scholarly journals Tectonic calibrations in molecular dating

2011 ◽  
Vol 57 (1) ◽  
pp. 116-124 ◽  
Author(s):  
Ullasa Kodandaramaiah
Keyword(s):  
Analytical Methods ◽  
Molecular Dating ◽  
Circular Reasoning ◽  
Geological Process ◽  
Major Drawback ◽  
Minimum Age ◽  
Geological Event ◽  
Almost All ◽  
Geological Constraints ◽  
Age Estimates

Abstract Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeography are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously believed that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicariance in several groups. Moreover, the possibility of speciation having occurred before the said geological event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations always result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided.

scholarly journals Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140677 ◽  
Author(s):  
Daniel T. Ksepka ◽  
Jessica L. Ware ◽  
Kristin S. Lamm
Keyword(s):  
Analytical Methods ◽  
Fossil Record ◽  
Tree Of Life ◽  
Temporal Information ◽  
Molecular Dating ◽  
Critical Nodes ◽  
Molecular Divergence ◽  
Divergence Dates ◽  
Divergence Estimates ◽  
Age Estimates

Major disparities are recognized between molecular divergence dates and fossil ages for critical nodes in the Tree of Life, but broad patterns and underlying drivers remain elusive. We harvested 458 molecular age estimates for the stem and crown divergences of 67 avian clades to explore empirical patterns between these alternate sources of temporal information. These divergence estimates were, on average, over twice the age of the oldest fossil in these clades. Mitochondrial studies yielded older ages than nuclear studies for the vast majority of clades. Unexpectedly, disparity between molecular estimates and the fossil record was higher for divergences within major clades (crown divergences) than divergences between major clades (stem divergences). Comparisons of dates from studies classed by analytical methods revealed few significant differences. Because true divergence ages can never be known with certainty, our study does not answer the question of whether fossil gaps or molecular dating error account for a greater proportion of observed disparity. However, empirical patterns observed here suggest systemic overestimates for shallow nodes in existing molecular divergence dates for birds. We discuss underlying biases that may drive these patterns.

scholarly journals Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
James A. Schulte
Keyword(s):  
Divergence Time ◽  
Penalized Likelihood ◽  
Molecular Data ◽  
Molecular Dating ◽  
Taxon Sampling ◽  
South American ◽  
The South ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Age Estimates

Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.

scholarly journals Harvesting methods of Cinnamomum tamala leaves in private land: a case study from Udayapur district, Nepal

1970 ◽  
Vol 19 (2) ◽  
pp. 20-24 ◽  
Author(s):  
D Lamichhane ◽  
NK Karna
Keyword(s):  
Forest Products ◽  
Private Land ◽  
Fresh Weight ◽  
High Positive Correlation ◽  
Cinnamomum Tamala ◽  
Non Timber Forest Products ◽  
Minimum Age ◽  
Level Of Significance ◽  
Almost All

Tejpat (Cinnamomum tamala) leaf is commercially one of the important non-timber forest products of Nepal. This paper attempts to elaborate and analyze the harvesting methods and techniques of Tejpat grown by the farmers in their private land. The study was conducted in the villages of Udayapur district where Tejpat was widely cultivated and harvested for income generation and trading purposes. Almost all farmers with private land had planted Tejpat. Complete lopping of leaves once a year was the exclusive practice for harvesting. The collection period for leaf was from Ashoj (October) to Magh (February) but the period for bark varied greatly, i.e. from Kartik to Poush (November to January) and Baisakh / Jestha (May / June). Bark collection was done only from old, dying, diseased and low leaf producing trees. Average number of trees per household ranged from 10 to 155. The mean diameter at breast height (DBH) of the trees was 39.58 cm. There was high positive correlation between the DBH and fresh weight of leaf. Fitting of linear regression of fresh weight of leaf with DBH proved that the relationship was statistically significant at 5% level of significance. The minimum age and size of trees for leaf harvesting were found to be five years and 16.18 cm, respectively. Keywords: Fresh weight; harvesting; private land; Tejpat DOI: 10.3126/banko.v19i2.2981 Banko Janakari, Vol. 19, No.2 2009 pp.20-24

scholarly journals Shape and size of the arenas affect amphipod behaviours: implications for ecotoxicology

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5271 ◽  
Author(s):  
Shanelle A. Kohler ◽  
Matthew O. Parker ◽  
Alex T. Ford
Keyword(s):  
False Negative ◽  
Careful Consideration ◽  
Negative Effects ◽  
Mean Velocity ◽  
Major Drawback ◽  
Test Species ◽  
Amphipod Crustacean ◽  
Almost All ◽  
Invertebrate Models ◽  
A Current

