Molecular evolution of the zinc-containing long-chain alcohol dehydrogenase genes

Phylogenetic relationships and rates of nucleotide substitution were studied for alcohol dehydrogenase (ADH) genes by using DNA sequences from mammals and plants. Mammalian ADH sequences include the three class I genes and a class II gene from humans and one gene each from baboon, rat, and mouse. Plant sequences include two ADH genes each from maize and rice, three genes from barley, and one gene each from wheat and two dicots, Arabidopsis and pea. Phylogenetic trees show that relationships among ADH genes are generally consistent with taxonomic relationships: mammalian and plant ADH genes are classified into two distinct groups; primate class I genes are clustered; and two dicot sequences are clustered separately from monocot sequences. Accelerated evolution has been detected among the duplicated ADH genes in plants, in which synonymous substitutions occurred more often within the coenzyme-binding domain than within the catalytic domains.     

Perils of paralogy: using HSP70 genes for inferring organismal phylogenies

Conserved genes have found their way into the mainstream of molecular systematics. Many of these genes are members of multigene families. A difficulty with using single genes of multigene families for phylogenetic inference is that genes from one species may be paralogous to those from another taxon. We focus attention on this problem using heat shock 70 (HSP70) genes. Using polymerase chain reaction techniques with genomic DNA, we isolated and sequenced 123 distinct sequences from 12 species of sharks. Phylogenetic analysis indicated that the sequences cluster with constituitively expressed cytoplasmic heat shock-like genes. Three highly divergent gene clades were sampled. A number of similar sequences were sampled from each species within each distinct gene clade. Comparison of published species trees with an HSP70 gene tree inferred using Bayesian phylogenetic analysis revealed several cases of gene duplication and differential sorting of gene lineages within this group of sharks. Gene tree parsimony based on the objective criteria of duplication and losses showed that previously published hypotheses of species relationships and two novel hypothesis based on Bayesian phylogenetics were concordant with the history of HSP70 gene duplication and loss. By contrast, two published hypotheses based on morphological data were not significantly different from the null hypothesis of a random association between species relatedness and the HSP70 gene tree. These results suggest that gene tree parsimony using data from multigene families can be used for inferring species relationships or testing published alternative hypotheses. More importantly, the results suggest that systematic studies relying on phylogenetic inferences from HSP70 genes may by plagued by unrecognized paralogy of sampled genes. Our results underscore the distinction between gene and species trees and highlight an underappreciated source of discordance between gene trees and organismal phylogeny, i.e., unrecognized paralogy of sampled genes.     

The molecular basis of quantitative variation in foliar secondary metabolites in Eucalyptus globulus

Eucalyptus is characterized by high foliar concentrations of plant secondary metabolites with marked qualitative and quantitative variation within a single species. Secondary metabolites in eucalypts are important mediators of a diverse community of herbivores. We used a candidate gene approach to investigate genetic associations between 195 single nucleotide polymorphisms (SNPs) from 24 candidate genes and 33 traits related to secondary metabolites in the Tasmanian Blue Gum (Eucalyptus globulus). We discovered 37 significant associations (false discovery rate (FDR) Q < 0.05) across 11 candidate genes and 19 traits. The effects of SNPs on phenotypic variation were within the expected range (0.018 < r(2) < 0.061) for forest trees. Whereas most marker effects were nonadditive, two alleles from two consecutive genes in the methylerythritol phosphate pathway (MEP) showed additive effects. This study successfully links allelic variants to ecologically important phenotypes which can have a large impact on the entire community. It is one of very few studies to identify the genetic variants of a foundation tree that influences ecosystem function.     

Genetic engineering of reproductive sterility in forest trees

Containment of transgenes inserted into genetically engineered forest trees will probably be necessary before most commercial uses are possible. This is a consequence of (1) high rates of gene dispersal by pollen and seed, (2) proximity of engineered trees in plantations to natural or feral stands of interfertile species, and (3) potentially undesirable ecological effects if certain transgenes become widely dispersed. In addition to gene containment, engineering of complete or male sterility may stimulate faster wood production, reduce production of allergenic pollen, and facilitate hybrid breeding. We review the regulatory and ecological rationale for engineering sterility, potentially useful floral genes, strategies for creating sterility-causing transgenes, and problems peculiar to engineering sterility in forest trees. Each of the two primary options — ablating floral tissuesvia floral promoter-cytotoxin fusions, and disrupting expression of essential floral genes by various methods of gene suppression — has advantages and disadvantages. Because promoters from structural and enzymatic floral-specific genes often work well in heterologous species, ablation methods based on these genes probably will not require cloning of homologs from angiosperm trees. Methods that inhibit gene expression will require cloning of tree genes and may be more prone to epigenetic variability, but should allow assay of transgene efficacy in seedlings. Practical constraints include the requirement for vegetative propagation if complete sterility is engineered and the need for highly stable forms of sterility in long-lived trees. The latter may require suppression of more than one floral gene or employment of more than one genetic mechanism for sterility.     

