The tree of life: introduction to an evolutionary debate

The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even some aspects of the standard evolutionary understanding of eukaryotes. These discussions have arisen out of a multidisciplinary collaboration of people with an interest in the Tree of Life, and we suggest that this sort of focused engagement enables a practical understanding of the relationships between biology, philosophy and history.     

Experimental analysis of character coupling across a complex life cycle: Pigment pattern metamorphosis in the tiger salamander,Ambystoma tigrinum tigrinum

Developmental relationships among characters are expected to bias patterns of morphological variation at the population level. Studies of character development thus can provide insights into processes of adaptation and the evolutionary diversification of morphologies. Here I use experimental manipulations to test whether larval and adult pigment patterns are coupled across metamorphosis in the tiger salamander, Ambystoma tigrinum tigrinum (Ambystomatidae). Previous investigations showed that the early larval pigment pattern depends on interactions between pigment cells and the lateral line sensory system. In contrast, the results of this study demonstrate that the major features of the adult pigment pattern develop largely independently of both the early larval pattern and the lateral lines. These results suggest that ontogenetic changes that occur across metamorphosis decouple larval and adult pigment patterns and could thereby facilitate independent evolutionary modifications to the patterns during different stages of the life cycle. J. Morphol. 237:53–67, 1998. © 1998 Wiley-Liss, Inc.     

Deep Phylogeny��How a Tree Can Help Characterize Early Life on Earth

The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history.

“You know, a tree is a tree.  How many more do you need to look at?”–Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966

The following article addresses a period in life most removed from life’s origins compared with other articles in this collection. The article discusses an advanced form of life that seems to have lived on the order of 3.5–4.0 billion years ago, around the time when life as we know it began to diversify in a Darwinian sense. The life from this geological period is located deep within an illustrated taxonomic tree of life. The hope is that by understanding how early life evolved, we can better understand how life originated. In this sense, the article attempts to travel backwards in time, starting from modern organisms, to understand life’s origin.The Darwinian concept of evolution suggests that all modern life shares a single common ancestor, often referred to as the last universal common ancestor (LUCA). Throughout evolutionary history, this ancestor has for the most part generated descendants as successive bifurcations in a tree-like manner. This so called Tree of Life, and phylogenetics in general provides much of the framework for the field of molecular evolution. Taxonomic trees allow us to better understand relationships and commonalities shared by life. For instance, a tree may tell us whether a trait or phenotype shared between two organisms is the result of shared-common ancestry (termed homologous traits) or whether the trait has evolved multiple times independent of ancestry (analogous traits such as wings).Taxonomic trees can be built using diverse sources of information. These can include morphological and phenotypic data at the macro-level down to DNA and protein sequence data at the micro-level. Ideally, trees built from multiple sources of input have identical taxonomic relationships and branching patterns, and such trees are said to be congruent. In practice, however, trees built from morphological data (say, presence or absence of wings) are often different than a tree built from molecular data (DNA or protein sequences). This requires the biologist to determine which of the two data sets is misleading and/or which taxonomic tree-building algorithm is most appropriate to use for a particular data set. Such an artform is common in the field of molecular evolution because rarely are trees congruent when built from two sources of input data.In light of this fact, we have provided the quote at the beginning of this article as a reflection about the field of molecular evolution and its interpretations of taxonomic trees. Although Reagan was not speaking about taxonomic trees in his quote, the same sort of disconnect exists between evolutionary biologists and molecular biologists (Woese and Goldenfeld 2009), as it did between conservationists and Ronald Reagan. A molecular biologist may be inclined to say that once you have seen one phylogenetic tree, you have seen them all. And in fairness, there is some validity to such a notion because historically a phylogenetic tree could not help a molecular biologist to better describe their system. An evolutionary biologist, however, will argue that individual trees have nuances that can dramatically alter our interpretation of evolutionary processes.We intend to show in this article that not all (taxonomic) trees look similar and describe identical evolutionary scenarios. We will discuss how our concept of the Tree of Life has changed over the past couple of decades, how trees can be interpreted, and what a tree can tell us about early life. In particular, the article will focus on the temperature conditions of early life because this topic has received much attention over the past few years as a direct result of improved DNA sequencing technology and a better understanding of molecular evolutionary processes. We will also describe how trees can be used to guide laboratory experiments in our attempt to understand ancient life. Lastly, we will discuss how phylogenetic trees will serve as the foundation for an “evolutionary synthetic biology” that should allow us to better understand the evolution of cellular pathways, macromolecular machines such as the ribosome, and other emergent properties of early life.     

