Review ["Telling the Evolutionary Time : Molecular Clocks and the Fossil Record" edited by Philip C. J. Donoghue and M. Paul Smith]

Determining the temporal scale of biological evolution has traditionally been the preserve of paleontology, with the timing of species originations and major diversifications all being read from the fossil record. However, the ages of the earliest (correctly identified) records will underestimate actual origins due to the incomplete nature of the fossil record and the necessity for lineages to have evolved sufficiently divergent morphologies in order to be distinguished. The possibility of inferring divergence times more accurately has been promoted by the idea that the accumulation of genetic change between modern lineages can be used as a molecular clock (Zuckerkandl and Pauling, 1965). In practice, though, molecular dates have often been so old as to be incongruent even with liberal readings of the fossil record. Prominent examples include inferred diversifications of metazoan phyla hundreds of millions of years before their Cambrian fossil record appearances (e.g., Nei et al., 2001) and a basal split between modern birds (Neoaves) that is almost double the age of their earliest recognizable fossils (e.g., Cooper and Penny, 1997).

Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas

The semiaquatic platypus and terrestrial echidnas (spiny anteaters) are the only living egg-laying mammals (monotremes). The fossil record has provided few clues as to their origins and the evolution of their ecological specializations; however, recent reassignment of the Early Cretaceous Teinolophos and Steropodon to the platypus lineage implies that platypuses and echidnas diverged >112.5 million years ago, reinforcing the notion of monotremes as living fossils. This placement is based primarily on characters related to a single feature, the enlarged mandibular canal, which supplies blood vessels and dense electrosensory receptors to the platypus bill. Our reevaluation of the morphological data instead groups platypus and echidnas to the exclusion of Teinolophos and Steropodon and suggests that an enlarged mandibular canal is ancestral for monotremes (partly reversed in echidnas, in association with general mandibular reduction). A multigene evaluation of the echidna–platypus divergence using both a relaxed molecular clock and direct fossil calibrations reveals a recent split of 19–48 million years ago. Platypus-like monotremes (Monotrematum) predate this divergence, indicating that echidnas had aquatically foraging ancestors that reinvaded terrestrial ecosystems. This ecological shift and the associated radiation of echidnas represent a recent expansion of niche space despite potential competition from marsupials. Monotremes might have survived the invasion of marsupials into Australasia by exploiting ecological niches in which marsupials are restricted by their reproductive mode. Morphology, ecology, and molecular biology together indicate that Teinolophos and Steropodon are basal monotremes rather than platypus relatives, and that living monotremes are a relatively recent radiation.

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

Lost in translation (and rotation) : rapid extrinsic calibration for 2D and 3D LIDARs

This paper describes a novel method for determining the extrinsic calibration parameters between 2D and 3D LIDAR sensors with respect to a vehicle base frame. To recover the calibration parameters we attempt to optimize the quality of a 3D point cloud produced by the vehicle as it traverses an unknown, unmodified environment. The point cloud quality metric is derived from Rényi Quadratic Entropy and quantifies the compactness of the point distribution using only a single tuning parameter. We also present a fast approximate method to reduce the computational requirements of the entropy evaluation, allowing unsupervised calibration in vast environments with millions of points. The algorithm is analyzed using real world data gathered in many locations, showing robust calibration performance and substantial speed improvements from the approximations.

Self-calibration of wireless cameras with restricted degrees of freedom

This paper presents an approach for the automatic calibration of low-cost cameras which are assumed to be restricted in their freedom of movement to either pan or tilt movements. Camera parameters, including focal length, principal point, lens distortion parameter and the angle and axis of rotation, can be recovered from a minimum set of two images of the camera, provided that the axis of rotation between the two images goes through the camera’s optical center and is parallel to either the vertical (panning) or horizontal (tilting) axis of the image. Previous methods for auto-calibration of cameras based on pure rotations fail to work in these two degenerate cases. In addition, our approach includes a modified RANdom SAmple Consensus (RANSAC) algorithm, as well as improved integration of the radial distortion coefficient in the computation of inter-image homographies. We show that these modifications are able to increase the overall efficiency, reliability and accuracy of the homography computation and calibration procedure using both synthetic and real image sequences

An investigation into factors affecting electron density calibration for a megavoltage cone-beam CT system

