Time resolved fission in metal clusters

We explore from a theoretical point of view pump and probe (P&P) analysis for fission of metal clusters where probe pulses are generalized to allow for scanning various frequencies. We show that it is possible to measure the time the system needs to develop to scission. This is achieved by a proper choice of both delay and frequency of the probe pulse. A more detailed analysis even allows to access the various intermediate stages of the fission process.Comment: 4 pages, 4 figure

The measure of success: geographic isolation promotes diversification in Pachydactylus geckos

Abstract Background Geckos of the genus Pachydactylus and their close relatives comprise the most species-rich clade of lizards in sub-Saharan Africa. Many explanations have been offered to explain species richness patterns of clades. In the Pachydactylus group, one possible explanation is a history of diversification via geographic isolation. If geographic isolation has played a key role in facilitating diversification, then we expect species in more species-rich subclades to have smaller ranges than species in less diverse subclades. We also expect traits promoting geographic isolation to be correlated with small geographic ranges. In order to test these expectations, we performed phylogenetic analyses and tested for correlations among body size, habitat choice, range sizes, and diversification rates in the Pachydactylus group. Results Both body size and habitat use are inferred to have shifted multiple times across the phylogeny of the Pachydactylus group, with large size and generalist habitat use being ancestral for the group. Geographic range size is correlated with both of these traits. Small-bodied species have more restricted ranges than large-bodied species, and rock-dwelling species have more restricted ranges than either terrestrial or generalist species. Rock-dwelling and small body size are also associated with higher rates of diversification, and subclades retaining ancestral conditions for these traits are less species rich than subclades in which shifts to small body size and rocky habitat use have occurred. The phylogeny also illustrates inadequacies of the current taxonomy of the group. Conclusions The results are consistent with a model in which lineages more likely to become geographically isolated diversify to a greater extent, although some patterns also resemble those expected of an adaptive radiation in which ecological divergence acts as a driver of speciation. Therefore, the Pachydactylus group may represent an intermediate between clades in which radiation is adaptive versus those in which it is non-adaptive.http://deepblue.lib.umich.edu/bitstream/2027.42/135714/1/12862_2016_Article_846.pd

Einstein-aether theory, violation of Lorentz invariance, and metric-affine gravity

We show that the Einstein-aether theory of Jacobson and Mattingly (J&M) can be understood in the framework of the metric-affine (gauge theory of) gravity (MAG). We achieve this by relating the aether vector field of J&M to certain post-Riemannian nonmetricity pieces contained in an independent linear connection of spacetime. Then, for the aether, a corresponding geometrical curvature-square Lagrangian with a massive piece can be formulated straightforwardly. We find an exact spherically symmetric solution of our model.Comment: Revtex4, 38 pages, 1 figur

Gecko diversity : a history of global discovery

1935 gecko species (and 224 subspecies) were known in December 2019 in seven families and 124 genera. These nearly 2000 species were described by ~950 individuals of whom more than 100 described more than 10 gecko species each. Most gecko species were discovered during the past 40 years. The primary type specimens of all currently recognized geckos (including subspecies) are distributed over 161 collections worldwide, with 20 collections having about two thirds of all primary types. The primary type specimens of about 40 gecko taxa have been lost or unknown. The phylogeny of geckos is well studied, with DNA sequences being available for ~76% of all geckos (compared to ~63% in other reptiles) and morphological characters now being collected in databases. Geographically, geckos occur on five continents and many islands but are most species-rich in Australasia (which also houses the greatest diversity of family-level taxa), Southeast Asia, Africa, Madagascar, and the West Indies. Among countries, Australia has the highest number of geckos (241 species), with India, Madagascar, and Malaysia being the only other countries with more than 100 described species each. As expected, when correcting for land area, countries outside the tropics have fewer geckos

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods

The development of cephalic armor in the tokay gecko (Squamata: Gekkonidae: Gekko gecko)

Armored skin resulting from the presence of bony dermal structures, osteoderms, is an exceptional phenotype in gekkotans (geckos and flap‐footed lizards) only known to occur in three genera: Geckolepis, Gekko, and Tarentola. The Tokay gecko (Gekko gecko LINNAEUS 1758) is among the best‐studied geckos due to its large size and wide range of occurrence, and although cranial dermal bone development has previously been investigated, details of osteoderm development along a size gradient remain less well‐known. Likewise, a comparative survey of additional species within the broader Gekko clade to determine the uniqueness of this trait has not yet been completed. Here, we studied a large sample of gekkotans (38 spp.), including 18 specimens of G. gecko, using X‐rays and high‐resolution computed tomography for visualizing and quantifying the dermal armor in situ. Results from this survey confirm the presence of osteoderms in a second species within this genus, Gekko reevesii GRAY 1831, which exhibits discordance in timing and pattern of osteoderm development when compared with its sister taxon, G. gecko. We discuss the developmental sequence of osteoderms in these two species and explore in detail the formation and functionality of these enigmatic dermal ossifications. Finally, we conducted a comparative analysis of endolymphatic sacs in a wide array of gekkotans to explore previous ideas regarding the role of osteoderms as calcium reservoirs. We found that G. gecko and other gecko species with osteoderms have highly enlarged endolymphatic sacs relative to their body size, when compared to species without osteoderms, which implies that these membranous structures might fulfill a major role of calcium storage even in species with osteoderms.Distribution of osteoderms in the skull of a large sized Tokay gecko (Gekko gecko).Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153558/1/jmor21092_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153558/2/jmor21092.pd