Pollen flow in Eucalyptus grandis determined by paternity analysis using microsatellite markers

Gene flow by pollen dispersal from forestry plantations containing introduced species, provenances or selected elite breeding material may impact on local native forest by changing the genetic diversity, introducing new genes or gene combinations, or causing the extinction of rare genotypes in adjacent native forest areas. Patterns of pollen flow can be used to assess the risk of genetic pollution of native forest areas from nearby plantations. Pollen flow in an artificial population of Eucalyptus grandis was estimated using molecular markers and paternity analysis. Microsatellite genotyping was used to identify pollen parents of progeny arrays from six mother trees. Of 329 progeny analysed, 178 (54%) were assigned to pollen parents within the population. Pollen parents located within the population were between 0–192 m from the respective mother trees, with an average pollination distance of 57.96 m. Pollination of mother trees was outcrossed, not by nearest neighbours, and displayed a preference for inter-provenance matings within the population. Progeny that could not be assigned pollen parents within the population (46%) were assumed to have resulted from pollen immigration from external sources. These pollen flow parameters provide useful information about the dynamics of pollen movement within E. grandis populations and may be used in risk assessment of gene flow from plantations to adjacent areas of native forest.     

Tree population studies in low-diversity forests, Guyana. II. Assessments on the distribution and abundance of non-timber forest products

Comparisons between two forest localities were undertaken to assess the potential availability of non-timber forest products (NTFPs) within the low-diversity forests of Guyana. Information on the abundance and distribution of tree species, and local and national ethnobotanical surveys were used classifying species into five categories (timber, construction, technological, edible and medicinal). A total of 152 species were recorded from the two localities; covering 236 different uses, 33 known commercial timber species and 106 species with potential non-timber product utilization. The most important plant families with the highest number of uses at both localities were Leguminosae (sub-families Caesalpinioideae and Mimosoideae), Arecaceae, Bombacaceae and Chrysobalanaceae, although these families were not the most abundant families at both localities. At both forest localities eight tree species represented over 50% of all the trees. At Kurupukari three species, each with more than three identified NTFPs, represented over 20% of the trees.Potential utilization of NTFPs are discussed in accordance with species richness, tree density, the number of different uses per species, and the percentage of trees represented by each utilizable species. Considering the constraints on the future potential commercialization of NTFPs, two scenarios for the extraction of NTFPs are discussed. Within relatively species-rich forest types the high diversity of products provides potentially viable multiple-species extractionism. In contrast, in low-diversity forest types, typical of the Guiana Shield, one or two NTFP species frequently represent over 50% of the canopy trees, and therefore substantially increase the potential sustainable extraction for single-species harvesting. It is suggested that these low-diversity types of forest are prioritized for conservation on the basis of ensuring future utilization, refuge, of non-timber forest products.     

Detecting highways of horizontal gene transfer

In a horizontal gene transfer (HGT) event, a gene is transferred between two species that do not have an ancestor-descendant relationship. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. We present a method for inferring such highways. Our method is based on the fact that the evolutionary histories of horizontally transferred genes disagree with the corresponding species phylogeny. Specifically, given a set of gene trees and a trusted rooted species tree, each gene tree is first decomposed into its constituent quartet trees and the quartets that are inconsistent with the species tree are identified. Our method finds a pair of species such that a highway between them explains the largest (normalized) fraction of inconsistent quartets. For a problem on n species and m input quartet trees, we give an efficient O(m + n(2))-time algorithm for detecting highways, which is optimal with respect to the quartets input size. An application of our method to a dataset of 1128 genes from 11 cyanobacterial species, as well as to simulated datasets, illustrates the efficacy of our method.     

