Clock Estimates Research Articles

Cyanobacteria and biogeochemical cycles through Earth history.

Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis, transforming the biology and chemistry of our planet. Genomic and evolutionary studies have revolutionized our understanding of early oxygenic phototrophs, complementing and dramatically extending inferences from the geologic record. Molecular clock estimates point to a Paleoarchean origin (3.6-3.2 billion years ago, bya) of the core proteins of Photosystem II (PSII) involved in oxygenic photosynthesis and a Mesoarchean origin (3.2-2.8 bya) for the last common ancestor of modern cyanobacteria. Nonetheless, most extant cyanobacteria diversified after the Great Oxidation Event (GOE), an environmental watershed ca. 2.45 bya made possible by oxygenic photosynthesis. Throughout their evolutionary history, cyanobacteria have played a key role in the global carbon cycle.

<i>Corrigendum to:</i> Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus <i>Stenopelmatus</i> (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data

The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American <i>Ammopelmatus</i>, and the Mexican, and central and northern South American <i>Stenopelmatus</i>. The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of <i>Stenopelmatus</i> is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of <i>Stenopelmatus</i>, with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within <i>Stenopelmatus</i>. Based on our results, we propose the existence of four species-groups within the genus (the <i>faulkneri</i>, <i>talpa</i>, Central America and <i>piceiventris</i> species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on <i>Stenopelmatus</i> to clarify its actual species richness and evolutionary history in Mesoamerica.

LS-VCE Applied to Stochastic Modeling of GNSS Observation Noise and Process Noise

Stochastic models play a crucial role in global navigation satellite systems (GNSS) data processing. Many studies contribute to the stochastic modeling of GNSS observation noise, whereas few studies focus on the stochastic modeling of process noise. This paper proposes a method that is able to jointly estimate the variances of observation noise and process noise. The method is flexible since it is based on the least-squares variance component estimation (LS-VCE), enabling users to estimate the variance components that they are specifically interested in. We apply the proposed method to estimate the variances for the dual-frequency GNSS observation noise and for the process noise of the receiver code bias (RCB). We also investigate the impact of the stochastic model upon parameter estimation, ambiguity resolution, and positioning. The results show that the precision of GNSS observations differs in systems and frequencies. Among the dual-frequency GPS, Galileo, and BDS code observations, the precision of the BDS B3 observations is highest (better than 0.2 m). The precision of the BDS phase observations is better than two millimeters, which is also higher than that of the GPS and Galileo observations. For all three systems, the RCB process noise ranges from 0.5 millimeters to 1 millimeter, with a data sampling rate of 30 s. An improper stochastic model of the observation noise results in an unreliable ambiguity dilution of precision (ADOP) and position dilution of precision (PDOP), thus adversely affecting the assessment of the ambiguity resolution and positioning performance. An inappropriate stochastic model of RCB process noise disturbs the estimation of the receiver clock and the ionosphere delays and is thus harmful for timing and ionosphere retrieval applications.

Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus

The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American Ammopelmatus, and the Mexican, and central and northern South American Stenopelmatus. The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of Stenopelmatus is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of Stenopelmatus, with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within Stenopelmatus. Based on our results, we propose the existence of four species-groups within the genus (the faulkneri, talpa, Central America and piceiventris species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on Stenopelmatus to clarify its actual species richness and evolutionary history in Mesoamerica.

On vectorial integer bootstrapping implementations in the estimation of satellite orbits and clocks based on small global networks

The estimation of satellite orbits and clocks plays a central role in different Global Navigation Satellite System (GNSS) domains, e.g. precise positioning or time transfer. Such products can be computed in the process of Orbit Determination and Time Synchronization (ODTS), which relies on a network of ground-based stations, well distributed around the globe. The mm-level precision of carrier-phase measurements is exploited in this network estimation following a correct resolution of their ambiguities. For several stations, satellites and/or signals, thousands of ambiguities have to be processed, which means having to deal with high-dimensional ambiguity resolution (HDAR) problems. In this research work, we firstly account for the impact of ambiguity resolution in a varying network size, based on GPS-only, Galileo-only and GPS+Galileo configurations. Using 25 or more stations, the accuracy (1D RMS orbital errors) of fixed solutions reaches a plateau at 1–2 cm. Hence, we focus on a small global network of 14 stations, where the model strength decreases, so does the reliability of the ambiguity fixing process and advantages over a float solution might become less evident. In order to allow reliable HDAR, two implementations of the Vectorial Integer Bootstrapping estimator are presented and evaluated with respect to their scalar counterpart. Finally, it is shown how the proposed fixing processes are more robust, still very efficient, and on certain days they provide a large improvement to satellite products. The orbital results are ultimately validated by considering the satellite midnight discontinuity errors over a 3-month period in 2019.

