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1
Rama, Taraka, and Søren Wichmann. "A test of Generalized Bayesian dating: A new linguistic dating method." PLOS ONE 15, no. 8 (August 12, 2020): e0236522. http://dx.doi.org/10.1371/journal.pone.0236522.
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Tintner, Johannes. "Recent developments in using the molecular decay dating method: a review." Annals of the New York Academy of Sciences 1493, no. 1 (January 14, 2021): 29–40. http://dx.doi.org/10.1111/nyas.14560.
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Tamura, Koichiro, Glen Stecher, and Sudhir Kumar. "MEGA11: Molecular Evolutionary Genetics Analysis Version 11." Molecular Biology and Evolution 38, no. 7 (April 23, 2021): 3022–27. http://dx.doi.org/10.1093/molbev/msab120.
Повний текст джерелаАнотація:
Abstract The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
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Wang, Hong, Stanley H. Ambrose, Kristin M. Hedman, and Thomas E. Emerson. "AMS 14C Dating of Human Bones Using Sequential Pyrolysis and Combustion of Collagen." Radiocarbon 52, no. 1 (2010): 157–63. http://dx.doi.org/10.1017/s0033822200045100.
Повний текст джерелаАнотація:
The Radiocarbon Dating Laboratory at the University of Illinois has been using the pyrolysis-combustion technique to separate pyrolysis-volatile (Py-V) or low molecular weight and pyrolysis-residue (Py-R) or high molecular weight compounds for 14C dating of organic remains since 2003. We have applied this method to human collagen dating to examine the 14C age difference between low and high molecular weight organic compounds. Results show that both fractions of late prehistoric period human bones from Illinois archaeological sites yield identical 14C dates but that Py-V or low molecular weight fractions of Archaic period human bones appear to be slightly contaminated. In this case, Py-V components or low molecular weight collagen fraction yield older 14C dates, which could result from contamination from old organic-rich sediments. The pyrolysis-combustion technique provides an economical alternative method to date bones that have not been satisfactorily dated using conventional purification techniques.
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Wilson, Moira A., Andrea Hamilton, Ceren Ince, Margaret A. Carter, and Christopher Hall. "Rehydroxylation (RHX) dating of archaeological pottery." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 468, no. 2147 (July 12, 2012): 3476–93. http://dx.doi.org/10.1098/rspa.2012.0109.
Повний текст джерелаАнотація:
We show that the rehydroxylation (RHX) method can be used to date archaeological pottery, and give the first RHX dates for three disparate items of excavated material. These are in agreement with independently assigned dates. We define precisely the mass components of the ceramic material before, during and after dehydroxylation. These include the masses of three types of water present in the sample: capillary water, weakly chemisorbed molecular water and chemically combined RHX water. We describe the main steps of the RHX dating process: sample preparation, drying, conditioning, reheating and measurement of RHX mass gain. We propose a statistical criterion for isolating the RHX component of the measured mass gain data after reheating and demonstrate how to calculate the RHX age. An effective lifetime temperature (ELT) is defined, and we show how this is related to the temperature history of a sample. The ELT is used to adjust the RHX rate constant obtained at the measurement temperature to the effective lifetime value used in the RHX age calculation. Our results suggest that RHX has the potential to be a reliable and technically straightforward method of dating archaeological pottery, thus filling a long-standing gap in dating methods.
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Xia, Xuhua, and Qun Yang. "A distance-based least-square method for dating speciation events." Molecular Phylogenetics and Evolution 59, no. 2 (May 2011): 342–53. http://dx.doi.org/10.1016/j.ympev.2011.01.017.
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Tao, Qiqing, Koichiro Tamura, Beatriz Mello, and Sudhir Kumar. "Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times." Molecular Biology and Evolution 37, no. 1 (October 22, 2019): 280–90. http://dx.doi.org/10.1093/molbev/msz236.
Повний текст джерелаАнотація:
Abstract Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in dating analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, that is, the actual time is contained within the CIs with a 94% probability. These developments will encourage broader use of computationally efficient RelTime approaches in molecular dating analyses and biological hypothesis testing.
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Schaeffer, O. A., R. W. Stoenner, and W. A. Bassett. "DATING OF TERTIARY VOLCANIC ROCKS BY THE POTASSIUM-ARGON METHOD*." Annals of the New York Academy of Sciences 91, no. 2 (December 15, 2006): 317–19. http://dx.doi.org/10.1111/j.1749-6632.1961.tb35467.x.
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ALFER, JOACHIM, AMIR FATTAHI, NATHALIE BLEISINGER, JÜRGEN KRIEG, ROLF BEHRENS, RALF DITTRICH, MATTHIAS W. BECKMANN, ARNDT HARTMANN, IRMGARD CLASSEN-LINKE, and ROXANA M. POPOVICI. "Endometrial Dating Method Detects Individual Maturation Sequences During the Secretory Phase." In Vivo 34, no. 4 (2020): 1951–63. http://dx.doi.org/10.21873/invivo.11992.
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dos Reis, Mario, Jun Inoue, Masami Hasegawa, Robert J. Asher, Philip C. J. Donoghue, and Ziheng Yang. "Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny." Proceedings of the Royal Society B: Biological Sciences 279, no. 1742 (May 23, 2012): 3491–500. http://dx.doi.org/10.1098/rspb.2012.0683.
Повний текст джерелаАнотація:
The fossil record suggests a rapid radiation of placental mammals following the Cretaceous–Paleogene (K–Pg) mass extinction 65 million years ago (Ma); nevertheless, molecular time estimates, while highly variable, are generally much older. Early molecular studies suffer from inadequate dating methods, reliance on the molecular clock, and simplistic and over-confident interpretations of the fossil record. More recent studies have used Bayesian dating methods that circumvent those issues, but the use of limited data has led to large estimation uncertainties, precluding a decisive conclusion on the timing of mammalian diversifications. Here we use a powerful Bayesian method to analyse 36 nuclear genomes and 274 mitochondrial genomes (20.6 million base pairs), combined with robust but flexible fossil calibrations. Our posterior time estimates suggest that marsupials diverged from eutherians 168–178 Ma, and crown Marsupialia diverged 64–84 Ma. Placentalia diverged 88–90 Ma, and present-day placental orders (except Primates and Xenarthra) originated in a ∼20 Myr window (45–65 Ma) after the K–Pg extinction. Therefore we reject a pre K–Pg model of placental ordinal diversification. We suggest other infamous instances of mismatch between molecular and palaeontological divergence time estimates will be resolved with this same approach.
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Lichtfouse, Eric. "13C-dating, the first method to calculate the relative age of molecular substance homologues in soil." Environmental Chemistry Letters 10, no. 1 (November 23, 2011): 97–103. http://dx.doi.org/10.1007/s10311-011-0334-2.
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Luo, Arong, David A. Duchêne, Chi Zhang, Chao-Dong Zhu, and Simon Y. W. Ho. "A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process." Systematic Biology 69, no. 2 (May 27, 2019): 325–44. http://dx.doi.org/10.1093/sysbio/syz038.
Повний текст джерелаАнотація:
Abstract Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth–death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth–death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth–death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth–death model, which will inform further development of the method and its application to key questions in evolutionary biology.
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Stafford, Thomas W., P. E. Hare, Lloyd Currie, A. J. T. Jull, and Douglas Donahue. "Accuracy of North American Human Skeleton Ages." Quaternary Research 34, no. 1 (July 1990): 111–20. http://dx.doi.org/10.1016/0033-5894(90)90076-w.
