Molecular Clock Calibration

Background: Celastraceae is a morphologically heterogeneous family. For this reason, the inclusion of some taxa within this group is controversial. Recently this problem has become significant since its fossil record is recognized as an important source of information for evolutionary studies, especially those using molecular clocks which require a robust, reliable fossil record. Questions: What are the most reliable fossil records of Celastraceae? What morphological characters are used to assign fossils in the family? Study site and dates: Compilation of records contained in paleontological databases, and paleobotanical literature, covering publications from 1869 to 2018. Methods: Published information on the Celastraceae fossil record was compiled and analyzed using the most recent classification system and specialized literature on the family. Results: A total of 168 fossil records were examined, of which nine are proposed for use as molecular clock calibration points. Each speci...

The Myristicaceae is a member of the early diverging angiosperm order Magnoliales; however, the family is poorly represented by fossil collections. We describe Virola dominicana sp. nov. (Myristicaceae), the first record of fossilized Myristicaceae flowers, from mid-Tertiary (45–15 million years ago) Dominican amber. The description is based on 24 male flowers in 17 pieces of amber, thus providing some indication of intraspecific variation, including a two-tepaled flower. Diagnostic characters of the new species are the long-simple or few-branched trichomes on the perianth margins, the small pollen grains, and a short staminal column. These fossils also show co-occurring insects, some of which could be Virola pollinators. It is speculated that V. dominicana disappeared from Hispaniola during the Pliocene–Pleistocene cooling events leaving no native members of the Myristicaceae in this region today. Additionally, these fossils demonstrate that Myristicaceae was present in the Western...

Synopsis Feeding is a complex process that involves an integrated response of multiple functional systems. Animals evolve phenotypic integration of complex morphological traits to covary and maximize performance of feeding behaviors. Specialization, such as feeding on dangerous prey, can further shape the integration of behavior and morphology as traits are expected to evolve and maintain function in parallel. Feeding on centipedes, with their powerful forcipules that pinch and inject venom, has evolved multiple times within snakes, including the genus Tantilla. However, the behavioral and morphological adaptations used to consume this dangerous prey are poorly understood. By studying snakes with varying degrees of dietary specialization, we can test the integration of diet, morphology, and behavior to better understand the evolution of consuming difficult prey. We studied the prey preference and feeding behavior of Tantilla using the flat-headed snake (T. gracilis) and the crowned ...

Phylogenies with estimates of divergence times are essential for investigating many evolutionary questions. In principle, "tip-dating" is arguably the most appropriate approach, with fossil and extant taxa analysed together in a single analysis, and topology and divergence times estimated simultaneously. However, "node-dating" (as used in many molecular clock analyses), in which fossil evidence is used to calibrate the age of particular nodes a priori, will probably remain the dominant approach, due to various issues with analysing morphological and molecular data together. Here, we provide a list of 25 well-justified node calibrations for primate divergences, following best practices: 16 within Haplorhini, four within Strepsirrhini, one for crown Primates, and four for older divergences within Euarchontoglires. In each case, we provide a hard minimum bound, and for 22 of these we also provide a soft maximum bound and a suggested prior distribution. For each calibrated node, we provide the age of the oldest fossil of each daughter lineage that descends from it, which allows use of the "CladeAge" method for specifying priors on node ages.

Phylogenies with estimates of divergence times are essential for investigating many evolutionary questions. In principle, "tip-dating" is arguably the most appropriate approach, with fossil and extant taxa analysed together in a single analysis, and topology and divergence times estimated simultaneously. However, "node-dating" (as used in many molecular clock analyses), in which fossil evidence is used to calibrate the age of particular nodes a priori, will probably remain the dominant approach, due to various issues with analysing morphological and molecular data together. Here, we provide a list of 25 well-justified node calibrations for primate divergences, following best practices: 16 within Haplorhini, four within Strepsirrhini, one for crown Primates, and four for older divergences within Euarchontoglires. In each case, we provide a hard minimum bound, and for 22 of these we also provide a soft maximum bound and a suggested prior distribution. For each calibrated node, we provide the age of the oldest fossil of each daughter lineage that descends from it, which allows use of the "CladeAge" method for specifying priors on node ages.

Understanding the origin and maintenance of functionally important subordinate traits is a major goal of evolutionary physiologists and ecomorphologists. Within the confines of a limbless body plan, snakes are diverse in terms of body size and ecology, but we know little about the functional traits that underlie this diversity. We used a phylogenetically diverse group of 131 snake species to examine associations between habitat use, sidewinding locomotion and constriction behaviour with the number of body vertebrae spanned by a single segment of the spinalis muscle, with total numbers of body vertebrae used as a covariate in statistical analyses. We compared models with combinations of these predictors to determine which best fit the data among all species and for the advanced snakes only (N = 114). We used both ordinary least-squares models and phylogenetic models in which the residuals were modelled as evolving by the Ornstein-Uhlenbeck process. Snakes with greater numbers of vertebrae tended to have spinalis muscles that spanned more vertebrae. Habitat effects dominated models for analyses of all species and advanced snakes only, with the spinalis length spanning more vertebrae in arboreal species and fewer vertebrae in aquatic and burrowing species. Sidewinding specialists had shorter muscle lengths than nonspecialists. The relationship between prey constriction and spinalis length was less clear. Differences among clades were also strong when considering all species, but not for advanced snakes alone. Overall, these results suggest that muscle morphology may have played a key role in the adaptive radiation of snakes.

