Considering the Case for Biodiversity Cycles: Reexamining the Evidence for Periodicity in the Fossil Record

Medvedev and Melott (2007) have suggested that periodicity in fossil biodiversity may be induced by cosmic rays which vary as the Solar System oscillates normal to the galactic disk. We re-examine the evidence for a 62 million year (Myr) periodicity in biodiversity throughout the Phanerozoic history of animal life reported by Rohde & Mueller (2005), as well as related questions of periodicity in origination and extinction. We find that the signal is robust against variations in methods of analysis, and is based on fluctuations in the Paleozoic and a substantial part of the Mesozoic. Examination of origination and extinction is somewhat ambiguous, with results depending upon procedure. Origination and extinction intensity as defined by RM may be affected by an artifact at 27 Myr in the duration of stratigraphic intervals. Nevertheless, when a procedure free of this artifact is implemented, the 27 Myr periodicity appears in origination, suggesting that the artifact may ultimately be based on a signal in the data. A 62 Myr feature appears in extinction, when this same procedure is used. We conclude that evidence for a periodicity at 62 Myr is robust, and evidence for periodicity at approximately 27 Myr is also present, albeit more ambiguous.Comment: Minor modifications to reflect final published versio

Facies and faunal assemblage changes in response to the Holocene transgression in the Lagoon of Mayotte (Comoro Archipelago, SW Indian Ocean)

This paper documents the facies change in response to the Holocene transgression within five sediment cores taken in the lagoon of Mayotte, which contain a Type-1 depositional sequence (lowstand, transgressive and highstand deposits underlain by an erosive sequence boundary). Quantitative compositional analysis and visual examination of the bioclasts were used to document the facies changes. The distribution of the skeletal and non-skeletal grains in the lagoon of Mayotte is clearly controlled by (1) the rate and amplitude of the Holocene sea-level rise, (2) the pre-Holocene basement topography and (3) the growth-potential of the barrier reef during sea-level rise, and the changes in bathymetry and continuity during this period. The sequence boundary consists of the glacial karst surface. The change-over from the glacial lowstand is marked by the occurrence of mangrove deposits. Terrigenous and/or mixed terrigenous-carbonate muds to sandy muds with a mollusc or mollusc-ostracod assemblage dominate the transgressive deposits. Mixed carbonate-siliciclastic or carbonate sand to gravel with a mollusc-foraminifer or mollusc-coral-foraminifer assemblage characterize the early highstand deposits on the inner lagoonal plains. The early highstand deposits in the outer lagoonal plains consist of carbonate muds with a mollusc-foraminifer assemblage. Late highstand deposits consist of terrigenous muds in the nearshore bays, mixed terrigenous-carbonate sandy muds to sands with a mollusc-foraminifer assemblage on the inner lagoonal plains and mixed muds with a mollusc-foraminifer assemblage on the outer deep lagoonal plains. The present development stage of the individual lagoons comprises semi-enclosed to open lagoons with fair or good water exchange with the open ocean

The Earliest Post-Paleozoic Freshwater Bivalves Preserved in Coprolites from the Karoo Basin, South Africa

Background: Several clades of bivalve molluscs have invaded freshwaters at various times throughout Phanerozoic history. The most successful freshwater clade in the modern world is the Unionoida. Unionoids arose in the Triassic Period, sometime after the major extinction event at the End-Permian boundary and are now widely distributed across all continents except Antarctica. Until now, no freshwater bivalves of any kind were known to exist in the Early Triassic. Principal Findings: Here we report on a faunule of two small freshwater bivalve species preserved in vertebrate coprolites from the Olenekian (Lower Triassic) of the Burgersdorp Formation of the Karoo Basin, South Africa. Positive identification of these bivalves is not possible due to the limited material. Nevertheless they do show similarities with Unionoida although they fall below the size range of extant unionoids. Phylogenetic analysis is not possible with such limited material and consequently the assignment remains somewhat speculative. Conclusions: Bivalve molluscs re-invaded freshwaters soon after the End-Permian extinction event, during the earliest part of the recovery phase during the Olenekian Stage of the Early Triassic. If the specimens do represent unionoids then these Early Triassic examples may be an example of the Lilliput effect. Since the oldest incontrovertible freshwater unionoids are also from sub-Saharan Africa, it is possible that this subcontinent hosted the initial freshwater radiation of the Unionoida. This find also demonstrates the importance of coprolites as microenvironments of exceptional preservation that contai

Auditory stimulation of opera music induced prolongation of murine cardiac allograft survival and maintained generation of regulatory CD4+CD25+ cells

