterogeneity in Mediterranean Basin Area

In this study, Borrelia lusitaniae DNA extracted from ticks and lizards was used to amplify the outer surface protein A (OspA) gene in order to increase knowledge about sequence variability in the Mediterranean basin area, to better understand how Borrelia lusitaniae has evolved and how its distribution has expanded. Phylogenetic trees including Italian and reference sequences showed a clear separation of B. lusitaniae OspA strains in two different major clades. North African isolates form a clade with Portuguese POTIB strains, whereas Italian samples are grouped with German strains and a human Portuguese strain. This subdivision was supported by very high posterior probability values in the trees, by both analysis of molecular variance and selective pressure. These results, based on phylogenetic information contained in the OspA gene sequences, show the presence of two different B. lusitaniae strains circulating in the Mediterranean basin area, suggesting two different evolution paths.     

The Potential Impact of An Introduced Shrub on Native Plant Diversity and Forest Regeneration

Over a period of 20 years, Chinese privet, Ligustrum sinense, invaded a mixed hardwood forest in western North Carolina, USA. The invasion penetrated about 30m under the canopy trees, providing 100% cover of the forest floor. Under the privets and in a nearby privet-poor reference area we marked off twenty, one square meter plots with string. All plants in each square meter of both areas were tallied in the spring of 1999 and young trees less than 1m high were again counted in September. We removed privets of the invaded area in November and again tallied all plants in both areas the following spring of 2000. In the spring of 1999, the mean number of herb species per square meter under the privet was 41%, and stem counts 75% less than in the reference area. 42% of herb species found in the reference area were missing under the privet. After removing the privets in the fall of 1999, the number of both native species and stems increased in the privet area the following spring. Plots of density of two native plants against privet density showed both native plants decreasing under increasing privet cover. In the spring of 1999, there were 4 species and 274 stems of tree seedlings in the privet area. In September of that year, we found only one small American holly tree, a highly shade-tolerant species, remaining under the privet. Our data support the thesis that Chinese privet can severely reduce herbaceous species and almost completely suppress tree regeneration in a mixed hardwood forest.     

Vegetative and generative dispersal capacity of field released transgenic aspen trees

Transfer of genes by pollen or wind-dispersed seed is considered a main potential risk when field release experiments with transgenic trees are initiated. In Germany, the first release experiment with genetically transformed trees was initiated in 1996. To ensure that the transgenic trees remained in the vegetative phase, the duration of the experiment was limited to 5 years. In total, 457 1-year-old trees including eight transgenic aspen lines carrying either the 35S- rolC or the rbcS- rolC gene construct, and three control clones were transferred to the field. In 1998 and 2000, 12 plants of transgenic lines all carrying the 35S- rolC gene construct formed female flower buds. Furthermore, one young aspen plant identified as a root sucker was observed in 1999 followed by an increasing number of root suckers derived from transgenic and non-transgenic trees in 2000 and 2001. In 2001, the last year of the field trial, 15 root suckers were detected outside the field. In total, 234 root suckers were harvested in 2000 and 2001 and analysed for their transgenic status. More than half of the roots suckers investigated showed the presence of the rbcS- rolC gene construct. We concluded that in addition to the widely accepted generative propagation, vegetative dispersal capacity of transgenic perennial plants is also important and must be included in risk assessment studies.     

Growth and crown efficiency of height repressed lodgepole pine; are suppressed trees more efficient?

Leaf area, crown projection area and growth over the last 5 years were measured to assess growth efficiency (GE) and crown efficiency (CE) of dominant (D), codominant (CD) and suppressed (SP) trees growing in height-repressed (P sites) and normally developing (M sites) lodgepole pine stands. Leaf area index (LAI), hydraulic characteristics, and needle nutrient concentrations were also measured. Volume growth of P site trees between 1994 and 1999 was 46% that of M site trees. Volume growth was closely associated with both hydraulic supply capacity (Q*) and leaf area. Height repression was not associated with lower GE, but P site trees had CE that was 24.5% lower than M site trees. Average GE of D and CD trees was 28% lower than that of SP trees, while mean CE for the D trees was 46% greater than that of CD, and 80% greater than for SP trees. Between M and P sites, canopy LAI and Q* per unit leaf area did not differ. Needle nitrogen (N) concentrations of M site trees were 7.6% greater than for P site trees. SP tree needles had the highest concentration of N and phosphorus. The nutrient advantage enjoyed by SP trees presumably allowed them to maintain higher GE for a given Q*/A_l. The fastest growing trees were the large D and CD trees from M sites. As LAI did not differ between sites, height repression on P sites may be a result of total leaf area being distributed among too many small trees.     