Combined BDS-2/BDS-3 real-time satellite clock estimation with the overlapping B1I/B3I signals

With the deployment of the global BeiDou navigation satellite system (BDS-3) constellation completed, the positioning service performance is significantly improved relative to the regional system (BDS-2). As one of the key prerequisite products for precise point positioning (PPP), the combined BDS-2/BDS-3 real-time satellite clock estimation method is investigated in this study. Since the code hardware delays of BDS-2/BDS-3 satellites might be inconsistent for some receiver types, the inter-system bias (ISB) is considered in the combination although the overlapping B1I/B3I signal is employed. The combination processing is comprehensively evaluated in terms of satellite tracking coverage, clock precision, and convergence time. The experiment results indicate that the standard deviation (STD) precision of the estimated clocks for BDS-2 medium Earth orbit (MEO) satellites is improved by 52.0% from 0.150 ns to 0.072 ns due to the improvement of satellite tracking coverage. Introducing the ISB parameter as piece-wise constants improves the STD of all clocks from 0.076 ns to 0.067 ns and BDS-3 clocks achieve a significant improvement from 0.065 ns to 0.053 ns. The real-time clock estimation is demonstrated to be robust for the clock datum transformation, and it converges after one hour to a stable precision but needs a long time to achieve the best performance. The BDS real-time clocks are estimated with the proposed strategy to support real-time PPP based on the predicted satellite orbits. Results show that the clock STD is about 0.1 ns for most BDS satellites and the positioning accuracy of about 10 cm is achieved after the convergence time of about half an hour. The clock precision for BDS-2 geostationary Earth orbit (GEO) satellites is degraded to 0.303 ns due to the impact of poor orbit prediction errors. The exclusion of GEO satellites improves the positioning accuracy by about 15% and reduces the convergence time by 22–34%.

A multi‐frequency method to improve the long‐term estimation of GNSS clock corrections and phase biases

<h3>Abstract</h3> The space segment of the Global Navigation Satellite System (GNSS) is equipped with highly stable atomic clocks. In order to use these clocks as references, their time offsets must be estimated from ground measurements as accurately as possible. This work presents a multi-frequency and multi-constellation method for estimating satellite and receiver clock corrections, starting from unambiguous, uncombined, and undifferenced carrier-phase measurements. A byproduct of the estimation process is phase biases (i.e., the hardware delays of the carrier-phase measurements occurring at receivers and satellites). The stability and predictability of our clock estimates for receivers and satellites (GPS and Galileo) are compared with those obtained by the International GNSS Service (IGS), whereas the phase biases are assessed against two independent determinations involving combinations of carrier-phase measurements. We conclude that the method reduces day boundary discontinuities in the clock corrections, and that the estimated phase biases reproduce variabilities already observed by other authors.

The Tuokko version of the Clock Drawing Test: A validation study in the Greek population

ABSTRACT Introduction The present study aims to be the first to validate the Tuokko version of the Clock Drawing Test (CDT) and estimate its cutoff score after its translation into the Greek language and administration in the Greek population. Methods One hundred and thirty-two individuals participated in this study [60 with Good Cognitive Health (GCH), 24 with Parkinson’s Disease (PD), 24 with Parkinson’s Disease Dementia (PDD) and 24 with Alzheimer’s Disease (AD)]. The CDT was administered to all participants. Additionally, the cognitive and mental status of the sample were estimated through the use of the Mini Mental State Examination (MMSE), Abbreviated Mental Test Score (AMTS), Arizona Battery for Communication Disorders of Dementia (ABCD), Instrumental Activities of Daily Living (IADL), the Neuropsychiatric Inventory (H-NPI) and the Geriatric Depression Scale −15 (GDS-15). Results Statistically significant differences were found between all groups on the CDT, with AD patients having lower scores than all subgroups in the study. The CDT showed a high internal consistency (Cronbach’s alpha = 0.832). The ROC analysis provided a cutoff point equal to 4.00 (AUC: 0.821, p < 0.001) between the Cognitively Unimpaired Group (CUG: GCH and PD group) and the Cognitively Impaired Group (CIG: PPD and AD patients), 5.00 (AUC: 0.845, p < 0.001) between the GCH group and the PDD group, and 4.00 (AUC: 0.780, p < 0.001) between the GCH group and the AD group. Finally, the cutoff point between the PD group and the PDD group was 4.00 (AUC: 0.896, p < 0.005), and 3.00 (AUC: 0.899, p < 0.001) between the PD group and the AD group. Significant positive Pearson’s correlations were observed between CDT and MMSE (r = 0.808, p < 0.001), CDT and AMTS (r = 0.688, p < 0.001), CDT and ABCD (r = 0.770, p < 0.001), CDT and the ABCD Visuospatial Construction subdomain (r = 0.880, p < 0.001); while a negative correlation was found between CDT and IADL (r = −0.627, p < 0.001) between the CUG and the CIG groups. Conclusion Given the results obtained, the CDT appears to be a clinically valid screening instrument for the assessment of visuospatial abilities, with high reliability in Greek populations with cognitive impairment.

