Fossil liberation: a model to explain high biodiversity in the Triassic Cassian Formation

With 1429 animal species, the Triassic Cassian Formation in the Dolomites, Southern Alps (Italy), yields the highest species richness reported from any spatially constrained pre-Quaternary formation known to science. The high preserved diversity is partly attributable to a high primary diversity governed by the tropical setting, increasing alpha diversity, and the breadth of habitats spurring beta diversity. More important is the excellent preservation of fossils and the ease with which they can be extracted from the poorly lithified sediments. We propose the term ‘liberation Lagerstätten’ to capture this preservational window. In contrast to conservation Lagerstätten, liberation Lagerstätten like the Cassian Formation originate from normal marine conditions but low-grade diagenesis. Molluscs contribute substantially to species richness, comprising 67% of all invertebrate species in the Cassian Formation. The gastropod dominance (39% of all species) is nearly as great as in Recent tropical settings, contradicting the concept of a substantial Cenozoic rise.     

Scaling of species diversity and body mass in mammals: Cope’s rule and the evolutionary cost of large size

Abstract

Equations are constructed describing the inverse correlation of species diversity and body mass in extant and Cenozoic mammals. Cope’s rule, the tendency for many mammal clades to increase in body size through time, through phyletic change in single lineages or turnover within species groups, is interpreted as a probability function reducing diversity potential as a tradeoff for ecological/evolutionary gains. The inverse rule predicts that large species in clades will be less diverse than smaller species and, unless origination rates remain high among smaller clade members, clades conforming to Cope’s rule will decline in diversity, moving towards extinction. This proposition is evaluated in the Cenozoic histories of five North American mammal clades; cotton rats, felids, canids, hyaenodontids, and equids. Diversity potential of different size classes within the 3.75 million year phyletic history of the muskrat, Ondatra zibethicus, is also examined. A corollary prediction of the inverse rule, that large species should have longer durations (species lifespans) than small species, is unresolved. Successful clades maintain small size or a significant number of smaller species relative to clade average size. The potential loss of unique extant large mammal species justifies the conservation effort to protect them. The similarity of scaling exponents of species diversity to mass around a slope of -1.0 suggests that species diversity is correlated with home range size, the latter related to the probability of population fragmentation.     

The fossil record of ichthyosaurs,completeness metrics and sampling biases

Ichthyosaurs were highly successful marine reptiles with an abundant and well‐studied fossil record. However, their occurrences through geological time and space are sporadic, and it is important to understand whether times of apparent species richness and rarity are real or the result of sampling bias. Here, we explore the skeletal completeness of 351 dated and identified ichthyosaur specimens, belonging to all 102 species, the first time that such a study has been carried out on vertebrates from the marine realm. No correlations were found between time series of different skeletal metrics and ichthyosaur diversity. There is a significant geographical variation in completeness, with the well‐studied northern hemisphere producing fossils of much higher quality than the southern hemisphere. Medium‐sized ichthyosaurs are significantly more complete than small or large taxa: the incompleteness of small specimens was expected, but it was a surprise that larger specimens were also relatively incomplete. Completeness varies greatly between facies, with fine‐grained, siliciclastic sediments preserving the most complete specimens. These findings may explain why the ichthyosaur diversity record is low at times, corresponding to facies of poor preservation potential, such as in the Early Cretaceous. Unexpectedly, we find a strong negative correlation between skeletal completeness and sea level, meaning the most complete specimens occurred at times of global low sea level, and vice versa. Completeness metrics, however, do not replicate the sampling signal and have limited use as a global‐scale sampling proxy.     

Dinosaur nest ecology and predation during the Late Cretaceous: was there a relationship between upper Cretaceous extinction and nesting behavior?

Many hypotheses have been advanced to explain the K/Pg extinctions, yet none closely examines the likely interactions between dinosaurs and contemporary taxa within their communities. The diversity of predators of dinosaur nests and hatchlings increased toward the end of the Cretaceous. In addition to large snakes having been found fossilized in the act of foraging in dinosaur nests, mammals and birds had also evolved new forms potentially capable of exploiting this resource. The constraints on mammal size and niche diversity lessened prior to the K/Pg boundary. Using comparisons of predator/prey size ratios between extant species and known fossils, we demonstrate that mammalian and avian clades had members large enough to prey on dinosaur eggs and hatchlings. We argue that the reproductive strategy of obligatory nest defense was likely practiced by most non-avian dinosaur species. This strategy was highly susceptible to the increasing numbers of mammalian, avian, and reptilian predators, which rendered this strategy obsolete. Continued selection against large oviparous species in the Cenozoic has limited this life-history strategy to habitats that provide concealment – primarily grasslands, a habitat that did not exist until the Miocene. We urge the evaluation of multiple, perhaps synergistic, hypotheses when considering extinction events of this magnitude.     

