Dynamic hierarchies in temporal directed networks

The outcome of interactions in many real-world systems can be often explained by a hierarchy between the participants. Discovering hierarchy from a given directed network can be formulated as follows: partition vertices into levels such that, ideally, there are only forward edges, that is, edges from upper levels to lower levels. In practice, the ideal case is impossible, so instead we minimize some penalty function on the backward edges. One practical option for such a penalty is agony, where the penalty depends on the severity of the violation. In this paper we extend the definition of agony to temporal networks. In this setup we are given a directed network with time stamped edges, and we allow the rank assignment to vary over time. We propose 2 strategies for controlling the variation of individual ranks. In our first variant, we penalize the fluctuation of the rankings over time by adding a penalty directly to the optimization function. In our second variant we allow the rank change at most once. We show that the first variant can be solved exactly in polynomial time while the second variant is NP-hard, and in fact inapproximable. However, we develop an iterative method, where we first fix the change point and optimize the ranks, and then fix the ranks and optimize the change points, and reiterate until convergence. We show empirically that the algorithms are reasonably fast in practice, and that the obtained rankings are sensible

Breeding young as a survival strategy during earth’s greatest mass extinction

Studies of the effects of mass extinctions on ancient ecosystems have focused on changes in taxic diversity, morphological disparity, abundance, behaviour and resource availability as key determinants of group survival. Crucially, the contribution of life history traits to survival during terrestrial mass extinctions has not been investigated, despite the critical role of such traits for population viability. We use bone microstructure and body size data to investigate the palaeoecological implications of changes in life history strategies in the therapsid forerunners of mammals before and after the Permo-Triassic Mass Extinction (PTME), the most catastrophic crisis in Phanerozoic history. Our results are consistent with truncated development, shortened life expectancies, elevated mortality rates and higher extinction risks amongst post-extinction species. Various simulations of ecological dynamics indicate that an earlier onset of reproduction leading to shortened generation times could explain the persistence of therapsids in the unpredictable, resource-limited Early Triassic environments, and help explain observed body size distributions of some disaster taxa (e.g., Lystrosaurus). Our study accounts for differential survival in mammal ancestors after the PTME and provides a methodological framework for quantifying survival strategies in other vertebrates during major biotic crises

A Comparison of the Effects of Random and Selective Mass Extinctions on Erosion of Evolutionary History in Communities of Digital Organisms

The effect of mass extinctions on phylogenetic diversity and branching history of clades remains poorly understood in paleobiology. We examined the phylogenies of communities of digital organisms undergoing open-ended evolution as we subjected them to instantaneous “pulse” extinctions, choosing survivors at random, and to prolonged “press” extinctions involving a period of low resource availability. We measured age of the phylogenetic root and tree stemminess, and evaluated how branching history of the phylogenetic trees was affected by the extinction treatments. We found that strong random (pulse) and strong selective extinction (press) both left clear long-term signatures in root age distribution and tree stemminess, and eroded deep branching history to a greater degree than did weak extinction and control treatments. The widely-used Pybus-Harvey gamma statistic showed a clear short-term response to extinction and recovery, but differences between treatments diminished over time and did not show a long-term signature. The characteristics of post-extinction phylogenies were often affected as much by the recovery interval as by the extinction episode itself

The Diversity of Coral Reefs: What Are We Missing?

Tropical reefs shelter one quarter to one third of all marine species but one third of the coral species that construct reefs are now at risk of extinction. Because traditional methods for assessing reef diversity are extremely time consuming, taxonomic expertise for many groups is lacking, and marine organisms are thought to be less vulnerable to extinction, most discussions of reef conservation focus on maintenance of ecosystem services rather than biodiversity loss. In this study involving the three major oceans with reef growth, we provide new biodiversity estimates based on quantitative sampling and DNA barcoding. We focus on crustaceans, which are the second most diverse group of marine metazoans. We show exceptionally high numbers of crustacean species associated with coral reefs relative to sampling effort (525 species from a combined, globally distributed sample area of 6.3 m2). The high prevalence of rare species (38% encountered only once), the low level of spatial overlap (81% found in only one locality) and the biogeographic patterns of diversity detected (Indo-West Pacific>Central Pacific>Caribbean) are consistent with results from traditional survey methods, making this approach a reliable and efficient method for assessing and monitoring biodiversity. The finding of such large numbers of species in a small total area suggests that coral reef diversity is seriously under-detected using traditional survey methods, and by implication, underestimated