Impact of Large Granular Lymphocyte Leukemia on Blood DNA Methylation and Epigenetic Clock Modeling in Fischer 344 Rats.

Age-dependent differences in methylation at specific cytosine-guanine (CpG) sites have been used in "epigenetic clock" formulas to predict age. Deviations of epigenetic age from chronological age are informative of health status and are associated with adverse health outcomes, including mortality. In most cases, epigenetic clocks are performed on methylation from DNA extracted from circulating blood cells. However, the effect of neoplastic cells in the circulation on estimation and interpretation of epigenetic clocks is not well understood. Here, we explored this using Fischer 344 (F344) rats, a strain that often develops large granular lymphocyte leukemia (LGLL). We found clear histological markers of LGLL pathology in the spleens and livers of 27 out of 61 rats aged 17-27 months. We assessed DNA methylation by reduced representation bisulfite sequencing with coverage of 3 million cytosine residues. Although LGLL broadly increased DNA methylation variability, it did not change epigenetic aging. Despite this, the inclusion of rats with LGLL in clock training sets significantly altered predictor selection probability at 83 of 121 commonly utilized CpG sites. Furthermore, models trained on rat samples that included individuals with LGLL had greater absolute age error than those trained exclusively rats free of LGLL (39% increase; p < .0001). We conclude that the epigenetic signals for aging and LGLL are distinct, such that LGLL assessment is not necessary for valid measures of epigenetic age in F344 rats. The precision and architecture of constructed epigenetic clock formulas, however, can be influenced by the presence of neoplastic hematopoietic cells in training set populations.

Fossil evidence unveils an early Cambrian origin for Bryozoa

Bryozoans (also known as ectoprocts or moss animals) are aquatic, dominantly sessile, filter-feeding lophophorates that construct an organic or calcareous modular colonial (clonal) exoskeleton1–3. The presence of six major orders of bryozoans with advanced polymorphisms in lower Ordovician rocks strongly suggests a Cambrian origin for the largest and most diverse lophophorate phylum2,4–8. However, a lack of convincing bryozoan fossils from the Cambrian period has hampered resolution of the true origins and character assembly of the earliest members of the group. Here we interpret the millimetric, erect, bilaminate, secondarily phosphatized fossil Protomelission gatehousei9 from the early Cambrian of Australia and South China as a potential stem-group bryozoan. The monomorphic zooid capsules, modular construction, organic composition and simple linear budding growth geometry represent a mixture of organic Gymnolaemata and biomineralized Stenolaemata character traits, with phylogenetic analyses identifying P. gatehousei as a stem-group bryozoan. This aligns the origin of phylum Bryozoa with all other skeletonized phyla in Cambrian Age 3, pushing back its first occurrence by approximately 35 million years. It also reconciles the fossil record with molecular clock estimations of an early Cambrian origination and subsequent Ordovician radiation of Bryozoa following the acquisition of a carbonate skeleton10–13.

Correction to: Inclusion of GPS clock estimates for satellites Sentinel-3A/3B in DORIS geodetic solutions

Correction to: Inclusion of GPS clock estimates for satellites Sentinel-3A/3B in DORIS geodetic solutions

Novel avian orthoavulavirus 13 in wild migratory waterfowl: biological and genetic considerations.

