cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.963510
title: The captorhinid reptile <i>Captorhinikos valensis</i> from the lower Permian Vale Formation of Texas, and the evolution of herbivory in eureptiles

description: ABSTRACT <i>Captorhinikos valensis</i> is a poorly known, multiple-tooth-rowed captorhinid reptile from the Lower Permian Vale Formation of Texas. Our reappraisal of <i>C. valensis</i> reveals it to be a small moradisaurine, exhibiting a maximum of five rows of bullet-shaped teeth in the multiple-rowed region of both the maxilla and the dentary. The slightly radiating organization of the tooth rows distinguishes <i>C. valensis</i> from the parallel arrangement of the tooth rows exhibited by all other moradisaurines. <i>Captorhinikos valensis</i> is also distinguishable from the coeval moradisaurine <i>Labidosaurikos meachami</i> by a more conspicuously denticulated, broader, ‘U’-shaped transverse flange of the pterygoid, a plesiomorphic morphology shared with the large, single-rowed captorhinid <i>Labidosaurus hamatus</i>. Postcranial information is limited to two short series of presacral vertebrae not associated with the cranial materials; open neurocentral sutures are present in one specimen, indicating immaturity at death. We investigated the relationships of <i>C. valensis</i> to other captorhinids by adding it to the data matrix of a previously published analysis that included several moradisaurine captorhinids. A branch-and-bound PAUP analysis discovered a single optimal tree. Whereas a previous analysis of captorhinid interrelationships found the (undifferentiated) genus <i>Captorhinikos</i> to fall outside of a clade composed of <i>L. hamatus</i> and the large moradisaurines, our analysis recovered <i>C. valensis</i> in a clade with the genera <i>Labidosaurikos</i>, <i>Gansurhinus</i>, <i>Moradisaurus</i>, and <i>Rothianiscus</i> (i.e., Moradisaurinae sensu stricto), and <i>Captorhinikos chozaensis</i> as the sister species of a clade that includes <i>L. hamatus</i> and Moradisaurinae s.s.; <i>Captorhinikos chozaensis</i> is no longer classifiable as a moradisaurine (according to our phylogenetic definition for the group), and should be assigned to a new genus. Stratigraphic calibration of our captorhinid phylogeny indicates that moradisaurines evolved by the middle Kungurian (middle Leonardian). SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.963511
title: Osteology, relationships, and ecology of <i>Annemys</i> (Testudines, Eucryptodira) from the Late Jurassic of Shar Teg, Mongolia, and phylogenetic definitions for Xinjiangchelyidae, Sinemydidae, and Macrobaenidae

description: ABSTRACTA complete description of the xinjiangchelyid turtles <i>Annemys levensis</i> and <i>A. latiens</i> is provided, based on all available material from the Upper Jurassic type locality of Shar Teg, Mongolia. <i>Annemys latiens</i> was previously known almost exclusively from shell material, but an undescribed skull from Shar Teg is referable to this species and its distinct morphology confirms the presence of two taxa at this locality. <i>Annemys latiens</i> has an elongated skull that markedly differs in proportions from those of <i>A</i>. <i>levensis</i> and resembles the shape of some recent, piscivorous turtles. The overall similarity of the shells of the two <i>Annemys</i> species combined with significant differences in the skull indicate that these turtles probably partitioned the aquatic niche by exploring different feeding strategies. Among xinjiangchelyids, at least three different skull morphotypes can be differentiated, which implies a moderate level of ecological diversification among Late Jurassic Asian turtles. Phylogenetic analysis weakly supports the inclusion of <i>Annemys</i> spp. into Xinjiangchelyidae and places xinjiangchelyids at the stem of Testudines, but the latter result is considered tentative. Phylogenetic definitions of Xinjiangchelyidae, Sinemydidae, and Macrobaenidae are provided for nomenclatural clarity and precision. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.963510.v1
title: The captorhinid reptile <i>Captorhinikos valensis</i> from the lower Permian Vale Formation of Texas, and the evolution of herbivory in eureptiles

