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Our understanding of life in the universe comes from one sample, life on Earth. Current and next-generation space missions will target exoplanets as well as planets and moons in our own solar system with the primary goal of detecting, interpreting and characterizing indications of possible biological activity. Thus, understanding life's fundamental characteristics is increasingly critical for detecting and interpreting potential biological signatures elsewhere in the universe. Astrobiologists have outlined the essential roles of carbon and water for life, but we have yet to decipher the rules governing the evolution of how living organisms use bioessential elements. Does the suite of life's essential chemical elements on Earth constitute only one possible evolutionary outcome? Are some elements so essential for biological functions that evolution will select for them despite low availability? How would this play out on other worlds that have different relative element abundances? When we look for life in the universe, or the conditions that could give rise to life, we must learn how to recognize it in extremely different chemical and environmental conditions from those on Earth. We argue that by exposing self-organizing biotic chemistries to different combinations of abiotic materials, and by mapping the evolutionary history of metalloenzyme biochemistry onto geological availabilities of metals, alternative element choices that are very different from life's present-day molecular structure might result. A greater understanding of the paleomolecular evolutionary history of life on Earth will create a predictive capacity for detecting and assessing life's existence on worlds where alternate evolutionary paths might have been taken.

International audience; The emergence of multicellular organisms was perhaps the most spectacular of the major transitions during the evolutionary history of life on this planet [1,2]. Despite decades of research aimed at understanding this important transition, many questions remain unanswered. This special issue, "Evolution of Multicellularity", which consists of reviews, an opinion piece and original research articles, highlights and addresses some of these questions. Together these articles look at several aspects of the evolution of multicellularity, ranging from the evolution of key molecular components to the emergence of cellular and organism-level features. They consider both early events at the transition between unicellularity and multicellularity and the subsequent complexification of multicellular organisms. Together the articles present several novel observations and propose interesting new hypotheses aimed at stimulating future research in this area. Research into the evolution of multicellularity tends to involve either studies that try to understand transitions from unicellularity to multicellularity or studies that focus on the subsequent step, corresponding to the emergence of complex multicellularity (i.e. the evolution of macroscopic organisms with multiple cell types such as animals and land plants). Kin and Schaap [3] argue that this distinction is somewhat artificial and point out that, in fact, lineages may exhibit a continuum of different levels of complexity and that this continuum can provide useful material for investigating the evolutionary origins of multicellularity. One such lineage is the dictyostelid social amoebas. Analysis of this lineage supports a broad hypothesis that is probably relevant to diverse multicellular lineages [4-7]: that the adaptation of what the authors call "proto cell-types" to particular environmental conditions may have laid the foundations for the later emergence of distinct cell types in a multicellular decedent.

International audience; Palaeontology relies on the description of fossil morphologies to understand the evolutionary history of life on Earth. Yet much remains unknown about the impact of fossilization processes, even though these may introduce biases into palaeobiological interpretations.Here, we report the characterization of fossilized remains of the earliest known woody plant Armoricaphyton chateaupannense preserved either in 2D (as flat carbonaceous films) or in 3D (as organo-mineral structures) in early Devonian shales (c. 407 Ma) of the Armorican Massif on the northern margin of Gondwana.To document the fine-scale structure and the chemistry of the tracheids of this ancient plant, we used propagation phase contrast synchrotron radiation X-ray microcomputed tomography (PPC-SR mu CT), transmission electron microscopy (TEM) and synchrotron-based scanning transmission X-ray microscopy (STXM) coupled with X-ray absorption near edge structure (XANES) spectroscopy. PPC-SR mu CT enables digital visualization of cell walls in unprecedented detail for the specimens preserved in 3D revealing structures similar to those observed in extant lignified cells, thereby strongly suggesting that the earliest woody plant A. chateaupannense originally contained lignin compounds. STXM-based XANES and TEM data show that, whatever the preservation modes (3D vs 2D), the remaining organic matter has a chemical composition rather typical of pyrobitumen compounds, raising the possibility of an original source other than lignin.The pyrobitumen compounds also contains automorphic Ti-nanominerals interpreted as a diagenetic feature. Altogether, the present study illustrates that anatomical and chemical preservations may not always be correlated.

