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Molecular Dating of Evolutionary Events . SpringerLink

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Inference of the age of evolutionary events using statistical analysis of rates of change of DNA or amino acid sequences. Molecular dating is used in the biological sciences to estimate the age of evolutionary events. Changes to DNA and amino acid sequences accumulate continuously in the genome over time, so comparing DNA sequences between lineages allows us to estimate the time since they last shared a common ancestor. However, the rate of change varies across the genome and among species. So in order to use molecular data to date evolutionary events, we need a way of estimating the rate of change in genetic sequences over time for any given dataset. Molecular dating requires a set of homologous genetic sequences all related by descent from a single ancestral sequence , a method for inferring the number of changes that have occurred during the evolution of these sequences, and calibrating information to estimate their rate of change.

Divergence time estimates were based on a single calibration point at the BEP-PACMAD node using phytolith data, which suggests that all major grass subfamilies had diverged by 35 mya [ 66 ]. A complete chronogram is shown in Fig. The estimated divergence date for Puelioideae was Divergence times of 30 species of Poaceae based on complete chloroplast sequences.

Apr 20, - PDF | This article addresses the challenges involved in estimating the ages of clades using fossils and DNA sequences. We review the. Molecular dating is used in the biological sciences to estimate the age of evolutionary events. Changes to DNA and amino acid sequences accumulate. Molecular dating has now become a common tool for many biologists and considerable methodological improvements have been made over the last few bellasoulshop.comg: molecules ?| Must include: molecules.

Values at nodes indicate divergence dates in millions of years. The four Urochloa species are shown in bold. With our taxon sampling, the date of the Setaria-Urochloa divergence was estimated at In the clade composed by U.

The Urochloa clade had an estimated date of origin at 7. Our results place the origins of U. These hybridizations would initially take place among sexual diploids, generating hybrids at different ploidy levels [ 88 ]. Gene exchange would still be possible for sexual triploids and tetraploids, but asexual reproduction in higher ploidy levels would lead to reproductive isolation and the occurrence of microspecies with discontinuous morphological variation.

Indeed, while most accessions of U. One hexaploid sexual accession of U. The similarity between chloroplast genomes of U.

The average divergence time between U. Given the high sequence similarity between their cpDNA genomes, these combined data would indicate that a single polyploidization event took place to establish the U. However, complementary analysis of cpDNA sequence data of germplasm accessions of both species would be necessary to confirm this hypothesis. The taxonomic complexity of the Urochloa genus is also characteristic of forage grass species in general [ 95 ]. Hybridization and allopolyploidization are probably common processes in Urochloa, leading to reticulate evolution events and to potential incongruences between nuclear and chloroplast phylogenies [ 59697 ].

A recent paper on the phylogeny of photosynthesis in Paniceae using a combination of chloroplast, mitochondrial and nuclear rDNA found that phylogenies from different types of markers did differ in certain areas of the trees [ 81 ].

In order to further investigate taxonomic relationships between the species described here, the inclusion of accessions of U. In addition to larger taxon sampling, a robust nuclear phylogeny [ 5 ] would be necessary to properly identify the most likely parent species of Urochloa polyploids used as forages. Use of low-coverage Illumina sequencing allowed the successful assembly and annotation of plastid genomes in four species of Urochloa extensively used as forages in the tropics U.

Comparative analyses of these chloroplast genomes allowed the identification of sequence and structural polymorphisms that will be useful for future genetic studies in Urochloa species. Results were consistent with previous phylogenies that group U. Future phylogenetic studies based on complete plastid sequences should include diploid samples of U. The increased throughput and reduced costs of next-generation sequencing technologies bring the opportunity for the execution of phylogenetic studies based on either complete or large fragments of plastids, including a high number of taxa.

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Seed abortion in the sexual counterpart of Brachiaria brizantha apomicts Poaceae. New sexual accessions in Brachiaria.

