Measuring phylogenetic signal between categorical traits and phylogenies

Borges, Rui; Machado, João Paulo; Gomes, Cidália; Rocha, Ana Paula; Antunes, Agostinho

doi:10.1093/bioinformatics/bty800

Cited by 90 publications

(107 citation statements)

References 34 publications

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“…The higher δ‐value is the less uncertainty there is in the ancestral reconstruction, i.e. stronger phylogenetic signal (Borges, Machado, Gomes, Rocha, & Antunes, ). Body size and activity times were found to be the most phylogenetically conserved traits (δ(activity time)=22.15; δ(diet)=12.18; δ(microhabitat)=6.67; λ(mass)=0.96).…”

Section: Methodsmentioning

confidence: 99%

The global biogeography of lizard functional groups

Vidan

Novosolov

Bauer

et al. 2019

Journal of Biogeography

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Aim Understanding the mechanisms determining species richness is a primary goal of biogeography. Richness patterns of sub‐groups within a taxon are usually assumed to be driven by similar processes. However, if richness of distinct ecological strategies respond differently to the same processes, inferences made for an entire taxon may be misleading. We deconstruct the global lizard assemblage into functional groups and examine the congruence among richness patterns between them. We further examine the species richness – functional richness relationship to elucidate the way functional diversity contributes to the overall species richness patterns. Location Global. Methods Using comprehensive biological trait databases we classified the global lizard assemblage into ecological strategies based on body size, diet, activity times and microhabitat preferences, using Archetypal Analysis. We then examined spatial gradients in the richness of each strategy at the one‐degree grid cell, biome, and realm scales. Results We found that lizards can best be characterized by seven “ecological strategies”: scansorial, terrestrial, nocturnal, herbivorous, fossorial, large, and semi‐aquatic. There are large differences among the global richness patterns of these strategies. While the major richness hotspot for lizards in general is in Australia, several strategies exhibit highest richness in the Amazon Basin. Importantly, the global maximum in lizard species richness is achieved at intermediate values of functional diversity and increasing functional diversity further result in a slow decline of species richness. Main conclusions The deconstruction of the global lizard assemblage along multiple ecological axes offers a new way to conceive lizard diversity patterns. It suggests that local lizard richness mostly increases when species belonging to particular ecological strategies become hyper‐diverse there, and not because more ecological types are present in the most species rich localities. Thus maximum richness and maximum ecological diversity do not overlap. These results shed light on the global richness pattern of lizards, and highlight previously unidentified spatial patterns in understudied functional groups.

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Section: Methodsmentioning

confidence: 99%

The global biogeography of lizard functional groups

Vidan

Novosolov

Bauer

et al. 2019

Journal of Biogeography

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“…Furthermore, the barn owl has a scarcely evident fovea (region of the retina that is rich in cone photoreceptors and responsible for color discrimination in bright environments), but instead has an abundance of rod cells (Harmening and Wagner 2011), which distinct from cones, gather light more efficiently in low-light (scotopic) environments (Hart 2001). Together, these features of the barn owl eye mirror patterns observed in the mammalian eye, which has also been hypothesized to have evolved specialized adaptations to nocturnal environments (Silva and Antunes 2017; Borges, Johnson, et al 2018; Borges, Machado, et al 2018).…”

Section: Introductionmentioning

confidence: 65%

“…The genetic changes we found in the barn owl are candidates that give the species its unique ocular features among birds, including high visual sensitivity and frontally orientated eyes, as well as these convergent innovations in nocturnal mammals (Khan et al. 2015; Borges, Johnson, et al 2018; Borges, Machado, et al 2018).…”