The use of behaviour in ecotoxicology is expanding, however the lack of standardisation and validation of these assays currently presents a major drawback in moving forward in the development of behavioural assays. Furthermore, there is a current paucity of control data on test species, particularly invertebrate models. In this study we assessed a range of behaviours associated with spatial distribution and locomotion in relation to arena size and shape in two species of amphipod crustacean (Echinogammarus marinus and Gammarus pulex). Arena shape had significant effects on almost all behavioural parameters analysed. Increasing arena size resulted in an increased mean velocity and activity plus increased proportional use of the central zones. These results indicate that ‘ceiling effects’ may occur in some ecotoxicological studies resulting in potentially ‘false’ negative effects if careful consideration is not paid to experimental design. Differences in behaviours were observed between the two species of amphipod. For example, G. pulex spend approximately five times (∼20%) more of the available time crossing the central zones of the arenas compared to E. marinus (∼4%) which could have implications on assessing anxiolytic behaviours. The results of this study highlight several behaviours with potential for use in behavioural ecotoxicology with crustaceans but also underscore the need for careful consideration when designing these behavioural assays.

scholarly journals Colonization time on island settings: lessons from the Hawaiian and Canary Island floras

2019 ◽  
Vol 191 (2) ◽  
pp. 155-163 ◽  
Author(s):  
C García-Verdugo ◽  
J Caujapé-Castells ◽  
I Sanmartín
Keyword(s):  
Molecular Dating ◽  
Plant Colonization ◽  
Endemic Plant ◽  
Biogeographic Patterns ◽  
Lineage Differentiation ◽  
Time Estimates ◽  
Colonization Time ◽  
Oceanic Archipelagos ◽  
Time Of Divergence ◽  
Age Estimates

Abstract Molecular dating offers a tool for inferring the time of divergence between two lineages. In this study, we discuss how dated molecular reconstructions are informative of two different, albeit often intermingled, time estimates with regard to a fundamental process in island biogeography: the time of island colonization (TIC). We illustrate how stem age estimates provide information on the divergence between the extant island lineage and their closest relatives (i.e. the onset of lineage differentiation). Such estimates, however, are typically poor TIC predictors, as they are strongly affected by spatial and temporal uncertainty, particularly in cases of deep stem ages. Crown ages of endemic island lineages, in contrast, provide information on the temporal onset of island in situ diversification, and may represent a better proxy for TIC when the associated uncertainty is taken into account. Thus, the geographic and temporal distance separating the island and mainland lineages in phylogenetic/phylogeographic reconstructions are key factors for determining the reliability of these two estimates as proxies of TIC. We show how divergence times can be used to investigate the biogeographic patterns of two well-studied oceanic archipelagos: Hawaii and the Canary Islands. A compilation of molecular age estimates for nearly one-third of the endemic plant lineages in each archipelago reveals that Canarian plant lineages exhibit significantly younger mean crown ages (2.1 ± 2.4 Myr) than Hawaiian lineages (3.5 ± 2.9 Myr), despite island substrates being much older in the Canarian archipelago. We postulate that this pattern suggests: (1) a more important role of submerged islands during plant colonization in Hawaii, and (2) higher taxon turnover in the Canaries, mediated by relatively young (Mediterranean) lineages, and probably facilitated by the combination of the high incidence of extinction for the last 5 Myr and the close proximity of mainland source areas as compared to Hawaii.

Chromium, Nickel and Iron as clues to the formation histories of exoplanetary bodies

2021 ◽  
Author(s):  
Andrew Buchan ◽  
Amy Bonsor ◽  
Oliver Shorttle ◽  
Jon Wade ◽  
John Harrison
Keyword(s):  
White Dwarfs ◽  
The Body ◽  
Subsequent Evolution ◽  
Geological Process ◽  
The Core ◽  
Novel Approach ◽  
Geological Constraints ◽  
Insight Into ◽  
Key Parameter

<p>We are now entering an era of rocky exoplanet detection. To determine whether an exoplanet is ‘Earth-like’, we must estimate not only its mass, radius and insolation, but also its geological composition. These geological constraints have wide ranging implications, not least for a planet’s subsequent evolution and habitability.</p><p>Polluted white dwarfs which have accreted fragments of planetary material provide a unique opportunity to probe exoplanetary interiors. We can also learn about their formation histories, including the geological process of core-mantle differentiation.</p><p>Cr, Ni and Fe behave differently during differentiation, depending on the conditions under which it occurs. This alters the Cr/Fe and Ni/Fe ratios in the core and mantle of differentiated bodies. The pressure inside the body is a key parameter, and depends on the body’s size.</p><p>In our work, we present a novel approach for modelling this behaviour and use it to gain crucial insight into the sizes of exoplanetary bodies which pollute white dwarfs.</p>

Amino Acid Geochemistry of Fossil Bones from the Rancho La Brea Asphalt Deposit, California

1982 ◽  
Vol 18 (2) ◽  
pp. 174-183 ◽  
Author(s):  
Mark A. S. McMenamin ◽  
David J. Blunt ◽  
Keith A. Kvenvolden ◽  
Scott E. Miller ◽  
Leslie F. Marcus ◽  
...  
Keyword(s):  
Amino Acids ◽  
Los Angeles ◽  
Aspartic Acid ◽  
Equivalent Age ◽  
Aspartic Acid Racemization ◽  
Wide Range ◽  
Fossil Bones ◽  
Minimum Age ◽  
Rancho La Brea ◽  
Age Estimates

AbstractLow aspartic acid d:l ratios and modern collagenlike concentration values indicate that amino acids in bones from the Rancho La Brea asphalt deposit, Los Angeles, California are better preserved than amino acids in bones of equivalent age that have not been preserved in asphalt. Amino acids were recovered from 10 Rancho La Brea bone samples which range in age from less than 200 to greater than 36,000 yr. The calibrated rates of aspartic acid racemization range from 2.1 to 5.0 × 10−6yr−1. Although this wide range of rate constants decreases the level of confidence for age estimates, use of the larger rate constant of 5.0 × 10−6yr−1provides minimum age estimates which fit the known stratigraphic and chronologic records of the Rancho La Brea deposits.