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, ...

The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of eight bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addressed. Here, we use a dataset of 60 µCT-scanned skulls and high-density geometric morphometric methods to address the origin and patterns of variation and integration in the feeding bones of aquatic-foraging snakes. By comparing alternate superimposition protocols allowing us to ana

We provide a detailed description of the hyoid apparatus and cranial osteology of the gymnophthalmid lizard Neusticurus ecpleopus , based on a series of 11 dry skeletal preparations and 22 cleared and double-stained specimens. Articulated and disarticulated material permit detailed descriptions of isolated bones as well as the overall architecture of the skull. Individual and ontogenetic variation within N. ecpleopus is discussed. The greatest intraspecific variation is reflected in features that vary during ontogeny, including firmness of articulation between bones of the dermatocranium, thickness of individual bones, degree of elongation or expansion of processes, relative width of the parietal table, elongation of the hyoid apparatus, lateral angulation of the first ceratobranchial and relatively late appearance of the second ceratobranchial. The skull of N. ecpleopus can be regarded as generally representative of the Gymnophthalmidae, but we provide preliminary discussion of areas where variation in gymnophthalmid skull configuration is pronounced.

Background: Celastraceae is a morphologically heterogeneous family. For this reason, the inclusion of some taxa within this group is controversial. Recently this problem has become significant since its fossil record is recognized as an important source of information for evolutionary studies, especially those using molecular clocks which require a robust, reliable fossil record. Questions: What are the most reliable fossil records of Celastraceae? What morphological characters are used to assign fossils in the family? Study site and dates: Compilation of records contained in paleontological databases, and paleobotanical literature, covering publications from 1869 to 2018. Methods: Published information on the Celastraceae fossil record was compiled and analyzed using the most recent classification system and specialized literature on the family. Results: A total of 168 fossil records were examined, of which nine are proposed for use as molecular clock calibration points. Each specimen has a description based on a character set used for its identification, a photograph and/or illustration, their geological age is well supported, their geographic origin is known, and the specimens are in accredited home institutions with publicly accessible collections. Conclusions: The identification and establishment of relationships between fossil and extant taxa have important limitations that depend on the critical interpretation of morphology in a phylogenetic context. Therefore, it is essential to incorporate only those morphological studies in Celastraceae that help clarify its fossil record.

Recent molecular analyses have changed key aspects of our understanding of snake phylogeny and evolution. While many morphological groupings have been upheld, such as the alethinophidians (all living snakes excluding blindsnakes) and caenophidians (filesnakes plus colubroids), others have been convincingly overturned. In particular, the large-gaped tropidophiines are very basal alethinophidians related to Anilius, while the relatively primitive Xenopeltis and Loxocemus are the nearest relatives of pythons. The new molecular phylogeny refutes the widespread view that snake evolution involved gradual elaboration of feeding mechanisms, culminating in an advanced "macrostomatan" clade. Instead, molecular evidence suggests large gape was primitive for snakes (or at least alethinophidians), and reduced repeatedly in many basal, burrowing alethinophidians as well as further elaborated at least twice; this view is consistent with some interpretations of the snake fossil record. Some (but not all) of the new molecular clades exhibit morphological novelties that support their reality. A revised molecular clock analysis of snakes, using five robust fossil calibrations, 2 produces more recent dates for all snake lineages compared to previous molecular clock studies. These shallower dates are much more consistent with the broader fossil record of reptiles, implying far shorter ghost lineages. vertebrae totally lacking neural spines but possessing enlarged subcentral foramina, and a short stumpy tail. A few other synapomorphies, however, are not obviously correlated with general habitus, leading to greater confidence in monophyly: these include the optic foramen located anteriorly (entirely within the frontal bone), and the frontal bones which overlap the nasals (rather than vice versa). 1.3.2 Basal alethinophidians and the evolution of gape size. All living snakes apart from blindsnakes form a clade, the alethinophidians, which is robustly

Background: The thin-spined porcupine, also known as the bristle-spined rat, Chaetomys subspinosus (Olfers, 1818), the only member of its genus, figures among Brazilian endangered species. In addition to being threatened, it is poorly known, and even its taxonomic status at the family level has long been controversial. The genus Chaetomys was originally regarded as a porcupine in the family Erethizontidae, but some authors classified it as a spiny-rat in the family Echimyidae. Although the dispute seems to be settled in favor of the erethizontid advocates, further discussion of its affinities should be based on a phylogenetic framework. In the present study, we used nucleotide-sequence data from the complete mitochondrial cytochrome b gene and karyotypic information to address this issue. Our molecular analyses included one individual of Chaetomys subspinosus from the state of Bahia in northeastern Brazil, and other hystricognaths.