There is a growing interest in the use of megavoltage cone-beam computed tomography (MV CBCT) data for radiotherapy treatment planning. To calculate accurate dose distributions, knowledge of the electron density (ED) of the tissues being irradiated is required. In the case of MV CBCT, it is necessary to determine a calibration-relating CT number to ED, utilizing the photon beam produced for MV CBCT. A number of different parameters can affect this calibration. This study was undertaken on the Siemens MV CBCT system, MVision, to evaluate the effect of the following parameters on the reconstructed CT pixel value to ED calibration: the number of monitor units (MUs) used (5, 8, 15 and 60 MUs), the image reconstruction filter (head and neck, and pelvis), reconstruction matrix size (256 by 256 and 512 by 512), and the addition of extra solid water surrounding the ED phantom. A Gammex electron density CT phantom containing EDs from 0.292 to 1.707 was imaged under each of these conditions. The linear relationship between MV CBCT pixel value and ED was demonstrated for all MU settings and over the range of EDs. Changes in MU number did not dramatically alter the MV CBCT ED calibration. The use of different reconstruction filters was found to affect the MV CBCT ED calibration, as was the addition of solid water surrounding the phantom. Dose distributions from treatment plans calculated with simulated image data from a 15 MU head and neck reconstruction filter MV CBCT image and a MV CBCT ED calibration curve from the image data parameters and a 15 MU pelvis reconstruction filter showed small and clinically insignificant differences. Thus, the use of a single MV CBCT ED calibration curve is unlikely to result in any clinical differences. However, to ensure minimal uncertainties in dose reporting, MV CBCT ED calibration measurements could be carried out using parameter-specific calibration measurements.

Applicability of the polysulphone horizontal calibration to differently inclined dosimeters

Polysulphone (PS) dosimetry has been a widely used technique for more than 30 years to quantify the erythemally effective UV dose received by anatomic sites (personal exposure). The calibration of PS dosimeters is an important issue as their spectral response is different from the erythemal action spectrum. It is performed exposing a set of PS dosimeters on a horizontal plane and measuring the UV doses received by dosimeters using calibrated spectroradiometers or radiometers. In this study, data collected during PS field campaigns (from 2004 to 2006), using horizontal and differently inclined dosimeters, were analyzed to provide some considerations on the transfer of the horizontal calibration to differently inclined dosimeters, as anatomic sites usually are. The role of sky conditions, of the angle of incidence between the sun and the normal to the slope, and of the type of surrounding surface on the calibration were investigated. It was concluded that PS horizontal calibrations apply to differently inclined dosimeters for incidence angles up to approximately 70 degrees and for surfaces excluding ones with high albedo. Caution should be used in the application of horizontal calibrations for cases of high-incidence angle and/or high albedo surfaces.

Distinguishing new science from calibration effects in the electron-volt neutron spectrometer VESUVIO at ISIS

The "standard" procedure for calibrating the Vesuvio eV neutron spectrometer at the ISIS neutron source, forming the basis for data analysis over at least the last decade, was recently documented in considerable detail by the instrument’s scientists. Additionally, we recently derived analytic expressions of the sensitivity of recoil peak positions with respect to fight-path parameters and presented neutron–proton scattering results that together called in to question the validity of the "standard" calibration. These investigations should contribute significantly to the assessment of the experimental results obtained with Vesuvio. Here we present new results of neutron–deuteron scattering from D2 in the backscattering angular range (theata > 90 degrees) which are accompanied by a striking energy increase that violates the Impulse Approximation, thus leading unequivocally the following dilemma: (A) either the "standard" calibration is correct and then the experimental results represent a novel quantum dynamical effect of D which stands in blatant contradiction of conventional theoretical expectations; (B) or the present "standard" calibration procedure is seriously deficient and leads to artificial outcomes. For Case(A), we allude to the topic of attosecond quantumdynamical phenomena and our recent neutron scattering experiments from H2 molecules. For Case(B),some suggestions as to how the "standard" calibration could be considerably improved are made.

Online calibration of stereo rigs for long-term autonomy

Stereo-based visual odometry algorithms are heavily dependent on an accurate calibration of the rigidly fixed stereo pair. Even small shifts in the rigid transform between the cameras can impact on feature matching and 3D scene triangulation, adversely affecting pose estimates and applications dependent on long-term autonomy. In many field-based scenarios where vibration, knocks and pressure change affect a robotic vehicle, maintaining an accurate stereo calibration cannot be guaranteed over long periods. This paper presents a novel method of recalibrating overlapping stereo camera rigs from online visual data while simultaneously providing an up-to-date and up-to-scale pose estimate. The proposed technique implements a novel form of partitioned bundle adjustment that explicitly includes the homogeneous transform between a stereo camera pair to generate an optimal calibration. Pose estimates are computed in parallel to the calibration, providing online recalibration which seamlessly integrates into a stereo visual odometry framework. We present results demonstrating accurate performance of the algorithm on both simulated scenarios and real data gathered from a wide-baseline stereo pair on a ground vehicle traversing urban roads.