Motivation Orthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target genes for biotechnological applications and revealing the evolutionary history of life. Although its importance keeps rising with the ever-growing number of sequenced genomes, existing tools are computationally demanding and difficult to employ. Results Here, we present SonicParanoid, which is faster than, but comparably accurate to, the well-established tools with a balanced precision-recall trade-off. Furthermore, SonicParanoid substantially relieves the difficulties of orthology inference for those who need to construct and maintain their own genomic datasets. Availability and implementation SonicParanoid is available with a GNU GPLv3 license on the Python Package Index and BitBucket. Documentation is available at http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid. Supplementary information Supplementary data are available at Bioinformatics online.

Geobiology is centered on interactions of the biosphere with the atmosphere, hydrosphere, and lithosphere. In deep time geobiology has focused on critical intervals of change for Earth and its biota. Such geobiological studies include data from palaeobiology, geochemistry and sedimentary geology within an interdisciplinary framework. Palaeogenomics has a variety of research agendas, and one of them is to understand the genes involved in key changes in the evolutionary history of life and when those genes and their interactions first evolved. The combination of geobiology and palaeogenomic studies is a powerful approach which leads to a more fundamental understanding of how Earth and life have changed through time. For example, linking palaeogenomic studies of biomineralization genes in modern organisms and when they first evolved in the Cambrian with geobiological studies of the impact this had on the production of carbonate sedimentary facies such as encrinites and the development of the Neritan ocean provides a unique perspective on how genes have shaped formation of the sedimentary record. Another component of the Cambrian explosion, the evolution of vertical bioturbation at the start of the Cambrian, has had significant effects on biogeochemical cycling and sediment production, and provides an inviting target for future genomic studies. The remaining Phanerozoic includes a broad variety of evolutionary innovations which within a joint geobiological and palaeogenomic context can also be profitably studied. In pelagic environments the genomic changes leading to evolution of the calcium carbonate biomineralized skeletons of coccolithophores contributed to the widespread deposition of carbonate sediment in deep settings and development in the Mesozoic of the Cretan ocean. On land, linking palaeogenomic studies of the genes that led to the Palaeozoic evolution of lignin and their associated geobiological effects, such as deposition of coal, provide another example of the effects of genes upon development of the sedimentary record. Such work will ultimately provide a history of genomic change and the environmental factors that influenced it, as well as how genomic change influenced environments.

© 2018 The Authors. Geobiology Published by John Wiley & Sons Ltd. Photosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

Ancestor microbes started colonizing inland habitats approximately 2.7 to 3.5 billion years ago. With some exceptions, the key physiological adaptations of microbiomes associated with marine-to-land transitions have remained elusive. This is essentially caused by the lack of suitable systems that depict changes in microbiomes across sufficiently large time scales. Here, we investigate the adaptive routes taken by microbiomes along a contemporary gradient of land formation. Using functional trait-based metagenomics, we show that a switch from a microbial ‘dispersal’ to a ‘competition’ response modus best characterizes the microbial trait changes during this eco-evolutionary trajectory. The ‘dispersal’ modus prevails in microbiomes at the boundary sites between land and sea. It encompasses traits conferring cell chemosensory and motile behaviors, thus allowing the local microbes to exploit short-lived nutritional patches in high-diffusion microhabitats. A systematic transition towards the ‘competition’ modus occurs progressively as the soil matures, which is likely due to forces of viscosity or strain that favor traits for competition and chemical defense. Concomitantly, progressive increases in the abundances of genes encoding antibiotic resistance and complex organic substrate degradation were found. Our findings constitute a novel perspective on the ecology and evolution of microbiome traits, tracking back one of the most seminal transitions in the evolutionary history of life.

