Contingency In Evolution Research Articles

The effects of host ecology and phylogeny on gut microbiota (non)parallelism across birds and mammals.

What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of "replaying life's tape." Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts.

EVOLUTION, CHANCE, NECESSITY, AND DESIGN

AbstractThis article represents comments arising from The Compatibility of Evolution and Design by Rope Kojonen (Palgrave Macmillan, 2021) concerning the role of chance and randomness in evolution (citations from this book are shown as page numbers in brackets). The various meanings of chance and randomness as used in descriptions of biological evolution are discussed and contrasted with their meanings in mathematics and metaphysics. The discussion relates to the role of contingency in evolution and to ideological and rhetorical extrapolations from biology into philosophical world views. Overall it is concluded that evolution is not a chance process, except in the epistemic sense of “chance.” Theologically, this has implications for the idea that God creates through “a free evolutionary process” and may also influence our perspectives on divine action and intentionality in evolutionary history.

Prediction and Contingency in Evolution by Natural Selection

Prediction and Contingency in Evolution by Natural Selection

The Evolutionary Dynamics of Mechanically Complex Systems

Animals use a diverse array of motion to feed, escape predators, and reproduce. Linking morphology, performance, and fitness is a foundational paradigm in organismal biology and evolution. Yet, the influence of mechanical relationships on evolutionary diversity remains unresolved. Here, I focus on the many-to-one mapping of form to function, a widespread, emergent property of many mechanical systems in nature, and discuss how mechanical redundancy influences the tempo and mode of phenotypic evolution. By supplying many possible morphological pathways for functional adaptation, many-to-one mapping can release morphology from selection on performance. Consequently, many-to-one mapping decouples morphological and functional diversification. In fish, for example, parallel morphological evolution is weaker for traits that contribute to mechanically redundant motions, like suction feeding performance, than for systems with one-to-one form–function relationships, like lower jaw lever ratios. As mechanical complexity increases, historical factors play a stronger role in shaping evolutionary trajectories. Many-to-one mapping, however, does not always result in equal freedom of morphological evolution. The kinematics of complex systems can often be reduced to variation in a few traits of high mechanical effect. In various different four-bar linkage systems, for example, mechanical output (kinematic transmission) is highly sensitive to size variation in one or two links, and insensitive to variation in the others. In four-bar linkage systems, faster rates of evolution are biased to traits of high mechanical effect. Mechanical sensitivity also results in stronger parallel evolution—evolutionary transitions in mechanical output are coupled with transition in linkages of high mechanical effect. In other words, the evolutionary dynamics of complex systems can actually approximate that of simpler, one-to-one systems when mechanical sensitivity is strong. When examined in a macroevolutionary framework, the same mechanical system may experience distinct selective pressures in different groups of organisms. For example, performance tradeoffs are stronger for organisms that use the same mechanical structure for more functions. In general, stronger performance tradeoffs result in less phenotypic diversity in the system and, sometimes, a slower rate of evolution. These macroevolutionary trends can contribute to unevenness in functional and lineage diversity across the tree of life. Finally, I discuss how the evolution of mechanical systems informs our understanding of the relative roles of determinism and contingency in evolution.

EVOLUTION, CONTINGENCY, AND CHRISTOLOGY

AbstractChristopher Southgate has made important contributions to theodicy and the theory of divine action in light of the contingency in evolution and the suffering of creation. What happens then when one thinks through the implications of contingency for Christology? One can admit that aesthetic and moral judgments are products of a contingent history and yet affirm that they really are valid. Similarly, we argue, one can acknowledge the contingency of Jesus’ existence, actions, and subsequent impact and still maintain that his will was uniquely united with the divine will. Following a critical engagement with the recent work of Keith Ward, we argue that a high Christology is compatible with the actual contingencies of evolutionary and social history, without the necessity of interventionist divine action.

Creatures of the semiosphere: A problematic third party in the ‘humans plus technology’ cognitive architecture of the future global superintelligence

Contrary to the prevailing pessimistic AI takeover scenarios, the theory of the Global Brain (GB) argues that this foreseen collective, distributed superintelligence is bound to include humans as its key beneficiaries. This prediction follows from the contingency of evolution: we, as already present intelligent forms of life, are in a position to exert selective pressures onto the emerging new ones. As a result, it is foreseen that the cognitive architecture of the GB will include human beings and such technologies, which will best prove to advance our collective wellbeing. This paper aims to nuance and problematize this forecast by offering a novel combination of several existing theories: Kauffmann's theory of adjacent possible, Lotman's concept of the semiosphere, Luhmann's theory of social systems, and Heylighen's theory of intelligence. The resulting framework allows for a reinterpretation of the history of the human species in a way which suggests that it may not be individual humans, but our social systems, who are the most advanced intelligence currently operating on Earth. Our unique social systems, emerging from as early as the Neolithic out of mutual interrelations of the occurrences of symbolic communication of humans, are argued to be capable of individuating into autonomous, intelligent agents. The resulting distributedness of the currently dominating form of intelligence might challenge the predicted cognitive architecture of the Global Brain, as it is likely to introduce additional powerful sources of selective pressures. Since the rapid evolution of interconnecting technologies appears to open up immense emancipatory possibilities not only for humans, but also for the intelligently evolving ‘creatures of the semiosphere’, it is concluded that in the context of the rapidly self-organizing Global Brain, a close watch needs to be kept over the dynamics of the latter.