Повний текст джерелаАнотація:
AbstractAccelerator mass spectrometry (AMS) radiocarbon dates fail to provide conclusive evidence that all New World human fossils are younger than approximately 11,000 yr. Because fossil bones vary widely in preservation, their radiocarbon dates are not equally accurate. Molecular-level radiocarbon dating, which used individual amino acids to assess fossil diagenesis, revealed that dates on known-age, noncollagenous bone were underestimated by at least 2000 to 9000 yr. The significance is that >11,000-yr-old fossil bones with poor preservation would yield Holocene and not Pleistocene radiocarbon ages, regardless of what chemical pretreatment or 14C counting method was used. Irreplaceable evidence for Pleistocene-age fossils in the New World could be lost if the diagenesis of fossil bones is not evaluated before the bones are radiocarbon dated. In contrast, radiocarbon ages for collagenous fossils can be determined more accurately if 14C is measured in several individual amino acids that are isolated from collagenous bone protein. Molecular-level radiocarbon dating will greatly improve not only the accuracy of chronologies for human migrations and animal extinctions, but of all late Quaternary chronologies that are based upon the 14C dating of fossil proteins.
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Tao, Qiqing, Koichiro Tamura, Fabia U. Battistuzzi, and Sudhir Kumar. "A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies." Molecular Biology and Evolution 36, no. 4 (January 23, 2019): 811–24. http://dx.doi.org/10.1093/molbev/msz014.
Повний текст джерелаАнотація:
Abstract New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here, we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies. CorrTest is computationally efficient and performs better than the available state-of-the-art method. Application of CorrTest reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, parasitic protozoans, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and nonmolecular evolutionary patterns, and they will foster unbiased and precise dating of the tree of life.
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Ohkouchi, Naohiko, Li Xu, Christopher M. Reddy, Daniel Montluçon, and Timothy I. Eglinton. "Radiocarbon Dating of Alkenones from Marine Sediments: I. Isolation Protocol." Radiocarbon 47, no. 3 (2005): 401–12. http://dx.doi.org/10.1017/s0033822200035189.
Повний текст джерелаАнотація:
The chemical and isotopic compositions of long-chain (C36–C39) unsaturated ketones (alkenones), a unique class of algal lipids, encode surface ocean properties useful for paleoceanographic reconstruction. Recently, we have sought to extend the utility of alkenones as oceanic tracers through measurement of their radiocarbon contents. Here, we describe a method for isolation of alkenones from sediments as a compound class based on a sequence of wet chemical techniques. The steps involved, which include silica gel column chromatography, urea adduction, and silver nitrate-silica gel column chromatography, exploit various structural attributes of the alkenones. Amounts of purified alkenones estimated by GC/FID measurements were highly correlated with CO2 yields after sample combustion, indicating purities of greater than 90% for samples containing ≥ 100 μg C. The degree of alkenone unsaturation (U37K′) also varied minimally through the procedure. We also describe a high-performance liquid chromatography (HPLC) method to isolate individual alkenones for molecular-level structural and isotopic determination.
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Moshynets, O. V., A. Koza, P. Dello Sterpaio, V. A. Kordium, and A. J. Spiers. "Up-dating the Cholodny method using PET films to sample microbial communities in soil." Biopolymers and Cell 27, no. 3 (May 20, 2011): 199–205. http://dx.doi.org/10.7124/bc.0000ba.
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Choe, Kyumin, Sujin Song, Jang Hoon Lee, Young Mi Song, Jin Kang, Myoung-ho Yun, and Jong Chan Kim. "A Study on Trapping CO2 Using Molecular Sieve for 14C AMS Sample Preparation." Radiocarbon 55, no. 2 (2013): 421–25. http://dx.doi.org/10.1017/s0033822200057556.
Повний текст джерелаАнотація:
At the Seoul National University accelerator mass spectrometry (AMS) laboratory, we are planning to develop an automated sample preparation system for higher throughput of radiocarbon dating. This system will consist of several sections, including a combustion line, CO2 trap, graphitization system, and so on. We usually collect CO2 by cryogenic trapping. However, since handling liquid nitrogen is expected to be rather difficult, we are interested in replacing the cryogenic method with the molecular sieve method for the collection of CO2. In this study, we compare the performance of the cryogenic trapping method and molecular sieve method. Zeolite 13X is used as a molecular sieve, and as test samples we use the oxalic acid standard (NIST SRM 4990C), high-purity graphite powder, and archaeological charcoals. The pMC values and the radiocarbon ages (BP) obtained from samples prepared by the above 2 methods are very similar. We especially focused on the memory effect of the molecular sieve, meaning the CO2 contamination from a previous sample, which can cause errors in age determination. To reduce this effect, we flowed He gas through a zeolite container for several minutes at a high temperature before the CO2 was introduced. By the adding this step, we have obtained more reliable results.
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Herrando-Pérez, Salvador. "Bone need not remain an elephant in the room for radiocarbon dating." Royal Society Open Science 8, no. 1 (January 13, 2021): 201351. http://dx.doi.org/10.1098/rsos.201351.
Повний текст джерелаАнотація:
Radiocarbon ( 14 C) analysis of skeletal remains by accelerator mass spectrometry is an essential tool in multiple branches of science. However, bone 14 C dating results can be inconsistent and not comparable due to disparate laboratory pretreatment protocols that remove contamination. And, pretreatments are rarely discussed or reported by end-users, making it an ‘elephant in the room’ for Quaternary scientists. Through a questionnaire survey, I quantified consensus on the reliability of collagen pretreatments for 14 C dating across 132 experts (25 countries). I discovered that while more than 95% of the audience was wary of contamination and would avoid gelatinization alone (minimum pretreatment used by most 14 C facilities), 52% asked laboratories to choose the pretreatment method for them, and 58% could not rank the reliability of at least one pretreatment. Ultrafiltration was highly popular, and purification by XAD resins seemed restricted to American researchers. Isolating and dating the amino acid hydroxyproline was perceived as the most reliable pretreatment, but is expensive, time-consuming and not widely available. Solid evidence supports that only molecular-level dating accommodates all known bone contaminants and guarantees complete removal of humic and fulvic acids and conservation substances, with three key areas of progress: (i) innovation and more funded research is required to develop affordable analytical chemistry that can handle low-mass samples of collagen amino acids, (ii) a certification agency overseeing dating-quality control is needed to enhance methodological reproducibility and dating accuracy among laboratories, and (iii) more cross-disciplinary work with better 14 C reporting etiquette will promote the integration of 14 C dating across disciplines. Those developments could conclude long-standing debates based on low-accuracy data used to build chronologies for animal domestications, human/megafauna extirpations and migrations, archaeology, palaeoecology, palaeontology and palaeoclimate models.
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Tao, Qiqing, Jose Barba-Montoya, and Sudhir Kumar. "Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies." Bioinformatics 37, Supplement_1 (July 1, 2021): i102—i110. http://dx.doi.org/10.1093/bioinformatics/btab307.
