Dinosaurs in decline tens of millions of years before their final extinction

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous–Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event.

A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids

Evolutionary innovations, traits that give species access to previously unoccupied niches, may promote speciation and adaptive radiation. Here, we show that such innovations can also result in competitive inferiority and extinction. We present evidence that the modified pharyngeal jaws of cichlid fishes and several marine fish lineages, a classic example of evolutionary innovation, are not universally beneficial. A large-scale analysis of dietary evolution across marine fish lineages reveals that the innovation compromises access to energy-rich predator niches. We show that this competitive inferiority shaped the adaptive radiation of cichlids in Lake Tanganyika and played a pivotal and previously unrecognized role in the mass extinction of cichlid fishes in Lake Victoria after Nile perch invasion.

The distributions, C- and O-isotopic compositions, and frequency of giant-ooids

Early Triassic oceans were characterized by deposition of a number of "anachronistic facies", including microbialites, seafloor carbonate cement fans, and giant ooids. Giant ooids were particularly prevalent in Lower Triassic sections across South China and exhibit unusual features that may provide insights into marine environmental conditions following the end-Permian mass extinction. The section at Moyang (Guizhou Province) contains abundant giant ooids ranging in size between 2 and 6 mm (maximum 12 mm) and exhibiting various cortical structures, including regular, deformed, compound, regenerated and "domed". Preservation of ooid cortical structure is generally good as indicated by petrographic observations, and trace element and carbon isotope analyses suggest that diagenesis occurred in a closed diagenetic system. All ooids exhibit fine concentric laminae, frequently alternating between light-colored coarsely crystalline and dark-colored finely crystalline layers probably reflecting variation in organic content or original mineralogy. Under scanning electron microscope, biomineralized filaments or biofilms and tiny carbonate fluorapatite (CFA) crystals are commonly found in the finely crystalline layers. We infer that the precipitation of CFA was related to adsorption of P via microbial activity on the surfaces of ooids following episodic incursions of deep waters rich in carbon dioxide, hydrogen sulfide and phosphate into shallow-marine environments. Giant ooid precipitation may have been promoted in shallow ramp settings during these events by increased watermass agitation and supersaturation with respect to calcium carbonate, as well as reduced carbonate removal rates through biotic skeletal formation. Spatio-temporal distribution data reveal that giant ooids were widespread in the Tethyan region during the Early Triassic, and that they were most abundant immediately after the end-Permian crisis and disappeared gradually as metazoans repopulated marine environments.

Lessons from the past: Biotic recoveries from mass extinctions

Although mass extinctions probably account for the disappearance of less than 5% of all extinct species, the evolutionary opportunities they have created have had a disproportionate effect on the history of life. Theoretical considerations and simulations have suggested that the empty niches created by a mass extinction should refill rapidly after extinction ameliorates. Under logistic models, this biotic rebound should be exponential, slowing as the environmental carrying capacity is approached. Empirical studies reveal a more complex dynamic, including positive feedback and an exponential growth phase during recoveries. Far from a model of refilling ecospace, mass extinctions appear to cause a collapse of ecospace, which must be rebuilt during recovery. Other generalities include the absence of a clear correlation between the magnitude of extinction and the pace of recovery or the resulting ecological and evolutionary disruption the presence of a survival interval, with few originations, immediately after an extinction and preceding the recovery phase, and the presence of many lineages that persist through an extinction event only to disappear during the subsequent recovery. Several recoveries include numerous missing lineages, groups that are found before the extinction, then latter in the recovery, but are missing during the initial survival–recovery phase. The limited biogeographic studies of recoveries suggest considerable variability between regions.

On the tracks of the earliest dinosaurs: implications for the hypothesis of dinosaurian monophyly

From the record of dinosaurian skeletal remains it has been inferred that the origin and initial diversification of dinosaurs were rapid events, occupying an interval of about 5 million years in the Late Triassic. By contrast numerous reports of dinosauroid tracks imply that the emergence of dinosaurs was a more protracted affair extending through much of the Early and Middle Triassic. This study finds no convincing evidence of dinosaur tracks before the late Ladinian. Each of the three dinosaurian clades - Theropoda, Sauropodomorpha, Ornithischia - produced a unique track morphotype that appears to be an independent modification of the chirotherioid pattern attributed to stem-group archosaurs (thecodontian reptiles). The existence of three divergent track morphotypes is consistent with the concept of dinosaurian polyphyly but can be reconciled with the hypothesis of dinosaurian monophyly only by invoking many and rapid reversals in the locomotor anatomy of early dinosaurs. The origin of dinosaurs was not the correlate or consequence of any single event or process, be it global change, competitive replacement, or opportunism in the wake of mass extinction. Instead the origin of dinosaurs is envisaged as a series of three cladogenetic events over an interval of at least 10 million years and possibly as much as 25 million years. This scenario of dinosaurian polyphyly is as well-supported by fossil evidence as is the currently favoured view of dinosaurian monophyly.