A case study in evolutionary contingency

Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit+), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit+ trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.

The Use of Weighted Graphs for Large-Scale Genome Analysis

There is an acute need for better tools to extract knowledge from the growing flood of sequence data. For example, thousands of complete genomes have been sequenced, and their metabolic networks inferred. Such data should enable a better understanding of evolution. However, most existing network analysis methods are based on pair-wise comparisons, and these do not scale to thousands of genomes. Here we propose the use of weighted graphs as a data structure to enable large-scale phylogenetic analysis of networks. We have developed three types of weighted graph for enzymes: taxonomic (these summarize phylogenetic importance), isoenzymatic (these summarize enzymatic variety/redundancy), and sequence-similarity (these summarize sequence conservation); and we applied these types of weighted graph to survey prokaryotic metabolism. To demonstrate the utility of this approach we have compared and contrasted the large-scale evolution of metabolism in Archaea and Eubacteria. Our results provide evidence for limits to the contingency of evolution.

Evolutionary contingency and SETI revisited

The well-known argument against the Search for ExtraTerrestrial Intelligence (SETI) due to George Gaylord Simpson is re-analyzed almost half a century later, in the light of our improved understanding of preconditions for the emergence of life and intelligence brought about by the ongoing “astrobiological revolution”. Simpson’s argument has been enormously influential, in particular in biological circles, and it arguably fueled the most serious opposition to SETI programmes and their funding. I argue that both proponents and opponents of Simpson’s argument have occasionally mispresented its core content. Proponents often oversimplify it as just another consequence of biological contingency, thus leaving their position open to general arguments limiting the scope of contingency in evolution (such as the recent argument of Geerat Vermeij based on selection effects in the fossil record). They also tend to neglect that the argument has been presented as essentially atemporal, while referring to entities and processes that are likely to change over time; this has become even less justifiable as our astrobiological knowledge increased in recent years. Opponents have failed to see that the weaknesses in Simpson’s position could be removed by restructuring of the argument; I suggest one way of such restructuring, envisioned long ago in the fictional context by Stanislaw Lem. While no firm consensus has emerged on the validity of Simpson’s argument so far, I suggest that, contrary to the original motivation, today it is less an anti-SETI argument, and more an astrobiological research programme. In this research programme, SETI could be generalized into a platform for testing some of the deepest assumptions about evolutionary continuity and the relative role of contingency versus convergence on unprecedented spatial and temporal scales.

Dynamic landscapes: A model of context and contingency in evolution

Although the basic mechanics of evolution have been understood since Darwin, debate continues over whether macroevolutionary phenomena are driven by the fitness structure of genotype space or by ecological interaction. In this paper we propose a simple model capturing key features of fitness-landscape and ecological models of evolution. Our model describes evolutionary dynamics in a high-dimensional, structured genotype space with interspecies interaction. We find promising qualitative similarity with the empirical facts about macroevolution, including broadly distributed extinction sizes and realistic exploration of the genotype space. The abstraction of our model permits numerous applications beyond macroevolution, including protein and RNA evolution.

The recurrent assembly of C4 photosynthesis, an evolutionary tale

Today, plants using C4 photosynthesis are widespread and important components of major tropical and subtropical biomes, but the events that led to their evolution and success started billions of years ago (bya). A CO2-fixing enzyme evolved in the early Earth atmosphere with a tendency to confuse CO2 and O2 molecules. The descendants of early photosynthetic organisms coped with this property in the geological eras that followed through successive fixes, the latest of which is the addition of complex CO2-concentrating mechanisms such as C4 photosynthesis. This trait was assembled from bricks available in C3 ancestors, which were altered to fulfill their new role in C4 photosynthesis. The existence of C4-suitable bricks probably determined the lineages of plants that could make the transition to C4 photosynthesis, highlighting the power of contingency in evolution. Based on the latest findings in C4 research, we present the evolutionary tale of C4 photosynthesis, with a focus on the general evolutionary phenomena that it so wonderfully exemplifies.