古生物多样性统计中的偏差及其校正

地质历史时期生物多样性统计中的偏差是普遍存在的。文中以奥陶纪海洋生物和二叠纪腕足动物分异度为例介绍和讨论古生物多样性统计中的偏差问题。认为在研究某些时段分异度时不能依靠单一的种、属或科的数量来建立分异度模式,而需要用生物分异度、灭绝率和新生率等多种计算方法来综合分析。同时古生物分异度的研究受到化石记录的完整性、研究、保存和采集程度、时间段的不均一性等多种因素影响,因此,大多需要应用稀疏标准化法等对不同时段或化石群在同等量化标准的基础上进行比较和校正后,才能得到比较符合实际的分异度模式。     

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 m(2)). 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.     

The complex effects of mass extinctions on morphological disparity

Studies of biodiversity through deep time have been a staple for biologists and paleontologists for over 60 years. Investigations of species richness (diversity) revealed that at least five mass extinctions punctuated the last half billion years, each seeing the rapid demise of a large proportion of contemporary taxa. In contrast to diversity, the response of morphological diversity (disparity) to mass extinctions is unclear. Generally, diversity and disparity are decoupled, such that diversity may decline as morphological disparity increases, and vice versa. Here, we develop simulations to model disparity changes across mass extinctions using continuous traits and birth-death trees. We find no simple null for disparity change following a mass extinction but do observe general patterns. The range of trait values decreases following either random or trait-selective mass extinctions, whereas variance and the density of morphospace occupation only decline following trait-selective events. General trends may differentiate random and trait-selective mass extinctions, but methods struggle to identify trait selectivity. Long-term effects of mass extinction trait selectivity change support for phylogenetic comparative methods away from the simulated Brownian motion toward Ornstein-Uhlenbeck and Early Burst models. We find that morphological change over mass extinction is best studied by quantifying multiple aspects of morphospace occupation.     

A re-examination of the expected effects of disturbance on diversity

Disturbance is often cited as one of the main factors determining patterns of species diversity. Several models have predicted qualitatively that species richness should be highest at intermediate intensities and/or frequencies of disturbances, but none indicate whether this effect should be strong (statistically accounting for much variability in diversity) or only subtle. Empirical evidence on the point is very mixed. This study examines Markov models of the dynamics of six real communities. We derive the predicted changes in species richness and evenness when these communities are subjected to quantified disturbance frequency and intensity gradients. We also use several different sampling intensities (i.e. numbers of individuals counted) to determine how this affects richness-disturbance relationships. Our models predict that peaked responses of diversity to disturbance should be less common than monotonic ones. Species richness should vary, on average, by only 3% over gradients of no disturbance to complete disturbance. In the most extreme case, richness varied two-fold over this gradient. Moreover, richness may increase monotonically, decrease monotonically, or be a peaked function of disturbance, interacting in a non-intuitive fashion with both the sampling intensity and the community in question. These results are broadly consistent with a review of published richness-disturbance relationships. Evenness varies somewhat more strongly along disturbance gradients, but the effect is still small. We conclude that extant models provide little reason to believe that disturbance should play more than a subtle role in determining patterns of diversity in nature, contrary to most contemporary literature.     