When and how oxygenic photosynthesis originated remains controversial. Wide uncertainties exist for the earliest detection of biogenic oxygen in the geochemical record or the origin of water oxidation in ancestral lineages of the phylum Cyanobacteria. A unique trait of oxygenic photosynthesis is that the process uses a Type I reaction centre with a heterodimeric core, also known as Photosystem I, made of two distinct but homologous subunits, PsaA and PsaB. In contrast, all other known Type I reaction centres in anoxygenic phototrophs have a homodimeric core. A compelling hypothesis for the evolution of a heterodimeric Type I reaction centre is that the gene duplication that allowed the divergence of PsaA and PsaB was an adaptation to incorporate photoprotective mechanisms against the formation of reactive oxygen species, therefore occurring after the origin of water oxidation to oxygen. Here I show, using sequence comparisons and Bayesian relaxed molecular clocks that this gene duplication event may have occurred in the early Archean more than 3.4 billion years ago, long before the most recent common ancestor of crown group Cyanobacteria and the Great Oxidation Event. If the origin of water oxidation predated this gene duplication event, then that would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

Certain lipids and biopolymers retain their original structure through sedimentary diagenesis and catagenesis that they can be assigned to a specific biological origin. These ‘‘taxon-specific biomarkers’’ (TSBs) can serve as chemical fossils that trace the evolution of life. TSBs in Early Precambrian rocks reveal the early evolution of archaea, cyanobacteria, and eukarya and the development of atmospheric free oxygen. Steroidal TSBs document the changing nature of marine phytoplankton from Neoproterozoic organic-walled acritarchs to the predominance of present day diatoms and terpanoid TSRs reveal the evolution of higher land plants. TSBs, used in conjunction with isotopic analysis, can identify the taxa of enigmatic fossils, provide important clues to the causes of mass extinctions, and describe the global changes in biotic diversity and Earth’s conditions as the biosphere recovers. Biomarkers record the evolutionary history of life on Earth and perhaps, other planets.

The evolution of microbes had been underway for about 3 billion years, covering much of the earlier evolutionary history of life. Many of the genes, molecular machines, regulatory, metabolic, and synthetic pathways found in all living organisms today evolved first in microorganisms. Even now, most of the biodiversity of life on Earth is microbial. The great diversity of microbes allows them to synthesize or break down a vast range of chemical substrates and govern biogeochemical cycles that make Earth a habitable planet. As such, microbes are essential to Earth’s functioning at every scale, and understanding them is essential for a complete understanding of life. As a brief introduction to this book, herein I highlight some of the reasons why understanding how microbes evolve is important to science and society and how challenging is to study microbial evolution.

Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces . Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution. IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces , with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.

The discovery and characterization of protist communities from diverse environments are crucial for understanding the overall evolutionary history of life on earth. However, major questions about the diversity, ecology, and evolutionary history of protists remain unanswered, notably because data obtained from natural protist communities, especially of heterotrophic species, remain limited. In this review, we discuss the challenges associated with "field protistology", defined here as the exploration, characterization, and interpretation of microbial eukaryotic diversity within the context of natural environments or field experiments, and provide suggestions to help fill this important gap in knowledge. We also argue that increased efforts in field studies that combine molecular and microscopical methods offer the most promising path toward (1) the discovery of new lineages that expand the tree of eukaryotes; (2) the recognition of novel evolutionary patterns and processes; (3) the untangling of ecological interactions and functions, and their roles in larger ecosystem processes; and (4) the evaluation of protist adaptations to a changing climate.

The timing of the origin of arthropods in relation to the Cambrian explosion is still controversial, as are the timing of other arthropod macroevolutionary events such as the colonization of land and the evolution of flight. Here we assess the power of a phylogenomic approach to shed light on these major events in the evolutionary history of life on earth. Analyzing a large phylogenomic dataset (122 taxa, 62 genes) with a Bayesian-relaxed molecular clock, we simultaneously reconstructed the phylogenetic relationships and the absolute times of divergences among the arthropods. Simulations were used to test whether our analysis could distinguish between alternative Cambrian explosion scenarios with increasing levels of autocorrelated rate variation. Our analyses support previous phylogenomic hypotheses and simulations indicate a Precambrian origin of the arthropods. Our results provide insights into the 3 independent colonizations of land by arthropods and suggest that evolution of insect wings happened much earlier than the fossil record indicates, with flight evolving during a period of increasing oxygen levels and impressively large forests. These and other findings provide a foundation for macroevolutionary and comparative genomic study of Arthropoda. (Arthropod; Bayesian relaxed clock; Cambrian explosion; comparative genomics; macroevolution; phylogenomics; timing of divergence) Arthropoda, as the largest animal phylum, may be considered the most successful group of living animal species. It includes the largest class of metazoans on earth, Insecta, which comprise more than half of all described species (Grimaldi and Engel 2005). Beyond sheer numbers, arthropods also exhibit an incredible range of morphological and ecological diversity and can be found in nearly all habitats on our planet. Understanding the evolutionary history of Arthropoda is therefore central to understanding the tempo and mode of evolution on earth. However, resolving the evolutionary history of the early arthropods is difficult as the fossil record is generally scant and episodic (Grimaldi and Engel 2005; Budd and Telford 2009). The timing of the origin of arthropods and its relation to the Cambrian explosion is still controversial, as are several macroevolutionary events, such as the colonization of land and the evolution of flight. Here we assess the power of a phylogenomic approach to shed light on these major events in the evolutionary history of life on earth.

