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The fossil record constitutes the primary source of information about the evolutionary history of extant and extinct groups, and many analyses of macroevolution rely on fossils that are accurately placed within phylogenies. To avoid misinterpretation of the fossil record, especially by non-palaeontologists, the proper assessment and communication of uncertainty in fossil placement is crucial. We here use Bayesian morphological phylogenetics to evaluate the classifications of fossil parasitoid wasps (Hymenoptera, Ichneumonidae) and introduce 'RoguePlots' to illustrate placement uncertainty on the phylogeny of extant taxa. Based on an extensive, newly constructed morphological matrix of 222 characters in 24 fossil and 103 extant taxa, we test three different aspects of models of morphological evolution. We find that a model that includes ordered characters, among-character rate variation, and a state-space restricted to observed states achieves the highest marginal likelihoods. The individual RoguePlots reveal large differences in confidence in the placement of the different fossils and allow some refinements to their classification: Polyhelictes bipolarus and Ichninsum appendicrassum are moved from an uncertain subfamily placement to Pimplinae, Plectiscidea lanhami is transferred to Allomacrus in Cylloceriinae (Allomacrus lanhami, comb. nov.), Lithotorus cressoni is moved from Diplazontinae to Orthocentrinae, and we note uncertainty in the generic placements of Rhyssella? vera and Xanthopimpla? messelensis. We discuss potential artefacts that might result in biased posterior probabilities in Bayesian morphological phylogenetic analyses, pertaining to character and taxon sampling, fossilization biases, and model misspecification. Finally, we suggest future directions both in ichneumonid palaeontology and in the way RoguePlots can improve both assessment and representation of placement uncertainty, both in fossils and other rogue taxa.

Estimates of evolutionary diversification rates – speciation and extinction – have been used extensively to explain global biodiversity patterns. Many studies have analyzed diversification rates derived from just two pieces of information: a clade’s age and its extant species richness. This “age-richness rate” (ARR) estimator provides a convenient shortcut for comparative studies, but makes strong assumptions about the dynamics of species richness through time. Here we demonstrate that use of the ARR estimator in comparative studies is problematic on both theoretical and empirical grounds. We prove mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversification is zero. Using paleontological time series, we demonstrate that the ARR estimator has no predictive ability for real datasets. These pathologies arise because the ARR inference procedure yields “point estimates” that have been computed under a saturated statistical model with zero degrees of freedom. Although ARR estimates remain useful in some contexts, they should be avoided for comparative studies of diversification and species richness. Age-richness rate (ARR) estimates of evolutionary diversification are widely used to study factors that influence species richness among clades. Here the authors show that ARR inference is based on problematic assumptions and recommend against its use in comparison of past diversity or diversification rates across clades.

Several hypotheses posit a link between the origin of Homo and climatic and environmental shifts between 3 and 2.5 Ma. Here we report on new results that shed light on the interplay between tectonics, basin migration and faunal change on the one hand and the fate of Australopithecus afarensis and the evolution of Homo on the other. Fieldwork at the new Mille-Logya site in the Afar, Ethiopia, dated to between 2.914 and 2.443 Ma, provides geological evidence for the northeast migration of the Hadar Basin, extending the record of this lacustrine basin to Mille-Logya. We have identified three new fossiliferous units, suggesting in situ faunal change within this interval. While the fauna in the older unit is comparable to that at Hadar and Dikika, the younger units contain species that indicate more open conditions along with remains of Homo . This suggests that Homo either emerged from Australopithecus during this interval or dispersed into the region as part of a fauna adapted to more open habitats. Key events in human evolution are thought to have occurred between 3 and 2.5 Ma, but the fossil record of this period is sparse. Here, Alemseged et al. report a new fossil site from this period, Mille-Logya, Ethiopia, and characterize the geology, basin evolution and fauna, including specimens of Homo .

Zoophycos is one of the most complex and enigmatic trace fossils recorded in marine strata from Cambrian to Quaternary worldwide, which is invaluable for the study of Phanerozoic development of organism–environment interactions. Here we address and demonstrate the macroevolution of Phanerozoic Zoophycos by assembling 448 points in constructing the Phanerozoic Zoophycos database based on 291 papers from 1821 to 2015 and 180 specimens from Cambrian to Palaeogene. The comprehensive dataset reveals, for the first time, five peaks and six depressions in Phanerozoic Zoophycos occurrence frequency. Secondly, the palaeogeographical distribution of Zoophycos is closely associated with the supercontinent Pangaea shifting, independent of the latitude. Our data also attest that the bathymetrical shift of Zoophycos from the littoral–neritic to bathyal environments is synchronized with the tiering shift from shallow to deep. By detailed comparison with body fossils, geochemical and palaeogeographical records, we conclude that the macroevolution of Phanerozoic Zoophycos is multi-affected by the global biodiversity expansion, benthic nutrient enhancement and the biotic macroevolution of the Zoophycos -producers. The macroevolution of development evidenced by the morphological changes of Zoophycos and other trace fossils, may have great implications on the behavioural and physiological adaptation of ancient animals to the environments.

