The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression

Through multifaceted genome-scale research involving phylogenomics, targeted gene surveys, and gene expression analyses in diverse basal lineages of angiosperms, our studies provide insights into the most recent common ancestor of all extant flowering plants. MADS-box gene duplications have played an important role in the origin and diversification of angiosperms. Furthermore, early angiosperms possessed a diverse tool kit of floral genes and exhibited developmental 'flexibility', with broader patterns of expression of key floral organ identity genes than are found in eudicots. In particular, homologs of B-function MADS-box genes are more broadly expressed across the floral meristem in basal lineages. These results prompted formulation of the 'fading borders' model, which states that the gradual transitions in floral organ morphology observed in some basal angiosperms (e.g. Amborella) result from a gradient in the level of expression of floral organ identity genes across the developing floral meristem.     

Phosphoglucose isomerase gene duplication in the bony fishes: An evolutionary history

Electrophoretic patterns of phosphoglucose isomerase (PGI) in bony fishes provide strong evidence for a model of genetic control by two independent structural gene loci, most likely resulting from a gene duplication. This model is confirmed by a comparison of certain kinetic and molecular properties of the PGI homodimers (PGI-1 and PGI-2) isolated from extracts of the teleost Astyanax mexicanus. In addition, in most higher teleosts examined, the PGI enzymes show a regular pattern of tissue distribution, with PGI-2 predominant in muscle, the heterodimer often strongest in the heart, and PGI-1 predominant in liver and other organs. An examination of 53 species of bony fishes belonging to 38 families indicates a widespread occurrence of duplicate PGI loci and an early origin of the gene duplication, perhaps in the Leptolepiformes. The apparent presence of three PGI loci in trout and goldfish exemplifies how new loci can be incorporated into the genome through polyploidization.This research was supported in part by a NSF graduate traineeship to J.C.A., by the Clayton Foundation for Research in Biochemistry (G.B.K.), by NSF Grant GB-15644 and NIH Grant GM-15769 to Robert K. Selander, and by contract AT(38-1)-310 between the University of Georgia and the U.S. Atomic Energy Commission.     

Phylogenetic and evolutionary analysis of the PLUNC gene family

The PLUNC family of human proteins are candidate host defense proteins expressed in the upper airways. The family subdivides into short (SPLUNC) and long (LPLUNC) proteins, which contain domains predicted to be structurally similar to one or both of the domains of bactericidal/permeability-increasing protein (BPI), respectively. In this article we use analysis of the human, mouse, and rat genomes and other sequence data to examine the relationships between the PLUNC family proteins from humans and other species, and between these proteins and members of the BPI family. We show that PLUNC family clusters exist in the mouse and rat, with the most significant diversification in the locus occurring for the short PLUNC family proteins. Clear orthologous relationships are established for the majority of the proteins, and ambiguities are identified. Completion of the prediction of the LPLUNC4 proteins reveals that these proteins contain approximately a 150-residue insertion encoded by an additional exon. This insertion, which is predicted to be largely unstructured, replaces the structure homologous to the 40s hairpin of BPI. We show that the exon encoding this region is anomalously variable in size across the LPLUNC proteins, suggesting that this region is key to functional specificity. We further show that the mouse and human PLUNC family orthologs are evolving rapidly, which supports the hypothesis that these proteins are involved in host defense. Intriguingly, this rapid evolution between the human and mouse sequences is replaced by intense purifying selection in a large portion of the N-terminal domain of LPLUNC4. Our data provide a basis for future functional studies of this novel protein family.     

The tree of life: introduction to an evolutionary debate

The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even some aspects of the standard evolutionary understanding of eukaryotes. These discussions have arisen out of a multidisciplinary collaboration of people with an interest in the Tree of Life, and we suggest that this sort of focused engagement enables a practical understanding of the relationships between biology, philosophy and history.     

