Chris L. Organ and Andrew M. Shedlock
Supplementary Figure 1: Pterodactylus (wing phalanx)
Supplementary Table 1: Summary of Bone Histology and Genome Size Data. Descriptive statistics of primary histological measurements. Gray text indicates data taken from Organ et al. 2007. The data from the extinct species were used to infer genome size using the Bayesian comparative method detailed below. Data from the genus Xenopus were included from Reumer and Thiebaud (1987), in which measurements of osteocyte lacunae were performed on the thin central area of the ossified suprascapular.
 is the standard deviation and C-Val is the haploid genome size in picograms.
Taxon Bone Element n
Lacunae
Avg Vol
(
 m3)
 C-Val
(pg)
Extant Taxa
Bison bison
Sorex araneus
Femur
Mandible
30
34
303.64
161.27
101.12
45.6
4.9
2.91
Loxodonta africana
Falco sparverius
Tyto alba
Corvus brachyrhynchos
Femur
Vomeronasal
Vomeronasal
Vomeronasal
29
20
208.68
58.52
87.84
25.95
4.28
1.43
27 128.39 41.57 1.63
28 37.99 12.78 1.25
Phalacrocorax auritus
Erinaceus europaeus
Regulus calendula
Xenopus laevis
Xenopus ruwenzoriensis
Xenopus vestitus
Vomeronasal
Tibia
Vomeronasal
Suprascapular
Suprascapular
Suprascapular
28
26 106.81 54.23 3.66
26
50
50
25
52 16.08 1.43
35.08
636
1143
14.08
180
1979 1535
757
1.33
3.3
7.9
6.1
Alligator mississippiensis
Ateles paniscus
Bos taurus
Femur
Turbinates
Tibia
33 197.98 25.56 2.49
20 290.3 50.55 3.47
37 207.04 20.45 3.59

Taxon Bone Element
Canis familiaris
Canis latrans
Capra hircus
Chrysemys picta
Corvus corax
Crocodylus niloticus
Dendroica dominica
Didelphis virginiana
Dromaius novaehollandiae
Eptesicus fuscus
Gekko sp.
Homo sapiens
Iguana iguana
Meleagris gallopavo
Turbinates
Femur
Tibia
Humerus
Turbinates
Humerus
Turbinates
Femur
Tibia
Turbinates
Skull
Femur
Skull
Femur
Ornithorhynchus anatinus
Oryctolagus cuniculus
Phylloderma stenops
Pteropus giganteus
Rana pipiens
Rattus norvegicus
Struthio camelus
Ursus arctos
Tibia
Femur
Turbinates
Turbinates
Ilium
Turbinates
Tibia
Femur
Varanus sp. Femur
Basal Archosauromorphs (extinct)
Champsosaurid indet. Femur, humerus
Desmatosuchus haploceros Scute
Basal alligatorid
(Leidyosuchus sp.)
Phytosaurid indet.
Scute
Scute
Postosuchus kirkpatricki
Rutiodon sp.
Typothorax meadei
Pterosaurs (extinct)
Humerus
Femur
Femur
Dimorphodon macronyx Tibia, wing phalanx
Rhamphorhynchus muensteri Radius
Pteranodon sp.
Pterodactylus sp.
Wing phalanx
Femur, wing phalanx n
Lacunae
Avg Vol
(
 m3)
 C-Val
(pg)
20 142.97 26.64 3.12
40 149.18 19.51 2.82
40 160.86 15.9 3.24
40 166.97 24.93 2.8
20 95.12 9.58 1.21
37 245.81 31.86 3.21
20 53.27
40 110.35
5.46 1.4
9.49 4.12
40 95.22 12.76 1.63
20 115.38 17.96 2.37
38 337.2 53.93 2.56
20 274.04 39.05 3.5
27
40
270.8
58.82
47.49
6.36
2.89
1.54
35 160.04 15.85 3.06
40 196.76 20.6 3.18
20 145.26 27.02 2.48
18 155.28 25.31 2.22
40 444.36 56.93 6.76
20 240.68 36.84 3.36
40
40
83.83
173.4
9.72
19.5
2.16
2.75
40 138.3 14.66 2.05
22
32
16
34
32
22
38
583.7 248.1 ?
340.4 130.91 ?
375.6 167.11 ?
16 429.04 196.91 ?
28 86.97 28.38 ?
27 100.29 27.67 ?
22 330.28 125.74 ?
81.19 32.64 ?
76.21 21.96 ?
84.95 24.25 ?
99.28 27.01 ?
For the cell size-genome size analysis tree topology and divergence times were maintained from
Organ et al. (2007), with divergence times for the additional extant taxa obtained using http://www.timetree.net
(Hedges et al. 2006) and data from the literature (Rest et al. 2003; Evans et al.
2004; Springer et al. 2004; Benton and Donoghue 2007). Topology and divergence times were estimated for the additional genera using a mixture of fossil and molecular divergence dates as follows:

