scholarly journals Sensitivity of biogeographic reconstructions to the use of differential extinction rates

2016 ◽  
Author(s):  
Jose Luis Pinzón
Keyword(s):  
Statistical Methods ◽  
Historical Biogeography ◽  
Range Estimation ◽  
Extinction Rates ◽  
Evolutionary Studies ◽  
Ancestral Range Estimation

Effects of differential extinction rates remain being an issue in biogeographic and evolutionary studies. Here, I use empirical examples and simulated datasets to asses how the specification of different extinction rates influences ancestral range estimation in historical biogeography. The results showed that variations in scale and asymmetry of extinction rates may have notorious effects in the accuracy of biogeographic inferences, specially when the rates of extinction are high. Further work may explore the behavior of current statistical methods of biogeographic inference with different estimates of extinction based on novel developments in this field.

scholarly journals Sensitivity of biogeographic reconstructions to the use of differential extinction rates

2016 ◽  
Author(s):  
Jose Luis Pinzón
Keyword(s):  
Statistical Methods ◽  
Historical Biogeography ◽  
Range Estimation ◽  
Extinction Rates ◽  
Evolutionary Studies ◽  
Ancestral Range Estimation

Effects of differential extinction rates remain being an issue in biogeographic and evolutionary studies. Here, I use empirical examples and simulated datasets to asses how the specification of different extinction rates influences ancestral range estimation in historical biogeography. The results showed that variations in scale and asymmetry of extinction rates may have notorious effects in the accuracy of biogeographic inferences, specially when the rates of extinction are high. Further work may explore the behavior of current statistical methods of biogeographic inference with different estimates of extinction based on novel developments in this field.

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.

Big data for a large clade: Bioregionalization and ancestral range estimation in the daisy family (Asteraceae)

2019 ◽  
Vol 46 (2) ◽  
pp. 255-267 ◽  
Author(s):  
Christiana McDonald-Spicer ◽  
Nunzio J. Knerr ◽  
Francisco Encinas-Viso ◽  
Alexander N. Schmidt-Lebuhn
Keyword(s):  
Big Data ◽  
Range Estimation ◽  
Ancestral Range Estimation

scholarly journals Into-India or out-of-India? Historical biogeography of the freshwater gastropod genus Pila (Caenogastropoda: Ampullariidae)

2020 ◽  
Vol 129 (3) ◽  
pp. 752-764 ◽  
Author(s):  
Maitreya Sil ◽  
N A Aravind ◽  
K Praveen Karanth
Keyword(s):  
Indian Subcontinent ◽  
Time Frame ◽  
Freshwater Snail ◽  
Historical Biogeography ◽  
Molecular Dating ◽  
Relative Importance ◽  
Tropical Asia ◽  
Relative Contribution ◽  
Freshwater Gastropod ◽  
Ancestral Range Estimation

Abstract The biota of the Indian subcontinent was assembled through multiple associations with various landmasses during a period spanning the Late Cretaceous to the present. It consists of Gondwanan elements that subsequently dispersed ‘out-of-India’ and biota that dispersed ‘into-India’ after the subcontinent collided with Asia. However, the relative contribution of these connections to the current biotic assembly of the subcontinent has been under-explored. Our aim here was to understand the relative importance of these various routes of biotic assembly in India by studying the historical biogeography of the tropical Old World freshwater snail genus Pila. We reconstructed a near-complete phylogeny, based on nuclear and mitochondrial markers, of Ampullariidae including all the described Pila species from India and Ampullariids worldwide. Thereafter, molecular dating and ancestral range estimation analyses were carried out to ascertain the time frame and route of colonization of India by Pila. The results showed that Pila dispersed into India as well as other parts of tropical Asia from Africa after both India and Africa collided with Eurasia. Furthermore, multiple dispersals took place between Southeast Asia and India. These findings corroborate increasing evidence that much of the current Indian assemblage of biota actually dispersed ‘into-India’ after it collided with Asia.