New beetles (Insecta,Coleoptera) from the Lower Triassic of European Russia

Fossil remains of beetles are described from two Lower Triassic localities: Entala (Induan) and Tikhvinskoe (Olenekian). Only one beetle fossil was previously known from the Lower Triassic of Tikhvinskoe. The fossils are rather few and poorly preserved, but they are worth describing as finds rare for the Lower Triassic. Five fossils from Entala most probably belong to beetles of the same species of the formal genus Pseudochrysomelites. Beetles of this genus are especially abundant in deposits close to the Permian–Triassic boundary and can be considered “disaster taxa.” There are no known cases, either in the Permian or in the Middle–Upper Triassic, of a random sample of five specimens belonging to a single species. This suggests that in the Entala oryctocenosis the species diversity of beetles is extremely low. All three beetle fossils found in Tikhvinskoe belong to beetles of different species, showing that diversity had already started to increase. However, it remained low, and all fossils belong to the formal family Schizocoleidae, and two of the three belong to the same genus, Pseudochrysomelites. The Khei-Yaga locality, which immediately follows Tikhvinskoe in time (topmost Olenekian or early Anisian), already contains beetles of the families Asiocoleidae and Permosynidae. In the Lower Anisian of the Buntsandstein, such typical Mesozoic beetles as Cupedidae and Coptoclavidae have been recorded. The appearance of such advanced beetles as early as the Lower Anisian suggests that the famous Permian–Triassic crisis was not as deep as it is usually believed, and many beetles survived it, disappearing, however, from the fossil record in the Early Triassic.     

A systematic overview of fossil osmundalean ferns in China: Diversity variation,distribution pattern,and evolutionary implications

The order Osmundales is a unique fern taxon with extensive fossil records in geological past. Diverse osmundalean fossils have been reported from China, ranging in age from the Late Palaeozoic to the Cenozoic. Most of them are based on leaf impressions/compressions, but permineralized rhizomes are also well documented. In this study, we provide a systematic overview on fossil osmundalean ferns in China with special references on diversity variations, distribution patterns, and evolutionary implications. Fossil evidence indicates that this fern lineage first appeared in the Late Palaeozoic in China. The Late Triassic to Middle Jurassic interval was the radiation stage. From the Late Jurassic onward, fossil diversity declined rapidly. Cenozoic osmundalean taxa are represented by the relict species of Osmunda. Geographically, osmundalean fossils are found from both the Northern and Southern phytoprovinces of China, though variations are documented for geographical ranges. The Chinese fossil records cover almost all important stages for the macroevolution of the Osmundales, and contribute to further understanding of evolutionary processes of this peculiar fern lineage.     

The challenge of small and rare species in marine biodiversity surveys: microgastropod diversity in a complex tropical coastal environment

Although molluscs feature prominently in the semi-popular and academic literature on marine biodiversity, field surveys largely ignore the small and rare species that form the majority of marine molluscan diversity. As a result of a massive effort to sample the benthic molluscs of a complex tropical coastal environment, 23,238 gastropod specimens representing 259 species of Triphoridae—a family with most adult species ranging from 2 to 10 mm—were obtained from a 45,000 hectares study area off the island of Espiritu Santo, Vanuatu. Most species are represented by fewer than 20 specimens and, despite the intensity of the sampling effort, 13% of the species are unique singletons. Spatial heterogeneity was high: out of 416 sampling events, 187 contained triphorids, and 42% of the species occurred at fewer than 5 stations. Most species were small (68% below 5 mm) or very small (22% below 3 mm). A faunal turnover was documented at around 10 m, and another at around 60 m, at the onset of the “twilight zone” that is particularly difficult to sample. On the order of 70% of the species are probably new to science. When dealing with taxonomically difficult groups a morphospecies segregation approach is operationally appropriate to detect patterns of richness, rarity and spatial turn-over. Very few, if any, conservation surveys have the human and funding resources to carry out baseline surveys of the intensity that generated the results presented here. However, as species numbers are often used to promote the conservation interest of a reef, a bay or a stretch of coast, it is essential to know how the numbers were generated: absolute numbers of species are meaningless unless sampling effort and techniques, area surveyed, and size classes targeted are described. This is very rarely the case, even in the academic literature.     

Epistemic values in the Burgess Shale debate

Focusing primarily on papers and books discussing the evolutionary and systematic interpretation of the Cambrian animal fossils from the Burgess Shale fauna, this paper explores the role of epistemic values in the context of a discipline (paleontology) striving to establish scientific authority within a larger domain of epistemic problems and issues (evolutionary biology). The focal point of this analysis is the repeated claims by paleontologists that the study of fossils gives their discipline a unique ‘historical dimension’ that makes it possible for them to unravel important aspects of evolution invisible to scientists who study the extant biosphere. The first part of the paper explores the shifting of emphasis in the writings of paleontologists between two strategies that employ opposing views on the classical positivist and physicalist ideal of science. The second part analyzes paleontologists’ claims of privileged access to life’s historical dimension in a situation where a theoretical upheaval occurring independent of the epistemical problem at hand completely shifts the standards for evaluating the legitimacy of various knowledge claims. Though the various strategies employed in defending the privileged historical perspective of paleontology have been disparate and, to an extent contradictory, each impinges on the acceptance of a specific epistemic ideal or set of values and success or failure of each depends on the compatibility of this ideal with the surrounding community of scientists.     

Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.     

Mitogenomic Evidence for an Indo-West Pacific Origin of the Clupeoidei (Teleostei: Clupeiformes)

The clupeoid fishes are distributed worldwide, with marine, freshwater and euryhaline species living in either tropical or temperate environments. Regional endemism is important at the species and genus levels, and the highest species diversity is found in the tropical marine Indo-West Pacific region. The clupeoid distribution follows two general pattern of species richness, the longitudinal and latitudinal gradients. To test historical hypotheses explaining the formation of these two gradients, we have examined the early biogeography of the Clupeoidei in reconstructing the evolution of their habitat preferences along with their ancestral range distributions on a time-calibrated mitogenomic phylogeny. The phylogenetic results support the distinction of nine main lineages within the Clupeoidei, five of them new. We infer several independent transitions from a marine to freshwater environment and from a tropical to temperate environment that occurred after the initial diversification period of the Clupeoidei. These results combined with our ancestral range reconstruction hypothesis suggest that the probable region of origin and diversification of the Clupeoidei during the Cretaceous period was the tropical marine precursor to the present Indo-West Pacific region. Thus, our study favors the hypotheses of “Region of origin” and “Tropical conservatism” to explain the origins of the longitudinal and latitudinal gradients of clupeoid species richness, respectively. Additional geological and paleontological evidence further define the tropical marine paleo-region of origin as the eastern Tethys Sea region. The Cretaceous fossil record of the Clupeoidei is partially incongruent with the results here as it contains taxa found outside this region. We discuss three possible causes of conflict between our biogeographical hypothesis and the distributions of the Cretaceous clupeoid fossils: regional extinction, incomplete taxonomic sampling and incorrect timescale estimation.     

Seaweeds, latitudinal diversity patterns, and Rapoport's Rule

We analysed the geographic distribution of 645 species of marine benthic algae along the Atlantic coast of Europe and Pacific coast of temperate South America to test for the existence of an association between geographic range size and latitude (Rapoport's Rule) and for three key components of the explanations offered for it. We found that species in high diversity areas are characterized by small geographic ranges and by low specific growth rates as compared to species with large geographic ranges, thus supporting the Rapoport-rescue hypothesis. However, the pattern is not related to species' tolerances, to abiotic conditions or to climatic variability. Further, the inverse latitudinal diversity pattern shown by the marine algal flora of temperate Pacific South America, and the opposite patterns shown by tropical and subantarctic species within this flora, stressed that small geographic ranges are linked to high diversity areas in general, and not only in relation to the pole to tropic species diversity gradient.     

INFLUENCE OF FRESHWATER FLOW REGIME ON FISH ASSEMBLAGES IN THE GREAT FISH RIVER AND ESTUARY

Summary

Two and a half years of data were collected from the lower Great Fish River, head region and estuary to determine the fish species composition within these areas. Gilchristella aestuaria, Liza dumerilii, Rhabdosargus holubi and Pomadasys commersonnii were the four most abundant species captured, with riverine flow rate having an important effect on both species composition and numbers of fishes in the different regions. Most marine species displayed a strong inverse relationship between catch per unit effort and elevated freshwater inputs. Euryhaline marine species dominated the catches at all sampling sites during low flows but were less common during high flow periods when catadromous species were most abundant. Based on the available evidence it is suggested that for most marine species in the river this decline in abundance is related to low conductivity levels following floods rather than avoidance of elevated flows. The impact of elevated suspensoid concentrations and lowered dissolved oxygen concentrations on freshwater and estuarine fish populations during major river flooding is also discussed.     