Mass extinctions drove increased global faunal cosmopolitanism on the supercontinent Pangaea

Mass extinctions have profoundly impacted the evolution of life through not only reducing taxonomic diversity but also reshaping ecosystems and biogeographic patterns. In particular, they are considered to have driven increased biogeographic cosmopolitanism, but quantitative tests of this hypothesis are rare and have not explicitly incorporated information on evolutionary relationships. Here we quantify faunal cosmopolitanism using a phylogenetic network approach for 891 terrestrial vertebrate species spanning the late Permian through Early Jurassic. This key interval witnessed the Permian–Triassic and Triassic–Jurassic mass extinctions, the onset of fragmentation of the supercontinent Pangaea, and the origins of dinosaurs and many modern vertebrate groups. Our results recover significant increases in global faunal cosmopolitanism following both mass extinctions, driven mainly by new, widespread taxa, leading to homogenous ‘disaster faunas’. Cosmopolitanism subsequently declines in post-recovery communities. These shared patterns in both biotic crises suggest that mass extinctions have predictable influences on animal distribution and may shed light on biodiversity loss in extant ecosystems

Global Taxonomic Diversity of Anomodonts (Tetrapoda, Therapsida) and the Terrestrial Rock Record Across the Permian-Triassic Boundary

The end-Permian biotic crisis (∼252.5 Ma) represents the most severe extinction event in Earth's history. This paper investigates diversity patterns in Anomodontia, an extinct group of therapsid synapsids (‘mammal-like reptiles’), through time and in particular across this event. As herbivores and the dominant terrestrial tetrapods of their time, anomodonts play a central role in assessing the impact of the end-Permian extinction on terrestrial ecosystems. Taxonomic diversity analysis reveals that anomodonts experienced three distinct phases of diversification interrupted by the same number of extinctions, i.e. an end-Guadalupian, an end-Permian, and a mid-Triassic extinction. A positive correlation between the number of taxa and the number of formations per time interval shows that anomodont diversity is biased by the Permian-Triassic terrestrial rock record. Normalized diversity curves indicate that anomodont richness continuously declines from the Middle Permian to the Late Triassic, but also reveals all three extinction events. Taxonomic rates (origination and extinction) indicate that the end-Guadalupian and end-Permian extinctions were driven by increased rates of extinction as well as low origination rates. However, this pattern is not evident at the final decline of anomodont diversity during the Middle Triassic. Therefore, it remains unclear whether the Middle Triassic extinction represents a gradual or abrupt event that is unique to anomodonts or more common among terrestrial tetrapods. The end-Permian extinction represents the most distinct event in terms of decline in anomodont richness and turnover rates

Complex body size trends in the evolution of sloths (Xenarthra: Pilosa)

Background Extant sloths present an evolutionary conundrum in that the two living genera are superficially similar (small-bodied, folivorous, arboreal) but diverged from one another approximately 30 million years ago and are phylogenetically separated by a radiation of medium to massive, mainly ground-dwelling, taxa. Indeed, the species in the two living genera are among the smallest, and perhaps most unusual, of the 50+ known sloth species, and must have independently and convergently evolved small size and arboreality. In order to accurately reconstruct sloth evolution, it is critical to incorporate their extinct diversity in analyses. Here, we used a dataset of 57 species of living and fossil sloths to examine changes in body mass mean and variance through their evolution, employing a general time-variable model that allows for analysis of evolutionary trends in continuous characters within clades lacking fully-resolved phylogenies, such as sloths. Results Our analyses supported eight models, all of which partition sloths into multiple subgroups, suggesting distinct modes of body size evolution among the major sloth lineages. Model-averaged parameter values supported trended walks in most clades, with estimated rates of body mass change ranging as high as 126 kg/million years for the giant ground sloth clades Megatheriidae and Nothrotheriidae. Inclusion of living sloth species in the analyses weakened reconstructed rates for their respective groups, with estimated rates for Megalonychidae (large to giant ground sloths and the extant two-toed sloth) were four times higher when the extant genus Choloepus was excluded. Conclusions Analyses based on extant taxa alone have the potential to oversimplify or misidentify macroevolutionary patterns. This study demonstrates the impact that integration of data from the fossil record can have on reconstructions of character evolution and establishes that body size evolution in sloths was complex, but dominated by trended walks towards the enormous sizes exhibited in some recently extinct forms