Apomixis Newsl. Development of microsatellite markers for Brachiaria humidicola Rendle Schweick. Conservation Genet Resour. Clayton WD. Tropical grasses. In: McIvor JG, editor. Bray RA. Reconstructing reticulate evolutionary histories of plants. Trends Plant Sci. Reconstructing patterns of reticulate evolution in plants. Download references. We thank Ediene G. Gouvea, Ana Luisa S. Accession codes for plastid sequences of Poaceae species used in this study are available on Additional file 1.

MPF and AMM performed DNA extractions, assembly and annotation of plastid genomes, sequence alignments, comparative analysis of plastid genomes, phylogenetic analysis, estimation of times of divergence, and drafted the manuscript. MEF allocated resources, designed the experiments, obtained the sequencing data, supervised the study and drafted the manuscript.

All authors read and contributed written sections of the final manuscript. All authors read and approved the final manuscript. This study has been conducted in accordance with the Brazilian legislation Law The selfed clone of U. All other plant accessions used in the study are commercial varieties of U.

Marandu is deposited under code BRA, U. Basilisk under code BRA, and U. Tupi under BRA To allow additional calibration points and the comparison of evolutionary rates among all angiosperms, taxa outside the grasses were added to this initial data set as follows: the three selected coding genes were first retrieved from complete plastid genomes available in NCBI database; then additional taxa were added that had available sequence data for all three plastid regions such that the complete data set contained representatives for most angiosperm orders and most monocot families.

Variable length segments that were ambiguously aligned were manually deleted. The final alignment included taxa sampled from across the angiosperm phylogeny grasses and 90 other angiosperms and was For comparative purposes, the same topology was used for all dating analyses Fig. In this topology, the relationships inside Poaceae were constrained to match the topology previously obtained with taxa Grass Phylogeny Working Group II and relationships among angiosperms outside Poaceae were set to those inferred with taxa and 17 concatenated genes Soltis et al.

Phylograms for plastid and nuclear markers. Branch lengths are shown for the different markers. To construct our nuclear data set, we focused on completely sequenced nuclear genomes of plants, which were screened for markers that can be compared across angiosperms.

Although considering sequenced transcriptomes would have allowed us to include a larger number of species, gene representation is generally sparse in transcriptomes, and numerous sequences are incomplete, hampering accurate phylogenetic reconstructions. Predicted gene coding sequences cDNAs from 26 complete nuclear genomes of angiosperms were downloaded from Phytozome Goodstein et al. This included 5 grasses and 21 eudicots.

The genome of the lycopod Selaginella was also downloaded and used as the outgroup. Selaginella is the closest relative of angiosperms that has been completely sequenced. In addition, the assembly 3. In order to obtain phylogenetically useful markers, we generated data sets composed of one predicted transcript per taxon that presented sufficient similarity for preliminary phylogenetic evaluation. Plant nuclear genomes undergo a high number of gene duplications followed by gene losses in some lineages, which complicates the assessment of orthology, a necessary assumption in phylogenetic analyses.

These were discarded after an assessment of orthology through phylogenetic analysis of data sets that passed a number of successive quality controls, which are described below.

Each predicted transcript considering only one transcript model per gene from the Sorghum genome, used here as the reference genome, was successively used as the query of a BLAST search against each of the other genomes with the program blastn and an e-value threshold of 0.

Only the markers from Sorghum that had at least one positive match in all of the other genomes were further considered. Each of these was used again as the query of a BLAST search against the genomes of the 26 other angiosperms with an e-value threshold that was raised to 10 to increase the length of the compared region. Only the best matching region returned by the BLAST search was considered, which removed segments of the predicted cDNA that were highly divergent between distantly related taxa and would be poorly aligned.

At this stage, matrices were discarded if the total alignment was smaller than bp or the smallest sequence was smaller than bp. A phylogenetic tree was inferred for each of the remaining single-gene matrices using PhyML Guindon and Gascuel under the substitution model deemed adequately parameter-rich for each data set using likelihood ratio tests done with PhyML while fixing the topology to that inferred under a HKY model.

