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PHYSIG specifications

Information


Unique identifier OMICS_12478
Name PHYSIG
Alternative name Phylogenetic Signal
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Theodore Garland

Publication for Phylogenetic Signal

PHYSIG citations

 (288)
call_split

Asynchronous evolution of interdependent nest characters across the avian phylogeny

2018
Nat Commun
PMCID: 5951845
PMID: 29760391
DOI: 10.1038/s41467-018-04265-x
call_split See protocol

[…] ore, by explicitly incorporating an evolutionary model, the EM-Mantel test provided a more realistic null hypothesis to test if correlation deviated from the model expectation and assess the level of phylogenetic signal. We modified the original R code provided by ref. for the EM-Mantel test to make it applicable to multiple character states within families using the Bray-Curtis dissimilarity stat […]

library_books

Mechanical adaptation of trabecular bone morphology in the mammalian mandible

2018
Sci Rep
PMCID: 5940912
PMID: 29740057
DOI: 10.1038/s41598-018-25597-0

[…] roduce contrasting trabecular structures (as was observed). As this study is an inter-species histomorphometric analysis it is important to note that the observed relationships could be influenced by phylogenetic signal present in the data. Due to the low sample size it is impossible to employ comparative methods within a robust statistical framework (see Blomberg et al.), and only future work bas […]

library_books

Dietary specialization is linked to reduced species durations in North American fossil canids

2018
R Soc Open Sci
PMCID: 5936914
PMID: 29765649
DOI: 10.1098/rsos.171861

[…] To test for phylogenetic signal in the two intrinsic traits (body size, diet) and two emergent properties (duration, occupancy), we computed Pagel's λ [] and Blomberg's K [] using the R package phytools []. To ac […]

library_books

Exploring the evolution of multicellularity in Saccharomyces cerevisiae under bacteria environment: An experimental phylogenetics approach

2018
Ecol Evol
PMCID: 5938455
PMID: 29760902
DOI: 10.1002/ece3.3979

[…] e statistically associated with the branching pattern of the diversification. In contrast, aggregative clusters appeared in twenty tips (only in the bacteria treatment), which also showed significant phylogenetic signal (observed number of transitions = 11; median of randomized transitions = 18; p < .001; Figure ). In other words, the distribution pattern of the aggregative phenotype in the result […]

call_split

Low acclimation capacity of narrow‐ranging thermal specialists exposes susceptibility to global climate change

2018
Ecol Evol
PMCID: 5938462
PMID: 29760904
DOI: 10.1002/ece3.4006
call_split See protocol

[…] nt Core Team, ). In all cases, lambda was chosen as the best model with lambda scores for traits between 0.00 and 0.086. These low lambda values indicate that these particular traits have very little phylogenetic signal, enabling us to use the original data without further concern for phylogenetic influence. […]

call_split

Study of morphological variation of northern Neotropical Ariidae reveals conservatism despite macrohabitat transitions

2018
BMC Evol Biol
PMCID: 5870521
PMID: 29587647
DOI: 10.1186/s12862-018-1152-y
call_split See protocol

[…] instead of the common biogeographic calibration point, the final closure of the Panamanian Isthmus. It was read in using read.nexus (ape).Blomberg’s K [] is an estimator that assesses the strength of phylogenetic signal in any quantitative variable. Phylogenetic signal in this context is the association of phenotypic similarity derived from Procrustes coordinates to phylogenetic relatedness among […]

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PHYSIG institution(s)
Department of Biology, University of California, Riverside, CA, USA; Department of Zoology, University of Wisconsin, Madison, WI, USA
PHYSIG funding source(s)
This work was supported by National Science Foundation grant DEB-0196384.

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