scholarly journals Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction.

Genetics ◽  
1993 ◽  
Vol 134 (3) ◽  
pp. 959-969 ◽  
Author(s):  
K A Crandall ◽  
A R Templeton

Abstract Empirical data sets of intraspecific restriction site polymorphism in Drosophila have been gathered in order to test hypotheses derived from coalescent theory. Three main ideas are tested: (1) haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, (2) the frequency of a haplotype is related to the number of mutational connections to other haplotypes in the cladogram and (3) geographic location can be used to infer topological positioning of haplotypes in a cladogram. These relationships can then be used to better estimate intraspecific phylogenies in two ways: (1) rooting the phylogeny and (2) resolving ambiguities in a cladogram. This information will allow one to reduce the number of alternative phylogenies and incorporate the uncertainties involved in reconstructing intraspecific phylogenies into subsequent analyses that depend heavily on the topology of the tree.

2012 ◽  
Vol 9 (10) ◽  
pp. 13439-13496 ◽  
Author(s):  
M. J. Smith ◽  
M. C. Vanderwel ◽  
V. Lyutsarev ◽  
S. Emmott ◽  
D. W. Purves

Abstract. The feedback between climate and the terrestrial carbon cycle will be a key determinant of the dynamics of the Earth System over the coming decades and centuries. However Earth System Model projections of the terrestrial carbon-balance vary widely over these timescales. This is largely due to differences in their carbon cycle models. A major goal in biogeosciences is therefore to improve understanding of the terrestrial carbon cycle to enable better constrained projections. Essential to achieving this goal will be assessing the empirical support for alternative models of component processes, identifying key uncertainties and inconsistencies, and ultimately identifying the models that are most consistent with empirical evidence. To begin meeting these requirements we data-constrained all parameters of all component processes within a global terrestrial carbon model. Our goals were to assess the climate dependencies obtained for different component processes when all parameters have been inferred from empirical data, assess whether these were consistent with current knowledge and understanding, assess the importance of different data sets and the model structure for inferring those dependencies, assess the predictive accuracy of the model, and to identify a methodology by which alternative component models could be compared within the same framework in future. Although formulated as differential equations describing carbon fluxes through plant and soil pools, the model was fitted assuming the carbon pools were in states of dynamic equilibrium (input rates equal output rates). Thus, the parameterised model is of the equilibrium terrestrial carbon cycle. All but 2 of the 12 component processes to the model were inferred to have strong climate dependencies although it was not possible to data-constrain all parameters indicating some potentially redundant details. Similar climate dependencies were obtained for most processes whether inferred individually from their corresponding data sets or using the full terrestrial carbon model and all available data sets, indicating a strong overall consistency in the information provided by different data sets under the assumed model formulation. A notable exception was plant mortality, in which qualitatively different climate dependencies were inferred depending on the model formulation and data sets used, highlighting this component as the major structural uncertainty in the model. All but two component processes predicted empirical data better than a null model in which no climate dependency was assumed. Equilibrium plant carbon was predicted especially well (explaining around 70% of the variation in the withheld evaluation data). We discuss the advantages of our approach in relation to advancing our understanding of the carbon cycle and enabling Earth System Models make better constrained projections.


2017 ◽  
pp. 99
Author(s):  
Pamela S. Soltis ◽  
Douglas E. Soltis

Technological advances in molecular biology have greatly increased the speed and efficiency of DNA sequencing, making it possible to construct large molecular data sets for phylogeny reconstruction relatively quickly. Despite their potential for improving our understanding of phylogeny, these large data sets also provide many challenges. In this paper, we discuss several of these challenges, including 1) the failure of a search to find the most parsimonious trees (the local optimum) in a reasonable amount of time, 2) the difference between a local optimum and the global optimum, and 3) the existence of multiple classes (islands) of most parsimonious trees. We also discuss possible strategies to improve the' likelihood of finding the most parsimonious tree(s) and present two examples from our work on angiosperm phylogeny. We conclude with a discussion of two alternatives to analyses of entire large data sets, the exemplar approach and compartmentalization, and suggest that additional consideration must be given to issues of data analysis for large data sets, whether morphological or molecular.