Paleontological and neontological systematics seek to answer evolutionary questions with different data sets. Phylogenies inferred for combined extant and extinct taxa provide novel insights into the evolutionary history of life. Primates have an extensive, diverse fossil record and molecular data for living and extinct taxa are rapidly becoming available. We used two models to infer the phylogeny and divergence times for living and fossil primates, the tip-dating (TD) and fossilized birth-death process (FBD). We collected new morphological data, especially on the living and extinct endemic lemurs of Madagascar. We combined the morphological data with published DNA sequences to infer near-complete (88% of lemurs) time-calibrated phylogenies. The results suggest that primates originated around the Cretaceous-Tertiary boundary, slightly earlier than indicated by the fossil record and later than previously inferred from molecular data alone. We infer novel relationships among extinct lemurs, and strong support for relationships that were previously unresolved. Dates inferred with TD were significantly older than those inferred with FBD, most likely related to an assumption of a uniform branching process in the TD compared with a birth-death process assumed in the FBD. This is the first study to combine morphological and DNA sequence data from extinct and extant primates to infer evolutionary relationships and divergence times, and our results shed new light on the tempo of lemur evolution and the efficacy of combined phylogenetic analyses.

About 80% of the evolutionary history of life on Earth is restricted to microorganisms which have had several billion years to speciate. The reasons for the origin (self-assembly) of life on Earth, bacterial cell division and why there are so many different bacteria and their global dispersal are discussed from an evolutionary perspective.

Ribozymes are RNA molecules that can carry out enzymatic function by speeding up the rate of a chemical reaction. There are nine known classes of ribozymes extant in nature, and many more that have been designed in the laboratory. The known biological ribozymes are phylogenetically widespread, although more have been discovered from viruses and bacteria than from other groups. Ribozymes play a central role in the evolutionary history of life on the Earth. They may in fact have been part of the first self-replicating biological entities that arose some 4 billion years ago, and today they are found in central positions in cellular biochemistry as a result of their antiquity.

Background The entire evolutionary history of life can be studied using myriad sequences generated by genomic research. This includes the appearance of the first cells and of superkingdoms Archaea, Bacteria, and Eukarya. However, the use of molecular sequence information for deep phylogenetic analyses is limited by mutational saturation, differential evolutionary rates, lack of sequence site independence, and other biological and technical constraints. In contrast, protein structures are evolutionary modules that are highly conserved and diverse enough to enable deep historical exploration. Results Here we build phylogenies that describe the evolution of proteins and proteomes. These phylogenetic trees are derived from a genomic census of protein domains defined at the fold family (FF) level of structural classification. Phylogenomic trees of FF structures were reconstructed from genomic abundance levels of 2,397 FFs in 420 proteomes of free-living organisms. These trees defined timelines of domain appearance, with time spanning from the origin of proteins to the present. Timelines are divided into five different evolutionary phases according to patterns of sharing of FFs among superkingdoms: (1) a primordial protein world, (2) reductive evolution and the rise of Archaea, (3) the rise of Bacteria from the common ancestor of Bacteria and Eukarya and early development of the three superkingdoms, (4) the rise of Eukarya and widespread organismal diversification, and (5) eukaryal diversification. The relative ancestry of the FFs shows that reductive evolution by domain loss is dominant in the first three phases and is responsible for both the diversification of life from a universal cellular ancestor and the appearance of superkingdoms. On the other hand, domain gains are predominant in the last two phases and are responsible for organismal diversification, especially in Bacteria and Eukarya. Conclusions The evolution of functions that are associated with corresponding FFs along the timeline reveals that primordial metabolic domains evolved earlier than informational domains involved in translation and transcription, supporting the metabolism-first hypothesis rather than the RNA world scenario. In addition, phylogenomic trees of proteomes reconstructed from FFs appearing in each of the five phases of the protein world show that trees reconstructed from ancient domain structures were consistently rooted in archaeal lineages, supporting the proposal that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.

