Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

Paleobiology ◽  
10.1666/13033 ◽  
2014 ◽  
Vol 40 (3) ◽  
pp. 331-351 ◽  
Author(s):  
David W. Bapst
Keyword(s):  
Fossil Record ◽  
Scaling Method ◽  
Short Branch ◽  
Time Scaling ◽  
Temporal Relationships ◽  
Branch Lengths ◽  
Scaling Methods ◽  
True Time ◽  
Fossil Data ◽  
Incomplete Sampling

Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect tree-based evolutionary analyses. I developed process-based simulations of the fossil record that allow the comparison of approximated time-scaled trees to true time-scaled trees. I used this simulation framework to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the stochastic “cal3”time-scaling method with ancestral assignment produced preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios that forced the insertion of many short branch lengths, a bias that is not solved by any of the considered time-scaling methods in all scenarios. Thecal3method of time-scaling can be recommended as the preferred time-scaling method among those tested, but caution must be exercised because tree-based analyses are prone to easily overlooked biases.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

Multiaxial Relaxation and Creep Damage Assessments—A Comparison of ASME N-47 and GLOSS Time-Scaling Methods

1993 ◽  
Vol 115 (1) ◽  
pp. 32-37 ◽  
Author(s):  
R. Seshadri
Keyword(s):  
Relaxation Process ◽  
Theoretical Basis ◽  
Creep Damage ◽  
Scaling Method ◽  
G Factor ◽  
Time Scaling ◽  
Scaling Methods ◽  
Asme Code

Two simplified methods for determining multiaxial relaxation and creep damage, the GLOSS time-scaling and the ASME Code Case N-47 method, are described in this paper. The theoretical basis and applicability of the methods to various pressure component configurations are discussed in detail. The G-factor in the ASME formula in effect speeds up or slows down the uniaxial relaxation process, similar to the GLOSS time-scaling method. The two methods are compared, and the differences are attributed to local follow-up not being accounted for in the ASME formula.

RANCANGAN MODEL PENILAIAN KINERJA DENGAN METODE MANAJEMEN BERDASARKAN SASARAN (MANAGEMENT BY OBJECTIVE) DAN PENSKALAAN GRAFIK DI PT ACI

2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Linda Mora Siregar
Keyword(s):  
Performance Appraisal ◽  
Job Analysis ◽  
Scaling Method ◽  
Scaling Methods ◽  
Questionnaire Method ◽  
A Performance

The purpose of this study is to design a performance appraisal model more effectively in accordance with the company's vision and mission, namely by combining management methods based on objectives (management by objective) and graph scaling methods. In the preparation of performance appraisal models with management methods based on objectives (management by objective) and graph scaling methods, carried out with several stages, namely the first stage is planning the making of performance appraisal models, the second is job analysis, third is the preparation of management methods based on objectives (management by objective), the fourth is the preparation of the scaling method and the fifth is the preparation of the performance appraisal form. The making of this performance appraisal design will use a questionnaire method, observation and also interviews to obtain and collect information and data.  Keywords: Performance Appraisal, Management Methods, Graph Scaling.   Tujuan penelitian ini adalah untuk merancang model penilaian kinerja secara lebih efektif sesuai dengan visi dan misi perusahaan, yaitu dengan menggabungkan metode manajemen berdasarkan sasaran (management by objective) dan metode penskalaan grafik. Dalam penyusunan model penilaian kinerja dengan metode manajemen berdasarkan sasaran (management by objective) dan metode penskalaan grafik, dilakukan dengan beberapa tahapan yaitu tahap pertama adalah perencanaan pembuatan model penilaian kinerja, kedua analisis jabatan, ketiga penyusunan metode manajemen berdasarkan sasaran (management by objective), keempat penyusunan metode penskalaan grafik dan kelima adalah penyusunan formulir penilaian kinerja. Pembuatan rancangan penilaian kinerja ini akan menggunakan metode kuesioner, observasi dan juga wawancara untuk mendapatkan dan mengumpulkan informasi dan data.   Kata Kunci: Penilaian kinerja, Metode Manajemen, Penskalaan Grafik.

scholarly journals Evidence for Range Expansion and Origins of an Invasive Hornet Vespa bicolor (Hymenoptera, Vespidae) in Taiwan, with Notes on Its Natural Status

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 320
Author(s):  
Sheng-Shan Lu ◽  
Junichi Takahashi ◽  
Wen-Chi Yeh ◽  
Ming-Lun Lu ◽  
Jing-Yi Huang ◽  
...  
Keyword(s):  
Range Expansion ◽  
Ecological Niche Modeling ◽  
Phylogenetic Analyses ◽  
Current Status ◽  
Mountain Areas ◽  
Colony Losses ◽  
Short Branch ◽  
Branch Lengths ◽  
The Government ◽  
Central Taiwan