A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions

2021 ◽  
Author(s):  
Wilson X Guillory ◽  
Jason L Brown
Keyword(s):  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Niche Modeling ◽  
New Method ◽  
Ancestral State ◽  
Range Estimation ◽  
Occurrence Data ◽  
Niche Models ◽  
Ancestral Range Estimation

Abstract Ancestral range estimation and projection of niche models into the past have both become common in evolutionary studies where the ancient distributions of organisms are in question. However, these methods are hampered by complementary hurdles: discrete characterization of areas in ancestral range estimation can be overly coarse, especially at shallow timescales, and niche model projection neglects evolution. Phylogenetic niche modeling accounts for both of these issues by incorporating knowledge of evolutionary relationships into a characterization of environmental tolerances. We present a new method for phylogenetic niche modeling, implemented in R. Given past and present climate data, taxon occurrence data, and a time-calibrated phylogeny, our method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. Models either at nodes or along branches of the phylogeny can be estimated. We demonstrate our method on a small group of dendrobatid frogs and show that it can make inferences given species with restricted ranges and little occurrence data. We also use simulations to show that our method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space. Our method brings together fields as disparate as ecological niche modeling, phylogenetics, and ancestral range estimation in a user-friendly package. [Ancestral range estimation; ancestral state reconstruction; biogeography; Dendrobatidae; ecological niche modeling; paleoclimate; phylogeography; species distribution modeling.]

Historical Biogeography of Holarctic Cymbiodyta Water Scavenger Beetles in the Times of Cenozoic Land Bridge Dispersal Routes

2019 ◽  
Vol 3 (5) ◽  
Author(s):  
Emmanuel F A Toussaint ◽  
Andrew E Z Short
Keyword(s):  
Evolutionary History ◽  
New Combination ◽  
Divergence Times ◽  
Range Estimation ◽  
Land Bridge ◽  
Palearctic Species ◽  
History Of ◽  
The Times ◽  
Ancestral Range Estimation

Abstract The genus Cymbiodyta Bedel, 1881 (Coleoptera: Hydrophilidae: Enochrinae) comprises 31 species distributed in both the Old and New World portions of the Holarctic realm. Although the species and taxonomy are relatively well known, the phylogenetic relationships among Cymbiodyta and the evolutionary history of the genus remain unexplored. To understand the systematics and evolution of this lineage, we sequenced five gene fragments for about half of the species in the genus, including most major morphological groups. We also estimated divergence times to test the hypothesis that Cymbiodyta beetles took advantage of the different land bridges connecting the Palearctic and Nearctic regions, that became subaerial in the Cretaceous and Paleocene. Our results recover the eastern Nearctic genus Helocombus Horn, 1890 nesting within Cymbiodyta. Therefore, we synonymize Helocombus syn. n. with Cymbiodyta, resulting in one new combination, Cymbiodyta bifidus (LeConte 1855) comb. n. Our dating analyses and ancestral range estimation support a Nearctic origin of Cymbiodyta in the late Cretaceous about 100 million year ago. The placement of the unique Palearctic species on a long branch as sister to the rest of the clade and the dating results cannot reject a role of the De Geer and/or Thulean routes in the colonization of the Palearctic region from the Nearctic; however, they do not support a role for Beringia in the more recent colonization of the Oriental region.

Statistics and parallaxes

1978 ◽  
Vol 48 ◽  
pp. 7-29
Author(s):  
T. E. Lutz
Keyword(s):  
Experimental Design ◽  
Statistical Methods ◽  
Review Paper ◽  
Systematic Errors ◽  
Past Experience ◽  
Random Errors ◽  
Trigonometric Parallaxes ◽  
Systematic And Random Errors

This review paper deals with the use of statistical methods to evaluate systematic and random errors associated with trigonometric parallaxes. First, systematic errors which arise when using trigonometric parallaxes to calibrate luminosity systems are discussed. Next, determination of the external errors of parallax measurement are reviewed. Observatory corrections are discussed. Schilt’s point, that as the causes of these systematic differences between observatories are not known the computed corrections can not be applied appropriately, is emphasized. However, modern parallax work is sufficiently accurate that it is necessary to determine observatory corrections if full use is to be made of the potential precision of the data. To this end, it is suggested that a prior experimental design is required. Past experience has shown that accidental overlap of observing programs will not suffice to determine observatory corrections which are meaningful.

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