Author(s):  
Lawrence Leemis

This chapter switches from the traditional analysis of Benford's law using data sets to a search for probability distributions that obey Benford's law. It begins by briefly discussing the origins of Benford's law through the independent efforts of Simon Newcomb (1835–1909) and Frank Benford, Jr. (1883–1948), both of whom made their discoveries through empirical data. Although Benford's law applies to a wide variety of data sets, none of the popular parametric distributions, such as the exponential and normal distributions, agree exactly with Benford's law. The chapter thus highlights the failures of several of these well-known probability distributions in conforming to Benford's law, considers what types of probability distributions might produce data that obey Benford's law, and looks at some of the geometry associated with these probability distributions.


1989 ◽  
Vol 65 (1) ◽  
pp. 155-160 ◽  
Author(s):  
Raymond Hubbard ◽  
Stuart J. Allen

Given nuances in the computer programs, unwary researchers performing a common factor analysis on the same set of data can be expected to arrive at very different conclusions regarding the number and nature of extracted factors if they use the BMDP, as opposed to the SPSSx (or SAS), statistical software package. This is illustrated using six well-known empirical data sets from the psychology literature.


1992 ◽  
Vol 6 ◽  
pp. 42-42
Author(s):  
Ann F. Budd ◽  
Kenneth G. Johnson

Scleractinian reef corals have a number of properties that are somewhat unique in morphometrics and therefore require methodologies different from those used in more structurally complex, non-colonial organisms with determinate growth. Most importantly, characters used in species recognition occur at two levels: (1) within modules and (2) among modules within colonies. Due to structural constraints imposed by radial symmetry and to the fact that growth is accomplished primarily by continuous accretion along the upper skeletal surface, most characters at the first level are continuous and consist either of architectural features related to coral lite size or to the upward growth of vertical structures forming the septa and columella. Because of high environmental variability, these features are best described using landmark based methods. Patterns of distribution of modules across colonies are best estimated using spatial statistics that can be related to underlying rules of budding and overall colony shape.Here we demonstrate how traditional multivariate statistical procedures can be applied to these two different levels of data to recognize species in the common branching and massive coral Porites, and to derive characters useful in phylogeny reconstruction. Discrete morphologic units are first identified by subdividing modules from the same colony into two groups of so-called “colony halves”, running cluster analysis on distances among halves, and using the relative positions of halves from the same colony and a modified jackknife procedure to establish cutoffs on the dendrogram for group recognition. The resulting clusters are tested using crossvalidation procedures in discriminant analysis which compare classification results for corallite level and colony level data sets, and similar results for different portions of the same colonies. Iterative procedures are then used to maximize the probability of correct group assignment for each colony. Using multiple comparisons among the resulting species, a set of independent characters that maximize group separation are selected for use in phylogeny reconstruction. Comparison with electrophoretic analyses on the same material shows high correspondence in both species assignments and phylogenetic trees based on the morphometric and allozyme approaches.


2020 ◽  
Vol 37 (11) ◽  
pp. 3380-3388
Author(s):  
Stephen A Smith ◽  
Nathanael Walker-Hale ◽  
Joseph F Walker

Abstract Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.


2013 ◽  
Vol 10 (1) ◽  
pp. 583-606 ◽  
Author(s):  
M. J. Smith ◽  
D. W. Purves ◽  
M. C. Vanderwel ◽  
V. Lyutsarev ◽  
S. Emmott

