Biological extinction in earth history

Demographic models predict end-Pleistocene arrival and rapid expansion of pre-agropastoralist humans in Cyprus

The antiquity of human dispersal into Mediterranean islands and ensuing coastal adaptation have remained largely unexplored due to the prevailing assumption that the sea was a barrier to movement and that islands were hostile environments to early hunter-gatherers [J. F. Cherry, T. P. Leppard, J. Isl. Coast. Archaeol. 13, 191-205 (2018), 10.1080/15564894.2016.1276489]. Using the latest archaeological data, hindcasted climate projections, and age-structured demographic models, we demonstrate evidence for early arrival (14,257 to 13,182 calendar years ago) to Cyprus and predicted that large groups of people (~1,000 to 1,375) arrived in 2 to 3 main events occurring within <100 y to ensure low extinction risk. These results indicate that the postglacial settlement of Cyprus involved only a few large-scale, organized events requiring advanced watercraft technology. Our spatially debiased and Signor-Lipps-corrected estimates indicate rapid settlement of the island within <200 y, and expansion to a median of 4,000 to 5,000 people (0.36 to 0.46 km-2) in <11 human generations (<300 y). Our results do not support the hypothesis of inaccessible and inhospitable islands in the Mediterranean for pre-agropastoralists, agreeing with analogous conclusions for other parts of the world [M. I. Bird et al., Sci. Rep. 9, 8220 (2019), 10.1038/s41598-019-42946-9]. Our results also highlight the need to revisit these questions in the Mediterranean and test their validity with new technologies, field methods, and data. By applying stochastic models to the Mediterranean region, we can place Cyprus and large islands in general as attractive and favorable destinations for paleolithic peoples.

Probing long-lived radioactive isotopes on the double-logarithmic Segrè chart

Isotopes have been widely applied in a variety of scientific subjects; many aspects of isotopes, however, remain not well understood. In this study, I investigate the relation between the number of neutrons (N) and the number of protons (Z) in stable isotopes of non-radioactive elements and long-lived isotopes of radioactive elements at the double-linear scale (conventional Segrè chart) and the double-logarithmic scale. Statistical analyses show that N is a power-law function of Z for these isotopes: N = 0.73 × Z 1.16. This power-law relation provides better predictions for the numbers of neutrons in stable isotopes of non-radioactive elements and long-lived isotopes of radioactive elements than the linear relation on the conventional Segrè chart. The power-law pattern reveled here offers empirical guidance for probing long-lived isotopes of unknown radioactive elements.

Fitness fluctuations in the Bak-Sneppen model

We study the one-dimensional Bak-Sneppen model for the evolution of species in an ecosystem. Of particular interest are the temporal fluctuations in fitness variables. We numerically compute the power spectral density and apply the finite-size scaling method to get data collapse. A clear signature of 1/f^{α} noise with α≈1.2 (long-time correlations) emerges for both local and global (or average) fitness noises. The limiting value of the spectral exponent, 0 or 2, corresponds to no interaction or a random neighbor version of the model, respectively. The local power spectra are spatially uncorrelated and also show an additional scaling, ∼1/L, in the frequency regime L^{-λ}≪f≪1/2, where L is the linear extent of the system.

Reduced strength and increased variability of extinction selectivity during mass extinctions

Two of the traits most often observed to correlate with extinction risk in marine animals are geographical range and body size. However, the relative effects of these two traits on extinction risk have not been investigated systematically for either background times or during mass extinctions. To close this knowledge gap, we measure and compare extinction selectivity of geographical range and body size of genera within five classes of benthic marine animals across the Phanerozoic using capture-mark-recapture models. During background intervals, narrow geographical range is strongly associated with greater extinction probability, whereas smaller body size is more weakly associated with greater extinction probability. During mass extinctions, the association between geographical range and extinction probability is reduced in every class and fully eliminated in some, whereas the association between body size and extinction probability varies in strength and direction across classes. While geographical range is universally the stronger predictor of survival during background intervals, variation among classes during mass extinction suggests a fundamental shift in extinction processes during these global catastrophes.