Orthology was assessed by comparing the inferred topology with the expected species tree based on Soltis et al. An accurate estimation of the P -value by the S-H test theoretically requires that a large pool of plausible trees be sampled Goldman et al. The selected data sets might consequently include some false negatives, especially in the case of closely related paralogs. The test however represents a rapid way to compare topologies for a large number of data sets and to identify most cases of paralogy problems.

Differences between nuclear and plastid phylogenies can also be caused by incomplete lineage sorting or hybridization, but with 27 species spread so broadly across angiosperms, the resulting topological differences would be small if existent at all Maddison and Knowlesand topology tests would likely not be significant.

On the other hand, significant topological differences due to lateral gene transfer between distantly related species cannot be differentiated from paralogy problems without a careful evaluation of the gene diversity present in diverse genomes Christin et al. Our approach removes such sequences and is consequently conservative.

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The remaining alignments were assumed to be composed of only co-orthologs sensu Sonnhammer and Koonin and were used for dating analyses.

The topology corresponding to the expected species tree based on Soltis et al. Of the 27, coding sequences predicted from the Sorghum bicolor genome, had a homolog in all of the 27 other plant genomes. After removing all the alignments that were too short data sets or that produced phylogenies incompatible with the species tree data setsa total of data sets were retained. Of these, 5 were further removed because they represented duplicates that arose in the ancestor of Sorghum after the diversification of Poaceae they matched the same loci as other Sorghum markers in at least some other grasses.

The final data set included loci for a total of 83, aligned bp. Each data set was analysed with two sets of calibration points see below and with four different methods. These methods all use a Bayesian procedure and allow for rate variation among branches of the phylogenetic tree, but they differ in their assumptions.

For analyses using BEAST, two independent MCMC tree searches were run for 20, generations, with a sampling frequency of generations after a burn-in period of 5, The adequacy of the length of the analysis and burn-in period was confirmed using Tracer Rambaut and Drummond through a visual inspection of the traces for the tree likelihood and the substitution model parameters and checking that their ESS was larger than The prior on the distribution of node ages was approximated by a Yule speciation process and evolutionary rates among branches followed a log-normal distribution.

The topology was kept constant throughout the analyses, which was necessary to directly compare results across multiple software programs, models, and priors. The different markers were concatenated into a single plastid and a single nuclear data set, which were first used without data partitioning.

Additional BEAST analyses of the plastid and genome data sets allowed different substitution model parameters for 1st, 2nd and 3rd positions of codons, which did not significantly alter the results Supplementary Fig. For all analyses, ages and rates were computed as the median across the set of sampled trees. In addition, standard deviations were calculated to obtain estimates comparable across software packages. The analyses were also done with the correlated CIR model Lepage et al. Ages were retrieved from the sampled trees, with a burn-in period of cycles and a sampling frequency of 10 cycles.

The MCMC procedure was run for 1, generations, with a sampling frequency of generations after a burn-in period ofThe effect of the prior was evaluated by rerunning the analysis under external calibration only see below with different values for four priors.

With the scale in twenties of million years ago, the mean and standard deviation of the rate at the root were set successively to 0. For each of these combinations, the mean and standard deviation of the Brownian motion constant were independently changed to the following values; 0.

For these additional analyses, the burn-in period was decreased to 10, generations and the sampling frequency and number of samples toto allow additional comparisons. To evaluate the effect of sampling density, the plastid data set was reanalysed with a species sampling similar to that of the nuclear genomes.

Plastid sequences for 28 species that were identical or closely related to those in the nuclear data set Fig. In addition, to evaluate the effect of sequence length, dating analyses were repeated with a number of nucleotides corresponding to the plastid data set sampled without replacement from the nuclear data set.

Dating analyses were run without taking into account Poaceae fossils, which were compared a posteriori to the ages inferred for various nodes within grasses Table 1. The exclusion of Poaceae fossils as calibration points in the initial analysis allowed their later use to validate or invalidate the results of alternative dating hypotheses.

