Autoregressive Models for Estimating Phylogenetic and Environmental Effects: Accounting for Within-species Variations

Cornillon, Pierre; Pontier, Dominique; Rochet, Marie-Joëlle

doi:10.1006/jtbi.1999.1040

Cited by 10 publications

(5 citation statements)

References 58 publications

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“…Also important for such attempts will be explicit incorporation of information on measurement error of various types. Such a comprehensive and practical method does not yet exist, but steps are being made in that direction (e.g., see Gittleman and Kot 1990, p. 231;Lynch 1991;Butler et al 2000;Cornillon et al 2000;Baum and Donoghue 2001;Housworth and Martins 2001;Orzack and Sober 2001;Martins et al 2002;Y. Desdevises, P. Legendre, L. Azouzi, and S. Morand, pers.…”

Section: Discussionmentioning

confidence: 99%

Testing for Phylogenetic Signal in Comparative Data: Behavioral Traits Are More Labile

2003

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Abstract. The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal ␣ ϭ 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the OrnsteinUhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25% of traits) and/or ACDC (40%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the ori...

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Section: Discussionmentioning

confidence: 99%

Testing for Phylogenetic Signal in Comparative Data: Behavioral Traits Are More Labile

2003

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“…However, most of our phylogenetic studies are carried out at much higher taxonomic levels, and intraspecific phylogenies are of course complicated by the possibility of rampant reticulate evolution, making these data challenging to obtain. The latter problem is being ameliorated by the development of a variety of novel methods capable of taking into account reticulation (Cornillon et al 2000;Posada and Crandall 2001), together with the use of combinations of nuclear and mitochondria/ chloroplast DNA data (Wendel et al 1991;Giebler 1997;Kenyon 1997).…”

Section: Toward a Research Program That Incorporates Genetic Assimilamentioning

confidence: 99%

Perspective: Genetic Assimilation and a Possible Evolutionary Paradox: Can Macroevolution Sometimes Be So Fast as to Pass Us By?

Pigliucci¹,

2003

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The idea of genetic assimilation, that environmentally induced phenotypes may become genetically fixed and no longer require the original environmental stimulus, has had varied success through time in evolutionary biology research. Proposed by Waddington in the 1940s, it became an area of active empirical research mostly thanks to the efforts of its inventor and his collaborators. It was then attacked as of minor importance during the "hardening" of the neo-Darwinian synthesis and was relegated to a secondary role for decades. Recently, several papers have appeared, mostly independently of each other, to explore the likelihood of genetic assimilation as a biological phenomenon and its potential importance to our understanding of evolution. In this article we briefly trace the history of the concept and then discuss theoretical models that have newly employed genetic assimilation in a variety of contexts. We propose a typical scenario of evolution of genetic assimilation via an intermediate stage of phenotypic plasticity and present potential examples of the same. We also discuss a conceptual map of current and future lines of research aimed at exploring the actual relevance of genetic assimilation for evolutionary biology.

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“…To find an estimation of the parameters, we used a maximum likelihood procedure (Kendall andStuart 1979, Cliff andOrd 1981). Further detail on model development and parameter estimation can be found in Cornillon et al (2000).…”

Section: A Family Of Autoregressive Modelsmentioning

confidence: 99%

“…Here our goals are to 1) better characterise life history patterns within a group of teleost fishes, 2) assess the magnitude of fishing effects on life history traits, 3) determine whether the slow-fast continuum observed in birds and mammals (Gaillard et al 1989, Promislow andHarvey 1990) and in lizards Charnov 1992, Clobert et al 1998) can be extended to fishes, 4) examine whether the decrease of adult survival due to fishing moves species towards the fast end of the continuum, irrespective of their position along this continuum. For that purpose, we developed a new comparative method designed to incorporate both inter-and intra-specific variation in life history traits (Cornillon et al 2000). This method is based on autoregressive methods whose aim is to separate environmental effects from phylogenetic influence (Cheverud et al 1985, Gittleman andKot 1990).…”

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confidence: 99%

Comparative analysis of phylogenetic and fishing effects in life history patterns of teleost fishes

Rochet¹,

Cornillon²,

Sabatier³

et al. 2000

Oikos

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Comparative analysis of phylogenetic and fishing effects in life history patterns of teleost fishes. -Oikos 91: 255 -270.The effects of fishing on life history traits and life history strategies of teleost fishes are analysed by a new comparative method that splits traits into an allometric part (size effect), an autoregressive phylogenetic component, and an environmental component (fishing effect). Both intra-and inter-specific variation of age and size at maturity, fecundity, adult size and egg size are analysed by comparing 84 populations of 49 species submitted to various fishing pressures. Two axes of life history diversification are found among teleosts. One is the well-known slow-fast continuum separating short-lived and early maturing species (like Clupeiformes) from longerlived species that mature late relative to their size and spawn larger eggs (like salmonids or Scorpaeniformes). An additional strategy involves the schedule of resource allocation to growth and reproduction. Indeterminate growth allows higher teleosts (e.g. Gadiformes) to reach a large size while maturing early and laying small eggs. Increasing fishing pressure decreases age at maturity and egg size, and increases fecundity at maturity, the slope of the fecundity-length relationship and relative size at maturity. These compensations for higher adult mortality differ among life history strategies. Indeterminate growth is associated with a greater flexibility in resource allocation to growth and reproduction that facilitates greater resilience to fishing mortality.M.-J. Rochet,

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Autoregressive Models for Estimating Phylogenetic and Environmental Effects: Accounting for Within-species Variations

Cited by 10 publications

References 58 publications

Testing for Phylogenetic Signal in Comparative Data: Behavioral Traits Are More Labile

Testing for Phylogenetic Signal in Comparative Data: Behavioral Traits Are More Labile

Perspective: Genetic Assimilation and a Possible Evolutionary Paradox: Can Macroevolution Sometimes Be So Fast as to Pass Us By?

Comparative analysis of phylogenetic and fishing effects in life history patterns of teleost fishes

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