Why lateral gene transfer is problematic for phylogeny

More controversial is the proposal that a the eukaryotic nucleus resulted from the fusion of archaeal and bacterial genomes; and that b Gram-negative bacteria, which have two membranes, resulted from the fusion of Archaea and Gram-positive bacteria, each of which has a single membrane. More recent work proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, did result from an endosymbiotic fusion of archaeal and bacterial species.

The double membrane would be a direct result of endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. A lot of skepticism still surrounds this hypothesis; the ideas are still debated within the biological science community. There are several other competing hypotheses as to the origin of eukaryotes and the nucleus.

One idea about how the eukaryotic nucleus evolved is that prokaryotic cells produced an additional membrane which surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes.

If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely-related to eukaryotes. Another hypothesis, the nucleus-first hypothesis, proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis, however, proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus by fusion or other mechanisms to become the first eukaryotic cell.

Most interestingly, the eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity. All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data. Three hypotheses of eukaryotic and prokaryotic evolution : Three alternate hypotheses of eukaryotic and prokaryotic evolution are a the nucleus-first hypothesis, b the mitochondrion-first hypothesis, and c the eukaryote-first hypothesis.

To more accurately describe the phylogenetic relationships of life, web and ring models have been proposed as updates to tree models. In , a phylogenetic model that resembles a web or a network more than a tree was proposed.

The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. Some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development in the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts.

Phylogenetic web of life model : In the a phylogenetic model proposed by W. Visually, this concept is better represented by b the multi-trunked Ficus than by the single trunk of the oak, similar to the tree drawn by Darwin. Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure. Using the conditioned reconstruction algorithm, it proposes a ring-like model in which species of all three domains Archaea, Bacteria, and Eukarya evolved from a single pool of gene-swapping prokaryotes.

This structure is proposed as the best fit for data from extensive DNA analyses; the ring model is the only one that adequately takes HGT and genomic fusion into account. However, phylogeneticists remain highly skeptical of this model. This does not mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life.

Privacy Policy. Skip to main content. Phylogenies and the History of Life. Search for:. Perspectives on the Phylogenetic Tree. Limitations to the Classic Model of Phylogenetic Trees The concepts of phylogenetic modeling are constantly changing causing limitations to the classic model to arise.

Learning Objectives Identify the limitations to the classic model of phylogenetic trees. This is one of the reasons why no attempt to fit the model to data was made in this study.

Ge et al. Our simulation study, finally, could serve the purpose of identifying features that might distinguish data generated with or without HGT. These trends, however, can hardly be used to decide whether a given data set has or has not undergone HGT. Again, real data sets can yield star-like estimated species trees and incongruent gene trees even in the absence of HGT. More interesting is the discovery that multigene data sets simulated without HGT frequently show a positive relationship between sequence length and gene tree congruence to the estimated species tree, whereas this is usually not the case with HGT, in which case even well-resolved gene trees can be incongruent with the species tree.

Although not fully discriminative, this criterion can help distinguishing between the two alternative models, as I now discuss for the three real data sets analyzed in this study. This appears consistent with our prior about the relative importance of HGT in the two domains.

This conclusion, however, is challenged by the gene-by-gene pattern of congruence. Surprisingly, a significant correlation between sequence length and gene tree congruence to the estimated species tree was detected in Bacteria, but not in Eucarya.

This suggests that the Daubin et al. Such a moderate amount of HGT apparently does not perturb much the phylogenetic inference: the reliability of the MRP method under condition c was hardly distinguishable from the reference condition c Table 1.

This supports again the conclusion that HGT is probably not the main problem we face in bacterial phylogenomics Daubin et al. The strong heterogeneity between gene trees is most likely the consequence of standard phylogenetic artefacts, due to the very old divergence between bacterial phyla. The MITO data set, although small in size and largely misleading, similarly showed a significant correlation between sequence length and congruence between gene trees, as expected for a data set immune of HGT.

The observed correlation coefficient was even higher than most values obtained under the c and c no HGT conditions Table 3. Gene trees supported by long sequences were not significantly closer to the estimated species tree than gene trees supported by short sequences.