Повний текст джерелаАнотація:
Abstract Motivation Precise time calibrations needed to estimate ages of species divergence are not always available due to fossil records' incompleteness. Consequently, clock calibrations available for Bayesian dating analyses can be few and diffused, i.e. phylogenies are calibration-poor, impeding reliable inference of the timetree of life. We examined the role of speciation birth–death (BD) tree prior on Bayesian node age estimates in calibration-poor phylogenies and tested the usefulness of an informative, data-driven tree prior to enhancing the accuracy and precision of estimated times. Results We present a simple method to estimate parameters of the BD tree prior from the molecular phylogeny for use in Bayesian dating analyses. The use of a data-driven birth–death (ddBD) tree prior leads to improvement in Bayesian node age estimates for calibration-poor phylogenies. We show that the ddBD tree prior, along with only a few well-constrained calibrations, can produce excellent node ages and credibility intervals, whereas the use of an uninformative, uniform (flat) tree prior may require more calibrations. Relaxed clock dating with ddBD tree prior also produced better results than a flat tree prior when using diffused node calibrations. We also suggest using ddBD tree priors to improve the detection of outliers and influential calibrations in cross-validation analyses. These results have practical applications because the ddBD tree prior reduces the number of well-constrained calibrations necessary to obtain reliable node age estimates. This would help address key impediments in building the grand timetree of life, revealing the process of speciation and elucidating the dynamics of biological diversification. Availability and implementation An R module for computing the ddBD tree prior, simulated datasets and empirical datasets are available at https://github.com/cathyqqtao/ddBD-tree-prior.
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Boudin, Mathieu, Marco Bonafini, Tess van den Brande, and Ina Vanden Berghe. "Cross-Flow Nanofiltration of Contaminated Protein-Containing Material: State of the Art." Radiocarbon 59, no. 6 (December 2017): 1793–807. http://dx.doi.org/10.1017/rdc.2017.137.
Повний текст джерелаАнотація:
ABSTRACTRadiocarbon (14C) dating of protein-containing material (collagen, hair/wool, silk, leather) contaminated with extraneous carbon (e.g. humic substances) might result in unreliable dates when pretreated with the conventional but inadequate protocols. In this study cross-flow nanofiltration was applied to pretreated, protein-containing material. This method is able to remove low-molecular and high-molecular weight contaminants as demonstrated in previous studies. The sample quality improvement by cross-flow nanofiltration is verified by measuring the C:N ratio before and after nanofiltration. If the C:N ratio of the permeate (sample after cross-flow nanofiltration) falls within the C:N boundaries for uncontaminated wool/hair, silk and bone collagen, it is assumed to be contamination free. In our study, we focused on wool, silk, and collagen samples of known historical age. All samples treated by cross-flow nanofiltration effectively outputs C:N ratios within the expected range and yield for more accurate 14C date in agreement with historical expectations whereas bulk samples with C:N ratio out of the expected ranges, give either younger or older dates. We thus highlight both that C:N ratio is a good indicator of contamination and that cross-flow nanofiltration is an efficient method to treat protein-containing materials prior to 14C dating.
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Senja, Garini Tiara, and Santi Delliana. "“CATFISHING” : EXPOSING TEEN RECEPTION ON MTV CATFISH ONLINE DATING." Profetik: Jurnal Komunikasi 15, no. 2 (November 19, 2022): 228. http://dx.doi.org/10.14421/pjk.v15i2.2380.
Повний текст джерелаАнотація:
Advanced technology has made meeting new people less conventional than it used to be. The Internet has taken romance into a whole different world and created a whole different threat with the idea of online dating. Internet users are faced with many threats every day, but online dating has caused a threat with a form of online identity deception called catfishing. Catfishing itself is the theme of an MTV reality show named Catfish: The TV Show. This study aims to find out about the reaction of adolescent online daters on catfishing on the program. This descriptive qualitative study uses Stuart Hall's Reception Analysis method and its three hypothetical positions, such as Dominant-Hegemonic position, Negotiated position, and Oppositional position. Results show different readings on each of the six pieces of information given in the chosen episode. Four pieces of information such as when the client first reached out to Catfish: The TV Show team, the team investigated the catfish, the team to arrange a meeting with the catfish, and the meeting with the catfish are dominated by the Dominant-Hegemonic Position. Meanwhile, the rest of the two pieces of information are dominated by the Negotiated position and the Oppositional position.However, the complete study result is dominated by the Oppositional position.
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King, Benedict, and Martin Rücklin. "Tip dating with fossil sites and stratigraphic sequences." PeerJ 8 (June 26, 2020): e9368. http://dx.doi.org/10.7717/peerj.9368.
Повний текст джерелаАнотація:
Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies. Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through the use of uniform tip age priors. However, the use of tip age priors has the unwanted effect of decoupling the ages of fossils from the same fossil site. Here we introduce a new Markov Chain Monte Carlo (MCMC) proposal, which allows fossils from the same site to have linked ages, while still incorporating uncertainty in the age of the fossil site itself. We also include an extension, allowing fossil sites to be ordered in a stratigraphic column with age bounds applied only to the top and bottom of the sequence. These MCMC proposals are implemented in a new open-source BEAST2 package, palaeo. We test these new proposals on a dataset of early vertebrate fossils, concentrating on the effects on two sites with multiple acanthodian fossil taxa but wide age uncertainty, the Man On The Hill (MOTH) site from northern Canada, and the Turin Hill site from Scotland, both of Lochkovian (Early Devonian) age. The results show an increased precision of age estimates when fossils have linked tip ages compared to when ages are unlinked, and in this example leads to support for a younger age for the MOTH site compared with the Turin Hill site. There is also a minor effect on the tree topology of acanthodians. These new MCMC proposals should be widely applicable to studies that employ tip dating, particularly when the terminals are coded as individual specimens.
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Sekhaneh, W. Al, Y. H. Akkam, G. Kamel, A. Drabee, and J. Popp. "Investigation of ancient teeth using Raman spectroscopy and synchrotron radiation Fourier-transform infrared (SR-µFTIR): mapping and novel method of dating." Digest Journal of Nanomaterials and Biostructures 16, no. 2 (2021): 713–24. http://dx.doi.org/10.15251/djnb.2021.162.713.
Повний текст джерелаАнотація:
Raman spectroscopy and Synchrotron Radiation Fourier-Transform Infrared (SR-µFTIR): Mapping have been increasingly applied as a good tool in archaeological research. The chronology of ancient samples is an essential step in archeology, and carbon dating using atomic force microscopy is the main technique. Nevertheless, the availability of instrumentation, sample preparation, and cost are barriers that limit the wide usage. The study was aimed to develop a method utilizing Raman spectroscopy and Synchrotron Radiation Fourier-Transform Infrared (SR-µFTIR) Mapping to identify ancient teeth and sort them chronologically. Furthermore, Raman spectroscopy was used to evaluate the preservation of collagen and the crystallinity of Apatite in ancient teeth. The age of fourteen ancient teeth descent from different individuals (8 from Roman period-1500BC and 4 from Byzantine period-641AD) was confirmed using carbon dating via atomic force spectrometry. The ancient teeth along with modern teeth were investigated using microRaman spectroscopy (oscillation and mapping). The typical Raman spectrum of the dentin for ancient samples was recorded and then compared to the modern teeth. The ratio of the phosphate 𝑃𝑂4 3− the band at 963 cm-1 to organic CH band at 2950 cm-1 was calculated for all samples. Raman mapping was recorded for cross-section teeth samples. The AMS data showed that the ages of the samples were 3400-3800 and 1240-1350 years for Roman and Byzantine teeth, respectively. The phosphate ν1 𝑃𝑂4 3− vibration band at (963 cm-1 ) in ancient teeth was shifted 3 cm-1 toward higher wavenumber compared to modern dentin samples (960 cm-1 ). The intensity and broadening of the carbonate apatite band at 1050 cm-1 were directly proportional to the aging. The intensity of the organic part triplet peaks at (2882, 2950, 2962) decreased with age. The ratio of phosphate band to organic C-H band was 0.346-0.388 and 0.122-0.136 for Roman and Byzantine teeth, respectively. According to the Raman mapping, the organic material in ancient teeth degraded and diffused, while in modern tooth it concentrated. Raman spectroscopy (intensity at 963 cm1 to 2950 cm-1) can be used as a qualitative tool to chronologically sort the archeological teeth samples before the use of carbon dating. The preliminary dating by Raman spectroscopy can recognize if a tooth or bone sample is archaeological or not. This step may save time and money and shall be assigned as a pre-request for AMS analysis. Raman mapping may help to explore archeological samples for best-preserved organic matter, hence identify the best candidates for further analysis (DNA extraction). In the future, the proposed method can be expanded and applied in specific cases in ancient osteology.