Rana and Xenopus (Evans et al. 2004; Marjanović and Laurin 2007); Phalacrocorax, Falco, Tyto, Corvus, and Regulus (Ericson et al. 2006); Erinaceus, Sorex, Loxodonta, Bison (Springer et al. 2003; Delsuc et al.
2004; Hassanin and Ropiquet 2004). Phylogenetic information for extinct species were also collected for Pterosauria (Kellner 2003; Unwin 2003), Archosauria (Benton 2004), Archosauromorpha (Gao and
Fox 1998; Modesto and Sues 2004). Portions of the avian tree are still unresolved (Brown et al. 2007).
For the body size, ancestral state reconstruction, and proportional evolution analysis divergence times and topologies were derived from the literature for: Amphibia (Evans et al. 2004; Benton and Donoghue
2007), Mammalia (Springer et al. 2004), Reptilia (Rest et al. 2003), Squamata (Rest et al. 2003; Vidal and
Hedges 2005; Wiens et al. 2006; Kumazawa 2007), Serpentes (Lawson et al. 2005; Lee et al. 2007; Vidal
et al. 2007), Testudines (Fujita et al. 2004; Near et al. 2005; Fritz and Bininda-Emonds 2007) and Aves
(Ericson et al. 2006; Brown et al. 2007).
Uncertain divergence times were estimated as half the span from the last common ancestor to the first descendant node. A polytomy within Aves was resolved to zero-length branches. Due to the constrained values of genome size within Aves, this polytomy is unlikely to adversely affect our results or conclusions. Phylogenetic trees were created in Mesquite v2.01 (Maddison and Maddison 2007) using the StratAdd (Faure et al. 2006) package to date nodes according to the geologic timescale
(Gradstein et al. 2004).
Hypothesis Testing. Statistical hypotheses are tested using Bayes factors. For two nested models this is twice the difference between the harmonic means from the last iteration of the Markov chains (Raftery 1996). A Bayes Factor greater than 3 is taken as positive evidence, greater than 5 as strong evidence, and over 10 are taken as very strong evidence (Raftery 1996).
Some tests for correlation are reported as p-values, which are determined by calculating the fraction of the posterior distribution that crosses zero. For likelihood ratio tests, significance was calculated for 2 x the likelihood ratio assuming a chi squared distribution and degrees of freedom equal to the difference in parameters of the models.
Regression Model and Inference. Genome size and cell size measurements were logarithmically transformed to normalize for the wide range in data values. The 12 extant taxa discussed above were added to a previous dataset (Organ et al. 2007) and the program BayesTraits
( http://www.evolution.rdg.ac.uk/BayesTraits.html
) was used to explore correlations (Pagel 1997; Pagel
1999) among character states using a Bayesian framework and tree #1 (see below; extinct taxa pruned).
BayesTraits uses a phylogenetic generalized least squares approach that corrects for the nonindependence of the species caused by shared evolutionary history. The derivation of this procedure can be found in (Organ et al. 2007).
Branch length scaling parameters were estimated simultaneously during the regression of genome size on osteocyte size in living tetrapods to better fit the data to the model. The MCMC had
5010000 iterations with a burn-in of 1000 and a rate deviation of 2. Uninformative priors were used for the alpha and beta parameters. With a Bayes factor of 20.5, there is very strong evidence for the correlation between genome size on osteocyte size. The results were explored in JMP 6.03
(SAS_Institute 2006) and are summarized in Supplementary Table 2.
Table 2: Summary of Posterior Regression Models of Genome Size on Osteocyte Size.
Alpha Beta r 2 Kappa Delta Lambda Acceptance n mean stdev
95% CI
50091
-0.81
0.42
0.0036
50091
0.35
0.07
0.0007
50091
0.43
0.06
0.0005
50091
1.95
0.92
0.0081
50091
1.19
0.68
0.006
50091
0.62
0.19
0.0016
50091
0.21
0.04
0.0004

