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PRESENCE OF A LARGE DASYPODIDAE GRAY, 1821 FROM THE CUVIERI CAVE, EASTERN BRAZIL

Cingulata represent a group of Xenarthra characterized by the presence of a carapace composed of bony plates (osteoderms). The Cuvieri Cave, located in the Lagoa Santa karst complex, presents a relevant quantity of vertebrate fossils, including extinct and extant species. Although several paleontological studies have been carried out, the material was reviewed from a taxonomic point of view, including Xenarthra material. Two osteoderms, initially attributed to the genus Euphractus, were found in Pleistocene deposits, but it was observed that the specimens did not belong to this genus. The aim of this study is to present the revision of these two specimens, now recognized as the first evidence of a large member of the family Dasypodidae in the Cuvieri Cave. The specimens were found in levels where both extant and extinct species from the Lagoa Santa region were found, but due to the paleoenvironmental changes of the Pleistocene-Holocene transition in Lagoa, it was not possible to determine the environment in which the specimen lived.

paleontology↗

THE FUNCTION AND EVOLUTION OF STEGOSAUR OSTEODERMS AND HYPOTHESIZED SEXUAL DIMORPHISM IN HESPEROSAURUS

Stegosaurus is one of the most iconic organisms in Earths history due to its impressive dermal osteoderms. These consisted of throat ossicles, two pairs of posterior tail spikes, and an estimated 18 large plates arranged in two staggered rows along the neck, back, and tail. The function and evolution of these structures in stegosaurs is a quintessential question in dinosaur paleontology. Although sociosexual display has become a popular explanation of plate function, sexual dimorphism in dinosaurs has been a contentious topic. Spikes are meanwhile often described as defensive structures, but we consider an additional intra-sex combat function worthy of further study. To investigate the questions surrounding stegosaur osteoderms, we reevaluate variation in North American stegosaur osteoderms, with attention to hypothesized sexual dimorphism in Hesperosaurus, a close relative of Stegosaurus with similar osteoderms. We correct errors in previous analyses, address challenges of the dimorphism hypothesis, and use outline analysis and effect size statistics to provide further statistical support that one sex possibly had larger, wide/broad plates (hypothesized male), while the other sex had smaller, tall/narrow plates (hypothesized female). Stegosaur plates are a difficult case study for sexual variation because the multiple plates borne by a single individual can result in datasets that violate assumptions of independence. Despite appreciable variation from head to tail along an individual, the variation in size and shape seen in Hesperosaurus plates is still consistent with the presence of sexual variation as evidenced by both size-independent, two-dimensional outline analysis as well as size-versus-shape regression analysis of principal component data, with high confidence in the latter. We note pathologies on stegosaur caudal vertebrae, particularly in old adults of wide-morph Hesperosaurus, as well as in Stegosaurus tail spikes. These pathologies are consistent with not just predator-prey interactions but also intraspecific combat. There currently is no unambiguous indication of dimorphism in stegosaur thagomizers because alternative hypotheses, such as ontogenetic or interspecific variation, are not yet fully tested. Finally, we present a hypothetical model of stegosaur osteoderm evolution and function based on fossil and extant evidence. Osteoderms adapted for defense in earlier thyreophorans likely became exapted for sexual display (i.e., plates) and intra-sex combat (e.g., tail spikes in stegosaurs, clubs in ankylosaurs). Therefore, sexual selection may have initiated the differentiation of plates from the terminal thagomizer and induced the unique asymmetry of staggered plates in Stegosaurus and Hesperosaurus. Osteoderm development in hypothesized males could have been driven to physiological upper limits by sexual selection, while the intensity of predation pressure dictated osteoderm development in hypothesized females. Increasing predation pressure might correlate with large body size, open habitats, spine-like plate processes, long tail spikes, and gular ossicles. Within this hypothetical evolutionary model, Hesperosaurus would represent a stegosaur taxon with a high magnitude of sexual dimorphism, consistent with its smaller body size, rounder plates, presumed lack of gular ossicles, and niche occupation within a wet, forested, vegetation-rich habitat in the northern Morrison foreland basin. The question of stegosaur plate function requires us to look more broadly at thyreophoran osteoderm variation and evolution and to consider complex, multifactor models that incorporate many previously proposed hypotheses. We must sort between primary versus secondary functions of plates, spikes, and ossicles and how these functions changed over time.

