PHYLOGENETIC ANCOVA AND PHENOTYPIC RADIATION:

CARNIVORAN POSTURE *
Jesualdo A. Fuentes , Elizabeth Housworth, P. David Polly, Emília P. Martins
Departments of Biology, Mathematics & Geology, Indiana University – Bloomington

INTRODUCTION TRANSFORMATIONS WITH A PHYLOGENY ANCOVA

• Regression residuals: Regression and subsequent ANOVA, • PGLS: Regress Y on X using Z as covariate,
When studying macroevolutionary patterns, we are commonly
interested in the functional relationship between traits and how they
but including phylogeny in a two step procedure (Fig.3): accounting for phylogeny (Fig.5): X
are related to ecological or evolutionary factors. For example, limb
Pattern may get
proportions in mammals are closely related to posture and
locomotion. Animals with proportionally long proximal and short distal diluted in
the two step
limb segments tend to have a slower, more powerful plantigrade Y
extension of the foot and those with long distal and short proximal procedure
segments tend to have a rapid digitigrade extension (Fig.1). This
system can be thought of in terms of three variables, two continuous
• Threshold model[9,10]: Estimate underlying
(Y and Z) and one categorical (X). Broad pattern is Homoscedasticity assumption
quantitative character (liability) for X.
Natural selection moving Y (0.31) and detected, but
Several methods have been proposed to analyze this type of data. • Phenotypic radiation[11]: Allowing
In this study we use some of the most prevalent, and introduce a new Z (0.95) in the same direction, but not the detailed
heteroscedasticity according to posture Z
approach that takes into account the problem of phenotypic radiation. contribution of X (0.001) not clear. relationships
(Fig.6) for different evolutionary processes Fig.5. Metatarsal III versus femur length; posture as indicated in the legend. Metatarsal and femur length
We test our approach using real data on hind limb segment ratios in (Table 1): are positively related, but posture categories have different lines

Carnivora in which we are able to control the correlation between the Parameter
Evolutionary AIC
variables to determine how well our method recovers it. process score
4.08 9.7 0.37 -0.21 70.28 - - 967.2
TIPS
Data 4.08 9.7 0.37 -0.21 76.54 68.42 - 969.1
2.42 10.7 0.34 -0.12 224.9 - - 932.6
• Variables: Linear measurements and postural BM
2.75 10.6 0.34 -0.12 245.81 219.6 - 934.5
categories for 135 species of the order OU
3.61 12.2 0.35 -0.17 85.2 - 1.97 928.9
Carnivora (Fig. 1). Data from Polly[1]. 4.34 11.5 0.35 -0.17 104.3 77.32 1.96 928.6
Z • Phylogeny: Backbone[2] with supplements for Table 1. ANCOVA models for different evolutionary processes: non-phylogenetic (TIPS),

Felidae[3], Canidae[4], Mustelidae[5],

Y Brownian Motion (BM) and Ornstein-Uhlenbeck (OU). For each evolutionary process, one
(light green) and two (dark green) variances are compared (Notation as in
Fig.6 for the two-variance case ). AIC scores provided for model comparison; the best model is
Mephitidae[6,7], and Procyonidae[8]. the OU process with two variances (bold).

Metatarsal length increases as femur

length increases, but the rate of
Plantigrady Digitigrady
change is higher for digitigrades
Fig.6. Carnivoran phylogeny with ancestral state reconstruction for posture. Plantigrady (A) and which also present smaller variance
digitigrady (B) can have different variances .

Y Z
Fig.3. Regression of metatarsal III on femur length, considering phylogenetic structure. The phylogeny is also used in the

X subsequent ANOVA, in which the resulting residuals (r) are not associated with X

Fig.1. Carnivoran hind limb (modified from Polly[1]). Y: Maximum length of the third Effect of posture on limb elongation is not detected
metatarsal; Z : Maximum length of the femur; X: Posture (Plantigrady, digitigrady).

TRANSFORMATIONS WITHOUT A PHYLOGENY SIMULATIONS

• Indices: Divide Y by Z and • ANCOVA: Simulation of Y, Z and X accounting for phylogeny,

apply ANOVA with the obtaining empirical null distributions for F-ratio and regression
resulting ratio, using X as coefficients (Fig.4). Randomization test applied comparing null
treatment (Fig.2): distributions with results of standard ANCOVA:
Strong focus on
hypothesis testing
Linear assumption; • MANOVA: Null distribution of test statistic obtained by new sets
deviations from the
of Y and Z as response variables on the phylogenetic tree. Null
Y/Z

general trend and

distribution is compared with standard MANOVA for testing:
measurement error
not considered Relationship between metatarsal
and femur length not explored
• Regression residuals:
Fig.4. Empirical null distribution from F-ratios for each simulation (1000
Regress Y on Z and apply generations). The test indicates that the relationship is stronger than expected by
chance (F: Observed=376.6 > Simulated=29.1 ). Empirical null distributions were
ANOVA with the X also obtained for the regression coefficients ( , but only was
Fig.2. Metatarsal III to femur ratio compared significant (Observed=-9.7, outside interval=-0.1, 0.1). Similarly, MANOVA indicates
residuals, using X as between posture categories. The ratio is higher for
digitigrades than for plantigrades (bb1=15.8, p<0.05).
that posture affects both metatarsal and femur length (Pillai-Barlett=0.3, p<0.05,
p(phy)=0.02)
treatment: The same trend results with the regression residuals
(b1=18.9, p<0.05).
Posture affects limbs,
Digitigrades have but relationship
larger relative between lengths
Independence assumption metatarsal length unknown

CONCLUSIONS
• Several methods are available for studying the
relationship among two continuous and one
categorical variable. Choosing one will depend
on the question at hand.
• In carnivores, shifts to digitigrady are not only
FUTURE DIRECTIONS
• Bayesian version: Considering uncertainty in
the phylogeny, the adaptive constraint
parameter, and the ancestral state
reconstruction.
• Adaptation-inertia[12]: Incorporating
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