Evolution of Rh Blood Group Genes Have Experienced Gene Conversions and Positive Selection

There are two tightly linked loci (D and CE) for the human Rh blood group. Their gene products are membrane proteins having 12 transmembrane domains and form a complex with Rh50 glycoprotein on erythrocytes. We constructed phylogenetic networks of human and nonhuman primate Rh genes, and the network patterns suggested the occurrences of gene conversions. We therefore used a modified site-by-site reconstruction method by using two assumed gene trees and detected 9 or 11 converted regions. After eliminating the effect of gene conversions, we estimated numbers of nonsynonymous and synonymous substitutions for each branch of both trees. Whichever gene tree we selected the branch connecting hominoids and Old World monkeys showed significantly higher nonsynonymous than synonymous substitutions, an indication of positive selection. Many other branches also showed higher nonsynonymous than synonymous substitutions; this suggests that the Rh genes have experienced some kind of positive selection. Received: 16 March 1999 / Accepted: 17 June 1999     

Identification of discriminative characteristics for clusters from biologic data with InforBIO software

Background  

There are a number of different methods for generation of trees and algorithms for phylogenetic analysis in the study of bacterial taxonomy. Genotypic information, such as SSU rRNA gene sequences, now plays a more prominent role in microbial systematics than does phenotypic information. However, the integration of genotypic and phenotypic information for polyphasic studies is necessary for the classification and identification of microbes. Thus, we devised an algorithm that objectively identifies discriminative characteristics for focused clusters on generated trees from a dataset composed of coded data, such as phenotypic information. Moreover, this algorithm has been integrated into the polyphasic analysis software, InforBIO.     

Imputing supertrees and supernetworks from quartets

Inferring species phylogenies is an important part of understanding molecular evolution. Even so, it is well known that an accurate phylogenetic tree reconstruction for a single gene does not always necessarily correspond to the species phylogeny. One commonly accepted strategy to cope with this problem is to sequence many genes; the way in which to analyze the resulting collection of genes is somewhat more contentious. Supermatrix and supertree methods can be used, although these can suppress conflicts arising from true differences in the gene trees caused by processes such as lineage sorting, horizontal gene transfer, or gene duplication and loss. In 2004, Huson et al. (IEEE/ACM Trans. Comput. Biol. Bioinformatics 1:151-158) presented the Z-closure method that can circumvent this problem by generating a supernetwork as opposed to a supertree. Here we present an alternative way for generating supernetworks called Q-imputation. In particular, we describe a method that uses quartet information to add missing taxa into gene trees. The resulting trees are subsequently used to generate consensus networks, networks that generalize strict and majority-rule consensus trees. Through simulations and application to real data sets, we compare Q-imputation to the matrix representation with parsimony (MRP) supertree method and Z-closure, and demonstrate that it provides a useful complementary tool.     

The nature of inbreeding in a seed orchard of Douglas fir as shown by an efficient multilocus model

Summary The amounts of self-fertilization versus consanguineous matings (as measured by effective selfing) was estimated in a seed orchard of Douglas-fir, using progeny array data at six allozyme loci. The orchard is family structured, consisting several grafts (clones) and/or open-pollinated (o-p) progeny from each of several plus-trees. Population-wide selfing rates were found to be 7% for the o-p trees and 2% for the cloned trees. Estimates of mating system parameters for individual trees showed this difference for average outcrossing rate t (1) still largely remained when outcrossingpollen gene frequency p was not allowed to vary among trees and (2) disappeared when p was allowed to vary among trees. Under this joint t and p estimation, o-p trees showed both significant variation of t (based upon a one-way ANOVA grouped by common plus-tree) and significant regressions of p on ovule genotype (indicative of consanguineous matings); cloned trees showed neither. This higher rate of consanguineous mating for o-p trees might be explained by the larger and more variable size of o-p families in the orchard. Estimates of outcrossing rate t and outcrossingpollen gene frequency p were based upon a multilocus model which makes full use of the information in the data. The increased information it gives over observed outcross models is equivalent to adding 30–50% more loci, and it gives enough degrees of freedom to jointly estimate t and p for individual trees (individual progeny arrays) under certain conditions. In addition, inclusion of megagametophyte data nearly doubles the information about the mating system of individual trees.     

Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data

Human microbiome research characterizes the microbial content of samples from human habitats to learn how interactions between bacteria and their host might impact human health. In this work a novel parametric statistical inference method based on object-oriented data analysis (OODA) for analyzing HMP data is proposed. OODA is an emerging area of statistical inference where the goal is to apply statistical methods to objects such as functions, images, and graphs or trees. The data objects that pertain to this work are taxonomic trees of bacteria built from analysis of 16S rRNA gene sequences (e.g. using RDP); there is one such object for each biological sample analyzed. Our goal is to model and formally compare a set of trees. The contribution of our work is threefold: first, a weighted tree structure to analyze RDP data is introduced; second, using a probability measure to model a set of taxonomic trees, we introduce an approximate MLE procedure for estimating model parameters and we derive LRT statistics for comparing the distributions of two metagenomic populations; and third the Jumpstart HMP data is analyzed using the proposed model providing novel insights and future directions of analysis.     