林木基因克隆研究进展

林木种质资源丰富, 种质间遗传差异大, 控制林木重要性状的基因克隆及转化对培育优良林木新品种具有很强的实用价值, 但许多具有潜在应用价值的林木基因未得到充分发掘和有效分离。近年来, 随着各种不同林木cDNA文库的建立, 大规模随机EST测序技术的运用以及克隆技术的不断完善, 特别是毛果杨(Populus trichocarpa)基因组测序计划的完成, 大量与林木重要性状相关的基因被分离和鉴定。这些重要基因的获得为利用转基因技术培育高产、优质、抗逆、抗病虫害的林木新品种奠定了一定的基础。该文综述了20多年来国内外林木基因克隆的研究进展, 对基因克隆及其应用过程中亟待解决的问题进行了讨论, 并对其发展趋势进行展望。     

Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

The root of the angiosperm tree has not yet been established. Major morphological and molecular differences between angiosperms and other seed plants have introduced ambiguities and possibly spurious results. Because it is unlikely that extant species more closely related to angiosperms will be discovered, and because relevant fossils will almost certainly not yield molecular data, the use of duplicate genes for rooting purposes may provide the best hope of a solution. Simultaneous analysis of the genes resulting from a gene duplication event along the branch subtending angiosperms would yield an unrooted network, wherein two congruent gene trees should be connected by a single branch. In these circumstances the best rooted species tree is the one that corresponds to the two gene trees when the network is rooted along the connecting branch. In general, this approach can be viewed as choosing among rooted species trees by minimizing hypothesized events such as gene duplication, gene loss, lineage sorting, and lateral transfer. Of those gene families that are potentially relevant to the angiosperm problem, phytochrome genes warrant special attention. Phylogenetic analysis of a sample of complete phytochrome (PHY) sequences implies that an initial duplication event preceded (or occurred early within) the radiation of seed plants and that each of the two resulting copies duplicated again. In one of these cases, leading to thePHYAandPHYClineages, duplication appears to have occurred before the diversification of angiosperms. Duplicate gene trees are congruent in these broad analyses, but the sample of sequences is too limited to provide much insight into the rooting question. Preliminary analyses of partialPHYAandPHYCsequences from several presumably basal angiosperm lineages are promising, but more data are needed to critically evaluate the power of these genes to resolve the angiosperm radiation.     

Testing hybridization hypotheses based on incongruent gene trees

Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence between gene trees. The incongruence, in turn, offers an opportunity to detect hybrid speciation. Here we characterized certain distinctions between hybridization and other biological processes, including lineage sorting, paralogy, and lateral gene transfer, that are responsible for topological incongruence between gene trees. Consider two incongruent gene trees with three taxa, A, B, and C, where B is a sister group of A on gene tree 1 but a sister group of C on gene tree 2. With a theoretical model based on the molecular clock, we demonstrate that time of divergence of each gene between taxa A and C is nearly equal in the case of hybridization (B is a hybrid) or lateral gene transfer, but differs significantly in the case of lineage sorting or paralogy. After developing a bootstrap test to test these alternative hypotheses, we extended the model and test to account for incongruent gene trees with numerous taxa. Computer simulation studies supported the validity of the theoretical model and bootstrap test when each gene evolved at a constant rate. The computer simulation also suggested that the model remained valid as long as the rate heterogeneity was occurring proportionally in the same taxa for both genes. Although the model could not test hypotheses of hybridization versus lateral gene transfer as the cause of incongruence, these two processes may be distinguished by comparing phylogenies of multiple unlinked genes.     

Spatial pattern and process in forest stands within the Virginia piedmont

Abstract. Question: Underlying ecological processes have often been inferred from the analysis of spatial patterns in ecosystems. Using an individual‐based model, we evaluate whether basic assumptions of species’life‐history, drought‐susceptibility, and shade tolerance generate dynamics that replicate patterns between and within forest stands. Location: Virginia piedmont, USA. Method: Model verification examines the transition in forest composition and stand structure between mesic, intermediate and xeric sites. At each site, tree location, diameter, and status were recorded in square plots ranging from 0.25 to 1.0 ha. Model validation examines the simulated spatial pattern of individual trees at scales of 1–25 m within each forest site using a univariate Ripley's K function. Results: 7512 live and dead trees were surveyed across all sites. All sites exhibit a consistent, significant shift in pattern for live trees by size, progressing from a clumped understorey (trees ± 0.1 m in diameter) to a uniform overstorey (trees > 0.25 m). Simulation results reflect not only the general shift in pattern of trees at appropriate scales within sites, but also the general transition in species composition and stand structure between sites. Conclusions: This shift has been observed in other forest ecosystems and interpreted as a result of competition; however, this hypothesis has seldom been evaluated using simulation models. These results support the hypothesis that forest pattern in the Virginia piedmont results from competition involving species’life‐history attributes driven by soil moisture availability between sites and light availability within sites.     