Protist homologs of the meiotic Spo11 gene and topoisomerase VI reveal an evolutionary history of gene duplication and lineage-specific loss

Spo11 is a meiotic protein of fundamental importance as it is a conserved meiosis-specific transesterase required for meiotic recombination initiation in fungi, animals, and plants. Spo11 is homologous to the archaebacterial topoisomerase VIA (Top6A) gene, and its homologs are broadly distributed among eukaryotes, with some eukaryotes having more than one homolog. However, the evolutionary relationships among these genes are unclear, with some debate as to whether eukaryotic homologs originated by lateral gene transfer. We have identified and characterized protist Spo11 homologs by degenerate polymerase chain reaction (PCR) and sequencing and by analyses of sequences from public databases. Our phylogenetic analyses show that Spo11 homologs evolved by two ancient eukaryotic gene duplication events prior to the last common ancestor of extant eukaryotes, resulting in three eukaryotic paralogs: Spo11-1, Spo11-2, and Spo11-3. Spo11-1 orthologs encode meiosis-specific proteins and are distributed broadly among eukaryotic lineages, though Spo11-1 is absent from some protists. This absence coincides with the presence of Spo11-2 orthologs, which are meiosis-specific in Arabidopsis and are found in plants, red algae, and some protists but absent in animals and fungi. Spo11-3 encodes a Top6A subunit that interacts with topoisomerase VIB (Top6B) subunits, which together play a role in vegetative growth in Arabidopsis. We identified Spo11-3 (Top6A) and Top6B homologs in plants, red algae, and a few protists, establishing a broader distribution of these genes among eukaryotes, indicating their likely vertical descent followed by lineage-specific loss.     

Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes

The human N-acetyltransferase genes NAT1 and NAT2 encode two phase-II enzymes that metabolize various drugs and carcinogens. Functional variability at these genes has been associated with adverse drug reactions and cancer susceptibility. Mutations in NAT2 leading to the so-called slow-acetylation phenotype reach high frequencies worldwide, which questions the significance of altered acetylation in human adaptation. To investigate the role of population history and natural selection in shaping NATs variation, we characterized genetic diversity through the resequencing and genotyping of NAT1, NAT2, and the pseudogene NATP in a collection of 13 different populations with distinct ethnic backgrounds and demographic pasts. This combined study design allowed us to define a detailed map of linkage disequilibrium of the NATs region as well as to perform a number of sequence-based neutrality tests and the long-range haplotype (LRH) test. Our data revealed distinctive patterns of variability for the two genes: the reduced diversity observed at NAT1 is consistent with the action of purifying selection, whereas NAT2 functional variation contributes to high levels of diversity. In addition, the LRH test identified a particular NAT2 haplotype (NAT2*5B) under recent positive selection in western/central Eurasians. This haplotype harbors the mutation 341T-->C and encodes the "slowest-acetylator" NAT2 enzyme, suggesting a general selective advantage for the slow-acetylator phenotype. Interestingly, the NAT2*5B haplotype, which seems to have conferred a selective advantage during the past approximately 6,500 years, exhibits today the strongest association with susceptibility to bladder cancer and adverse drug reactions. On the whole, the patterns observed for NAT2 well illustrate how geographically and temporally fluctuating xenobiotic environments may have influenced not only our genome variability but also our present-day susceptibility to disease.     

Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life

Background  

The root of the tree of life has been a holy grail ever since Darwin first used the tree as a metaphor for evolution. New methods seek to narrow down the location of the root by excluding it from branches of the tree of life. This is done by finding traits that must be derived, and excluding the root from the taxa those traits cover. However the two most comprehensive attempts at this strategy, performed by Cavalier-Smith and Lake et al., have excluded each other's rootings.     

Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification

Denitrification is a facultative respiratory pathway in which nitrite (NO2(-)), nitric oxide (NO), and nitrous oxide (N2O) are successively reduced to nitrogen gas (N(2)), effectively closing the nitrogen cycle. The ability to denitrify is widely dispersed among prokaryotes, and this polyphyletic distribution has raised the possibility of horizontal gene transfer (HGT) having a substantial role in the evolution of denitrification. Comparisons of 16S rRNA and denitrification gene phylogenies in recent studies support this possibility; however, these results remain speculative as they are based on visual comparisons of phylogenies from partial sequences. We reanalyzed publicly available nirS, nirK, norB, and nosZ partial sequences using Bayesian and maximum likelihood phylogenetic inference. Concomitant analysis of denitrification genes with 16S rRNA sequences from the same organisms showed substantial differences between the trees, which were supported by examining the posterior probability of monophyletic constraints at different taxonomic levels. Although these differences suggest HGT of denitrification genes, the presence of structural variants for nirK, norB, and nosZ makes it difficult to determine HGT from other evolutionary events. Additional analysis using phylogenetic networks and likelihood ratio tests of phylogenies based on full-length sequences retrieved from genomes also revealed significant differences in tree topologies among denitrification and 16S rRNA gene phylogenies, with the exception of the nosZ gene phylogeny within the data set of the nirK-harboring genomes. However, inspection of codon usage and G + C content plots from complete genomes gave no evidence for recent HGT. Instead, the close proximity of denitrification gene copies in the genomes of several denitrifying bacteria suggests duplication. Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, our analysis suggests that other phenomena, such gene duplication/divergence and lineage sorting, may have differently influenced the evolution of each denitrification gene.     