Avian orthoavulavirus 13 (AOAV-13), formerly known as Avian paramyxovirus 13 (APMV-13), is found scatteredly in wild birds around the world. Although four complete genome sequences of AOAV-13 had been identified since the first discovery in Japan in 2003, the information available on the genetic variation and biological characteristics of AOAV-13 is still limited. In the present study, we isolated six AOAV-13 strains from fecal samples of wild migratory waterfowls during annual (2014-2018) viral surveillance of wild bird populations from wetland and domestic poultry of live bird markets (LBMs) in China. The phylogenetic analyses based on the HN and F genes showed that they had very close relationship and the molecular clock estimations showed a low evolutionary rate of AOAV-13. However, Bean goose/Hubei/V97-1/2015 is 1953nt in size (ORF, 1, 776nt), which is a unique size and longer than other reported AOAV-13 strains. Additionally, four repeats of conserved sequences "AAAAAT" was presented in the 5'-end trailer region of Swan goose/Hubei/VI49-1/2016, which is unprecedented in the AOAV-13. These findings highlight the importance of continuous monitoring the specific species of APMVs.

Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses.

The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably in recent years. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the evolutionary interactions among these lagovirus variants, we monitored their geographical distribution and relative incidence over time in a continental-scale competition study. Within 3 years of the incursion of rabbit haemorrhagic disease virus 2 (RHDV2, denoted genotype GI.1bP-GI.2 [polymerase genotype]P-[capsid genotype]) into Australia, two novel recombinant lagovirus variants emerged: RHDV2-4e (genotype GI.4eP-GI.2) in New South Wales and RHDV2-4c (genotype GI.4cP-GI.2) in Victoria. Although both novel recombinants contain non-structural genes related to those from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that the determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the RHDV2-4c recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both the new RHDV2-4e and -4c recombinant variants replaced the previous dominant parental RHDV2 (genotype GI.1bP-GI.2) in their respective geographical areas, despite sharing an identical or near-identical (i.e. single amino acid change) VP60 major capsid protein with the parental virus. This suggests that the observed replacement by these recombinants was not driven by antigenic variation in VP60, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the RHDV2-4e recombination event in early to mid-2015, while the five RHDV2-4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a 2-year period highlights the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.

Impact of GPS/BDS Satellite Attitude Quaternions on Precise Point Positioning with Ambiguity Resolution

Precise point positioning with ambiguity resolution (PPP-AR) based on multiple global navigation satellite system (multi-GNSS) constellations is an important high-precision positioning tool. However, some unmodeled satellite and receiver biases (such as errors in satellite attitude) make it difficult to fix carrier-phase ambiguities. In order to fix ambiguities of eclipsing satellites, accurate integer clock and satellite attitude products (i.e., attitude quaternion) have been provided by the International GNSS Service (IGS). Nevertheless, the quality of these products and their positioning performance in multi-GNSS PPP-AR have not been investigated yet. Using the PRIDE PPP-AR II software associated with the corresponding rapid satellite orbit, integer clock and attitude quaternion products of Wuhan University (WUM), we carried out GPS/BDS PPP-AR using 30 days of data in an eclipsing season of 2020. We found that about 75% of GPS, 60% of BDS-2 and 57% of BDS-3 narrow-lane ambiguity residuals after integer clock corrections fall within ±0.1 cycles in the case of using nominal attitudes. However, when using attitude quaternions, these percentages will rise to 80% for GPS, 70% for BDS-2 and 60% for BDS-3. GPS/BDS daily kinematic PPP-AR after integer clock and nominal attitude corrections can usually achieve a positioning precision of about 10, 10 and 30 mm for the east, north and up components, respectively. In contrast, the counterparts are 8, 8 and 20 mm when using attitude quaternions. Compared with the case of using attitude quaternions only at the network end for the integer clock estimation, using attitude quaternions only at the user end shows a pronounced improvement of 15% in the east component and less than 10% in the north and up components. Therefore, we suggest PPP users apply integer clock and satellite attitude quaternion products to realize more efficient ambiguity fixing, especially in satellite eclipsing seasons.