Genotypic but not phenotypic historical contingency revealed by viral experimental evolution

BackgroundThe importance of historical contingency in determining the potential of viral populations to evolve has been largely unappreciated. Identifying the constraints imposed by past adaptations is, however, of importance for understanding many questions in evolutionary biology, such as the evolution of host usage dynamics by multi-host viruses or the emergence of escape mutants that persist in the absence of antiviral treatments. To address this issue, we undertook an experimental approach in which sixty lineages of Tobacco etch potyvirus that differ in their past evolutionary history and degree of adaptation to Nicotiana tabacum were allowed to adapt to this host for 15 rounds of within host multiplication and transfer. We thereafter evaluated the degree of adaptation to the new host as well as to the original ones and characterized the consensus sequence of each lineage.ResultsWe found that past evolutionary history did not determine the phenotypic outcome of this common host evolution phase, and that the signal of local adaptation to past hosts had largely disappeared. By contrast, evolutionary history left footprints at the genotypic level, since the majority of host-specific mutations present at the beginning of this experiment were retained in the end-point populations and may have affected which new mutations were consequently fixed. This resulted in further divergence between the sequences despite a shared selective environment.ConclusionsThe present experiment reinforces the idea that the answer to the question “How important is historical contingency in evolution?” strongly depends on the level of integration of the traits studied. A strong historical contingency was found for TEV genotype, whereas a weak effect of on phenotypic evolution was revealed. In an applied context, our results imply that viruses are not easily trapped into suboptimal phenotypes and that (re)emergence is not evolutionarily constrained.

Epistasis can lead to fragmented neutral spaces and contingency in evolution

In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space—namely, that networks of genomes encoding the same phenotype may not be connected by single mutational moves. We use the folding of RNA sequences into secondary structures as a model genotype–phenotype map and explore the neutral spaces corresponding to networks of genotypes with the same phenotype. In most of these networks, we find that it is not possible to connect all genotypes to one another by single point mutations. Instead, a network for a phenotypic structure withnbonds typically fragments into at least 2nneutral components, often of similar size. While components of the same network generate the same phenotype, they show important variations in their properties, most strikingly in their evolvability and mutational robustness. This heterogeneity implies contingency in the evolutionary process.

Convergence and Parallelism in Evolution: A Neo-Gouldian Account

Determining whether a homoplastic trait is the result of convergence or parallelism is central to many of the most important contemporary discussions in biology and philosophy: the relation between evolution and development, the importance of constraints on variation, and the role of contingency in evolution. In this article, I show that two recent attempts to draw a black-or-white distinction between convergence and parallelism fail, albeit for different reasons. Nevertheless, I argue that we should not be afraid of gray areas: a clarified version of S. J. Gould's earlier account, based on a separation of underlying developmental mechanisms from the realized trait, still represents a useful approach. 1 Introduction2 The Topological Approach3 The Screening-Off Approach4 The Neo-Gouldian Approach5 Conclusion

Historical contingency and the evolution of a key innovation in an experimental population ofEscherichia coli

The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations ofEscherichia coliwere founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, whichE. colicannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that “replayed” evolution from different points in that population's history. We observed no Cit+mutants among 8.4 × 1012ancestral cells, nor among 9 × 1012cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

Persistence of foot-and-mouth disease virus in cell culture revisited: implications for contingency in evolution

If we could rewind the tape of evolution and play it again, would it turn out to be similar to or different from what we know? Obviously, this key question can only be addressed by fragmentary experimental approaches. Twenty-two years ago, we described the establishment of BHK-21 cells persistently infected with foot-and-mouth disease virus (FMDV), a system that displayed as its major biological feature a coevolution of the cells and the resident virus in the course of persistence. Now we report the establishment of two persistently infected cell lines in parallel, starting with the same clones of FMDV and BHK-21 cells used 22 years ago. We have asked whether the evolution of the two newly established cell lines and of the earlier cell line would be similar or different. The main conclusions of the study are: (i) the basic behaviour characterized by virus-cell coevolution is similar in the three carrier cell lines, despite differences in some genetic alterations of FMDV; (ii) a strikingly parallel behaviour has been observed with the two newly established cell lines passaged in parallel, unveiling a deterministic virus behaviour during persistence; and (iii) selective RT-PCR amplifications have detected imbalances in the proportion of positive- versus negative-strand viral RNA, mediated by both viral and cellular factors. The results confirm coevolution of cells and virus as a major and reproducible feature of FMDV persistence in cell culture, and suggest that rapidly evolving viruses may constitute adequate test systems to probe the influence of historical contingency on evolutionary events.