paleontology↗

Occurrence of Gray, 1838, (Chiroptera: Phyllostomidae) in Quaternary deposits of Lagoa Santa, Brazil

Fossils of bats (Order Chiroptera) are considered rare due to the fragility of their bone structure, and are commonly represented only by fragments. In Brazil, most records correspond to extant species, with Desmodus draculae standing out as the only extinct species identified. The Lagoa Santa karst system is widely recognized for its paleontological and archaeological sites. Although many of its caves contain bat remains, detailed studies focusing on this group remain scarce. This study reports the first record of the species Anoura geoffroyi in Quaternary deposits. The skull was found in Cuvieri Cave, in a superficial layer associated with vertebrate remains currently present in the local fauna. Although the exact age of the specimen is uncertain, the presence of carbonate incrustations suggests that the skull remained exposed in the cave for an extended period before its final burial. Despite the impossibility of precisely defining the corresponding paleoenvironment, the current wide distribution of Anoura geoffroyi in the Cerrado Biome (Brazilian Savanna) suggests that the specimen may have lived in the region at a time when this biome was already predominant.

paleontology↗

Unique fingerprint of marine ectotherm body size change during hyperthermal crises

The term Lilliput Effect describes a substantial decrease in the average body size of fossil assemblages during major environmental perturbations in Earths history, which is reported in many paleontological studies. The limited regional, temporal and taxonomic focus of most studies, however, has sparked discussions concerning its generality. Additionally, even though a negative relationship between warming and body size has been established in recent marine ectotherms, the environmental and mechanistic drivers of the Lilliput effect are still debated. We compiled close to 9000 body size changes from fossil, historical and modern body size studies, to show that a decrease in body size is indeed a general response of marine ectotherms to environmental crises. The magnitude and temporal variability of size changes at the species-level are significantly higher during hyperthermal than non-hyperthermal events, suggesting differing mechanisms of body size decrease depending on the environmental stressor. Our results further show that ancient environmental perturbations with a higher magnitude of warming were associated with a greater dwarfing. This implies that warming was a major driver of body size decreases during hyperthermal events throughout the Phanerozoic, and future warming will impact current trajectories of body size reduction in modern marine ectotherms. Significance StatementDwarfing is a common response of marine ectotherms to both anthropogenic warming and similar environmental crises throughout Earths history. However, the underlying mechanisms and parallels between fossil and modern observations are still debated. We show, using newly compiled data from fossil, historical and modern studies, that warming events elicit especially strong species body size changes, suggesting similar mechanisms linking modern and fossil body size reductions to warming stress. A correlation between the magnitude of warming during ancient crises and the observed dwarfing indicates that trajectories of body size reduction can be projected into the future depending on climate-change scenarios.

paleontology↗

The skull of Tonatia bidens Spix, 1823, found in ancient deposits of Abismo Ponta de Flecha Cave, Ribeira Valley, Southeastern Brazil

The Ribeira Valley, located in the southern part of Sao Paulo State, contains an extensive cave system where vertebrate fossils from the Late Pleistocene and Holocene have been found. The Abismo Ponta de Flecha Cave, a vertical cave rich in osteological material, is subdivided into lateral galleries known as Jazidas. Previous paleontological studies have described several extinct and extant species, but chiropterans were only briefly mentioned in the initial study of this cave, with only a single fragmented skull reported. This study presents that skull and briefly discusses the locality where it was found. The specimen belonged to an adult individual of Tonatia bidens, discovered in Jazida 6, an intermediate level located some distance from the cave entrance. Bat osteological remains are fragile and easily destroyed in high-energy environments; therefore, the preservation observed in this Jazida may indicate that the specimen died in situ, without being transported. Although this area experienced intense sediment remobilization in the past, Jazida 6 shows evidence of stability and minimal reworking activity, as indicated by the preservation of fragile specimens, sometimes still in their anatomical position at death.

paleontology↗

What do ossification sequences tell us about the origin of extant amphibians?