In the last thirty years systematics has transformed itself from a discipline concerned with classification into a discipline concerned with reconstructing the evolutionary history of life. This transformation has been driven by cladistic analysis, a set of techniques for reconstructing evolutionary trees. Long interested in the large-scale structure of evolutionary history, cladistically oriented systematists have recently begun to apply «tree thinking» to problems near the species level. In any local («non-dimensional») situation, species are usually well-defined, but across space and time the grouping of organisms into species is often problematic. Three views of species are in common use today: the biological species concept, the evolutionary species concept, and the phylogenetic species concept

RNA has played a variety of roles in the evolutionary history of life on the Earth. While this molecule was once considered a poor cousin of the more influential polymers in the cell, namely DNA and proteins, a string of important discoveries over the last 50 years has revealed that RNA may in fact be the cornerstone of biological function. In particular, the finding that RNA can be catalytic, and thus possess both a genotype and a phenotype, has forced us to consider the possibility that life's origins began with RNA, and that the subsequent diversification of life is aptly described as a string of innovations by RNA to adapt to a changing environment. Some of these adaptations include riboswitches, ribonucleoproteins (RNPs), RNA editing, and RNA interference (RNAi). Although many of these functions may seem at first glance to be recent evolutionary developments, it may be the case that all of their catalytic activities trace their roots back to a primordial 'RNA World' some four billion years ago, and that RNA's diversity has a continuous thread that pervades life from its very origins.

The enormous amount of data generated by the various genome-sequencing projects has led to a plethora of studies addressing the evolutionary history of life on Earth.

The evolutionary history of life is inscribed in the DNA and protein sequences of living organisms, and we can infer evolutionary trees from these sequences. DNAs and proteins are sequences of four types of bases and of twenty types of amino acids, respectively. At each site of a sequence, one type of base or amino acid may change to another one during evolution, and the substitutions occur independently between lineages after they separate in an evolutionary tree. These substitutions can be best regarded as stochastic, and therefore, it is appropriate to infer evolutionary trees in the framework of maximum likelihood (ML) based on a statistical model for base or amino acid substitutions.

A famous poster shows earthrise seen from the moon. The beautiful image of the blue oceans and white clouds emphasizes that, despite its name, Earth is a planet of water. Most of the evolutionary history of life has been played out in the medium of water. The interactions between organisms and their abiotic environment and between organisms themselves have provided the dynamic for evolution by natural selection. Ecology is the study of those interactions. Its central question is what abiotic and biotic conditions are required for organisms to successfully reproduce themselves? The problems in ecology come not from the difficulties of the questions but from the complexities of the potential answers.