'Nothing exists for one cause' : putting biology back into evolution

The opening phrase of the title is from Charles Darwin’s notebooks (Schweber 1977). It is a double reminder, firstly that mainstream evolutionary theory is not just about describing nature but is particularly looking for mechanisms or ‘causes’, and secondly, that there will usually be several causes affecting any particular outcome. The second part of the title is our concern at the almost universal rejection of the idea that biological mechanisms are sufficient for macroevolutionary changes, thus rejecting a cornerstone of Darwinian evolutionary theory. Our primary aim here is to consider ways of making it easier to develop and to test hypotheses about evolution. Formalizing hypotheses can help generate tests. In an absolute sense, some of the discussion by scientists about evolution is little better than the lack of reasoning used by those advocating intelligent design. Our discussion here is in a Popperian framework where science is defined by that area of study where it is possible, in principle, to find evidence against hypotheses – they are in principle falsifiable. However, with time, the boundaries of science keep expanding. In the past, some aspects of evolution were outside the current boundaries of falsifiable science, but increasingly new techniques and ideas are expanding the boundaries of science and it is appropriate to re-examine some topics. It often appears that over the last few decades there has been an increasingly strong assumption to look first (and only) for a physical cause. This decision is virtually never formally discussed, just an assumption is made that some physical factor ‘drives’ evolution. It is necessary to examine our assumptions much more carefully. What is meant by physical factors ‘driving’ evolution, or what is an ‘explosive radiation’. Our discussion focuses on two of the six mass extinctions, the fifth being events in the Late Cretaceous, and the sixth starting at least 50,000 years ago (and is ongoing). Cretaceous/Tertiary boundary; the rise of birds and mammals. We have had a long-term interest (Cooper and Penny 1997) in designing tests to help evaluate whether the processes of microevolution are sufficient to explain macroevolution. The real challenge is to formulate hypotheses in a testable way. For example the numbers of lineages of birds and mammals that survive from the Cretaceous to the present is one test. Our first estimate was 22 for birds, and current work is tending to increase this value. This still does not consider lineages that survived into the Tertiary, and then went extinct later. Our initial suggestion was probably too narrow in that it lumped four models from Penny and Phillips (2004) into one model. This reduction is too simplistic in that we need to know about survival and ecological and morphological divergences during the Late Cretaceous, and whether Crown groups of avian or mammalian orders may have existed back into the Cretaceous. More recently (Penny and Phillips 2004) we have formalized hypotheses about dinosaurs and pterosaurs, with the prediction that interactions between mammals (and groundfeeding birds) and dinosaurs would be most likely to affect the smallest dinosaurs, and similarly interactions between birds and pterosaurs would particularly affect the smaller pterosaurs. There is now evidence for both classes of interactions, with the smallest dinosaurs and pterosaurs declining first, as predicted. Thus, testable models are now possible. Mass extinction number six: human impacts. On a broad scale, there is a good correlation between time of human arrival, and increased extinctions (Hurles et al. 2003; Martin 2005; Figure 1). However, it is necessary to distinguish different time scales (Penny 2005) and on a finer scale there are still large numbers of possibilities. In Hurles et al. (2003) we mentioned habitat modification (including the use of Geogenes III July 2006 31 fire), introduced plants and animals (including kiore) in addition to direct predation (the ‘overkill’ hypothesis). We need also to consider prey switching that occurs in early human societies, as evidenced by the results of Wragg (1995) on the middens of different ages on Henderson Island in the Pitcairn group. In addition, the presence of human-wary or humanadapted animals will affect the distribution in the subfossil record. A better understanding of human impacts world-wide, in conjunction with pre-scientific knowledge will make it easier to discuss the issues by removing ‘blame’. While continued spontaneous generation was accepted universally, there was the expectation that animals continued to reappear. New Zealand is one of the very best locations in the world to study many of these issues. Apart from the marine fossil record, some human impact events are extremely recent and the remains less disrupted by time.