The observed correlation between sequence length and congruence was lower than in most data sets simulated under conditions c or c no HGT but was typical for data sets simulated under condition c with HGT; see Table 3. This result, of course, does not demonstrate that metazoa and fungi genomes have undergone HGT.

In real data, sequence length is probably less strongly correlated to the amount of phylogenetic information carried by each gene than in simulated data. It should also be noted that the species tree reconstructed in this study is nonoptimal. When the tree recovered by the detailed analysis of Philippe et al. Gene and genome duplications are frequent in Eucarya.

Like HGT, hidden paralogy can lead to incongruent gene trees, and presumably to a removal of the relationship between sequence length and congruence. The correlation between sequence length and gene tree congruence to the estimated species tree is proposed as a new potential criterion for detecting HGT in phylogenomics. Its empirical relevance obviously requires further assessment.

This study suggests that even a moderate amount of HGT essentially removes any influence of gene length on gene tree accuracy. So detecting a significant correlation should be taken as solid evidence that the considered data set is largely immune from HGT.

The reciprocal statement is less clear, however. Not observing a correlation between sequence length and gene-tree congruence to the supertree can probably happen for many reasons, as discussed above; one should not claim for the occurrence of HGT based on this sole evidence. Thanks to the use of a new stochastic model, this study suggests that supertree methods are robust enough to the occurrence of HGT, at least when HGT events occur randomly. A new criterion having some power to distinguish between HGT and other confounding factors in phylogenomics is proposed, namely the correlation between sequence length and gene tree congruence to the estimated species tree.

Further assessment of the empirical relevance of this criterion is needed. Additional perspectives include extending the approach to supermatrix methods and taking into account the statistical support for internal branches. The author thanks H. Philippe and V. Daubin for sharing data sets, and N.

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Huelsenbeck J. It is found that supertree methods are quite robust to HGT, keeping high levels of performance even when gene trees are largely incongruent with each other. Gene tree incongruence per se is not indicative of HGT. Determining if a given collection of characters is compatible or not is called the perfect phylogeny problem or character compatibility problem. It is, in general, NP-complete The Quartet fit tree similarity measure 72 , Qfit for short is a measure that receives two trees and computes the number of quartets shared by them, relative to the total number of induced quartets.

In this paper we use a variant of this measure that was first introduced in 48 : for two trees t 1 , t 2 we define. We note that according to this definition of Qfit, the mean Qfit score of two randomly chosen trees is zero see One can apply Eq.

The Robinson-Foulds symmetric difference 73 , RF for short measures the distance between two trees by counting the number of different non-trivial splits in those trees, and dividing it by the total number of non-trivial tree splits. We were interested in tree similarity, and therefore counted the number of non-trivial splits shared by the two trees in question.

Real data trees were taken from 18 for our analysis. A total of gene trees were analyzed, based on species of prokaryotes 41 archaea and 59 bacteria. The full list of species is found in 18 and is also provided in S1 table for completeness.

For the simulation study, we used our own scripts to create simulated species trees and simulated gene trees. Qfit was calculated using our own script, RF similarity was calculated using Phylip Determining if a tree was perfect with respect to a given character was done using our own script. Tree reconstruction was done using wQMC For example, given a pair of two bacteria chosen as the recipient and donor of an HGT event, and assuming that the intra-bacteria HGT rate is 0.

HGT rates were divided into four categories: archaea to archaea; archaea to bacteria; bacteria to archaea; bacteria to bacteria. Thus, a total of 64 groups of gene trees were generated for each species tree, differing in their sets of HGT rates. The simulation procedure is described in full in S 1 file, Appendix A.

As detailed in Section 2. Branch lengths in the wQMC output tree are undetermined. It is easy to see that there may be three different quartet topologies based on this 4-taxaset, namely a , b c , d , a , c b , d , and a , d b , c. We denote these three topologies as q 1 , q 2 , and q 3 respectively. We assume that among all gene trees examined, N 1 trees induce the topology q 1 , and similarly N 2 N 3 trees induce the topology q 2 q 3.

This weighting scheme is justified by the theoretical work of All data generated or analyzed during this study are included in this published article, and in the supporting files of the following previously published paper: P.

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