The Origin of Species, 150 years after ANTONIO FONTDEVILA

The biological species concept has not solved the problem of the species identity because current studies of comparative genomics have revealed a higher than expected frequency of introgression. This evidence casts serious doubts on the prime role of the reproductive isolation in the origin and maintenance of species. The allopatric model of speciation, formerly viewed as the most frequent, fails to explain many well documented cases of sympatric speciation. Rather the allo- sympatric model, in which several allopatric and sympatric episodes are interspersed in time, is currently favoured to explain many speciation case studies such as the origin of cichlid fishes. Moreover, the gene exchange through hybridisation, without whole genome duplication, is often the starting point of new species in many plants and also in . In many of these cases, as in the homoploid hybrid species of Helianthus, the selection for fertility and the ecological selection have been documented, bolstering the decisive role of natural selection in speciation. Last but not least, comparative phylogenetic studies have shown that horizontal gene exchange is also a plausible phenomenon both in prokaryote and eukaryote domains of life. Taken together, all this evidence suggests that biodiversity should be viewed rather as the outcome of an evolutionary web of life, in which both genetic vertical transmissions and horizontal gene exchanges coexist. But, what is most relevant, it vindicates Darwin’s tenet that natural selection, versus reproductive isolation, is the prime mechanism in the origin and maintenance of species.

Evolution in the Deep Sea ADOLF SEILACHER

Today, paleontologists generally accept in the Darwinian mode. In the fossil record, however, they also observe long-term modulations of this ongoing intrinsic process by extrinsic factors. Negative effects of such macroevolution reach from minor and local background extinctions to global mass extinctions, the causes of which have been widely discussed. In contrast, the positive side of the modulation has received less attention. It is expressed by “Golden Ages”, in which various groups of organisms reach unusually high levels of diversity as well as disparity. As such periods commonly coincide with “greenhouse” states of earth climate, they may be compared to latitudinal gradients in the present biosphere, where rich faunas (tropical reefs and rain forests and other “Golden Biotopes”) result from accelerated speciation and reduced background extinction.

As ongoing speciation and niche partitioning in an ecosystem necessarily leads to increased specialization, the historical link between Golden Ages and following Mass Extinctions is neither surprising: Whatever the killer, its impact will increase with the level of specialization, and thereby the vulnerability, of the biosphere.

On this background, the macroevolutionary behavior of the deep sea fauna is particularly interesting. For Darwin, the deep sea was a zone, in which animals could not live due to lightlessness, extreme pressures, low temperature and the lack of photosynthetic primary production. Modern deep-sea research has revised this picture. The biggest surprise, however, was the unbelievable diversity and monstrosity of this fauna — a Golden Biotope in spite of unfavorable conditions and low population densities. Howard Sander’s time stability hypothesis accounts for this paradox The large number of “living fossils” in this biotope supports his view.

Natural Selection: intrinsic and extrinsic factors ANTONIO GARCIA-BELLIDO

Evolution offers the most beautiful perspective of . The appropriated focus to study of evolution is to analyze its beginning in contrast with the current approach from the end results, the present forms. Darwin and Wallace only contemplated a post-Cambrian scenario, where diversity prevails over complexity and Natural selection is clearly operative.

When we contemplate evolution from the beginning we uncover invariant principles. They are explicit in different levels of organic complexity or in their orthogonal expansion manifested in diversity. Both cooperation and conflict are at work in these processes. The outcome is maximal energetic efficiency in molecular interactions. In such interactions coupling of elements takes place by molecular recognition with minimal loss of free energy, quasi-maximal molecular matching. This is what maintains together the biological world. Hereditary amplification is based on molecular copying and leads to the spreading of mutational novelties. Energy transaction pathways incorporate new partners and thus gain energetic efficiency. Molecular recognition, on the other hand represents inertia to variation. It is an evolutionary constraint, from which only iterations and combinations allows for novelty. Novelty also results from genetic transfer among species, sex, haplodiploidy and recombinant variations.

Evolution uses combinations of molecular modules, both stable and transient, in genetic interactions, to generate morphologies. These combinations allow for an increase in degrees of freedom, thus providing organisms with tolerance to changes in the external world. Physiological efficiency more than final observable forms appears to be the subject of selection and evolution.

