Inferring functional linkages between proteins from evolutionary scenarios

Identifying potential protein interactions is of great importance in understanding the topologies of cellular networks, which is much needed and valued in current systematic biological studies. The development of our computational methods to predict protein-protein interactions have been spurred on by the massive sequencing efforts of the genomic revolution. Among these methods is phylogenetic profiling, which assumes that proteins under similar evolutionary pressures with similar phylogenetic profiles might be functionally related. Here, we introduce a method for inferring functional linkages between proteins from their evolutionary scenarios. The term evolutionary scenario refers to a series of events that occurred in speciation over time, which can be reconstructed given a phylogenetic profile and a species tree. Common evolutionary pressures on two proteins can then be inferred by comparing their evolutionary scenarios, which is a direct indication of their functional linkage. This scenario method has proven to have better performance compared with the classical phylogenetic profile method, when applied to the same test set. In addition, predicted results of the two methods are found to be fairly different, suggesting the possibility of merging them in order to achieve a better performance. We analyzed the influence of the topology of the phylogenetic tree on the performance of this method, and found it to be robust to perturbations in the topology of the tree. However, if a completely random tree is incorporated, performance will decline significantly. The evolutionary scenario method was used for inferring functional linkages in 67 species, and 40,006 linkages were predicted. We examine our prediction for budding yeast and find that almost all predicted linkages are supported by further evidence.     

The future of evolutionary diversity in reef corals

One-third of the world''s reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in conjunction with geographical distributions of living reef coral species to model how extinctions are likely to affect evolutionary diversity across different ecoregions. Based on two measures—phylogenetic diversity and phylogenetic species variability—we highlight regions with the largest losses of evolutionary diversity and hence of potential conservation interest. Notably, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle, while many regions with fewer species stand to lose much larger shares of their diversity. We also suggest that for complex ecosystems like coral reefs it is important to consider changes in phylogenetic species variability; areas with disproportionate declines in this measure should be of concern even if phylogenetic diversity is not as impacted. These findings underscore the importance of integrating evolutionary history into conservation planning for safeguarding the future diversity of coral reefs.     

A framework for estimating niche metrics using the resemblance between qualitative resources

Despite the central importance of the niche concept for the ecological theory, current methods to quantify the species niche from qualitative resources, such as food or habitat types, remain insufficiently developed. Classically, information theory and diversity measures have formed the toolbox used for calculating resource niche metrics on species preference data for a set of qualitative resources. We provide a comprehensive framework that extends these classical approaches by incorporating the resemblance between resources into the calculation of resource niche metrics. This does not only allow estimation of the niche centre, breadth, overlap and displacement with greater accuracy, but also makes the estimates less influenced by the way the resources are subdivided. In addition, all niche metrics can be calculated while taking into account the variation in resource availability, and confidence intervals can be obtained by bootstrapping. We illustrate the utility of the framework with an analysis of dietary preferences in feral pigeons Columba livia.     

Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting

Analyses of the increasingly available genomic data continue to reveal the extent of hybridization and its role in the evolutionary diversification of various groups of species. We show, through extensive coalescent-based simulations of multilocus data sets on phylogenetic networks, how divergence times before and after hybridization events can result in incomplete lineage sorting with gene tree incongruence signatures identical to those exhibited by hybridization. Evolutionary analysis of such data under the assumption of a species tree model can miss all hybridization events, whereas analysis under the assumption of a species network model would grossly overestimate hybridization events. These issues necessitate a paradigm shift in evolutionary analysis under these scenarios, from a model that assumes a priori a single source of gene tree incongruence to one that integrates multiple sources in a unifying framework. We propose a framework of coalescence within the branches of a phylogenetic network and show how this framework can be used to detect hybridization despite incomplete lineage sorting. We apply the model to simulated data and show that the signature of hybridization can be revealed as long as the interval between the divergence times of the species involved in hybridization is not too small. We reanalyze a data set of 106 loci from 7 in-group Saccharomyces species for which a species tree with no hybridization has been reported in the literature. Our analysis supports the hypothesis that hybridization occurred during the evolution of this group, explaining a large amount of the incongruence in the data. Our findings show that an integrative approach to gene tree incongruence and its reconciliation is needed. Our framework will help in systematically analyzing genomic data for the occurrence of hybridization and elucidating its evolutionary role.     

