Hanley, Cassey & Doucet
Appendix 1
Appendix 1
Comparison between museums and measurement protocols
When conducting a multi-species comparative study, it is important to consider the sources of
variation among the species you are comparing (Garamszegi and Møller 2010). Although interspecific
variation is usually greater than intraspecific variation, sources of variation that are not accounted for
may introduce biases into datasets, and it is therefore important to consider alternative sources of
variation, particularly those introduced due to measurement error and differences in protocol. In this
study, we combined two datasets containing reflectance measurements that were obtained with subtly
different measurement techniques from four natural history museums (for details, see Methods). To
justify combining these datasets, we examine the effect of measurement protocol on the eggshell
reflectance spectra we use for our comparative tests.
Methods
We used a general linear mixed model to examine the effect of species (as a random variable), and
museum on the calculated colorimetric variables presented in our paper (brightness, UV chroma, bluegreen chroma, and brown chroma) for species that were measured using both data collection protocols
(N = 25 species). Although it is important to control for the influence of phylogeny, each species is
represented twice in this analysis, which is not conducive to phylogenetic controls. Therefore, we have
chosen to classify species as a random effect, which controls for non-independence. We present the
least square means from these analyses to examine the influence of measurement protocol and museum
on our analyses. We expect that interspecific variation will be greater than the variation between
institutions, just as we expect interspecific variation to be greater than other possible sources of
variation (between clutches, between regions on the egg, between eggs collected at different stages,
Hanley, Cassey & Doucet
Appendix 1
etc.). In addition, if the different measurement protocol used at the Natural History Museum at Tring
introduced biases (rather than legitimate differences in egg color), we would expect a post-hoc
examination to show that the least square means from this institution are significantly different from all
other institutions.
Results & Conclusions
Although there were differences in eggshell reflectance between museums (Table A1, Fig. A1), there
were no consistent differences attributed to measurement protocol (Fig. A2). Moreover, variation
attributable to species was far greater than that attributable to the institution that the egg was measured
in. This suggests that although there were differences between institutions, possibly due to the
individual histories of the specimens, much of the variation represents true differences in colour
between the eggs that were collected. These data suggest that for inter-specific comparisons, the
combination of data collected with these two measurement protocols was justified, perhaps because the
sampling procedure, white standard, and spectrometer configurations were identical. Differences
between sampling procedures or spectrometer spectral range could conceivably produce larger
differences between reflectance measurements (but see Moreno et al. 2006).
Literature cited
Garamszegi, L. Z., and A. P. Møller. 2010. Effects of sample size and intraspecific variation in
phylogenetic comparative studies: a meta-analytic review. Biol. Rev. 85:797-805.
Moreno, J., E. Lobato, J. Morales, S. Merino, G. Tomás, J. Martínez-de la Puente, J. J. Sanz, R. Mateo,
and J. J. Soler. 2006. Experimental evidence that egg color indicates female condition at laying
in a songbird. Behav. Ecol. 17:651-655.
Hanley, Cassey & Doucet
Appendix 2
Appendix 2
Phylogenetic reconstruction
We used Mesquite (v2.6) to reconstruct a composite supertree (Fig. A3) following a recent
hypothesis for the phylogenic relationships among birds (Hackett et al., 2008) for the basis of the major
phylogenetic relationships. Within Passeriformes, we based our placement of species on phylogenetic
positions suggested by a large-scale (1723 extant species) supertree (Jønsson & Fjeldså, 2006). We
relied on a ‘direct’ phylogenetic substitution method; however, not all taxonomic units are
monophyletic, therefore we did not rely on taxonomy for the basis of our decision, but instead relied on
available published molecular (or combined molecular and morphological) phylogenies for species
placement. When the exact placement of a species was ambiguous the species were collapsed into a
polytomy.