Many aspects of the drivers for, and evolutionary dynamics of, the Cambrian Explosion are poorly understood. Here we quantify high-resolution changes in species body size in major metazoan groups on the Siberian Platform during the early Cambrian (ca. 540–510 Million years ago (Ma)). Archaeocyath sponges, hyolith lophophorates, and helcionelloid mollusc species show dynamic and synchronous trends over million-year timescales, with peaks in body size during the latest Tommotian/early Atbadanian and late Atdabanian/early Botoman, and notably small body sizes in the middle Atdabanian and after the Sinsk anoxic extinction event, starting ca. 513 Ma. These intervals of body size changes are also mirrored in individual species and correlate positively with increased rates of origination and broadly with total species diversity. Calcitic brachiopods (rhynchonelliformeans), however, show a general increase in body size following the increase in species diversity through this interval: phosphatic brachiopods (linguliformeans) show a body size decrease that negatively correlates with diversity. Both brachiopod groups show a rapid recovery at the Sinsk Event. The synchronous changes in these metrics in archaeocyath, hyoliths and helcionelloids suggest the operation of external drivers through the early Cambrian, such as episodic changes in oxygenation or productivity. But the trends shown by brachiopods suggests a differing physiological response. Together, these dynamics created both the distinct evolutionary record of metazoan groups during the Cambrian Explosion and determined the nature of its termination.

In this study we analyzed the relationships and patterns of spatial variation from morphological cranial variability of 17 population samples representing the ancient inhabitants of the central territory of Argentina (archaeologically known as “Sierras Centrales”) and other pre-Hispanic populations from different ecological and geographic regions of the Southern Cone of South America (Argentina and Uruguay), based on the analysis of 10 craniofacial measurements. Results obtained from D2 distances can be interpreted as evidence of a similar biological history for the populations that inhabited the Sierras Centrales and the population of Santiago del Estero. Matrix correlation analysis demonstrated that craniometric variation is significantly influenced by geography, suggesting that populations that lived at lower geographical distance share more biological similarity. Global spatial autocorrelation analysis suggests a clinal pattern for the biological variation, although Moran's I estimates calculated for each variable demonstrate that only nasal height and breadth show this spatial pattern of variation. Results from spatial regression techniques show a significant effect of altitude modeling nasal shape, in agreement with previous studies suggesting that nasal morphology is strongly influenced by environment variables.

Long-term transitions in the composition of Earth's marine biota during the Phanerozoic have historically been explained in two different ways. One view is that they were mediated through biotic interactions among organisms played out over geologic time. The other is that mass extinctions transcended any such interactions and governed diversity over the long term by resetting the relative diversities of higher taxa. However, a growing body of evidence suggests that macroevolutionary processes effecting biotic transitions during background times were not fundamentally different from those operating during mass extinctions. Physical perturbations at many geographic scales combined to produce the long-term trajectory of Phanerozoic diversity.

It has long been suspected that trends in global marine biodiversity calibrated for the Phanerozoic may be affected by sampling problems. However, this possibility has not been evaluated definitively, and raw diversity trends are generally accepted at face value in macroevolutionary investigations. Here, we analyze a global-scale sample of fossil occurrences that allows us to determine directly the effects of sample size on the calibration of what is generally thought to be among the most significant global biodiversity increases in the history of life: the Ordovician Radiation. Utilizing a composite database that includes trilobites, brachiopods, and three classes of molluscs, we conduct rarefaction analyses to demonstrate that the diversification trajectory for the Radiation was considerably different than suggested by raw diversity time-series. Our analyses suggest that a substantial portion of the increase recognized in raw diversity depictions for the last three Ordovician epochs (the Llandeilian, Caradocian, and Ashgillian) is a consequence of increased sample size of the preserved and catalogued fossil record. We also use biometric data for a global sample of Ordovician trilobites, along with methods of measuring morphological diversity that are not biased by sample size, to show that morphological diversification in this major clade had leveled off by the Llanvirnian. The discordance between raw diversity depictions and more robust taxonomic and morphological diversity metrics suggests that sampling effects may strongly influence our perception of biodiversity trends throughout the Phanerozoic.

Encrusting bryozoans provide one of the few systems in the fossil record in which ecological competition can be observed directly at local scales. The macroevolutionary history of diversity of cyclostome and cheilostome bryozoans is consistent with a coupled-logistic model of clade displacement predicated on species within clades interacting competitively. The model matches observed diversity history if the model is perturbed by a mass extinction with a position and magnitude analogous to the Cretaceous/Tertiary boundary event. Although it is difficult to measure all parameters in the model from fossil data, critical factors are intrinsic rates of extinction, which can be measured. Cyclostomes maintained a rather low rate of extinction, and the model solutions predict that they would lose diversity only slowly as competitively superior species of cheilostomes diversified into their environment. Thus, the microecological record of preserved competitive interactions between cyclostome and cheilostome bryozoans and the macroevolutionary record of global diversity are consistent in regard to competition as a significant influence on diversity histories of post-Paleozoic bryozoans.

Eight major episodes of biological extinction of marine families over the past 250 million years stand significantly above local background (P < 0.05). These events are more pronounced when analyzed at the level of genus, and generic data exhibit additional apparent extinction events in the Aptian (Cretaceous) and Pliocene (Tertiary) Stages. Time-series analysis of these records strongly suggests a 26-million-year periodicity. This conclusion is robust even when adjusted for simultaneous testing of many trial periods. When the time series is limited to the four best-dated events (Cenomanian, Maestrichtian, upper Eocene, and middle Miocene), the hypothesis of randomness is also rejected for the 26-million-year period (P < 0.0002).