生命之树与进化模式:导言

One and half centuries ago, Charles Darwin (1859) presented overwhelming evidence and argued that all life on the earth shared common descent, and "from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved". Ernst Haeckel (1886) and several of his contemporaries attempted to trace the pattern of descent among all extant and extinct forms in what Darwin referred to as "the great Tree of Life". Ever since then, systematists and evolutionary biologists have been exploring morphological, cytogenetic, chemical, developmental and molecular characters, and actively developing theories and methods to infer phylogenetic relationships among organisms from these characters. This endeavor has been especially stimulated by the rise of molecular biology and the emergence of computer science over the past 50 years. At the beginning of the 21st century, we are presented with an unprecedented opportunity to reconstruct the entire Tree of Life, and further, to study evolutionary processes and mechanisms in the context of a robust phylogenetic framework.     

Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.     

Neutral biodiversity theory can explain the imbalance of phylogenetic trees but not the tempo of their diversification

Numerous evolutionary studies have sought to explain the distribution of diversity across the limbs of the tree of life. At the same time, ecological studies have sought to explain differences in diversity and relative abundance within and among ecological communities. Traditionally, these patterns have been considered separately, but models that consider processes operating at the level of individuals, such as neutral biodiversity theory (NBT), can provide a link between them. Here, we compare evolutionary dynamics across a suite of NBT models. We show that NBT can yield phylogenetic tree topologies with imbalance closely resembling empirical observations. In general, metacommunities that exhibit greater disparity in abundance are characterized by more imbalanced phylogenetic trees. However, NBT fails to capture the tempo of diversification as represented by the distribution of branching events through time. We suggest that population-level processes might therefore help explain the asymmetry of phylogenetic trees, but that tree shape might mislead estimates of evolutionary rates unless the diversification process is modeled explicitly.     

Cave-adapted evolution in the North American amblyopsid fishes inferred using phylogenomics and geometric morphometrics

Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to pigmentation and eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. We use the North American amblyopsid fishes, a family spanning a wide degree of cave adaptation, to examine the impact of cave specialization on the modes and tempo of evolution. We reconstruct evolutionary relationships using ultraconserved element loci, estimate the ancestral histories of eye-state, and examine the impact of cave adaptation on body shape evolution. Our phylogenomic analyses provide a well-supported hypothesis for amblyopsid evolutionary relationships. The obligate blind cavefishes form a clade and the cave-facultative eyed spring cavefishes are nested within the obligate cavefishes. Using ancestral state reconstruction, we find support for at least two independent subterranean colonization events within the Amblyopsidae. Eyed and blind fishes have different body shapes, but not different rates of body shape evolution. North American amblyopsids highlight the complex nature of cave-adaptive evolution and the necessity to include multiple lines of evidence to uncover the underlying processes involved in the loss of complex traits.     

BOOM AND BUST: ANCIENT AND RECENT DIVERSIFICATION IN BICHIRS (POLYPTERIDAE: ACTINOPTERYGII), A RELICTUAL LINEAGE OF RAY‐FINNED FISHES

Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species‐rich clades, but also those that maintain species‐poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species‐poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray‐finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray‐finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5–83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high‐diversity intervals in the geological past suggest a “boom and bust” pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so‐called “living fossils.”     

Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)

The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts in diversification rates and if exceptional species richness can be explained by clade age alone. A single significant rapid rate shift increase is detected within the evolutionary history of the African subfamily Pseudocrenilabrinae, which includes the haplochromins of the East African Great Lakes. Several lineages from the subfamilies Pseudocrenilabrinae (Australotilapiini, Oreochromini) and Cichlinae (Heroini) exhibit exceptional species richness given their clade age, a net rate of diversification, and relative rates of extinction, indicating that clade age alone is not a sufficient explanation for their increased diversity. Our results indicate that the Neotropical Cichlinae includes lineages that have not experienced a significant rapid burst in diversification when compared to certain African lineages (rift lake). Neotropical cichlids have remained comparatively understudied with regard to macroevolutionary patterns relative to African lineages, and our results indicate that of Neotropical lineages, the tribe Heroini may have an elevated rate of diversification in contrast to other Neotropical cichlids. These findings provide insight into our understanding of the diversification patterns across taxonomically disparate lineages in this diverse clade of freshwater fishes and one of the most species-rich families of vertebrates.     

