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1.
Shalchian-Tabrizi K Skånseng M Ronquist F Klaveness D Bachvaroff TR Delwiche CF Botnen A Tengs T Jakobsen KS 《Molecular biology and evolution》2006,23(8):1504-1515
Serial transfer of plastids from one eukaryotic host to another is the key process involved in evolution of secondhand plastids. Such transfers drastically change the environment of the plastids and hence the selection regimes, presumably leading to changes over time in the characteristics of plastid gene evolution and to misleading phylogenetic inferences. About half of the dinoflagellate protists species are photosynthetic and unique in harboring a diversity of plastids acquired from a wide range of eukaryotic algae. They are therefore ideal for studying evolutionary processes of plastids gained through secondary and tertiary endosymbioses. In the light of these processes, we have evaluated the origin of 2 types of dinoflagellate plastids, containing the peridinin or 19'-hexanoyloxyfucoxanthin (19'-HNOF) pigments, by inferring the phylogeny using "covarion" evolutionary models allowing the pattern of among-site rate variation to change over time. Our investigations of genes from secondary and tertiary plastids derived from the rhodophyte plastid lineage clearly reveal "heterotachy" processes characterized as stationary covarion substitution patterns and changes in proportion of variable sites across sequences. Failure to accommodate covarion-like substitution patterns can have strong effects on the plastid tree topology. Importantly, multigene analyses performed with probabilistic methods using among-site rate and covarion models of evolution conflict with proposed single origin of the peridinin- and 19'-HNOF-containing plastids, suggesting that analysis of secondhand plastids can be hampered by convergence in the evolutionary signature of the plastid DNA sequences. Another type of sequence convergence was detected at protein level involving the psaA gene. Excluding the psaA sequence from a concatenated protein alignment grouped the peridinin plastid with haptophytes, congruent with all DNA trees. Altogether, taking account of complex processes involved in the evolution of dinoflagellate plastid sequences (both at the DNA and amino acid level), we demonstrate the difficulty of excluding independent, tertiary origin for both the peridinin and 19'-HNOF plastids involving engulfment of haptophyte-like algae. In addition, the refined topologies suggest the red algal order, Porphyridales, as the endosymbiont ancestor of the secondary plastids in cryptophytes, haptophytes, and heterokonts. 相似文献
2.
It is a central assumption of evolution that gene duplications provide the genetic raw material from which to create proteins with new functions. The increasing availability in multigene family sequences that has resulted from genome projects has inspired the creation of novel in silico approaches to predict details of protein function. The underlying principle of all such approaches is to compare the evolutionary properties of homologous sequence positions in paralogous proteins. It has been proposed that the positions that show switches in substitution rate over time-i.e., "heterotachous sites," are good indicators of functional divergence. Here, we analyzed the alpha and beta paralogous subunits of hemoglobin in search for such signatures. We found as many heterotachous sites in comparisons between groups of paralogous subunits (alpha/beta) as between orthologous ones (alpha/alpha, beta/beta). Thus, the importance of substitution rate shifts as predictors of specialization between protein subfamilies might be reconsidered. Instead, such shifts may reflect a more general process of protein evolution, consistent with the fact that they can be compatible with function conservation. As an alternative, we focused on those residues showing highly constrained states in two sequence groups, but different in each group, and we named them CBD (for "constant but different"). As opposed to heterotachous positions, CBD sites were markedly overrepresented in paralogous (alpha/beta) comparisons, as opposed to orthologous ones (alpha/alpha, beta/beta), identifying them as likely signatures of functional specialization between the two subunits. When superimposed onto the three-dimensional structure of hemoglobin, CBD positions consistently appeared to cluster preferentially on inter-subunit surfaces, two contact areas crucial to function in vertebrate tetrameric hemoglobin. The identification and analysis of CBD sites by complementing structural information with evolutionary data may represent a promising direction for future studies dealing with the functional characterization of a growing number of multigene families identified by complete genome analyses. 相似文献
3.