Earth's interior dynamics drive marine fossil diversity cycles of tens of millions of years

The fossil record reveals that biotic diversity has fluctuated quasi-cyclically through geological time. However, the causal mechanisms of biotic diversity cycles remain unexplained. Here, we highlight a common, correlatable 36 ± 1 Myr (million years) cycle in the diversity of marine genera as well as in tectonic, sea-level, and macrostratigraphic data over the past 250 Myr of Earth history. The prominence of the 36 ± 1 Myr cycle in tectonic data favors a common-cause mechanism, wherein geological forcing mechanisms drive patterns in both biological diversity and the preserved rock record. In particular, our results suggest that a 36 ± 1 Myr tectono-eustatically driven sea-level cycle may originate from the interaction between the convecting mantle and subducting slabs, thereby pacing mantle-lithospheric deep-water recycling. The 36 ± 1 Myr tectono-eustatic driver of biodiversity is likely related to cyclic continental inundations, with expanding and contracting ecological niches on shelves and in epeiric seas.

Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber

BACKGROUND

Ponerine ants are almost exclusively predatory and comprise many of the largest known ant species. Within this clade, the genus Neoponera is among the most conspicuous Neotropical predators. We describe the first fossil member of this lineage: a worker preserved in Miocene-age Dominican amber from Hispaniola.

RESULTS

Neoponera vejestoria sp. nov. demonstrates a clear case of local extinction-there are no known extant Neoponera species in the Greater Antilles. The species is attributable to an extant and well-defined species group in the genus, which suggests the group is older than previously estimated. Through CT scan reconstruction and linear morphometrics, we reconstruct the morphospace of extant and fossil ants to evaluate the history and evolution of predatory taxa in this island system.

CONCLUSIONS

The fossil attests to a shift in insular ecological community structure since the Miocene. The largest predatory taxa have undergone extinction on the island, but their extant relatives persist throughout the Neotropics. Neoponera vejestoria sp. nov. is larger than all other predatory ant workers known from Hispaniola, extant or extinct. Our results empirically demonstrate the loss of a functional niche associated with body size, which is a trait long hypothesized to be related to extinction risk.

Ecological complexity and the biosphere: the next 30 years

Global warming, habitat loss and overexploitation of limited resources are leading to alarming biodiversity declines. Ecosystems are complex adaptive systems that display multiple alternative states and can shift from one to another in abrupt ways. Some of these tipping points have been identified and predicted by mathematical and computational models. Moreover, multiple scales are involved and potential mitigation or intervention scenarios are tied to particular levels of complexity, from cells to human–environment coupled systems. In dealing with a biosphere where humans are part of a complex, endangered ecological network, novel theoretical and engineering approaches need to be considered. At the centre of most research efforts is biodiversity, which is essential to maintain community resilience and ecosystem services. What can be done to mitigate, counterbalance or prevent tipping points? Using a 30-year window, we explore recent approaches to sense, preserve and restore ecosystem resilience as well as a number of proposed interventions (from afforestation to bioengineering) directed to mitigate or reverse ecosystem collapse. The year 2050 is taken as a representative future horizon that combines a time scale where deep ecological changes will occur and proposed solutions might be effective.

