Journal articles on the topic 'Tip-dating'
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Bapst, D. W., A. M. Wright, N. J. Matzke, and G. T. Lloyd. "Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)." Biology Letters 12, no. 7 (July 2016): 20160237. http://dx.doi.org/10.1098/rsbl.2016.0237.
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Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.
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Crouch, Nicholas M. A., Karolis Ramanauskas, and Boris Igić. "Tip-dating and the origin of Telluraves." Molecular Phylogenetics and Evolution 131 (February 2019): 55–63. http://dx.doi.org/10.1016/j.ympev.2018.10.006.
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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.
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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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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.
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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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Matzke, Nicholas J., and Randall B. Irmis. "Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data." PeerJ 6 (April 6, 2018): e4553. http://dx.doi.org/10.7717/peerj.4553.
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Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping information, so many character matrices have an ascertainment bias: they omit autapomorphies (unique derived character states), which are considered uninformative. There has been no study of the effect of this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based inference. We expected that excluding autapomorphies would shorten the morphological branchlengths of terminal branches, and thus bias downwards the time branchlengths inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates are virtually unchanged when autapomorphies are excluded, although we find large changes in morphological rate estimates and small effects on topological and dating confidence. We hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of the eureptile data. We confirm this explanation by simulating strict clock and non-clock datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A theoretical solution to ascertainment bias is computing the ascertainment bias correction (Mkparsinf), but we explore this correction in detail, and show that it is computationally impractical for typical datasets with many character states and taxa. Therefore we recommend that palaeontologists collect autapomorphies whenever possible when assembling character matrices.
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Zhang, Chi, and Min Wang. "Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds." Royal Society Open Science 6, no. 7 (July 2019): 182062. http://dx.doi.org/10.1098/rsos.182062.
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Recently, comprehensive morphological datasets including nearly all the well-recognized Mesozoic birds became available, making it feasible for statistically rigorous methods to unveil finer evolutionary patterns during early avian evolution. Here, we exploited the advantage of Bayesian tip dating under relaxed morphological clocks to estimate both the divergence times and evolutionary rates while accounting for their uncertainties. We further subdivided the characters into six body regions (i.e. skull, axial skeleton, pectoral girdle and sternum, forelimb, pelvic girdle and hindlimb) to assess evolutionary rate heterogeneity both along the lineages and across partitions. We observed extremely high rates of morphological character changes during early avian evolution, and the clock rates are quite heterogeneous among the six regions. The branch subtending Pygostylia shows an extremely high rate in the axial skeleton, while the branches subtending Ornithothoraces and Enantiornithes show notably high rates in the pectoral girdle and sternum and moderately high rates in the forelimb. The extensive modifications in these body regions largely correspond to refinement of the flight capability. This study reveals the power and flexibility of Bayesian tip dating implemented in MrBayes to investigate evolutionary dynamics in deep time.
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Lee, Michael S. Y. "Multiple morphological clocks and total-evidence tip-dating in mammals." Biology Letters 12, no. 7 (July 2016): 20160033. http://dx.doi.org/10.1098/rsbl.2016.0033.
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Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or ‘pacemaker’. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths in a heterodox position as stem placentals, but multi-clock analyses retrieved a more plausible and orthodox position within crown placentals. Several shortcomings (including uneven character sampling) currently impact upon the accuracy of total-evidence dating, but this study suggests that when sufficiently large and appropriately constructed phenotypic datasets become more commonplace, multi-clock approaches are feasible and can affect both divergence dates and phylogenetic relationships.
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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.
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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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Matzke, Nicholas J., and April Wright. "Inferring node dates from tip dates in fossil Canidae: the importance of tree priors." Biology Letters 12, no. 8 (August 2016): 20160328. http://dx.doi.org/10.1098/rsbl.2016.0328.
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Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and M r B ayes v. 3.2.5. We find that for key nodes ( Canis, approx. 3.2 Ma, Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic versus non-mechanistic) and their applicability to fossil datasets.
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Lartillot, Nicolas, Matthew J. Phillips, and Fredrik Ronquist. "A mixed relaxed clock model." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1699 (July 19, 2016): 20150132. http://dx.doi.org/10.1098/rstb.2015.0132.
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Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.
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Brocklehurst, Neil. "Olson's Gap or Olson's Extinction? A Bayesian tip-dating approach to resolving stratigraphic uncertainty." Proceedings of the Royal Society B: Biological Sciences 287, no. 1928 (June 10, 2020): 20200154. http://dx.doi.org/10.1098/rspb.2020.0154.
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Adaptive radiations and mass extinctions are of critical importance in structuring terrestrial ecosystems. However, the causes and progress of these transitions often remain controversial, in part because of debates surrounding the completeness of the fossil record and biostratigraphy of the relevant fossil-bearing formations. The early–middle Permian, when a substantial faunal turnover in tetrapods coincided with a restructuring of the trophic structure of ecosystems, is such a time. Some have suggested the transition is obscured by a gap in the tetrapod fossil record (Olson's Gap), while others suggest a correlation between North American and Russian tetrapod-bearing formations allows the interval to be documented in detail. The latter biostratigraphic scheme has been used to support a mass extinction at this time (Olson's Extinction). Bayesian tip-dating methods used frequently in phylogenetics are employed to resolve this debate. Bayes factors are used to compare the results of analyses incorporating tip age priors based on different stratigraphic hypotheses, to show which stratigraphic scheme best fits the morphological data and phylogeny. Olson's Gap is rejected, and the veracity of Olson's Extinction is given further support. Tip-dating approaches have great potential to resolve debates surrounding the stratigraphic ages of critical formations where appropriate morphological data is available.
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Cannatella, David. "Xenopus in Space and Time: Fossils, Node Calibrations, Tip-Dating, and Paleobiogeography." Cytogenetic and Genome Research 145, no. 3-4 (2015): 283–301. http://dx.doi.org/10.1159/000438910.