We then used BayesTraits to generate phylogenetically informed posterior distributions of genome size inferences that take into account uncertainty in the regression model parameters and aspects of the phylogenetic tree. These estimations included cell size data (Supplementary Table 1) and phylogenetic information (from tree #1, see below). BayesTraits settings and scaling parameters were the same as the regression analysis discussed above. The results are listed in Supplementary Table 4 below.
Tree #3 below was used in these test with the following scaling parameters

= 0.00,

= 0.50, and

= 1.00 (Pagel 1999).
Table 3: Genome Size Inferences for Pterosaurs and Basal Archosauromorphs. Descriptive statistics from the posterior distributions of haploid genome size for seven extinct species of basal archosauromorphs and four pterosaurs.
Taxon
Champsosaurid indet.
C-Val mean
4.07
C-Val stdev
1.28
Rutiodon sp.
Desmatosuchus haploceros
Typothorax meadei
Postosuchus kirkpatricki
2.12
3.22
3.19
2
0.21
0.33
0.32
0.2
Leidyosuchus sp.
Dimorphodon macronyx
Rhamphorhynchus muensteri
Pterodactylus sp.
3.43
1.94
1.93
2.12
0.66
0.23
0.25
0.25
Pteranodon sp. 2.01 0.35
Phylogenetic t-Test using Multiple Regression: Dummy variables were used to divide species into groups. For example, we divided the taxa into groups A, B, and C, and it is A and B that we are interested in. Two dummy variables were then coded, the first assigns 1's to A's and 0's to B’s and C’s.
The second dummy variable assigns 1's to C’s and 0's to A’s and B’s. B's are assigned 0's for both dummy variables. A continuous multiple regression model was then generated using MCMC in
BayesTraits in which the two dummy variables (independent variables) predict a third dependent variable, say, genome size. Significance of

(the proportion of the posterior distribution that crosses
0) indicates that A and B differ when the data are normalized for phylogeny. Tree #3 below was used in these tests with the following scaling parameters

= 0.00,

= 0.50, and

= 1.00 (Pagel 1999).
Node Values: Ancestral genome size was estimated by inserting 0-branch length dummy nodes and using the random walk (Model A) analysis in BayesTraits. We used the MCMC mode to generate posterior distributions of the trait values (genome size). Node values are presented in Figure 2 of the main text.
Proportional Rates of Evolution. The PDAP package (Midford et al. 2005) for Mesquite was used to estimated node values and the amount of change in immediate descendants (standardized contrasts) in 130 tetrapods, including the inferred genome size for the basal archosaurs, pterosaurs, and non-avian dinosaurs. An ordinary least square model was then fit to the natural log transformed node values and standardized contrasts.