Fossils with reliable dates and taxonomic placement for eudicots and non-grass monocots were used to set minimal ages on stem nodes of clades to which they have been previously assigned.

These calibration densities are not equal to the marginal prior distributions, which are also influenced by the topological constraints and tree prior Heled and Drummond BEAST analyses were first run without molecular data, which showed that the marginal prior distributions take non-uniform distributions when the topology is fixed Supplementary Figs.

Based on the review by Magallon and Sandersonminimal bounds were set at In addition, a minimal age of Ma was set on the stem node of core eudicots, based on the appearance of tricolpate pollen in the fossil record Friis et al. The appearance of tricolpate pollen was also used to set a maximal age for the crown of core eudicots at Ma. The rationale behind this constraint is that, given the rich fossil record of pollen and the distinctive morphology of tricolpate pollen, it is unlikely that tricolpate pollen grains would be undetected for a long period of time after their evolution Anderson et al.

The use of maximal age constraints is controversial, but its absence can lead to unacceptably ancient divergence time estimates Hug and Roger ; Ho and Phillips Compatibility of dating analyses with fossil evidence a.

Ages not compatible with fossil evidence are indicated by an asterisk; b Elias ; c Crepet and Feldman ; d Herendeen and Cranecompared with age of the crown Poaceae; e Fox and Kochcompared with stem of core Chloridoideae; fg Prasad et al. These nine constraints are congruent with each other Christin et al.

Not all of the calibration points listed above could be placed in the phylogeny based on markers from whole genomes or the reduced phylogeny based on plastid markers.

Because of the reduced species sampling, the corresponding node was not present in these smaller phylogenies. Consequently, constraints on Buxales, Typhales, Liliales and Zingiberales were not used for these analyses.

Phytoliths are microscopic silica bodies precipitated in and around plant cells in many land plants that remain in the soil when plants die and decay Piperno The morphology of grass phytoliths varies among extant taxa, suggesting that fossil phytoliths might be assigned to specific taxonomic groups and be informative regarding the timing of speciation events Prasad et al.

Fossilized phytoliths, and especially the associated cuticles, are relatively rare in ancient soils and the described fossils are unlikely to represent the earliest appearance of the group. The 67 Ma phytoliths fossils were consequently included as a minimal age on the stem of Oryzeae last common ancestor of Oryza sativa and Microlaena stipoides. In the nuclear genomes data set, O. Strong variation in branch lengths was present in the plastid phylogeny Fig. In particular, the average length from the root of the tree to the tips of the BEP-PACMAD clade greatly exceeded that of branches leading to most other monocots, including the other graminid lineages sensu Givnish et al.

Feb 18, - Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: new insights into convergent evolution of. Apr 6, - DNA holds the story of our ancestry – how we're related to the familiar faces at family reunions as well as more ancient affairs: how we're. Jul 6, - Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. Marco Pessoa-Filho.

Comparison of the fit of different molecular clock models a. The ages estimated by BEAST are compatible with the known macrofossils, but not with phytoliths attributed to Oryzeae, even if these are attributed to more ancient ancestors of Oryzeae Table 1.

Effect of different calibrations on inferred evolutionary rates. The distribution of rates in expected mutations per site per billion years inferred by BEAST for different taxonomic groups is indicated by boxplots for external calibration only black and external calibration plus phytoliths grayfor a plastid markers and b nuclear markers.

Ages estimated under external calibration only a. In contrast, the correlated log-normal model implemented in the same software led to younger estimates for nodes within graminids, as well as older estimates for multiple nodes outsides graminids Fig.

If the prior for the standard deviation of the Brownian motion constant is very small 0. We interpreted age estimates to be incompatible with the fossil record if the maximum credible age for a given node was younger than a known fossil belonging to that clade. Comparison of age estimates produced by different methods on plastid markers. For external calibration only, ages estimated by BEAST in million years ago are compared with those produced by other methods. Black lines indicate relationships.

Using phytolith fossils as a calibration point external calibration plus phytoliths strongly affected estimated ages with all methods Table 4.