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Published data from DNA sequences, morphology of 11 extant and 15 extinct frog taxa, and stratigraphic ranges of fossils were integrated to open a window into the deep-time evolution of Xenopus. The ages and morphological characters of fossils were used as independent datasets to calibrate a chronogram. We found that DNA sequences, either alone or in combination with morphological data and fossils, tended to support a close relationship between Xenopus and Hymenochirus, although in some analyses this topology was not significantly better than the Pipa + Hymenochirus topology. Analyses that excluded DNA data found strong support for the Pipa + Hymenochirus tree. The criterion for selecting the maximum age of the calibration prior influenced the age estimates, and our age estimates of early divergences in the tree of frogs are substantially younger than those of published studies. Node-dating and tip-dating calibrations, either alone or in combination, yielded older dates for nodes than did a root calibration alone. Our estimates of divergence times indicate that overwater dispersal, rather than vicariance due to the splitting of Africa and South America, may explain the presence of Xenopus in Africa and its closest fossil relatives in South America.
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Donoghue, Philip C. J., and Ziheng Yang. "The evolution of methods for establishing evolutionary timescales." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1699 (July 19, 2016): 20160020. http://dx.doi.org/10.1098/rstb.2016.0020.
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The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.
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Rossavik, Ivor K. "The tip of the iceberg and the best fit in ultrasonographic dating of pregnancy." American Journal of Obstetrics and Gynecology 166, no. 6 (June 1992): 1867–68. http://dx.doi.org/10.1016/0002-9378(92)91588-2.
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Arcila, Dahiana, R. Alexander Pyron, James C. Tyler, Guillermo Ortí, and Ricardo Betancur-R. "An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)." Molecular Phylogenetics and Evolution 82 (January 2015): 131–45. http://dx.doi.org/10.1016/j.ympev.2014.10.011.
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Rieux, Adrien, and Camilo E. Khatchikian. "tipdatingbeast : an r package to assist the implementation of phylogenetic tip-dating tests using beast." Molecular Ecology Resources 17, no. 4 (October 25, 2016): 608–13. http://dx.doi.org/10.1111/1755-0998.12603.
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Beck, Robin M. D., Dorien de Vries, Mareike C. Janiak, Ian B. Goodhead, and Jean P. Boubli. "Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches." Journal of Human Evolution 174 (January 2023): 103293. http://dx.doi.org/10.1016/j.jhevol.2022.103293.
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Xia, Xuhua. "Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes." Viruses 13, no. 9 (September 8, 2021): 1790. http://dx.doi.org/10.3390/v13091790.
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All dating studies involving SARS-CoV-2 are problematic. Previous studies have dated the most recent common ancestor (MRCA) between SARS-CoV-2 and its close relatives from bats and pangolins. However, the evolutionary rate thus derived is expected to differ from the rate estimated from sequence divergence of SARS-CoV-2 lineages. Here, I present dating results for the first time from a large phylogenetic tree with 86,582 high-quality full-length SARS-CoV-2 genomes. The tree contains 83,688 genomes with full specification of collection time. Such a large tree spanning a period of about 1.5 years offers an excellent opportunity for dating the MRCA of the sampled SARS-CoV-2 genomes. The MRCA is dated 16 August 2019, with the evolutionary rate estimated to be 0.05526 mutations/genome/day. The Pearson correlation coefficient (r) between the root-to-tip distance (D) and the collection time (T) is 0.86295. The NCBI tree also includes 10 SARS-CoV-2 genomes isolated from cats, collected over roughly the same time span as human COVID-19 infection. The MRCA from these cat-derived SARS-CoV-2 is dated 30 July 2019, with r = 0.98464. While the dating method is well known, I have included detailed illustrations so that anyone can repeat the analysis and obtain the same dating results. With 16 August 2019 as the date of the MRCA of sampled SARS-CoV-2 genomes, archived samples from respiratory or digestive tracts collected around or before 16 August 2019, or those that are not descendants of the existing SARS-CoV-2 lineages, should be particularly valuable for tracing the origin of SARS-CoV-2.
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Emerson, Brent C., Diego F. Alvarado-Serrano, and Michael J. Hickerson. "Comment on Rieux and Balloux: calibration from tip-dating can compromise topological accuracy and evolutionary inference." Molecular Ecology 26, no. 10 (December 31, 2016): 2623–24. http://dx.doi.org/10.1111/mec.13951.
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Jones, Bradley R., Natalie N. Kinloch, Joshua Horacsek, Bruce Ganase, Marianne Harris, P. Richard Harrigan, R. Brad Jones, et al. "Phylogenetic approach to recover integration dates of latent HIV sequences within-host." Proceedings of the National Academy of Sciences 115, no. 38 (September 5, 2018): E8958—E8967. http://dx.doi.org/10.1073/pnas.1802028115.
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Given that HIV evolution and latent reservoir establishment occur continually within-host, and that latently infected cells can persist long-term, the HIV reservoir should comprise a genetically heterogeneous archive recapitulating within-host HIV evolution. However, this has yet to be conclusively demonstrated, in part due to the challenges of reconstructing within-host reservoir establishment dynamics over long timescales. We developed a phylogenetic framework to reconstruct the integration dates of individual latent HIV lineages. The framework first involves inference and rooting of a maximum-likelihood phylogeny relating plasma HIV RNA sequences serially sampled before the initiation of suppressive antiretroviral therapy, along with putative latent sequences sampled thereafter. A linear model relating root-to-tip distances of plasma HIV RNA sequences to their sampling dates is used to convert root-to-tip distances of putative latent lineages to their establishment (integration) dates. Reconstruction of the ages of putative latent sequences sampled from chronically HIV-infected individuals up to 10 y following initiation of suppressive therapy revealed a genetically heterogeneous reservoir that recapitulated HIV’s within-host evolutionary history. Reservoir sequences were interspersed throughout multiple within-host lineages, with the oldest dating to >20 y before sampling; historic genetic bottleneck events were also recorded therein. Notably, plasma HIV RNA sequences isolated from a viremia blip in an individual receiving otherwise suppressive therapy were highly genetically diverse and spanned a 20-y age range, suggestive of spontaneous in vivo HIV reactivation from a large latently infected cell pool. Our framework for reservoir dating provides a potentially powerful addition to the HIV persistence research toolkit.
