The last universal common ancestor (LUCA), simple or complex?

The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA

The existence of LUCA in the distant past is the logical consequence of the binary mechanism of cell division. The biosphere in which LUCA and contemporaries were living was the product of a long cellular evolution from the origin of life to the second age of the RNA world. A parsimonious scenario suggests that the molecular fabric of LUCA was much simpler than those of modern organisms, explaining why the evolutionary tempo was faster at the time of LUCA than it was during the diversification of the three domains. Although LUCA was possibly equipped with a RNA genome and most likely lacked an ATP synthase, it was already able to perform basic metabolic functions and to produce efficient proteins. However, the proteome of LUCA and its inferred metabolism remains to be correctly explored by in-depth phylogenomic analyses and updated datasets. LUCA was probably a mesophile or a moderate thermophile since phylogenetic analyses indicate that it lacked reverse gyrase, an enzyme systematically present in all hyperthermophiles. The debate about the position of Eukarya in the tree of life, either sister group to Archaea or descendants of Archaea, has important implications to draw the portrait of LUCA. In the second alternative, one can a priori exclude the presence of specific eukaryotic features in LUCA. In contrast, if Archaea and Eukarya are sister group, some eukaryotic features, such as the spliceosome, might have been present in LUCA and later lost in Archaea and Bacteria. The nature of the LUCA virome is another matter of debate. I suggest here that DNA viruses only originated during the diversification of the three domains from an RNA-based LUCA to explain the odd distribution pattern of DNA viruses in the tree of life.

The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.

Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present

Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins are mainly due to their involvement in protein-DNA and protein-protein complexes. Mutations and consequential structural alteration in the OB-fold proteins often lead to severe diseases. Here, we have investigated the structure, function and mode of action of OB-fold proteins (RPA, BRCA2, DNA ligases and SSBs1/2) in cellular pathways and their relationship with diseases and their possible use in therapeutic intervention. Due to the crucial role of OB-fold proteins in regulating the key physiological process, a detailed structural understanding in the context of underlying mechanism of action and cellular complexity offers a new avenue to target OB-proteins for therapeutic intervention.

Microbially Mediated Ore-Forming Processes and Cell Mineralization

Sedimentary black shale-hosted manganese carbonate and oxide ores were studied by high-resolution in situ detailed optical and cathodoluminescence microscopy, Raman spectroscopy, and FTIR spectroscopy to determine microbial contribution in metallogenesis. This study of the Urucum Mn deposit in Brazil is included as a case study for microbially mediated ore-forming processes. The results were compared and interpreted in a comparative way, and the data were elaborated by a complex, structural hierarchical method. The first syngenetic products of microbial enzymatic oxidation were ferrihydrite and lepidocrocite on the Fe side, and vernadite, todorokite, birnessite, and manganite on the Mn side, formed under obligatory oxic (Mn) and suboxic (Fe) conditions and close to neutral pH. Fe- and Mn-oxidizing bacteria played a basic role in metallogenesis based on microtextural features, bioindicator minerals, and embedded variable organic matter. Trace element content is determined by source of elements and microbial activity. The present Urucum (Brazil), Datangpo (China), and Úrkút (Hungary) deposits are the result of complex diagenetic processes, which include the decomposition and mineralization of cell and extracellular polymeric substance (EPS) of Fe and Mn bacteria and cyanobacteria. Heterotrophic cell colonies activated randomly in the microbialite sediment after burial in suboxic neutral/alkaline conditions, forming Mn carbonates and variable cation-bearing oxides side by side with lithification and stabilization of minerals. Deposits of variable geological ages and geographical occurrences show strong similarities and indicate two-step microbial metallogenesis: a primary chemolithoautotrophic, and a diagenetic heterotrophic microbial cycle, influenced strongly by mineralization of cells and EPSs. These processes perform a basic role in controlling major and trace element distribution in sedimentary environments on a global level and place biogeochemical constraints on the element content of natural waters, precipitation of minerals, and water contaminants.

Photoactivatable oligonucleotide probes to trap single-stranded DNA binding proteins: Updating the potential of 4-thiothymidine from a comparative study

