Pre-Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift.

The cause, or causes, of the Pleistocene megafaunal extinctions have been difficult to establish, in part because poor spatiotemporal resolution in the fossil record hinders alignment of species disappearances with archeological and environmental data. We obtained 172 new radiocarbon dates on megafauna from Rancho La Brea in California spanning 15.6 to 10.0 thousand calendar years before present (ka). Seven species of extinct megafauna disappeared by 12.9 ka, before the onset of the Younger Dryas. Comparison with high-resolution regional datasets revealed that these disappearances coincided with an ecological state shift that followed aridification and vegetation changes during the Bølling-Allerød (14.69 to 12.89 ka). Time-series modeling implicates large-scale fires as the primary cause of the extirpations, and the catalyst of this state shift may have been mounting human impacts in a drying, warming, and increasingly fire-prone ecosystem.

On Information Rank Deficiency in Phenotypic Covariance Matrices.

This article investigates a form of rank deficiency in phenotypic covariance matrices derived from geometric morphometric data, and its impact on measures of phenotypic integration. We first define a type of rank deficiency based on information theory then demonstrate that this deficiency impairs the performance of phenotypic integration metrics in a model system. Lastly, we propose methods to treat for this information rank deficiency. Our first goal is to establish how the rank of a typical geometric morphometric covariance matrix relates to the information entropy of its eigenvalue spectrum. This requires clear definitions of matrix rank, of which we define three: the full matrix rank (equal to the number of input variables), the mathematical rank (the number of nonzero eigenvalues), and the information rank or "effective rank" (equal to the number of nonredundant eigenvalues). We demonstrate that effective rank deficiency arises from a combination of methodological factors-Generalized Procrustes analysis, use of the correlation matrix, and insufficient sample size-as well as phenotypic covariance. Secondly, we use dire wolf jaws to document how differences in effective rank deficiency bias two metrics used to measure phenotypic integration. The eigenvalue variance characterizes the integration change incorrectly, and the standardized generalized variance lacks the sensitivity needed to detect subtle changes in integration. Both metrics are impacted by the inclusion of many small, but nonzero, eigenvalues arising from a lack of information in the covariance matrix, a problem that usually becomes more pronounced as the number of landmarks increases. We propose a new metric for phenotypic integration that combines the standardized generalized variance with information entropy. This metric is equivalent to the standardized generalized variance but calculated only from those eigenvalues that carry nonredundant information. It is the standardized generalized variance scaled to the effective rank of the eigenvalue spectrum. We demonstrate that this metric successfully detects the shift of integration in our dire wolf sample. Our third goal is to generalize the new metric to compare data sets with different sample sizes and numbers of variables. We develop a standardization for matrix information based on data permutation then demonstrate that Smilodon jaws are more integrated than dire wolf jaws. Finally, we describe how our information entropy-based measure allows phenotypic integration to be compared in dense semilandmark data sets without bias, allowing characterization of the information content of any given shape, a quantity we term "latent dispersion". [Canis dirus; Dire wolf; effective dispersion; effective rank; geometric morphometrics; information entropy; latent dispersion; modularity and integration; phenotypic integration; relative dispersion.].

Morphology-based diagnostics of "protodogs." A commentary to Galeta et al., 2021, Anatomical Record, 304, 42-62, doi: 10.1002/ar.24500.

In a recent article in this journal, Galeta et al., (2020) discussed eight Pleistocene "protodogs" and seven Pleistocene wolves. Those "protodogs" had been diagnosed in earlier publications, based on skull morphology. We re-examined the Galeta et al. paper to offer comments on their observed outcomes, and the conclusion of presumed domestication. Of seven metrics that the authors used, five differed statistically between their two groups. However, from more elaborate studies, some of those same metrics had been rejected previously as not valid species-distinguishing traits. In this respect, we do accept cranium size and wider palate as species-distinguishing metrics. The physical size of their specimens was much larger than other archaeological specimens that have been accepted as dogs. Additionally, their sample size was small, compared to the number of available specimens, as shown from previous publications by the same group. Thus, we considered statistical differences that were found between groups in their study, and assessed whether the outcomes could have resulted from natural morphological variation. We examined a group of 73 dire wolves ((Aenocyon [Canis] dirus; Perri et al., 2021), using the same methods as used by Galeta et al., (2020). We could segregate two distinct morphological groups in our study, one having outcomes that were identical to the "protodogs" in Galeta et al. (2020). For the specimens of extinct dire wolves to segregate in the same way as the subjects from Galeta et al. indicates that natural variation probably was the driver of their observed outcomes, domestication being an unlikely assumption.