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Wright, David F. "Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)." Journal of Paleontology 91, no. 4 (February 8, 2017): 799–814. http://dx.doi.org/10.1017/jpa.2016.141.
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AbstractKnowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian ‘tip-dating’ approaches to phylogeny estimation is especially promising for paleosystematists because time-stamped comparative data can be combined with probabilistic models tailored to accommodate the study of fossil taxa. Under a Bayesian framework, the recently developed fossilized birth–death (FBD) process provides a more realistic tree prior model for paleontological data that accounts for macroevolutionary dynamics, preservation, and sampling when inferring phylogenetic trees containing fossils. In addition, the FBD tree prior allows for the possibility of sampling ancestral morphotaxa. Although paleontologists are increasingly embracing probabilistic phylogenetic methods, these recent developments have not previously been applied to the deep-time invertebrate fossil record. Here, I examine phylogenetic relationships among Ordovician through Devonian crinoids using a Bayesian tip-dating approach. Results support several clades recognized in previous analyses sampling only Ordovician taxa, but also reveal instances where phylogenetic affinities are more complex and extensive revisions are necessary, particularly among the Cladida. The name Porocrinoidea is proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids and hybocrinids. The Eucladida is proposed as a clade name for the sister group of the Flexibilia herein comprised of cladids variously considered ‘cyathocrines,’ ‘dendrocrines,’ and/or ‘poteriocrines’ by other authors.
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Lee, Michael S. Y., and Adam M. Yates. "Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record." Proceedings of the Royal Society B: Biological Sciences 285, no. 1881 (June 27, 2018): 20181071. http://dx.doi.org/10.1098/rspb.2018.1071.
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Simultaneously analysing morphological, molecular and stratigraphic data suggests a potential resolution to a major remaining inconsistency in crocodylian evolution. The ancient, long-snouted thoracosaurs have always been placed near the Indian gharial Gavialis , but their antiquity ( ca 72 Ma) is highly incongruous with genomic evidence for the young age of the Gavialis lineage ( ca 40 Ma). We reconcile this contradiction with an updated morphological dataset and novel analysis, and demonstrate that thoracosaurs are an ancient iteration of long-snouted stem crocodylians unrelated to modern gharials. The extensive similarities between thoracosaurs and Gavialis are shown to be an almost ‘perfect storm’ of homoplasy, combining convergent adaptions to fish-eating, as well resemblances between genuinely primitive traits (thoracosaurs) and atavisms ( Gavialis ). Phylogenetic methods that ignore stratigraphy (parsimony and undated Bayesian methods) are unable to tease apart these similarities and invariably unite thoracosaurs and Gavialis. However, tip-dated Bayesian approaches additionally consider the large temporal gap separating ancient (thoracosaurs) and modern ( Gavialis ) iterations of similar long-snouted crocodyliforms. These analyses robustly favour a phylogeny which places thoracosaurs basal to crocodylians, far removed from modern gharials, which accordingly are a very young radiation. This phylogenetic uncoupling of ancient and modern gharial-like crocs is more consistent with molecular clock divergence estimates, and also the bulk of the crocodylian fossil record (e.g. all unequivocal gharial fossils are very young). Provided that the priors and models attribute appropriate relative weights to the morphological and stratigraphic signals—an issue that requires investigation—tip-dating approaches are potentially better able to detect homoplasy and improve inferences about phylogenetic relationships, character evolution and divergence dates.
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Sauzier, Georgina, Jasmine McGann, Simon W. Lewis, and Wilhelm van Bronswijk. "A study into the ageing and dating of blue ball tip inks on paper using in situ visible spectroscopy with chemometrics." Analytical Methods 10, no. 47 (2018): 5613–21. http://dx.doi.org/10.1039/c8ay01418c.
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Poinar, Jr., George O., Kenton L. Chambers, Urszula T. Iwaniec, and Fernando E. Vega. "Valviloculus pleristaminis gen. et sp. nov., a Lauralean fossil flower with valvate anthers from mid-Cretaceous Myanmar amber." Journal of the Botanical Research Institute of Texas 14, no. 2 (December 7, 2020): 359–66. http://dx.doi.org/10.17348/jbrit.v14.i2.1014.
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The flower described here as Valviloculus pleristaminis, a new genus and species of fossil angiosperms, was obtained from Myanmar amber deposits dating to the mid-Cretaceous period. The flower is staminate, with an ovoid, hollow floral cup. The perianth consists of 6 tepals, one of which was lost prior to preservation. Numerous helically arranged stamens are borne at the summit of the flower. The anthers are bilocular, with pollen sacs that dehisce by laterally hinged valves. The tip of the connective bears a cup-shaped appendage. The gynoecium is represented only by a cluster of vestigial styles centered among the stamens. The fossil is provisionally assigned to order Laurales, its closest affinities being with the families Monimiaceae and Atherospermataceae.
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Sallam, Hesham M., and Erik R. Seiffert. "New phiomorph rodents from the latest Eocene of Egypt, and the impact of Bayesian “clock”-based phylogenetic methods on estimates of basal hystricognath relationships and biochronology." PeerJ 4 (March 1, 2016): e1717. http://dx.doi.org/10.7717/peerj.1717.