‘High up in the North in the land called Svithjod, there stands a rock. It is a hundred miles high and a hundred miles wide. Once every thousand years a little bird comes to the rock to sharpen its beak.When the rock has thus been worn away, then a single day of eternity will have gone by.’Hendrick Van Loon [1xThe Story of Mankind. Van Loon, H. See all References][1]It cannot be disputed that the time dimension is of fundamental importance in understanding the processes and patterns of ecology and evolution. In his book Basin and Range [2xBasin and Range. McPhee, J. See all References][2], the natural-history author John McPhee coined the term ‘Deep Time’ in reference to geological timescales. Whereas most modern biologists are interested in seconds, days, months and years, paleobiologists delve into timescales that are unfathomable to the human mind's experience or comprehension, ranging from many thousands to millions of years. Starting in this issue of TREE [3xFifty millennia of catastrophic extinctions after human contact. Burney, D.A. and Flannery, T.F. Trends Ecol. Evol. 2005; Abstract | Full Text | Full Text PDF | PubMed | Scopus (186)See all References][3], a new series of articles presents studies of vertebrate ecology and evolution in Deep Time. These articles address macroevolutionary and macroecological phenomena, such as adaptation, climatic influences, growth, reconstructing behavior and ecology, extinction, and biogeography, in vertebrate groups ranging from dinosaurs to mammals, including humans.Ever since the publication of Evolution: The Modern Synthesis [4xEvolution: The Modern Synthesis. Huxley, J. See all References][4], it has been realized that paleontology (also termed ‘paleobiology’) is a fundamental part of biology, particularly in relation to the lessons that can be learned from the evolutionary history of life over long periods of time. Simpson [5xThe Major Features of Evolution. Simpson, G.G. See all References][5] termed this ‘quantum evolution,’ which is the same as the modern concept of ‘macroevolution’ [6xMacroevolution Pattern and Process. Stanley, S.M. See all References][6] [i.e. the study of higher-level (species, genera, and above) evolution that occurs on geological timescales]. Although the fossil record provides abundant evidence of evolutionary patterns, evolutionary processes are more difficult to interpret. Nevertheless, recent studies have integrated observed morphological change in fossils with developmental biology [7xPatterns and Processes of Vertebrate Evolution. Carroll, R.L. See all References][7], such as the genomic mechanism for the acquisition of jaws and paired appendages in vertebrates 400 million years ago. Likewise, Gould's forward-thinking book Ontogeny and Phylogeny [8xOntogeny and Phylogeny. Gould, S.J. See all References][8] stimulated the investigation of how the timing of developmental events changes in ancestral–descendant sequences (i.e. ‘heterochrony’).Just as paleontology has contributed to evolutionary thinking, so too has it fundamentally contributed to ecology, particularly with regard to our knowledge of historical biogeography, global climate change, ancient guild structure and faunal evolution (‘chronofaunas’) through time. In the context of modern biology, macroecology [9xMacroecology. Brown, J.H. See all References][9] is the study of the relationships between organisms and their environment that result in broad-scale patterns of abundance, diversity and distribution. The fossil record has much to contribute to macroecology by providing the evolutionary context that results in these broad-scale patterns, as well as a unique understanding of the history of climate change. Recent biogeochemical studies of ancient ecosystems, and even broader geographical regions (e.g. the use of carbon isotopes to understand the evolution of C4 grasslands and grazing by late Cenozoic mammals), are contributing a great deal to our comprehension of the interaction between organisms and their environments in Deep Time.Ecological and evolutionary patterns and processes are ongoing through time. To only have knowledge of the present-day is similar to one landing of the Svithjod bird [1xThe Story of Mankind. Van Loon, H. See all References][1]. The Paleontology series beginning in this issue will integrate the lessons learned from Deep Time into a forward-thinking perspective about modern ecology and evolution.

W e are part of a tree of life that germinated at the dawn of evolutionary history and encompasses a vast diversity that we are only beginning to understand. Since the advent of molecular techniques for studying phylogenies, there has been active and sometimes acrimonious debate concerning the relative reliability and accuracy of the molecular and fossil records. These debates have involved not only questions of phylogenetic relationships but also the dating of the origins of the major branches of the tree. As more data accumulate from both sources, there are encouraging signs of rapprochement, as discussed by Benton and Ayala (p. [1698][1]). One of the most elusive nodes of the tree has been the origin of the eukaryotes. Molecular phylogenetic data have largely resolved the systematics of the eukaryotes, but, as Baldauf shows (p. [1703][2]), the latest data are suggesting a radical reinterpretation of the position of the root of the eukaryote branch of the tree. This identity crisis has been further fueled by the recent discovery of ultrasmall eukaryotes. But the question remains of how best to come up with phylogenies, particularly ones that link vast numbers of organisms. Indeed, just identifying all the species that constitute the twigs of this grand tree of life is a daunting task; even conservative estimates of the number of unknown species approach 4 million. A few enterprising researchers are coming up with ways to simplify and speed up this much-needed assessment of biodiversity. Others have pushed their colleagues into new ways of thinking about creating phylogenies, as they build ever-larger trees on their way to the one grand tree of life (see News story by Pennisi on p. [1692][3]). A sketch of the tree of life itself is shown on p. [1694][4]. Far from a final answer, it illustrates how complex a unified tree of life will be. This cataloging of life is not an empty exercise, but one that has practical implications. At various points in evolutionary history, the tree of life has lost limbs in major extinction events. As humans wield the ax, Mace et al. (p. 1707) consider the consequences and discuss how phylogenies might help us assess the priorities for conservation. The cross-talk between evolution and genomics has been so fruitful for each field that a new field has emerged: “phylogenomics” (Eisen and Fraser, p. 1706), which is providing insights into areas so seemingly removed as the evolution of metabolic pathways (Chothia et al. , p. [1701][5]). [1]: /lookup/doi/10.1126/science.1077795 [2]: /lookup/doi/10.1126/science.1085544 [3]: /lookup/doi/10.1126/science.300.5626.1692 [4]: /lookup/doi/10.1126/science.300.5626.1694 [5]: /lookup/doi/10.1126/science.1085371

