The Role of Subjectivity in Reconstructing Ancestral Character States: A Bayesian Approach to Unknown Rates, States, and Transformation Asymmetries

Schultz, Ted R.; Churchill, Gary A.

doi:10.1080/106351599260229

Cited by 122 publications

(79 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…3 in Garland et al, 1999). In the present study, it is hoped that the inclusion of several outgroup taxa has countered this possibility with respect to inferring ancestral values at the base of the Phrynosomatidae (see also Garland et al, 1997;Schultz and Churchill, 1999;Polly, 2001). …”

Section: Discussionmentioning

confidence: 80%

Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states

Bonine

Gleeson

Garland

2005

Journal of Experimental Biology

View full text Add to dashboard Cite

Previously, we found that phrynosomatid lizards, a diverse group common in the southwestern USA, vary markedly in fiber-type composition of the iliofibularis (a hindlimb muscle important in locomotion). Phrynosomatidae comprises three subclades: the closely related sand and horned lizards, and their relatives the Sceloporus group. The variation in muscle fiber-type composition for 11 phrynosomatid species is attributable mainly to differences between the sand-and horned-lizard subclades. Here, we expand the phrynosomatid database with three additional species and compare these results with data collected for 10 outgroup (distantly related) species. Our goal was to determine if the patterns found in Phrynosomatidae hold across a broader phylogenetic range of the extant lizards and to elucidate the evolution of muscle fiber-type composition and related traits. To allow for meaningful comparisons, data were collected from species that are primarily terrestrial and relatively small in size (3.5-65·g body mass). Results indicate that the fiber-type variation observed within the Phrynosomatidae almost spans the range of variation observed in our sample of 24 species from eight families.However, one species of Acanthodactylus (Lacertidae) had a consistent region of large tonic fibers (that did not stain darkly for either succinic dehydrogenase or myosin ATPase activity), a fiber-type only occasionally seen in the other 23 species examined. Many species have a large proportion of either fast-twitch glycolytic (FG; e.g. sand lizards and Aspidoscelis) or fast-twitch oxidative-glycolytic (FOG) fibers (e.g. horned lizards), with the slow-oxidative proportion occupying only 1-17% of the iliofibularis. Importantly, the negative relationship between FG and FOG composition observed in Phrynosomatidae appears to be a characteristic of lizards in general, and could lead to functional trade-offs in aspects of locomotor performance, as has previously been reported for Lacertidae. Reconstruction of ancestral trait values by use of phylogenetically based statistical methods indicates especially large changes in fiber-type composition during the evolution of horned lizards.

show abstract

Section: Discussionmentioning

confidence: 80%

Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states

Bonine

Gleeson

Garland

2005

Journal of Experimental Biology

View full text Add to dashboard Cite

show abstract

“…We coded spectral tuning as UVS (0) or VS (1) based on measured l max and/or DNA sequence predictions. We estimated character evolution priors [63] using the MCMC method described in SIMMAP (cycles: 100 000; sampling freq: 200; burnin: 10 000; rate upper bound: 1000): (i) photic niche: rate prior parameter a ¼ 26.128, b ¼ 2006.996; (ii) spectral tuning: rate prior parameter a ¼ 8.870, b ¼ 3616.625, bias parameter a ¼ 85.737. We set the bias parameter for photic niche to empirical, and used the default number of categories (k) for the priors (bias ¼ 31; rate ¼ 60).…”

mentioning

confidence: 99%

Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution

et al. 2015

View full text Add to dashboard Cite

Retinal opsin photopigments initiate mammalian vision when stimulated by light. Most mammals possess a short wavelength-sensitive opsin 1 (SWS1) pigment that is primarily sensitive to either ultraviolet or violet light, leading to variation in colour perception across species. Despite knowledge of both ultraviolet-and violet-sensitive SWS1 classes in mammals for 25 years, the adaptive significance of this variation has not been subjected to hypothesis testing, resulting in minimal understanding of the basis for mammalian SWS1 spectral tuning evolution. Here, we gathered data on SWS1 for 403 mammal species, including novel SWS1 sequences for 97 species. Ancestral sequence reconstructions suggest that the most recent common ancestor of Theria possessed an ultraviolet SWS1 pigment, and that violet-sensitive pigments evolved at least 12 times in mammalian history. We also observed that ultraviolet pigments, previously considered to be a rarity, are common in mammals. We then used phylogenetic comparative methods to test the hypotheses that the evolution of violet-sensitive SWS1 is associated with increased light exposure, extended longevity and longer eye length. We discovered that diurnal mammals and species with longer eyes are more likely to have violet-sensitive pigments and less likely to possess UV-sensitive pigments. We hypothesize that (i) as mammals evolved larger body sizes, they evolved longer eyes, which limited transmittance of ultraviolet light to the retina due to an increase in Rayleigh scattering, and (ii) as mammals began to invade diurnal temporal niches, they evolved lenses with low UV transmittance to reduce chromatic aberration and/or photo-oxidative damage.

show abstract

“…19) been widely applied in other contexts. Stochastic models have been used to estimate ancestral states (Schluter, 1995;Schluter et al, 1997;Cunningham, 1999;Mooers and Schluter, 1999;Pagel, 1999b;Schultz and Churchill, 1999) and to establish correlation in characters (Pagel, 1994(Pagel, , 1999a). More recently, Lewis (2001) argued that phylogeny should be estimated using stochastic models of morphological character change.…”

Section: Character Correlationmentioning

confidence: 99%

“…The question of the appropriate rate for the morphological characters was then addressed. We adopted the approach advocated by Schultz and Churchill (1999) in which prior probability distributions are placed on the overall rate of change for the morphological characters and on the bias parameter (zo or rl for the two-state model). Specifically, we placed a gamma prior on the rate of substitution and a beta prior on the bias parameter.…”

Section: Sampling Character Historiesmentioning

confidence: 99%

Stochastic Mapping of Morphological Characters

2003

View full text Add to dashboard Cite

The Role of Subjectivity in Reconstructing Ancestral Character States: A Bayesian Approach to Unknown Rates, States, and Transformation Asymmetries

Cited by 122 publications

References 22 publications

Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states

Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states

Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution

Stochastic Mapping of Morphological Characters

Contact Info

Product

Resources

About