We will here explore how much short-term, adaptive, immediate and “externally” driven in contrast with long-term, parsimonious, cumulative and “internally” driven selection operate in Evolution. Whereas long-term selection dominates the changes in levels of complexity, short-term selection prevails in the generation of diversity in different complexity levels.

Fossil links JUAN LUIS ARSUAGA

In the distant future I see open fields for far more important researches. Psychology will be based on a new foundation, that of the necessary acquirement of each mental power and capacity by gradation. Light will be thrown on the origin of man and his history”. So wrote Charles Darwin 150 years ago in “On the origin of Species”.

We are unique and alone now in the world. There is no other species that truly resembles our own. A physical and mental chasm separates us from all other living creatures. There is no other bipedal mammal. No other mammal controls and uses fire, write books, travels in space, paints portraits, or prays. This is not a question of degree. It is all or nothing: there is no semi-bipedal animal, none that makes only small fires, writes only short sentences, builds only rudimentary spaceships, draws just a little bit or prays just occasionally.

Darwin needed links, transitional forms, either living or fossil, to fill the gap between the great biological groups, and especially between human and apes. By 1859 the Neanderthals had already been discovered, but Darwin did not see them as the desired missing links. They were too human.

Phylogenetic, developmental and paleontological arguments for a gradual (darwinian) scenario at the origin of the bilateria. JAUME BAGUÑÀ

Morphological gaps and morphological innovations with little evidence of how they evolved (no transitional forms) were, as Darwin himself acknowledged, a serious threat to one of the basic tenets of his theory: the gradual nature of adaptive changes. Another category of gap, the apparent appearance in the fossil record (circa 530-520 million years) of many animal phyla (namely bilaterians) with few or no antecedents (known today as the Cambrian ‘explosion’), caused also great trouble to Darwin. While in the last 50 years many transitional forms have filled the first type of discontinuities, the very sparse fossil record at the Ediacara period (635-543 million years) and the current poor understanding of the molecular genetic determination of characters have fuelled a continuous debate on the nature of the first bilaterian, on the tempo of origin of bilaterian phyla, and on its proximate causes.

Here we advance some arguments for a gradual emergence of bilaterian groups based on different sets of data. First, molecular phylogenies, phylogenomics, and qualitative molecular changes show acoelomate groups emerging first at the base of the bilaterians, deuterostomates, and lophotrochozoans; hence, the Last Common Bilaterian Ancestor (LCBA) should have morphological features simpler than those envisaged in the complex Urbilateria hypothesis. Second, expression of genes involved in patterning body axes and germ layers in cnidarians and bilaterians indicate a piecemeal evolution as well as hypothetical axial shifts to decouple gastrulation from oral and neural embryonic domains. Finally, the scarcity of unambiguous sponges, cnidarians and ctenophores at the Ediacara, the presence of rare stem bilaterians in the last Ediacaran period, and the parallel radiation of crown sponges and cnidarians along with crown bilaterians in the Cambrian suggest, taphonomic explanations aside, that stem sponges and cnidarians were tiny organisms like sponge/cnidarian larvae today from which simple stem bilaterians gradually evolve.

Why evolution is predictable SIMON CONWAY MORRIS

A central tenet of the neo-Darwinian enterprise is that the evolutionary process is open-ended and indeterminate, lacking any predictable outcomes. An important metaphysical trope arising from this world-picture is that intelligence and cognitive capacitance are flukes, and correspondingly humans are an evolutionary accident. Nor does this seem unreasonable given the emphasis on randomness, be it at the level of mutation and historical contigencies such as mass extinctions. So too nobody can fail to be impressed at the immense ramifications of the Tree of Life. Nevertheless I will argue this view is fundamentally incorrect.

There are five lines of evidence against received wisdom: a) the ubiquity of evolutionary convergence, b) the fact that complex evolutionary outcomes are largely dependent on prior molecular constructions and there is rampant (but not unorganized!) co-option, c) the under-appreciated versatility of molecules (the "Swiss Army Knife Syndrome", d) the divergences that produce the Tree of Life are very far from random, and e) much of biological complexity arises from processes of self-organization. This programme has no quarrel with the Darwinian mechanism, other than it is rather boring, in fact about as interesting (and important) as ionic bonding. Welcome to the post-Darwinian world.

