Molecular phylogenies in angiosperm evolution

A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes

Background

Accurate estimation of the divergence time of the extant eukaryotes is a fundamentally important but extremely difficult problem owing primarily to gross violations of the molecular clock at long evolutionary distances and the lack of appropriate calibration points close to the date of interest. These difficulties are intrinsic to the dating of ancient divergence events and are reflected in the large discrepancies between estimates obtained with different approaches. Estimates of the age of Last Eukaryotic Common Ancestor (LECA) vary approximately twofold, from ~1,100 million years ago (Mya) to ~2,300 Mya.

Results

We applied the genome-wide analysis of rare genomic changes associated with conserved amino acids (RGC_CAs) and used several independent techniques to obtain date estimates for the divergence of the major lineages of eukaryotes with calibration intervals for insects, land plants and vertebrates. The results suggest an early divergence of monocot and dicot plants, approximately 340 Mya, raising the possibility of plant-insect coevolution. The divergence of bilaterian animal phyla is estimated at ~400-700 Mya, a range of dates that is consistent with cladogenesis immediately preceding the Cambrian explosion. The origin of opisthokonts (the supergroup of eukaryotes that includes metazoa and fungi) is estimated at ~700-1,000 Mya, and the age of LECA at ~1,000-1,300 Mya. We separately analyzed the red algal calibration interval which is based on single fossil. This analysis produced time estimates that were systematically older compared to the other estimates. Nevertheless, the majority of the estimates for the age of the LECA using the red algal data fell within the 1,200-1,400 Mya interval.

Conclusion

The inference of a "young LECA" is compatible with the latest of previously estimated dates and has substantial biological implications. If these estimates are valid, the approximately 1 to 1.4 billion years of evolution of eukaryotes that is open to comparative-genomic study probably was preceded by hundreds of millions years of evolution that might have included extinct diversity inaccessible to comparative approaches.

Reviewers

This article was reviewed by William Martin, Herve Philippe (nominated by I. King Jordan), and Romain Derelle.

A molecular phylogenomic analysis of the ILR1-like family of IAA amidohydrolase genes

The ILR1-like family of hydrolase genes was initially isolated in Arabidopsis thaliana and is thought to help regulate levels of free indole-3-acetic-acid.We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve orthologous genes. The relationships among these sequences were assessed employing phylogenomic analyses to examine molecular evolution and phylogeny. The members of the ILR1-like family analysed were ILL1, ILL2, ILL3, ILL6, ILR1 and IAR3. Present evidence suggests that IAR3 has undergone the least evolution and is most conserved. This conclusion is based on IAR3 having the largest number of total interspecific orthologues, orthologous species and unique orthologues. Although less conserved than IAR3, DNA and protein sequence analyses of ILL1 and ILR1 suggest high conservation. Based on this conservation, IAR3, ILL1 and ILR1 may have had major roles in the physiological evolution of 'higher' plants. ILL3 is least conserved, with the fewest orthologous species and orthologues. The monocotyledonous orthologues for most family-members examined have evolved into two separate molecular clades from dicotyledons, indicating active evolutionary change. The monocotyledon clades are: (a) those possessing a putative endoplasmic reticulum localizing signal; and (b) those that are putative cytoplasmic hydrolases. IAR3, ILL1 and ILL6 are all highly orthologous to a gene in the gymnosperm Pinus taeda, indicating an ancient enzymatic activity. No orthologues could be detected in Chlamydomonas, moss and fern databases.

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes

We estimated the dates of the monocot-dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li-Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot-dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li-Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li-Tanimura method, we propose that monocots branched off from dicots 140-150 Myr ago (late Jurassic-early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100-115 Myr ago (Albian-Aptian of the Cretaceous). These estimates indicate that both the monocot-dicot divergence and the core eudicot's age are older than their respective fossil records.

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes

We estimated the dates of the monocot-dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li-Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot-dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li-Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li-Tanimura method, we propose that monocots branched off from dicots 140-150 Myr ago (late Jurassic-early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100-115 Myr ago (Albian-Aptian of the Cretaceous). These estimates indicate that both the monocot-dicot divergence and the core eudicot's age are older than their respective fossil records.

Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils

Many efforts to date evolutionary divergences by using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies often are attributed to the inadequacy of the fossil record, but many potential sources of error can affect molecular-based estimates. In this study, we minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes. Age estimates varied because of gene effects, codon position, lineage effects, method of inferring branch lengths, and whether or not rate constancy was assumed. However, even methods designed to ameliorate the effects of rate heterogeneity among lineages could not accommodate the substantially slower rates observed in Marattia + Angiopteris and in the tree ferns. Both of these clades of ferns have undergone dramatic decelerations in their rates of molecular evolution and are "molecular living fossils," consistent with their relative morphological stasis for the past 165-200 million years. Similar discrepancies between the fossil record and molecular-based age estimates noted in other studies may also be explained in part by violations of rate constancy among lineages.