Shalchian-Tabrizi K Minge MA Cavalier-Smith T Nedreklepp JM Klaveness D Jakobsen KS 《The Journal of eukaryotic microbiology》2006,53(3):217-224
Dinoflagellates harbour diverse plastids obtained from several algal groups, including haptophytes, diatoms, cryptophytes, and prasinophytes. Their major plastid type with the accessory pigment peridinin is found in the vast majority of photosynthetic species. Some species of dinoflagellates have other aberrantly pigmented plastids. We sequenced the nuclear small subunit (SSU) ribosomal RNA (rRNA) gene of the "green" dinoflagellate Gymnodinium chlorophorum and show that it is sister to Lepidodinium viride, indicating that their common ancestor obtained the prasinophyte (or other green alga) plastid in one event. As the placement of dinoflagellate species that acquired green algal or haptophyte plastids is unclear from small and large subunit (LSU) rRNA trees, we tested the usefulness of the heat shock protein (Hsp) 90 gene for dinoflagellate phylogeny by sequencing it from four species with aberrant plastids (G. chlorophorum, Karlodinium micrum, Karenia brevis, and Karenia mikimotoi) plus Alexandrium tamarense, and constructing phylogenetic trees for Hsp90 and rRNAs, separately and together. Analyses of the Hsp90 and concatenated data suggest an ancestral origin of the peridinin-containing plastid, and two independent replacements of the peridinin plastid soon after the early radiation of the dinoflagellates. Thus, the Hsp90 gene seems to be a promising phylogenetic marker for dinoflagellate phylogeny. 相似文献
4.
Covarion models of molecular evolution allow the rate of evolution of a site to vary through time. There are few simple and effective tests for covarion evolution, and consequently, little is known about the presence of covarion processes in molecular evolution. We describe two new tests for covarion evolution and demonstrate with simulations that they perform well under a wide range of conditions. A survey of covarion evolution in sequenced plastid genomes found evidence of covarion drift in at least 26 out of 57 genes. Covarion evolution is most evident in first and second codon positions of the plastid genes, and there is no evidence of covarion evolution in third codon positions. Therefore, the significant covarion tests are likely due to changes in the selective constraints of amino acids. The frequency of covarion evolution within the plastid genome suggests that covarion processes of evolution were important in generating the observed patterns of sequence variation among plastid genomes. 相似文献
5.
Wilson RJ 《Journal of molecular biology》2002,319(2):257-274
This review offers a snapshot of our current understanding of the origin, biology, and metabolic significance of the non-photosynthetic plastid organelle found in apicomplexan parasites. These protists are of considerable medical and veterinary importance world-wide, Plasmodium spp., the causative agent of malaria being foremost in terms of human disease. It has been estimated that approximately 8% of the genes currently recognized by the malarial genome sequencing project (now nearing completion) are of bacterial/plastid origin. The bipartite presequences directing the products of these genes back to the plastid have provided fresh evidence that secondary endosymbiosis accounts for this organelle's presence in these parasites. Mounting phylogenetic evidence has strengthened the likelihood that the plastid originated from a red algal cell. Most importantly, we now have a broad understanding of several bacterial metabolic systems confined within the boundaries of the parasite plastid. The primary ones are type II fatty acid biosynthesis and isoprenoid biosynthesis. Some aspects of heme biosynthesis also might take place there. Retention of the plastid's relict genome and its still ill-defined capacity to participate in protein synthesis might be linked to an important house-keeping process, i.e. guarding the type II fatty acid biosynthetic pathway from oxidative damage. Fascinating observations have shown the parasite plastid does not divide by constriction as in typical plants, and that plastid-less parasites fail to thrive after invading a new cell. The modes of plastid DNA replication within the phylum also have provided surprises. Besides indicating the potential of the parasite plastid for therapeutic intervention, this review exposes many gaps remaining in our knowledge of this intriguing organelle. The rapid progress being made shows no sign of slackening. 相似文献
6.
The genes for both subunits of Rubisco (rbcL, rbcS) are located on the plastome of the brown alga Ectocarpus siliculosus (Chromophyta, Phaeophyceae). The organization of these genes in the form of an operon was similar to that found in rhodoplasts, cyanobacteria and the plastids of Cryptomonas . Sequence analysis of the complete operon revealed a high degree of homology and great structural similarities to corresponding genes from two red algae. In contrast, sequence homology to Rubisco genes from chloroplasts and cyanobacteria was much lower. This clearly indicated a close phylogenetic relationship between the plastids of Rhodophyta and Chromophyta which seem to have evolved independently from the chloroplasts (polyphyletic origin). Our data suggest that the plastids of Chromophyta and Cryptophyta have originated from endosymbiotic unicellular red algae. Surprisingly, red and brown algal Rubiscos show a significantly higher degree of homology to that from a hydrogen bacterium than to those from cyanobacteria. 相似文献
7.