description: ABSTRACT <i>Captorhinikos valensis</i> is a poorly known, multiple-tooth-rowed captorhinid reptile from the Lower Permian Vale Formation of Texas. Our reappraisal of <i>C. valensis</i> reveals it to be a small moradisaurine, exhibiting a maximum of five rows of bullet-shaped teeth in the multiple-rowed region of both the maxilla and the dentary. The slightly radiating organization of the tooth rows distinguishes <i>C. valensis</i> from the parallel arrangement of the tooth rows exhibited by all other moradisaurines. <i>Captorhinikos valensis</i> is also distinguishable from the coeval moradisaurine <i>Labidosaurikos meachami</i> by a more conspicuously denticulated, broader, ‘U’-shaped transverse flange of the pterygoid, a plesiomorphic morphology shared with the large, single-rowed captorhinid <i>Labidosaurus hamatus</i>. Postcranial information is limited to two short series of presacral vertebrae not associated with the cranial materials; open neurocentral sutures are present in one specimen, indicating immaturity at death. We investigated the relationships of <i>C. valensis</i> to other captorhinids by adding it to the data matrix of a previously published analysis that included several moradisaurine captorhinids. A branch-and-bound PAUP analysis discovered a single optimal tree. Whereas a previous analysis of captorhinid interrelationships found the (undifferentiated) genus <i>Captorhinikos</i> to fall outside of a clade composed of <i>L. hamatus</i> and the large moradisaurines, our analysis recovered <i>C. valensis</i> in a clade with the genera <i>Labidosaurikos</i>, <i>Gansurhinus</i>, <i>Moradisaurus</i>, and <i>Rothianiscus</i> (i.e., Moradisaurinae sensu stricto), and <i>Captorhinikos chozaensis</i> as the sister species of a clade that includes <i>L. hamatus</i> and Moradisaurinae s.s.; <i>Captorhinikos chozaensis</i> is no longer classifiable as a moradisaurine (according to our phylogenetic definition for the group), and should be assigned to a new genus. Stratigraphic calibration of our captorhinid phylogeny indicates that moradisaurines evolved by the middle Kungurian (middle Leonardian). SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.963511.v1
title: Osteology, relationships, and ecology of <i>Annemys</i> (Testudines, Eucryptodira) from the Late Jurassic of Shar Teg, Mongolia, and phylogenetic definitions for Xinjiangchelyidae, Sinemydidae, and Macrobaenidae

description: ABSTRACTA complete description of the xinjiangchelyid turtles <i>Annemys levensis</i> and <i>A. latiens</i> is provided, based on all available material from the Upper Jurassic type locality of Shar Teg, Mongolia. <i>Annemys latiens</i> was previously known almost exclusively from shell material, but an undescribed skull from Shar Teg is referable to this species and its distinct morphology confirms the presence of two taxa at this locality. <i>Annemys latiens</i> has an elongated skull that markedly differs in proportions from those of <i>A</i>. <i>levensis</i> and resembles the shape of some recent, piscivorous turtles. The overall similarity of the shells of the two <i>Annemys</i> species combined with significant differences in the skull indicate that these turtles probably partitioned the aquatic niche by exploring different feeding strategies. Among xinjiangchelyids, at least three different skull morphotypes can be differentiated, which implies a moderate level of ecological diversification among Late Jurassic Asian turtles. Phylogenetic analysis weakly supports the inclusion of <i>Annemys</i> spp. into Xinjiangchelyidae and places xinjiangchelyids at the stem of Testudines, but the latter result is considered tentative. Phylogenetic definitions of Xinjiangchelyidae, Sinemydidae, and Macrobaenidae are provided for nomenclatural clarity and precision. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.963507
title: The first discovery of an alligatorid (Crocodylia, Alligatoroidea, Alligatoridae) in the Eocene of China

description: SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.963508
title: Taxonomy and phylogeny of the turtle <i>Tropidemys langii</i> Rütimeyer, 1873, based on new specimens from the Kimmeridgian of the Swiss Jura Mountains