We compared the head skeleton (skull and lower jaw) of juvenile and adult specimens of five snake species [Anilios (=Ramphotyphlops) bicolor, Cylindrophis ruffus, Aspidites melanocephalus, Acrochordus arafurae, and Notechis scutatus] and two lizard outgroups (Ctenophorus decresii, Varanus gilleni). All major ontogenetic changes observed were documented both qualitatively and quantitatively. Qualitative comparisons were based on high-resolution micro-CT scanning of the specimens, and detailed quantitative analyses were performed using three-dimensional geometric morphometrics. Two sets of landmarks were used, one for accurate representation of the intraspecific transformations of each skull and jaw configuration, and the other for comparison between taxa. Our results document the ontogenetic elaboration of crests and processes for muscle attachment (especially for cervical and adductor muscles); negative allometry in the braincase of all taxa; approximately isometric growth of the snout of all taxa except Varanus and Anilios (positively allometric); and positive allometry in the quadrates of the macrostomatan snakes Aspidites, Acrochordus and Notechis, but also, surprisingly, in the iguanian lizard Ctenophorus. Ontogenetic trajectories from principal component analysis provide evidence for paedomorphosis in Anilios and peramorphosis in Acrochordus. Some primitive (lizard-like) features are described for the first time in the juvenile Cylindrophis. Two distinct developmental trajectories for the achievement of the macrostomatan (large-gaped) condition in adult snakes are documented, driven either by positive allometry of supratemporal and quadrate (in pythons), or of quadrate alone (in sampled caenophidians); this is consistent with hypothesised homoplasy in this adaptive complex. Certain traits (e.g. shape of coronoid process, marginal tooth counts) are more stable throughout postnatal ontogeny than others (e.g. basisphenoid keel), with implications for their reliability as phylogenetic characters.

Several studies have reported the occurrence of fossil remains of a now extinct Boa snake from the upper Pleistocene of Marie-Galante Island, French West Indies. However, these remains have never been fully investigated and no complete description of this possible new species has been published. In this paper, we try to bridge this gap by providing a
detailed morphological study of the Boa remains discovered in the three major fossil deposits of Marie-Galante Island. Our study reveals the specific morphological aspects of this fossil snake and allows us to identify it as a new species, Boa blanchardensis. We also reconstructed its body size, carried out a paleohistological investigation, and suggest that this snake may have been a dwarf species. We then discuss the possible explanation for the extinction of this snake on Marie-Galante Island and possibly also on other Guadeloupe islands.

The grass snake (Natrix natrix) is Europe's most widely distributed and, in many regions, most common snake species, with many morphologically defined subspecies. Yet, the taxonomy of grass snakes is relatively little studied and recent work has shown major conflicts between morphologically defined subspecies and phylogeographical differentiation. Using external morphology, osteological characters, and information from 13 microsatellite loci and two mitochondrial markers, we examine differentiation of the subspecies N. n. astreptophora from the North African Maghreb region, the Iberian Peninsula and neighbouring France. According to previous studies, N. n. astreptophora corresponds to a deeply divergent mitochondrial clade and constitutes the sister taxon of all remaining grass snakes. In the French Pyrenees region, there is a contact zone of N. n. astreptophora with another subspecies, N. n. helvetica. Our analyses of microsatellites and mitochondrial DNA reveal that the distribution ranges of the two taxa abut there, but both hybridize only exceptionally. Even though many morphological characters are highly variable and homoplastic in grass snakes, N. n. astreptophora differs consistently from all other grass snakes by its reddish iris coloration and in having significantly fewer ventral scales and another skull morphology. Considering further the virtual absence of gene flow between N. n. astreptophora and N. n. helvetica, and acknowledging the morphological distinctiveness of N. n. astreptophora and its sister group relationship to all remaining subspecies of grass snakes, we conclude that Natrix astreptophora (Seoane, 1884) should be recognized as a distinct species. Further research is needed to explore whether N. astreptophora is polytypic because a single sample of N. astreptophora from Tunisia turned out to be genetically highly distinct from its European conspecifics.

RESUMO O Comportamento de Constrição em Boideos: Há uma Dominância de Lado? O comportamento de constrição enfocando a dominância de lado foi estuda-da nos boídeos neotropicais Boa constrictor e Epicrates cenchria em experimen-tos de predação sobre ratos. Os dados sugeriram que não há uma tendência à do-minância de lado de constricção ao nível específico, embora esta tendência possa ocorrer ao nível individual para as duas espécies. ABSTRACT Constriction behavior focusing on side dominance was studied iIl the neotropica1 boids Boa constrictor and Epicrates cenchria preying on rats. The data showed no tendency of side dominance at specific levei a1though it may occur at individuallevel for both species.

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, ...

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation.We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.

371 Introduction 372 Morphological and molecular data 373 Methods 375 Separate analyses 375 Combined parsimony analyses 375 Combined Bayesian analyses 375 Combined likelihood analyses 376 Results 378 Separate analyses 378 Combined analyses 380 Discussion 383 Weighting morphology and molecules in parsimony and likelihood 383 Snake phylogeny and taxonomy 387