Photoaffinity labeling (PAL) in combination with recent developments in mass spectrometry is a powerful tool for studying nucleic acid-protein interactions, enabling crosslinking of both partners through covalent bond formation. Such a strategy requires a preliminary study of the most judicious photoreactive group to crosslink efficiently with the target protein. In this study, we report a survey of three different photoreactive nucleobases (including a guanine functionalized with a benzophenone or a diazirine and the zero-length agent 4-thiothymine) incorporated in 30-mer oligonucleotides (ODN) containing a biotin moiety for selective trapping and enrichment of single-stranded DNA binding proteins (SSB). First, the conditions and efficiency of the photochemical reaction with a purified protein using human replication protein A as the relevant model was studied. Secondly, the ability of the probe as bait to photocrosslink and enrich SSB in cell lysate was addressed. Among the different ODN probes studied, we showed that 4-thiothymine was the most relevant: i) it allows efficient and specific trapping of SSB in whole cell extracts in a similar extent as the widely used diazirine, ii) it features the advantages of a zero-length agent thus retaining the physicochemical properties of the ODN bait; iii) ODN including this photochemical agent are easily accessible. In combination with mass spectrometry, the probes incorporating this nucleobase are powerful tools for PAL strategies and can be added in the toolbox of the traditional photocrosslinkers for studying DNA-protein interactions.

A Proposal of the Ur-proteome

Herein we outline a plausible proteome, encoded by assuming a primeval RNY genetic code. We unveil the primeval phenotype by using only the RNA genotype; it means that we recovered the most ancestral proteome, mostly made of the 8 amino acids encoded by RNY triplets. By looking at those fragments, it is noticeable that they are positioned, not at catalytic sites, but in the cofactor binding sites. It implies that the stabilization of a molecule appeared long before its catalytic activity, and therefore the Ur-proteome comprised a set of proteins modules that corresponded to Cofactor Stabilizing Binding Sites (CSBSs), which we call the primitive bindome. With our method, we reconstructed the structures of the "first protein modules" that Sobolevsky and Trifonov (2006) found by using only RMSD. We also examine the probable cofactors that bound to them. We discuss the notion of CSBSs as the first proteins modules in progenotes in the context of several proposals about the primitive forms of life.

Ancient, highly conserved proteins from a LUCA with complex cell biology provide evidence in support of the nuclear compartment commonality (NuCom) hypothesis

The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya.

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

The literature is replete with manuscripts describing the origin of eukaryotic cells. Most of the models for eukaryogenesis are either autogenous (sometimes called slow-drip), or symbiogenic (sometimes called big-bang). In this article, we use large and diverse suites of 'Omics' and other data to make the inference that autogeneous hypotheses are a very poor fit to the data and the origin of eukaryotic cells occurred in a single symbiosis.

The origins of cellular life

All life on earth can be naturally classified into cellular life forms and virus-like selfish elements, the latter being fully dependent on the former for their reproduction. Cells are reproducers that not only replicate their genome but also reproduce the cellular organization that depends on semipermeable, energy-transforming membranes and cannot be recovered from the genome alone, under the famous dictum of Rudolf Virchow, Omnis cellula e cellula. In contrast, simple selfish elements are replicators that can complete their life cycles within the host cell starting from genomic RNA or DNA alone. The origin of the cellular organization is the central and perhaps the hardest problem of evolutionary biology. I argue that the origin of cells can be understood only in conjunction with the origin and evolution of selfish genetic elements. A scenario of precellular evolution is presented that involves cohesion of the genomes of the emerging cellular life forms from primordial pools of small genetic elements that eventually segregated into hosts and parasites. I further present a model of the coevolution of primordial membranes and membrane proteins, discuss protocellular and non-cellular models of early evolution, and examine the habitats on the primordial earth that could have been conducive to precellular evolution and the origin of cells.

Oxygen levels and the regulation of cell adhesion in the nervous system: a control point for morphogenesis in development, disease and evolution?

In this article, I discuss the hallmarks of hypoxia in vitro and in vivo and review work showing that many types of stem cell proliferate more robustly in lowered oxygen. I then discuss recent studies showing that alterations in the levels and the types of cell and substrate adhesion molecules are a notable response to reduced O(2) levels in both cultured primary neural stem cells and brain tissues in response to hypoxia in vivo. The ability of O(2) levels to regulate adhesion molecule expression is linked to the Wnt signaling pathway, which can control and be controlled by adhesion events. The ability of O(2) levels to influence cell adhesion also has far-reaching implications for development, ischemic trauma and neural regeneration, as well as for cancer and other diseases. Finally I discuss the possibility that the fluctuations in O(2) levels known to have occurred over evolutionary time could, by influencing adhesion systems, have contributed to early symbiotic events in unicellular organisms and to the emergence of multicellularity. It is not my intention to be exhaustive in these domains, which are far from my own field of study. Rather this article is meant to provoke and stimulate thinking about molecular evolution involving O(2) sensing and signaling during eras of geologic and atmospheric change that might inform modern studies on development and disease.