The following data were used to detect the influence of population dynamics and neutral evolutionary patterns were conducted by evaluating (as discussed above for differences in character states) the evidence for differences in body size as a proxy for population size (Lynch 2006; Lynch 2007b; Lynch
2007a) vs. genome size change as discussed in the primary text. Tree #2 below was used in analyzing body mass and genome size with the following scaling parameters

= 0.42,

= 0.28, and

= 1.00
(Pagel 1999).
Table 4: Body Size and Genome Size Data for Tetrapods. Body size data were obtained from the references listed in the table and references contained therein. Genome sizes were downloaded from www.genomesize.com
.
Taxa References Body
Size
(ln g)
Genome
Size
(ln pg)
Agama agama, Agama atra, Agama
impalearis (GS), Agama impalearis (BS)
Alligator mississippiensis
4
10.93
0.48 (Nagy et al. 1999)
0.91 (Lewis and Gatten 1985)
Ambystoma maculatum 1.45 3.5 (Vinogradov and Anatskaya 2006)
3.09
2.35
0.97 (Alonso et al. 2004)
0.74 (Alonso et al. 2004)
Anguis fragilis
Anolis aeneus, Anolis auratus, Anolis carolinensis, Anolis cf. nitens, Anolis
equestris, Anolis sagraei (GS), Anolis
auratus (BS)
Anoura caudifera, Anoura geoffroyi
Apalone spinifera (=Trionyx spiniferus; GS)
Trionyx ferox (BS)
Ardea herodias
Artibeus glaucus, Artibeus jamaicensis,
Artibeus lituratus (GS), Artibeus jamaicensis
(BS)
Bison bison
Boa constrictor
Bombina bombina
Bos taurus
Bradypus variegatus
Bufo bufo
Canis familiaris
Canis latrans
Canis lupus
Chalcides chalcides
Chamaeleo ceylanicus, Chamaeleo dilepis,
Chamaeleo hoehnelli, Chamaeleo jacksoni
(GS), Chamaeleo lateralis (BS)
Chelonia mydas
Chelydra serpentina
Coluber constrictor, Coluber najadum,
Coluber nummifer, Coluber ravergieri,
Coluber schmidti, Coluber viridiflavus (GS),
2.44
8.09
7.53
3.81
13.71
8.4
1.39
13.68
8.24
3.93
10.2
9.21
10.53
1.86
2.39
11.65
8.15
4.88
0.99 (Nagy et al. 1999)
0.99 (Vinogradov and Anatskaya 2006)
0.38 (Bennett and Harvey 1987)
0.97 (White and Seymour 2003)
1.59 (Garland 1983)
0.84 (Alonso et al. 2004)
2.44 (Vinogradov and Anatskaya 2006)
1.28 (Owen-Smith 1992)
1.44 (White and Seymour 2003)
1.9 (Vinogradov and Anatskaya 2006)
1.14 (Vinogradov 1995)
1.04 (White and Seymour 2003)
1.03 (Nagy et al. 1999)
0.46 (Alonso et al. 2004)
0.9 (Alonso et al. 2004)
0.97 (Alonso et al. 2004)
0.97 (Guppy and Withers 1999)
0.65 (Nagy et al. 1999)