Wonderful strife: systematics, stem groups, and the phylogenetic signal of the Cambrian radiation

Gould's Wonderful Life (1989) was a landmark in the investigation of the Cambrian radiation. Gould argued that a number of experimental body plans (“problematica”) had evolved only to become extinct, and that the Cambrian was a time of special fecundity in animal design. He focused attention on the meaning and significance of morphological disparity versus diversity, and provoked attempts to quantify disparity as an evolutionary metric. He used the Burgess Shale as a springboard to emphasize the important role of contingency in evolution, an idea that he reiterated for the next 13 years. These ideas set the agenda for much subsequent research. Since 1989 cladistic analyses have accommodated most of the problematic Cambrian taxa as stem groups of living taxa. Morphological disparity has been shown to be similar in Cambrian times as now. Konservat-Lagerstatten other than the Burgess Shale have yielded important new discoveries, particularly of arthropods and chordates, which have extended the range of recognized major clades still further back in time. The objective definition of a phylum remains controversial and may be impossible: it can be defined in terms of crown or total group, but the former reveals little about the Cambrian radiation. Divergence times of the major groups remain to be resolved, although molecular and fossil dates are coming closer. Although “superphyla” may have diverged deep in the Proterozoic, “explosive” evolution of these clades near the base of the Cambrian remains a possibility. The fossil record remains a critical source of data on the early evolution of multicellular organisms.

Macaque evolution and dispersal in insular south-east Asia

The evolution of primates is usually approached from the standpoint of adaptation and interspecific competition. However, climatic and eustatic changes associated with periodic glaciations have had a profound influence on their geographical distribution, favouring the intervention of contingency in evolution. This paper deals with the role of chance and competition in the dispersal and stocking of macaques in the islands of south-east Asia. The genus Macaca is unique among non-human primates for the range of habitats colonized, from continents to islands. We first review current knowledge about the zoogeography of macaques in Sundaland. We point out the inconsisten- cies present in the hypotheses thus far proposed to account for the colonization of shallow- and deep-water islands. We then propose a new perspective of macaque dispersal through the Indonesian archipelago, which takes into account sea-level changes, as well as latitudinal and altitudinal rainforest shifts following climatic cycles during the Quaternary. We envision three steps: (i) dispersal and partial disappearance of the first radiation of macaques; (ii) primary mainland recolonization by pigtailed and longtailed macaques; and (iii) secondary sea-rafting colo- nization by longtailed macaques. This model implies that liontailed, Sulawesi and Mentawai macaques stemmed from pre-glacial remnant populations, whereas pigtailed macaques originated in post-glacial populations that diverged later on. The model accounts for the distribution of longtailed macaques throughout the Indonesian archi- pelago. The riverine habits of this species would have favoured its dispersal by sea rafting, which was otherwise extremely rare for other primate species. Stocking would have been successful for longtailed macaques only in islands where no other macaque competitors were already present. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 75, 555-576. ADDITIONAL KEYWORDS: biogeography - colonization - competition - contingency - island - Macaca - Quaternary - Sunda shelf.

Evolution and the genetic analysis of populations: 1950–2000

SummaryBachmann, K.: Evolution and the genetic analysis of populations: 1950–2000. – Taxon 50: 7–45. 2001. – ISSN 0040–0262.Population genetics had played a key role in the fusion of Mendelian genetics and Darwinian natural selection into the Synthetic Theory of Evolution. The realization that all basic processes of evolution occur in or among populations suggested that evolutionary processes at all levels could be extrapolated from observations on living populations. In plants, an active tradition in ecological genetics had prepared the ground for the Synthesis, and the new initiative of “biosystematics” made full use of experimental and analytical techniques for systematics, especially at the level of species. This development got caught up in the “hardening of the Synthesis”, the defensive persistence on a simplified core theory in the face of challenges from known facts and new discoveries, especially in molecular genetics. Enzyme electrophoresis was the first molecular method to be introduced into population biology. The new results revealed unexpectedly high levels of variation within populations and precipitated discussion about the selective neutrality of protein polymorphisms. This discussion distracted attention from the population genetic basis of organismic evolution. Together with the widespread adoption of molecular marker methods at the expense of other approaches, population genetics was in danger of losing its central relevance and its variety of experimental approaches. Since the end of the 1970s, calls for new initiatives have drawn attention to the importance of historical contingency in evolution, especially in the form of developmental constraints. A population genetic application of these ideas initially faced immense technical problems. A succession of new molecular marker systems suitable for the genetic analysis of populations added new resolving power, but introduced new problems with the inference of processes from basically static and descriptive data. Only very recently, methods have advanced to the point that molecular markers can help in the experimental analysis of morphological and physiological evolution. The coming challenge will be to adapt results from detailed analyses of individual plants to broadly comparative population genetic studies. The accumulated new insights of the last 50 years show that the pervasive influence of historical contingency has non–trivial consequences for evolutionary biology and taxonomy. These are strikingly exemplified by a completely changed picture of genome structure and evolution. The time seems to be right for a paradigm shift in evolutionary biology.