Evolution of the angiosperms: calibrating the family tree

Growing evidence of morphological diversity in angiosperm flowers, seeds and pollen from the mid Cretaceous and the presence of derived lineages from increasingly older geological deposits both imply that the timing of early angiosperm cladogenesis is older than fossil-based estimates have indicated. An alternative to fossils for calibrating the phylogeny comes from divergence in DNA sequence data. Here, angiosperm divergence times are estimated using non-parametric rate smoothing and a three-gene dataset covering ca. 75% of all angiosperm families recognized in recent classifications. The results provide an initial hypothesis of angiosperm diversification times. Using an internal calibration point, an independent evaluation of angiosperm and eudicot origins is performed. The origin of the crown group of extant angiosperms is indicated to be Early to Middle Jurassic (179-158 Myr), and the origin of eudicots is resolved as Late Jurassic to mid Cretaceous (147-131 Myr). Both estimates, despite a conservative calibration point, are older than current fossil-based estimates.

Early Cretaceous lineages of monocot flowering plants

The phylogeny of flowering plants is now rapidly being disclosed by analysis of DNA sequence data, and currently, many Cretaceous fossils of flowering plants are being described. Combining molecular phylogenies with reference fossils of known minimum age makes it possible to date the nodes of the phylogenetic tree. The dating may be done by counting inferred changes in sequenced genes along the branches of the phylogeny and calculating change rates by using the reference fossils. Plastid DNA rbcL sequences and eight reference fossils indicate that approximately 14 of the extant monocot lineages may have diverged from each other during the Early Cretaceous >100 million years B.P. The lineages are very different in size and geographical distribution and provide perspective on flowering plant evolution.

East Gondwana ancestry of the sunflower alliance of families

The sunflower alliance of families comprises nearly 10% of all flowering plant species and includes the largest of all plant families, the sunflower family Asteraceae, which has 23,000 species, and the bellflower family Campanulaceae. Both are worldwide in distribution, but the majority of their species occur in the northern hemisphere. Recently it has been shown that a number of small, woody families from the Australian-Southwest Pacific area also belong in this relationship. Here we add yet another such family and present phylogenetic, biogeographic, and chronological analyses elucidating the origin of this large group of plants. We show that the ancestral lineages are confined to Malesia, Australia, New Guinea, and New Zealand and that the sunflower and bellflower families represent phylogenetically derived lineages within a larger group with a Cretaceous and southern-hemisphere, presumably East Gondwana, ancestry. Their highly derived position in the flowering plant phylogeny makes this significant for understanding the evolution of flowering plants in general.

Classification and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes

The MADS-box encodes a novel type of DNA-binding domain found so far in a diverse group of transcription factors from yeast, animals, and seed plants. Here, our first aim was to evaluate the primary structure of the MADS-box. Compilation of the 107 currently available MADS-domain sequences resulted in a signature which can strictly discriminate between genes possessing or lacking a MADS-domain and allowed a classification of MADS-domain proteins into several distinct subfamilies. A comprehensive phylogenetic analysis of known eukaryotic MADS-box genes, which is the first comprising animal as well as fungal and plant homologs, showed that the vast majority of subfamily members appear on distinct subtrees of phylogenetic trees, suggesting that subfamilies represent monophyletic gene clades and providing the proposed classification scheme with a sound evolutionary basis. A reconstruction of the history of the MADS-box gene subfamilies based on the taxonomic distribution of contemporary subfamily members revealed that each subfamily comprises highly conserved putative orthologs and recent paralogs. Some subfamilies must be very old (1,000 MY or more), while others are more recent. In general, subfamily members tend to share highly similar sequences, expression patterns, and related functions. The defined species distribution, specific function, and strong evolutionary conservation of the members of most subfamilies suggest that the establishment of different subfamilies was followed by rapid fixation and was thus highly advantageous during eukaryotic evolution. These gene subfamilies may have been essential prerequisites for the establishment of several complex eukaryotic body structures, such as muscles in animals and certain reproductive structures in higher plants, and of some signal transduction pathways. Phylogenetic trees indicate that after establishment of different subfamilies, additional gene duplications led to a further increase in the number of MADS-box genes. However, several molecular mechanisms of MADS-box gene diversification were used to a quite different extent during animal and plant evolution. Known plant MADS-domain sequences diverged much faster than those of animals, and gene duplication and sequence diversification were extensively used for the creation of new genes during plant evolution, resulting in a relatively large number of interacting genes. In contrast, the available data on animal genes suggest that increase in gene number was only moderate in the lineage leading to mammals, but in the case of MEF2-like gene products, heterodimerization between different splice variants may have increased the combinatorial possibilities of interactions considerably. These observations demonstrate that in metazoan and plant evolution, increased combinatorial possibilities of MADS-box gene product interactions correlated with the evolution of increasingly complex body plans.

