Academic literature on the topic 'Tip-dating'
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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’.
Dissertations / Theses on the topic "Tip-dating"
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Chatterji, Ray. "The Evolution of Sea Turtles." Thesis, 2021. https://hdl.handle.net/2440/134280.
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Chelonioidea (sea turtles) are a group where available morphological evidence for crown group relationships are incongruent with those established using molecular data. However, morphological surveys of crown group taxa tend to focus on a recurring subset of the extant species. The Australian flatback sea turtle, Natator depressus, is often excluded from comparisons and it is the most poorly known of the seven extant species of Chelonioidea. Previous descriptions of its skull morphology are limited and conflict. Here we describe two skulls of adult N. depressus and re-examine the phylogenetic relationships according to morphological character data. Using X-ray micro Computed Tomography we describe internal structures of the braincase and identify new phylogenetically informative characters not previously reported. Phylogenetic analysis using a Bayesian approach strongly supports a sister group relationship between Chelonia mydas and N. depressus, a topology which wasn’t supported by previous analyses of morphological data but one that matches the topology supported by analysis of molecular data. Our results highlight the general need to sample the morphological anatomy of crown group taxa more thoroughly before concluding that morphological and molecular evidence is incongruous.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 2021
Books on the topic "Tip-dating"
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Henningsen, Christopher W. Dating Tip Basics: For The Newly Single Man. PublishAmerica, 2005.
Find full textBook chapters on the topic "Tip-dating"
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Xia, Xuhua. "Improved Method for Rooting and Tip-Dating a Viral Phylogeny." In Springer Handbooks of Computational Statistics, 397–410. Berlin, Heidelberg: Springer Berlin Heidelberg, 2022. http://dx.doi.org/10.1007/978-3-662-65902-1_19.
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Colón, José. "The Gastrointestinal System, Nutrition, and Sleep." In Integrative Sleep Medicine, edited by Valerie Cacho and Esther Lum, 149–70. Oxford University Press, 2021. http://dx.doi.org/10.1093/med/9780190885403.003.0010.
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Dating back to 400 bc, Hippocrates of Kos recognized the importance of nutrition and gut health, as well as that of sleep, in maintaining wellness. The gastrointestinal system (GI) is one of the largest organ system of the body and was once viewed as merely for alimentation and energy production. We now recognize the GI system’s influence on nearly every body system through the gut–brain connection and that it has bidirectional correlates with sleep health. Historical medicinal treatments that aided sleep and nervousness commonly were equally used for GI ailments. Within the GI system melatonin and neurotransmitters are synthesized and affect sleep. Circadian disturbances affect our microbiome and impact GI disorders such as gastroesophageal reflux, irritable bowel syndrome, and inflammatory bowel disease. Sleep restriction influences the types of foods eaten, and nutrition influences sleep health on both macronutrient and micronutrient levels. In 1989, J. Allen Hobson said “More has been learned about sleep in the last 60 years than in the preceding 6,000.” Today we may say the same thing about the microbiome, but what we know about the bidirectional nature of GI and sleep health is only the tip of the iceberg.
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Mitchell, Peter. "South America I: Caribbean Deserts and Tropical Savannahs." In Horse Nations. Oxford University Press, 2015. http://dx.doi.org/10.1093/oso/9780198703839.003.0012.
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These two quotations, dating to within almost a decade of each other, refer to very different parts of South America, the first the La Guajira Peninsula at its northern tip, the second the savannahs of the Gran Chaco at its very heart. The Wayúu, dwelling in the first, had no direct connection with the Mbayá of whom Dobrizhoffer wrote here (though he is more famous for his work on their cousins, the Abipones). Nevertheless, both regions shared aspects of their respective experiences of colonial intrusion and settlement: the frequent adoption not just of horses but also of other exotic species like cattle and sheep; Spanish use of missionaries to try and pacify their Indigenous inhabitants; and the fact that the latter could play off one European power, or Spanish province, against another, thereby maintaining their own freedom of action. Aiding the Native peoples in this was their geographically, politically, and economically marginal position with respect to the main foci of colonial power in the Andes and along the Atlantic. Spain began exploiting Venezuela’s pearl fisheries as early as 1508, even settling on the mainland from 1522, but the real impetus to conquest in South America came only with Francisco Pizarro’s invasion of the Inka Empire in 1533. The highlands of Peru, Bolivia, Ecuador, and Colombia (the latter never part of Inka domains), the lowlands between them and the Pacific Ocean, the northern half of Chile, and the northwestern corner of Argentina all passed quickly—if not always easily—under Spanish control. So too did parts of Paraguay, settled by following rivers inland from the Atlantic. Portugal, on the other hand, secured for herself the coast of Brazil, eventually expanding her reach across virtually the entire Amazon Basin. Horses were as much a part of the conquistadores’ repertoire in South America as in Mexico. They sowed panic when Pizarro first confronted Inka troops at Cajamarca in 1533, but Native American surprise and fear did not last. Inka armies quickly devised tactics to neutralize the effects of horses on the battlefield in vain efforts to expel the invader.
