Assessing phenotypic correlation through the multivariate phylogenetic latent liability model

Cybis, Gabriela Bettella; Sinsheimer, Janet S.; Bedford, Trevor; Mather, Alison E.; Lemey, Philippe; Suchard, Marc A.

doi:10.1214/15-aoas821

Cited by 43 publications

(93 citation statements)

References 47 publications

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“…Although there are precedents to this approach [60,61], theoretical and simulation studies show that the evolutionary analysis of principal components can yield biased results under some conditions [62]. Unfortunately, no current phylogenetic models can efficiently analyze high-dimensional datasets such as spectral data despite recent methodological advances [63], pointing to an important future research direction.…”

Section: Caveats and Limitsmentioning

confidence: 99%

Associations of Leaf Spectra with Genetic and Phylogenetic Variation in Oaks: Prospects for Remote Detection of Biodiversity

Cavender‐Bares

Meireles

Couture³

et al. 2016

Remote Sensing

144

116

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Species and phylogenetic lineages have evolved to differ in the way that they acquire and deploy resources, with consequences for their physiological, chemical and structural attributes, many of which can be detected using spectral reflectance from leaves. Recent technological advances for assessing optical properties of plants offer opportunities to detect functional traits of organisms and differentiate levels of biological organization across the tree of life. Here, we connect leaf-level full range spectral data (400-2400 nm) of leaves to the hierarchical organization of plant diversity within the oak genus (Quercus) using field and greenhouse experiments in which environmental factors and plant age are controlled. We show that spectral data significantly differentiate populations within a species and that spectral similarity is significantly associated with phylogenetic similarity among species. We further show that hyperspectral information allows more accurate classification of taxa than spectrally-derived traits, which by definition are of lower dimensionality. Finally, model accuracy increases at higher levels in the hierarchical organization of plant diversity, such that we are able to better distinguish clades than species or populations. This pattern supports an evolutionary explanation for the degree of optical differentiation among plants and demonstrates potential for remote detection of genetic and phylogenetic diversity.

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Section: Caveats and Limitsmentioning

confidence: 99%

Associations of Leaf Spectra with Genetic and Phylogenetic Variation in Oaks: Prospects for Remote Detection of Biodiversity

Cavender‐Bares

Meireles

Couture³

et al. 2016

Remote Sensing

144

116

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“…Correlates of diet evolution in mullets We explored evolutionary 690 correlations between feeding preference and several other variables in 691 mullets under the latent-liability model [69]. Specifically, we evaluated all 692 pairwise correlations between two continuous traits-trophic index and 693 total length-and two discrete traits-habitat type (marine, non-marine), 694 and geographic distribution (tropical, non-tropical).…”

Section: /56mentioning

confidence: 99%

“…Numbers adjacent to internal nodes indicate the corresponding marginal probabilities; the three circled nodes indicate the location of the corresponding fossil calibrations (see Table 2). Estimates are based on analyses of the 100-species dataset under the latent-liability model [69]. Traits (abbreviations) [and states] include: trophic index (TI); total length (TL) [centimeters]; habitat type (Habitat) [marine, non-marine]; and distribution (Distribution) [tropical, non-tropical].…”

Section: Mugil Liza 298mentioning

confidence: 99%

“…We explored correlations between traits in the 64-species tree using the latent-liability model [69]. The four traits included two continuous and two discrete variables: trophic index (TI, continuous), total length (TL, continuous), habitat (Hab, discrete), and geographic distribution (Dist, discrete).…”

Section: Ancestral-state Estimationmentioning

confidence: 99%

“…The shading of internal branches indicates the corresponding node probabilities (see inset legend), the numbered internal nodes indicate the location of the corresponding fossil calibrations (see Table 2), and the bar plots on nodes indicate the corresponding 95% HPD interval of divergence times. Estimates are based on analyses of the 100-species dataset under the latent-liability model [69]. We explored correlations between two discrete and two continuous traits.…”

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confidence: 99%

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Bayesian Inference of Divergence Times and Feeding Evolution in Grey Mullets (Mugilidae)