The myth of bacterial species and speciation

The Tree of Life hypothesis frames the evolutionary process as a series of events whereby lineages diverge from one another, thus creating the diversity of life as descendent lineages modify properties from their ancestors. This hypothesis is under scrutiny due to the strong evidence for lateral gene transfer between distantly related bacterial taxa, thereby providing extant taxa with more than one parent. As a result, one argues, the Tree of Life becomes confounded as the original branching structure is gradually superseded by reticulation, ultimately losing its ability to serve as a model for bacterial evolution. Here we address a more fundamental issue: is there a Tree of Life that results from bacterial evolution without considering such lateral gene transfers? Unlike eukaryotic speciation events, lineage separation in bacteria is a gradual process that occurs over tens of millions of years, whereby genetic isolation is established on a gene-by-gene basis. As a result, groups of closely related bacteria, while showing robust genetic isolation as extant lineages, were not created by an unambiguous series of lineage-splitting events. Rather, a temporal fragmentation of the speciation process results in cognate genes showing different genetic relationships. We argue that lineage divergence in bacteria does not produce a tree-like framework, and inferences drawn from such a framework have the potential to be incorrect and misleading. Therefore, the Tree of Life is an inappropriate paradigm for bacterial evolution regardless of the extent of gene transfer between distantly related taxa.     

Rates of morphological evolution are correlated with species richness in salamanders

The tempo and mode of species diversification and phenotypic evolution vary widely across the tree of life, yet the relationship between these processes is poorly known. Previous tests of the relationship between rates of phenotypic evolution and rates of species diversification have assumed that species richness increases continuously through time. If this assumption is violated, simple phylogenetic estimates of net diversification rate may bear no relationship to processes that influence the distribution of species richness among clades. Here, we demonstrate that the variation in species richness among plethodontid salamander clades is unlikely to have resulted from simple time-dependent processes, leading to fundamentally different conclusions about the relationship between rates of phenotypic evolution and species diversification. Morphological evolutionary rates of both size and shape evolution are correlated with clade species richness, but are uncorrelated with simple estimators of net diversification that assume constancy of rates through time. This coupling between species diversification and phenotypic evolution is consistent with the hypothesis that clades with high rates of morphological trait evolution may diversify more than clades with low rates. Our results indicate that assumptions about underlying processes of diversity regulation have important consequences for interpreting macroevolutionary patterns.     

DO REEFS DRIVE DIVERSIFICATION IN MARINE TELEOSTS? EVIDENCE FROM THE PUFFERFISH AND THEIR ALLIES (ORDER TETRAODONTIFORMES)

A major challenge in evolutionary biology lies in explaining patterns of high species numbers found in biodiversity hot spots. Tropical coral reefs underlie most marine hot spots and reef-associated fish faunas represent some of the most diverse assemblages of vertebrates on the planet. Although the standing diversity of modern reef fish clades is usually attributed to their ecological association with corals, untangling temporal patterns of codiversification has traditionally proved difficult. In addition, owing to uncertainty in higher-level relationships among acanthomorph fish, there have been few opportunities to test the assumption that reef-association itself leads to higher rates of diversification compared to other habitats. Here we use relaxed-clock methods in conjunction with statistical measures of species accumulation and phylogenetic comparative methods to clarify the temporal pattern of diversification in reef and nonreef-associated lineages of tetraodontiforms, a morphologically diverse order of teleost fish. We incorporate 11 fossil calibrations distributed across the tetraodontiform tree to infer divergence times and compare results from models of autocorrelated and uncorrelated evolutionary rates. All major tetraodontiform reef crown groups have significantly higher rates of diversification than the order as a whole. None of the nonreef-associated families show this pattern with the exception of the aracanid boxfish. Independent contrasts analysis also reveals a significantly positive relationship between diversification rate and proportion of reef-associated species within each family when aracanids are excluded. Reef association appears to have increased diversification rate within tetraodontiforms. We suggest that both intrinsic factors of reef habitat and extrinsic factors relating to the provincialization and regionalization of the marine biota during the Miocene (about 23-5 MY) played a role in shaping these patterns of diversity.     