We recognize that other techniques for supertree construction that take conflicting hypotheses
on phylogenetic positions into account (Bininda-Emonds et al., 2002). Matrix representation with
parsimony (MRP) is one such technique and is the most popular method for what is referred to as
‘indirect’ supertree construction (Baum, 1992; Ragan, 1992). This method has already been applied
broadly (Bininda-Emonds et al., 2002; Bininda-Emonds, 2004) and can utilize all available information
from published phylogenies to arrive at the best possible current hypothesis and therefore is more
objective and repeatable than previous methods.
Both ‘direct’ and ‘indirect’ methods have advantages and drawbacks (Sanderson et al., 1998);
however, we choose to rely on a ‘direct’ method that will not be overly influenced by poorly resolved
or erroneous phylogenetic hypotheses. While future work may provide better resolution to in various
lineages of birds that we have collapsed into polytomies within our supertree, we follow the viewpoint
Hanley, Cassey & Doucet
Appendix 2
that there should be a single correct hypothesis for the relationships between organisms. ‘Indirect’
methods for phylogenetic reconstruction can be thought of as “summaries of summaries” (BinindaEmonds, 2004), however not all source phylogenies adequately approach the truth. In this way, some
level of discretion is necessary for both ‘indirect’ and ‘direct’ methods, with ‘direct’ methods allowing
for a larger degree of researcher discretion. Direct methods are conservative (Sanderson et al., 1998;
Bininda-Emonds et al., 2002), which may be statistically limiting (e.g., lower power). However, we
chose to take this conservative approach for resolving the phylogenetic hypotheses, due to the broad
interest, and sometimes contentious views of the adaptive evolution of eggshell colouration (Kilner,
2006; Reynolds et al., 2009; Cherry & Gosler, 2010).
Here we provide references that we used to decide on the placement of the species in our
dataset. We relied on better-resolved phylogenetic information, particularly where more recent
information improved upon previous species placement, to form the basis of our phylogeny (Jønsson &
Fjeldså, 2006; Hackett et al., 2008).
Orders
Struthioniformes (Harshman et al., 2008)
Tinamiformes (Bertelli & Porzecanski, 2004)
Sphenisciformes (Bertelli & Giannini, 2005)
Gaviiformes (Boertmann, 1990)
Podicepidiformes (Livezey, 1989)
Hanley, Cassey & Doucet
Appendix 2
Procellariformes (Nunn & Stanley, 1998)
Pelecaniformes (Friesen & Anderson, 1997; Kennedy et al., 2000; Kennedy & Spencer, 2004; Hackett
et al., 2008)
Ciconiiformes Sheldon et al., 1995; Sheldon & Slikas, 1997; Sheldon et al., 2000)
Phoenicopteriformes (Hackett et al., 2008)
Anseriformes (Johnson et al., 1999; Donne-Goussé et al., 2002)
Falconiformes (Griffiths et al., 2004; Lerner & Mindell, 2005; Hackett et al., 2008)
Galliformes (Crowe et al., 2006)
Gruiformes (Fain et al., 2007)
Charadriformes (Whittingham et al., 2000; Thomas et al., 2004; Baker et al., 2007; Hackett et al.,
2008)
Columbidae (Johnson & Clayton, 2000; Johnson et al., 2001; Shapiro et al., 2002; Clements, 2007;
Pereira et al., 2007)
Pscittaciformes (de Kloet & de Kloet, 2005; Ericson et al., 2006a; Tavares et al., 2006; Hackett et al.,
2008; Wright et al., 2008)
Cuculiformes (Veron, 2000; Sorenson & Payne, 2005)
Strigiformes (Hackett et al., 2008; Wink et al., 2008)
Camprimulgiformes (Barrowclough et al., 2006; Larsen et al., 2007)
Apodiformes (Price, 2004; McGuire et al., 2008)
Hanley, Cassey & Doucet
Appendix 2
Coliiformes (Mayr et al., 2003; Ericson et al., 2006a)