The invasive alien species (IAS) Vespa bicolor is the first reported hornet that has established in Taiwan and is concerning as they prey on honeybee Apis mellifera, which leads to colony losses and public concerns. Thus, the aim of this study was to assess the current status of V. bicolor abundance, dispersal, and impact and to trace the origins of Taiwan’s V. bicolor population. Our studies took place in five areas in northern to central Taiwan. We used mtDNA in the phylogenetic analyses. Field survey and ecological niche modeling (ENM) were used to understand the origins and current range of the invasive species. Two main subgroups of V. bicolor in the phylogenetic tree were found, and a clade with short branch lengths in Southeastern China and Taiwan formed a subgroup, which shows that the Taiwan population may have invaded from a single event. Evidence shows that V. bicolor is not a severe pest to honeybees in the study area; however, using ENM, we predict the rapid dispersion of this species to the cooler and hilly mountain areas of Taiwan. The management of V. bicolor should also involve considering it a local pest to reduce loss by beekeepers and public fear in Taiwan. Our findings highlight how the government, beekeepers, and researchers alike should be aware of the implications of V. bicolor’s rapid range expansion in Taiwan, or in other countries.

scholarly journals Predicting the Impact of Describing New Species on Phylogenetic Patterns

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
D C Blackburn ◽  
G Giribet ◽  
D E Soltis ◽  
E L Stanley
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Length Variation ◽  
Tree Shape ◽  
Branch Lengths ◽  
Taxonomic History ◽  
Ecological Patterns ◽  
The Impact ◽  
Incomplete Sampling

Abstract Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

scholarly journals A comparison of the modern Lie scaling method to classical scaling techniques

2016 ◽  
Vol 20 (7) ◽  
pp. 2669-2678 ◽  
Author(s):  
James Polsinelli ◽  
M. Levent Kavvas
Keyword(s):  
Lie Group ◽  
Overland Flow ◽  
New Technology ◽  
Scaling Method ◽  
Lie Group Of Transformations ◽  
Key Points ◽  
Scaling Transformation ◽  
Scaling Models ◽  
Scaling Methods ◽  
Channel Hydraulics

Abstract. In the past 2 decades a new modern scaling technique has emerged from the highly developed theory on the Lie group of transformations. This new method has been applied by engineers to several problems in hydrology and hydraulics, including but not limited to overland flow, groundwater dynamics, sediment transport, and open channel hydraulics. This study attempts to clarify the relationship this new technology has with the classical scaling method based on dimensional analysis, non-dimensionalization, and the Vaschy–Buckingham-Π theorem. Key points of the Lie group theory, and the application of the Lie scaling transformation, are outlined and a comparison is made with two classical scaling models through two examples: unconfined groundwater flow and contaminant transport. The Lie scaling method produces an invariant scaling transformation of the prototype variables, which ensures the dynamics between the model and prototype systems will be preserved. Lie scaling can also be used to determine the conditions under which a complete model is dynamically, kinematically, and geometrically similar to the prototype phenomenon. Similarities between the Lie and classical scaling methods are explained, and the relative strengths and weaknesses of the techniques are discussed.

Stratigraphic biases in the analysis of taxonomic survivorship

Paleobiology ◽  
1975 ◽  
Vol 1 (4) ◽  
pp. 343-355 ◽  
Author(s):  
J. John Sepkoski
Keyword(s):  
Simple Model ◽  
Lognormal Distribution ◽  
Fossil Record ◽  
The Other ◽  
Time Intervals ◽  
Survivorship Analysis ◽  
Other Hand ◽  
Incomplete Sampling ◽  
Biologic Factors

Taxonomic survivorship curves may reflect stratigraphic as well as biologic factors. The approximately lognormal distribution of lengths of Phanerozoic time intervals produces an error in the estimation of taxonomic durations that is also lognormally distributed. As demonstrated by several simulated examples, this error may cause concave taxonomic survivorship curves to appear linear, especially if the maximum durations involved are relatively short. The error of estimation also makes highly concave taxonomic survivorship curves virtually unrecognizable. Incomplete sampling of the fossil record, on the other hand, may not be a serious problem in survivorship analysis. Simulated paleontological sampling employing a simple model suggests that survivorship curves tend to retain their original shapes even when as few as 20% of the taxa have been discovered. However, concave taxonomic survivorship curves tend to lose their concavity as efficiency of sampling declines.

scholarly journals More Than Names: The role of updated taxonomy in palaeontology collections