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The Fayum Depression of Egypt has yielded fossils of hystricognathous rodents from multiple Eocene and Oligocene horizons that range in age from ∼37 to ∼30 Ma and document several phases in the early evolution of crown Hystricognathi and one of its major subclades, Phiomorpha. Here we describe two new genera and species of basal phiomorphs,Birkamys koraiandMubhammys vadumensis, based on rostra and maxillary and mandibular remains from the terminal Eocene (∼34 Ma) Fayum Locality 41 (L-41).Birkamysis the smallest known Paleogene hystricognath, has very simple molars, and, like derived Oligocene-to-Recent phiomorphs (but unlike contemporaneous and older taxa) apparently retained dP4∕4late into life, with no evidence for P4∕4eruption or formation.Mubhammysis very similar in dental morphology toBirkamys, and also shows no evidence for P4∕4formation or eruption, but is considerably larger. Though parsimony analysis with all characters equally weighted placesBirkamysandMubhammysas sister taxa of extantThryonomysto the exclusion of much younger relatives of that genus, all other methods (standard Bayesian inference, Bayesian “tip-dating,” and parsimony analysis with scaled transitions between “fixed” and polymorphic states) place these species in more basal positions within Hystricognathi, as sister taxa of Oligocene-to-Recent phiomorphs. We also employ tip-dating as a means for estimating the ages of early hystricognath-bearing localities, many of which are not well-constrained by geological, geochronological, or biostratigraphic evidence. By simultaneously taking into account phylogeny, evolutionary rates, and uniform priors that appropriately encompass the range of possible ages for fossil localities, dating of tips in this Bayesian framework allows paleontologists to move beyond vague and assumption-laden “stage of evolution” arguments in biochronology to provide relatively rigorous age assessments of poorly-constrained faunas. This approach should become increasingly robust as estimates are combined from multiple independent analyses of distantly related clades, and is broadly applicable across the tree of life; as such it is deserving of paleontologists’ close attention. Notably, in the example provided here, hystricognathous rodents from Libya and Namibia that are controversially considered to be of middle Eocene age are instead estimated to be of late Eocene and late Oligocene age, respectively. Finally, we reconstruct the evolution of first lower molar size among Paleogene African hystricognaths using a Bayesian approach; the results of this analysis reconstruct a rapid latest Eocene dwarfing event along the lineage leading toBirkamys.
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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.
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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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Flammensbeck, Christina K., Jürgen Pollerspöck, Frederic D. B. Schedel, Nicholas J. Matzke, and Nicolas Straube. "Of teeth and trees: A fossil tip-dating approach to infer divergence times of extinct and extant squaliform sharks." Zoologica Scripta 47, no. 5 (August 2, 2018): 539–57. http://dx.doi.org/10.1111/zsc.12299.
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Pettersson, John H. O., and Omar Fiz-Palacios. "Dating the origin of the genus Flavivirus in the light of Beringian biogeography." Journal of General Virology 95, no. 9 (September 1, 2014): 1969–82. http://dx.doi.org/10.1099/vir.0.065227-0.
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The genus Flavivirus includes some of the most important human viral pathogens, and its members are found in all parts of the populated world. The temporal origin of diversification of the genus has long been debated due to the inherent problems with dating deep RNA virus evolution. A generally accepted hypothesis suggests that Flavivirus emerged within the last 10 000 years. However, it has been argued that the tick-borne Powassan flavivirus was introduced into North America some time between the opening and closing of the Beringian land bridge that connected Asia and North America 15 000–11 000 years ago, indicating an even older origin for Flavivirus. To determine the temporal origin of Flavivirus, we performed Bayesian relaxed molecular clock dating on a dataset with high coverage of the presently available Flavivirus diversity by combining tip date calibrations and internal node calibration, based on the Powassan virus and Beringian land bridge biogeographical event. Our analysis suggested that Flavivirus originated ~85 000 (64 000–110 000) or 120 000 (87 000–159 000) years ago, depending on the circumscription of the genus. This is significantly older than estimated previously. In light of our results, we propose that it is likely that modern humans came in contact with several members of the genus Flavivirus much earlier than suggested previously, and that it is possible that the spread of several flaviviruses coincided with, and was facilitated by, the migration and population expansion of modern humans out of Africa.
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Sallam, Hesham M., and Erik R. Seiffert. "Revision of Oligocene ‘Paraphiomys’ and an origin for crown Thryonomyoidea (Rodentia: Hystricognathi: Phiomorpha) near the Oligocene–Miocene boundary in Africa." Zoological Journal of the Linnean Society 190, no. 1 (December 30, 2019): 352–71. http://dx.doi.org/10.1093/zoolinnean/zlz148.
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Abstract ‘Paraphiomys’ simonsi is a phiomorph rodent from the early Oligocene of Egypt (~29–30 Mya) that has historically been aligned with much younger (< ~20 Mya) Miocene species of the genera Paraphiomys and Neosciuromys. Here, we use Bayesian tip-dating analysis of a 109-character morphological matrix containing 57 living and extinct ctenohystricans to test these proposed placements for ‘Paraphiomys’ simonsi. Our analyses provide support for the exclusion of ‘Paraphiomys’ simonsi from both Paraphiomys and Neosciuromys and justify the establishment of a new genus (Monamys gen. nov.) for this stem thryonomyoid. These analyses also indicate that the divergence of the extant dassie rat Petromus from the extant cane rat Thryonomys (i.e. origin of crown Thryonomyoidea) occurred ~23.7 Mya, close to the Oligocene–Miocene boundary and in close agreement with recent molecular estimates for this split. Miocene Neosciuromys, Paraulacodus, Protohummus and the type species of Paraphiomys are identified as stem thryonomyids, whereas the Namibian species Apodecter stromeri, Tufamys woodi, ‘Paraphiomys’ australis and ‘Paraphiomys’ roessneri are identified for the first time as stem petromurids, raising the possibility of a long period of endemic petromurid evolution in south-west Africa. Comparison of molecular divergence estimates with our optimal tip-dated topology suggests that stem bathyergoids are most likely to have arisen from late Eocene and early Oligocene ‘phiomyids’.
