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22 de mayo de 2014

Que es "señal filogenética" en los datos morfométricos?

Primero hay que considerar el concepto, que es "señal filogenetica" en terminos generales?
Luego hay que visualizar las alternativas sobre como medir dicha señal. Por ejemplo, como se mide "señal filogenetica" en los datos moleculares? ... en los datos morfológicos? ... en los datos conductuales? .... etc.
El concepto de "señal filogenetica" no deberia ser diferente en el caso de los datos de forma. Por lo tanto, cuantas maneras hay de medir "señal filogenetica" en los datos morfometricos?

Aqui va un articulo reciente que me hizo divagar sobre sobre "señal filogenetica". Los datos son  morfometricos de ontogenias. Los análisis son en el contexto de los metodos comparativos. Las conclusiones son: las ontogenias contienen poca informacion filogenetica, y se cuestiona su eficacia para la inferencia de filogenia. Mi opinion: califican el uso, sin usar los datos para inferir filogenia.

Pregunta: Para poder concluir asi, acaso no deberian USARSE  los datos para INFERIR de hecho la filogenia? Dado que producir arboles es diferente de mapear los datos en un arbol dado, se puede concluir sobre la señal filogenetica y si son eficaces o no, solo si se intenta usarlos para producir arboles. Como ven?

Aqui el articulo:

J Evol Biol. 2014 May 19. doi: 10.1111/jeb.12382. [Epub ahead of print]
The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics.


The degree to which the ontogeny of organisms could facilitate our understanding of phylogenetic relationships has long been a subject of contention in evolutionary biology. The famed notion that 'ontogeny recapitulates phylogeny' has been largely discredited, but there remains an expectation that closely related organisms undergo similar morphological transformations throughout ontogeny. To test this assumption, we used three-dimensional geometric morphometric methods to characterize the cranial morphology of 10 extant crocodylian species and construct allometric trajectories that model the post-natal ontogenetic shape changes. Using time-calibrated molecular and morphological trees, we employed a suite of comparative phylogenetic methods to assess the extent of phylogenetic signal in these trajectories. All analyses largely demonstrated a lack of significant phylogenetic signal, indicating that ontogenetic shape changes contain little phylogenetic information. Notably, some Mantel tests yielded marginally significant results when analysed with the morphological tree, which suggest that the underlying signal in these trajectories is correlated with similarities in the adult cranial morphology. However, despite these instances, all other analyses, including more powerful tests for phylogenetic signal, recovered statistical and visual evidence against the assumption that similarities in ontogenetic shape changes are commensurate with phylogenetic relatedness and thus bring into question the efficacy of using allometric trajectories for phylogenetic inference.
© 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.
Crocodylia, allometry, geometric morphometrics, ontogeny, phylogenetic signal
[PubMed - as supplied by publisher]
Definiciones de "señal filogenetica"
1. En el contexto de los metodos comparativos: aka mapeando caracteres! (Opinión: esto no es señal filogenetica!)
Basicamente es la relacion o dependencia de las observaciones con un arbol. Los datos tienen estructura filogenetica?
phylogenetic signal - which is recognized when closely related species tend to be more similar to one another than expected by chance - is a central concept in comparative biology. ...
If a character exhibits phylogenetic signal, we expect that the phylogeny will be helpful in explaining the distribution of character values among terminal taxa.
Revell et al 2011 Syst. Biol. 57, 591-601
Throughout this article, we represent and interpret phylogenetic signal—the statistical dependence among observations for species related by a phylogenetic tree—as a consequence of the phylogenetic covariance between species. Phylogenetic covariance is the covariance between species values for a given trait that is due to the shared history of taxa. The measurement of phylogenetic signal involves comparing the variability of species trait values to the residual trait variability when the expected covariances among observations are first incorporated.

One of the questions to ask is whether your data (rather the residuals; Revell 2010) are phylogenetically structured. In other words, do your data show phylogenetic signal? Two common methods are the K statistics of Blomberg et al. (2003) and Pagel's lambda (Pagel, 1999).  
The multivariate version of K for phylogenetic signal in shape:
Adams, D.C. 2014. A generalized K statistic for estimating phylogenetic signal
from shape and other high-dimensional multivariate data. Systematic
Biology 63:685-697. This is implemented in the function physignal of geomorph
R package.

2. En el contexto de los metodos filogeneticos: aka incluyendo caracteres! (Opinión: esto si es señal filogenetica!)
Basicamente "señal filogenética" es homologia filogenética, es decir, la relacion o dependencia de las observaciones con otras observaciones (congruencia de caracteres). Mapeando no se mide congruencia.

Helm-Bychowski & Cracraft 1993. Molecular Biology and Evolution 10: 1196-1214.
"It is suggested, on the other hand, that congruence in cladistic signal across different data sets may be a potentially more useful method for evaluating the reliability of the signal of any one data set.  "
 Mardulyn & Whitfield 1999. Mol. Phyl Evol. 12: 282-294.
"We explore here the phylogenetic signal in three gene (mitochondrial COI and 16S, and nuclear 28S) fragments as an assessment of their utility in resolving generic relationships within this species-rich insect group. .... The phylogenetic signal, if present, is therefore concentrated on a few well-supported clades."
Clouse et al 2010. Phylogenetic signal in morphometric data. Cladistics 27: 1-4.
"phylogenetic signal: ... our best measure of success ... is whether the resulting trees bear any resemblance to hypothesis derived from other sources of evidence "


3. La señal filogenetica de dos juegos de datos puede ser conflictiva
Huelsenbeck & Bull 1995. Syst. Biol 45: 92-98.

"We describe a novel likelihood ratio test that compares different topologies (each estimated from a different data partition for the same taxa) to determine if they are significantly different. The results of this test indicate that different genes provide significantly different phylogenies for amniotes, supporting earlier suggestions based on less direct tests. These results suggest that some molecular data can give misleading information about evolutionary history."

es lo mismo señal filogenetica que phylogenetic reliability and congruence?

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