This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

The Mesozoic terminated in boreal spring

The Cretaceous-Palaeogene mass extinction around 66 million years ago was triggered by the Chicxulub asteroid impact on the present-day Yucatán Peninsula^1,2. This event caused the highly selective extinction that eliminated about 76% of species^3,4, including all non-avian dinosaurs, pterosaurs, ammonites, rudists and most marine reptiles. The timing of the impact and its aftermath have been studied mainly on millennial timescales, leaving the season of the impact unconstrained. Here, by studying fishes that died on the day the Mesozoic era ended, we demonstrate that the impact that caused the Cretaceous-Palaeogene mass extinction took place during boreal spring. Osteohistology together with stable isotope records of exceptionally preserved perichondral and dermal bones in acipenseriform fishes from the Tanis impact-induced seiche deposits⁵ reveal annual cyclicity across the final years of the Cretaceous period. Annual life cycles, including seasonal timing and duration of reproduction, feeding, hibernation and aestivation, vary strongly across latest Cretaceous biotic clades. We postulate that the timing of the Chicxulub impact in boreal spring and austral autumn was a major influence on selective biotic survival across the Cretaceous-Palaeogene boundary.

Mass extinctions alter extinction and origination dynamics with respect to body size

Whether mass extinctions and their associated recoveries represent an intensification of background extinction and origination dynamics versus a separate macroevolutionary regime remains a central debate in evolutionary biology. The previous focus has been on extinction, but origination dynamics may be equally or more important for long-term evolutionary outcomes. The evolution of animal body size is an ideal process to test for differences in macroevolutionary regimes, as body size is easily determined, comparable across distantly related taxa and scales with organismal traits. Here, we test for shifts in selectivity between background intervals and the 'Big Five' mass extinction events using capture-mark-recapture models. Our body-size data cover 10 203 fossil marine animal genera spanning 10 Linnaean classes with occurrences ranging from Early Ordovician to Late Pleistocene (485-1 Ma). Most classes exhibit differences in both origination and extinction selectivity between background intervals and mass extinctions, with the direction of selectivity varying among classes and overall exhibiting stronger selectivity during origination after mass extinction than extinction during the mass extinction. Thus, not only do mass extinction events shift the marine biosphere into a new macroevolutionary regime, the dynamics of recovery from mass extinction also appear to play an underappreciated role in shaping the biosphere in their aftermath.

The role of vicariance and dispersal on the temporal range dynamics of forest vipers in the Neotropical region

The emergence of the diagonal of open/dry vegetations, including Chaco, Cerrado and Caatinga, is suggested to have acted as a dispersal barrier for terrestrial organisms by fragmenting a single large forest that existed in South America into the present Atlantic and Amazon forests. Here we tested the hypothesis that the expansion of the South American diagonal of open/dry landscapes acted as a vicariant process for forest lanceheads of the genus Bothrops, by analyzing the temporal range dynamics of those snakes. We estimated ancestral geographic ranges of the focal lancehead clade and its sister clade using a Bayesian dated phylogeny and the BioGeoBEARS package. We compared nine Maximum Likelihood models to infer ancestral range probabilities and their related biogeographic processes. The best fitting models (DECTS and DIVALIKETS) recovered the ancestor of our focal clade in the Amazon biogeographic region of northwestern South America. Vicariant processes in two different subclades resulted in disjunct geographic distributions in the Amazon and the Atlantic Forest. Dispersal processes must have occurred mostly within the Amazon and the Atlantic Forest and not between them. Our results suggest the fragmentation of a single ancient large forest into the Atlantic and Amazon forests acting as a driver of vicariant processes for the snake lineage studied, highlighting the importance of the diagonal of open/dry landscapes in shaping distribution patterns of terrestrial biota in South America.

Evolutionary legacies in contemporary tetrapod imperilment

The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns - but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.

On the Evolution of the Biological Framework for Insight

The details of abiogenesis, to date, remain a matter of debate and constitute a key mystery in science and philosophy. The prevailing scientific hypothesis implies an evolutionary process of increasing complexity on Earth starting from (self-) replicating polymers. Defining the cut-off point where life begins is another moot point beyond the scope of this article. We will instead walk through the known evolutionary steps that led from these first exceptional polymers to the vast network of living biomatter that spans our world today, focusing in particular on perception, from simple biological feedback mechanisms to the complexity that allows for abstract thought. We will then project from the well-known to the unknown to gain a glimpse into what the universe aims to accomplish with living matter, just to find that if the universe had ever planned to be comprehended, evolution still has a long way to go.