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Bradfield, Justin. "Identifying Bone-Tipped Arrow Types in the Archaeological Record of Southern Africa: The Contribution of Use-Trace Studies." Journal of African Archaeology 13, no. 2 (November 1, 2015): 135–47. http://dx.doi.org/10.3213/2191-5784-10278.
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This study presents a historical review of the different types of southern African hunter-gatherer arrows employing a piece of bone situated at or near the tip of the arrow, which I call the apical bone component. The results of an extensive use-trace study of bone points and fragments thereof from twelve archaeological sites spanning the last 18,000 years show that it is possible to identify arrow types based on associated use-trace features. Five possible arrow types are identified from the archaeological sample, all dating to within the last 4000–6000 years. Using use-trace studies it is possible to identify now-missing components of the arrows, such as metal, mastic or stone inserts. Contrary to recent claims, I do not find evidence for bone-tipped arrows evolving along a continuum. Rather, some arrow types may have a much greater antiquity than previously thought.
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Campos, Paola E., Clara Groot Crego, Karine Boyer, Myriam Gaudeul, Claudia Baider, Damien Richard, Olivier Pruvost, et al. "First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence." PLOS Pathogens 17, no. 7 (July 29, 2021): e1009714. http://dx.doi.org/10.1371/journal.ppat.1009714.
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Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.
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Wright, David F., and Ursula Toom. "New crinoids from the Baltic region (Estonia): fossil tip-dating phylogenetics constrains the origin and Ordovician-Silurian diversification of the Flexibilia (Echinodermata)." Palaeontology 60, no. 6 (August 30, 2017): 893–910. http://dx.doi.org/10.1111/pala.12324.
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Lloyd, G. T., D. W. Bapst, M. Friedman, and K. E. Davis. "Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds." Biology Letters 12, no. 11 (November 2016): 20160609. http://dx.doi.org/10.1098/rsbl.2016.0609.
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Branch lengths—measured in character changes—are an essential requirement of clock-based divergence estimation, regardless of whether the fossil calibrations used represent nodes or tips. However, a separate set of divergence time approaches are typically used to date palaeontological trees, which may lack such branch lengths. Among these methods, sophisticated probabilistic approaches have recently emerged, in contrast with simpler algorithms relying on minimum node ages. Here, using a novel phylogenetic hypothesis for Mesozoic dinosaurs, we apply two such approaches to estimate divergence times for: (i) Dinosauria, (ii) Avialae (the earliest birds) and (iii) Neornithes (crown birds). We find: (i) the plausibility of a Permian origin for dinosaurs to be dependent on whether Nyasasaurus is the oldest dinosaur, (ii) a Middle to Late Jurassic origin of avian flight regardless of whether Archaeopteryx or Aurornis is considered the first bird and (iii) a Late Cretaceous origin for Neornithes that is broadly congruent with other node- and tip-dating estimates. Demonstrating the feasibility of probabilistic time-scaling further opens up divergence estimation to the rich histories of extinct biodiversity in the fossil record, even in the absence of detailed character data.
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Fei, L., and P. Fraundorf. "Evidence for a raised rim on pits in mica induced by keV/nucleon ions." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 390–91. http://dx.doi.org/10.1017/s0424820100138324.
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Nuclear tracks have been extensively studied and widely used in applications like archeological and geological dating, solar flare iostope determination, extraterrestrial material studies, super heavy elementary particle searches, etc. for more than three decades. Recently, scanning force microscopy (SFM) has proven to be useful for studying the pits induced by ions in the track recording energy range from several keV to several MeV per nucleaon on track recording material (e.g. mica) surfaces. SFM can provide topographical information on chemically etched or unetched track pits at near atomic resolution in all three dimensions.We report here using a commercial SFM (NanoScope III, Digital Instruments, CA) in the study of a muscovite mica surfaces irradiated with 150keV Ar+ ions. The mica was freshly cleaved before the irradiation. The SFM was operated with the amplitude resonance (tapping) mode to lower the interaction between a tip and specimen. We found pits on the mica surface after, but not before the irradiation, like those shown in Fig. la. Their number density was orders of magnitude less than the expected argon flux.
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Baral, Upendra, Ding Lin, Khum N. Paudayal, Deepak Chamlagain, and Qasim Muhammad. "Erosional unroofing of Himalaya in far western Nepal: a detrital zircon U-Pb geochronology and petrography study." Journal of Nepal Geological Society 53 (December 31, 2017): 1–8. http://dx.doi.org/10.3126/jngs.v53i0.23795.
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Since the collision between the Indian and Asian plates, several peripheral foreland basin were formed, and started to accumulate the sediments from the hinterland Himalayan orogeny. The sediments deposited at the northern tip of the Greater India have been uplifted, exhumed after the activation of several south propagating thrusts and finally transported to the foreland basin by southward flowing fluvial system. We present petrography and detrital zircon dating for the interpretation of possible provenance of the Neogene Siwalik foreland basin sediments in far western Nepal. The QFL ternary plot for provenance analysis show a 'recycled orogeny' field for the studied sandstone samples, indicating Tethys Himalaya, Higher Himalaya and Lesser Himalaya as the source of the foreland basin sediments. The detrital zircon U-Pb ages of the studied samples have shown that during the time of deposition there was dominant numbers of detritus supplied from the Tethys and upper Lesser Himalaya. Subsequently the amount of the Higher and Lower Lesser Himalaya increased during the time of deposition of the Middle Siwalik.
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Gryseels, Sophie, Thomas D. Watts, Jean-Marie Kabongo Mpolesha, Brendan B. Larsen, Philippe Lemey, Jean-Jacques Muyembe-Tamfum, Dirk E. Teuwen, and Michael Worobey. "A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue." Proceedings of the National Academy of Sciences 117, no. 22 (May 19, 2020): 12222–29. http://dx.doi.org/10.1073/pnas.1913682117.
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With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 (“DRC66”)—a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.