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Behnamian, Sara, Umberto Esposito, Grace Holland, Ghadeer Alshehab, Ann M. Dobre, Mehdi Pirooznia, Conrad S. Brimacombe, and Eran Elhaik. "Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years." Cell Reports Methods 2, no. 8 (August 2022): 100270. http://dx.doi.org/10.1016/j.crmeth.2022.100270.
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Patry, Wyatt L., MacKenzie Bubel, Cypress Hansen, and Thomas Knowles. "Diffusion tubes: a method for the mass culture of ctenophores and other pelagic marine invertebrates." PeerJ 8 (April 7, 2020): e8938. http://dx.doi.org/10.7717/peerj.8938.
Повний текст джерелаАнотація:
The culture of pelagic marine invertebrates, especially the ctenophore Mnemiopsis leidyi, has been demonstrated in past studies dating back to the 1960s; however, the mass culture of delicate pelagic invertebrates has remained elusive. By using a pair of acrylic tubes and enabling water diffusion between them, we have been able to reliably and cost effectively mass culture several genera of ctenophores (Pleurobrachia, Hormiphora, Bolinopsis, Mnemiopsis and Leucothea), one species of siphonophore (Nanomia) and one species of larvacean (Oikopleura). The simple, compact method is effective enough to support two permanent exhibits of ctenophores at the Monterey Bay Aquarium while minimizing live food culture requirements with the potential to support further investigation of pelagic marine invertebrate ontogeny, ecology and genomics.
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King, Benedict, and Robin M. D. Beck. "Tip dating supports novel resolutions of controversial relationships among early mammals." Proceedings of the Royal Society B: Biological Sciences 287, no. 1928 (June 10, 2020): 20200943. http://dx.doi.org/10.1098/rspb.2020.0943.
Повний текст джерелаАнотація:
The estimation of the timing of major divergences in early mammal evolution is challenging owing to conflicting interpretations of key fossil taxa. One contentious group is Haramiyida, the earliest members of which are from the Late Triassic. Many phylogenetic analyses have placed haramiyidans in a clade with multituberculates within crown Mammalia, thus extending the minimum divergence date for the crown group deep into the Triassic. A second taxon of interest is the eutherian Juramaia from the Middle–Late Jurassic Yanliao Biota, which is morphologically very similar to eutherians from the Early Cretaceous Jehol Biota and implies a very early origin for therian mammals. Here, we apply Bayesian tip-dated phylogenetic methods to investigate these issues. Tip dating firmly rejects a monophyletic Allotheria (multituberculates and haramiyidans), which are split into three separate clades, a result not found in any previous analysis. Most notably, the Late Triassic Haramiyavia and Thomasia are separate from the Middle Jurassic euharamiyidans. We also test whether the Middle–Late Jurassic age of Juramaia is ‘expected’ given its known morphology by assigning an age prior without hard bounds. Strikingly, this analysis supports an Early Cretaceous age for Juramaia , but similar analyses on 12 other mammaliaforms from the Yanliao Biota return the correct, Jurassic age. Our results show that analyses incorporating stratigraphic data can produce results very different from other methods. Early mammal evolution may have involved multiple instances of convergent morphological evolution (e.g. in the dentition), and tip dating may be a method uniquely suitable to recognizing this owing to the incorporation of stratigraphic data. Our results also confirm that Juramaia is anomalous in exhibiting a much more derived morphology than expected given its age, which in turn implies very high rates of evolution at the base of therian mammals.
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Pardo-Seco, Jacobo, Xabier Bello, Alberto Gómez-Carballa, Federico Martinón-Torres, José Ignacio Muñoz-Barús, and Antonio Salas. "A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations." International Journal of Molecular Sciences 23, no. 21 (October 25, 2022): 12899. http://dx.doi.org/10.3390/ijms232112899.
Повний текст джерелаАнотація:
Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an unknown SARS-CoV-2 genome in a population (hereafter, estimated time of a queried genome [QG]; tE-QG) can be easily predicted using a phylogenetic model based on a robust reference genome database of the virus, and information on their sampling dates. We evaluate several phylogeny-based approaches, including modeling evolutionary (substitution) rates of the SARS-CoV-2 genome (~10−3 substitutions/nucleotide/year) and the mutational (substitutions) differences separating the QGs from the reference genomes (RGs) in the database. Owing to the mutational characteristics of the virus, the present Viral Molecular Clock Dating (VMCD) method covers timeframes going backwards from about a month in the past. The method has very low errors associated to the tE-QG estimates and narrow intervals of tE-QG, both ranging from a few days to a few weeks regardless of the mathematical model used. The SARS-CoV-2 model represents a proof of concept that can be extrapolated to any other microorganism, provided that a robust genome sequence database is available. Besides obvious applications in epidemiology and microbiology investigations, there are several contexts in forensic casework where estimating tE-QG could be useful, including estimation of the postmortem intervals (PMI) and the dating of samples stored in hospital settings.
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Gray, Russell D., Quentin D. Atkinson, and Simon J. Greenhill. "Language evolution and human history: what a difference a date makes." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1567 (April 12, 2011): 1090–100. http://dx.doi.org/10.1098/rstb.2010.0378.
Повний текст джерелаАнотація:
Historical inference is at its most powerful when independent lines of evidence can be integrated into a coherent account. Dating linguistic and cultural lineages can potentially play a vital role in the integration of evidence from linguistics, anthropology, archaeology and genetics. Unfortunately, although the comparative method in historical linguistics can provide a relative chronology, it cannot provide absolute date estimates and an alternative approach, called glottochronology, is fundamentally flawed. In this paper we outline how computational phylogenetic methods can reliably estimate language divergence dates and thus help resolve long-standing debates about human prehistory ranging from the origin of the Indo-European language family to the peopling of the Pacific.
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Duchen, Pablo. "Métodos de reconstrucción filogenética II: inferencia bayesiana." Tequio 4, no. 11 (January 27, 2021): 81–89. http://dx.doi.org/10.53331/teq.v4i11.0055.
