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Figure 1 from: Aung AT, Huang J, Do TV, Song A, Liu J, Zhou Z-K, Su T (2020) Three new fossil records of Equisetum (Equisetaceae) from the Neogene of south-western China and northern Vietnam. In: Jin X-H, Xia N-H, Tan Y-H (Eds) Plant diversity of Southeast Asia-II. PhytoKeys 138: 3-15. https://doi.org/10.3897/phytokeys.138.38674
Figure 1 Map showing the locations of the fossils collected in this study. 1. Sanzhangtian, Zhenyuan County, Yunnan, south-western China (the middle Miocene); 2. Hop Thanh Village, Tuy Loc Commune, Yen Bai Province, northern Vietnam (the late Miocene); 3. Longmen, Yongping County, Yunnan Province, south-western China (the late Pliocene).
Figure 3 from: Aung AT, Huang J, Do TV, Song A, Liu J, Zhou Z-K, Su T (2020) Three new fossil records of Equisetum (Equisetaceae) from the Neogene of south-western China and northern Vietnam. In: Jin X-H, Xia N-H, Tan Y-H (Eds) Plant diversity of Southeast Asia-II. PhytoKeys 138: 3-15. https://doi.org/10.3897/phytokeys.138.38674
Figure 3 Equisetum yongpingense A.T.Aung, T.Su & Z.K.Zhou, sp. nov. Specimen numbers: A XTBGYP0748 B XTBGYP0747 C XTBGYP1014 D XTBGYP1015 E XTBGYP0750 F XTBGYP0749. Scale bars: 1cm.
Figure 2 from: Aung AT, Huang J, Do TV, Song A, Liu J, Zhou Z-K, Su T (2020) Three new fossil records of Equisetum (Equisetaceae) from the Neogene of south-western China and northern Vietnam. In: Jin X-H, Xia N-H, Tan Y-H (Eds) Plant diversity of Southeast Asia-II. PhytoKeys 138: 3-15. https://doi.org/10.3897/phytokeys.138.38674
Figure 2 A–BEquisetum cf. pratense Ehrhart C–FEquisetum yenbaiense A.T.Aung, T.Su, T.V.Do & Z.K.Zhou, sp. nov. Specimen numbers: A–B XTBGSZTF0001 (counterparts) C XTBGVNMN4002 D XTBGVNMN4001 E XTBGVNMN4003 F XTBGVNMN4004. n = node; r = ridge. Scale bars: 1cm.
FIGURE 3 in First fossil record of a nymph (Ephemeroptera, Teloganellidae) from the Indian subcontinent
FIGURE 3. Numbered abdominal segments of Teloganella gurhaensis Agnihotri et al., sp. nov.
Data from: The greatest hits of all time: the histories of dominant genera in the fossil record
Certain taxa are noticeably common within collections, widely distributed, and frequently long-lived. We have examined these dominant genera as compared to rarer genera, with a focus on their temporal histories. Using occurrence data from the Paleobiology Database, we determined which genera belonging to six target groups ranked among the most common within each of 49 temporal bins based on occurrences. The turnover among these dominant taxa from bin-to-bin was then determined for each of these groups and all six groups pooled. Although dominant genera are only a small fraction of all genera, the patterns of turnover mimic those seen in much larger compilations of total biodiversity. We also found that differences in patterns of turnover at the top ranks among the higher taxa reflect previously documented comparison of overall turnover among these classes. Both dominant and non-dominant genera exhibit on average symmetrical patterns of rise and fall between first and last appearances. Dominant genera rarely begin at high ranks, but nevertheless tend to be more common when they first appear than non-dominant genera. Moreover, dominant genera rarely are in the Top 20 when they last appear, but still typically occupy more localities than non-dominant genera occupy in their last interval. The mechanism(s) that produce dominant genera remain unclear. Nearly half of dominant genera are the type genus of a family or subfamily. This is consistent with a simple model of morphological and phylogenetic diversification and sampling.