Multiple human single-stranded DNA binding proteins function in genome maintenance: structural, biochemical and functional analysis

DNA exists predominantly in a duplex form that is preserved via specific base pairing. This base pairing affords a considerable degree of protection against chemical or physical damage and preserves coding potential. However, there are many situations, e.g. during DNA damage and programmed cellular processes such as DNA replication and transcription, in which the DNA duplex is separated into two single-stranded DNA (ssDNA) strands. This ssDNA is vulnerable to attack by nucleases, binding by inappropriate proteins and chemical attack. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB). All known SSBs use an oligosaccharide/oligonucleotide binding (OB)-fold domain for DNA binding. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating strand-exchange proteins and helicases, and mediation of protein-protein interactions. Recently two additional human SSBs have been identified that are more closely related to bacterial and archaeal SSBs. Prior to this it was believed that replication protein A, RPA, was the only human equivalent of bacterial SSB. RPA is thought to be required for most aspects of DNA metabolism including DNA replication, recombination and repair. This review will discuss in further detail the biological pathways in which human SSBs function.

On the origin of cells and viruses: primordial virus world scenario

It is proposed that the precellular stage of biological evolution unraveled within networks of inorganic compartments that harbored a diverse mix of virus‐like genetic elements. This stage of evolution might makes up the Last Universal Cellular Ancestor (LUCA) that more appropriately could be denoted Last Universal Cellular Ancestral State (LUCAS). Such a scenario recapitulates the ideas of J. B. S. Haldane sketched in his classic 1928 essay. However, unlike in Haldane's day, considerable support for this scenario exits today: lack of homology between core DNA replication system components in archaea and bacteria, distinct membrane chemistries and enzymes of lipid biosynthesis in archaea and bacteria, spread of several viral hallmark genes among diverse groups of viruses, and the extant archaeal and bacterial chromosomes appear to be shaped by accretion of diverse, smaller replicons. Under the viral model of precellular evolution, the key components of cells originated as components of virus‐like entities. The two surviving types of cellular life forms, archaea and bacteria, might have emerged from the LUCAS independently, along with, probably, numerous forms now extinct.

The origin of modern terrestrial life

The study of the origin of life covers many areas of expertise and requires the input of various scientific communities. In recent years, this research field has often been viewed as part of a broader agenda under the name of "exobiology" or "astrobiology." In this review, we have somewhat narrowed this agenda, focusing on the origin of modern terrestrial life. The adjective "modern" here means that we did not speculate on different forms of life that could have possibly appeared on our planet, but instead focus on the existing forms (cells and viruses). We try to briefly present the state of the art about alternative hypotheses discussing not only the origin of life per se, but also how life evolved to produce the modern biosphere through a succession of steps that we would like to characterize as much as possible.

Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes

Multicellular organization arose several times by convergence during the evolution of eukaryotes (e.g., in terrestrial plants, several lineages of "algae," fungi, and metazoans). To reconstruct the evolutionary transitions between unicellularity and multicellularity, we need a proper understanding of the origin and diversification of regulatory molecules governing the construction of a multicellular organism in these various lineages. Homeodomain (HD) proteins offer a paradigm for studying such issues, because in multicellular eukaryotes, like animals, fungi and plants, these transcription factors are extensively used in fundamental developmental processes and are highly diversified. A number of large eukaryote lineages are exclusively unicellular, however, and it remains unclear to what extent this condition reflects their primitive lack of "good building blocks" such as the HD proteins. Taking advantage from the recent burst of sequence data from a wide variety of eukaryote taxa, we show here that HD-containing transcription factors were already existing and diversified (in at least two main classes) in the last common eukaryote ancestor. Although the family was retained and independently expanded in the multicellular taxa, it was lost in several lineages of unicellular parasites or intracellular symbionts. Our findings are consistent with the idea that the common ancestor of eukaryotes was complex in molecular terms, and already possessed many of the regulatory molecules, which later favored the multiple convergent acquisition of multicellularity.

The origin and evolution of Archaea: a state of the art

Environmental surveys indicate that the Archaea are diverse and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the planet. Archaea display unique capacities, such as methanogenesis and survival at temperatures higher than 90 degrees C, that make them crucial for understanding the nature of the biota of early Earth. Molecular, genomics and phylogenetics data strengthen Woese's definition of Archaea as a third domain of life in addition to Bacteria and Eukarya. Phylogenomics analyses of the components of different molecular systems are highlighting a core of mainly vertically inherited genes in Archaea. This allows recovering a globally well-resolved picture of archaeal evolution, as opposed to what is observed for Bacteria and Eukarya. This may be due to the fact that no rapid divergence occurred at the emergence of present-day archaeal lineages. This phylogeny supports a hyperthermophilic and non-methanogenic ancestor to present-day archaeal lineages, and a profound divergence between two major phyla, the Crenarchaeota and the Euryarchaeota, that may not have an equivalent in the other two domains of life. Nanoarchaea may not represent a third and ancestral archaeal phylum, but a fast-evolving euryarchaeal lineage. Methanogenesis seems to have appeared only once and early in the evolution of Euryarchaeota. Filling up this picture of archaeal evolution by adding presently uncultivated species, and placing it back in geological time remain two essential goals for the future.