Повний текст джерелаАнотація:
Phylogenetic reconstruction through Bayesian inference is currently widely used. The main advantage of this method is the direct output of posterior probabilities for each clade on the final phylogeny. Thus, it does not require bootstrapping as a measure of uncertainty. Moreover, Bayesian inference is perfectly fit for dating phylogenies through molecular clocks. In this paper, the basics of Bayesian inference applied to phylogenetic reconstruction are described, starting with an explanation of Bayes’ theorem. Then, the use of the Metropolis-Hastings algorithm to sample topologies from the posterior distribution is characterized and illustrated through a simple example. At the end, there is a mention of the software used for Bayesian phylogeny reconstruction.
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Marić, Ana, Danica Srećković Batoćanin, Dubravka Škraba Jurlina, Miloš Brkušanin, Jelena Karanović, Tamara Kanjuh, Vera Nikolić, Danilo Mrdak, and Predrag Simonović. "A treatise about reliability in dating events of evolutionary history of brown trout Salmo cf. trutta (Actinopterygii) at Western Balkans: Impassable barriers, isolation of populations and assistance of geological timeframe." Acta Ichthyologica et Piscatoria 53 (February 27, 2023): 1–18. http://dx.doi.org/10.3897/aiep.53.97702.
Повний текст джерелаАнотація:
A pool of data already existing about D-loop, i.e., the Control Region (CR) haplotypes of the mitochondrial DNA (mtDNA) of brown trout, Salmo trutta Linnaeus, 1758, tentative Adriatic trout Salmo farioides Karaman, 1938, and tentative Macedonian trout, Salmo macedonicus (Karaman, 1924), and their reconstructed phylogeography makes a good starting point for resolving their evolutionary history. That includes the dating of particular events in it. The events have hitherto been dated using the method of a molecular clock. Various calibrations were applied for the mutation rate, owing to the incongruence between the time of divergence that various authors notified and general knowledge about events in geological history and the periods in which they occurred in the Mediterranean region. Since geological history events were mandatory for setting the scene for the evolutionary history of brown trout, the incongruence between them has questioned the molecular clock calibration’s validity. From results about both the phylogeography and phylogenetic relations between native haplotypes (both partial and whole CR sequences) and the population genetics that characterized particular populations, we calculated the time of divergence between haplotypes in the regions of the western part of the Balkans: Iron Gate broader area in eastern Serbia, continental Montenegro and south-eastern Serbia. The distinct status of adjacent populations was verified by frequencies of microsatellites’ alleles and the STRUCTURE analysis that examined the significance of differences between them. In particular, we examined the populations that were clearly separated either by physical barriers, such as a waterfall in eastern Serbia (e.g., the upper and lower River Rečka supplemented by nearby rivers Vratna and Zamna), or by underground drops in Montenegro (e.g., upper and lower River Zeta, and rivers Nožica and lower River Mrtvica as isolated counterparts). We used the so far most common substitution rate of 1% in a million years’ (MY) period. The divergence times we obtained were compared to the events known for the region from available geological history data. There was a fairly good congruence between the dating obtained by the molecular clock method and that by geological history where the advanced, i.e., modern haplotypes, were concerned. In contrast, the congruence was worse for dating of divergence when more ancient haplotypes were in question, being much better if the mutational rate would be decreased to lower rates. That supported results both from the Rate Correlation Test about the independence of evolutionary rates in different lineages of brown trout, and from the Molecular Clock Test, which revealed that the evolutionary rate throughout the phylogenetic tree is not equal. That implies a difference in the speed of evolution in them, which was likely slower and faster, in the ancient, pre-Pleistocene haplotypes and the advanced, Pleistocene ones, respectively. The setting of the variable, or non-linear (i.e., logarithmic) speed of evolving seems helpful, since the early cladogenesis with the dominance of mutations was most likely combined afterwards with the acting of other evolutionary mechanisms, especially of genetic drift in populations that passed through the bottleneck episodes of the abrupt decrease in population size during the unfavourable periods of their evolutionary history.
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Brock, Fiona, Michael Dee, Andrew Hughes, Christophe Snoeck, Richard Staff, and Christopher Bronk Ramsey. "Testing the Effectiveness of Protocols for Removal of Common Conservation Treatments for Radiocarbon Dating." Radiocarbon 60, no. 1 (August 9, 2017): 35–50. http://dx.doi.org/10.1017/rdc.2017.68.
Повний текст джерелаАнотація:
AbstractTo achieve a reliable radiocarbon (14C) date for an object, any contamination that may be of a different age must be removed prior to dating. Samples that have been conserved with treatments such as adhesives, varnishes or consolidants can pose a particular challenge to 14C dating. At the Oxford Radiocarbon Accelerator Unit (ORAU), common examples of such substances encountered include shellac, the acrylic polymers Paraloid B-67 and B-72, and vinyl acetate-derived polymers (e.g. PVA). Here, a non-carbon-containing absorbent substrate called Chromosorb® was deliberately contaminated with a range of varieties or brands of these conservation treatments, as well as two cellulose nitrate lacquers. A selection of chemical pretreatments was tested for their efficiency at removing them. While the varieties of shellac and Paraloid tested were completely removed with some treatments (water/methanol and acetone/methanol/chloroform sequential washes, respectively), no method was found that was capable of completely removing any of the vinyl acetate-derived materials or the cellulose nitrate lacquers. While Chromosorb is not an exact analog of archaeological wood or bone, for example, this study suggests that it may be possible to remove aged shellac and Paraloid from archaeological specimens with standard organic solvent-acid-base-acid pretreatments, but it may be significantly more difficult to remove vinyl acetate-derived polymers and cellulose nitrate lacquers sufficiently to provide reliable 14C dates. The four categories of conservation treatment studied demonstrate characteristic FTIR spectra, while highlighting subtle chemical and molecular differences between different varieties of shellac, Paraloid and cellulose nitrate lacquers, and significant differences between the vinyl acetate derivatives.
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Lin, Wei, Greig A. Paterson, Qiyun Zhu, Yinzhao Wang, Evguenia Kopylova, Ying Li, Rob Knight, et al. "Origin of microbial biomineralization and magnetotaxis during the Archean." Proceedings of the National Academy of Sciences 114, no. 9 (February 13, 2017): 2171–76. http://dx.doi.org/10.1073/pnas.1614654114.
Повний текст джерелаАнотація:
Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from theNitrospiraephylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between theNitrospiraeandProteobacteria. This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth’s dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.
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Giribet, Gonzalo, and Gregory D. Edgecombe. "Stable phylogenetic patterns in scutigeromorph centipedes (Myriapoda : Chilopoda : Scutigeromorpha): dating the diversification of an ancient lineage of terrestrial arthropods." Invertebrate Systematics 27, no. 5 (2013): 485. http://dx.doi.org/10.1071/is13019.
