Search

Phylogenetic comparative methods (PCMs) have become a sophisticated suite of techniques for analyzing trait evolution. Powerful PCMs incorporate branch length estimates. Phylogenetic trees with branches scaled to time are called chronograms, and those to substitution are called phylograms. Given identical topologies, chronograms and phylograms may have branch lengths proportional to one another, as expected from the molecular clock hypothesis. However, this hypothesis is often violated. Unlike phylograms, chronograms, coupled with the Brownian motion model, assume that a trait evolves at a constant rate over time and across species. This assumption is unrealistic. Researchers have developed methods to allow variable rates of trait evolution, but why add complexity if phylograms are sufficient at explaining trait variation? We assembled published pairs of chronograms and phylograms with identical topologies (n = 100 jawed vertebrate species) and six phenotypic trait datasets. Phylograms better fit the evolution of the six traits after accounting for model complexity than do chronograms. Also, the variable-rates method we used rescales (modifies) phylogram branch lengths less than chronograms, indicating a better match to trait data. This work will improve comparative studies by refining how researchers employ phylogenies in fields ranging from ecology and biomedicine to linguistics and anthropology.

Genome size has long been hypothesized to affect the metabolic rate in various groups of animals. The mechanism behind this proposed association is the nucleotypic effect, in which large nucleus and cell sizes influence cellular metabolism through surface area-to-volume ratios. Here, we provide a review of the recent literature on the relationship between genome size and metabolic rate. We also conduct an analysis using phylogenetic comparative methods and a large sample of extant vertebrates. We find no evidence that the effect of genome size improves upon models in explaining metabolic rate variation. Not surprisingly, our results show a strong positive relationship between metabolic rate and body mass, as well as a substantial difference in metabolic rate between endothermic and ectothermic vertebrates, controlling for body mass. The presence of endothermy can also explain elevated rate shifts in metabolic rate whereas genome size cannot. We further find no evidence for a punctuated model of evolution for metabolic rate. Our results do not rule out the possibility that genome size affects cellular physiology in some tissues, but they are consistent with previous research suggesting little support for a direct functional connection between genome size and basal metabolic rate in extant vertebrates.This article is part of the theme issue ‘Vertebrate palaeophysiology’.

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments1. Among amniotes, genome sequences are available for mammals2 and birds3–5, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes3. Also, A. carolinensis mobile elements are very young and diverse – more so than in any other sequenced amniote genome. This lizard genome’s GC content is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds6. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