Association genetics in Corymbia citriodora subsp. variegata identifies single nucleotide polymorphisms affecting wood growth and cellulosic pulp yield

Wood is an important biological resource which contributes to nutrient and hydrology cycles through ecosystems, and provides structural support at the plant level. Thousands of genes are involved in wood development, yet their effects on phenotype are not well understood. We have exploited the low genomic linkage disequilibrium (LD) and abundant phenotypic variation of forest trees to explore allelic diversity underlying wood traits in an association study. Candidate gene allelic diversity was modelled against quantitative variation to identify SNPs influencing wood properties, growth and disease resistance across three populations of Corymbia citriodora subsp. variegata, a forest tree of eastern Australia. Nine single nucleotide polymorphism (SNP) associations from six genes were identified in a discovery population (833 individuals). Associations were subsequently tested in two smaller populations (130-160 individuals), 'validating' our findings in three cases for actin 7 (ACT7) and COP1 interacting protein 7 (CIP7). The results imply a functional role for these genes in mediating wood chemical composition and growth, respectively. A flip in the effect of ACT7 on pulp yield between populations suggests gene by environment interactions are at play. Existing evidence of gene function lends strength to the observed associations, and in the case of CIP7 supports a role in cortical photosynthesis.     

Biodiversity and spatial distribution of vascular epiphytes in two biotopes of the Cameroonian semi-deciduous rain forest

The diversity and spatial distribution of vascular epiphytes were surveyed in two biotopes (dryland forest and swamp-inundated forest) of the semi-deciduous rain forest area in Cameroon. Eight sites in each biotope were selected, which included 530 individuals of phorophytes in dryland forest and 460 in swamp-inundated forest. A total of 148 epiphyte species were recorded, which showed that semi-deciduous rain forests represent a major source of African-epiphyte diversity. Dryland forest hosted 110 epiphyte species, while the swamp-inundated forest harboured 108. A total of 56 species were found only in the dryland forest and 60 were restricted to the swamp-inundated forest. At family level, Orchidaceae exhibited the highest-species richness within both biotopes. Pteridophytes were more abundant in the swamp-inundated forest. A TWINSPAN analysis of the floristic similarities separated the two investigated forest types very clearly. No significant difference existed between the two biotopes regarding vertical distribution of epiphytes within single trees. The swamp-inundated forests may serve as a refuge for many epiphytes that occur in the outer canopy of the dryland forests, both because they are inherently less vulnerable to timber extraction, and enjoy better protection by legislation.     

Gene flow among established Puerto Rican populations of the exotic tree species, Albizia lebbeck

We estimate gene flow and patterns of genetic diversity in Albizia lebbeck, an invasive leguminous tree in the dry forest of southwestern Puerto Rico. Genetic diversity estimates calculated for 10 populations of 24 trees each indicated that these populations may have been formed from multiple introductions. The presence of unique genotypes in the northernmost populations suggests that novel genotypes are still immigrating into the area. This combination of individuals from disparate locations led to high estimates of genetic diversity (He = 0.266, P = 0.67). Indirect estimates of gene flow indicate that only 0.69 migrants per generation move between populations, suggesting that genetic diversity within populations should decrease due to genetic drift. Since migration-drift equilibrium was not found, however, this estimate needs to be viewed with caution. The regular production of pods in this outcrossing species (tm = 0.979) indicates that sufficient outcross pollen is received to insure successful reproduction. Direct estimates of gene flow indicate that between 44 and 100% of pollen received by trees in four small stands of trees (n < 11) was foreign. The role of gene flow in facilitating the spread of this invasive plant species is discussed.     

A support vector machine based test for incongruence between sets of trees in tree space

ABSTRACT: BACKGROUND: The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. RESULTS: Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. CONCLUSIONS: The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license.     