C. W. Cunningham H. Zhu D. M. Hillis 《Evolution; international journal of organic evolution》1998,52(4):978-987
Despite the proliferation of increasingly sophisticated models of DNA sequence evolution, choosing among models remains a major problem in phylogenetic reconstruction. The choice of appropriate models is thought to be especially important when there is large variation among branch lengths. We evaluated the ability of nested models to reconstruct experimentally generated, known phylogenies of bacteriophage T7 as we varied the terminal branch lengths. Then, for each phylogeny we determined the best-fit model by progressively adding parameters to simpler models. We found that in several cases the choice of best-fit model was affected by the parameter addition sequence. In terms of phylogenetic performance, there was little difference between models when the ratio of short: long terminal branches was 1:3 or less. However, under conditions of extreme terminal branch-length variation, there were not only dramatic differences among models, but best-fit models were always among the best at overcoming long-branch attraction. The performance of minimum-evolution-distance methods was generally lower than that of discrete maximum-likelihood methods, even if maximum-likelihood methods were used to generate distance matrices. Correcting for among-site rate variation was especially important for overcoming long-branch attraction. The generality of our conclusions is supported by earlier simulation studies and by a preliminary analysis of mitochondrial and nuclear sequences from a well-supported four-taxon amniote phylogeny. 相似文献
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Rates of molecular evolution in tree ferns are associated with body size,environmental temperature,and biological productivity 下载免费PDF全文
Luis E. Eguiarte 《Evolution; international journal of organic evolution》2018,72(5):1050-1062
Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population‐level factors to better understand the processes affecting the tempo of evolution at the molecular level. 相似文献
10.
Sedoheptulose-1,7-bisphosphatase (SBPase) and fructose-1,6-bisphosphatase (FBPase) are essential nuclear-encoded enzymes involved in land plant Calvin cycle and gluconeogenesis. In this study, we cloned seven SBP and seven FBP cDNAs/genes and established sequences from all lineages of photosynthetic eukaryotes, in order to investigate their origin and evolution. Our data are best explained by a single recruitment of plastid-targeted SBP in Plantae after primary endosymbiosis and a further distribution to algae with complex plastids. While SBP is universally found in photosynthetic lineages, its presence in apicomplexa, ciliates, trypanosomes, and ascomycetes is surprising given that no metabolic function beyond the one in the plastid Calvin cycle is described so far. Sequences of haptophytes, cryptophytes, diatoms, and peridinin-containing dinoflagellates (complex red lineage) strongly group together in the SBP tree and the same assemblage is recovered for plastid-targeted FBP sequences, although this is less supported. Both SBP and plastid-targeted FBP are most likely of red algal origin. Including phosphoribulokinase, fructose bisphosphate aldolase, and glyceraldehyde-3-phosphate dehydrogenase, a total of five independent plastid-related nuclear-encoded markers support a common origin of all complex rhodoplasts via a single secondary endosymbiosis event. However, plastid phylogenies are incongruent with those of the host cell, as illustrated by the cytosolic FBP isoenzyme. These results are discussed in the context of Cavalier-Smith's far-reaching chromalveolate hypothesis. In our opinion, a more plausible evolutionary scenario would be the establishment of a unique secondary rhodoplast and its subsequent spread via tertiary endosymbioses. 相似文献
11.
The photosynthetic chloroplast is the hallmark organelle of green plants. During the endosymbiotic evolution of chloroplasts, the vast majority of genes from the original cyanobacterial endosymbiont were transferred to the host cell nucleus. Chloroplast biogenesis therefore requires the import of nucleus-encoded proteins from their site of synthesis in the cytosol. The majority of proteins are imported by the activity of Toc and Tic complexes located within the chloroplast envelope. In addition to chloroplasts, plants have evolved additional, non-photosynthetic plastid types that are essential components of all cells. Recent studies indicate that the biogenesis of various plastid types relies on distinct but homologous Toc-Tic import pathways that have specialized in the import of specific classes of substrates. These different import pathways appear to be necessary to balance the essential physiological role of plastids in cellular metabolism with the demands of cellular differentiation and plant development. 相似文献
12.
Dong Zhang Liping Yan Ming Zhang Hongjun Chu Jie Cao Kai Li Defu Hu Thomas Pape 《International journal of biological sciences》2016,12(5):489-504
The complete mitogenome of the horse stomach bot fly Gasterophilus pecorum (Fabricius) and a near-complete mitogenome of Wohlfahrt''s wound myiasis fly Wohlfahrtia magnifica (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, Pollenia + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included. 相似文献
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Bodył A 《Plant biology (Stuttgart, Germany)》2004,6(5):e1-e1
Plastids with four envelope membranes have evolved from red and green algae engulfed by phagotrophic protozoans. It is assumed that the Sec translocon resides in their outermost membrane, while in the two innermost membranes the Toc-Tic supercomplex is embedded. However, such a single Sec/single Toc-Tic model cannot explain the passage of proteins across the second (or periplastid) membrane which represents the endosymbiont plasmalemma. One of the most recent models postulates that this membrane contains the Toc75 channel which was relocated here from the endosymbiont plastid. Unfortunately, the precursor of this protein carries a bipartite presequence, which means that its insertion into the new membrane would require relocation and/or modification of two different processing peptidases. I suggest that these obstacles can be easily bypassed by the assumption that the mitochondrial Tim23 channel was inserted into the endosymbiont plasmalemma. In contrast to Toc75, this protein has an internal, uncleavable targeting signal and its insertion into the new membrane would require neither relocation nor modification of additional proteins. Besides, such a relocated Tim23 channel could import not only plastid, but also mitochondrial proteins. I hypothesize that from the latter proteins, initially directed to the endosymbiont mitochondrion, periplastid proteins have evolved which are now targeted to the former cytosol and/or nucleus of the eukaryotic algal endosymbiont. 相似文献
15.