<p>Abstract</p> <p>Background</p> <p>Interactions between the immune response and brain functions such as olfactory, auditory, and visual sensations are likely. This study investigated the effect of sounds on alloimmune responses in a murine model of cardiac allograft transplantation.</p> <p>Methods</p> <p>Naïve CBA mice (H2^k) underwent transplantation of a C57BL/6 (B6, H2^b) heart and were exposed to one of three types of music--opera (<it>La Traviata</it>), classical (Mozart), and New Age (Enya)--or one of six different single sound frequencies, for 7 days. Additionally, we prepared two groups of CBA recipients with tympanic membrane perforation exposed to opera for 7 days and CBA recipients exposed to opera for 7 days before transplantation (pre-treatment). An adoptive transfer study was performed to determine whether regulatory cells were generated in allograft recipients. Immunohistochemical, cell-proliferation, cytokine, and flow cytometry assessments were also performed.</p> <p>Results</p> <p>CBA recipients of a B6 cardiac graft that were exposed to opera music and Mozart had significantly prolonged allograft survival (median survival times [MSTs], 26.5 and 20 days, respectively), whereas those exposed to a single sound frequency (100, 500, 1000, 5000, 10,000, or 20,000 Hz) or Enya did not (MSTs, 7.5, 8, 9, 8, 7.5, 8.5 and 11 days, respectively). Untreated, CBA mice with tympanic membrane perforations and CBA recipients exposed to opera for 7 days before transplantation (pre-treatment) rejected B6 cardiac grafts acutely (MSTs, 7, 8 and 8 days, respectively). Adoptive transfer of whole splenocytes, CD4⁺cells, or CD4⁺CD25⁺cells from opera-exposed primary allograft recipients resulted in significantly prolonged allograft survival in naive secondary recipients (MSTs, 36, 68, and > 100 days, respectively). Proliferation of splenocytes, interleukin (IL)-2 and interferon (IFN)-γ production was suppressed in opera-exposed mice, and production of IL-4 and IL-10 from opera-exposed transplant recipients increased compared to that from splenocytes of untreated recipients. Flow cytometry studies showed an increased CD4⁺CD25⁺Forkhead box P3 (Foxp3)⁺cell population in splenocytes from those mice.</p> <p>Conclusion</p> <p>Our findings indicate that exposure to opera music, such as La traviata, could affect such aspects of the peripheral immune response as generation of regulatory CD4⁺CD25⁺cells and up-regulation of anti-inflammatory cytokines, resulting in prolonged allograft survival.</p

Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

<p>Abstract</p> <p>Background</p> <p>The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and others have previously shown that binding sites of these two transcription factors show a high degree of overlap and are associated with the majority of genes upregulated during differentiation of murine 3T3-L1 adipocytes.</p> <p>Results</p> <p>Here we have mapped all binding sites of C/EBPα and PPARγ in human SGBS adipocytes and compared these with the genome-wide profiles from mouse adipocytes to systematically investigate what biological features correlate with retention of sites in orthologous regions between mouse and human. Despite a limited interspecies retention of binding sites, several biological features make sites more likely to be retained. First, co-binding of PPARγ and C/EBPα in mouse is the most powerful predictor of retention of the corresponding binding sites in human. Second, vicinity to genes highly upregulated during adipogenesis significantly increases retention. Third, the presence of C/EBPα consensus sites correlate with retention of both factors, indicating that C/EBPα facilitates recruitment of PPARγ. Fourth, retention correlates with overall sequence conservation within the binding regions independent of C/EBPα and PPARγ sequence patterns, indicating that other transcription factors work cooperatively with these two key transcription factors.</p> <p>Conclusions</p> <p>This study provides a comprehensive and systematic analysis of what biological features impact on retention of binding sites between human and mouse. Specifically, we show that the binding of C/EBPα and PPARγ in adipocytes have evolved in a highly interdependent manner, indicating a significant cooperativity between these two transcription factors.</p

Early Stage Biomineralization in the Periostracum of the ‘Living Fossil’ Bivalve Neotrigonia