Abstract. The feedback between climate and the terrestrial carbon cycle will be a key determinant of the dynamics of the Earth System (the thin layer that contains and supports life) over the coming decades and centuries. However, Earth System Model projections of the terrestrial carbon-balance vary widely over these timescales. This is largely due to differences in their terrestrial carbon cycle models. A major goal in biogeosciences is therefore to improve understanding of the terrestrial carbon cycle to enable better constrained projections. Utilising empirical data to constrain and assess component processes in terrestrial carbon cycle models will be essential to achieving this goal. We used a new model construction method to data-constrain all parameters of all component processes within a global terrestrial carbon model, employing as data constraints a collection of 12 empirical data sets characterising global patterns of carbon stocks and flows. Our goals were to assess the climate dependencies inferred for all component processes, assess whether these were consistent with current knowledge and understanding, assess the importance of different data sets and the model structure for inferring those dependencies, assess the predictive accuracy of the model and ultimately to identify a methodology by which alternative component models could be compared within the same framework in the future. Although formulated as differential equations describing carbon fluxes through plant and soil pools, the model was fitted assuming the carbon pools were in states of dynamic equilibrium (input rates equal output rates). Thus, the parameterised model is of the equilibrium terrestrial carbon cycle. All but 2 of the 12 component processes to the model were inferred to have strong climate dependencies, although it was not possible to data-constrain all parameters, indicating some potentially redundant details. Similar climate dependencies were obtained for most processes, whether inferred individually from their corresponding data sets or using the full terrestrial carbon model and all available data sets, indicating a strong overall consistency in the information provided by different data sets under the assumed model formulation. A notable exception was plant mortality, in which qualitatively different climate dependencies were inferred depending on the model formulation and data sets used, highlighting this component as the major structural uncertainty in the model. All but two component processes predicted empirical data better than a null model in which no climate dependency was assumed. Equilibrium plant carbon was predicted especially well (explaining around 70% of the variation in the withheld evaluation data). We discuss the advantages of our approach in relation to advancing our understanding of the carbon cycle and enabling Earth System Models to make better constrained projections.


Radiocarbon ◽  
2015 ◽  
Vol 57 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Laia Andreu-Hayles ◽  
Guaciara M Santos ◽  
David A Herrera-Ramírez ◽  
Javier Martin-Fernández ◽  
Daniel Ruiz-Carrascal ◽  
...  

This study used high-precision radiocarbon bomb-pulse dating of selected wood rings to provide an independent validation of the tree growth periodicity of Pseudolmedia rigida (Klotzsch & H. Karst) Cuatrec. from the Moraceae family, collected in the Madidi National Park in Bolivia. 14C content was measured by accelerator mass spectrometry (AMS) in 10 samples from a single tree covering over 70 yr from 1939 to 2011. These preliminary calendar dates were determined by dendrochronological techniques and were also used to select the samples for 14C AMS. In order to validate these preliminary dates using the established Southern Hemisphere (SH) 14C atmospheric concentration data set, the targeted rings were selected to be formed during periods before and after the 14C bomb spike nuclear tests (i.e. 1950s–1960s). The excellent agreement of the dendrochronological dates and the 14C signatures in tree rings associated with the same dates provided by the bomb-pulse 14C atmospheric values for the SH (SHCal zone 1–2) confirms the annual periodicity of the observed growth layers, and thus the high potential of this species for tree-ring analysis. The lack of discrepancies between both data sets also suggests that there are no significant latitudinal differences between the 14C SHCal zone 1–2 curve and the 14C values obtained from the selected tree rings at this geographic location (14°33′S, 68°49′W) in South America. The annual resolution of P. rigida tree rings opens the possibility of broader applications of dendrochronological analysis for ecological and paleoclimatic studies in the Bolivian tropics, as well as the possibility of using wood samples from some tree species from this region to improve the quality of the bomb-pulse 14C SHCal curve at this latitude.


2010 ◽  
Vol 47 (8) ◽  
pp. 1079-1091 ◽  
Author(s):  
John Shaw ◽  
Carl L. Amos ◽  
David A. Greenberg ◽  
Charles T. O’Reilly ◽  
D. Russell Parrott ◽  
...  

Tidal models for the Bay of Fundy, Canada — site of the highest recorded modern tide — show that tidal amplification began in the early Holocene and by ca. 5000 BP the range was almost 80% of the present range. Empirical data consisting of 146 sea-level index points and other observations appear to contradict model results. Aggregated relative sea-level data for Chignecto Bay and Minas Basin show that rapid tidal expansion began ca. 3400 BP. However, if we separate these two geographically separate data sets, evidence for this rapid late-Holocene tidal expansion is confined to Minas Basin. We explain this singularity by positing a barrier at the mouth of Minas Basin, at the Minas Passage, that delayed tidal expansion. With the rapid breakdown of this barrier and near-instantaneous tidal expansion, water temperature dropped, tidal currents and turbidity increased, and the form of the inner estuary was changed from lagoonal–mesotidal to macrotidal. We argue that the catastrophic breakdown of the barrier is related in the aboriginal legend of Glooscap, showing that aboriginal peoples observed the rapid environmental changes and preserved an oral record for 3400 years.


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