Evolutionary Uniformitarianism DOUGLAS H. ERWIN

The development of evolutionary theory from the publication of The Origin of Species through the late 1800s was heavily influenced by the example Newton's laws of physics, which established the importance of identifying universals that did not vary through time or space, and the debate between the geological uniformitarianism of Hutton and Lyell and catastrophism. Lyell's influence on Darwin's views on geology is widely known. Less appreciated is the extent to which Darwin and later evolutionary biologists adopted a sort of evolutionary uniformitarianism. To win acceptance of evolution, they implicitly assumed that the rates and processes of evolution operating today were sufficient to explain the ; no additional mechanisms, or extraordinary rates were required. There were good reasons for this assumption: it allowed experimental investigation of evolutionary processes, particularly with the advent of genetics after 1900, and led to the elimination of untestable and non uniformitarian hypotheses such as . Additional mechanisms (e.g. drift) have been added to our views of evolutionary change, and we appreciate that evolution encompasses a spectrum of evolutionary rates. The hierarchical expansion of evolution by macroevolution and levels of selection arguments have also expanded the range of evolutionary mechanisms, yet all have been essentially uniformitarian. But the underlying assumption remains that there has been no temporal asymmetry to the operation of different mechanisms. Studies of major evolutionary transitions have broken down this barrier, however, describing a series of mechanisms that repackage genetic information as new evolutionary entities are created. In particular, the elucidation of gene regulatory networks reveals a hierarchical structure that ‘packages’ elements of these networks. This reflects a more general pattern in which the nature of variation exposed to selection has itself evolved over time.

Viral quasispecies: A model of molecular

ESTEBAN DOMINGO

Darwin’s concept of natural selection shattered the understanding of the biological world by providing convincing evidence that evolution did occur, and that humans are a product of biological evolution. Darwinism influenced not only biology but also sociology and physics. Darwinian processes currently under study include cosmological natural selection, brain function, and the transition that led to the origin of life from simple organic molecules. Quasispecies was formulated as a theory of the origin of life, based on the self-organization of primitive RNA-like molecules subjected to sequence variation, competition and selection. The theory was developed by Manfred Eigen and Peter Schuster in the 1970’s, and represented a link between the principles of Darwinian evolution and classical information theory. Interestingly, quasispecies theory has found an application in the study of the population dynamics of present day RNA viruses.

Viruses with RNA as genetic material mutate at rates about one-million fold higher than cellular DNA. Error-prone replication, together with short replication cycles render RNA viruses highly dynamic mutant spectra, as predicted by quasispecies theory. Main biological consequences of quasispecies dynamics for viruses are: (i) adaptability prompted by selection acting on the multitudes of different genomes that compose mutant spectra, with a number of disease implications; (ii) the presence of “memory” genomes in evolving viral lineages (with some analogy to neurological memory); and (iii) the establishment of positive and negative interactions among components of a mutant spectrum. Internal cohesions and repulsions within quasispecies render viral populations integrated units of selection, which marks a crucial difference with respect to classical Wright-Fisher models of mutation-selection equilibrium. Quasispecies dynamics has opened the way towards a new antiviral strategy termed lethal mutagenesis, based on elevating mutation rates artificially, above the maximum level compatible with maintenance of the genetic information of the virus. This practical development illustrates how a purely theoretical concept such as quasispecies, based on the principles of natural selection, can find an application in treatment of viral disease