Echinocereus is a morphologically diverse genus that includes 64 species grouped into eight taxonomic sections based on morphological traits. In previous molecular phylogenetic analyses, the relationships amongst Echinocereus species were not entirely revealed and useful characters to recognize clades were not provided. The inclusion of several sources of evidence in a phylogenetic analysis is likely to produce more supported hypotheses. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses were mostly congruent. However, the relationships of E. poselgeri were not consistent between analyses. A second Bayesian analysis using a long-branch extraction test resulted in a topology with the morphological position of E. poselgeri congruent with that in parsimony analysis. Parsimony and Bayesian analyses corroborated the monophyly of Echinocereus, which included eight monophyletic groups. The combined phylogeny integrated into different clades those taxa that were not determined in previous analyses and changed the relationships of some recognized clades. The clades did not recover the recent infrageneric classification. In the present study, a new sectional classification for Echinocereus is proposed based on the eight recovered clades, which is supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included. 相似文献
16.
JÉRÔME SUEUR DAN VANDERPOOL CHRIS SIMON DAVID OUVRARD THIERRY BOURGOIN 《Biological journal of the Linnean Society. Linnean Society of London》2007,91(4):611-626
To estimate the potential contribution of ethological and ecological parameters to the mechanisms of species formation and species isolation in the Palearctic cicada genus Tibicina , we constructed a molecular phylogenetic hypothesis of extant Tibicina species. Seven mitochondrial genes and a fragment of a nuclear gene were sequenced (3046 bp). Mitochondrial genes included 547 informative sites but the nuclear gene was too conserved to be included in the analysis. The tree was characterized by a basal polytomy indicating that Tibicina species arose rapidly. Such rapid radiation might explain the low divergence in the acoustic communication observed between species. Parameters describing habitat selection and acoustic communication were mapped onto the tree. A shift in habitat selection accompanied by acoustic changes might have contributed to one speciation event. The stochastic distribution of the same acoustic characters on the other branches of the tree implies, however, that the subtle acoustic differences between species could be the result of previous speciation events and independent evolutionary histories, rather than having contributed themselves in the speciation and isolation processes. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 611–626. 相似文献
17.
Hervé PHILIPPE 《植物分类学报》2008,46(3):274-286
Phylogenomics, the inference of phylogenetic trees using genome-scale data, is becoming the rule for resolving difficult parts of the tree of life. Its promise resides in the large amount of information available, which should eliminate stochastic error. However, systematic error, which is due to limitations of reconstruction methods, is becoming more apparent. We will illustrate, using animal phylogeny as a case study, the three most efficient approaches to avoid the pitfalls of phylogenomics (1) using a dense taxon sampling, (2) using probabilistic methods with complex models of sequence evolution that more accurately detect multiple substitutions, and (3) removing the fastest evolving part of the data (e.g., species and positions). The analysis of a dataset of 55 animal species and 102 proteins (25712 amino acid positions) shows that standard site-homogeneous model inference is sensitive to long-branch attraction artifact, whereas the site-heterogeneous CAT model is less so. The latter model correctly locates three very fast evolving species, the appendicularian tunicate Oikopleura, the acoel Convoluta and the myxozoan Buddenbrockia. Overall, the resulting tree is in excellent agreement with the new animal phylogeny, confirming that "simple" organisms like platyhelminths and nematodes are not necessarily of basal emergence. This further emphasizes the importance of secondary simplification in animals, and for organismal evolution in general. 相似文献
18.
We investigate the relationship between cultural complexity and population size in a non-technological cultural domain for which we have suitable quantitative records: folktales. We define three levels of complexity for folk narratives: the number of tale types, the number of narrative motifs, and, finally, the number of traits in variants of the same type, for two well-known tales for which we have data from previous studies. We found a positive relationship between number of tale types and population size, a negative relationship for the number of narrative motifs, and no relationship for the number of traits. The absence of a consistent relationship between population size and complexity in folktales provides a novel perspective on the current debates in cultural evolution. We propose that the link between cultural complexity and demography could be domain dependent: in some domains (e.g. technology) this link is important, whereas in others, such as folktales, complex traditions can be easily maintained in small populations as well as large ones, as they may appeal to universal cognitive biases. 相似文献
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