A detailed investigation of the shell formation of the palaeoheterodont ‘living fossil’ Neotrigonia concentrated on the timing and manufacture of the calcified ‘bosses’ which stud the outside of all trigonioid bivalves (extant and fossil) has been conducted. Electron microscopy and optical microscopy revealed that Neotrigonia spp. have a spiral-shaped periostracal groove. The periostracum itself is secreted by the basal cell, as a thin dark pellicle, becoming progressively transformed into a thin dark layer by additions of secretions from the internal outer mantle fold. Later, intense secretion of the internal surface of the outer mantle fold forms a translucent layer, which becomes transformed by tanning into a dark layer. The initiation of calcified bosses occurred at a very early stage of periostracum formation, deep within the periostracal groove immediately below the initialmost dark layer. At this stage, they consist of a series of polycyclically twinned crystals. The bosses grow as the periostracum traverse through the periostracal groove, in coordination with the thickening of the dark periostracal layer and until, upon reaching the mantle edge, they impinge upon each other and become transformed into large prisms separated by dark periostracal walls. In conclusion, the initial bosses and the external part of the prismatic layer are fully intraperiostracal. With later growth, the prisms transform into fibrous aggregates, although the details of the process are unknown. This reinforces the relationships with other groups that have the ability to form intraperiostracal calcifications, for example the unionoids with which the trigonioids form the clade Paleoheterodonta. The presence of similar structures in anomalodesmatans and other euheterodonts raises the question of whether this indicates a relationship or represents a convergence. The identification of very early calcification within an organic sheet has interesting implications for our understanding of how shells may have evolved.Coordinated Research Projects CGL2010-20748-C02-01 (AGC, EMH) and 02 (CS) (DGI, Spanish MICINN); the Research Group RNM363 (Consejería de Economía, Investigación, Ciencia y Empleo, Junta de Andalucía); and the FP7 COST Action TD0903 of the European Community

Chess databases as a research vehicle in psychology : modeling large data

The game of chess has often been used for psychological investigations, particularly in cognitive science. The clear-cut rules and well-defined environment of chess provide a model for investigations of basic cognitive processes, such as perception, memory, and problem solving, while the precise rating system for the measurement of skill has enabled investigations of individual differences and expertise-related effects. In the present study, we focus on another appealing feature of chess—namely, the large archive databases associated with the game. The German national chess database presented in this study represents a fruitful ground for the investigation of multiple longitudinal research questions, since it collects the data of over 130,000 players and spans over 25 years. The German chess database collects the data of all players, including hobby players, and all tournaments played. This results in a rich and complete collection of the skill, age, and activity of the whole population of chess players in Germany. The database therefore complements the commonly used expertise approach in cognitive science by opening up new possibilities for the investigation of multiple factors that underlie expertise and skill acquisition. Since large datasets are not common in psychology, their introduction also raises the question of optimal and efficient statistical analysis. We offer the database for download and illustrate how it can be used by providing concrete examples and a step-by-step tutorial using different statistical analyses on a range of topics, including skill development over the lifetime, birth cohort effects, effects of activity and inactivity on skill, and gender differences

Genetic Structure, Nestmate Recognition and Behaviour of Two Cryptic Species of the Invasive Big-Headed Ant Pheidole megacephala

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The multi-peak adaptive landscape of crocodylomorph body size evolution

Background: Little is known about the long-term patterns of body size evolution in Crocodylomorpha, the > 200-million-year-old group that includes living crocodylians and their extinct relatives. Extant crocodylians are mostly large-bodied (3–7 m) predators. However, extinct crocodylomorphs exhibit a wider range of phenotypes, and many of the earliest taxa were much smaller ( Results: Crocodylomorphs reached an early peak in body size disparity during the Late Jurassic, and underwent an essentially continual decline since then. A multi-peak Ornstein-Uhlenbeck model outperforms all other evolutionary models fitted to our data (including both uniform and non-uniform), indicating that the macroevolutionary dynamics of crocodylomorph body size are better described within the concept of an adaptive landscape, with most body size variation emerging after shifts to new macroevolutionary regimes (analogous to adaptive zones). We did not find support for a consistent evolutionary trend towards larger sizes among lineages (i.e., Cope’s rule), or strong correlations of body size with climate. Instead, the intermediate to large body sizes of some crocodylomorphs are better explained by group-specific adaptations. In particular, the evolution of a more aquatic lifestyle (especially marine) correlates with increases in average body size, though not without exceptions. Conclusions: Shifts between macroevolutionary regimes provide a better explanation of crocodylomorph body size evolution on large phylogenetic and temporal scales, suggesting a central role for lineage-specific adaptations rather than climatic forcing. Shifts leading to larger body sizes occurred in most aquatic and semi-aquatic groups. This, combined with extinctions of groups occupying smaller body size regimes (particularly during the Late Cretaceous and Cenozoic), gave rise to the upward-shifted body size distribution of extant crocodylomorphs compared to their smaller-bodied terrestrial ancestors.</p