A model of autowave self-organization as a hierarchy of active media in the biological evolution

Within the framework of the active media concept, we develop a biophysical model of autowave self-organization which is treated as a hierarchy of active media in the evolution of the biosphere. We also propose a mathematical model of the autowave process of speciation in a flow of mutations for the three main taxonometric groups (prokaryotes, unicellular and multicellular eukaryotes) with a naturally determined lower boundary of living matter (the appearance of prokaryotes) and an open upper boundary for the formation of new species. It is shown that the fluctuation-bifurcation description of the evolution for the formation of new taxonometric groups as a trajectory of transformation of small fluctuations into giant ones adequately reflects the process of self-organization during the formation of taxa. The major concepts of biological evolution, conditions of hierarchy formation as a fundamental manifestation of self-organization and complexity in the evolution of biological systems are considered.

Coral mass mortalities in the Chagos Archipelago over 40 years: Regional species and assemblage extinctions and indications of positive feedbacks

The global decline of reef corals has been driven largely by several marine heatwaves. This has greatly reduced coral cover but has reduced coral diversity also. While there is a lack of data in most locations to detect coral species losses, reefs of the Chagos Archipelago, central Indian Ocean, have long term monitoring data extending back to the late 1970s. Severe declines in cover have occurred since the 1970s, with regional extinctions of some species and key species assemblages. There is a severe decline in coral settlement, along with a substantial loss of habitat quality which has reduced the habitat available for settlement. This is a clear precursor to positive feedback. Regional species extinctions here occur mainly when total coral cover is <10% of pre-warming levels. Climate models predict more frequent and more severe marine heatwaves, and even if this ecosystem recovers it will contain fewer species.

Farming the Sea: The Only Way to Meet Humanity's Future Food Needs

A major change began 10,000-12,000 years ago when humans began to practice agriculture. A series of "green revolutions" enabled the human population to explode, but these advancements have dramatically changed the planet. The United Nations predicts that we will need to produce 50% more food by 2050 to feed another 2.5 billion people, but this will be challenging with tighter land and water resources and a changing climate. Responsible marine aquaculture can complement responsible land-based agriculture and aquaculture and well-managed fisheries to increase the global supply of nutritious food.

Stratigraphic signatures of mass extinctions: ecological and sedimentary determinants

Stratigraphic patterns of last occurrences (LOs) of fossil taxa potentially fingerprint mass extinctions and delineate rates and geometries of those events. Although empirical studies of mass extinctions recognize that random sampling causes LOs to occur earlier than the time of extinction (Signor–Lipps effect), sequence stratigraphic controls on the position of LOs are rarely considered. By tracing stratigraphic ranges of extant mollusc species preserved in the Holocene succession of the Po coastal plain (Italy), we demonstrated that, if mass extinction took place today, complex but entirely false extinction patterns would be recorded regionally due to shifts in local community composition and non-random variation in the abundance of skeletal remains, both controlled by relative sea-level changes. Consequently, rather than following an apparent gradual pattern expected from the Signor–Lipps effect, LOs concentrated within intervals of stratigraphic condensation and strong facies shifts mimicking sudden extinction pulses. Methods assuming uniform recovery potential of fossils falsely supported stepwise extinction patterns among studied species and systematically underestimated their stratigraphic ranges. Such effects of stratigraphic architecture, co-produced by ecological, sedimentary and taphonomic processes, can easily confound interpretations of the timing, duration and selectivity of mass extinction events. Our results highlight the necessity of accounting for palaeoenvironmental and sequence stratigraphic context when inferring extinction dynamics from the fossil record.