The phylogenetic significance of peptidoglycan types: Molecular analysis of the genera Microbacterium and Aureobacterium based upon sequence comparison of gyrB, rpoB, recA and ppk and 16SrRNA genes

The type strains of 27 species of the genus Microbacterium, family Microbacteriaceae, were analyzed with respect to the phylogeny of the housekeeping genes coding for DNA gyrase subunit B (gyrB), RNA-polymerase subunit B (rpoB), recombinase A (recA) and polyphosphate kinase (ppk). The resulting gene trees were compared to the 16S rRNA gene phylogeny of the same species. The topology of neighbour-joining and maximum parsimony phylogenetic trees based upon nucleic acid sequences and protein sequences of housekeeping genes differed among each other and no gene tree was identical to that of the 16S rRNA gene tree. Only some species showed consistent clustering by all genes analyzed, but the majority of species branched with different neighbours in most gene trees. The failure to phylogenetically cluster type strains into two groups based upon differences in the amino acid composition of peptidoglycan on the basis of 16S rRNA gene sequence similarity, once leading to the union of the genera Microbacterium and Aureobacterium, was also seen in the analysis of recA, rpoB and gyrB gene and protein phylogenies. Analysis of the pkk gene and protein as well as of a concatenate tree, combining sequences of all five genes (total of 3.700 nucleotides), sees members of the former genus Aureobacterium and other type strains with lysine as diagnostic diamino acid to form a coherent cluster that branches within the radiation of Microbacterium species with ornithine in the peptidoglycan.     

Comparative genomics provides evidence for an ancient genome duplication event in fish

There are approximately 25 000 species in the division Teleostei and most are believed to have arisen during a relatively short period of time ca. 200 Myr ago. The discovery of 'extra' Hox gene clusters in zebrafish (Danio rerio), medaka (Oryzias latipes), and pufferfish (Fugu rubripes), has led to the hypothesis that genome duplication provided the genetic raw material necessary for the teleost radiation. We identified 27 groups of orthologous genes which included one gene from man, mouse and chicken, one or two genes from tetraploid Xenopus and two genes from zebrafish. A genome duplication in the ancestor of teleost fishes is the most parsimonious explanation for the observations that for 15 of these genes, the two zebrafish orthologues are sister sequences in phylogenies that otherwise match the expected organismal tree, the zebrafish gene pairs appear to have been formed at approximately the same time, and are unlinked. Phylogenies of nine genes differ a little from the tree predicted by the fish-specific genome duplication hypothesis: one tree shows a sister sequence relationship for the zebrafish genes but differs slightly from the expected organismal tree and in eight trees, one zebrafish gene is the sister sequence to a clade which includes the second zebrafish gene and orthologues from Xenopus, chicken, mouse and man. For these nine gene trees, deviations from the predictions of the fish-specific genome duplication hypothesis are poorly supported. The two zebrafish orthologues for each of the three remaining genes are tightly linked and are, therefore, unlikely to have been formed during a genome duplication event. We estimated that the unlinked duplicated zebrafish genes are between 300 and 450 Myr. Thus, genome duplication could have provided the genetic raw material for teleost radiation. Alternatively, the loss of different duplicates in different populations (i.e. 'divergent resolution') may have promoted speciation in ancient teleost populations.     

海南地区螺旋粉虱种群mtDNA-COI和rDNA-ITS1基因的序列及系统发育分析

螺旋粉虱Aleurodicus dispersus Russell在海南是一种重要的农林害虫。本研究对海南地区不同螺旋粉虱种群的mtDNA-COI和rDNA-ITS1基因片段进行了测定并对其系统发育进行了分析。mtDNA-COI和rDNA-ITS1的序列比较发现, 海南16个县市螺旋粉虱种群的mtDNA-COI序列基本一致, 只有文昌番石榴Psidium guajava种群的序列发生变异, 在476 bp位点的碱基C突变为碱基T。不同螺旋粉虱种群的rDNA-ITS1序列也无差异。基于mtDNA COI序列的不同螺旋粉虱种群的系统发育树表明, 已传入我国海南地区的螺旋粉虱未发生明显的遗传分化; 研究还发现海南的螺旋粉虱种群与台湾的种群遗传距离最近, 表明海南地区的螺旋粉虱可能由台湾传入的。基于mtDNA-COI和rDNA-ITS1序列构建的不同粉虱种群的系统发育树表明, 粉虱科分为复孔粉虱亚科（Aleurodicinae）和粉虱亚科（Aleyrodinae）, 这一结果与其他研究结果一致。