Apr 18, - These molecular dating methods require some direct or indirect input from fossil or other geological data, but they offer the hope of dating. Mar 20, - As molecular dating methods grow more sophisticated, the number of assumptions we must make about the evolutionary process increases. Jan 10, - We show that molecular dating based on a data set of plastid markers is strongly dependent on the model assumptions. In particular, an  ?Abstract · ?Methods · ?Discussion · ?Conclusion.

As illustrated with BEAST results, this extra calibration point leads to older estimates for all nodes within graminids, but has little effect on nodes within eudicots Fig. Ages estimated by BEAST in million years ago under external calibration plus phytoliths are plotted against those obtained under external calibration only. The black line indicates relationship. Ages estimated from plastid markers under external calibration plus phytoliths a. Differences in root-to-tip length between BEP-PACMAD and other taxa was smaller in the trees inferred with nuclear genomes than in those from plastid markers, with the exception of the Brassicaceae which had longer root-to-tip distances than other taxa Fig.

In the absence of constraints within grasses, the ages estimated from the transcripts were very similar among the different methods, with an age for the crown of BEP-PACMAD at With the exception of one node within eudicots at the base of Brassicaceaethese ages were, moreover, very similar to those inferred from plastid markers with BEAST Fig.

However, they were not compatible with putative Oryzeae phytoliths at 67 Ma, as the crown of the BEP clade the group containing Oryzeae was estimated at Differences between plastid and nuclear markers were not due to different species numbers or sequence length, as the data sets sampled to the same size produced similar results Supplementary Fig.

The evolutionary rates of grasses inferred from the transcripts were similar to those inferred for other groups Supplementary Fig. For external calibration only, the age estimates in million years ago are represented for nodes that were shared between phylogenetic trees of plastid and nuclear markers. Taxonomic groups are indicated on the bottom.

The last point corresponds to the crown of BEP, and the horizontal bar indicates the minimal age for the clade that would be congruent with the 67 Ma phytolith fossil Prasad et al. This constraint led to the inference of lower evolutionary rates within grasses, which fell below those for the root and most branches in eudicots and monocots Fig.

The investigated plastid genes show strong variation in branch lengths Fig. Since the time elapsed from the root to the tips is the same for all extant species, this branch-length variation must be interpreted as strong differences in evolutionary rates Gaut et al. First, higher evolutionary rates could have been sustained throughout the whole history of the clade, which would mean that the clade is of relatively recent origin.

Second, evolutionary rates could have been high during the early evolution of the clade and then later decreased, in which case the clade would be older, a scenario favored in several recent studies Leebens-Mack et al. The ages produced under these hypotheses are, however, incompatible with macrofossil evidence, as the estimated ages for most nodes are more recent than the corresponding fossils Table 1. The ages estimated with these methods are compatible with macrofossil evidence as well as geochemical proxy data i.

It has been demonstrated that both types of methods are strongly misled when their underlying model is violated Ho et al. This increase of mutation accumulation is followed by a return to rates that are typical of angiosperms in descendant taxa, as inferred by previous authors Zhong et al. Several phenomena have been presented as potential explanations for this pattern of rate variation e. In all cases, the strong rate variation observed in chloroplasts of Poaceae and other graminids is a great challenge for dating analyses, and explains the incongruence between previous angiosperm-wide analyses and our current understanding of Poaceae evolutionary history based on fossil evidence.

Due to the rate heterogeneity among lineages in the plastid genome, dating methods that differ in their assumptions produce incongruent results. Markers from other genomes can provide support in favor of one method or the other, but most phylogenetic studies in plants rely solely on markers that are easy to amplify, such as plastid markers and the nuclear internal transcribed spacers ITSthe latter being extremely difficult to align among distant taxa Smith and Donoghue ; Soltis et al.

Genome projects are generating nuclear genetic markers for an increasing number of angiosperms, which can provide new insights into plant evolution Cibrian-Jaramillo et al.

Extracting phylogenetically informative markers from these genomes is not straightforward because repeated gene duplications and losses in nuclear genomes makes the assessment of orthology difficult Chiu et al.