Data from: Does exceptional preservation distort our view of disparity in the fossil record?
How much of evolutionary history is lost because of the unevenness of the fossil record? Lagerstätten, sites of exceptional fossil preservation, provide remarkable, yet distorting insights into past life. When examining macroevolutionary trends in the fossil record, they can generate an uneven sampling signal for taxonomic diversity; by comparison, their effect on morphological variety (disparity) is poorly understood. We show here that lagerstätten impact the disparity of ichthyosaurs, Mesozoic marine reptiles, by preserving higher diversity and more complete specimens. Elsewhere in the fossil record, undersampled diversity and more fragmentary specimens produce spurious results. We identify a novel effect, that a taxon moves towards the centroid of a Generalised Euclidean dataset as its proportion of missing data increases. We term this effect 'centroid slippage', as a disparity-based analogue of phylogenetic stemward slippage. Our results suggest that uneven sampling presents profound issues for our view of disparity in the fossil record, but that this is also dependent on the methodology used, especially true with widely used Generalised Euclidean distances. Mitigation of missing cladistic data is possible by phylogenetic gap filling, and heterogeneous effects of lagerstätten on disparity may be accounted for by understanding the factors affecting their spatiotemporal distribution.
Data from: Assessing the completeness of the fossil record: comparison of different methods applied to parareptilian tetrapods (Vertebrata: Sauropsida)
As paleontological studies are generally distorted by gaps and biases in the fossil record, it is important to assess its completeness. Here we address the fossil record of Parareptilia, a Permian–Triassic amniote clade, applying two measures of specimen completeness: the skeletal completeness metric (SCM) and the character completeness metric (CCM). The SCM quantifies how much of the skeletal material of a taxon is preserved, whereas the CCM measures the amount of phylogenetic information available. The latter was implemented using two different approaches. In this study, we compare three completeness metrics. Two CCM implementations show a strong correlation with each other, but only the second implementation of the CCM correlates significantly with the SCM, possibly due to character selection in phylogenetic data sets. There is no correlation between diversity of parareptiles and their completeness, implying that the observed fluctuations in diversity are not driven by the completeness of the fossils. The mean completeness of parareptiles through time is consistently high compared with previously studied tetrapod clades, suggesting that most parareptile taxa are based on reasonably complete specimens. Clade-specific differences reveal no link between body size and completeness. However, the analyses confirm the impact of ecology, with aquatic mesosaurids being better preserved than terrestrial taxa.
Data from: Quantifying the completeness of the bat fossil record
Bats (Chiroptera) are one of the most successful extant mammalian orders, uniquely capable of powered flight and laryngeal echolocation. The timing and evidence for evolution of their novel adaptations has been difficult to ascertain from the fossil record due to chronological gaps (e.g. during the Palaeocene) and the fragmentary nature of most fossil bat material. Changes in fossil specimen completeness through time and space can bias our understanding of macroevolutionary processes. Here, we quantify the quality of the bat fossil record using skeletal and character completeness metrics, which respectively document what proportion of a complete skeleton is preserved for a specimen, and the proportion of phylogenetic characters that can be scored for a specimen. Completeness scores were collected from the literature for 441 valid fossil bat species in 167 genera from the Eocene to Pleistocene. All metrics record similar temporal patterns: peak completeness in the Lutetian Stage reflects the presence of Lagerstätten, while subsequent stages have very low completeness with the exception of an Aquitanian high and a Pleistocene peak in skeletal completeness. Bat completeness is not correlated with intensity of sampling through geological time but has a weak negative correlation with publication date. There is no correlation between taxonomic richness and completeness, as the bat fossil record predominately consists of diagnostic but isolated teeth. Consequently, bat skeletal completeness is the lowest of any previously assessed tetrapod group, but character completeness is similar to parareptiles and birds. Bats have significantly higher character completeness in the northern hemisphere, likely due to heightened historical interest and presence of Lagerstätten. Taxa derived from caves, fissure fills and sink holes are more complete than those from fluviolacustrine and marine deposits, but do not preserve highly complete specimens.