ABSTRACTThe controversial origin of extant amphibians has been studied using several sources of data and methods, including phylogenetic analyses of morphological data, molecular dating, stratigraphic data, and integration of ossification sequence data, but a consensus has failed to emerge. We have compiled five datasets to assess the relative support for six competing hypotheses about the origin of extant amphibians: a monophyletic origin among temnospondyls, a monophyletic origin among lepospondyls, a diphyletic origin among both temnospondyls and lepospondyls, a diphyletic origin among temnospondyls alone, and two variants of a triphyletic origin, in which anurans and urodeles come from different temnospondyl taxa while caecilians come from lepospondyls and are either closer to anurans and urodeles or to amniotes. Our datasets comprise ossification sequences of up to 107 terminal taxa and up to eight cranial bones, and up to 65 terminal taxa and up to seven appendicular bones, respectively. Among extinct taxa, only two or three temnospondyl can be analyzed simultaneously for cranial data, but this is not an insuperable problem because each of the six tested hypotheses implies a different position of temnospondyls and caecilians relative to other sampled taxa. For appendicular data, more extinct taxa can be analyzed, including some lepospondyls and the finned tetrapodomorph Eusthenopteron, in addition to temnospondyls. The data are analyzed through maximum likelihood, and the AICc (corrected Akaike Information Criterion) weights of the six hypotheses allow us to assess their relative support. By an unexpectedly large margin, our analyses of the cranial data support a monophyletic origin among lepospondyls; a monophyletic origin among temnospondyls, the current near-consensus, is a distant second. All other hypotheses are exceedingly unlikely according to our data. Surprisingly, analysis of the appendicular data supports triphyly of extant amphibians within a clade that unites lepospondyls and temnospondyls, contrary to all molecular and recent paleontological phylogenies, but this conclusion is not very robust.View Full Text

paleontology↗

Inferring lifestyle for Aves and Theropoda: a model based on curvatures of extant avian ungual bones

Claws are involved in a number of behaviours including locomotion and prey capture, and as a result animals evolve claw morphologies that enable these functions. Past authors have found geometry of the keratinous sheath of the claw to correlate with mode of life for extant birds and squamates; this relationship has frequently been cited to infer lifestyles for Mesozoic theropods including Archaeopteryx. However, claw sheaths rarely fossilise and are prone to deformation; past inferences are thus compromised. As the ungual phalanx within the claw is relatively resistant to deformation and more commonly preserved in the fossil record, geometry of this bone would provide a more useful metric for paleontological analysis. In this study, ungual bones of 108 birds and 5 squamates were imaged using X-ray techniques and a relationship was found between curvatures of the ungual bone within the claw of pedal digit III and four modes of life; ground-dwelling, perching, predatory, and scansorial; using linear discriminant analysis with Kappa equal to 0.69. Our model predicts arboreal lifestyles for certain key taxa Archaeopteryx and Microraptor and a predatory ecology for Confuciusornis. These findings demonstrate the utility of our model in answering questions of palaeoecology, the theropod-bird transition, and the evolution of avian flight.View Full Text

paleontology↗

Automated Microfossil Identification and Segmentation Using a Deep Learning Approach

