A Primer on Phylogenetic Generalised Least Squares

Symonds, Matthew R. E.; Blomberg, Simon P.

doi:10.1007/978-3-662-43550-2_5

Cited by 351 publications

(363 citation statements)

References 55 publications

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“…Pagel's λ was then estimated from the posterior distribution, along with the 95% credibility intervals. The significance of the deviation of Pagel's λ from 0 and 1 was tested with mean values for all extant taxa using the gls function in the R package nlme, version 3.1-113 (59). Results are presented in SI Appendix, Tables S9 and S10.…”

Section: Methodsmentioning

confidence: 99%

The integration of quantitative genetics, paleontology, and neontology reveals genetic underpinnings of primate dental evolution

Hlusko

Schmitt

Monson

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

107

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Developmental genetics research on mice provides a relatively sound understanding of the genes necessary and sufficient to make mammalian teeth. However, mouse dentitions are highly derived compared with human dentitions, complicating the application of these insights to human biology. We used quantitative genetic analyses of data from living nonhuman primates and extensive osteological and paleontological collections to refine our assessment of dental phenotypes so that they better represent how the underlying genetic mechanisms actually influence anatomical variation. We identify ratios that better characterize the output of two dental genetic patterning mechanisms for primate dentitions. These two newly defined phenotypes are heritable with no measurable pleiotropic effects. When we consider how these two phenotypes vary across neontological and paleontological datasets, we find that the major Middle Miocene taxonomic shift in primate diversity is characterized by a shift in these two genetic outputs. Our results build on the mouse model by combining quantitative genetics and paleontology, and thereby elucidate how genetic mechanisms likely underlie major events in primate evolution.paleontology | quantitative genetics | primates | neontology | dental variation T he relationship between genotype and phenotype is critical to evolutionary biology, because it influences how phenotypes respond to selective pressures and evolve (1, 2). Paleontologists have long sought to incorporate the etiology of the dental phenotype to inform on questions of environmental, dietary, and adaptive change over time (3)(4)(5)(6). This research has been advanced significantly by the revolution in developmental genetics over the past few decades (7). Experimental research on mice has yielded tremendous biological insight (8). However, for human phenotypes, ranging from inflammation (9) to placentation (10), the limitations of the mouse model due to the ∼140 million years ago of evolution that have occurred since our last common ancestor ∼70 Ma (11) are starting to be recognized. Here, we demonstrate how to overcome the limitations of the mouse model's application to the primate dentition by integrating research from quantitative genetics, neontology, and paleontology. The insights gained from this transdisciplinary approach have implications for all of these seemingly disparate subdisciplines of biology.

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Section: Methodsmentioning

confidence: 99%

The integration of quantitative genetics, paleontology, and neontology reveals genetic underpinnings of primate dental evolution

Hlusko

Schmitt

Monson

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

107

View full text Add to dashboard Cite

show abstract

“…The assumption is that species that are closely related will be more similar to one another in the trait of interest, and thus will have more similar residuals from the least squares regression line. Thus, phylogenetic relatedness generates an expected covariance structure for the residuals, which can then be used to modify estimates of the slope and intercept of the regression line, correcting for phylogeny (for a recent review, see Symonds and Blomberg, 2014).…”

Section: Database Of Acuity For Use In Analysesmentioning

confidence: 99%

Visual acuity in ray-finned fishes correlates with eye size and habitat

Caves

Sutton

Johnsen

2017

Journal of Experimental Biology

101

137

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Visual acuity (the ability to resolve spatial detail) is highly variable across fishes. However, little is known about the evolutionary pressures underlying this variation. We reviewed published literature to create an acuity database for 159 species of ray-finned fishes (Actinopterygii). Within a subset of those species for which we had phylogenetic information and anatomically measured acuity data (n=81), we examined relationships between acuity and both morphological (eye size and body size) and ecological (light level, water turbidity, habitat spatial complexity and diet) variables. Acuity was significantly correlated with eye size (P<0.001); a weaker correlation with body size occurred via a correlation between eye and body size (P<0.001). Acuity decreased as light level decreased and turbidity increased; however, these decreases resulted from fishes in dark or murky environments having smaller eyes and bodies than those in bright or clear environments. We also found significantly lower acuity in horizon-dominated habitats than in featureless or complex habitats. Higher acuity in featureless habitats is likely due to species having absolutely larger eyes and bodies in that environment, though eye size relative to body size is not significantly different from that in complex environments. Controlling for relative eye size, we found that species in complex environments have even higher acuity than predicted. We found no relationship between visual acuity and diet. Our results show that eye size is a primary factor underlying variation in fish acuity. We additionally show that habitat type is an important ecological factor that correlates with acuity in certain species.

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“…As a result, more similar residuals are produced from a least squares regression line. PGLS takes into account the expected covariance structure of these residuals, and generates new slope and intercept estimates to account for interspecific autocorrelation due to phylogeny (Symonds and Blomberg, 2014). To account for phylogenetic …”

Section: Evolutionary Analysesmentioning

confidence: 99%

The evolution of jaw protrusion mechanics has been tightly coupled to bentho-pelagic divergence in damselfishes (Pomacentridae)

Cooper

Carter

Conith

et al. 2016

Journal of Experimental Biology

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Most species-rich lineages of aquatic organisms have undergone divergence between forms that feed from the substrate (benthic feeding) and forms that feed from the water column ( pelagic feeding). Changes in trophic niche are frequently accompanied by changes in skull mechanics, and multiple fish lineages have evolved highly specialized biomechanical configurations that allow them to protrude their upper jaws toward the prey during feeding. Damselfishes (family Pomacentridae) are an example of a species-rich lineage with multiple trophic morphologies and feeding ecologies. We sought to determine whether bentho-pelagic divergence in the damselfishes is tightly coupled to changes in jaw protrusion ability. Using high-speed video recordings and kinematic analysis, we examined feeding performance in 10 species that include three examples of convergence on herbivory, three examples of convergence on omnivory and two examples of convergence on planktivory. We also utilized morphometrics to characterize the feeding morphology of an additional 40 species that represent all 29 damselfish genera. Comparative phylogenetic analyses were then used to examine the evolution of trophic morphology and biomechanical performance. We find that pelagic-feeding damselfishes ( planktivores) are strongly differentiated from extensively benthic-feeding species (omnivores and herbivores) by their jaw protrusion ability, upper jaw morphology and the functional integration of upper jaw protrusion with lower jaw abduction. Most aspects of cranial form and function that separate these two ecological groups have evolved in correlation with each other and the evolution of the functional morphology of feeding in damselfishes has involved repeated convergence in form, function and ecology.

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A Primer on Phylogenetic Generalised Least Squares

Cited by 351 publications

References 55 publications

The integration of quantitative genetics, paleontology, and neontology reveals genetic underpinnings of primate dental evolution

The integration of quantitative genetics, paleontology, and neontology reveals genetic underpinnings of primate dental evolution

Visual acuity in ray-finned fishes correlates with eye size and habitat

The evolution of jaw protrusion mechanics has been tightly coupled to bentho-pelagic divergence in damselfishes (Pomacentridae)

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