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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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Kinloch, Natalie N., Daniel R. MacMillan, Anh Q. Le, Laura A. Cotton, David R. Bangsberg, Susan Buchbinder, Mary Carrington, et al. "Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic." Journal of Virology 90, no. 3 (November 11, 2015): 1244–58. http://dx.doi.org/10.1128/jvi.02353-15.
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ABSTRACTHuman leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989;n= 338) and modern (2001 to 2011;n= 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era.IMPORTANCEHLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may accumulate in circulation over time, potentially undermining host antiviral immunity to the transmitted viral strain. We studied >600 experimentally collected HIV-1 polymerase sequences linked to host HLA information dating back to 1979, along with phylogenetically reconstructed HIV-1 sequences dating back to the virus' introduction into North America. Overall, our results support the gradual spread of many—though not all—HIV-1 polymerase immune escape mutations in circulation over time. This is consistent with recent observations from other global regions, though the extent of polymorphism accumulation in North America appears to be lower than in populations with high seroprevalence, older epidemics, and/or limited HLA diversity. Importantly, the risk of acquiring an HIV-1 polymerase sequence at transmission that is substantially preadapted to one's HLA profile remains relatively low in North America, even in the present era.
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Congreve, Curtis R., Mark E. Patzkowsky, and Peter J. Wagner. "An early burst in brachiopod evolution corresponding with significant climatic shifts during the Great Ordovician Biodiversification Event." Proceedings of the Royal Society B: Biological Sciences 288, no. 1958 (September 2021): 20211450. http://dx.doi.org/10.1098/rspb.2021.1450.
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We employ modified tip-dating methods to date divergence times within the Strophomenoidea, one of the most abundant and species-rich brachiopod clades to radiate during the Great Ordovician Biodiversification Event (GOBE), to determine if significant environmental changes at this time correlate with the diversification of the clade. Models using origination, extinction and sampling rates to estimate prior probabilities of divergence times strongly support both high rates of anatomical change per million years and rapid divergences shortly before the clade first appears in the fossil record. These divergence times indicate much higher rates of cladogenesis than are typical of brachiopods during this interval. The correspondence of high speciation rates and high anatomical disparity suggests punctuated (speciational) change drove the high frequencies of early anatomical change, which in turn suggests increased ecological opportunities rather than shifting developmental constraints account for high rates of anatomical change. The pulse of rapid evolution began coincident with cooling temperatures, the start of major oscillations in sea level and increased levels of atmospheric oxygen. Our results suggest that these factors permitted major geographical and ecological expansion of strophomenoids with intervals of geographical isolation, resulting in elevated speciation rates and corresponding elevated frequencies of punctuated change.
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LEE, Michael S. Y., Matthew G. BARON, David B. NORMAN, and Paul M. BARRETT. "Dynamic biogeographic models and dinosaur origins." Earth and Environmental Science Transactions of the Royal Society of Edinburgh 109, no. 1-2 (March 2018): 325–32. http://dx.doi.org/10.1017/s1755691018000920.
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ABSTRACTA comprehensive analysis of early dinosaur relationships raised the possibility that the group may have originated in Laurasia (Northern Hemisphere), rather than Gondwana (Southern Hemisphere) as often thought. However, that study focused solely on morphology and phylogenetic relationships and did not quantitatively evaluate this issue. Here, we investigate dinosaur origins using a novel Bayesian framework uniting tip-dated phylogenetics with dynamic, time-sliced biogeographic methods, which explicitly account for the age and locality of fossils and the changing interconnections of areas through time due to tectonic and eustatic change. Our analysis finds strong support for a Gondwanan origin of Dinosauria, with 99 % probability for South America (83 % for southern South America). Parsimony analysis gives concordant results. Inclusion of time-sliced biogeographic information affects ancestral state reconstructions (e.g., high connectivity between two regions increases uncertainty over which is the ancestral area) and influences tree topology (disfavouring uniting fossil taxa from localities that were widely separated during the relevant time slice). Our approach directly integrates plate tectonics with phylogenetics and divergence dating, and in doing so reaffirms southern South America as the most likely area for the geographic origin of Dinosauria.
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Madzia, Daniel, and Andrea Cau. "Inferring ‘weak spots’ in phylogenetic trees: application to mosasauroid nomenclature." PeerJ 5 (September 15, 2017): e3782. http://dx.doi.org/10.7717/peerj.3782.
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Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the ‘weak spots’ in the phylogeny of mosasauroids, we revise the nomenclature of the ‘traditionally’ recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.
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Wibowo, Marsha C., Zhen Yang, Maxime Borry, Alexander Hübner, Kun D. Huang, Braden T. Tierney, Samuel Zimmerman, et al. "Reconstruction of ancient microbial genomes from the human gut." Nature 594, no. 7862 (May 12, 2021): 234–39. http://dx.doi.org/10.1038/s41586-021-03532-0.
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AbstractLoss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.
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Robertson, J., G. P. Roberts, F. Iezzi, M. Meschis, D. M. Gheorghiu, D. Sahy, C. Bristow, and C. Sgambato. "Distributed normal faulting in the tip zone of the South Alkyonides Fault System, Gulf of Corinth, constrained using 36Cl exposure dating of late-Quaternary wave-cut platforms." Journal of Structural Geology 136 (July 2020): 104063. http://dx.doi.org/10.1016/j.jsg.2020.104063.
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Paterson, John R., Gregory D. Edgecombe, and Michael S. Y. Lee. "Trilobite evolutionary rates constrain the duration of the Cambrian explosion." Proceedings of the National Academy of Sciences 116, no. 10 (February 19, 2019): 4394–99. http://dx.doi.org/10.1073/pnas.1819366116.