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Although stable and well-supported relationships are in place for the three main clades (families) of Scutigeromorpha, the interrelationships of particular taxa within the most diverse family, Scutigeridae, are less clearly resolved. Novel molecular data for taxa from Mesoamerica, the Caribbean, southern Africa, New Guinea and previously unsampled parts of the Pacific are incorporated into phylogenetic analyses. Relationships across the tree are stable under variable analytical conditions, whether these are homology-based (multiple sequence alignment versus implied alignment; untrimmed versus trimmed datasets) or method-based (parsimony versus maximum likelihood). Hypervariable regions, contrary to common belief, add phylogenetic structure to the data, as measured by the increased support for many nodes when compared with the same alignments trimmed with Gblocks. Our analyses show that a Yule-3-rate model best explained the diversification of Scutigeromorpha during their 400 million years of history. More complete molecular data for the New Guinea genus Ballonema stabilise its position as sister group to Thereuoneminae. To reconcile scutigeromorph systematics with the phylogeny, the monotypic genus Madagassophora Verhoeff, 1936, is placed in synonymy with Scutigerina Silvestri, 1901 (n. syn.), its type species M. hova becoming Scutigerina hova (de Saussure & Zehntner, 1902) new comb. (from Scutigera), and Lassophora Verhoeff, 1905, is re-established for an Afro-Malagasy clade containing Lassophora nossibei (de Saussure & Zehntner, 1902) new comb. (from Scutigera) and a newly sequenced species from Mozambique that diverged at the base of the lineage to Thereuoneminae. The dated phylogeny of Scutigeromorpha is more consistent with ancient vicariant splits between Madagascar–southern Africa and Australia–New Caledonia than with younger dispersal scenarios, though some geologically young Pacific islands that harbour lineages dating to the Cretaceous demonstrate the potential for trans-oceanic dispersal.
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Salemi, Marco, Korbinian Strimmer, William W. Hall, Margaret Duffy, Eric Delaporte, Souleymane Mboup, Martine Peeters, and Anne‐Mieke Vandamme. "Dating the common ancestor of SIVcpz and HIV‐1 group M and the origin of HIV‐1 subtypes by using a new method to uncover clock‐like molecular evolution." FASEB Journal 15, no. 2 (December 8, 2000): 276–78. http://dx.doi.org/10.1096/fj.00-0449fje.
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Sorin, Deacu, Neculai-Cândea Lavinia, Pricop Ștefan, Gheorghe Emma, Mocanu Liliana, and Popa Marius Florentin. "HMGB1-RAGE, A Useful Partnership in Vital Response?" ARS Medica Tomitana 27, no. 2 (May 1, 2021): 99–105. http://dx.doi.org/10.2478/arsm-2021-0018.
Повний текст джерелаАнотація:
Abstract Introduction: In forensic practice, it is well known that the mechanism and dating of traumatic injuries is one of the primary responsibilities of this specialty. Currently, it is a subject still debated by researchers, and so far, an infallible marker that would objectively support their intravitam/postmortem occurrence has not yet been identified. However, studies have shown that the HMGB1-RAGE axis is rapidly activated after trauma and might be an essential element to help solve the forensic problem of wound dating. Purpose: To compare the values of HMGB1-RAGE expression occurring in wounds produced intravitally shortly before death and in wounds produced postmortem and to quantify the differences arising between them. Material and method: For this prospective study, skin fragments were collected from the site of wounds in autopsied cadavers at the County Clinical Service of Forensic Medicine Constanta (SCJML Constanta), wounds produced intravitally and with a maximum survival time of 60 minutes. Postmortem wounds and control fragments from volunteers undergoing surgery for skin tumours were also collected. The main conditions were: chronological documentation of the lesion and absence of neoplastic or inflammatory conditions. Ninety-six autopsy cases between 2021–2022 met the criteria for inclusion in the study. A control fragment accompanied each fragment from the wound. Routine Hematoxylin-Eosin (HE), Perls and Van Gieson Werhoeffstaining, as well as immunohistochemistry with HMGB1 and RAGE markers were performed on each fragment and a score based on staining intensity was determined. Results: Routine staining was not useful in assessing vitality in segments with survival time up to 30 min. Immunohistochemically, both markers showed increased values compared to control values (p<0.0001) and to lesions produced postmortem. An interesting aspect is the lack of reactivity in the lesion’s margins for both markers. Conclusions: Although further research is needed, the results of our study support the hypothesis that the HMGB1-RAGE axis is useful in assessing the vital reaction in skin wounds.
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BHATTACHARYA, D. "Dating Algal Origin Using Molecular Clock Methods." Protist 155, no. 1 (March 2004): 9–10. http://dx.doi.org/10.1078/1434461000157.
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Marshall, Charles R. "Confidence intervals on stratigraphic ranges." Paleobiology 16, no. 1 (1990): 1–10. http://dx.doi.org/10.1017/s0094837300009672.
Повний текст джерелаАнотація:
Observed stratigraphic ranges almost always underestimate true longevities. Strauss and Sadler (1987, 1989) provide a method for calculating confidence intervals on the endpoints of local stratigraphic ranges. Their method can also be applied to composite sections; confidence intervals may be placed on times of origin and extinction for entire species or lineages. Confidence interval sizes depend only on the length of the stratigraphic range and the number of fossil horizons. The technique's most important assumptions are that fossil horizons are distributed randomly and that collecting intensity has been uniform over the stratigraphic range. These assumptions are more difficult to test and less likely to be fulfilled for composite sections than for local sections.Confidence intervals give useful baseline estimates of the incompleteness of the fossil record, even if the underlying assumptions cannot be tested. Confidence intervals, which can be very large, should be calculated when the fossil record is used to assess absolute rates of molecular or morphological evolution, especially for poorly preserved groups. Confidence intervals have other functions: to determine how rich the fossil record has to be before radiometric dating errors become the dominant source of error in estimated times of origin or extinction; to predict future fossil finds; to predict which species with fossil records should be extant; and to assess phylogenetic hypotheses and taxonomic assignments.
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Kodandaramaiah, Ullasa. "Tectonic calibrations in molecular dating." Current Zoology 57, no. 1 (February 1, 2011): 116–24. http://dx.doi.org/10.1093/czoolo/57.1.116.
Повний текст джерелаАнотація:
Abstract Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeography are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously believed that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicariance in several groups. Moreover, the possibility of speciation having occurred before the said geological event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations always result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided.
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Pérez-Miranda, Fabian, Omar Mejia, Benjamín López, and Oldřich Říčan. "Molecular clocks, biogeography and species diversity in Herichthys with evaluation of the role of Punta del Morro as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification." PeerJ 8 (April 29, 2020): e8818. http://dx.doi.org/10.7717/peerj.8818.
Повний текст джерелаАнотація:
Using molecular dated phylogenies and biogeographic reconstructions, the species diversity, biogeography and time frame of evolution of the genus Herichthys were evaluated. In particular, we test the role of Punta del Morro (PdM) as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification using several sets of calibrations. Species diversity in Herichthys is complex and the here employed dating methods suggest young age and rapid divergence for many species while species delimitation methods did not resolve these young species including both sympatric species pairs. Based on our molecular clock dating analyses, Herichthys has colonized its present distribution area significantly prior to the suggested vicariance by PdM (10–17.1 Ma vs. 5 to 7.5 Ma). The PdM constraint is in conflict with all other paleogeographic and fossil constraints including novel ones introduced in this study that are, however, congruent among each other. Our study demonstrates that any cichlid datings significantly older or younger than the bounds presented by our analyses and discussion have to be taken as highly questionable from the point of view of Middle American paleogeography and cichlid biogeography unless we allow the option that cichlid biogeography is completely independent from ecological and geological constraints.
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McLay, Todd G. B., Michael J. Bayly, and Pauline Y. Ladiges. "Is south-western Western Australia a centre of origin for eastern Australian taxa or is the centre an artefact of a method of analysis? A comment on Hakea and its supposed divergence over the past 12 million years." Australian Systematic Botany 29, no. 2 (2016): 87. http://dx.doi.org/10.1071/sb16024.