Not so arbitrary: Sexual and social selection as drivers of evolutionary change

JUAN MORENO

Many traits show no obvious signs of adaptation by natural selection and have been frequently interpreted as products of genetic drift or evidence of neutral variation. Stephen J. Gould was the main proponent of a certain look on evolution as essentially driven by random forces. However, a brief look at the recent evolutionary ecology literature reveals strong evidence that many apparently arbitrary traits are being socially and sexually selected at present. These traits range from morphology to behaviour and may strongly affect all aspects of organismic function. Studies in molecular genetics are discovering how gene regulation involved in developmental processes creates morphological ornaments used in social and sexual selection. Moreover, sympatric speciation is being increasingly linked to sexually selected traits, while prezygotic barriers to gene exchange often involve traits formerly interpreted as selected for species recognition but increasingly reevaluated as signalling phenotypic quality to mates or social partners. Studies of the fossil record are uncovering clear signs of the strength of sexual selection also in the evolutionary past. Many structures which now appear as adaptations for survival may in fact have started their evolutionary career as sexual signals. Taking into consideration the available body of evidence from evolutionary ecology, developmental biology, speciation studies and makes many claims about the evolutionary importance of drift and neutrality rather dubious. Ornaments may appear arbitrary to us because of lack of knowledge but be closely associated with genetic success in natural populations of real organisms, not the organisms built in modellers’ morphospaces. Charles Darwin was fully aware of the strength of social and sexual selection and opened many lines of productive research by the opposite strategy to that of Gould, namely avoiding randomness as an explanation as much as possible. The lesson taught by Darwin is that things in biology are not so arbitrary as they may look, and that their selective substrate merits to be researched before making rash conclusions. Denying the strength of selection because of ignorance of past and present forces as has been systematically done by proponents of pervasive randomness appears increasingly like a heuristically self-defeating and epistemologically failed strategy.

The evolving genome in early metazoans

JAMES W. VALENTINE1 AND CHARLES R. MARSHALL2

Comparison of the whole-genomes of living taxa that span the transition from sponge-grade animals to the first bilaterians suggests a change in the mode of metazoan genome evolution during this transition. The core elements of the bilaterian developmental system first evolved in sponge-grade organisms prior to 635 million years ago (Ma), and was characterized by the appearance of many novel gene families with regulatory functions, both in signaling and transcriptional control. An episode of even greater genomic innovation was associated with the origin and patterning of the ectoderm as the first eumetazoans, the diploblasts, emerged (near 600 Ma?). Strikingly, there was relatively little fundamental regulatory innovation associated with the emergence of the bilaterian (triploblastic) phyla, implying that many of the regulatory genes that bestow bilaterian-specific morphologies were already functioning in the early-branching phyla even though these phyla lacked bilaterian morphologies. Thus, while early bilaterian genome evolution (560?-543 Ma) was associated with expansions of many regulatory gene families, evidently these did not substantially increase the fundamental morphogenetic potential of the bilaterian developmental system. Stem lineages of the bilaterian phyla are first found during the (530-520 Ma), while crown lineages largely replaced stem groups during the great Ordovician biodiversifications (after 489 Ma), and here too there is little evidence of important genomic innovations during those and later events.

Thus, in the early non-bilaterian metazoans selection for new morphologies was commonly accommodated through the evolution of new regulatory domains, while in bilaterians, even though they show a much greater range of morphologies, novelty was largely achieved through the recruitment of already existing regulatory domains to novel functions, and through the expansion of existing regulatory gene families. This shift in the developmental basis of morphological innovation appears to represent a shift in genomic responses to selection, a change from reliance on innovation within the protein-coding regions of the genome to a primary reliance on cis-regulatory evolution (and including expansion of the regulatory RNA repertoire) to accommodate selection for novel morphologies.

Symbiogenesis as source of evolutionary innovation

LYNN MARGULIS

Evolution is no single fact, The process depends on at least four observables. First, life requires the incessant flow of energy and matter to survive. Second, a species- specific biotic potential, a measurable quantity, is assignable: the number of offspring that, in principle, can be produced per generation. Third, as Malthus indicated, all populations grow at rates more rapidly than their immediate environment can sustain. What Darwin called "Natural Selection" is simply this fact of elimination. Never do 100% of the offspring continue to survive and reproduce. Biotic potential is not reached except for very short periods of time under extraordinarily permissive enviromental conditions. Biotic potential is only reached when it can be measured. Finally, offspring are not identical to their parents. Inherited (genetic) change is easily observable but less easily measured. From these observables Darwin correctly inferred that all extant life “descended with modification” from common ancestors.

Symbiosis is simply the living together of organisms that are different from each other. Originally coined by Heinrich Anton de Bary (1831-1888) the term symbiosis referred to living together of “differently named organisms”. Symbioses are physical associations that endure for at least half the life history of one of the partners. Endosymbiosis, a topological condition, is a kind of symbiosis where one partner lives inside another. When different types of organisms associate, fuse and in the merger make a third kind ecology becomes evolution: this is symbiogenesis. The fusion is never random, it is environmentally contingent. Symbioses usually, if not always, depend on environmental conditions. Symbiosis, not an evolutionary process per se, refers to physiological, temporal or topological associations with environmentally determined fates. Symbiogenesis, however, implies the appearance of new tissues, new organs, physiologies or other new features that result from protracted symbiotic association. At least two classes of eukaryotic cell organelles, plastids and mitochondria, evolved symbiogenetically. I will argue that cilia and other microtubular structure are legacies of an even earlier symbiogenetic event that marked the origin of nucleated cells.