Taxa
Coluber constrictor (BS)
Corvus brachyrhynchos
Crocodylus niloticus, Crocodylus siamensis
(GS), Crocodylus acutus (BS)
Dasypus hybridus, Dasypus kappleri,
Dasypus novemcinctus, Dasypus pilosus,
Dasypus sabanicola, Dasypus
septemcinctus (BS), Dasypus novemcinctus
(BS)
Delphinapterus leucas
Dendroica dominica
Desmodus rotundus
Desmognathus fuscus
Didelphis virginiana
Dromaius novaehollandiae
Eptesicus furinalis
Equus caballus
Erinaceus europaeus
Eumops perotis
Falco peregrinus
Felis catus
Felis lynx
Gallus gallus
Gekko gecko
Gopherus agassizii
Gorilla gorilla
Hemidactylus leightoni (GS), Hemidactylus
mabouia (BS)
Homo sapiens
Hyla savignyi
Iguana iguana
Kinixys belliana
Kinosternon subrubrum (GS), Kinosternon
avescens (BS)
Lacerta viridis
Larus atricilla
Loxodonta africana
Macropus rufus
Myotis myotis (GS), Myotis lucifugus (BS)
Natrix natrix
Ornithorhynchus anatinus
Oryctolagus cuniculus
Panthera tigris
Body
Size
(ln g)
Genome
Size
(ln pg)
References
5.95
11.81
9.01
0.22 (Bennett and Harvey 1987)
1.17 (Alonso et al. 2004)
1.63 (White and Seymour 2003)
14.22
2.28
3.38
0.69
7.82
10.57
2.34
12.9
6.62
4.03
4.76
8.01
10.52
7.9
4
7.66
12.21
0.92
11.16
3.56
6.76
6.54
5.19
3.38
5.62
15.61
10.39
1.65
4.31
6.54
7.6
11.83
1.19 (O'Corry-Crowe 2002)
0.34 (Bennett and Harvey 1987)
0.98 (White and Seymour 2003)
2.79 (Vinogradov and Anatskaya 2006)
1.42 (White and Seymour 2003)
0.43 (Bennett and Harvey 1987)
0.85 (White and Seymour 2003)
1.17 (White and Seymour 2003)
1.3 (White and Seymour 2003)
0.94 (White and Seymour 2003)
0.36 (Bennett and Harvey 1987)
1.13 (Vinogradov 1995)
1.12 (White and Seymour 2003)
0.22 (Bennett and Harvey 1987)
0.94 (Alonso et al. 2004)
1.07 (Nagy et al. 1999)
1.35 (Vinogradov and Anatskaya 2006)
0.74 (Alonso et al. 2004)
1.25 (Vinogradov 1995)
1.28 (Vinogradov and Anatskaya 2006)
1.06 (Nagy et al. 1999)
1.09 (Guppy and Withers 1999)
1 (Guppy and Withers 1999)
0.68 (Bennett and Dawson 1976)
0.37 (Bennett and Harvey 1987)
1.45 (Garland 1983)
1.14 (White and Seymour 2003)
0.76 (Nagy et al. 1999)
1.06 (Alonso et al. 2004)
1.12 (White and Seymour 2003)
1.16 (White and Seymour 2003)
1 (White and Seymour 2003)

Taxa
Pelobates fuscus
Phalacrocorax auritus
Plethodon cinereus
Podarcis sicula (GS), Podarcis lilfordi (BS)
Procavia capensis
Python reticulatus
Rana pipiens
Rattus norvegicus
Regulus calendula
Sauromalus obesus
Sceloporus magister, Sceloporus
occidentalis(GS), Sceloporus graciosus (BS)
Setifer setosus
Sorex araneus
Spheniscus demersus
Struthio camelus
Sus scrofa
Tachyglossus aculeatus
Tarsius syrichta
Tonatia bidens, Tonatia evotis (GS), Tonatia
bidens (BS)
Trachemys scripta
Triturus cristatus
Trogonophis wiegmanni
Tursiops truncatus
Tyto alba
Ursus arctos (GS), Ursus horribilis (BS)
Varanus komodoensis
Varanus salvator
Vipera aspis
Xenopus laevis
6.55
1.39
1.87
13.38
6.21
12.61
10.72
7.85
4.23
4.01
6.27
2.09
8.06
11.39
11.23
7.91
4.73
3.21
Body
Size
(ln g)
2.77
7.19
1.36
2
7.78
8.72
3.56
5.47
1.7
5.12
1.6
Genome
Size
(ln pg)
References
1.53 (Vinogradov and Anatskaya 2006)
0.36 (Bennett and Harvey 1987)
3.36 (Gatten et al. 1992)
0.7 (Nagy et al. 1999)
1.4 (White and Seymour 2003)
0.47 (Vinogradov and Anatskaya 2006)
1.91 (Gatten et al. 1992)
1.21 (Vinogradov 1995)
0.29 (Bennett and Harvey 1987)
0.98 (Nagy et al. 1999)
0.94 (Nagy et al. 1999)
1.62 (White and Seymour 2003)
1.07 (White and Seymour 2003)
0.49 (Nagy et al. 1999)
0.77 (Nagy et al. 1999)
1.15 (Vinogradov 1995)
1.06 (Nagy et al. 1999)
1.66 (White and Seymour 2003)
0.85 (White and Seymour 2003)
0.87 (Montes et al. 2007)
3.12 (Vinogradov and Anatskaya 2006)
0.5 (Alonso et al. 2004)
1.15 (Reidenberg and Laitman 2002)
0.49 (Vinogradov and Anatskaya 2006)
1.01 (Garland 1983)
0.66 (Nagy et al. 1999)
0.72 (Nagy et al. 1999)
1.07 (Alonso et al. 2004)
1.19 (Gatten et al. 1992)

