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To model distribution ranges, the most popular methods of phylogenetic biogeography divide Earth into a handful of predefined areas. Other methods use explicit geographic ranges, but unfortunately, these methods assume a static Earth, ignoring the effects of plate tectonics and the changes in the landscape. To address this limitation, I propose a method that uses explicit geographic ranges and incorporates a plate motion model and a paleolandscape model directly derived from the models used by geologists in their tectonic and paleogeographic reconstructions. The underlying geographic model is a high-resolution pixelation of a spherical Earth. Biogeographic inference is based on diffusion, approximates the effects of the landscape, uses a time-stratified model to take into account the geographic changes, and directly integrates over all probable histories. By using a simplified stochastic mapping algorithm, it is possible to infer the ancestral locations as well as the distance traveled by the ancestral lineages. For illustration, I applied the method to an empirical phylogeny of the Sapindaceae plants. This example shows that methods based on explicit geographic data, coupled with high-resolution paleogeographic models, can provide detailed reconstructions of the ancestral areas but also include inferences about the probable dispersal paths and diffusion speed across the taxon history. The method is implemented in the program PhyGeo.
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Biogeographic studies have generally relied on methods that use a few, large predefined areas, which may overlook fine-scale patterns. Here we test previous hypotheses about the biogeographic history of a diverse bat clade regarding its association with major Neotropical geological formations, particularly the Antilles, the South American Dry Diagonal, the Andes and the Panamanian land bridge, by applying a recently available method that uses actual distributions instead of predefined areas. We compiled and curated spatially explicit, georeferenced data of 173 bat species (Mammalia: Chiroptera: Noctilionoidea) from the online database Global Biodiversity Information Facility. By taking a previous comprehensive phylogeny as an evolutionary framework, we performed computationally intensive analyses using the Geographically-explicit Event Model. This method uses the observed species distributions to reconstruct the ancestral areas and biogeographic events at each phylogeny node. We found that sympatric speciation was the most frequently reconstructed event, and involved mainly the Panamanian Isthmus and northern South America (SA), but all sympatry reconstructions were different and specific to each node. Allopatric events were important in the Andes; vicariance caused both west/east and north/south disjunctions that went unnoticed previously. Founder events indicated bidirectional dispersal between the mainland and the Antilles since the Miocene, and across the incomplete Panamanian bridge and the SA Dry Diagonal since the early Pliocene. Overall, we found support for previous hypotheses on the influence of major Neotropical paleogeographic events in the diversification of the group, but additionally revealed multi-scale patterns that are embedded within the mainland and were previously overlooked. Our results highlight a trans-isthmian centre of diversification in the biogeographic history of Noctilionoidea including the Panamanian Isthmus and Northern SA.
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A likelihood method that approximates the behaviour of implied weighting is described. This approach provides a likelihood perspective on several aspects of implied weighting, such as guidance for the choice of concavity values, a justification to use different concavities for different numbers of taxa, and a natural basis for extended implied weighting. In this approach, the number of free parameters in the estimation depends on C, the number of characters (in contrast to the standard Mk model, which estimates 2T-3 parameters for T taxa). Depending on the characteristics of the dataset, the likelihood obtained with this approach may in some cases be similar or superior to that of the Mk model, but with fewer parameters being adjusted. Because of that tradeoff, testing against the Mk model by means of the Akaike information criterion on a set of 182 morphological datasets indicated many cases (36) in which the likelihood approximation to implied weighting is the best method, from an information-theoretic point of view. Given that it is expected to produce (almost) the same results as this maximum-likelihood approximation, implied weighting can therefore be seen as a valid alternative to the Mk model often used for morphological datasets, on the basis of a criterion for model fit widely advocated by likelihoodists.
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One of the lasting controversies in phylogenetic inference is the degree to which specific evolutionary models should influence the choice of methods. Model-based approaches to phylogenetic inference (likelihood, Bayesian) are defended on the premise that without explicit statistical models there is no science, and parsimony is defended on the grounds that it provides the best rationalization of the data, while refraining from assigning specific probabilities to trees or character-state reconstructions. Authors who favour model-based approaches often focus on the statistical properties of the methods and models themselves, but this is of only limited use in deciding the best method for phylogenetic inference-such decision also requires considering the conditions of evolution that prevail in nature. Another approach is to compare the performance of parsimony and model-based methods in simulations, which traditionally have been used to defend the use of models of evolution for DNA sequences. Some recent papers, however, have promoted the use of model-based approaches to phylogenetic inference for discrete morphological data as well. These papers simulated data under models already known to be unfavourable to parsimony, and modelled morphological evolution as if it evolved just like DNA, with probabilities of change for all characters changing in concert along tree branches. The present paper discusses these issues, showing that under reasonable and less restrictive models of evolution for discrete characters, equally weighted parsimony performs as well or better than model-based methods, and that parsimony under implied weights clearly outperforms all other methods.