The applicability of computational analysis to paleontological images ranges from the study of the animals, plants and evolution of microorganisms to the simulation of the habitat of living beings of a given epoch. It also can be applied in several niches, such as oil exploration, where there are several factors to be analyzed in order to minimize the expenses related to the oil extraction process. One factor is the characterization of the environment to be explored. This analysis can occur in several ways: use of probes, extraction of samples for petrophysical components evaluation, the correlation with logs of other drilling wells and so on. In the samples extraction part the Computed Tomography (CT) is of importance because it preserves the sample and makes it available for several analyzes. Based on 3D images generated by CT, several analyzes and simulations can be performed and processes, currently performed manually and exhaustively, can be automated. In this work we propose and validate a method for fully automated microfossil identification and extraction. A pipeline is proposed that begins in the scanning process and ends in an identification process. For the identification a Deep Learning approach was developed, which resulted in a high rate of correct microfossil identification (98% of Intersection Over Union). The validation was performed both through an automated quantitative analysis based upon ground truths generated by specialists in the micropaleontology field and visual inspection by these specialists. We also present the first fully annotated MicroCT-acquired publicly available microfossils dataset.View Full Text

paleontology↗

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 1: Osteometry

AO_SCPLOWBSTRACTC_SCPLOWTaxonomic identification of animal bone remains from archaeological and paleontological contexts is usually conducted by comparison with modern skeletal specimens, an approach that is relatively straightforward in temperate or insular regions. In contrast, it is more challenging in continental tropical areas, where rich biodiversity makes it difficult to assemble exhaustive modern references. This situation is well illustrated in continental Southeast Asia, where studies of large mammal assemblages have largely focused on teeth and cranial elements, while postcranial remains are rarely investigated. To address this issue, we established an osteometric reference dataset of the limb bones from Southeast Asian ruminant species and analyzed both the potential of raw measurements and osteometric ratios to identify the different taxa. The results reveal significant differences between genera and species, allowing size-based grouping and precise taxonomic identification in some cases. These data were subsequently used to develop an easy-to-use identification tool based solely on measurements. The performance of this tool was tested against previously published datasets, allowing confirmation of existing results, and discussion of potential biases associated with identification based on measurements alone. This new methodological framework provides a solid foundation to be combined with qualitative morphological criteria to enhance the precision and robustness of the taxonomic identifications of subfossil bones from continental southeast Asia.

paleontology↗

Phylogenetic inference from an incomplete fossil record

Fossil data is crucial to construct phylogenetic time trees, which serve as the basis to test a wide range of evolutionary hypotheses. While the fossil record is known to be incomplete, modern stratigraphy provides predictions of the structure of the fossil record as expressed by gap location and duration. Advances in phylogenetic model development allow us to propagate this information into Bayesian phylogenetic inference in the form of priors on time-variable fossil sampling. However, the impact and role of stratigraphic architectures on time tree inference has so far remained unexplored. We introduce a novel simulation framework that combines realistic stratigraphic forward models with phylogenetic simulations. Using this framework, we examine (1) how stratigraphically plausible model violations of fossil sampling due to gaps affect total-evidence inference under the fossilized birth-death model and (2) if stratigraphic knowledge on gap duration and timing improves inference when incorporated in priors on fossil sampling. We find that total-evidence analysis is robust to stratigraphically plausible distribution of gaps in disparate stratigraphic architectures, with results being instead dominated by the number of morphological characters. Surprisingly, incorporating information on prominent gaps in the stratigraphic record does not improve phylogenetic inference. Our results suggest that phylogenetic inference is robust to model violations introduced by stratigraphic gaps over short timescales, with results being dominated by a priori known data availability constraints such as morphological character matrix size. This research establishes the foundations for joint modeling of phylogenetic and stratigraphic processes and narrows the knowledge gap between paleontology, stratigraphy, and neontology.

paleontology↗

An exact version of Hunt's ancestor-descendant directional random walk parameterization

Hunt's ancestor-descendant parameterization for fitting of evolutionary models to empirical paleontological sequences assumes independent log-likelihoods for the transitions between populations (Hunt, 2006). This is not quite correct, as he also pointed out in his paper. The reason is that adjacent trait differences share a trait mean value and its sampling error, and ignorance of this fact may give large errors in the estimated step size. Here, the problem is solved by use of the N-1 dimensional normal density for a random vector, where N is the number of samples. This results in a tridiagonal covariance matrix instead of Hunt s diagonal matrix, and the estimated step sizes, and thus prediction slopes, in cases where the estimated step variance is zero will then be identical to those found by weighted least squares estimation.