2019 ◽  
Vol 3 ◽  
Author(s):  
Ricardo Paredes
Keyword(s):  
Fossil Record ◽  
Marine Invertebrate ◽  
Research Community ◽  
Type Material ◽  
Museum Collections ◽  
Web Based ◽  
2D Imaging ◽  
Visual Impact ◽  
Fossil Data

The accuracy on taxonomic determinations of palaeontology collections may have significant consequences in estimations of organism diversity through time. This justifies the need of taxonomic standardization of palaeontological collections. The perception of palaeodiversity through Phanerozoic time has significantly improved since the Sepkoski showed the marine invertebrate taxonomic data in diversity graphs, organized in orders (Sepkoski 1978) and families (Sepkoski 1979, Sepkoski 1984). The visual impact of these graphs engaged palaeontologists into gathering quantitative macroevolution in order to better understand marine palaeodiversity. Alroy et al. (2008) presented a rebuilt diversity curve based on genus-level in a large sample record. These and other statistically sound and standardized datasets of fossil occurrences have combined sources as literature, databases, and museum collections data as a foundation. Integration of these datasets with the entire fossil record based on individual specimens in space and time would be the ideal approach to species-level taxonomy standards determinations. An example showing how this approach may be achieved is the use of initiatives such as the Web-based data facility Palaeontology Database (PdB) which includes a large amount of fossil record data from throughout the world. The major advantage of that is to gather institucional and also private palaeontological collections with taxonomy experts validation. The core of these datasets is the taxon, with the species as the expected most reliable unit. Taxonomy is therefore the discipline enrolled in the process with the taxonomist at the centre of the process. Updated taxonomy is crucial to create reliable datasets and a careful approach should prevent biased data due to under- or overestimation of diversity. Palaeontological museum collections are known to be one of the largest repositories of fossil data. Taxonomic standardization of palaeontology collections in the context of a museum should: Engage taxonomists in revising fossil clades of the museum material; Promote networking and museum researcher peers involved in similar collections activities; Avoid replication of errors in taxonomic determinations (e.g. exclusive use of Web-based databases sources of taxonomy); Use type material to compare with the collection specimens; Critically analyse previous taxonomic determinations on old labels and associated specimen information; Promote the accessibility of the collection to the research community; Emphasize digitisation of specimen catalogue records as well as 2D imaging of the specimens. Engage taxonomists in revising fossil clades of the museum material; Promote networking and museum researcher peers involved in similar collections activities; Avoid replication of errors in taxonomic determinations (e.g. exclusive use of Web-based databases sources of taxonomy); Use type material to compare with the collection specimens; Critically analyse previous taxonomic determinations on old labels and associated specimen information; Promote the accessibility of the collection to the research community; Emphasize digitisation of specimen catalogue records as well as 2D imaging of the specimens. These practices are valuable complements to current methodologies adopted to improve the taxonomy of collections, resulting in more reliable data which further enables museum-based research focusing on palaeodiversity estimations.

First study of the bat fossil record of the mid-Atlantic volcanic islands

2021 ◽  
pp. 1-15
Author(s):  
Javier GONZÁLEZ-DIONIS ◽  
Carolina CASTILLO RUIZ ◽  
Penélope CRUZADO-CABALLERO ◽  
Elena CADAVID-MELERO ◽  
Vicente D. CRESPO
Keyword(s):  
Atlantic Ocean ◽  
Iberian Peninsula ◽  
Central Europe ◽  
Canary Islands ◽  
Fossil Record ◽  
Dental Morphology ◽  
Lava Tubes ◽  
El Hierro ◽  
Volcanic Islands ◽  
Fossil Data

ABSTRACT Bats are one of the most abundant and important mammals in ecosystems. However, their fossil record is scarce and fragile, making them difficult to find. Accordingly, there is no record of this group in the volcanic islands of the mid-Atlantic Ocean apart from the Canary Islands. This paper studies the first bat fossil record of the Canary Islands (Spain). The material studied is found within two Quaternary lava tubes, Cueva de los Verdes on Lanzarote and Cueva Roja on the island of El Hierro. The dental and humeral morphology and biometry are analysed and compared with current specimens. Among our results we highlight the first fossil data of two species endemic to the islands of the mid-Atlantic Ocean, Plecotus teneriffae and Pipistrellus maderensis, the former from the Canary Islands and the latter from the Azores, Madeira and the Canary Islands. We also confirm the presence of Pipistrellus kuhlii in the fossil record of the island of Lanzarote. No differences are observed between the dental morphology of the current and the fossil populations of P. maderensis and Pl. teneriffae. In the case of P. kuhlii, the populations of the Canary Islands and the Iberian Peninsula show differences in the paraconule with respect to the populations from central Europe. Palaeoecological studies of these taxa suggest that these islands presented a similar habitat when the sites were formed to the present-day habitat.

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