description: ABSTRACTThe fossil turtle <i>Tropidemys langii</i> is a representative of Plesiochelyidae, a traditionally recognized group of Late Jurassic turtles diagnosed by the presence of three cervical scutes and adapted to life in the sea. <i>Tropidemys langii</i> was previously only known from fossilized carapaces and, possibly, plastra from Europe, most notably the famous ‘Solothurn Turtle Limestone’ of Switzerland. Due to the sparse fossil record of <i>Tropidemys langii</i>, several questions concerning its taxonomy and phylogeny have remained unanswered. Here, new material of <i>Tropidemys langii</i> is reported from the Kimmeridgian of Porrentruy, Canton Jura, Switzerland. In addition to three well-preserved carapaces, associated plastra and limb bones (humerus and femur) are described for the first time. The type specimens of ‘<i>Tropidemys valanginiensis</i>’ and ‘<i>Pelobatochelys blakii</i>’ lack diagnostic characters, but can nevertheless be referred to <i>Tropidemys</i>. A potential extension of the lineage into the Early Cretaceous is uncertain, however, because the type locality of ‘<i>Tropidemys valanginiensis</i>’ is dubious. A cladistic analysis shows that <i>Tropidemys langii</i> is sister to <i>Plesiochelys solodurensis</i>, thereby tentatively confirming for the first time the monophyly of Plesiochelyidae using cladistic arguments. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.963508.v1
title: Taxonomy and phylogeny of the turtle <i>Tropidemys langii</i> Rütimeyer, 1873, based on new specimens from the Kimmeridgian of the Swiss Jura Mountains

description: ABSTRACTThe fossil turtle <i>Tropidemys langii</i> is a representative of Plesiochelyidae, a traditionally recognized group of Late Jurassic turtles diagnosed by the presence of three cervical scutes and adapted to life in the sea. <i>Tropidemys langii</i> was previously only known from fossilized carapaces and, possibly, plastra from Europe, most notably the famous ‘Solothurn Turtle Limestone’ of Switzerland. Due to the sparse fossil record of <i>Tropidemys langii</i>, several questions concerning its taxonomy and phylogeny have remained unanswered. Here, new material of <i>Tropidemys langii</i> is reported from the Kimmeridgian of Porrentruy, Canton Jura, Switzerland. In addition to three well-preserved carapaces, associated plastra and limb bones (humerus and femur) are described for the first time. The type specimens of ‘<i>Tropidemys valanginiensis</i>’ and ‘<i>Pelobatochelys blakii</i>’ lack diagnostic characters, but can nevertheless be referred to <i>Tropidemys</i>. A potential extension of the lineage into the Early Cretaceous is uncertain, however, because the type locality of ‘<i>Tropidemys valanginiensis</i>’ is dubious. A cladistic analysis shows that <i>Tropidemys langii</i> is sister to <i>Plesiochelys solodurensis</i>, thereby tentatively confirming for the first time the monophyly of Plesiochelyidae using cladistic arguments. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.963507.v1
title: The first discovery of an alligatorid (Crocodylia, Alligatoroidea, Alligatoridae) in the Eocene of China

description: SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.963492
title: Influence of Methanogenic Populations in Holocene Lacustrine Sediments Revealed by Clone Libraries and Fatty Acid Biogeochemistry

description: Methanogenic populations were investigated in subsaline Laguna Potrok Aike sediments, southern Argentina. Microbial density and activity were assessed via cell count and <i>in situ</i> ATP detection for the last ∼11K years. Methanogen phylogenetics highlighted species stratification throughout depth, whereas CO<sub>2</sub> reduction was the major pathway leading to methane production. Organic substrates, characterized using pore water analysis, bulk organic fractions and saturated fatty acids, showed a clear link between sediment colonization and initial organic sources. Concentrations and δ<sup>13</sup>C compositions of methane and fatty acids provided final evidence of a microbial imprint on Holocene organic proxies in the most colonized intervals.
DOI: 10.6084/m9.figshare.963491
title: Metagenomic Evidence for Sulfide Oxidation in Extremely Acidic Cave Biofilms