Pattern, process, inference and prediction in extinction biology

Extinction is a key feature of the evolutionary history of life, and assessments of extinction risk are essential for the effective protection of biodiversity. The goal in assembling this special issue of Biology Letters was to highlight problems and questions at the research frontier of extinction biology, with an emphasis on recent developments in the methodology of inferring the patterns and processes of extinction from a background of often noisy and sparse data. In selecting topics, we sought to illustrate how extinction is not simply a self-evident phenomenon, but the subject of a dynamic and quantitatively rigorous field of natural science, with practical applications to conservation.

Thresholds of catastrophe in the Earth system

The history of the Earth system is a story of change. Some changes are gradual and benign, but others, especially those associated with catastrophic mass extinction, are relatively abrupt and destructive. What sets one group apart from the other? Here, I hypothesize that perturbations of Earth's carbon cycle lead to mass extinction if they exceed either a critical rate at long time scales or a critical size at short time scales. By analyzing 31 carbon isotopic events during the past 542 million years, I identify the critical rate with a limit imposed by mass conservation. Identification of the crossover time scale separating fast from slow events then yields the critical size. The modern critical size for the marine carbon cycle is roughly similar to the mass of carbon that human activities will likely have added to the oceans by the year 2100.

The Invertebrate Invasion and Evolution of Mesozoic Soil Ecosystems: The Ichnofossil Record of Ecological Innovations

Mesozoic soil ecosystems are intriguing because they are the products of many unique factors and events in geologic history. One of the most notable events that likely shaped Mesozoic soil ecosystems was the Permo-Triassic extinction. At that time, estimates of 20% of plant species, 50% of tetrapod genera, roughly 60% of insect families, and approximately 91 to 97% of shallow marine life became extinct (e.g., Padian and Clemens, 1985; Raup, 1986; Niklas et al., 1980; Wing and Sues, 1992; Labandeira and Sepkoski, 1993; and references therein). Over the span of the next 180 million years the supercontinent Pangea disassembled and the continents moved toward the configuration we see today (Scotese and Golonka, 1992); the Pangean mega-monsoonal climate pattern deteriorated into more zonal climates through to the Cretaceous (e.g., Parrish et al., 1982; Dubiel et al., 1991; Parrish, 1993); sea-level rose and flooded continental interiors, reaching its second greatest maximum since the Ordovician (e.g., Haq et al., 1987, 1988); and several major evolutionary episodes occurred, including the evolution and diversification of the angiosperms, mammals, birds, and many of the neopteran insects (Lillegraven et al., 1979; Carpenter and Burham, 1985; Friis et al., 1987; Wing and Sues, 1992; Labandeira and Sepkoski, 1993).

The Pace of Taxonomic Evolution

G. Udny Yule (1924) was perhaps the first to examine the subject of rates of taxonomic evolution mathematically, but George Gaylord Simpson was the first to examine the subject from within the confines of the so-called Modern Synthesis of Biology (Simpson, 1944). In that sense, therefore, Simpson's can be regarded as the first modern study of rates of taxonomic evolution. Although he is almost universally regarded as the catalyst behind the current interest in taxonomic evolutionary rates, it is a remarkable fact that Simpson's aims were almost entirely different from those of current workers. In a very important sense, Simpson's taxonomic rates of evolution were not taxonomic at all, but were morphological, or even more to the point, genetic.

Models of life: epigenetics, diversity and cycles

This review emphasizes aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and to punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is the minimal number of rules to sustain specific states of complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that restitute the system to a potentially new metastable state.

Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

High-order species interactions shape ecosystem diversity

Classical theory shows that large communities are destabilized by random interactions among species pairs, creating an upper bound on ecosystem diversity. However, species interactions often occur in high-order combinations, whereby the interaction between two species is modulated by one or more other species. Here, by simulating the dynamics of communities with random interactions, we find that the classical relationship between diversity and stability is inverted for high-order interactions. More specifically, while a community becomes more sensitive to pairwise interactions as its number of species increases, its sensitivity to three-way interactions remains unchanged, and its sensitivity to four-way interactions actually decreases. Therefore, while pairwise interactions lead to sensitivity to the addition of species, four-way interactions lead to sensitivity to species removal, and their combination creates both a lower and an upper bound on the number of species. These findings highlight the importance of high-order species interactions in determining the diversity of natural ecosystems.

Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night

Competition among organisms has ecological and evolutionary consequences. However, whether the consequences of competition are manifested and measureable on macroevolutionary time scales is equivocal. Marine bivalves and brachiopods have overlapping niches such that competition for food and space may occur. Moreover, there is a long-standing debate over whether bivalves outcompeted brachiopods evolutionarily, because brachiopod diversity declined through time while bivalve diversity increased. To answer this question, we estimate the origination and extinction dynamics of fossil marine bivalve and brachiopod genera from the Ordovician through to the Recent while simultaneously accounting for incomplete sampling. Then, using stochastic differential equations, we assess statistical relationships among diversification and sampling dynamics of brachiopods and bivalves and five paleoenvironmental proxies. None of these potential environmental drivers had any detectable influence on brachiopod or bivalve diversification. In contrast, elevated bivalve extinction rates causally increased brachiopod origination rates, suggesting that bivalves have suppressed brachiopod evolution.

Extinction events can accelerate evolution

Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term.

Evolutionary food web model based on body masses gives realistic networks with permanent species turnover

The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the complexity and stability of such food webs, we developed an eco-evolutionary model in which new species emerge as modifications of existing ones and dynamic ecological interactions determine which species are viable. The food-web structure thereby emerges from the dynamical interplay between speciation and trophic interactions. The proposed model is less abstract than earlier evolutionary food web models in the sense that all three evolving traits have a clear biological meaning, namely the average body mass of the individuals, the preferred prey body mass, and the width of their potential prey body mass spectrum. We observed networks with a wide range of sizes and structures and high similarity to natural food webs. The model networks exhibit a continuous species turnover, but massive extinction waves that affect more than 50% of the network are not observed.

Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians

Despite an explosion in the amount of sequence data, phylogenomics has failed to settle controversy regarding some critical nodes on the animal tree of life. Understanding relationships among Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera is essential for studying how complex traits such as neurons, muscles, and gastrulation have evolved. Recent studies have cast doubt on the historical viewpoint that sponges are sister to all other animal lineages with recent studies recovering ctenophores as sister. However, the ctenophore-sister hypothesis has been criticized as unrealistic and caused by systematic error. We review past phylogenomic studies and potential causes of systematic error in an effort to identify areas that can be improved in future studies. Increased sampling of taxa, less missing data, and a priori removal of sequences and taxa that may cause systematic error in phylogenomic inference will likely be the most fruitful areas of focus when assembling future datasets. Ultimately, we foresee metazoan relationships being resolved with higher support in the near future, and we caution against dismissing novel hypotheses merely because they conflict with historical viewpoints of animal evolution.

Can oncology recapitulate paleontology? Lessons from species extinctions

Although we can treat cancers with cytotoxic chemotherapies, target them with molecules that inhibit oncogenic drivers, and induce substantial cell death with radiation, local and metastatic tumours recur, resulting in extensive morbidity and mortality. Indeed, driving a tumour to extinction is difficult. Geographically dispersed species of organisms are perhaps equally resistant to extinction, but >99.9% of species that have ever existed on this planet have become extinct. By contrast, we are nowhere near that level of success in cancer therapy. The phenomena are broadly analogous--in both cases, a genetically diverse population mutates and evolves through natural selection. The goal of cancer therapy is to cause cancer cell population extinction, or at least to limit any further increase in population size, to prevent the tumour burden from overwhelming the patient. However, despite available treatments, complete responses are rare, and partial responses are limited in duration. Many patients eventually relapse with tumours that evolve from cells that survive therapy. Similarly, species are remarkably resilient to environmental change. Paleontology can show us the conditions that lead to extinction and the characteristics of species that make them resistant to extinction. These lessons could be translated to improve cancer therapy and prognosis.