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Scincidae is one of the most species-rich and cosmopolitan clades of squamate reptiles. Abundant disarticulated fossil material has also been attributed to this group, however, no complete pre-Cenozoic crown-scincid specimens have been found. A specimen in Burmite (99 MYA) is the first fossil that can be unambiguously referred to this clade. Our analyses place it as nested within extant skinks, supported by the presence of compound osteoderms formed by articulated small ostedermites. The specimen has a combination of dorsal and ventral compound osteoderms and overlapping cycloid scales that is limited to skinks. We propose that this type of osteoderm evolved as a response to an increased overlap of scales, and to reduced stiffness of the dermal armour. Compound osteoderms could be a key innovation that facilitated diversification in this megadiverse family.
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Ámbar , Fósiles , Animales , Fósiles/anatomía & histología , Lagartos/anatomía & histología , Filogenia , Evolución BiológicaRESUMEN
We here report on a well-preserved juvenile lizard specimen in Albian amber (ca. 110 mya) from the Hkamti site (Myanmar). This new taxon is represented by an articulated skull and the anterior portion of the trunk, including the pectoral girdle and forelimbs. The scleral ossicles and eyelid are also visible, and the specimen exhibits pristine detail of the integument (of both head and body). In a combined molecular and morphological analysis, it was consistently recovered as a scincoid lizard (Scinciformata), as sister to Tepexisaurus + Xantusiidae. However, the phylogenetic position of the new taxon should be interpreted with caution as the holotype is an immature individual. We explored the possibility of miscoding ontogenetically variable characters by running alternative analyses in which these characters were scored as missing data for our taxon. With the exception of one tree, in which it was sister to Amphisbaenia, the specimen was recovered as a Pan-xantusiid. Moreover, we cannot rule out the possibility that it represents a separate lineage of uncertain phylogenetic position, as it is the case for many Jurassic and Cretaceous taxa. Nonetheless, this fossil offers a rare opportunity to glimpse the external appearance of one group of lizards during the Early Cretaceous.
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Ámbar , Fósiles/anatomía & histología , Integumento Común/anatomía & histología , Lagartos/anatomía & histología , Animales , Evolución Biológica , Fósiles/diagnóstico por imagen , Integumento Común/diagnóstico por imagen , Lagartos/genética , Mianmar , Filogenia , Microtomografía por Rayos XRESUMEN
Based on Hovenkamp's ideas on historical biogeography, we present a method for analysis of taxon history, spatial analysis of vicariance, which uses observed distributions as data, thus requiring neither predefined areas nor assumptions of hierarchical relations between areas. The method is based on identifying sister nodes with disjunct (allopatric/vicariant) distributions. To do this across the tree, internal nodes are assigned distributions (as the sum of the distributions of the descendant nodes). When distributions are less than ideal, ignoring the distribution of the problematic node(s) when assigning a distribution to their ancestors may allow us to consider additional sister nodes (i.e. those resulting from splits basal to the problematic node) as having disjunct distributions. The optimality criterion seeks to find the best (possibly weighted) compromise between the maximum possible number of disjunct sister nodes and the minimum number of eliminated distributions. The method can also take overlap into account. The methodology presented is implemented in VIP, a computer program available at http://www.zmuc.dk/public/phylogeny/vip. © The Willi Hennig Society 2011.
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Oculudentavis khaungraae was described based on a tiny skull trapped in amber. The slender tapering rostrum with retracted narial openings, large eyes, and short vaulted braincase led to its identification as the smallest avian dinosaur on record, comparable to the smallest living hummingbirds. Despite its bird-like appearance, Oculudentavis showed several features inconsistent with its original phylogenetic placement. Here, we describe a more complete specimen that demonstrates Oculudentavis is actually a bizarre lizard of uncertain position. The new specimen is described as a new species within the genus Oculudentavis. The new interpretation and phylogenetic placement highlight a rare case of convergent evolution in skull proportions but apparently not in morphological characters. Our results re-affirm the importance of Myanmar amber in yielding unusual taxa from a forest ecosystem rarely represented in the fossil record.
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Dinosaurios , Fósiles , Lagartos , Ámbar , Animales , Aves , Dinosaurios/anatomía & histología , Ecosistema , Lagartos/anatomía & histología , FilogeniaRESUMEN
Albanerpetontids are tiny, enigmatic fossil amphibians with a distinctive suite of characteristics, including scales and specialized jaw and neck joints. Here we describe a new genus and species of albanerpetontid, represented by fully articulated and three-dimensional specimens preserved in amber. These specimens preserve skeletal and soft tissues, including an elongated median hyoid element, the tip of which remains embedded in a distal tongue pad. This arrangement is very similar to the long, rapidly projecting tongue of chameleons. Our results thus suggest that albanerpetontids were sit-and-wait ballistic tongue feeders, extending the record of this specialized feeding mode by around 100 million years.
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Anfibios/clasificación , Extinción Biológica , Fósiles , Cráneo/anatomía & histología , Ámbar , Anfibios/anatomía & histología , Animales , Mianmar , FilogeniaRESUMEN
Faith and Trueman [Syst. Biol. (2001) 331] recently proposed "Profile Parsimony" (PP) as a new form of phylogenetic analysis, but it is equivalent to the Implied Weights (IW) method when certain functions are used. The PP method cannot accommodate missing/inapplicable cells and/or multistate characters. Finally we demonstrate that, as defined, PP scores are not random, and there is no need to generate random trees as proposed by Faith and Trueman.