Alonso, P. D., Milner, A. C., Ketcham, R. A., Cookson, M. J. & Rowe, T. B. 2004 The avian nature of the brain and inner ear of Archaeopteryx. Nature 430, 666-669.
Bennett, A. F. & Dawson, W. R. 1976 Metabolism. Biology of the Reptilia. 5, C. Gans and W. R. Dawson,
Eds. New York, Academic Press.
Bennett, P. M. & Harvey, P. H. 1987 Active and resting metabolic rate in birds: allometry, phylogeny, and ecology. J. Zool. 213, 327–363.
Benton, M. & Donoghue, P. 2007 Paleontological evidence to date the tree of life. Molecular Biology
and Evolution 24, 26-53.
Benton, M. J. 2004 Origin and Relationships of Dinosauria. The Dinosauria. D. B. Weishampel, P. Dodson and H. Osmólska. Berkeley, University of California Press, 7-19.
Brown, J. W., Payne, R. B. & Mindell, D. P. 2007 Nuclear DNA does not reconcile 'rocks' and 'clocks' in
Neoaves: A Comment on Ericson et al. Biology Letters 3, 257-259.
Delsuc, F., Vizcaíno, S. F. & Douzery, E. J. 2004 Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans. BMC Evolutionary Biology 4, 11.
Ericson, P. G., Anderson, C. L., Britton, T., Elzanowski, A., Johansson, U. S., Kallersjo, M., Ohlson, J. I.,
Parsons, T. J., Zuccon, D. & Mayr, G. 2006 Diversification of Neoaves: integration of molecular sequence data and fossils. Biol Lett 2, 543-547.
Evans, B. J., Kelley, D. B., Tinsley, R. C., Melnick, D. J. & Cannatellae, D. C. 2004 A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution.
Molecular Phylogenetics and Evolution 33, 197–213.
Faure, E., Lony, E., Lovigny, R., Menegoz, A., Ting, Y. & Laurin, M. (2006). StratAdd module for
Mesquite.
Fritz, U. & Bininda-Emonds, O. R. P. 2007 When genes meet nomenclature: Tortoise phylogeny and the shifting generic concepts of Testudo and Geochelone. Zoology 110, 298-307.
Fujita, M. K., Engstrom, T. N., Starkey, D. E. & Shaffer, H. B. 2004 Turtle phylogeny: insights from a novel nuclear intron. Molecular Phylogenetics and Evolution 31, 1031–1040.
Gao, K. & Fox, R. C. 1998 New choristoderes (Reptilia: Diapsida) from the Upper Cretaceous and
Palaeocene, Alberta and Saskatchewan, Canada, and phylogenetic relationships of
Choristodera. Zool. J. Linnean Soc. 124, 303-353.
Garland, T. J. 1983 The relation between maximal running speed and body mass in terrestrial mammals.
J. Zool. 199, 157-170.
Gatten, R. E., Jr., Miller, K. & Full, R. J. 1992 Energetics at rest and during locomotion. Environmental
Physiology of the Amphibians. M. E. Feder and W. W. Burggren. Chicago, University of Chicago
Press, 314–377.
Gradstein, F. M., Ogg, J. G., Smith, A. G., Agterberg, F. P., Bleeker, W., Cooper, R. A., Davydov, V.,
Gibbard, P., Hinnov, L. A., House, M. R., Lourens, L., Luterbacher, H. P., McArthur, J., Melchin,
M. J., L. J. Robb, L. J., Shergold, J., Villeneuve, M., Wardlaw, B. R., Ali, J., Brinkhuis, H., Hilgen, F.
J., Hooker, J., Howarth, R. J., Knoll, A. H., Laskar, J., Monechi, S., Plumb, K. A., Powell, J., Raffi, I.,
Röhl, U., Sadler, P., Sanfilippo, A., Schmitz, B., Shackleton, N. J., Shields, G. A., Strauss, H., Van
Dam, J., van Kolfschoten, T., Veizer, J. & Wilson, D. M. 2004 A Geologic Time Scale 2004, Eds.
Cambridge, Cambridge University Press, 589.
Guppy, M. & Withers, P. 1999 Metabolic depression in animals: physiological perspectives and biochemical generalizations. Biol. Rev. Camb. Philos. Soc. 74, 1-40.
Hassanin, A. & Ropiquet, A. 2004 Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937. Molecular Phylogenetics and
Evolution 33, 896-907.
Hedges, S. B., Dudley, J. & Kumar, S. (2006). TimeTree: A public knowledge-base. ( www.timetree.net) ,
Pennsylvania and Arizona State Universities, USA.