The appearance of the first abundant skeletal organisms in the earliest Cambrian was a quantum leap in the evolutionary history of life. It provided the foundations of the animal kingdom from Cambrian times onwards. This paper demonstrates that this evolutionary process resulted from a combination of environmental and biological factors. The author maintains that the appearance of the oldest shelly fossils is a reasonable criterion for defining the Precambrian–Cambrian boundary. This arises not only from the viewpoint of taking the Cambrian Period as the first period in the Palaeozoic Era, but is also a logical extension of regarding the history of life as being divisible into a series of developmental stages.

Systematics, defined here as the study of the evolutionary history of life, plays a vital role in biology. Together with studies of evolutionary mechanisms, it gives special meaning to biology; it is the unifying force in biology. As a result of recent developments in techniques useful to systematics and in philosophical approaches to systematics, it will be possible for vertebrate systematics to make major advances. Comparative morphological studies of extant and extinct species will play the dominant role in our understanding of the overall pattern of vertebrate phylogeny. For extant species, data from immunological, electrophoretic, and amino acid sequence studies will be important, but the major advances will come from studies of mitochondrial DNA and DNA–DNA hybridization. Examples of phylogenetic controversies that should be resolved in the next 25 years concern the following: the ancestral group of jawed vertebrates, the relationships of Latimeria, the ancestral group of tetrapods, the interrelationships of birds and mammals to each other, and the closest living relatives of man. Both cladistic and synthetic classifications will survive; each serves a useful purpose in translating phylogenetic ideas. Systematics, together with evolution, is a fundamental aspect of biology and should be included in the undergraduate program of all biology students; all biology departments should have a research program in systematics involving graduate students and staff. In addition, museums are a vital part of biology departments, in both their teaching and research functions, and their existence within universities must be nourished.

The vast majority of species that have ever lived went extinct sometime other than during one of the great mass extinction events. In spite of this, mass extinctions are thought to have outsized effects on the evolutionary history of life. While part of this effect is certainly due to the extinction itself, I here consider how the aftermaths of mass extinctions might contribute to the evolutionary importance of such events. Following the mass loss of taxa from the fossil record are prolonged intervals of ecological upheaval that create a selective regime unique to those times. The pacing and duration of ecosystem change during extinction aftermaths suggests strong ties between the biosphere and geosphere, and a previously undescribed macroevolutionary driver - earth system succession. Earth system succession occurs when global environmental or biotic change, as occurs across extinction boundaries, pushes the biosphere and geosphere out of equilibrium. As species and ecosystems re-evolve in the aftermath, they change global biogeochemical cycles - and in turn, species and ecosystems - over timescales typical of the geosphere, often many thousands to millions of years. Earth system succession provides a general explanation for the pattern and timing of ecological and evolutionary change in the fossil record. Importantly, it also suggests that a speed limit might exist for the pace of global biotic change after massive disturbance - a limit set by geosphere-biosphere interactions. For mass extinctions, earth system succession may drive the ever-changing ecological stage on which species evolve, restructuring ecosystems and setting long-term evolutionary trajectories as they do.