Testing alternative hypotheses for evolutionary diversification in an African songbird: rainforest refugia versus ecological gradients

Geographic isolation in rainforest refugia and local adaptation to ecological gradients may both be important drivers of evolutionary diversification. However, their relative importance and the underlying mechanisms of these processes remain poorly understood because few empirical studies address both putative processes in a single system. A key question is to what extent is divergence in signals that are important in mate and species recognition driven by isolation in rainforest refugia or by divergent selection across ecological gradients? We studied the little greenbul, Andropadus virens, an African songbird, in Cameroon and Uganda, to determine whether refugial isolation or ecological gradients better explain existing song variation. We then tested whether song variation attributable to refugial or ecological divergence was biologically meaningful using reciprocal playback experiments to territorial males. We found that much of the existing song variation can be explained by both geographic isolation and ecological gradients, but that divergence across the gradient, and not geographic isolation, affects male response levels. These data suggest that ecologically divergent traits, independent of historical isolation during glacial cycles, can promote reproductive isolation. Our study provides further support for the importance of ecology in explaining patterns of evolutionary diversification in ecologically diverse regions of the planet.     

Regional variation in the historical components of global avian species richness

Aim Using a global data base of the distribution of extant bird species, we examine the evidence for spatial variation in the evolutionary origins of contemporary avian diversity. In particular, we assess the possible role of the timing of mountain uplift in promoting diversification in different regions. Location Global. Methods We mapped the distribution of avian richness at four taxonomic levels on an equal‐area 1° grid. We examined the relationships between richness at successive taxonomic levels (e.g. species richness vs. genus richness). We mapped the residuals from linear regressions of these relationships to identify areas that are exceptional in the number of lower taxa relative to the number of higher taxa. We use generalized least squares models to test the influence of elevation range and temperature on lower‐taxon richness relative to higher‐taxon richness. Results Peaks of species richness in the Neotropics were congruent with patterns of generic richness, whilst peaks in Australia and the Himalayas were congruent with patterns of both genus and family richness. Hotspots in the Afrotropics did not reflect higher‐taxon patterns. Regional differences in the relationship between richness at successive taxonomic levels revealed variation in patterns of taxon co‐occurrence. Species and genus co‐occurrence was positively associated with elevational range across much of the world. Taxon occurrence in the Neotropics was associated with a positive interaction between elevational range and temperature. Conclusions These results demonstrate that contemporary patterns of richness show different associations with higher‐taxon richness in different regions, which implies that the timing of historical effects on these contemporary patterns varies across regions. We suggest that this is due to dispersal limitation and phylogenetic constraints on physiological tolerance limits promoting diversification. We speculate that diversification rates respond to long‐term changes in the Earth's topography, and that the role of tropical mountain ranges is implicated as a correlate of contemporary diversity, and a source of diversification across avian evolutionary history.     

New insights into the phylogenetic relationships, character evolution, and phytogeographic patterns of Calceolaria (Calceolariaceae)

Biogeographical patterns and diversification processes in Andean and Patagonian flora are not yet well understood. Calceolaria is a highly diversified genus of these areas, representing one of the most specialized plant-pollinator systems because flowers produce nonvolatile oils, a very unusual floral reward. Phylogenetic analyses with molecular (ITS and matK) and morphological characters from 103 Calceolaria species were conducted to examine relationships, to understand biogeographic patterns, and to detect evolutionary patterns of floral and ecological characters. Total evidence analysis retrieved three major clades, which strongly correspond to the three previously recognized subgenera, although only subgenus Rosula was retrieved as a monophyletic group. A single historical event explains the expansion from the southern to central Andes, while different parallel evolutionary lines show a northward expansion from the central to northern Andes across the Huancabamba Deflection, an important geographical barrier in northern Peru. Polyploidy, acquisition of elaiophores, and a nototribic pollination mechanism are key aspects of the evolutionary history of Calceolaria. Pollination interactions were more frequently established with Centris than with Chalepogenus oil-collecting bee species. The repeated loss of the oil gland and shifts to pollen as the only reward suggest an evolutionary tendency from highly to moderately specialized pollination systems.     

What causes latitudinal gradients in species diversity? Evolutionary processes and ecological constraints on swallowtail biodiversity

The latitudinal diversity gradient (LDG) is one of the most striking ecological patterns on our planet. Determining the evolutionary causes of this pattern remains a challenging task. To address this issue, previous LDG studies have usually relied on correlations between environmental variables and species richness, only considering evolutionary processes indirectly. Instead, we use a phylogenetically integrated approach to investigate the ecological and evolutionary processes responsible for the global LDG observed in swallowtail butterflies (Papilionidae). We find evidence for the 'diversification rate hypothesis' with different diversification rates between two similarly aged tropical and temperate clades. We conclude that the LDG is caused by (1) climatically driven changes in both clades based on evidence of responses to cooling and warming events, and (2) distinct biogeographical histories constrained by tropical niche conservatism and niche evolution. This multidisciplinary approach provides new findings that allow better understanding of the factors that shape LDGs.     