Повний текст джерелаАнотація:
Lamont et al. (2016) concluded that the Australian sclerophyllous genus Hakea (Proteaceae) arose 18million years ago in the South West of Western Australia (SWA) and dispersed 18 times to eastern (EA) and central Australia (CA) only 12million years ago (mid-Miocene). Their explanation of the biogeographic history of Hakea was based on the following: accepting a fully resolved molecular phylogenetic tree, although ~40% of nodes had posterior probability values below 0.95; using all nodes including geographically paralogous nodes to determine ancestral area probabilities; and applying a strict clock to estimate clade divergence times. Our re-analyses of the same dataset using a relaxed clock model pushes the age of Hakea to 32.4 (21.8–43.7) million years ago relative to its nearest outgroups, and the age of the divergence of two major clades (A and B) to 24.7 (17.2–33.7) million years ago. Calibration based on a new finding of Late Cretaceous fossil Banksia pushes these dates to 48.0 (24.3–75.2) million years ago and 36.6 (18.5–55.4) million years ago respectively. We confirm that each of the two main clades includes lineages in SWA, CA and EA. At the basal node of Clade A, two eastern Australian species form the sister group to three SWA scrub–heath–Eremaean species. These two groups together are sister to a large, mostly unresolved clade of SWA, CA and EA taxa. Similarly, at the base of Clade B is a polytomy of lineages from the SWA, CA and EA, with no resolution of area relationships. There is no evidence of a centre of origin and diversification of the genus is older than the mid-Miocene, being at least Oligocene, and probably older, although calibration points for molecular dating are too far removed from the ingroup to provide any great confidence in the methodology. Consideration should be given to the possibility of vicariance of multiple, widespread ancestral lineages as an explanation for lineages now disjunct between EA and SWA.
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Halász, Júlia, Andrzej Pedryc, Sezai Ercisli, Kadir Ugurtan Yilmaz, and Attila Hegedűs. "S-genotyping Supports the Genetic Relationships between Turkish and Hungarian Apricot Germplasm." Journal of the American Society for Horticultural Science 135, no. 5 (September 2010): 410–17. http://dx.doi.org/10.21273/jashs.135.5.410.
Повний текст джерелаАнотація:
The S-genotypes of a set of Turkish and Hungarian apricot (Prunus armeniaca L.) cultivars were determined by polymerase chain reaction (PCR) amplification of their S-RNase intron regions. In addition, the S-genotyping method was extended to the SFB gene to detect the non-functional SC-haplotype and hence reliably identify self-compatible apricot cultivars. We determined the complete S-genotype of 51 cultivars and the partial S-genotype of four cultivars. A total of 32 different S-genotypes were assigned to the 51 cultivars, and many of them (28) were classified into newly established cross-incompatibility groups III through XIV. Another 12 cultivars demonstrated unique incompatible genotypes and seven self-compatible cultivars were identified in the examined accessions. The fact that Turkish and Hungarian apricot cultivars carry 12 and five S-alleles, respectively, and all five alleles detected in Hungarian cultivars were also present in Turkish apricots furnished molecular evidence supporting the long-suspected historical connection between Hungarian and Turkish apricots. The connection between these two gene pools appeared to be relatively recent and associated with historical events dating back 300 years. Our results confirm that Turkish germplasm contributed considerably to the development of several desirable Hungarian apricot cultivars. Results suggest that the mutation rendering the SC-haplotype non-functional might have occurred somewhere east of central Turkey.
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Borths, Matthew R., Patricia A. Holroyd, and Erik R. Seiffert. "Hyainailourine and teratodontine cranial material from the late Eocene of Egypt and the application of parsimony and Bayesian methods to the phylogeny and biogeography of Hyaenodonta (Placentalia, Mammalia)." PeerJ 4 (November 10, 2016): e2639. http://dx.doi.org/10.7717/peerj.2639.
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Hyaenodonta is a diverse, extinct group of carnivorous mammals that included weasel- to rhinoceros-sized species. The oldest-known hyaenodont fossils are from the middle Paleocene of North Africa and the antiquity of the group in Afro-Arabia led to the hypothesis that it originated there and dispersed to Asia, Europe, and North America. Here we describe two new hyaenodont species based on the oldest hyaenodont cranial specimens known from Afro-Arabia. The material was collected from the latest Eocene Locality 41 (L-41, ∼34 Ma) in the Fayum Depression, Egypt.Akhnatenavus nefertiticyonsp. nov. has specialized, hypercarnivorous molars and an elongate cranial vault. InA. nefertiticyonthe tallest, piercing cusp on M1–M2is the paracone.Brychotherium ephalmosgen. et sp. nov. has more generalized molars that retain the metacone and complex talonids. InB. ephalmosthe tallest, piercing cusp on M1–M2is the metacone. We incorporate this new material into a series of phylogenetic analyses using a character-taxon matrix that includes novel dental, cranial, and postcranial characters, and samples extensively from the global record of the group. The phylogenetic analysis includes the first application of Bayesian methods to hyaenodont relationships.B. ephalmosis consistently placed within Teratodontinae, an Afro-Arabian clade with several generalist and hypercarnivorous forms, andAkhnatenavusis consistently recovered in Hyainailourinae as part of an Afro-Arabian radiation. The phylogenetic results suggest that hypercarnivory evolved independently three times within Hyaenodonta: in Teratodontinae, in Hyainailourinae, and in Hyaenodontinae. Teratodontines are consistently placed in a close relationship with Hyainailouridae (Hyainailourinae + Apterodontinae) to the exclusion of “proviverrines,” hyaenodontines, and several North American clades, and we propose that the superfamily Hyainailouroidea be used to describe this relationship. Using the topologies recovered from each phylogenetic method, we reconstructed the biogeographic history of Hyaenodonta using parsimony optimization (PO), likelihood optimization (LO), and Bayesian Binary Markov chain Monte Carlo (MCMC) to examine support for the Afro-Arabian origin of Hyaenodonta. Across all analyses, we found that Hyaenodonta most likely originated in Europe, rather than Afro-Arabia. The clade is estimated by tip-dating analysis to have undergone a rapid radiation in the Late Cretaceous and Paleocene; a radiation currently not documented by fossil evidence. During the Paleocene, lineages are reconstructed as dispersing to Asia, Afro-Arabia, and North America. The place of origin of Hyainailouroidea is likely Afro-Arabia according to the Bayesian topologies but it is ambiguous using parsimony. All topologies support the constituent clades–Hyainailourinae, Apterodontinae, and Teratodontinae–as Afro-Arabian and tip-dating estimates that each clade is established in Afro-Arabia by the middle Eocene.
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Lyu, Rudan, Jiamin Xiao, Mingyang Li, Yike Luo, Jian He, Jin Cheng, and Lei Xie. "Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data." International Journal of Molecular Sciences 24, no. 3 (February 3, 2023): 3056. http://dx.doi.org/10.3390/ijms24033056.
Повний текст джерелаАнотація:
The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.
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Kim, K. J., W. Hong, J. H. Park, H. J. Woo, G. Hodgins, and A. J. T. Jull. "Development of Radiocarbon Dating Methods for Modern Bone Collagenization." Radiocarbon 52, no. 4 (2010): 1657–59. http://dx.doi.org/10.1017/s0033822200056381.