The genetic material, deoxyribonucleic acid (DNA), contains information about the evolutionary history of life. Both the relationships amongst organisms and the times of their divergence can be inferred from DNA sequences. Anthropological geneticists use DNA sequences to infer the evolutionary history of humans and their primate relatives. We review the basic methodology used to infer these relationships. We then review the anthropological genetic evidence for modern human origins. We conclude that modern humans evolved recently in Africa and then left to colonize the rest of the world within the last 50,000 years, largely replacing the other human groups that they encountered. Modern humans likely exchanged genes with Neanderthals prior to or early during their expansion out of Africa.

During the voyage of the H.M.S. Beagle, Charles Darwin quickly realized that geographic isolation led to significant changes in the adaptation of local flora and fauna (Darwin 1859). Genetic isolation is one of the well-known mechanisms by which adaptation (allopatric speciation) can occur (Palumbi, Annu Rev Ecol Syst 25:547–72, 1994; Ricklefs, J Avian Biol 33:207–11, 2002; Burns et al., Evolution 56:1240–52, 2002; Hendry et al., Science 290:516–8, 2009). Evolutionary changes can also occur when landmasses converge or are “bridged.” An important and relatively recent (Pliocene Epoch) example known as the “Great American Biotic Interchange” allowed for the migration of previously isolated species into new ecological niches between North and South America (Webb 1985, Ann Mo Bot Gard 93:245–57, 2006; Kirby and MacFadden, Palaeogeogr Palaeoclimatol Palaeoecol 228:193–202, 2005). Geographic isolation (vicariance) or geographic merging (geodispersal) can occur for a variety of reasons (sea level rise, splitting of continents, mountain building). In addition, the growth of a large supercontinent (or breakup) may change the climatic zonation on the globe and form a different type of barrier for species migration. This short review paper focuses on changing paleogeography throughout the Phanerozoic and the close ties between paleogeography and the evolutionary history of life on Earth.

Exceptionally preserved fossils provide major insights into the evolutionary history of life. Microbial activity is thought to play a pivotal role in both the decay of organisms and the preservation of soft tissue in the fossil record, though this has been the subject of very little experimental investigation. To remedy this, we undertook an experimental study of the decay of the brine shrimp Artemia , examining the roles of autolysis, microbial activity, oxygen diffusion and reducing conditions. Our findings indicate that endogenous gut bacteria are the main factor controlling decay. Following gut wall rupture, but prior to cuticle failure, gut-derived microbes spread into the body cavity, consuming tissues and forming biofilms capable of mediating authigenic mineralization, that pseudomorph tissues and structures such as limbs and the haemocoel. These observations explain patterns observed in exceptionally preserved fossil arthropods. For example, guts are preserved relatively frequently, while preservation of other internal anatomy is rare. They also suggest that gut-derived microbes play a key role in the preservation of internal anatomy and that differential preservation between exceptional deposits might be because of factors that control autolysis and microbial activity. The findings also suggest that the evolution of a through gut and its bacterial microflora increased the potential for exceptional fossil preservation in bilaterians, providing one explanation for the extreme rarity of internal preservation in those animals that lack a through gut.

Photosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

When and how oxygenic photosynthesis originated remains controversial. Wide uncertainties exist for the earliest detection of biogenic oxygen in the geochemical record or the origin of water oxidation in ancestral lineages of the phylum Cyanobacteria. A unique trait of oxygenic photosynthesis is that the process uses a Type I reaction centre with a heterodimeric core, also known as Photosystem I, made of two distinct but homologous subunits, PsaA and PsaB. In contrast, all other known Type I reaction centres in anoxygenic phototrophs have a homodimeric core. A compelling hypothesis for the evolution of a heterodimeric Type I reaction centre is that the gene duplication that allowed the divergence of PsaA and PsaB was an adaptation to incorporate photoprotective mechanisms against the formation of reactive oxygen species, therefore occurring after the origin of water oxidation to oxygen. Here I show, using sequence comparisons and Bayesian relaxed molecular clocks that this gene duplication event may have occurred in the early Archean more than 3.4 billion years ago, long before the most recent common ancestor of crown group Cyanobacteria and the Great Oxidation Event. If the origin of water oxidation predated this gene duplication event, then that would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.