Evidence that the root of the tree of life is not within the Archaea

The Archaea occupy uncommon and extreme habitats around the world. They manufacture unusual compounds, utilize novel metabolic pathways, and contain many unique genes. Many suspect, due to their novel properties, that the root of the tree of life may be within the Archaea, although there is little direct evidence for this root. Here, using gene insertions and deletions found within protein synthesis factors present in all prokaryotes and eukaryotes, we present statistically significant evidence that the root of life is outside the Archaea.     

慢生根瘤菌属结瘤基因的进化及遗传分析

根瘤菌中存在一系列控制固氮结瘤因子(lipo-chito-oligosaccharides)合成的结瘤基因(nodulation genes)。其中, nodA基因是合成结瘤因子所必需的, 该基因负责酰基转移酶的合成, 能将不饱和脂肪酸转移到结瘤因子寡聚糖骨架上; 基因nodZ, nolL和noeI为宿主专一性结瘤基因, 分别转录合成岩藻糖基转移酶, 岩藻糖乙酰化酶和岩藻糖甲基化酶。通过GenBank调取慢生根瘤菌属及其他根瘤菌属的结瘤基因nodA, nodZ, nolL和noeI, 构建系统发育树, 进行进化和遗传分析。结果表明, 慢生根瘤菌属各个菌株的nodA, nodZ, nolL和noeI具有很高的相关性, 但是与根据保守基因16S rDNA和dnaK分类情况不完全相符。这表明慢生根瘤菌属的结瘤基因主要是通过直系遗传的, 同时可能为适应宿主及环境条件, 结瘤基因有少量的平行转移。结果表明, 慢生根瘤菌属各个菌株的nodA, nodZ, nolL和noeI具有很高的同源性, 同时发现基于保守基因16S rDNA和dnaK对慢生根瘤菌的分类情况与慢生根瘤菌属各菌株在nodA, nodZ, nolL和noeI具有较高同源性的事实不完全相符。这表明慢生根瘤菌属的结瘤基因主要是通过直系遗传的, 同时可能为适应宿主及环境条件, 结瘤基因有少量的平行转移。     

Cloning and nucleotide sequence of an archaebacterial glutamine synthetase gene: Phylogenetic implications

Summary The glnA gene of the thermophilic sulphur-dependent archaebacterium Sulfolobus solfataricus was identified by hybridization with the corresponding gene of the cyanobacterium Spirulina platensis and cloned in Escherichia coli. The nucleotide sequence of the 1696 bp DNA fragment containing the structural gene for glutamine synthetase was determined, and the derived amino acid sequence (471 residues) was compared to the sequences of glutamine synthetases from eubacteria and eukaryotes. The homology between the archaebacterial and the eubacterial enzymes is higher (42%–49%) than that found with the eukaryotic counterpart (less than 20%). This was true also when the five most conserved regions, which it is possible to identify in both eubacterial and eukaryotic glutamine synthetases, were analysed.     

Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history

We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.     

Evidence that Tn5565, which includes the enterotoxin gene in Clostridium perfringens, can have a circular form which may be a transposition intermediate

The Clostridium perfringens enterotoxin gene is on a transposon-like element, Tn5565, integrated in the chromosome in human food poisoning strains. The flanking IS elements, IS1470 A and B, are related to IS30. The IS element found in the transposon, IS1469, is related to IS200 and has been found upstream of cpe in all Type A strains. PCR and sequencing studies from cell extracts and plasmid isolations of C. perfringens indicate that Tn5565 can form a circular form with the tandem repeat (IS1470)₂, similar to the transposition intermediates described for a number of IS elements.     

Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature

Bacterial tmRNA mediates a trans-translation reaction, which permits the recycling of stalled ribosomes and probably also contributes to the regulated expression of a subset of genes. Its action results in the addition of a small number of C-terminal amino acids to protein whose synthesis had stalled and these constitute a proteolytic recognition tag for the degradation of these incompletely synthesized proteins. Previous work has identified pseudoknots and stem-loops that are widely conserved in divergent bacteria. In the present work an alignment of tmRNA gene sequences within 13 beta-proteobacteria reveals an additional sub-structure specific for this bacterial group. This sub-structure is in pseudoknot Pk2, and consists of one to two additional stem-loop(s) capped by stable GNRA tetraloop(s). Three-dimensional models of tmRNA pseudoknot 2 (Pk2) containing various topological versions of the additional sub-structure suggest that the sub-structures likely point away from the core of the RNA, containing both the tRNA and the mRNA domains. A putative tertiary interaction has also been identified.     

Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history

Background

Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions.

Methology/Principal Findings

Based on a long-term (1972–2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns.

Conclusion/Significance

Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependant on recent ecological processes.     

Telling the tree: Narrative representation and the study of evolutionary history

Accounts of the evolutionary past have as much in common with works of narrative history as they do with works of science. Awareness of the narrative character of evolutionary writing leads to the discovery of a host of fascinating and hitherto unrecognized problems in the representation of evolutionary history, problems associated with the writing of narrative. These problems include selective attention, narrative perspective, foregrounding and backgrounding, differential resolution, and the establishment of a canon of important events. The narrative aspects of evolutionary writing, however, which promote linearity and cohesiveness in conventional stories, conflict with the underlying chronicle of evolution, which is not linear, but branched, and which does not cohere, but diverges. The impulse to narrate is so great, however, and is so strongly reinforced by traditional schemes of taxonomic attention, that natural historians have more often abandoned the diverging tree than they have abandoned the narrative mode of representation. If we are to understand the true nature of the evolutionary past then we must adopt tree thinking, and develop new and creative ways, both narrative and non-narrative, of telling the history of life.     

The Pleistocene history of the sheepshead minnow (Cyprinodon variegatus): Non-equilibrium evolutionary dynamics within a diversifying species complex

The sheepshead minnow, Cyprinodon variegatus, is a widespread fish species that typically inhabits coastal tidal marsh and mangrove swamp environments, ranging from Cape Cod, Massaschusetts to northern Mexico and into the Caribbean. This wide range crosses several biogeographic boundaries which are coincident with genetic structuring within numerous species originating in the Pleistocene. In addition, the more northerly reaches of this species range have been further subject to the evolutionary consequences of Pleistocene glaciation due to local extinction and recolonization of formerly glaciated sites. C. variegatus thus provides an excellent vertebrate model system within which to test the extent of genetic differentiation among populations in a dominant coastal ecosystem and examine patterns of historical demography in populations distributed along a latitudinal gradient. Using mitochondrial control region and ND2 sequence data, we discovered monophyletic clades within C. variegatus with divergence times within the Pleistocene, and very low gene flow between most sites. Intraspecific genetic breaks appear to correspond broadly to biogeographic or oceanic boundaries. Pleistocene climate change appears to have had dramatic impacts on the size and distribution of populations within and near the glacial margins, but has also affected populations far from formerly glaciated regions.     

Human asparaginyl-tRNA synthetase: molecular cloning and the inference of the evolutionary history of Asx-tRNA synthetase family.

We have cloned and sequenced a cDNA encoding human cytoplasmic asparaginyl-tRNA synthetase (AsnRS). The N-terminal appended domain of 112 amino acid represents the signature sequence for the eukaryotic AsnRS and is absent from archaebacterial or eubacterial enzymes. The canonical ortholog for AsnRS is absent from most archaebacterial and some eubacterial genomes, indicating that in those organisms, formation of asparaginyl-tRNA is independent of the enzyme. The high degree of sequence conservation among asparaginyl- and aspartyl-tRNA synthetases (AsxRS) made it possible to infer the evolutionary paths of the two enzymes. The data show the neighbor relationship between AsnRS and eubacterial aspartyl-tRNA synthetase, and support the occurrence of AsnRS early in the course of evolution, which is in contrast to the proposed late occurrence of glutaminyl-tRNA synthetase.     

Congruence of evidence for a Methanopyrus-proximal root of life based on transfer RNA and aminoacyl-tRNA synthetase genes

Among 60 organisms, the intraspecies genetic distances between tRNAs cognate for different amino acids, between the initiator and elongator tRNAs for Met, and between potentially paralogous pairs of aminoacyl-tRNA synthetases are found to be at a minimum within the Methanopyrus kandleri genome. These results indicate an exact congruence between the evidence from tRNA and aminoacyl-tRNA synthetase genes locating the root of life closest to this organism.