The Cotton tensor in Riemannian spacetimes

Recently, the study of three-dimensional spaces is becoming of great interest. In these dimensions the Cotton tensor is prominent as the substitute for the Weyl tensor. It is conformally invariant and its vanishing is equivalent to conformal flatness. However, the Cotton tensor arises in the context of the Bianchi identities and is present in any dimension. We present a systematic derivation of the Cotton tensor. We perform its irreducible decomposition and determine its number of independent components for the first time. Subsequently, we exhibit its characteristic properties and perform a classification of the Cotton tensor in three dimensions. We investigate some solutions of Einstein's field equations in three dimensions and of the topologically massive gravity model of Deser, Jackiw, and Templeton. For each class examples are given. Finally we investigate the relation between the Cotton tensor and the energy-momentum in Einstein's theory and derive a conformally flat perfect fluid solution of Einstein's field equations in three dimensions.Comment: 27 pages, revtex

Reappraising the Evolutionary History of the Largest Known Gecko, the Presumably Extinct \u3cem\u3eHoplodactylus delcourti\u3c/em\u3e, via High-Throughput Sequencing of Archival DNA

Hoplodactylus delcourti is a presumably extinct species of diplodactylid gecko known only from a single specimen of unknown provenance. It is by far the largest known gekkotan, approximately 50% longer than the next largest-known species. It has been considered a member of the New Zealand endemic genus Hoplodactylus based on external morphological features including shared toe pad structure. We obtained DNA from a bone sample of the only known specimen to generate high-throughput sequence data suitable for phylogenetic analysis of its evolutionary history. Complementary sequence data were obtained from a broad sample of diplodactylid geckos. Our results indicate that the species is not most closely related to extant Hoplodactylus or any other New Zealand gecko. Instead, it is a member of a clade whose living species are endemic to New Caledonia. Phylogenetic comparative analyses indicate that the New Caledonian diplodactylid clade has evolved significantly more disparate body sizes than either the Australian or New Zealand clades. Toe pad structure has changed repeatedly across diplodactylids, including multiple times in the New Caledonia clade, partially explaining the convergence in form between H. delcourti and New Zealand Hoplodactylus. Based on the phylogenetic results, we place H. delcourti in a new genus

The Angolan bushveld lizards, genus Heliobolus Fitzinger, 1843 (Squamata: Lacertidae): Integrative taxonomy and the description of two new species

The genus Heliobolus comprises four recognized species, all endemic to sub-Saharan Africa. Of these, only Heliobolus lugubris occurs in southern Africa, its distribution extending from Angola in the west to Mozambique in the east and reaching as far south as parts of northern South Africa. Like many of the reptile species that occur in southern Africa, Heliobolus lugubris is poorly studied, and preliminary investigation suggested that it may contain cryptic diversity. The present work focusses on the Angolan population of H. lugubris and uses an integrative taxonomic approach based on morphological, coloration and DNA sequence data. The results indicate that some of the current and historical specimens of H. lugubris from Angola do not correspond to the nominotypical form, and that differences between specimens suggest the presence of two additional species, described here as Heliobolus bivari sp. nov. from the southernmost xeric/desertic regions and plateau of Namibe Province, southwestern Angola and H. crawfordi sp. nov. from the Serra da Neve inselberg north through the sub-desert coastal regions of northern Namibe, Benguela, and Kwanza Sul provinces. Nominotypical Heliobolus lugubris is confirmed to occur in Cuando Cubango Province, southeastern Angola

Exposure of African ape sites to climate change impacts

Large gaps remain in our understanding of the vulnerability of specific animal taxa and regions to climate change, especially regarding extreme climate impact events. Here, we assess African apes, flagship and highly important umbrella species for sympatric biodiversity. We estimated past (1981–2010) and future exposure to climate change impacts across 363 sites in Africa for RCP2.6 and RCP6.0 for near term (2021–2050) and long term (2071–2099). We used fully harmonized climate data and data on extreme climate impact events from the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP). Historic data show that 171 sites had positive temperature anomalies for at least nine of the past ten years with the strongest anomalies (up to 0.56°C) estimated for eastern chimpanzees. Climate projections suggest that temperatures will increase across all sites, while precipitation changes are more heterogeneous. We estimated a future increase in heavy precipitation events for 288 sites, and an increase in the number of consecutive dry days by up to 20 days per year (maximum increase estimated for eastern gorillas). All sites will be frequently exposed to wildfires and crop failures in the future, and the latter could impact apes indirectly through increased deforestation. 84% of sites are projected to be exposed to heatwaves and 78% of sites to river floods. Tropical cyclones and droughts were only projected for individual sites in western and central Africa. We further compiled available evidence on how climate change impacts could affect apes, for example, through heat stress and dehydration, a reduction in water sources and fruit trees, and reduced physiological performance, body condition, fertility, and survival. To support necessary research on the sensitivity and adaptability of African apes to climate change impacts, and the planning and implementation of conservation measures, we provide detailed results for each ape site on the open-access platform A.P.E.S. Wiki