A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective

Using an algorithm for ancestral state inference of gene content, given a large number of extant genome sequences and a phylogenetic tree, we aim to reconstruct the gene content of the last universal common ancestor (LUCA), a hypothetical life form that presumably was the progenitor of the three domains of life. The method allows for gene loss, previously found to be a major factor in shaping gene content, and thus the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized. More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree. Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology.

Protein content of minimal and ancestral ribosome

Minimal genome approaches seek to define the smallest gene complement compatible with modern-type cellular life on Earth. A consensus of computational and experimental approaches indicates that a minimal genome is close to 300 protein-coding genes, if a rich medium is provided for cell growth. I relate ribosomal gene content in completely sequenced genomes to ribosomal subunit structure and approximate the protein components of the putative minimal ribosome and the ribosome of the Last Universal Common Ancestor of Life. Both sets contain between 35 and 40 proteins. There is evidence of protein-protein and protein-RNA displacement in the evolution of both ribosomal subunits.

Did life begin on the beach?

Water is one of the prerequisites of life. Further requirements are the existence of a system of interacting organic molecules capable of capturing and converting the supply of external energy and elaborating the replicating function that is needed for propagation. None of this would be possible without the existence of some means of concentrating, selecting, and then containing these mutually interacting substances in proximity to one another, i.e., a primitive cell. Starting from this hypothesis we propose a model for the development of life on Earth. Our model embodies the following new features: (1) rapid cycles of catalysis and transport of material, (2) desegregation (separation by tidal action and degradation by catalysis) as well as segregation (by chromatography on tidal beaches), (3) cross-catalysis instead of auto-catalysis, as well as (4) compartmentalization, although the latter idea is of course not new. But our "lipid first" model, in contrast to earlier "peptide first" or "RNA first" models, provides for the compartments needed to act as a cradle for the subsequent development of information- rich molecules like peptides and RNA. If anything, the earliest information-rich molecules were probably membrane-spanning peptides/proteins.

A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts

BACKGROUND

Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction.

RESULTS

This paper presents results of a comprehensive census of signal transduction proteins--histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases--encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false-negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. The total number of signal transduction proteins grows approximately as a square of genome size. While histidine kinases are found in representatives of all phyla and are distributed according to the power law, other signal transducers are abundant in certain phylogenetic groups but virtually absent in others.

CONCLUSION

The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters. The number of encoded signal transducers (or their fraction in the total protein set) can be used as a measure of the organism's ability to adapt to diverse conditions, the 'bacterial IQ', while the ratio of transmembrane receptors to intracellular sensors can be used to define whether the organism is an 'extrovert', actively sensing the environmental parameters, or an 'introvert', more concerned about its internal homeostasis. Some of the microorganisms with the highest IQ, including the current leader Wolinella succinogenes, are found among the poorly studied beta-, delta- and epsilon-proteobacteria. Among all bacterial phyla, only cyanobacteria appear to be true introverts, probably due to their capacity to conduct oxygenic photosynthesis, using a complex system of intracellular membranes. The census data, available at http://www.ncbi.nlm.nih.gov/Complete_Genomes/SignalCensus.html, can be used to get an insight into metabolic and behavioral propensities of each given organism and improve prediction of the organism's properties based solely on its genome sequence.

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

BACKGROUND

Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task.

RESULTS

We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs). We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes) of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains). We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain) are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA) of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties indicates that, even with a gain penalty of 1 (equal weights assigned to a gain and a loss), the set of 572 genes assigned to LUCA might be nearly sufficient to sustain a functioning organism. Under this gain penalty value, the numbers of horizontal gene transfer and gene loss events are nearly identical. This result holds true for two alternative topologies of the species tree and even under random shuffling of the tree. Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes.

CONCLUSIONS

The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree. Algorithms were developed for constructing parsimonious evolutionary scenarios, which include gene loss and gain events, for orthologous gene sets, given a species tree. This analysis shows, contrary to expectations, that the number of predicted HGT events that occurred during the evolution of prokaryotes might be approximately the same as the number of gene losses. The approach to the reconstruction of evolutionary scenarios employed here is conservative with regard to the detection of HGT because only patterns of gene presence-absence in sequenced genomes are taken into account. In reality, horizontal transfer might have contributed to the evolution of many other genes also, which makes it a dominant force in prokaryotic evolution.

Ancient phylogenetic relationships

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.