The origin of cyclical high- and low-Cr basalts with continental crust trace element signatures in the Kalkarindji Large Igneous Province

The 510 million year old Kalkarindji Large Igneous Province correlates in time with the first major extinction event after the Cambrian explosion of life. Large igneous provinces correlate with all major mass extinction events in the last 500 million years. The genetic link between large igneous provinces and mass extinction remains unclear. My work is a contribution towards understanding magmatic processes involved in the generation of Large Igneous Provinces. I concentrate on the origin of variation in Cr in magmas and have developed a model in which high temperature melts intrude into and assimilate large amounts of upper continental crust.

Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds”

Jarvis et al. (Research Articles, 12 December 2014, p. 1320) presented molecular clock analyses that suggested that most modern bird orders diverged just after the mass extinction event at the Cretaceous-Paleogene boundary (about 66 million years ago). We demonstrate that this conclusion results from the use of a single inappropriate maximum bound, which effectively precludes the Cretaceous diversification overwhelmingly supported by previous molecular studies.

Assessment of some physico-chemical parameters of River Ogun (Abeokuta, Ogun State, southwestern Nigeria) in comparison with national and international standards

This study assessed the physico-chemical quality of River Ogun, Abeokuta, Ogun state, Southwestern Nigeria. Four locations were chosen spatially along the water course to reflect a consideration of all possible human activities that are capable of changing the quality of river water. The water samples were collected monthly for seven consecutive months (December 2011 – June 2012) at the four sampling stations. pH, air temperature (℃), water temperature (℃), conductivity (µs/cm) and total dissolved solids (mg/L) were conducted in-situ with the use of HANNA Combo pH and EC multi meter Hi 98129 and Mercury-in-glass thermometer while dissolved oxygen (mg/L), nitrate (mg/L), phosphate (mg/L), alkalinity (mg/L) and hardness (mg/L) were determined ex-situ using standard methods. Results showed that dissolved oxygen, hydrogen ion concentration, total hardness and nitrate were above the maximum permissible limit of National Administration for Food, Drugs and Control (NAFDAC), Standard Organization of Nigeria (SON), Federal Environmental Protection Agency (FEPA), United States Environmental Protection Agency (USEPA), European Union (EU) and World Health Organization (WHO) for drinking water during certain months of the study period. Results also showed that water temperature and conductivity were within the permissible limits of all the standards excluding FEPA. However, total dissolved solids and alkalinity were within the permissible limits of all the standards. Adejuwon and Adelakun, (2012) also reported similar findings on Rivers Lala, Yobo and Agodo in Ewekoro local government area of Ogun state, Nigeria. Since most of the parameters measured were above the maximum permissible limits of the national and international standards, it can be concluded that the water is unfit for domestic uses, drinking and aquacultural purposes and therefore needs to be treated if it is to be used at all. The low dissolved oxygen values for the first four months was too low i.e. < 5 mg/L. This is most likely as a result of the amount of effluents discharged into the river. To prevent mass extinction of aquatic organisms due to anoxic conditions, proper regulations should be implemented to reduce the organic load the river receives.

The Origin and Diversification of Birds.

Birds are one of the most recognizable and diverse groups of modern vertebrates. Over the past two decades, a wealth of new fossil discoveries and phylogenetic and macroevolutionary studies has transformed our understanding of how birds originated and became so successful. Birds evolved from theropod dinosaurs during the Jurassic (around 165-150 million years ago) and their classic small, lightweight, feathered, and winged body plan was pieced together gradually over tens of millions of years of evolution rather than in one burst of innovation. Early birds diversified throughout the Jurassic and Cretaceous, becoming capable fliers with supercharged growth rates, but were decimated at the end-Cretaceous extinction alongside their close dinosaurian relatives. After the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.