Sludge characterization: the rôle of physical consistency

2004 ◽  
Vol 49 (10) ◽  
pp. 59-65 ◽  
Author(s):  
L. Spinosa ◽  
K. Wichmann
Keyword(s):  
Sewage Sludge ◽  
Analytical Methods ◽  
Field Tests ◽  
Treatment Utilization ◽  
European Directives ◽  
Boundary Limit ◽  
Sludge Characterization ◽  
Almost All ◽  
All Treatment

The physical consistency is an important parameter in sewage sludge characterization as it strongly affects almost all treatment, utilization and disposal operations. In addition, in many European Directives a reference to the physical consistency is reported as a characteristic to be evaluated for fulfilling the regulations’ requirements. Further, in many analytical methods for sludge, different procedures are indicated depending on whether a sample is liquid or not, is solid or not. Three physical behaviours (liquid, paste-like and solid) can be observed with sludges, so the development of analytical procedures to define the boundary limit between liquid and paste-like behaviours (flowability) and that between solid and pastelike ones (solidity) is of growing interest. Several devices can be used for evaluating the flowability and solidity properties, but often they are costly and difficult to be operated in the field. Tests have been carried out to evaluate the possibility to adopt a simple extrusion procedure for flowability measurements, and a Vicat needle for solidity ones.

scholarly journals Analyzing statistical age models to determine the equivalent dose and burial age using a Markov chain Monte Carlo method

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Jun Peng
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Likelihood Estimation ◽  
Equivalent Dose ◽  
Mcmc Method ◽  
Minimum Age ◽  
Age Model ◽  
Multiple Samples ◽  
Age Estimates

AbstractIn optically stimulated luminescence (OSL) dating, statistical age models for equivalent dose (De) distributions are routinely estimated using the maximum likelihood estimation (MLE) method. In this study, a Markov chain Monte Carlo (MCMC) method was used to analyze statistical age models, including the central age model (CAM), the minimum age model (MAM), the maximum age model (MXAM), etc. This method was first used to obtain sampling distributions on parameters of interest in an age model using De distributions from individual sedimentary samples and subsequently extended to simultaneously extract age estimates from multiple samples with stratigraphic constraints. The MCMC method allows for the use of Bayesian inference to refine chronological sequences from multiple samples, including both fully and partially bleached OSL dates. This study designed easily implemented open-source numeric programs to perform MCMC sampling. Measured and simulated De distributions are used to validate the reliability of dose (age) estimates obtained by this method. Findings from this study demonstrate that estimates obtained by the MCMC method can be used to informatively compare results obtained by the MLE method. The application of statistical age models to multiple OSL dates with stratigraphic orders using the MCMC method may significantly improve both the precision and accuracy of burial ages.

scholarly journals Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3373 ◽  
Author(s):  
Friðgeir Grímsson ◽  
Paschalia Kapli ◽  
Christa-Charlotte Hofmann ◽  
Reinhard Zetter ◽  
Guido W. Grimm
Keyword(s):  
Fossil Record ◽  
Middle Miocene ◽  
Molecular Data ◽  
Late Eocene ◽  
Molecular Dating ◽  
The Family ◽  
Minimum Age ◽  
Age Constraints ◽  
Scanning Electron ◽  
Lineage Diversification

BackgroundWe revisit the palaeopalynological record of Loranthaceae, using pollen ornamentation to discriminate lineages and to test molecular dating estimates for the diversification of major lineages.MethodsFossil Loranthaceae pollen from the Eocene and Oligocene are analysed and documented using scanning-electron microscopy. These fossils were associated with molecular-defined clades and used as minimum age constraints for Bayesian node dating using different topological scenarios.ResultsThe fossil Loranthaceae pollen document the presence of at least one extant root-parasitic lineage (Nuytsieae) and two currently aerial parasitic lineages (Psittacanthinae and Loranthinae) by the end of the Eocene in the Northern Hemisphere. Phases of increased lineage diversification (late Eocene, middle Miocene) coincide with global warm phases.DiscussionWith the generation of molecular data becoming easier and less expensive every day, neontological research should re-focus on conserved morphologies that can be traced through the fossil record. The pollen, representing the male gametophytic generation of plants and often a taxonomic indicator, can be such a tracer. Analogously, palaeontological research should put more effort into diagnosing Cenozoic fossils with the aim of including them into modern systematic frameworks.

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