Geographical variation in shell shape of the pod razor shell Ensis siliqua (Bivalvia: Pharidae)

The present study assessed the existence of variation in the shell shape of the pod razor shell (Ensis siliqua) throughout its distributional range in the north- eastern Atlantic. Shells of E. siliqua caught at seven collecting sites (three in Portugal, three in Spain and one in Ireland) were studied by geometric morphometric methods, using both landmark- and contour-based methods. Both approaches (landmarks inside the valves and shell outline) discriminated the shells from Aveiro (centre of Portugal) and Strangford Lough (Ireland) from those caught in the nearby localities (remaining Portuguese and Spanish sites,maximum distance of 550 km by sea). Landmark analysis revealed that shells from Aveiro were more similar to shells from Ireland (*1,500 km far away). Contour anal- ysis revealed that shells from Aveiro had a shape with a comparatively larger height-to-width ratio, whereas shells from Ireland showed a slightly more curved outline than in the remaining sites. Landmark- and contour-based methods provided coherent complementary information, confirming the usefulness of geometric morphometric analyses for discerning differences in shell shape among populations of E. siliqua. A brief review of previous applications of geometric morphometric methods to modern bivalve spe- cies is also provided.The authors would like to thank Dr. Dai Roberts and Adele Cromie for providing samples of pod razor shells from Ireland. This study was funded by Community Initiative Programmes (INTERREG-IIIB, Atlantic Area) Sustainable HARvesting of Ensis (090–SHARE) and Towards Integrated Management of Ensis Stocks (206–TIMES) from the European Community. Marta M. Rufino and Paulo Vasconcelos benefited from postdoctoral grants (SFRH/BPD/14935/2004 and SFRH/BPD/26348/2006, respectively) awarded by the Fundação para a Ciência e Tecnologia (FCT—Portugal). Finally, the authors acknowledge three anonymous referees for valuable comments and suggestions that greatly improved the revised manuscript.publishe

Reining in the Red Queen: The dynamics of adaptation and extinction reexamined

One of the most enduring evolutionary metaphors is Van Valen's (1973) Red Queen. According to this metaphor, as one species in a community adapts by becoming better able to acquire and defend resources, species with which it interacts are adversely affected. If those other species do not continuously adapt to compensate for this biotically caused deterioration, they will be driven to extinction. Continuous adaptation of all species in a community prevents any single species from gaining a long-term advantage; this amounts to the Red Queen running in place. We have critically examined the assumptions on which the Red Queen metaphor was founded. We argue that the Red Queen embodies three demonstrably false assumptions: (1) evolutionary adaptation is continuous; (2) organisms are important agents of extinction; and (3) evolution is a zero-sum process in which living things divide up an unchanging quantity of resources. Changes in the selective regime need not always elicit adaptation, because most organisms function adequately under many "suboptimal" conditions and often compensate by demonstrating adaptive flexibility. Likewise, ecosystems are organized in such a way that they tend to be robust and capable of absorbing invasions and extinctions, at least up to a point. With a simple evolutionary game involving three species, we show that Red Queen dynamics (continuous adaptation by all interacting species) apply in only a very small minority of possible outcomes. Importantly, cooperation and facilitation among species enable competitors to increase ecosystem productivity and therefore to enlarge the pool and turnover of resources. The Red Queen reigns only under a few unusual circumstances. © 2013 The Paleontological Society. All rights reserved