Molecular evolution of nitrate reductase genes

To understand the evolutionary mechanisms and relationships of nitrate reductases (NRs), the nucleotide sequences encoding 19 nitrate reductase (NR) genes from 16 species of fungi, algae, and higher plants were analyzed. The NR genes examined show substantial sequence similarity, particularly within functional domains, and large variations in GC content at the third codon position and intron number. The intron positions were different between the fungi and plants, but conserved within these groups. The overall and nonsynonymous substitution rates among fungi, algae, and higher plants were estimated to be 4.33 x 10(-10) and 3.29 x 10(-10) substitutions per site per year. The three functional domains of NR genes evolved at about one-third of the rate of the N-terminal and the two hinge regions connecting the functional domains. Relative rate tests suggested that the nonsynonymous substitution rates were constant among different lineages, while the overall nucleotide substitution rates varied between some lineages. The phylogenetic trees based on NR genes correspond well with the phylogeny of the organisms determined from systematics and other molecular studies. Based on the nonsynonymous substitution rate, the divergence time of monocots and dicots was estimated to be about 340 Myr when the fungi-plant or algae-higher plant divergence times were used as reference points and 191 Myr when the rice-barley divergence time was used as a reference point. These two estimates are consistent with other estimates of divergence times based on these reference points. The lack of consistency between these two values appears to be due to the uncertainty of the reference times.

Genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution

The gene encoding the monolignol biosynthetic enzyme cinnamyl alcohol dehydrogenase (CAD, E.C. 1.1.1.195) can be expressed in response to different developmental and environmental cues. Control of Cad gene expression could involve either differential regulation of more than one Cad gene or, alternatively combinatorial regulation of a single Cad gene. In loblolly pine (Pinus taeda L.), we found several electrophoretic variants (allozymes) of CAD and a high level of heterozygosity (he = 0.46). Analysis of inheritance patterns of pine CAD allozymes gave segregation ratios that were consistent with Mendelian expectations for a single functional gene. The identity of the full-length Cad cDNA sequence was confirmed by alignment with peptide sequences obtained from purified active enzyme and by extensive similarity to Cad sequences from other species. Southern blot analysis of genomic DNA using the Cad cDNA as a hybridization probe gave simple patterns, consistent with our interpretation that pine Cad is a single-copy gene. Phylogenetic analysis and evolution rate estimates showed that Cad sequences are diverging less rapidly in the gymnosperms than in the angiosperms. The Cad mRNA was present in both lignifying tissues and a non lignifying tissue (the megagametophyte) of pine. The presence of a single gene suggests that different regulatory mechanisms for a single Cad gene, rather than differential regulation of several genes, can account for its expression in response to different cues.

Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants

We have estimated the time for the last common ancestor of extant seed plants by using molecular clocks constructed from the sequences of the chloroplastic gene coding for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and the nuclear gene coding for the small subunit of rRNA (Rrn18). Phylogenetic analyses of nucleotide sequences indicated that the earliest divergence of extant seed plants is likely represented by a split between conifer-cycad and angiosperm lineages. Relative-rate tests were used to assess homogeneity of substitution rates among lineages, and annual angiosperms were found to evolve at a faster rate than other taxa for rbcL and, thus, these sequences were excluded from construction of molecular clocks. Five distinct molecular clocks were calibrated using substitution rates for the two genes and four divergence times based on fossil and published molecular clock estimates. The five estimated times for the last common ancestor of extant seed plants were in agreement with one another, with an average of 285 million years and a range of 275-290 million years. This implies a substantially more recent ancestor of all extant seed plants than suggested by some theories of plant evolution.

Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes

Higher plants process two distinct, nuclear gene-encoded glyceraldehyde-3-phosphate dehydrogenase (GAPDH) proteins, a Calvin-cycle enzyme active within chloroplasts and a glycolytic enzyme active within the cytosol. The gene for the chloroplast enzyme was previously suggested to be of endosymbiotic origin. Since the ancestors of plastids were related to cyanobacteria, we have studied GAPDH genes in the cyanobacterium Anabaena variabilis. Our results confirm that the nuclear gene for higher plant chloroplast GAPDH indeed derives from the genome of a cyanobacterium-like endosymbiont. But two additional GAPDH genes were found in the Anabaena genome and, surprisingly, one of these sequences is very similar to nuclear genes encoding the GAPDH enzyme of glycolysis in plants, animals, and fungi. Evidence that the eukaryotic nuclear genes for glycolytic GAPDH, as well as the Calvin-cycle genes, are of eubacterial origin suggests that eukaryotic genomes are more highly chimeric than previously assumed.