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Trilobites are often considered exemplary for understanding the Cambrian explosion of animal life, due to their unsurpassed diversity and abundance. These biomineralized arthropods appear abruptly in the fossil record with an established diversity, phylogenetic disparity, and provincialism at the beginning of Cambrian Series 2 (∼521 Ma), suggesting a protracted but cryptic earlier history that possibly extends into the Precambrian. However, recent analyses indicate elevated rates of phenotypic and genomic evolution for arthropods during the early Cambrian, thereby shortening the phylogenetic fuse. Furthermore, comparatively little research has been devoted to understanding the duration of the Cambrian explosion, after which normal Phanerozoic evolutionary rates were established. We test these hypotheses by applying Bayesian tip-dating methods to a comprehensive dataset of Cambrian trilobites. We show that trilobites have a Cambrian origin, as supported by the trace fossil record and molecular clocks. Surprisingly, they exhibit constant evolutionary rates across the entire Cambrian, for all aspects of the preserved phenotype: discrete, meristic, and continuous morphological traits. Our data therefore provide robust, quantitative evidence that by the time the typical Cambrian fossil record begins (∼521 Ma), the Cambrian explosion had already largely concluded. This suggests that a modern-style marine biosphere had rapidly emerged during the latest Ediacaran and earliest Cambrian (∼20 million years), followed by broad-scale evolutionary stasis throughout the remainder of the Cambrian.
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Hervé, Francisco, Jorge Lobato, Ignacio Ugalde, and Robert J. Pankhurst. "The geology of Cape Dubouzet, northern Antarctic Peninsula: continental basement to the Trinity Peninsula Group?" Antarctic Science 8, no. 4 (December 1996): 407–14. http://dx.doi.org/10.1017/s0954102096000582.
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Cape Dubouzet is mainly composed of a volcanic-subvolcanic complex of extrusive rhyolitic breccias, a banded rhyolite and a semi-annular body of dacite porphyry rich in xenoliths of metamorphic rocks. Major and REE geochemistry indicate that the volcanic rocks are calc-alkaline and that they are genetically related by fractional crystallization of a plagioclase-bearing assemblage from a common magma. Rb-Sr data suggest that the rhyolitic complex is of Middle-to-Late Jurassic age, and that it is intruded by Late Cretaceous stocks of banded diorite and gabbro. All these rocks are partially covered by moraines whose clasts are of local provenance. Xenoliths in the dacite porphyry suggest that the northern tip of the Antarctic Peninsula is underlain by a metamorphic complex composed of amphibolites, meta-tonalites and pelitic gneiss containing garnet, sillimanite, cordierite, hercynite, and andalucite. Such rocks are not known in the Scotia metamorphic complex, nor in the Trinity Peninsula Group and its low grade metamorphic derivatives, which also occur as rare xenoliths in the dacite. Previous dating of xenoliths collected from the moraines suggested a late Carboniferous age for this amphibolite-grade metamorphism. Both the Jurassic-Cenozoic magmatic arc of the Antarctic Peninsula and the accretionary complex rocks of the Trinity Peninsula Group were thus developed, at least in part, over pre-existing continental crust.
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Timberlake, Simon. "Prehistoric Copper Extraction in Britain: Ecton Hill, Staffordshire." Proceedings of the Prehistoric Society 80 (December 23, 2013): 159–206. http://dx.doi.org/10.1017/ppr.2013.17.
Full textAbstract:
Major investigations were undertaken of the Ecton Copper Mines, Staffordshire, following the discovery of hammerstones and a red deer antler tool dating to the Early Bronze Age during surface and underground exploration in the 1990s. Ecton Hill was surveyed, the distribution of hammerstone tools examined, and two identified sites of potential prehistoric mining close to the summit of the hill excavated in 2008 & 2009. Excavations at Stone Quarry Mine revealed noin situprehistoric mining activity, but hammerstones and Early Bronze Age bone mining tools from upcast suggest that an historic mine shaft had intersected Bronze Age workings at around 10–25 m depth. On The Lumb one trench revealed evidence for medieval lead mining, while another examined the lowest of four primitive mines associated with cave-like mine entrances along the base of a small cliff. Evidence for prehistoric mining was recorded within a shallow opencut formed by during extraction of malachite from a layer of mineralised dolomite. Traces of the imprint of at least 18 bone and stone tools could be seen and seven different types of working were identified. Most prehistoric mining debris appears to have been cleared out during the course of later, medieval–post-medieval prospection; some bone and stone tools were recovered from this spoil. The tip of a worn and worked (cut) antler tine point was the only such mining tool foundin situat this site but nine tools were radiocarbon dated toc.1880–1640 calbc. Bayesian modelling of the dates from both sites probably indicates mining over a much briefer period (perhaps 20–50 years) at 1800–1700 calbc, with mining at Stone Quarry possibly beginning earlier and lasting longer than on The Lumb. A single date from The Lumb suggests possible renewed mining activity (or prospection?) during the Middle Bronze Age. The dating of this mining activity is consistent with the idea that mining and prospection moved eastwards from Ireland to Wales, then to central England, at the beginning of the 2nd millenniumbc. At Ecton the extraction of secondary ores may have produced only a very small tonnage of copper metal. The mine workers may have been Early Bronze Age farmers who occupied this part of the Peak District seasonally in a transhumant or sustained way
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Poinar, Jr., George O., and Kenton L. Chambers. "Fossil flowers of Lachnociona camptostylus sp. nov., a second record for the genus in mid-Cretaceous Myanmar Amber." Journal of the Botanical Research Institute of Texas 12, no. 2 (November 20, 2018): 655–66. http://dx.doi.org/10.17348/jbrit.v12.i2.966.