Interaction network of vascular epiphytes and trees in a subtropical forest

The commensalistic interaction between vascular epiphytes and host trees is a type of biotic interaction that has been recently analysed with a network approach. This approach is useful to describe the network structure with metrics such as nestedness, specialization and interaction evenness, which can be compared with other vascular epiphyte-host tree networks from different forests of the world. However, in several cases these comparisons showed different and inconsistent patterns between these networks, and their possible ecological and evolutionary determinants have been scarcely studied. In this study, the interactions between vascular epiphytes and host trees of a subtropical forest of sierra de San Javier (Tucuman, Argentina) were analysed with a network approach. We calculated metrics to characterize the network and we analysed factors such as the abundance of species, tree size, tree bark texture, and tree wood density in order to predict interaction frequencies and network structure. The interaction network analysed exhibited a nested structure, an even distribution of interactions, and low specialization, properties shared with other obligated vascular epiphyte-host tree networks with a different assemblage structure. Interaction frequencies were predicted by the abundance of species, tree size and tree bark texture. Species abundance and tree size also predicted nestedness. Abundance indicated that abundant species interact more frequently; and tree size was an important predictor, since larger-diameter trees hosted more vascular epiphyte species than small-diameter trees. This is one of the first studies analyzing interactions between vascular epiphytes and host trees using a network approach in a subtropical forest, and taking the whole vascular epiphyte assemblage of the sampled community into account.     

The components of biodiversity,with a particular focus on phylogenetic information

We present a framework for biodiversity metrics that organizes the growing panoply of metrics. Our framework distinguishes metrics based on the type of information–abundance, phylogeny, function–and two common properties–magnitude and variability. Our new metrics of phylogenetic diversity are based on a partition of the total branch lengths of a cladogram into the proportional share of each species, including: a measure of divergence which standardizes the amount of evolutionary divergence by species richness and time depth of the cladogram; a measure of regularity which is maximal when the tree is perfectly symmetrical so that all species have the same proportional branch lengths; a measure that combines information on the magnitude and variability of abundance with phylogenetic variability, and a measure of phylogenetically weighted effective mean abundance; and indicate how those metrics can be decomposed into α and β components. We illustrate the utility of these new metrics using empirical data on the bat fauna of Manu, Peru. Divergence was greatest in lowland rainforest and at the transition between cloud and elfin forests, and least in upper elfin forests and in cloud forests. In contrast, regularity was greatest in lowland rainforest, dipping to its smallest values in mid‐elevation cloud forests, and then increasing in high elevation elfin forests. These patterns indicate that the first species to drop out with increasing elevation are ones that are closely related to other species in the metacommunity. Measures of the effective number of phylogenetically independent or distinct species decreased very rapidly with elevation, and β‐diversity was larger. In contrast, a comparison of feeding guilds shows a different effect of phylogenetic patterning. Along the elevational gradient, each guild generally loses some species from each clade–rather than entire clades–explaining the maintenance of functional diversity as phylogenetic diversity decreases.     

Is phylogenetic relatedness to native species important for the establishment of reptiles introduced to California and Florida?

Aim Charles Darwin posited that introduced species with close relatives were less likely to succeed because of fiercer competition resulting from their similarity to residents. There is much debate about the generality of this rule, and recent studies on plant and fish introductions have been inconclusive. Information on phylogenetic relatedness is potentially valuable for explaining invasion outcomes and could form part of screening protocols for minimizing future invasions. We provide the first test of this hypothesis for terrestrial vertebrates using two new molecular phylogenies for native and introduced reptiles for two regions with the best data on introduction histories. Location California and Florida, USA. Methods We performed an ordination of ecological traits to confirm that ecologically similar species are indeed closely related phylogenetically. We then inferred molecular phylogenies for introduced and native reptiles using sequence data for two nuclear and three mitochondrial genes. Using these phylogenies, we computed two distance metrics: the mean phylogenetic distance (MPD) between each introduced species and all native species in each region (which indicates the potential interactions between introduced species and all native species in the community) and the distance of each introduced species to its nearest native relative – NN (indicating the degree of similarity and associated likelihood of competition between each introduced species and its closest evolutionary analogue). These metrics were compared for introduced species that established and those that failed. Results We demonstrate that phylogenetically related species do share similar ecological functions. Furthermore, successfully introduced species are more distantly related to natives (for NN and MPD) than failed species, although variation is high. Main conclusions The evolutionary history of a region has value for explaining and predicting the outcome of human‐driven introductions of reptiles. Phylogenetic metrics are thus useful inputs to multi‐factor risk assessments, which are increasingly required for screening introduced species.     

Phylogeny of the Oriental Drosophila melanogaster species group: a multilocus reconstruction

The melanogaster species group of Drosophila (subgenus Sophophora) has long been a favored model for evolutionary studies because of its morphological and ecological diversity and wide geographic distribution. However, phylogenetic relationships among species and subgroups within this lineage are not well understood. We reconstructed the phylogeny of 17 species representing 7 "oriental" species subgroups, which are especially closely related to D. melanogaster. We used DNA sequences of four nuclear and two mitochondrial loci in an attempt to obtain the best possible estimate of species phylogeny and to assess the extent and sources of remaining uncertainties. Comparison of trees derived from single-gene data sets allowed us to identify several strongly supported clades, which were also consistently seen in combined analyses. The relationships among these clades are less certain. The combined data set contains data partitions that are incongruent with each other. Trees reconstructed from the combined data set and from internally homogenous data sets consisting of three or four genes each differ at several deep nodes. The total data set tree is fully resolved and strongly supported at most nodes. Statistical tests indicated that this tree is compatible with all individual and combined data sets. Therefore, we accepted this tree as the most likely model of historical relationships. We compared the new molecular phylogeny to earlier estimates based on morphology and chromosome structure and discuss its taxonomic and evolutionary implications.     