Impact of biased sampling effort and spatial uncertainty of locations on models of plant invasion patterns in Croatia

Very frequently biological databases are used for analysing distribution of different taxa. These databases are usually the result of variable sampling effort and location uncertainty. The aim of this study was to test the influence of geographically biased sampling effort and spatial uncertainty of locations on models of species richness. For this purpose, we assessed the pattern of invasive alien plants in Croatia using the Flora Croatica Database. The procedure applied in testing of the sensitivity of models consisted of sample area sectioning into coherent ecological classes (hereinafter Gower classes). The quadrants were then ranked based on sampling effort per class. This resulted in creation of models using varying numbers of quadrants whose performance was tested with independent validation points. From this the best fitting model was determined, as well as a threshold of sampling effort. The data from quadrants with sampling effort below the threshold were considered too unreliable for modelling. Further, spatial uncertainty was simulated by adding a random term to each location and re-running the models using the simulated locations. Biased sampling effort and spatial uncertainty of locations had similar effects on model performance in terms of the magnitude of the affected area, as in both cases 7% of the quadrants showed statistically significant deviations in alien plant species richness. The model using only on the quandrants with the highest 35% quantile sampling effort best balanced the sampling effort per quadrant and overall geographical coverage. It predicted a mean number of 3.2 invasive alien plant species per quadrant for the Alpine region, 5.2 for the Continental, 6.1 for the Mediterranean and 5.3 for the Pannonian region of Croatia. Thus, the observational databases can be considered as a reliable source for species richness models and, most likely, for other types of species distribution models, given that their limitations are accounted for in the data selection process. In order to obtain precise estimates of species richness it is required to sample the whole range of ecological conditions of the study area.     

Cyclicity in the fossil record mirrors rock outcrop area

In a recent article, Rohde & Muller (Rohde & Muller 2005 Nature 434, 208-210) identified a strong 62 Myr cyclicity in the history of marine diversity through the Phanerozoic. The data they presented were highly convincing, yet they were unable to explain what process might have generated this pattern. A significant correlation between observed genus-level diversity (after removal of long-term trends) and the amount of marine sedimentary rock measured at a surface outcrop in Western Europe is demonstrated. This suggests that cyclicity originates from long-term changes in sedimentary depositional and erosional regimes, and raises the strong possibility that the cyclicity apparent in the record of marine fossils is not a biological signal but a sampling signal.     

Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution

Testing models of macroevolution, and especially the sufficiency of microevolutionary processes, requires good collaboration between molecular biologists and paleontologists. We report such a test for events around the Late Cretaceous by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describe the gradual decline of pterosaurs at the same time modern birds radiate. The penguin fossils comprise four naturally associated skeletons from the New Zealand Waipara Greensand, a Paleocene (early Tertiary) formation just above a well-known Cretaceous/Tertiary boundary site. The fossils, in a new genus (Waimanu), provide a lower estimate of 61-62 Ma for the divergence between penguins and other birds and thus establish a reliable calibration point for avian evolution. Combining fossil calibration points, DNA sequences, maximum likelihood, and Bayesian analysis, the penguin calibrations imply a radiation of modern (crown group) birds in the Late Cretaceous. This includes a conservative estimate that modern sea and shorebird lineages diverged at least by the Late Cretaceous about 74 +/- 3 Ma (Campanian). It is clear that modern birds from at least the latest Cretaceous lived at the same time as archaic birds including Hesperornis, Ichthyornis, and the diverse Enantiornithiformes. Pterosaurs, which also coexisted with early crown birds, show notable changes through the Late Cretaceous. There was a decrease in taxonomic diversity, and small- to medium-sized species disappeared well before the end of the Cretaceous. A simple reading of the fossil record might suggest competitive interactions with birds, but much more needs to be understood about pterosaur life histories. Additional fossils and molecular data are still required to help understand the role of biotic interactions in the evolution of Late Cretaceous birds and thus to test that the mechanisms of microevolution are sufficient to explain macroevolution.     

Of beta diversity,variance, evenness,and dissimilarity

The amount of variation in species composition among sampling units or beta diversity has become a primary tool for connecting the spatial structure of species assemblages to ecological processes. Many different measures of beta diversity have been developed. Among them, the total variance in the community composition matrix has been proposed as a single‐number estimate of beta diversity. In this study, I first show that this measure summarizes the compositional variation among sampling units after nonlinear transformation of species abundances. Therefore, it is not always adequate for estimating beta diversity. Next, I propose an alternative approach for calculating beta diversity in which variance is substituted by a weighted measure of concentration (i.e., an inverse measure of evenness). The relationship between this new measure of beta diversity and so‐called multiple‐site dissimilarity measures is also discussed.