Full textAbstract:
Two flowers embedded in a single block of amber from Myanmar are here proposed as a second species of the previously described fossil genus Lachnociona. The mid-Cretaceous age of the fossils was earlier established through paleontological and U-Pb isotope dating methods. Because they lie within millimeters of each other in the amber, the flowers are assumed to have come from the same parent plant. One flower is hermaphrodite while the other is functionally pistillate. They differ by the number of styles—4 in the perfect flower and 5 in the unisexual one—and most notably by the presence, in the perfect flower, of 10 conspicuous nectar glands forming a disc above the whorl of stamens. The pistillate flower has no such glands. In the new species, the arched styles are widely divergent and the ovary is fully inferior, while in the earlier-described Lachnociona terriae, the flower is functionally pistillate, with styles that are erect and connivent or connate. It could not be determined whether the ovary is superior or half-inferior. The best-preserved anther in the perfect flower of L. camptostylus resembles, in its dorsal filament attachment and hooked filament tip, a vestigial anther present in the flower of L. terriae. Pollen of the new species is tri- or tetracolpate. As proposed in the previous paper, the genus may have participated in the early diversification of the rosid clade of eudicots.
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Marivaux, Laurent, and Myriam Boivin. "Emergence of hystricognathous rodents: Palaeogene fossil record, phylogeny, dental evolution and historical biogeography." Zoological Journal of the Linnean Society 187, no. 3 (September 4, 2019): 929–64. http://dx.doi.org/10.1093/zoolinnean/zlz048.
Full textAbstract:
AbstractAlthough phylogenetic trees imply Asia as the ancestral homeland of the Hystricognathi clade (Rodentia: Ctenohystrica), curiously the oldest known fossil occurrences of hystricognathous rodents are not from Asia, but from Africa and South America, where they appear suddenly in the fossil record of both landmasses by the Late Middle Eocene. Here we performed cladistic and Bayesian (standard and tip-dating analyses) assessments of the dental evidence documenting early ctenohystricans, including several Asian ‘ctenodactyloids’, virtually all Palaeogene Asian and African hystricognaths known thus far and two representatives of the earliest known South American hystricognaths. Our results provide a phylogenetic context of early hystricognaths (with implications on systematics) and suggest that some Eocene Asian ‘ctenodactyloids’ could be considered as stem hystricognaths and pre-hystricognaths, although they were not recognized as such originally. However, this view does not fill the gap of the Eocene Asian hystricognath record, as the proposed results imply many ghost lineages extending back to the Middle Eocene for several Asian and African taxa. They also imply a complex early historical biogeography of the group, involving multiple dispersal events from Asia to Africa (and possibly from Africa back to Asia) and then to South America sometime during the Middle Eocene. Based on these phylogenetic considerations, we discuss the emergence of hystricognathous rodents from a morpho-anatomical perspective by analysing the differentiation of their masticatory apparatus and chewing movements, notably through the evolution of their dental patterns.
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Campbell, Kenneth E., Paul B. O’Sullivan, John G. Fleagle, Dorien de Vries, and Erik R. Seiffert. "An Early Oligocene age for the oldest known monkeys and rodents of South America." Proceedings of the National Academy of Sciences 118, no. 37 (September 7, 2021): e2105956118. http://dx.doi.org/10.1073/pnas.2105956118.
Full textAbstract:
The Santa Rosa fossil locality in eastern Perú produced the first Paleogene vertebrate fauna from the Amazon Basin, including the oldest known monkeys from South America. This diverse paleofauna was originally assigned an Eocene age based largely on the stage of evolution of the site’s caviomorph rodents and marsupials. Here, we present detrital zircon dates that indicate that the maximum composite age of Santa Rosa is 29.6 ± 0.08 Ma (Lower Oligocene), although several zircons from Santa Rosa date to the Upper Oligocene. The first appearance datum for Caviomorpha in South America is purported to be the CTA-27 site in the Contamana region of Perú, which is hypothesized to be ∼41 Ma (Middle Eocene) in age. However, the presence of the same caviomorph species and/or genera at both CTA-27 and at Santa Rosa is now difficult to reconcile with a >11-My age difference. To further test the Middle Eocene age estimate for CTA-27, we ran multiple Bayesian tip-dating analyses of Caviomorpha, treating the ages of all Paleogene species from Perú as unknown. These analyses produced mean age estimates for Santa Rosa that closely approximate the maximum 29.6 ± 0.08 Ma composite date provided by detrital zircons, but predict that CTA-27 is much younger than currently thought (∼30 Ma). We conclude that the ∼41 Ma age proposed for CTA-27 is incorrect, and that there are currently no compelling Eocene records of either rodents or primates in the known fossil record of South America.
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Sun, X., P. Andersson, C. Humborg, B. Gustafsson, D. J. Conley, P. Crill, and C. M. Mörth. "Climate dependent diatom production is preserved in biogenic Si isotope signatures." Biogeosciences 8, no. 11 (November 29, 2011): 3491–99. http://dx.doi.org/10.5194/bg-8-3491-2011.
Full textAbstract:
Abstract. The aim of this study was to reconstruct diatom production in the subarctic northern tip of the Baltic Sea, Bothnian Bay, based on down-core analysis of Si isotopes in biogenic silica (BSi). Dating of the sediment showed that the samples covered the period 1820 to 2000. The sediment core record can be divided into two periods, an unperturbed period from 1820 to 1950 and a second period affected by human activities (from 1950 to 2000). This has been observed elsewhere in the Baltic Sea. The shift in the sediment core record after 1950 is likely caused by large scale damming of rivers. Diatom production was inferred from the Si isotope composition which ranged between δ30Si −0.18‰ and +0.58‰ in BSi, and assuming fractionation patterns due to the Raleigh distillation, the production was shown to be correlated with air and water temperature, which in turn were correlated with the mixed layer (ML) depth. The sedimentary record showed that the deeper ML depth observed in colder years resulted in less production of diatoms. Pelagic investigations in the 1990's have clearly shown that diatom production in the Baltic Sea is controlled by the ML depth. Especially after cold winters and deep water mixing, diatom production was limited and dissolved silicate (DSi) concentrations were not depleted in the water column after the spring bloom. Our method corroborates these findings and offers a new method to estimate diatom production over much longer periods of time in diatom dominated aquatic systems, i.e. a large part of the world's ocean and coastal seas.