Data from: The generification of the fossil record
Many modern paleobiological analyses are conducted at the generic level, a practice predicated on the validity of genera as meaningful proxies for species. Uncritical application of genera in such analyses, however, has led, perhaps inadvertently, to the unjustified reification of genera in an evolutionary context. While the utility of genera as proxies for species in evolutionary studies should be evaluated as an empirical issue, in practice it is increasingly assumed (rather than demonstrated) that genera are suitable proxies for species. This is problematic on both ontological and epistemological grounds. Genera are arbitrarily circumscribed, non-equivalent, often paraphyletic, and sometimes polyphyletic collections of species. They are useful tools for communication, but have no theoretical or biological reality of their own and, whether monophyletic or not, cannot themselves operate in the evolutionary process. Attributes considered important for understanding macroevolution (e.g., geographic ranges, niche breadths, and taxon durations) are frequently variable among species within genera and will be inflated at the generic level, especially in species-rich genera. Consequently, the meanings of results attained at the generic level may not "trickle down" in any obvious way that elucidates our understanding of evolution at the species level. Ideally, then, evolutionary studies that are actually about species should be studied using species-level data rather than proxy data tabulated using genera. Where genera are used, greater critical attention should be focused on the degree to which attributes tabulated at the generic level reflect biological properties and processes at the species level.
Data from: Phylogeny, ancestors, and anagenesis in the hominin fossil record
Probabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary patterns by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary divergence. Recent methodological developments have integrated ancestral relationships into probabilistic phylogenetic methods. These new approaches rely on parameter-rich models and sophisticated inferential methods, potentially obscuring the respective contributions of data and models. In this study, we describe a simple likelihoodist approach that combines probabilistic models of morphological evolution and fossil preservation to reconstruct both cladogenetic and anagenetic relationships. By applying this approach to a data set of fossil hominins, we demonstrate the capability of existing models to unveil evidence for anagenesis presented by morphological and temporal data. This evidence was previously recognized by qualitative assessments, but largely ignored by quantitative phylogenetic analyses. For example, we find support for directly ancestral relationships in multiple lineages: Sahelanthropus is ancestral to later hominins; Australopithecus anamensis is ancestral to Australopithecus afarensis; Australopithecus garhi is ancestral to Homo; Homo antecessor is ancestral to Homo heidelbergensis, which in turn is ancestral to both Homo sapiens and Homo neanderthalensis. By accommodating direct ancestry in phylogenetics, quantitative results align more closely with previous qualitative expectations.
Data from: Spatiotemporal sampling patterns in the 230 million year fossil record of terrestrial crocodylomorphs and their impact on diversity
The 24 extant crocodylian species are the remnants of a once much more diverse and widespread clade. Crocodylomorpha has an approximately 230 million year evolutionary history, punctuated by a series of radiations and extinctions. However, the group's fossil record is biased. Previous studies have reconstructed temporal patterns in subsampled crocodylomorph palaeobiodiversity, but have not explicitly examined variation in spatial sampling, nor the quality of this record. We compiled a dataset of all taxonomically diagnosable non‐marine crocodylomorph species (393). Based on the number of phylogenetic characters that can be scored for all published fossils of each species, we calculated a completeness value for each taxon. Mean average species completeness (56%) is largely consistent within subgroups and for different body size classes, suggesting no significant biases across the crocodylomorph tree. In general, average completeness values are highest in the Mesozoic, with an overall trend of decreasing completeness through time. Many extant taxa are identified in the fossil record from very incomplete remains, but this might be because their provenance closely matches the species' present‐day distribution, rather than through autapomorphies. Our understanding of nearly all crocodylomorph macroevolutionary 'events' is essentially driven by regional patterns, with no global sampling signal. Palaeotropical sampling is especially poor for most of the group's history. Spatiotemporal sampling bias impedes our understanding of several Mesozoic radiations, whereas molecular divergence times for Crocodylia are generally in close agreement with the fossil record. However, the latter might merely be fortuitous, i.e. divergences happened to occur during our ephemeral spatiotemporal sampling windows.
Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record
Background: The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Results: Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Conclusions: Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction.
Data from: Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction
There is a well-established discrepancy between paleontological and molecular data regarding the timing of the origin and diversification of placental mammals. Molecular estimates place interordinal diversification dates in the Cretaceous, whilst no unambiguous crown placental fossils have been found prior to the end-Cretaceous mass extinction. Here, the completeness of the eutherian fossil record through geological time is evaluated in order to assess the suggestion that a poor fossil record is largely responsible for the difference in estimates of placental origins. The completeness of fossil specimens was measured using the Character Completeness Metric, a metric that quantifies the completeness of fossil taxa as the percentage of phylogenetic characters that are available to be scored for any given taxon. Our dataset was comprised of 33 published cladistic matrices representing 445 genera, of which 333 were coded at the species-level. There was no significant difference in eutherian completeness across the Cretaceous/Palaeogene boundary. This suggests that the lack of placental mammal fossils in the Cretaceous is not due to a poor fossil record, but more likely represents a genuine absence of placental mammals in the Cretaceous. This result supports the 'explosive model' of early placental evolution, whereby placental mammals originated around the time of the Cretaceous/Palaeogene boundary and diversified soon after the event. No correlation was found between the completeness pattern observed in this study and those of previous completeness studies on birds and sauropodomorph dinosaurs, suggesting that different factors affect the preservation of these groups. No correlations were found with various isotope proxy measures, but Akaike Information Criterion analysis found that eutherian Character Completeness Metric scores were best explained by models involving the marine carbonate strontium isotope ratios (87Sr/86Sr), suggesting that the tectonic activity might play a role in controlling the completeness of the eutherian fossil record.
FIGURES 8–9 in First record of fossil Priacma (Coleoptera: Archostemata: Cupedidae) from the Jehol Biota of western Liaoning, China
FIGURES 8–9. Priacma latidentata sp. nov., holotype. 8— head, 9—metaventrite.
FIGURES 17–18 in First record of fossil Priacma (Coleoptera: Archostemata: Cupedidae) from the Jehol Biota of western Liaoning, China
FIGURES 17–18. Priacma clavata sp. nov., holotype. 17—head, 18—metaventrite.
FIGURES 13–14 in First record of fossil Priacma (Coleoptera: Archostemata: Cupedidae) from the Jehol Biota of western Liaoning, China
FIGURES 13–14. Priacma tuberculosa sp. nov., holotype. 13—head, 14—elytral cells.
FIGURES 15–16 in First record of fossil Priacma (Coleoptera: Archostemata: Cupedidae) from the Jehol Biota of western Liaoning, China
FIGURES 15–16. Priacma clavata sp. nov., holotype. 15—dorsal view, 16—ventral view.
FIGURE 4 in The earliest fossil record of the wasp subfamily Pelecininae (Hymenoptera: Proctotrupoidea: Pelecinidae) from the Yixian Formation of China
FIGURE 4. Shoushida regilla gen. et sp. nov., line drawing of wing venation, No. CNU–HYM–LB2006074.
FIGURE 1B. Aradus andancensis n in A new record and a new species of Aradidae fossils (Hemiptera: Heteroptera)
FIGURE 1B. Aradus andancensis n. sp., holotype, dorsal view. Scale: 1 mm.
FIGURE 3. Amber piece 2 in Further records of Amphipoda from Baltic Eocene amber with first evidence of prae-copulatory behaviour in a fossil amphipod and remarks on the taxonomic position of Palaeogammarus Zaddach, 1864
FIGURE 3. Amber piece 2, individuals of Synurella indicated with letters (scale bar in mm).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.