Inferring phylogenetic relationships avoiding forbidden rooted triplets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set C and none of the rooted triplets in another given set F. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.     

Inferring phylogenetic networks by the maximum parsimony criterion: a case study

Horizontal gene transfer (HGT) may result in genes whose evolutionary histories disagree with each other, as well as with the species tree. In this case, reconciling the species and gene trees results in a network of relationships, known as the "phylogenetic network" of the set of species. A phylogenetic network that incorporates HGT consists of an underlying species tree that captures vertical inheritance and a set of edges which model the "horizontal" transfer of genetic material. In a series of papers, Nakhleh and colleagues have recently formulated a maximum parsimony (MP) criterion for phylogenetic networks, provided an array of computationally efficient algorithms and heuristics for computing it, and demonstrated its plausibility on simulated data. In this article, we study the performance and robustness of this criterion on biological data. Our findings indicate that MP is very promising when its application is extended to the domain of phylogenetic network reconstruction and HGT detection. In all cases we investigated, the MP criterion detected the correct number of HGT events required to map the evolutionary history of a gene data set onto the species phylogeny. Furthermore, our results indicate that the criterion is robust with respect to both incomplete taxon sampling and the use of different site substitution matrices. Finally, our results show that the MP criterion is very promising in detecting HGT in chimeric genes, whose evolutionary histories are a mix of vertical and horizontal evolution. Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history.     

The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa.     

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation.     

A guide to phylogenetic metrics for conservation,community ecology and macroecology

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.     

Phylogenomic assessment of the role of hybridization and introgression in trait evolution

Trait evolution among a set of species—a central theme in evolutionary biology—has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding of trait evolution. For a trait whose states are incongruent with the branching patterns in the species tree, the same state could have arisen independently in different species (homoplasy) or followed the branching patterns of gene trees, incongruent with the species tree (hemiplasy). Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is gene flow between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of polymorphic or monomorphic binary traits. We apply the method to simulated evolutionary scenarios to demonstrate the interplay between the parameters of the evolutionary history and the role of introgression in a binary trait’s evolution (which we call xenoplasy). Very importantly, we demonstrate, including on a biological data set, that inferring a species tree and using it for trait evolution analysis in the presence of gene flow could lead to misleading hypotheses about trait evolution.     

Evolutionarily distinctive species often capture more phylogenetic diversity than expected

Evolutionary distinctiveness measures of how evolutionarily isolated a species is relative to other members of its clade. Recently, distinctiveness metrics that explicitly incorporate time have been proposed for conservation prioritization. However, we found that such measures differ qualitatively in how well they capture the total amount of evolution (termed phylogenetic diversity, or PD) represented by a set of species. We used simulation and simple graph theory to explore this relationship with reference to phylogenetic tree shape. Overall, the distinctiveness measures capture more PD on more unbalanced trees and on trees with many splits near the present. The rank order of performance was robust across tree shapes, with apportioning measures performing best and node-based measures performing worst. A sample of 50 ultrametric trees from the literature showed the same patterns. Taken together, this suggests that distinctiveness metrics may be a useful addition to other measures of value for conservation prioritization of species. The simplest measure, the age of a species, performed surprisingly well, suggesting that new measures that focus on tree shape near the tips may provide a transparent alternative to more complicated full-tree approaches.     

How well are biodiversity drivers reflected in protected areas? A representativeness assessment of the geohistorical gradients that shaped endemic flora in Japan

Protected areas function as a lifeboat that can preserve the origins and maintenance of biodiversity. We assessed the representativeness of biodiversity in existing protected areas in Japan using a distribution dataset and phylogenetic tree for 5565 Japanese vascular plant species. We first examined the overlap of species distribution with the existing protected areas and identified the minimum set representing all plant species. Second, we evaluated the relative importance of environmental variables in explaining the spatial arrangement of protected areas using a random forest model. Finally, we clarified how potential drivers of plant diversity were sufficiently captured within the protected areas network. Although the protected areas captured the majority of species, nearly half of the minimum set areas were selected from outside the existing protected areas. The locations of existing protected areas are mainly associated with geographical and socio-economic factors rather than key biodiversity features (including evolutionary distinctiveness). Moreover, critical biodiversity drivers, which include current climate, paleoclimatic stability, and geographical isolation, were biasedly emulated within the existing protected areas. These findings demonstrate that current conservation planning fails to represent the ecological and evolutionary processes relevant to species sorting, dispersal limitation, and allopatric speciation. In particular, under-representativeness of historically stable habitats that function as evolutionary hotspots or refugia in response to climate changes may pose a threat to the long-term persistence of Japan’s endemic biota. This study provides a fundamental basis for developing prioritization measures to retain species assembly processes and in situ diversification along current climatic and geohistorical gradients.     