description: Snottites are extremely acidic (pH 0–2) biofilms that form on the walls and ceilings of hydrogen sulfide-rich caves. Recent work suggests that microbial communities including snottites and related cave wall biofilms accelerate cave formation by oxidizing sulfide to sulfuric acid. Therefore, we used full-cycle rRNA methods and metagenomics to explore the community composition and sulfur metabolism of snottites from the sulfidic Frasassi and Acquasanta cave systems, Italy. Acquasanta snottites were dominated by strains of <i>Acidithiobacillus thiooxidans</i>, with a smaller population of <i>Ferroplasma</i> sp. Frasassi snottites were also dominated by <i>At. thiooxidans</i> but with a more diverse community including relatives of ‘G-plasma’ (Thermoplasmatales), <i>Acidimicrobium</i>, and rare taxa. We identified diverse homologues of sulfide:quinone oxidoreductase (SQR) in the metagenomic datasets. Based on phylogenetic analysis, the numerically dominant <i>At. thiooxidans</i> populations have four different types of SQR, while <i>Ferroplasma</i> has two and <i>Acidimicrobium</i> and G-plasma each have one. No other genetic evidence for sulfur oxidation was detected for either <i>Acidimicrobium</i> or G-plasma, suggesting that they do not generate sulfuric acid. Our results confirm earlier findings that <i>At. thiooxidans</i> is the dominant primary producer and sulfide oxidizer in sulfidic cave snottites.
DOI: 10.6084/m9.figshare.963491.v1
title: Metagenomic Evidence for Sulfide Oxidation in Extremely Acidic Cave Biofilms

description: Snottites are extremely acidic (pH 0–2) biofilms that form on the walls and ceilings of hydrogen sulfide-rich caves. Recent work suggests that microbial communities including snottites and related cave wall biofilms accelerate cave formation by oxidizing sulfide to sulfuric acid. Therefore, we used full-cycle rRNA methods and metagenomics to explore the community composition and sulfur metabolism of snottites from the sulfidic Frasassi and Acquasanta cave systems, Italy. Acquasanta snottites were dominated by strains of <i>Acidithiobacillus thiooxidans</i>, with a smaller population of <i>Ferroplasma</i> sp. Frasassi snottites were also dominated by <i>At. thiooxidans</i> but with a more diverse community including relatives of ‘G-plasma’ (Thermoplasmatales), <i>Acidimicrobium</i>, and rare taxa. We identified diverse homologues of sulfide:quinone oxidoreductase (SQR) in the metagenomic datasets. Based on phylogenetic analysis, the numerically dominant <i>At. thiooxidans</i> populations have four different types of SQR, while <i>Ferroplasma</i> has two and <i>Acidimicrobium</i> and G-plasma each have one. No other genetic evidence for sulfur oxidation was detected for either <i>Acidimicrobium</i> or G-plasma, suggesting that they do not generate sulfuric acid. Our results confirm earlier findings that <i>At. thiooxidans</i> is the dominant primary producer and sulfide oxidizer in sulfidic cave snottites.
DOI: 10.6084/m9.figshare.963492.v1
title: Influence of Methanogenic Populations in Holocene Lacustrine Sediments Revealed by Clone Libraries and Fatty Acid Biogeochemistry

description: Methanogenic populations were investigated in subsaline Laguna Potrok Aike sediments, southern Argentina. Microbial density and activity were assessed via cell count and <i>in situ</i> ATP detection for the last ∼11K years. Methanogen phylogenetics highlighted species stratification throughout depth, whereas CO<sub>2</sub> reduction was the major pathway leading to methane production. Organic substrates, characterized using pore water analysis, bulk organic fractions and saturated fatty acids, showed a clear link between sediment colonization and initial organic sources. Concentrations and δ<sup>13</sup>C compositions of methane and fatty acids provided final evidence of a microbial imprint on Holocene organic proxies in the most colonized intervals.
DOI: 10.6084/m9.figshare.963486
title: Robust Estimation for Generalized Additive Models

description: This article studies <i>M</i>-type estimators for fitting robust generalized additive models in the presence of anomalous data. A new theoretical construct is developed to connect the costly <i>M</i>-type estimation with least-squares type calculations. Its asymptotic properties are studied and used to motivate a computational algorithm. The main idea is to decompose the overall <i>M</i>-type estimation problem into a sequence of well-studied conventional additive model fittings. The resulting algorithm is fast and stable, can be paired with different nonparametric smoothers, and can also be applied to cases with multiple covariates. As another contribution of this article, automatic methods for smoothing parameter selection are proposed. These methods are designed to be resistant to outliers. The empirical performance of the proposed methodology is illustrated via both simulation experiments and real data analysis. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.963485
title: Label Switching in Bayesian Mixture Models: Deterministic Relabeling Strategies