paleontology↗

NOTE ON RHEIFORMES (AVES: PALAEOGNATHAE) FROM A QUATERNARY CAVE IN THE LAGOA SANTA KARST, EASTERN BRAZIL

Rheiformes are a South American lineage of large, flightless palaeognathous birds, currently represented by the genus Rhea and the two extant species R. americana and R. pennata. The fossil record of the group extends back to the Eocene, with its greatest diversification occurring during the Neogene. During the Quaternary, Rheiformes were widely distributed across southern and central South America. The Lagoa Santa region is particularly notable for its rich paleontological and archaeological record. Quaternary records of Rheiformes from caves in this region provide important evidence for understanding the distribution of the group in Brazil, although their chronological context remains uncertain owing to the absence of direct dating. Here, we describe and illustrate two rheiform bones recovered from a cave in the Lagoa Santa karst region. The material comprises a partially complete tibiotarsus and a fragmented tarsometatarsus, interpreted as belonging to a single individual. Comparative anatomical and morphometric analyses support their attribution to Rhea americana, based on morphological features and dimensions consistent with adult specimens of the species. This occurrence extends the Quaternary record of Rheiformes in the Lagoa Santa region and contributes to the fossil and subfossil record of Rhea in Brazil. The absence of stratigraphic and geochronological control precludes a precise age determination. Although the association with an extinct dasypodid indicates the presence of Late Pleistocene or Early Holocene faunal elements at the locality, a Holocene or even recent age for the rheiform remains cannot be excluded.

paleontology↗

A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data

Our understanding of macroevolutionary patterns of adaptive evolution has greatly increased with the advent of large-scale phylogenetic comparative methods. Widely used Ornstein-Uhlenbeck (OU) models can describe an adaptive process of divergence and selection. However, inference of the dynamics of adaptive landscapes from comparative data is complicated by interpretational difficulties, lack of identifiability among parameter values and the common requirement that adaptive hypotheses must be assigned a priori. Here we develop a reversible-jump Bayesian method of fitting multi-optima OU models to phylogenetic comparative data that estimates the placement and magnitude of adaptive shifts directly from the data. We show how biologically informed hypotheses can be tested against this inferred posterior of shift locations using Bayes Factors to establish whether our a priori models adequately describe the dynamics of adaptive peak shifts. Furthermore, we show how the inclusion of informative priors can be used to restrict models to biologically realistic parameter space and test particular biological interpretations of evolutionary models. We argue that Bayesian model-fitting of OU models to comparative data provides a framework for integrating of multiple sources of biological data--such as microevolutionary estimates of selection parameters and paleontological timeseries--allowing inference of adaptive landscape dynamics with explicit, process-based biological interpretations.

Evolutionary Biology↗

Burrow architectural types of the Atlantic ghost crab, Ocypode quadrata (Fabricius, 1787) (Brachyura: Ocypodidae), in Brazil

A broad range of aspects from paleontology to physiology of the ghost crabs Ocypode quadrata have been studied worldwide. These crabs have been used as ecological indicators of the levels of anthropogenic impacts on sandy beaches. Our aim is to report the variety of burrow architecture types constructed by ghost crabs Ocypode quadrata on beaches of Maceio, Brazil. We found 20 types of burrows that differ in shape (number of axes, number of openings, orientation of blind end, number of branches). The slash-shaped burrows (type C) were the most frequent shape, followed by types K (spiral) and E (Y-shaped). Type C also showed the largest opening diameter and length ranges. Burrow types F, J, P, S and T were the least frequent. The G-test for goodness of fit to a time-independent uniform frequency distribution (G = 417.61; d.f. = 18; p < 0.005) reject the hypothesis that burrow types are constructed randomly (uniform distribution). The dominance of type C burrows and other simple-type burrows over more elaborate types indicates preference for simplicity.