A Method to Accelerate the Convergence of Satellite Clock Offset Estimation Considering the Time-Varying Code Biases

Continuous and stable precision satellite clock offsets are an important guarantee for real-time precise point positioning (PPP). However, in real-time PPP, the estimation of a satellite clock is often interrupted for various reasons such as network fluctuations, which leads to a long time for clocks to converge again. Typically, code biases are assumed to stay constant over time in clock estimation according to the current literature. In this contribution, it is shown that this assumption reduces the convergence speed of estimation, and the satellite clocks are still unstable for several hours after convergence. For this reason, we study the influence of different code bias extraction schemes, that is, taking code biases as constants, extracting satellite code biases (SCBs), extracting receiver code biases (RCBs) and simultaneously extracting SCBs and RCBs, on satellite clock estimation. Results show that, the time-varying SCBs are the main factors leading to the instability of satellite clocks, and considering SCBs in the estimation can significantly accelerate the filter convergence and improve the stability of clocks. Then, the products generated by introducing SCBs in the clock estimation based on undifferenced observations are applied to PPP experiments. Compared with the original undifferenced model, clocks estimated using the new method can significantly accelerate the convergence speed of PPP and improve the positioning accuracy, which illustrates that our estimated clocks are effective and superior.

Validation of molecular clock inferred HIV infection ages: Evidence for accurate estimation of infection dates.

Improving HIV diagnosis, access to care and effective antiretroviral treatment provides our global strategy to reduce HIV incidence. To reach this goal we need to increase our knowledge about local epidemics. HIV infection dates would be an important information towards this goal, but they are largely unknown. To date, methods to estimate the dates of HIV infection are based mainly on laboratory or molecular methods. Our aim was to validate molecular clock inferred infection dates that were estimated by analysing sequences from 145 people living with HIV (PLHIV) with known transmission dates (clinically estimated infection dates). All HIV sequences were obtained by Sanger sequencing and were previously found to belong to well-established molecular transmission clusters (MTCs). Our analysis showed that the molecular clock inferred infection dates were correlated with the clinically estimated ones (Spearman's Correlation coefficient = 0.93, p < 0.001) and that there was an agreement between them (Lin's concordance correlation coefficient = 0.92, p < 0.001). For the 61.4% of cases the molecular clock inferred preceded the clinically estimated infection dates. The median difference between clinically and molecularly estimated dates of infection was of 0.18 (IQR: -0.21, 0.89) years. The lowest differences were identified in people who inject drugs of our study population. The estimated time to more recent common ancestor (tMRCA) of nodes within clusters provides a reliable approximation of HIV infections for PLHIV infected within MTCs. Next-generation sequencing data and molecular clock estimates based on heterochronous sequences provide, probably, more reliable methods for inferring infection dates. However, since these data are not available in most of the HIV clinical laboratories, our approach, under specific conditions, can provide a reliable estimation of HIV infection dates and can be used for HIV public health interventions.

The CODE ambiguity-fixed clock and phase bias analysis products: generation, properties, and performance

The generation and use of GNSS analysis products that allow—particularly for the needs of single-receiver applications—precise point positioning with ambiguity resolution (PPP-AR) are becoming more and more popular. A general uncertainty concerns the question on how the necessary phase bias information should be provided to the PPP-AR user. Until now, each AR-enabling clock/bias representation method had its own practice to provide the necessary bias information. We have generalized the observable-specific signal bias (OSB) representation, as introduced in Villiger (J Geod 93:1487–1500, 2019) originally exclusively for pseudorange measurements, to carrier phase measurements. The existing common clock (CC) approach has been extended in a way that OSBs allowing for flexible signal and frequency handling between multiple GNSS become possible. Advantages of the proposed OSB-based PPP-AR approach are: GNSS biases can be provided in a consistent way for phase and code measurements and it is capable of multi-GNSS and suitable for standardization. This new, extended PPP-AR approach has been implemented by the Center for Orbit Determination in Europe (CODE). CODE clock products that adhere to the integer-cycle property have been submitted to the International GNSS Service (IGS) since mid of 2018 for three analysis lines: Rapid, Final, and MGEX (Multi-GNSS Extension). Ambiguity fixing is performed not only for GPS but also for Galileo. The integer-cycle property of between-satellite clock differences is of fundamental importance when comparing satellite clock estimates among various analysis lines, or at day boundaries. Both kinds of comparisons could be exploited at a very high level of consistency. Any retrieved comparison essentially indicated a standard deviation for between-satellite clocks from CODE of the order of 5 ps (1.5 mm in range). Finally, the integer-cycle property that may be recovered between the CODE Final clock and the accompanying bias product of consecutive daily sessions (using clock estimates additionally provided for the second midnight epoch) allows us to deduce GPS satellite clock and phase bias information that is consistent and continuous with respect to carrier phase observation data over two, three, or, in principle, yet more days. Phase-based clock densification from initially estimated integer-cycle-conform clock corrections at intervals of 300 s to 30 s (5 s in case of our Final clock product) is a matter of particular interest. Based on direct product comparisons and GRACE K-band ranging (KBR) data analysis, the quality of accordingly densified clock corrections could be confirmed to be on a level similar to that of “anchor” (300 s) clock corrections.