Kellner, A. W. A. 2003 Pterosaur phylogeny and comments on the evolutionary history of the group.
Evolution and Palaeobiology of Pterosaurs. E. Buffetaut and J.-M. Mazin. London, Geological
Society of London, Special Publications 217, 105-138.
Kumazawa, Y. 2007 Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations. Gene 388, 19-26.
Lawson, R., Slowinski, J. B., Crother, B. I. & Burbrink, F. T. 2005 Phylogeny of the Colubroidea
(Serpentes): New evidence from mitochondrial and nuclear genes. Molecular Phylogenetics and
Evolution 37, 581–601.
Lee, M. S. Y., Hugall, A. F., Lawson, R. & Scanlon, J. D. 2007 Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood, Bayesian and parsimony analyses. Systematics
and Biodiversity 5, 371–389.
Lewis, L. Y. & Gatten, R. E. J. 1985 Aerobic metabolism of American alligators, Alligator mississippiensis, under standard conditions and during voluntary activity. Comp. Biochem. Physiol. 80A, 441–
447.
Lynch, M. 2006 The origins of eukaryotic gene structure. Molecular Biology and Evolution 23, 450-468
Lynch, M. 2007a Colloquium Papers: The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl. Acad. Sci. U. S. A. 104, 8597-8604.
Lynch, M. 2007b The Origins of Genome Architecture, Eds. Sunderland, Sinauer Associates, 389.
Maddison, W. P. & Maddison, D. R. 2007 Mesquite: a modular system for evolutionary analysis.
Version 2.01 http://mesquiteproject.org
.
Marjanović, D. & Laurin, M. 2007 Fossils, molecules, divergence times, and the origin of lissamphibians.
Systematic Biology 56, 369 - 388.
Midford, P. E., Garland, T. J. & Maddison, W. P. 2005 PDAP Package of Mesquite. Version 1.07.
Modesto, S. P. & Sues, H.-D. 2004 The skull of the Early Triassic archosauromorph reptile Prolacerta
broomi and its phylogenetic significance. Zool. J. Linnean Soc. 140, 335–351.
Montes, L., Le Roy, N., Perret, M., De Buffrenil, V., Castanet, J. & Cubo, J. 2007 Relationships between bone growth rate, body mass and resting metabolic rate in growing amniotes: a phylogenetic approach. Biological Journal of the Linnean Society 92, 63-76.
Nagy, K. A., Girard, I. A. & Brown, T. K. 1999 Energetics of free-ranging mammals, reptiles, and birds.
Annu. Rev. Nutr. 19, 247–277.
Near, T., Meylan, P. & Shaffer, H. B. 2005 Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. The American Naturalist 165, 137-146.
O'Corry-Crowe, G. M. 2002 Beluga whale (Delphinapterus leucas). Encyclopedia of Marine Mammals. W.
F. Perrin, B. Würsig and J. G. M. Thewissen. San Diego, CA, Academic Press, 94–99.
Organ, C. L., Shedlock, A. M., Meade, A., Pagel, M. & Edwards, S. V. 2007 Origin of avian genome size and structure in nonavian dinosaurs. Nature 446, 180-184.
Owen-Smith, R. N. 1992 Megaherbivores: The Influence of Very Large Body Size on Ecology, Eds. New
York, Cambridge University Press.
Pagel, M. D. 1997 Inferring evolutionary processes from phylogenies. Zool. Scripta 26, 331-348.
Pagel, M. D. 1999 Inferring the historical patterns of biological evolution. Nature 401, 877-884.
Raftery, A. E. 1996 Hypothesis testing and model selection. Markov Chain Monte Carlo in Practice. W. R.
Gilks, S. Richardson and D. J. Spiegelhalter. London, Chapman and Hall, 163-188.
Reidenberg, J. S. & Laitman, J. T. 2002 Prenatal development in cetaceans. Encyclopedia of Marine
Mammals. W. F. Perrin, B. Würsig and J. G. M. Thewissen. San Diego, CA, Academic Press, 998-
1007.
Rest, J. S., Ast, J. C., Austin, C. C., Waddell, P. J., Tibbetts, E. A., Hay, J. M. & Mindella, D. P. 2003
Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.
Molecular Phylogenetics and Evolution 29, 289–297.
Reumer, J. W. F. & Thiebaud , C. H. 1987 Osteocyte lacunae size in the genus Xenopus (Pipidae).
Amphibia-Reptilia 8, 315-320.
SAS_Institute (2006). JMP, Version 6.03. Cary, NC, SAS Institute Inc.