Section: Discussionmentioning

confidence: 93%

Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype

Borges

Fonseca

Gomes

et al. 2019

Genome Biology and Evolution

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Typical avian eyes are phenotypically engineered for photopic vision (daylight). In contrast, the highly derived eyes of the barn owl (Tyto alba) are adapted for scotopic vision (dim light). The dramatic modifications distinguishing barn owl eyes from other birds include: 1) shifts in frontal orientation to improve binocularity, 2) rod-dominated retina, and 3) enlarged corneas and lenses. Some of these features parallel mammalian eye patterns, which are hypothesized to have initially evolved in nocturnal environments. Here, we used an integrative approach combining phylogenomics and functional phenotypes of 211 eye-development genes across 48 avian genomes representing most avian orders, including the stem lineage of the scotopic-adapted barn owl. Overall, we identified 25 eye-development genes that coevolved under intensified or relaxed selection in the retina, lens, cornea, and optic nerves of the barn owl. The agtpbp1 gene, which is associated with the survival of photoreceptor populations, was pseudogenized in the barn owl genome. Our results further revealed that barn owl retinal genes responsible for the maintenance, proliferation, and differentiation of photoreceptors experienced an evolutionary relaxation. Signatures of relaxed selection were also observed in the lens and cornea morphology-associated genes, suggesting that adaptive evolution in these structures was essentially structural. Four eye-development genes (ephb1, phactr4, prph2, and rs1) evolved in positive association with the orbit convergence in birds and under relaxed selection in the barn owl lineage, likely contributing to an increased reliance on binocular vision in the barn owl. Moreover, we found evidence of coevolutionary interactions among genes that are expressed in the retina, lens, and optic nerve, suggesting synergetic adaptive events. Our study disentangles the genomic changes governing the binocularity and low-light perception adaptations of barn owls to nocturnal environments while revealing the molecular mechanisms contributing to the shift from the typical avian photopic vision to the more-novel scotopic-adapted eye.

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“…Phylogenetic signal for the type of multilayer on the throat and the back was computed using the δ Bayesian approach for discrete characters described in Borges et al [35]. Larger values of δ express a higher level stronger phylogenetic signal, i.e.…”

Section: Methodsmentioning

confidence: 99%

Hummingbird iridescence: an unsuspected structural diversity influences colouration at multiple scales

Gruson

Élias

Djédiat

et al. 2019

Preprint

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10Iridescent colours are colours that change depending on the angle of illumination or observation. They are 11 produced when light is reflected by multilayer structures or diffracted by gratings. While this phenomenon is well 12 understood for simple optical systems, it remains unclear how complex biological structures interact with light 13 to produce iridescence. There are very few comparative studies at interspecific level (often focusing on a single 14 colour patch for each species), resulting in an underestimation of structure diversity. Using an interdisciplinary 15 approach combining physics and biology, we here quantify the colour and structure of 36 hummingbirds species evenly 16 distributed across the phylogeny. We explore at least 2 patches per species, which are assumed to be under different 17 selective regimes. For each patch, we measure structural features (number of layers, layer width, irregularity, spacing, 18 etc.) of the feathers at different scales using both optical and electronic microscopy and we measure colour using a 19 novel approach we developed to encompass the full complexity of iridescence, including its angular dependency. We 20 discover an unsuspected diversity of structures producing iridescence in hummingbirds. We also study the effect of 21 several structural features on the colour of the resulting signal, using both an empirical and modelling approach. Our 22 findings demonstrate the need to take into account multiple patches per species and suggest possible evolutionary 23 pressures causing the evolutionary transitions from one melanosome type to another. 24 Hummingbirds are famous for their bright and shiny colours which change with the illumination or observation 26 angle: a phenomenon known as iridescence. Iridescent colours are produced by the interaction of light with periodic 27 nanometre-scale structures such as multilayers or diffraction gratings and are widespread among many taxa [1]. But few 28 taxa display colours as bright and as saturated as the hummingbirds (Trochilidae family). Most hummingbird species 29 harbour two visually distinct types of iridescent colour patches, as illustrated in fig. S1: directional patches, which are 30 only visible at a very narrow angle range [2] and are often very bright and saturated, and diffuse patches, for which 31 some colour is visible from any angle [2] and that are often not as bright as directional patches. Directional patches are 32 often located on facial or ventral patches and thought to be involved in communication while diffuse patches are often 33 located on dorsal patches and thought to be involved in camouflage [3]. Additionally, although all hummingbird species 34 display some degree of iridescence, striking differences can be noticed between the various species and body patches in 35 terms of brightness (describing how much light is reflected by the object), saturation (describing the colour "purity") 36 and directionality [4]. 37Yet, the structural bases of this intra-individual and interspecific diversity...

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Measuring phylogenetic signal between categorical traits and phylogenies

Cited by 90 publications

References 34 publications

The global biogeography of lizard functional groups

The global biogeography of lizard functional groups

Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype

Hummingbird iridescence: an unsuspected structural diversity influences colouration at multiple scales

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