Extinction can be estimated from moderately sized molecular phylogenies

Hundreds of studies have been dedicated to estimating speciation and extinction from phylogenies of extant species. Although it has long been known that estimates of extinction rates using trees of extant organisms are often uncertain, an influential paper by Rabosky (2010) suggested that when birth rates vary continuously across the tree, estimates of the extinction fraction (i.e., extinction rate/speciation rate) will appear strongly bimodal, with a peak suggesting no extinction and a peak implying speciation and extinction rates are approaching equality. On the basis of these results, and the realistic nature of this form of rate variation, it is now generally assumed by many practitioners that extinction cannot be understood from molecular phylogenies alone. Here, we reevaluated and extended the analyses of Rabosky (2010) and come to the opposite conclusion-namely, that it is possible to estimate extinction from molecular phylogenies, even with model violations due to heritable variation in diversification rate. Note that while it may be tempting to interpret our study as advocating the application of simple birth-death models, our goal here is to show how a particular model violation does not necessitate the abandonment of an entire field: use prudent caution, but do not abandon all hope.

Climate-driven extinctions shape the phylogenetic structure of temperate tree floras

When taxa go extinct, unique evolutionary history is lost. If extinction is selective, and the intrinsic vulnerabilities of taxa show phylogenetic signal, more evolutionary history may be lost than expected under random extinction. Under what conditions this occurs is insufficiently known. We show that late Cenozoic climate change induced phylogenetically selective regional extinction of northern temperate trees because of phylogenetic signal in cold tolerance, leading to significantly and substantially larger than random losses of phylogenetic diversity (PD). The surviving floras in regions that experienced stronger extinction are phylogenetically more clustered, indicating that non-random losses of PD are of increasing concern with increasing extinction severity. Using simulations, we show that a simple threshold model of survival given a physiological trait with phylogenetic signal reproduces our findings. Our results send a strong warning that we may expect future assemblages to be phylogenetically and possibly functionally depauperate if anthropogenic climate change affects taxa similarly.

Taxamatch, an algorithm for near ('fuzzy') matching of scientific names in taxonomic databases

Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical.

Punctuated equilibrium and shock waves in molecular models of biological evolution

We consider the dynamics in infinite population evolution models with a general symmetric fitness landscape. We find shock waves, i.e., discontinuous transitions in the mean fitness, in evolution dynamics even with smooth fitness landscapes, which means that the search for the optimal evolution trajectory is more complicated. These shock waves appear in the case of positive epistasis and can be used to represent punctuated equilibria in biological evolution during long geological time scales. We find exact analytical solutions for discontinuous dynamics at the large-genome-length limit and derive optimal mutation rates for a fixed fitness landscape to send the population from the initial configuration to some final configuration in the fastest way.

Function relaxation followed by diversifying selection after whole-genome duplication in flowering plants

Episodes of whole-genome duplication (WGD) followed by gene loss dominate the evolutionary history of flowering plants. Despite the importance of understanding gene evolution following WGD, little is known about the evolutionary dynamics of this process. In this study, we analyzed duplicated genes from three WGD events in the Arabidopsis (Arabidopsis thaliana) lineage using multiple data types. Most duplicated genes that have survived from the most recent WGD (α) are under purifying selection in modern Arabidopsis populations. Using the number of identified protein-protein interactions as a proxy for functional divergence, approximately 92.7% of α-duplicated genes were diverged in function from one another in modern Arabidopsis populations, indicating that their preservation is no longer explicable by dosage balance. Dosage-balanced retention declines with antiquity of duplication: 24.1% of α-duplicated gene pairs in Arabidopsis remain in dosage balance with interacting partners, versus 12.9% and 9.4% for the earlier β-duplication and γ-triplication. GO-slim (a cut-down version of gene ontologies) terms reinforce evidence from protein-protein interactions, showing that the putatively diverged gene pairs are adapted to different cellular components. We identified a group of α-duplicated genes that show higher than average single-nucleotide polymorphism density, indicating that a period of positive selection, potentially driving functional divergence, may have preceded the current phase of purifying selection. We propose three possible paths for the evolution of duplicated genes following WGD.