The Evolution of Segmentation Mechanisms in Arthropods

MICHAEL AKAM

A great deal is known about the molecular mechanisms that generate the segmented body plan of Drosophila. However, it is already clear that one of the key segmentation genes in Drosophila is a relatively recent invention of the higher Diptera, and there is strong circumstantial evidence to suggest that the mechanisms of segment generation in some other arthropod groups are fundamentally different from those used in the higher insects.

I will review what is known of segmentation mechanisms in arthropods, as well as data for relevant outgroups, including onychophorans and annelids. I will discuss work which suggests that in at least one myriapod lineage, segments are generated not through a mechanism dependent on the interpretation of unique spatial cues, but through a mechanism that involves repetitive cycles of gene activity, more akin to the mechanisms that underlie vertebrate somitogenesis. I will consider how the derived Drosophila segmentation machinery may have evolved from more basal mechanisms.

Finally, in the light of this evidence I will consider arguments for and against the proposal that the last common ancestor of the protostomes and deuterostomes was itself segmented.

Developmental Insights from the Study of Newly Emerging Model Species

NIPAM H. PATEL

A relatively small number of model species have provided the majority of our insights into the mechanisms that guide development. Recently, however, many of the tools developed in model species can now be applied to studying the development of a wide range of species. These studies of have provided us with some remarkable insights into the evolution and flexibility of developmental systems. I will describe two examples of recent work from my lab where the study of new species has led to some especially unexpected discoveries regarding developmental evolution and the possible adaptive significance of developmental variation. First, the study of germline formation in the crustacean, Parhyale, suggests that post-embryonic replacement of the germline is possible, even in animals without extensive regenerative capabilities. Second, a bioinformatic approach to studying butterfly wing patterning reveals an unexpected subdivision of the traditional compartments of the wing during development.

3D Plate Tectonic, Paleogeographic and Paleoclimatic Maps and Animations: The PALEOMAP Project PaleoAtlas for ArcGIS

CHRISTOPHER R. SCOTESE

The PALEOMAP Project is known for its synthesis of the plate tectonic, paleogeographic, and paleoclimatic history of ocean basins and continents during the last 1100 million years. In this talk, 3D paleogeographic, plate tectonic, and paleoclimatic maps and animations for Precambrian, Paleozoic, Mesozoic, and Cenozoic will be presented. Projections of future plate motions and the assembly of the future supercontinent — “PANGEA PROXIMA” will also shown.

The PALEOMAP PaleoAtlas for ArcGIS is composed of >50 digital maps illustrating the plate tectonic and paleogeographic development of the continents and ocean basins during the Late Precambrian and Phanerozoic (Figure 1). Stored as map projects in ArcGIS, each time interval has up to 12 thematic layers illustrating: geology, paleogeography, plate motion vectors, as well as modern and geographic and cultural features.

These plate tectonic reconstructions are the basis for a new set a paleoclimatic simulations (FOAM) that illustrate ancient: temperature, winds, rainfall, runoff, river drainage, ocean circulation, and upwelling (see Figure 2 & 3). The GANDOLPH project is an industry-sponsored project that uses the plate tectonic reconstructions together with simulations of atmospheric and oceanographic conditions to predict source and reservoir rock occurrences during the last 600 million years.

*All intellectual property rights belong to the author. Total or partial reproduction of the work without express permission of the author is forbidden. © FUNDACIÓN RAMÓN ARECES. All rights reserved.

All maps are made in ArcGIS by ESRI. The software that will be demonstrated includes: The PALEOMAP GIS PaleoAtlas, PlateTracker for ArcGIS, and PaleoGIS.

Figure 1. Example Paleogeographic Map from PALEOMAP GIS PaleoAtlas

Figure 2. Paleoclimatic Reconstruction from PALEOMAP GIS PaleoAtlas (GANDDOLPH Project)

Figure 3. PALEOMAP Paleoclimatic Simulation Time-Slices