Повний текст джерелаАнотація:
The relationship between temperature and time required for collagenization using modern bone samples was investigated. Gelatinized samples of bone collagen were filtered to selectively collect different molecular weight fractions. The results of this study suggest that heating to 70 ° for a duration of 12 hr provides the optimal conditions for gelatinization.
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Forni, Diego, Chiara Pontremoli, Mario Clerici, Uberto Pozzoli, Rachele Cagliani, and Manuela Sironi. "Recent Out-of-Africa Migration of Human Herpes Simplex Viruses." Molecular Biology and Evolution 37, no. 5 (January 9, 2020): 1259–71. http://dx.doi.org/10.1093/molbev/msaa001.
Повний текст джерелаАнотація:
Abstract Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results indicated that HSV-1 populations have limited geographic structure and the most evident clustering by geography is likely due to recent bottlenecks. For HSV-2, the only level of population structure is accounted for by the so-called “worldwide” and “African” lineages. Analysis of ancestry components and nucleotide diversity, however, did not support the view that the worldwide lineage followed early humans during out-of-Africa dispersal. Although phylogeographic analysis confirmed an African origin for both viruses, molecular dating with a method that corrects for the time-dependent rate phenomenon indicated that HSV-1 and HSV-2 migrated from Africa in relatively recent times. In particular, we estimated that the HSV-2 worldwide lineage left the continent in the 18th century, which corresponds to the height of the transatlantic slave trade, possibly explaining the high prevalence of HSV-2 in the Americas (second highest after Africa). The limited geographic clustering of HSV-1 makes it difficult to date its exit from Africa. The split between the basal clade, containing mostly African sequences, and all other strains was dated at ∼5,000 years ago. Our data do not imply that herpes simplex viruses did not infect early humans but show that the worldwide distribution of circulating strains is the result of relatively recent events.
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Jofré-Briceño, Constanza, Felipe Muñoz-La Rivera, Edison Atencio, and Rodrigo F. Herrera. "Implementation of Facility Management for Port Infrastructure through the Use of UAVs, Photogrammetry and BIM." Sensors 21, no. 19 (October 8, 2021): 6686. http://dx.doi.org/10.3390/s21196686.
Повний текст джерелаАнотація:
The maintenance of port infrastructures presents difficulties due to their location: an aggressive environment or the variability of the waves can cause progressive deterioration. Maritime conditions make inspections difficult and, added to the lack of use of efficient tools for the management of assets, planning maintenance, important to ensure operability throughout the life cycle of port infrastructures, is generally not a priority. In view of these challenges, this research proposes a methodology for the creation of a port infrastructure asset management tool, generated based on the Design Science Research Method (DSRM), in line with Building Information Modeling (BIM) and digitization trends in the infrastructure sector. The proposal provides workflows and recommendations for the survey of port infrastructures from UAVs, the reconstruction of digital models by photogrammetry (due to scarce technical documentation), and the reconstruction of BIM models. Along with this, the bidirectional linking of traditional asset management spreadsheets with BIM models is proposed, by visual programming, allowing easy visualization of the status and maintenance requirements. This methodology was applied to a port infrastructure, where the methodology demonstrated the correct functionality of the asset management tool, which allows a constant up-dating of information regarding the structural state of the elements and the necessary maintenance activities.
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Unterberger, Seraphin H., Cordula Berger, Michael Schirmer, Anton Kasper Pallua, Bettina Zelger, Georg Schäfer, Christian Kremser, et al. "Morphological and Tissue Characterization with 3D Reconstruction of a 350-Year-Old Austrian Ardea purpurea Glacier Mummy." Biology 12, no. 1 (January 11, 2023): 114. http://dx.doi.org/10.3390/biology12010114.
Повний текст джерелаАнотація:
Glaciers are dwindling archives, releasing animal mummies preserved in the ice for centuries due to climate changes. As preservation varies, residual soft tissues may differently expand the biological information content of such mummies. DNA studies have proven the possibility of extracting and analyzing DNA preserved in skeletal residuals and sediments for hundreds or thousands of years. Paleoradiology is the method of choice as a non-destructive tool for analyzing mummies, including micro-computed tomography (micro-CT) and magnetic resonance imaging (MRI). Together with radiocarbon dating, histo-anatomical analyses, and DNA sequencing, these techniques were employed to identify a 350-year-old Austrian Ardea purpurea glacier mummy from the Ötztal Alps. Combining these techniques proved to be a robust methodological concept for collecting inaccessible information regarding the structural organization of the mummy. The variety of methodological approaches resulted in a distinct picture of the morphological patterns of the glacier animal mummy. The BLAST search in GenBank resulted in a 100% and 98.7% match in the cytb gene sequence with two entries of the species Purple heron (Ardea purpurea; Accession number KJ941160.1 and KJ190948.1) and a 98% match with the same species for the 16 s sequence (KJ190948.1), which was confirmed by the anatomic characteristics deduced from micro-CT and MRI.
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Warnock, Rachel C. M., Ziheng Yang, and Philip C. J. Donoghue. "Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution." Proceedings of the Royal Society B: Biological Sciences 284, no. 1857 (June 21, 2017): 20170227. http://dx.doi.org/10.1098/rspb.2017.0227.
Повний текст джерелаАнотація:
Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions.
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Chen, Yangkang, Yi Wang, Jialiang Li, Wentao Wang, Duanyu Feng, and Kangshan Mao. "Principles, error sources and application suggestions of prevailing molecular dating methods." Biodiversity Science 29, no. 5 (2021): 629–46. http://dx.doi.org/10.17520/biods.2020273.
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E. Grammatikakis, Kyriakidis, D. Demadis, Cabeza Diaz, and Leon-Reina. "Mineralogical Characterization and Firing Temperature Delineation on Minoan Pottery, Focusing on the Application of Micro-Raman Spectroscopy." Heritage 2, no. 3 (September 17, 2019): 2652–64. http://dx.doi.org/10.3390/heritage2030163.
Повний текст джерелаАнотація:
Ceramic objects in whole or in fragments usually account for the majority of findings in an archaeological excavation. Thus, through examination of the values these items bear, it is possible to extract important information regarding raw materials provenance and ceramic technology. For this purpose, either traditional examination protocols could be followed, focusing on the macroscopic/morphological characteristics of the ancient object, or more sophisticated physicochemical techniques are employed. Nevertheless, there are cases where, due to the uniqueness and the significance of an object of archaeological value, sampling is impossible. Then, the available analytical tools are extremely limited, especially when molecular information and mineral phase identification is required. In this context, the results acquired from a multiphase clay ceramic dated on Early Neopalatioal period ΜΜΙΙΙΑLMIA (1750 B.C.E.–1490 B.C.E.), from the Minoan Bronze Age site at Philioremos (Crete, Greece) through the application of Raman confocal spectroscopy, a nondestructive/ noninvasive method are reported. The spectroscopic results are confirmed through the application of Xray microdiffraction and scanning electron microscopy coupled with energy dispersive Xray spectrometry. Moreover, it is demonstrated how it is made possible through the application of microRaman (μRaman) spectroscopy to examine and collect crucial information from very small inclusions in the ceramic fabric. The aim of this approach is to develop an analytical protocol based on μRaman spectroscopy, for extracting firing temperature information from other ceramic finds (figurines) where due to their uniqueness sampling and analyses through other techniques is not possible. This information can lead to dating but also to firing kiln technology extrapolations that are very significant in archaeology.