Environmental effects of Deccan volcanism across the Cretaceous-Tertiary transition in Meghalaya, India

The Um Sohryngkew section of Meghalaya, NE India, located 800–1000 km from the Deccan volcanic province, is one of the most complete Cretaceous–Tertiary boundary (KTB) transitions worldwide with all defining and supporting criteria present: mass extinction of planktic foraminifera, first appearance of Danian species, δ13C shift, Ir anomaly (12 ppb) and KTB red layer. The geochemical signature of the KTB layer indicates not only an extraterrestrial signal (Ni and all Platinum Group Elements (PGEs)) of a second impact that postdates Chicxulub, but also a significant component resulting from condensed sedimentation (P), redox fluctuations (As, Co, Fe, Pb, Zn, and to a lesser extent Ni and Cu) and volcanism. From the late Maastrichtian C29r into the early Danian, a humid climate prevailed (kaolinite: 40–60%, detrital minerals: 50–80%). During the latest Maastrichtian, periodic acid rains (carbonate dissolution; CIA index: 70–80) associated with pulsed Deccan eruptions and strong continental weathering resulted in mesotrophic waters. The resulting super-stressed environmental conditions led to the demise of nearly all planktic foraminiferal species and blooms (> 95%) of the disaster opportunist Guembelitria cretacea. These data reveal that detrimental marine conditions prevailed surrounding the Deccan volcanic province during the main phase of eruptions in C29r below the KTB. Ultimately these environmental conditions led to regionally early extinctions followed by global extinctions at the KTB.

Radiative forcing of the direct aerosol effect from AeroCom Phase II simulations

We report on the AeroCom Phase II direct aerosol effect (DAE) experiment where 16 detailed global aerosol models have been used to simulate the changes in the aerosol distribution over the industrial era. All 16 models have estimated the radiative forcing (RF) of the anthropogenic DAE, and have taken into account anthropogenic sulphate, black carbon (BC) and organic aerosols (OA) from fossil fuel, biofuel, and biomass burning emissions. In addition several models have simulated the DAE of anthropogenic nitrate and anthropogenic influenced secondary organic aerosols (SOA). The model simulated all-sky RF of the DAE from total anthropogenic aerosols has a range from −0.58 to −0.02Wm−2, with a mean of −0.27Wm−2 for the 16 models. Several models did not include nitrate or SOA and modifying the estimate by accounting for this with information from the other AeroCom models reduces the range and slightly strengthens the mean. Modifying the model estimates for missing aerosol components and for the time period 1750 to 2010 results in a mean RF for the DAE of −0.35Wm−2. Compared to AeroCom Phase I (Schulz et al., 2006) we find very similar spreads in both total DAE and aerosol component RF. However, the RF of the total DAE is stronger negative and RF from BC from fossil fuel and biofuel emissions are stronger positive in the present study than in the previous AeroCom study.We find a tendency for models having a strong (positive) BC RF to also have strong (negative) sulphate or OA RF. This relationship leads to smaller uncertainty in the total RF of the DAE compared to the RF of the sum of the individual aerosol components. The spread in results for the individual aerosol components is substantial, and can be divided into diversities in burden, mass extinction coefficient (MEC), and normalized RF with respect to AOD. We find that these three factors give similar contributions to the spread in results.

Sources, sinks, and transatlantic transport of North African dust aerosol: a multimodel analysis and comparison with remote sensing data

This study evaluates model-simulated dust aerosols over North Africa and the North Atlantic from five global models that participated in the Aerosol Comparison between Observations and Models phase II model experiments. The model results are compared with satellite aerosol optical depth (AOD) data from Moderate Resolution Imaging Spectroradiometer (MODIS), Multiangle Imaging Spectroradiometer (MISR), and Sea-viewing Wide Field-of-view Sensor, dust optical depth (DOD) derived from MODIS and MISR, AOD and coarse-mode AOD (as a proxy of DOD) from ground-based Aerosol Robotic Network Sun photometer measurements, and dust vertical distributions/centroid height from Cloud Aerosol Lidar with Orthogonal Polarization and Atmospheric Infrared Sounder satellite AOD retrievals. We examine the following quantities of AOD and DOD: (1) the magnitudes over land and over ocean in our study domain, (2) the longitudinal gradient from the dust source region over North Africa to the western North Atlantic, (3) seasonal variations at different locations, and (4) the dust vertical profile shape and the AOD centroid height (altitude above or below which half of the AOD is located). The different satellite data show consistent features in most of these aspects; however, the models display large diversity in all of them, with significant differences among the models and between models and observations. By examining dust emission, removal, and mass extinction efficiency in the five models, we also find remarkable differences among the models that all contribute to the discrepancies of model-simulated dust amount and distribution. This study highlights the challenges in simulating the dust physical and optical processes, even in the best known dust environment, and stresses the need for observable quantities to constrain the model processes.