Springer, M. S., Murphy, W. J., Eizirik, E. & O'Brien, S. J. 2003 Placental mammal diversification and the
Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. U. S. A. 100, 1056-61.
Springer, M. S., Stanhope, M. J., Madsen, O. & de Jong, W. W. 2004 Molecules consolidate the placental mammal tree. Trends in Ecology & Evolution 19, 430-438.
Unwin, D. M. 2003 On the phylogeny and evolutionary history of pterosaurs. Evolution and
Palaeobiology of Pterosaurs. E. Buffetaut and J.-M. Mazin. London, Geological Society of
London, Special Publications 217, 139-190.
Vidal, N., Delmas, A.-S., David, P., Cruaud, C., Couloux, A. & Hedges, S. B. 2007 The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes.
Comptes Rendus Biologies 330, 182–187.
Vidal, N. & Hedges, S. B. 2005 The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. Comptes Rendus Biologies
328, 1000-1008.
Vinogradov, A. E. 1995 Nucleotypic effect in homeotherms: body-mass-corrected basal metabolic rate of mammals is related to genome size. Evolution 49, 1249-1259
Vinogradov, A. E. & Anatskaya, O. V. 2006 Genome size and metabolic intensity in tetrapods: a tale of two lines. Proc. R. Soc. B 273, 27-32.
White, C. R. & Seymour, R. S. 2003 Mammalian basal metabolic rate is proportional to body mass 2/3 .
Proc. Natl. Acad. Sci. U. S. A. 100, 4046–4049.
Wiens, J. J., Brandley, M. C. & Reeder, T. W. 2006 Why does a trait evolve multiple times within a clade? Repeated evolution of snake-like body form in squamate reptiles. Evolution 60, 123–141.