Temperature dependence of evolutionary diversification: differences between two contrasting model taxa support the metabolic theory of ecology

Biodiversity patterns are largely determined by variation of diversification rates across clades and geographic regions. Although there are multiple reasons for this variation, it has been hypothesized that metabolic rate is the crucial driver of diversification of evolutionary lineages. According to the metabolic theory of ecology (MTE), metabolic rate – and consequently speciation – is driven mainly by body size and environmental temperature. As environmental temperature affects metabolic rate in ecto‐ and endotherms differently, its impact on diversification rate should also differ between the two types of organisms. Employing two independent approaches, we analysed correlates of speciation rates and, ultimately, net diversification rates for two contrasting taxa: plethodontid salamanders and carnivoran mammals. Whereas in the ectothermic plethodontids speciation rates positively correlated with environmental temperature, in the endothermic carnivorans a reverse, negative correlation was detected. These findings comply with predictions of the MTE and suggest that similar geographic patterns of biodiversity across taxa (e.g. ecto‐ and endotherms) might have been generated by different ecological and evolutionary processes.     

Biological factors contributing to bark and ambrosia beetle species diversification

The study of species diversification can identify the processes that shape patterns of species richness across the tree of life. Here, we perform comparative analyses of species diversification using a large dataset of bark beetles. Three examined covariates—permanent inbreeding (sibling mating), fungus farming, and major host type—represent a range of factors that may be important for speciation. We studied the association of these covariates with species diversification while controlling for evolutionary lag on adaptation. All three covariates were significantly associated with diversification, but fungus farming showed conflicting patterns between different analyses. Genera that exhibited interspecific variation in host type had higher rates of species diversification, which may suggest that host switching is a driver of species diversification or that certain host types or forest compositions facilitate colonization and thus allopatric speciation. Because permanent inbreeding is thought to facilitate dispersal, the positive association between permanent inbreeding and diversification rates suggests that dispersal ability may contribute to species richness. Bark beetles are ecologically unique; however, our results indicate that their impressive species diversity is largely driven by mechanisms shown to be important for many organism groups.     

113 Toward Resolution of the Fuzzy Nodes in Green Plant Phylogeny

We are funded to resolve the primary pattern of evolutionary diversification among green plants, and to establish a model for doing so that will be applicable to other groups of organisms with long evolutionary histories. To achieve this goal we will 1) complete a matrix of whole genome sequences for chloroplast and mitochondria and develop either nuclear or organellar bacterial artificial chromosome, BAC, libraries for about 50 representatives of the critical deep-branching lineages of green plants; 2) produce a comprehensive set of comparable morphological and ultrastructural data for these same taxa; 3) incorporate inferences from across the phylogenetic hierarchy in green plants using methods designed to permit scaling across studies. We shall indicate how this work will link to other research being conducted on green plants and various scales, especially the concatenation of our data sets with theirs. We will present the fuzzy nodes we have chosen to resolve and discuss our choices of taxa in this preliminary report. Funded by NSF's Tree of Life Program, 2002–2006, DEB #0228655 (lead institution), #228432, #0228679, #0228729, #0228660, #0228576.     

Large-scale genome clustering across life based on a linguistic approach

With the availability of genome sequences, the possibility of new phylogenetic reconstructions arises in order to reveal genomic relationships among organisms. According to the compositional-spectra (CS) approach proposed in our previous studies, any genomic sequence can be characterized by a distribution of frequencies of imperfect matching of words (oligonucleotides). In the current application of CS-analysis, we attempted to analyze the cluster structure of genomes across life. It appeared that compositional spectra show a clear three-group clustering of the compared prokaryotic and eukaryotic genomes. Unexpectedly, this grouping seriously differs from the classical Universal Tree of Life structure represented by common kingdoms known as Eubacteria, Archaebacteria, and Eukarya. The revealed CS-clustering displays high stability, putatively reflecting its objective nature, and still enigmatic biological significance that may result from convergent evolution driven by ecological selection. We believe that our approach provides a new and wider (compared to traditional methods) perspective of extracting genomic information of high evolutionary relevance.