treespace: Statistical exploration of landscapes of phylogenetic trees

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace , combines tree metrics and multivariate analysis to provide low‐dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group‐specific consensus phylogenies. treespace also provides a user‐friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results.     

Brain reorganization,not relative brain size,primarily characterizes anthropoid brain evolution

Comparative analyses of primate brain evolution have highlighted changes in size and internal organization as key factors underlying species diversity. It remains, however, unclear (i) how much variation in mosaic brain reorganization versus variation in relative brain size contributes to explaining the structural neural diversity observed across species, (ii) which mosaic changes contribute most to explaining diversity, and (iii) what the temporal origin, rates and processes are that underlie evolutionary shifts in mosaic reorganization for individual branches of the primate tree of life. We address these questions by combining novel comparative methods that allow assessing the temporal origin, rate and process of evolutionary changes on individual branches of the tree of life, with newly available data on volumes of key brain structures (prefrontal cortex, frontal motor areas and cerebrocerebellum) for a sample of 17 species (including humans). We identify patterns of mosaic change in brain evolution that mirror brain systems previously identified by electrophysiological and anatomical tract-tracing studies in non-human primates and functional connectivity MRI studies in humans. Across more than 40 Myr of anthropoid primate evolution, mosaic changes contribute more to explaining neural diversity than changes in relative brain size, and different mosaic patterns are differentially selected for when brains increase or decrease in size. We identify lineage-specific evolutionary specializations for all branches of the tree of life covered by our sample and demonstrate deep evolutionary roots for mosaic patterns associated with motor control and learning.     

MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes

The identification of orthologous genes shared by multiple genomes plays an important role in evolutionary studies and gene functional analyses. Based on a recently developed accurate tool, called MSOAR 2.0, for ortholog assignment between a pair of closely related genomes based on genome rearrangement, we present a new system MultiMSOAR 2.0, to identify ortholog groups among multiple genomes in this paper. In the system, we construct gene families for all the genomes using sequence similarity search and clustering, run MSOAR 2.0 for all pairs of genomes to obtain the pairwise orthology relationship, and partition each gene family into a set of disjoint sets of orthologous genes (called super ortholog groups or SOGs) such that each SOG contains at most one gene from each genome. For each such SOG, we label the leaves of the species tree using 1 or 0 to indicate if the SOG contains a gene from the corresponding species or not. The resulting tree is called a tree of ortholog groups (or TOGs). We then label the internal nodes of each TOG based on the parsimony principle and some biological constraints. Ortholog groups are finally identified from each fully labeled TOG. In comparison with a popular tool MultiParanoid on simulated data, MultiMSOAR 2.0 shows significantly higher prediction accuracy. It also outperforms MultiParanoid, the Roundup multi-ortholog repository and the Ensembl ortholog database in real data experiments using gene symbols as a validation tool. In addition to ortholog group identification, MultiMSOAR 2.0 also provides information about gene births, duplications and losses in evolution, which may be of independent biological interest. Our experiments on simulated data demonstrate that MultiMSOAR 2.0 is able to infer these evolutionary events much more accurately than a well-known software tool Notung. The software MultiMSOAR 2.0 is available to the public for free.     

Multiple genome rearrangement: a general approach via the evolutionary genome graph

MOTIVATION: In spite of a well-known fact that genome rearrangements are supposed to be viewed in the light of the evolutionary relationships within and between the species involved, no formal underlying framework based on the evolutionary considerations for treating the questions arising in the area has been proposed. If such an underlying framework is provided, all the basic questions in the area can be posed in a biologically more appropriate and useful form: e.g., the similarity between two genomes can then be computed via the nearest ancestor, rather than 'directly', ignoring the evolutionary connections. RESULTS: We outline an evolution-based general framework for answering questions related to the multiple genome rearrangement. In the proposed model, the evolutionary genome graph (EG-graph) encapsulates an evolutionary history of a genome family. For a set of all EG-graphs, we introduce a family of similarity measures, each defined via a fixed set of genome transformations. Given a set of genomes and restricting ourselves to the transpositions, an algorithm for constructing an EG-graph is presented. We also present the experimental results in the form of an EG-graph for a set of concrete genomes (for several species). This EG-graph turns out to be very close to the corresponding known phylogenetic tree.