Nevertheless, we have shown here that a large number of reliable markers can be obtained from these genomes, which help disentangle contrasting evolutionary scenarios.

The nuclear data sets we investigated are not free of branch-length variation, but the variation is less pronounced than with plastid markers, especially in grasses Fig. Differences in model assumptions were therefore less important than with plastid markers and the different methods yielded similar results Fig. Moreover, unlike analyses based on plastid markers, the estimated dates are compatible with Poaceae macrofossils Table 1increasing our confidence in molecular dating analyses conducted with nuclear markers for the grasses.

The low number of nuclear markers presently available however limits the evolutionary insights that can be gained because many questions require large species sampling. The problem is likely to decrease with the rapid accumulation of nuclear data sets based on genome-scale projects. In the meantime, phylogenetic data sets composed of a large number of nuclear markers and multiple species can be generated through high-throughput sequencing following target enrichment e. Faircloth et al. Nevertheless, it is possible to integrate the phytolith fossils as a calibration point and obtain dates that are compatible with our current knowledge of the ages of other major angiosperm lineages; the putative Oryzeae phytoliths merely imply lower rates of molecular evolution in BEP-PACMAD grasses and higher rates in other graminids Fig.

Fossil remains provide an independent proxy for divergence times, but a reliable assignment to a specific group requires synapomorphies that are unlikely to be shared with other groups Parham et al. The only characters exclusively shared by some phytolith fossils and extant Oryzeae are the distribution of vertical bilobates in costal rows and their scooped shape Prasad et al.

Whether these traits evolved only once is unknown. A reevaluation of Poaceae diversification and therefore evolutionary rates should wait until the potential homoplasy of these phytolith characters has been adequately assessed through comparative studies based on a wide sample of extant monocots. In the meantime, our analyses can predict the consequences of the phytolith-based hypothesis for evolutionary and ecological scenarios.

If these splits occurred at or after 55 Ma Table 3then grass lineages must have spread from their Gondwanan center s of origin Bremer ; Bremer and Janssen ; Bouchenak-Khelladi et al. In contrast, under the phytolith-based age hypothesis, these divergences would have occurred during a time when there were still land connections between the southern continents; hence, vicariance may have played a larger role in early grass diversification Prasad et al.

The earliest C 4 acquisition occurred in Chloridoideae, by at least The younger of these two dates places the oldest origin of C 4 Chloridoideae potentially after the drop in pCO 2 in the early Oligocene Pagani et al. In contrast, the phytolith-based ages for Poaceae result in a scenario by which C 4 grasses appeared in the Eocene, when atmospheric CO 2 was elevated Zachos et al. Although this would necessitate a reevaluation of potential environmental drivers Urban et al.

Finally, based on analyses that did not include the fossil phytoliths from India, it has been suggested that core Pooideae evolved cold tolerance in response to climatic cooling following the Eocene—Oligocene boundary If the phytolith-based ages are used, core Pooideae are significantly older than Microfossils offer the potential to add a great deal of data to an otherwise scant grass fossil record, but until the phylogenetic informativeness of their characters is better known, their placement should be considered as hypothetical.

With the current state of knowledge, we suggest that the dates obtained with phytolith evidence should be considered as an alternative to those obtained with macrofossils only. Molecular dating methods are widely used in ecology and evolution to address diverse questions, but sufficient attention is not always given to the influence of the underlying model assumptions and placement of fossils.

Unfortunately, the estimates of evolutionary rate variation linked to the model assumptions and divergence times of key nodes linked to the placement of fossils are tightly connected and one can be confidently estimated only with an accurate knowledge of the other Magallon The comparison of different molecular markers, different calibration points and different models of evolution must be advocated to evaluate the uncertainties linked to the inferred dates and evolutionary rates.

Using the grasses as a case study, we show that strong rate variation of plastid markers among branches of the phylogeny mislead analyses when using a method that assumes an autocorrelation of evolutionary rates.


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