The fossil record of phenotypic integration and modularity: A deep-time perspective on developmental and evolutionary dynamics.

Variation is the raw material for natural selection, but the factors shaping variation are still poorly understood. Genetic and developmental interactions can direct variation, but there has been little synthesis of these effects with the extrinsic factors that can shape biodiversity over large scales. The study of phenotypic integration and modularity has the capacity to unify these aspects of evolutionary study by estimating genetic and developmental interactions through the quantitative analysis of morphology, allowing for combined assessment of intrinsic and extrinsic effects. Data from the fossil record in particular are central to our understanding of phenotypic integration and modularity because they provide the only information on deep-time developmental and evolutionary dynamics, including trends in trait relationships and their role in shaping organismal diversity. Here, we demonstrate the important perspective on phenotypic integration provided by the fossil record with a study of Smilodon fatalis (saber-toothed cats) and Canis dirus (dire wolves). We quantified temporal trends in size, variance, phenotypic integration, and direct developmental integration (fluctuating asymmetry) through 27,000 y of Late Pleistocene climate change. Both S. fatalis and C. dirus showed a gradual decrease in magnitude of phenotypic integration and an increase in variance and the correlation between fluctuating asymmetry and overall integration through time, suggesting that developmental integration mediated morphological response to environmental change in the later populations of these species. These results are consistent with experimental studies and represent, to our knowledge, the first deep-time validation of the importance of developmental integration in stabilizing morphological evolution through periods of environmental change.

Evolution and homology of the astragalus in early amniotes: new fossils, new perspectives.

The reorganization of the ankle in basal amniotes has long been considered a key innovation allowing the evolution of more terrestrial and cursorial behavior. Understanding how this key innovation arose is a complex problem that largely concerns the homologizing of the amniote astragalus with the various ossifications in the anamniote tarsus. Over the last century, several hypotheses have been advanced homologizing the amniote astragalus with the many ossifications in the ankle of amphibian-grade tetrapods. There is an emerging consensus that the amniote astragalus is a complex structure emerging via the co-ossification of several originally separate elements, but the identities of these elements remain unclear. Here we present new fossil evidence bearing on this contentious question. A poorly ossified, juvenile astragalus of the large captorhinid Moradisaurus grandis shows clear evidence of four ossification centers, rather than of three centers or one center as posited in previous models of astragalus homology. Comparative material of the captorhinid Captorhinikos chozaensis is also interpretable as demonstrating four ossification centers. A new, four-center model for the homology of the amniote astragalus is advanced, and is discussed in the context of the phylogeny of the Captorhinidae in an attempt to identify the developmental transitions responsible for the observed pattern of ossification within this clade. Lastly, the broader implications for amniote phylogeny are discussed, concluding that the neomorphic pattern of astragalus ossification seen in all extant reptiles (including turtles) arose within the clade Diapsida.

Permian tetrapods from the Sahara show climate-controlled endemism in Pangaea.

New fossils from the Upper Permian Moradi Formation of northern Niger provide an insight into the faunas that inhabited low-latitude, xeric environments near the end of the Palaeozoic era (approximately 251 million years ago). We describe here two new temnospondyl amphibians, the cochleosaurid Nigerpeton ricqlesi gen. et sp. nov. and the stem edopoid Saharastega moradiensis gen. et sp. nov., as relicts of Carboniferous lineages that diverged 40-90 million years earlier. Coupled with a scarcity of therapsids, the new finds suggest that faunas from the poorly sampled xeric belt that straddled the Equator during the Permian period differed markedly from well-sampled faunas that dominated tropical-to-temperate zones to the north and south. Our results show that long-standing theories of Late Permian faunal homogeneity are probably oversimplified as the result of uneven latitudinal sampling.