Protein sequences from bone-derived collagen as old as 68 million years have been detected by using mass spectrometry (1, 2). A BLAST search of the resulting peptide sequences found the highest similarities between the collagen peptides obtained from extracts of Tyrannosaurus rex fossil bone and those ofbirds (Gallus gallus) and between mastodon (Mammut americanum) and other mam­ mals, including elephant (Loxodonta africana). We performed phylogenetic analyses to infer the evolutionary relationships of the T. rex [Museum of the Rockies (MOR) 1125] and mastodon (MOR 605). The results extend our knowledge of trait evo­ lution within nonavian dinosaurs into the macro­ molecular level of biological organization. We used 21 extant organisms in the analyses. Collagen a 1(I) and a2(I) protein sequences from 19 extant organisms (3) were obtained from the National Center for Biotechnology Information (NCBI) and ENSEMBL databases. Collagen a1(I) and a2(I) peptide sequences from a metacarpal of Alligator mississippiensis were obtained by mi­ crocapillary liquid chromatography tandem mass spectrometry (LC/MS/MS) with an ion trap mass spectrometer using the Sequest algorithm (1, 2) and the Paragon algorithm (4). Ostrich collagen se­ quences were determined elsewhere (1, 2). Sequences from alligator (Crocodilia) and ostrich (Aves) rep­ resent 63% and 43% of the full-length collagen a1(I) protein available for other organisms, respec­ tively. The collagen a1(I) and a2(I) sequences for elephant (L. africana), tenrec (Echinops telfairi), and green anole (Anolis carolinensis) were ob­ tained by using gene translations from online databases (5). P ' Bayesian, likelihood, parsimony, and dis­ tance methods were used to generate evolu­ tionary trees (6). In the Bayesian analysis, the posterior distribution of trees reconstructed all extant groups in generally agreed-upon rela­ tionships (the posterior probability of clades ranged from 0.80 to 1.00), with the exception of green anole (A. carolinensis), which is in­ ferred here to lie at the base of amniotes in­ stead ofgrouping as the sister taxon to alligator and birds (archosaurs) (Fig. 1). LC/MS/MS from tryptic digests produces fragmentary pro­ tein sequence data; however, we found unequivocal support (posterior probability of 1.00) uniting mastodon with elephant as members of Elephantinae, which together group with tenrec (E. telfairi) as members of the mam­ malian group Afrotheria (7). Maximum likeli­ hood produces the same groupings, although with less support (approximate likelihood ratio test; aLRT = 0.855 for Elephantinae and 0.872 for Afrotheria). Maximum parsimony analysis also groups mastodon, elephant, and tenrec together (fig. S1, B to D). For the T. rex sample, we used five peptide sequences from collagen a1(I) and one from collagen a2(I) (1, 2, 8) for a total of 89 amino acids (Fig. 1). The T. rex clusters within the Archosauria (posterior probability of 0.92), more closely related to birds (chicken and ostrich, 0.9) than alligator, although a lack of informative sites in the ostrich and T. rex leaves Dinosauria unresolved. The likelihood tree is identical to the Bayesian tree, except for higher support at these locations in the tree (aLRT = 0.969 for Archosauria and 0.907 for Dinosauria). Branch lengths (expected rates of change per site) indicate a relatively stable and uniform rate of evolution, lacking evidence for a deviation from a molecular clock. Maximum par­ simony analysis also groups the T. rex with the chicken and ostrich, although bootstrap support is low (fig. S1, B to D). Neighbor joining groups the T. rex with the birds, but miscalculates the branching order and misplaces alligator, mastodon, and several extant organisms (fig. S1, B to D). The slight disagreement between the distance results compared with the Bayesian, likelihood, and parsimony results (all three of which are concordant) are predictable given that distance methods perform poorly for taxa with large amounts of missing data (9). Nevertheless, there is congruence between three out of the four methods for the mastodon and four out of four methods for the T. rex despite the problem of missing sequence data. The recovered sequences contain informative phylogenetic signal consistent with predictions based on genetic and morphological data for mastodon (10, 11) and on morphological data for T. rex (12, 13) These results support the endogenous origin of the preserved collagen molecules and confirm the prediction based on morphology that, ifbiomolecules could be retrieved from a nonavian dinosaur, they would share a higher degree of similarity with birds than with other extant vertebrates. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas of the vertebrate evolutionary tree that have, so far, been intractable. The findings presented here also bolster the use ofmorphology in phylogenetics because our results are consistent with studies on the evolutionary relationships of fossil forms that rely on morphology (12, 13)., Published as part of Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley & John M. Asara, 2008, Molecular phylogenetics of Mastodon and Tyrannosaurus rex, pp. 499 in Science 320 on page 499, DOI: 10.1126/science.1154284, http://zenodo.org/record/3942979, {"references":["1. J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, L. C. Cantley, Science 316, 280 (2007).","2. J. M. Asara et al., Science 317, 1324 (2007).","4. I. V. Shilov et al., Mol. Cell. Proteomics 6, 1638 (2007).","7. M. S. Springer, W. J. Murphy, E. Eizirik, S. J. O'Brien, Proc. Natl. Acad. Sci. U. S. A. 100, 1056 (2003).","8. J. M. Asara, M. H. Schweitzer, Science 319, 33 (2008).","9. J. J. Wiens, Syst. Biol. 52, 528 (2003).","12. M. J. Benton, in The Dinosauria, D. B. Weishampel, P. Dodson, H. Osmolska, Eds. (Univ. of California Press, Berkeley, 2004), pp. 7 - 19.","13. T. R. Holtz, H. Osmolska, in The Dinosauria, D. B. Weishampel, P. Dodson, H. Osmolska, Eds. (Univ. of California Press, Berkeley, 2004), pp. 21 - 24."]}