description: Label switching is a well-known problem in the Bayesian analysis of mixture models. On the one hand, it complicates inference, and on the other hand, it has been perceived as a prerequisite to justify Markov chain Monte Carlo (MCMC) convergence. As a result, nonstandard MCMC algorithms that traverse the symmetric copies of the posterior distribution, and possibly genuine modes, have been proposed. To perform component-specific inference, methods to undo the label switching and to recover the interpretation of the components need to be applied. If latent allocations for the design of the MCMC strategy are included, and the sampler has converged, then labels assigned to each component may change from iteration to iteration. However, observations being allocated together must remain similar, and we use this fundamental fact to derive an easy and efficient solution to the label switching problem. We compare our strategy with other relabeling algorithms on univariate and multivariate data examples and demonstrate improvements over alternative strategies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.963483
title: Generalized Isotonic Regression

description: We present a new computational and statistical approach for fitting isotonic models under convex differentiable loss functions through recursive partitioning. Models along the partitioning path are also isotonic and can be viewed as regularized solutions to the problem. Our approach generalizes and subsumes the well-known work of Barlow and Brunk on fitting isotonic regressions subject to specially structured loss functions, and expands the range of loss functions that can be used (e.g., adding Huber loss for robust regression). This is accomplished through an algorithmic adjustment to a recursive partitioning approach recently developed for solving large-scale ł<sub>2</sub>-loss isotonic regression problems. We prove that the new algorithm solves the generalized problem while maintaining the favorable computational and statistical properties of the <i>l</i><sub>2</sub> algorithm. The results are demonstrated on both real and synthetic data in two settings: fitting count data using negative Poisson log-likelihood loss, and fitting robust isotonic regressions using Huber loss. Proofs of theorems and a MATLAB-based software package implementing our algorithm are available in the online supplementary materials.
DOI: 10.6084/m9.figshare.963482
title: Modeling and Anomalous Cluster Detection for Point Processes Using Process Convolutions

description: We present a model using process convolutions, which describes spatial and temporal variations of the intensity of events that occur at random geographical locations. An inhomogeneous Poisson process is used to model the intensity over a spatial region with multiplicative spatial and temporal covariate effects. Temporal variation in the structure of the intensity is obtained by employing a time-varying process for the convolution. Use of a compactly supported kernel in the convolution improves the computational efficiency. Additionally, anomalous cluster detection in the event rates is developed based on exceedance probabilities. The methods are demonstrated on data of major crimes in Cincinnati during 2006. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.963486.v1
title: Robust Estimation for Generalized Additive Models

description: This article studies <i>M</i>-type estimators for fitting robust generalized additive models in the presence of anomalous data. A new theoretical construct is developed to connect the costly <i>M</i>-type estimation with least-squares type calculations. Its asymptotic properties are studied and used to motivate a computational algorithm. The main idea is to decompose the overall <i>M</i>-type estimation problem into a sequence of well-studied conventional additive model fittings. The resulting algorithm is fast and stable, can be paired with different nonparametric smoothers, and can also be applied to cases with multiple covariates. As another contribution of this article, automatic methods for smoothing parameter selection are proposed. These methods are designed to be resistant to outliers. The empirical performance of the proposed methodology is illustrated via both simulation experiments and real data analysis. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.963485.v1
title: Label Switching in Bayesian Mixture Models: Deterministic Relabeling Strategies

description: Label switching is a well-known problem in the Bayesian analysis of mixture models. On the one hand, it complicates inference, and on the other hand, it has been perceived as a prerequisite to justify Markov chain Monte Carlo (MCMC) convergence. As a result, nonstandard MCMC algorithms that traverse the symmetric copies of the posterior distribution, and possibly genuine modes, have been proposed. To perform component-specific inference, methods to undo the label switching and to recover the interpretation of the components need to be applied. If latent allocations for the design of the MCMC strategy are included, and the sampler has converged, then labels assigned to each component may change from iteration to iteration. However, observations being allocated together must remain similar, and we use this fundamental fact to derive an easy and efficient solution to the label switching problem. We compare our strategy with other relabeling algorithms on univariate and multivariate data examples and demonstrate improvements over alternative strategies. Supplementary materials for this article are available online.