Trogoniformes (Hackett et al., 2008)
Coraciformes (Moyle, 2006; Hackett et al., 2008)
Galbuliformes (Johansson & Ericson, 2003; Mayr et al., 2003)
Bucerotiformes (Hackett et al., 2008)
Piciformes (Johansson & Ericson, 2003; Mayr et al., 2003; Webb & Moore, 2005)
Passeriformes (Subocines) (Irestedt et al., 2004; Moyle et al., 2009a)
Passeriformes (Oscines) (Murray et al., 1994; Lanyon & Omland, 1999; Lovette, 1999; Omland et al.,
1999; Zink et al., 1999; Cicero & Johnson, 2001; Cicero & Johnson, 2002; Lovette, 2002; Yuri &
Mindell, 2002; Carson & Spicer, 2003; Cibois, 2003; Ericson & Johansson, 2003; Barker, 2004; Barker
et al., 2004; Cibois, 2004; Sheldon et al., 2005; Alström et al., 2006; Ericson et al., 2006b; Jønsson &
Fjeldså, 2006; Mann et al., 2006; Pasquet et al., 2006; Arnaiz-Villena et al., 2007; Barker, 2007;
Bonaccorso & Peterson, 2007; Klicka & Spellman, 2007; Lovette & Rubenstein, 2007; Nguembock et
al., 2007; Voelker et al., 2007; Chaves et al., 2008; Jønsson et al., 2008; Ohlson et al., 2008; Spellman
et al., 2008; Voelker & Klicka, 2008; da Costa et al., 2009; Gelang et al., 2009; Irestedt et al., 2009;
Moyle et al., 2009b; Nguembock et al., 2009)
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Appendix 2
Table A1
Results of a general mixed-effect model predicting color from species and the institution at which the
eggs were measured. In these models, species was considered a random covariate, while institution was
considered a fixed effect.
Fig. A1
Spectral reflectance of eggshells from species laying white Apus apus A), blue-green Aplonis tabuensis
B), and brown Pica pica C) eggshells measured at three institutions using a 45 degree coincident
oblique measurement angle (black line ± SE) and the eggs measured at the National History Museum at
Tring with a coincident normal measurement angle (red line ± SE).
Fig. A2
Brightness A), blue-green B), brown C), and ultraviolet chroma D) from general linear mixed models
controlling for species as a random effect and institution (AMNH = American Museum of Natural
History, FMNH = Field Museum of Natural History, TRING = National History Museum at Tring, and
UMMZ = University of Michigan Museum of Zoology). Data are least squares means ± SE and Tukey
HSD post hoc comparisons are indicated in italic letters.
Fig. A3
A visual depiction of the phylogeny (to the family level) that formed the basis for our comparative
analyses. For convenience, all Passeriformes are shown to the right. We used a ‘direct’ method of
supertree construction to build this phylogeny, and relied on both molecular and combined molecular
and morphological phylogenies. We follow Jønsson and Fjeldså (2006) for the relationships within
Hanley, Cassey & Doucet
Appendix 2
Passeriformes. In cases where families were paraphyletic, we used numbers to indicate the position of
species that are not grouped with the other representatives of their families (nomenclature follows
Clement’s Checklist 6th edition (2007)).
Table A1
Brightness
UV chroma
Blue-green chroma
Brown chroma
Whole model
Species
Institution
Whole model
Species
Institution
Whole model
Species
Institution
Whole model
Species
Institution
F
24.58
25.95
13.36
19.66
20.42
5.00
25.62
30.00
4.48
24.05
25.12
11.34
r2
0.82
0.79
0.83
0.82
df
28,147
25,175
3,175
28,147
25,175
3,175
28,147
25,175
3,175
28,147
25,175
3,175
P
< 0.0001
< 0.0001
< 0.0001
< 0.0001
< 0.0001
0.003
< 0.0001
< 0.0001
0.005
< 0.0001
< 0.0001
< 0.0001
Hanley, Cassey & Doucet
Fig. A1
Appendix 2
Hanley, Cassey & Doucet
Fig. A2
Appendix 2
Hanley, Cassey & Doucet
Fig. A3
Appendix 2