Bivalve network reveals latitudinal selectivity gradient at the end-Cretaceous mass extinction

Biogeographic patterns of survival help constrain the causal factors responsible for mass extinction. To test whether biogeography influenced end-Cretaceous (K-Pg) extinction patterns, we used a network approach to delimit biogeographic units (BUs) above the species level in a global Maastrichtian database of 329 bivalve genera. Geographic range is thought to buffer taxa from extinction, but the number of BUs a taxon occurred in superseded geographic range as an extinction predictor. Geographically, we found a latitudinal selectivity gradient for geographic range in the K-Pg, such that higher latitude BUs had lower extinction than expected given the geographic ranges of the genera, implying that (i) high latitude BUs were more resistant to extinction, (ii) the intensity of the K-Pg kill mechanism declined with distance from the tropics, or (iii) both. Our results highlight the importance of macroecological structure in constraining causal mechanisms of extinction and estimating extinction risk of taxa.

Disturbances, organisms and ecosystems: a global change perspective

The present text exposes a theory of the role of disturbances in the assemblage and evolution of species within ecosystems, based principally, but not exclusively, on terrestrial ecosystems. Two groups of organisms, doted of contrasted strategies when faced with environmental disturbances, are presented, based on the classical r-K dichotomy, but enriched with more modern concepts from community and evolutionary ecology. Both groups participate in the assembly of known animal, plant, and microbial communities, but with different requirements about environmental fluctuations. The so-called "civilized" organisms are doted with efficient anticipatory mechanisms, allowing them to optimize from an energetic point of view their performances in a predictable environment (stable or fluctuating cyclically at the scale of life expectancy), and they developed advanced specializations in the course of evolutionary time. On the opposite side, the so-called "barbarians" are weakly efficient in a stable environment because they waste energy for foraging, growth, and reproduction, but they are well adapted to unpredictably changing conditions, in particular during major ecological crises. Both groups of organisms succeed or alternate each other in the course of spontaneous or geared successional processes, as well as in the course of evolution. The balance of "barbarians" against "civilized" strategies within communities is predicted to shift in favor of the first type under present-day anthropic pressure, exemplified among others by climate warming, land use change, pollution, and biological invasions.

Instability in evolutionary games

Background

Phenomena of instability are widely observed in many dissimilar systems, with punctuated equilibrium in biological evolution and economic crises being noticeable examples. Recent studies suggested that such instabilities, quantified by the abrupt changes of the composition of individuals, could result within the framework of a collection of individuals interacting through the prisoner's dilemma and incorporating three mechanisms: (i) imitation and mutation, (ii) preferred selection on successful individuals, and (iii) networking effects.

Methodology/Principal Findings

We study the importance of each mechanism using simplified models. The models are studied numerically and analytically via rate equations and mean-field approximation. It is shown that imitation and mutation alone can lead to the instability on the number of cooperators, and preferred selection modifies the instability in an asymmetric way. The co-evolution of network topology and game dynamics is not necessary to the occurrence of instability and the network topology is found to have almost no impact on instability if new links are added in a global manner. The results are valid in both the contexts of the snowdrift game and prisoner's dilemma.

Conclusions/Significance

The imitation and mutation mechanism, which gives a heterogeneous rate of change in the system's composition, is the dominating reason of the instability on the number of cooperators. The effects of payoffs and network topology are relatively insignificant. Our work refines the understanding on the driving forces of system instability.