LASER: A Maximum Likelihood Toolkit for Detecting Temporal Shifts in Diversification Rates From Molecular Phylogenies

By D. Rabosky. Evolutionary bioinformatics online, 2006

348 citations recorded by the source corpus.

Rates of species origination and extinction can vary over time during evolutionary radiations, and it is possible to reconstruct the history of diversification using molecular phylogenies of extant taxa only. Maximum likelihood methods provide a useful framework for inferring temporal variation in diversification rates. LASER is a package for the R programming environment that implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time. LASER contrasts the likelihood of phylogenetic data under models where diversification rates have changed over time to alternative models where rates have remained constant over time. Major strengths of the package include the ability to detect temporal increases in diversification rates and the inference of diversification parameters under multiple rate-variable models of diversification. The program and associated documentation are freely available from the R package archive at http://cran.r-project.org.

Subfields: Ecology, Genetics, Paleontology

View Paper: https://www.semanticscholar.org/paper/468b551cbce751e1b54550dc2ff1473104a67949

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Genetics

In Paleontology

Citations in the corpus

Species delimitation, patterns of diversification and historical biogeography of the Neotropical frog genus Adenomera (Anura, Leptodactylidae) (2014, methodology): “Rd function of the laser package (Rabosky, 2006) under R 2.”
Early evolutionary history of the flowering plant family Annonaceae: steady diversification and boreotropical geodispersal (2011, positive): “To provide an indication of net diversification rates within the family, we generated a semi-logarithmic lineage-through-time (LTT) plot of the resulting dated trees using the laser package version 2.2 (Rabosky, 2006).”
The age of the grasses and clusters of origins of C4 photosynthesis (2008, methodology): “With LASER (Rabosky, 2006), we created 1000 simulated datasets, each with as many transitions in photosynthetic pathway as observed, generated under a pure birth constant rate speciation model (Rabosky, 2006).”
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates (2009, methodology): “We used R (44) to perform all diversification analyses using the following libraries: Ape (45), Geiger (46), and Laser (47).”
The beetle tree of life reveals that Coleoptera survived end‐Permian mass extinction to diversify during the Cretaceous terrestrial revolution (2015, methodology): “, 2008, 2011) and Laser (Rabosky, 2007), following the methods of Alfaro et al.”
Phylogenetic scale in ecology and evolution (2016, background): “Gamma statistic (Pybus & Harvey, 2000) laser (Rabosky, 2007) Community ecology and biogeography Community structure and phylogenetic diversity Phylometrics (NRI, NTI, MNND, MPD, PD) (Faith, 1992; Swenson, 2009; Webb et al., 2002) picante (Kembel et al., 2010), Phy-loMeasures (Tsirogiannis & Sandel,…”
Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini) (2010, positive): “The R framework with packages ape (Paradis et al., 2004), laser (Rabosky, 2006) and geiger (Harmon et al., 2007) was used to implement the Monte Carlo constantrates (MCCR) test following Pybus & Harvey (2000) and to create a lineage-through-time plot as a graphical representation of the ultrametric…”
GEIGER: investigating evolutionary radiations (2008, methodology): “GEIGER is written in the cross-platform software language R and complements four other packages: APE (Paradis et al ., 2004), apTreeshape (Bortolussi et al ., 2006), OUCH (Butler and King, 2004) and LASER (Rabosky, 2006).”
Biogeographical diversification of mainland Asian Dendrobium (Orchidaceae) and its implications for the historical dynamics of evergreen broad‐leaved forests (2016, positive): “The calculations were performed using laser 2.3 (Rabosky, 2006a).”
Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. II. Diversification history and origin of regional assemblages (2013, methodology): “3 (Rabosky, 2006).”
Tree of Life Reveals Clock-Like Speciation and Diversification (2014, methodology): “Gamma Test The gamma statistic (Pybus and Harvey 2000) was employed on 59 clades (all eukaryotes plus 58 clades listed in supplementary table S5, Supplementary Material online) to detect decrease in speciation rate over the history of the tree (LASER package; Rabosky and Schliep 2013).”
A simple polytomy resolver for dated phylogenies (2011, methodology): “(2009), using the r library laser (Rabosky 2006) and additional code kindly provided by Dan Rabosky.”