Ecology↗

A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary

The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting mass-extinction events from phylogenies estimated from molecular sequence data. We develop our approach in a Bayesian statistical framework, which enables us to harness prior information on the frequency and magnitude of mass-extinction events. The approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between rate-shift events. We model three types of events: (1) instantaneous tree-wide shifts in speciation rate; (2) instantaneous tree-wide shifts in extinction rate, and; (3) instantaneous tree-wide mass-extinction events. Each of the events is described by a separate compound Poisson process (CPP) model, where the waiting times between each event are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-type specific prior distribution. Parameters of the model are then estimated using a reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events, provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e., below 5%) false discovery rate even in the case of background diversification rate variation. Finally, we provide an empirical application of this approach to conifers, which reveals that this group has experienced two major episodes of mass extinction. This new approach--the CPP on Mass Extinction Times (CoMET) model--provides an effective tool for identifying mass-extinction events from molecular phylogenies, even when the history of those groups includes more prosaic temporal variation in diversification rate.

Evolutionary Biology↗

Estimating diversification rates from the fossil record

Diversification rates are estimated from phylogenies, typically without fossils, except in paleontological studies. By nature, rate estimations depend heavily on the time data provided in phylogenies, which are divergence times and (when used) fossil ages. Among these temporal data, fossil ages are by far the most precisely known (divergence times are inferences calibrated with fossils). We propose a method to compute the likelihood of a phylogenetic tree with fossils in which the only known time information is the fossil ages.\n\nTesting our approach on simulated data shows that the maximum likelihood rate estimates from the phylogenetic tree shape and the fossil dates are almost as accurate as the ones obtained by taking into account all the data, including the divergence times. Moreover they are substantially more accurate than the estimates obtained only from the exact divergence times (without taking into account the fossil record).

Evolutionary Biology↗

A new model for ancient DNA decay based on paleogenomic meta-analysis

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time is likely due to a bulk diffusion process, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation.

genomics↗

The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

Divergence time estimation -- the calibration of a phylogeny to geological time -- is a integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more. While the incompleteness of the fossil record is a common concern, issues of data limitation and model inadequacy are viable (if underexplored) alternative explanations. In this vein, Beaulieu et al. (2015) convincingly demonstrated how methods of divergence time inference can be misled by both (i) extreme state-dependent molecular substitution rate heterogeneity and (ii) biased sampling of representative major lineages. While these (essentially model-violation) results are robust (and probably common in empirical data sets), we note a further alternative: that the configuration of the statistical inference problem alone (i.e., the parameters, their relationships, and associated priors) precluded the reconstruction of the paleontological timeframe for the crown age of angiosperms. We demonstrate, through sampling from the joint prior (formed by combining the tree (diversification) prior with the various calibration densities specified for fossil-calibrated nodes), that with no data present at all, an Early Cretaceous crown angiosperms is rejected (i.e., has essentially zero probability). More worrisome, however, is that for the 24 nodes calibrated by fossils, almost all have indistinguishable marginal prior and posterior age distributions, indicating an absence of relevant information in the data. Given that these calibrated nodes are strategically placed in disparate regions of the tree, they essentially anchor the tree scaffold, and so the posterior inference for the tree as a whole is largely determined by the pseudo-data present in the (often arbitrary) calibration densities. We recommend, as for any Bayesian analysis, that marginal prior and posterior distributions be carefully compared, especially for parameters of direct interest. Finally, we note that the results presented here do not refute the biological modelling concerns identified by Beaulieu et al. (2015). Both sets of issues remain apposite to the goals of accurate divergence time estimation, and only by considering them in tandem can we move forward more confidently. [marginal priors; information content; diptych; divergence time estimation; fossil record; BEAST; angiosperms.]

evolutionary biology↗