Calibration of the electron volt spectrometer, a deep inelastic neutron scattering spectrometer at the ISIS pulsed neutron spallation source

The electron Volt Spectrometer (eVS) is an inverse geometry filter difference spectrometer that has been optimised to measure the single atom properties of condensed matter systems using a technique known as Neutron Compton Scattering (NCS) or Deep Inelastic Neutron Scattering (DINS). The spectrometer utilises the high flux of epithermal neutrons that are produced by the ISIS neutron spallation source enabling the direct measurement of atomic momentum distributions and ground state kinetic energies. In this paper the procedure that is used to calibrate the spectrometer is described. This includes details of the method used to determine detector positions and neutron flight path lengths as well as the determination of the instrument resolution. Examples of measurements on 3 different samples are shown, ZrH2, 4He and Sn which show the self-consistency of the calibration procedure.

Calibration of the electron volt spectrometer, a deep inelastic neutron scattering spectrometer at the ISIS pulsed neutron spallation source

The electron Volt Spectrometer (eVS) is an inverse geometry filter difference spectrometer that has been optimised to measure the single atom properties of condensed matter systems using a technique known as Neutron Compton Scattering (NCS) or Deep Inelastic Neutron Scattering (DINS). The spectrometer utilises the high flux of epithermal neutrons that are produced by the ISIS neutron spallation source enabling the direct measurement of atomic momentum distributions and ground state kinetic energies. In this paper the procedure that is used to calibrate the spectrometer is described. This includes details of the method used to determine detector positions and neutron flight path lengths as well as the determination of the instrument resolution. Examples of measurements on 3 different samples are shown, ZrH2, 4He and Sn which show the self-consistency of the calibration procedure.

Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene–Holocene cave deposit on Kangaroo Island, South Australia

Fossils and sediments preserved in caves are an excellent source of information for investigating impacts of past environmental changes on biodiversity. Until recently studies have relied on morphology-based palaeontological approaches, but recent advances in molecular analytical methods offer excellent potential for extracting a greater array of biological information from these sites. This study presents a thorough assessment of DNA preservation from late Pleistocene–Holocene vertebrate fossils and sediments from Kelly Hill Cave Kangaroo Island, South Australia. Using a combination of extraction techniques and sequencing technologies, ancient DNA was characterised from over 70 bones and 20 sediment samples from 15 stratigraphic layers ranging in age from >20 ka to ∼6.8 ka. A combination of primers targeting marsupial and placental mammals, reptiles and two universal plant primers were used to reveal genetic biodiversity for comparison with the mainland and with the morphological fossil record for Kelly Hill Cave. We demonstrate that Kelly Hill Cave has excellent long-term DNA preservation, back to at least 20 ka. This contrasts with the majority of Australian cave sites thus far explored for ancient DNA preservation, and highlights the great promise Kangaroo Island caves hold for yielding the hitherto-elusive DNA of extinct Australian Pleistocene species.

Autonomous movement-driven place recognition calibration for generic multi-sensor robot platforms

In this paper we present a method for autonomously tuning the threshold between learning and recognizing a place in the world, based on both how the rodent brain is thought to process and calibrate multisensory data and the pivoting movement behaviour that rodents perform in doing so. The approach makes no assumptions about the number and type of sensors, the robot platform, or the environment, relying only on the ability of a robot to perform two revolutions on the spot. In addition, it self-assesses the quality of the tuning process in order to identify situations in which tuning may have failed. We demonstrate the autonomous movement-driven threshold tuning on a Pioneer 3DX robot in eight locations spread over an office environment and a building car park, and then evaluate the mapping capability of the system on journeys through these environments. The system is able to pick a place recognition threshold that enables successful environment mapping in six of the eight locations while also autonomously flagging the tuning failure in the remaining two locations. We discuss how the method, in combination with parallel work on autonomous weighting of individual sensors, moves the parameter dependent RatSLAM system significantly closer to sensor, platform and environment agnostic operation.