Diversification dynamics of total-, stem-, and crown-groups are compatible with molecular clock estimates of divergence times.

Molecular evolutionary time scales are expected to predate the fossil evidence, but, particularly for major evolutionary radiations, they can imply extremely protracted stem lineages predating the origin of living clades, leading to claims of systematic overestimation of divergence times. We use macroevolutionary birth-death models to describe the range of total-group and crown-group ages expected under constant rates of speciation and extinction. We extend current predictions on origination times for crown- and total-groups, and extinction of stem-groups, demonstrating that there is broad variance in these predictions. Under constant rates of speciation and extinction, we show that the distribution of expected arthropod total-group ages is consistent with molecular clock estimates. The fossil record cannot be read literally, and our results preclude attempts to interpret the antiquity of clades based on the co-occurrence of stem- and crown-representatives.

Phylogeography of the widespread fern Lemmaphyllum in East Asia: species differentiation and population dynamics in response to change in climate and geography

AbstractPast climatic oscillations and complex geodynamic processes had tremendous effects on the current distributions of species in East Asia. Previous studies have revealed that spermatophytes experienced different demographic histories and survived in multiple refuges. However, very few studies involving ferns have been conducted over a large geographical area like East Asia. The monophyletic epiphytic fern genus Lemmaphyllum, which is composed of four species, is widespread in East Asia and offers a good model for exploring how geoclimatic oscillations influence the diversification and demographic history of fern species. We studied the phylogeography of Lemmaphyllum based on 115 populations using plastid sequences and ecological niche modeling. A total of 91 haplotypes were found in Lemmaphyllum. Molecular clock estimation revealed that speciation coincided with the three phases of the Qingzang Movement at beginning of the third uplift of Qinghai‐Tibetan Plateau. The “Tanaka‐Kaiyong Line” demarcated lineages within L. carnosum. The split of the mainland and island lineages of L. rostratum and L. carnosum var. microphyllum may have resulted from ancestral isolation whereby land‐bridges acted as a “barrier” rather than as a “corridor” between mainland and island lineages. Multiple glacial refuges such as Sichuan Basin, Jinggangshan region, YGG region, HDM region, and the islands of the China East Sea during the LGM were revealed. The entities of Lemmaphyllum experienced species‐specific demographic histories in response to the Pleistocene climate change. The case study of epiphytic ferns may provide evidences for understanding the migration of evergreen broad‐leaf forest under climate oscillation.

LEO satellite clock analysis and prediction for positioning applications

ABSTRACT The positioning service aided by low Earth orbit (LEO) mega-constellations has become a hot topic in recent years. To achieve precise positioning, accuracy of the LEO clocks is important for single-receiver users. To bridge the gap between the applicable time of the clock products and the time of positioning, the precise LEO clocks need to be predicted over a certain period depending on the sampling interval of the clock products. This study discusses the prediction errors for periods from 10 s to 1 h for two typical LEO clock types, i.e. the ultra-stable oscillator (USO) and the oven-controlled crystal oscillator (OCXO). The prediction is based on GNSS-determined precise clock estimates, where the clock stability is related to the GNSS estimation errors, the behaviors of the oscillators themselves, the systematic effects related to the environment and the relativistic effects, and the stability of the time reference. Based on real data analysis, LEO clocks of the two different types are simulated under different conditions, and a prediction model considering the systematic effects is proposed. Compared to a simple polynomial fitting model usually applied, the proposed model can significantly reduce the prediction errors, i.e. by about 40%-70% in simulations and about 5%-30% for real data containing different miss-modeled effects. For both clock types, short-term prediction of 1 min would result in a root mean square error (RMSE) of a few centimeters when using a very stable time reference. The RMSE amounts to about 0.1 m, when a typical real-time time reference of the national center for space studies (CNES) real-time clocks was used. For long-term prediction of 1 h, the RMSE could range from below 1 m to a few meters for the USOs, depending on the complexity of the miss-modeled effects. For OCXOs, the 1 h prediction could lead to larger errors with an RMSE of about 10 m.