Conference papers on the topic "Tip-dating"
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Landman, Neil H., Selina R. Cole, David F. Wright, and Melanie J. Hopkins. "PHYLOGENETIC ANALYSIS OF THE SCAPHITIDAE (AMMONOIDEA) USING PARSIMONY AND BAYESIAN TIP-DATING APPROACHES." In GSA Annual Meeting in Phoenix, Arizona, USA - 2019. Geological Society of America, 2019. http://dx.doi.org/10.1130/abs/2019am-335959.
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Wagner, Peter J. "PALEOBIOLOGICAL DIVERSIFICATION METRICS AND BIRTH-DEATH MODELS AS CONTROLS FOR THE EFFECTS OF RATE HETEROGENEITIES ON TIP-DATING." In GSA Annual Meeting in Denver, Colorado, USA - 2016. Geological Society of America, 2016. http://dx.doi.org/10.1130/abs/2016am-285563.
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Wright, David F. "BAYESIAN TIP-DATING AND TREE-BASED ANALYSES OF MORPHOLOGIC EVOLUTION: AN EMPIRICAL ASSESSMENT OF RATE HETEROGENEITY AND MORPHOSPACE OCCUPATION AMONG PALEOZOIC CRINOIDS." In GSA Annual Meeting in Denver, Colorado, USA - 2016. Geological Society of America, 2016. http://dx.doi.org/10.1130/abs/2016am-283590.
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А.Е., Леонтьев,, Бейлекчи, В.В., and Бейлекчи, В.В. "RESEARCH OF VYZSHEGSHA HILLFORT, 2020." In Археология Владимиро-Суздальской земли. Crossref, 2021. http://dx.doi.org/10.25681/iaras.2021.978-5-94375-365-7.38-50.
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В раскопе на центральной площадке городища были открыты остатки наземной постройки. Многочисленные находки мелких слитков и лома цветных металлов, литейных форм, обломка тигля указывают на ее вероятное использование в качестве литейной мастерской. Вывод подтверждает химический анализ культурного слоя заполнения постройки, который показал повышенное содержание в его составе элементов меди, свинца, олова. Находка ножа характерной формы позволяет датировать постройку не ранее второй половины VIII в. В коллекции находок многочисленны элементы украшений, характерных для костюма раннесредневекового финского населения Поволжья, в их числе редкий образец височного лопастного кольца. Второй раскоп находился в северо-восточной оконечности центральной площадки городища. Специфика отложений позволяет полагать, что обследованный участок поселения использовался для добычи камня. Лидарная аэросъемка окрестностей городища позволила обнаружить на противоположном левом берегу р. Черной 3 группы курганов Remnants of an above-ground structure were discovered in excavation site 1at the central area of the fortified settlement. Numerous findings of small ingots and scarps of nonferrous metals and findings of casting forms, fragments of troughs indicate that the structure was possibly used as a casting workshop. This conclusion is reinforced by analysis of the occupation layer that filled the structure. Analysis showed an increased content of copper, lead and tin in the occupation layer. Finding of a knife of a very specific shape allows dating the structure which is no earlier than the second half of the 8 century. Numerous elements of adornments specific for dressing of early medieval Finnish population are included in collection of findings. The second excavation site was at the of north-east tip of the central ground of the fortified settlement. Specificity of depositions allows to suppose that that area of settlements wasused for quarrying. The lidar aerial survey allowed discovering three groups of burial mounds at the opposite (left) bank of the Chernaya river and probable location of a fortified settlement that was hitherto unknown.