Prediction of treatment response using gene expression profiles

This paper concerns prediction of clinical outcome from gene expression profiles using work in a different area, nonlinear system identification. In particular, the approach can predict long-term treatment response from data of a landmark article by Golub et al. (Golub, T. R.; Slonim, D. K.; Tamayo, P.; Huard, C.; Gaasenbeek, M.; Mesirov, J. P. et al. Science 1999, 286, 531-537) that has not previously been achieved with these data. The present paper shows that, for these data, gene expression profiles taken at time of diagnosis of acute myeloid leukemia contain information predictive of eventual response to chemotherapy. This was not evident in previous work; indeed, the Golub et al. article did not find a set of genes strongly correlated with clinical outcome. However, the present approach can accurately predict outcome class of gene expression profiles even when the genes do not have large differences in expression levels between the classes.     

iGTP: A software package for large-scale gene tree parsimony analysis

Background  

The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.     

洞庭湖水系(湖南地区)主要防护型经济树种草种生态类型区选择研究

为了减少或避免在农林业生产中因土壤、气候不适宜造成的冻害或其它自然灾害造成的不必要的损失,最大限度地利用洞庭湖水系(湖南地区)区域内的气候资源、水热资源以及土壤资源,本文依据洞庭湖水系(湖南地区)区域内89个样本县(市)气象台(站)30年的气候资料及其地貌、土壤等生态环境特性值,采用主分量(PCA)分析的方法,并结合定性分桥,对洞庭湖水系(湖南地区)进行了生态类型区划分的研究,其结果将该区域划分成5个生态类型区,并结合26个主要经济树种草种分布的气候、水热条件、地貌和土壤等生态环境的差异性,对26个树种草种进行了最适宜、适宜、较适宜栽培的生态类型区的选择研究,相应地对各生态类型区进行了主栽树种和辅栽树种的分析。     

Forest Structure and Primary Productivity in a Bornean Heath Forest

Aboveground forest structure, biomass, and primary productivity in a tropical heath forest in Central Kalimantan (Indonesian Borneo) were examined using data from 1-ha plots and stand-level allometric equations developed from harvested tree samples. The study site experienced a severe drought in 1997–1998 associated with the El Niño Southern Oscillation event. The drought effect on heath forest productivity was also assessed by evaluating changes in wood mass increment rates. Allometric relationships suggested that heath forest trees had leaves with smaller specific leaf area (SLA), and large heath forest trees allocate more to leaf mass compared to mixed dipterocarp forest trees. Aboveground biomass (for trees ≥ 4.8 cm DBH) in two 1-ha plots, P1 and P4, totaled 244.8 and 232.0 Mg/ha. Aboveground wood mass increment rate was –0.1 and 4.7 Mg/ha/yr in P1 and P4 during the drought period (from February to August 1998), while it quickly recovered to 8.1 and 8.5 Mg/ha/yr during the post-drought period (from August 1998 to August 1999 for P1 and from August 1998 to November 1999 for P4). This suggests a severe impact of the drought on heath forest productivity. Leaf characteristics of heath forest such as small SLA and long-lived leaves probably play a significant role in effective assimilation and maintenance of heath forest productivity under stressful conditions.     

南亚热带季风常绿阔叶林锥栗-荷木-黄果厚壳桂群落发展趋势探讨

 根据广东省中部鼎湖山自然保护区季风常绿阔叶林锥栗_荷木_黄果厚壳桂(Castanopsis chinensis_Schima superba_Cryptocarya concinna)群落8年的监测,用成对双样本均值分析的方法对群落个体数、生物量等进行了对比研究,初步揭示了群落真正时间意义上的变化：1）群落个体数呈逐年递减的趋势,1992、1994、1999年分别为3 979、3 822、3 531 株·hm-2,1994、1999年比1992年分别减少了3.9%、11.3%,经t_检验,差异极显著。类似的,群落生物量大体上也呈下降的趋势,1992、1994和1999年分别为293.1、304.3和248.5 t·hm-2,1994、1999年分别为1992年的103.8%、84.8%,差异不显著。2）不同径级树木个体数和生物量年间存在差异。胸径≤30 cm的树木个体数年间差异极显著。胸径90 cm以上的树木个体数在1992～1999年间减少50%。胸径40 cm以下和90 cm以上树木生物量年间差异不显著。1994、1999年中径级（尤其是40～50 cm）树木的生物量有一定的发展, 分别增长了1.36%、8.7%。3）黄果厚壳桂、云南银柴物种个体数极显著减少,锥栗1992～1999年间生物量减少31.1%,黄果厚壳桂1999年生物量显著低于1992年。4）鼎湖山季风常绿阔叶林正朝着中生顶级群落演替。5）顺行演替过程中群落出现波动,这是群落演替、自然稀疏、自然灾害等共同作用的结果。