Santini

Carnevale

et al. 2015

Preprint

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Grey mullets (Mugilidae, Ovalentariae) are coastal fishes found in near-shore environments of tropical, subtropical, and temperate regions within marine, brackish, and freshwater habitats throughout the world. This group is noteworthy both for the highly conserved morphology of its members-which complicates species identification and delimitation-and also for the uncommon herbivorous or detritivorous diet of most mullets. In this study, we first attempt to identify the number of mullet species, and then-for the resulting species-estimate a densely sampled time-calibrated phylogeny using three mitochondrial gene regions and three fossil calibrations. Our results identify two major subgroups of mullets that diverged in the Paleocene/Early Eocene, followed by an Eocene/Oligocene radiation across both tropical and subtropical habitats. We use this phylogeny to explore the evolution of feeding preference in mullets, which indicates multiple independent origins of both herbivorous and detritivorous diets within this group. We also explore correlations between feeding preference and other variables, including body size, habitat (marine, brackish, or freshwater), and geographic distribution (tropical, subtropical, or temperate). Our analyses reveal: (1) a positive correlation between trophic index and habitat (with herbivorous and/or detritivorous species predominantly occurring in marine habitats); (2) a negative correlation between trophic index and geographic distribution (with herbivorous species occurring predominantly in subtropical and temperate regions), and; (3) a negative correlation between body size and geographic distribution (with larger species occurring predominantly in subtropical and temperate regions). PLOS1/56 1 Grey mullets (Mugilidae, Ovalentariae) occur in coastal waters worldwide 2 and represent an important food source in several European and Pacific 3 countries. Mugilids are geographically widespread, with species ranging 4 from the tropics to northern Europe, and vary greatly in body size, with 5 species ranging from 10 − 120 cm in total length (TL). Despite this 6 variation, the morphology of mullets is extremely conservative; all species 7 share a torpedo-shaped body form with a similar overall appearance, 8 which makes accurate species identification exceptionally challenging [1]. 9 Most mullet species are euryhaline and may spend at least part of their 10 life cycle in brackish or freshwater habitats, even though the majority of 11 the adult life-stage and reproduction typically occur in marine habitats. 12 However, a few species (e.g., Liza abu, Agonostomus monticula and A. 13 catalai) are exclusively freshwater [1-4]. 14 The diet of grey mullets is unusual among marine fishes: most mullet 15 species feed predominantly on food items-such as detritus and 16 filamentous algae-with relatively low calories and/or protein per unit 17 mass (i.e., "low-quality food resources" [5]). Mullets have evolved a 18 number of morphological adaptations associated with this diet, including 19 a stomach with...

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Progesterone Response Element Variation in the OXTR Promoter Region and Paternal Care in New World Monkeys

et al. 2016

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Paternal care is a complex social behavior common in primate species with socially monogamous mating systems and twin births. Evolutionary causes and consequences of such behavior are not well understood, nor are their neuroendocrine and genetic bases. However, the neuropeptide oxytocin (OXT) and its receptor (OXTR) are associated with parental care in mammalian lineages. Here we investigated the interspecific variation in the number of progesterone response elements (PREs) in the OXTR promoter region of 32 primate species, correlating genetic data with behavior, social systems, and ecological/life-history parameters, while controlling for phylogeny. We verified that PREs are only present in New World monkeys and that PRE number is significantly correlated with the presence of paternal care in this branch. We suggest that PRE number could be an essential part of the genetic repertoire that allowed the emergence of taxon-specific complex social behaviors, such as paternal care in marmosets and tamarins.

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Assessing phenotypic correlation through the multivariate phylogenetic latent liability model

Cited by 43 publications

References 47 publications

Associations of Leaf Spectra with Genetic and Phylogenetic Variation in Oaks: Prospects for Remote Detection of Biodiversity

Associations of Leaf Spectra with Genetic and Phylogenetic Variation in Oaks: Prospects for Remote Detection of Biodiversity

Bayesian Inference of Divergence Times and Feeding Evolution in Grey Mullets (Mugilidae)

Progesterone Response Element Variation in the OXTR Promoter Region and Paternal Care in New World Monkeys

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