scholarly journals To Hop or Not to Hop? The Answer Is in the Bird Trees

2020 ◽  
Vol 69 (5) ◽  
pp. 962-972 ◽  
Author(s):  
Pauline Provini ◽  
Elizabeth Höfling
Keyword(s):  
Bird Species ◽  
Appendicular Skeleton ◽  
Character State ◽  
Micro Computed Tomography ◽  
Avian Evolution ◽  
Terrestrial Locomotion ◽  
Ancestral Character State ◽  
Hind Limbs ◽  
Knee Muscle ◽  
3D Landmarks

Abstract Birds can use different types of gaits to move on the ground: they either walk, hop, or run. Although velocity can easily explain a preference for running, it remains unclear what drives a bird species to favor hopping over walking. As many hopping birds are relatively small and arboreal, we wanted to test the link between size, arboreality, and hopping ability. First, we carried out ancestral character state reconstructions of size range, hopping ability, and habitat traits on over 1000 species of birds. We found that both hopping ability and arboreality were derived and significantly correlated traits in avian evolution. Second, we tested the influence of hopping ability on the morphology of the lower appendicular skeleton by quantifying the shape differences of the pelvis and the three long bones of the hind limbs in 47 avian species with different habitats and gait preferences. We used geometric morphometrics on 3D landmarks, digitized on micro–computed tomography (micro-CT) and surface scans of the pelvis, femur, tibiotarsus, and tarsometatarsus. Locomotion habits significantly influence the conformation of the pelvis, especially at the origin of hip and knee muscle extensors. Interestingly, habitat, more than locomotion habits, significantly changed tarsometatarsus conformation. The morphology of the distal part of the tarsometatarsus constrains digit orientation, which leads to a greater ability to perch, an advantageous trait in arboreality. The results of this work suggest an arboreal origin of hopping and illuminate the evolution of avian terrestrial locomotion.[Anatomy; avian; gait; leg; lifestyle; pelvis; tree-dwelling.]

scholarly journals Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

2019 ◽  
Vol 3 ◽  
Author(s):  
Sergei Tarasov ◽  
Istvan Miko ◽  
Matthew Yoder ◽  
Josef Uyeda
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Ancestral Reconstruction ◽  
Anatomy Ontology ◽  
Insect Order ◽  
Ancestral Character State ◽  
Body Regions ◽  
Individual Traits ◽  
History Of ◽  
Complex Characters

Ancestral character state reconstruction has been long used to gain insight into the evolution of individual traits in organisms. However, organismal anatomies (= entire phenotypes) are not merely ensembles of individual traits, rather they are complex systems where traits interact with each other due to anatomical dependencies (when one trait depends on the presence of another trait) and developmental constraints. Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of entire organismal anatomies or organismal body regions. Herein, we present a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies, Tarasov and Uyeda 2019) that takes into account anatomical dependencies and uses stochastic maps (i.e., phylogenetic trees with an instance of mapped evolutionary history of characters, Huelsenbeck et al. 2003) along with anatomy ontologies to reconstruct organismal anatomies. Our approach treats the entire phenotype or its component body regions as single complex characters and allows exploring and comparing phenotypic evolution at different levels of anatomical hierarchy. These complex characters are constructed by ontology-informed amalgamation of elementary characters (i.e., those coded in character matrix) using stochastic maps. In our approach, characters are linked with the terms from an anatomy ontology, which allows viewing them not just as an ensemble of character state tokens but as entities that have their own biological meaning provided by the ontology. This ontology-informed framework provides new opportunities for tracking phenotypic radiations and anatomical evolution of organisms, which we explore using a large dataset for the insect order Hymenoptera (sawflies, wasps, ants and bees).

scholarly journals Terrestrial force production by the limbs of a semi-aquatic salamander provides insight into the evolution of terrestrial locomotor mechanics

2021 ◽  
Author(s):  
Sandy Momoe Kawano ◽  
Richard W. Blob
Keyword(s):  
Adult Life ◽  
Force Production ◽  
Rear Wheel ◽  
Ambystoma Tigrinum ◽  
Terrestrial Locomotion ◽  
Hind Limbs ◽  
Wheel Drive ◽  
Reaction Forces ◽  
Pleurodeles Waltl ◽  
Insight Into

Amphibious fishes and salamanders are valuable functional analogs for vertebrates that spanned the water-to-land transition. However, investigations of walking mechanics have focused on terrestrial salamanders and, thus, may better reflect the capabilities of stem tetrapods that were already terrestrial. The earliest tetrapods were aquatic, so salamanders that are not primarily terrestrial may yield more appropriate data for modelling the incipient stages of terrestrial locomotion. In the present study, locomotor biomechanics were quantified from semi-aquatic Pleurodeles waltl, a salamander that spends most of its adult life in water, and then compared to a primarily terrestrial salamander (Ambystoma tigrinum) and semi-aquatic fish (Periophthalmus barbarus) to evaluate whether walking mechanics show greater similarity between species with ecological versus phylogenetic similarities. Ground reaction forces (GRFs) from individual limbs or fins indicated that the pectoral appendages of each taxon had distinct patterns of force production, but hind limb forces were comparable between the salamanders. The rate of force development ('yank') was sometimes slower in P. waltl but generally comparable between the three species. Finally, medial inclination of the GRF in P. waltl was intermediate between semi-aquatic fish and terrestrial salamanders, potentially elevating bone stresses among more aquatic taxa as they move on land. These data provide a framework for modelling stem tetrapods using an earlier stage of quadrupedal locomotion that was powered primarily by the hind limbs (i.e., "rear-wheel drive"), and reveal mechanisms for appendages to generate propulsion in three locomotor strategies that are presumed to have occurred across the water-to-land transition in vertebrate evolution.

TAIL MUSCLE ACTIVITY PATTERNS IN WALKING AND FLYING PIGEONS (COLUMBA LIVIA)

1993 ◽  
Vol 176 (1) ◽  
pp. 55-76 ◽  
Author(s):  
S. M. Gatesy ◽  
K. P. Dial
Keyword(s):  
Muscle Activity ◽  
High Speed ◽  
Activity Patterns ◽  
Columba Livia ◽  
Trunk Muscles ◽  
Avian Evolution ◽  
Terrestrial Locomotion ◽  
Temporal Flexibility ◽  
High Speed Cinematography ◽  
Tail Muscle

The electrical activity of major caudal muscles of the pigeon (Columba livia) was recorded during five modes of aerial and terrestrial locomotion. Tail muscle electromyograms were correlated with movement using high-speed cinematography and compared to activity in selected muscles of the wings, legs and trunk. During walking, the pectoralis and most tail muscles are normally inactive, but levator muscle activity alternates with the striding legs. In flight, caudal muscles are phasically active with each wingbeat and undergo distinct changes in electromyographic pattern between liftoff, takeoff, slow level flapping and landing modes. The temporal flexibility of tail muscle activity differs significantly from the stereotypic timing of wing muscles in pigeons performing the same flight modes. These neural programs may represent different solutions to the control of flight surfaces in the rapidly oscillating wing and the relatively stationary caudal skeleton. Birds exhibit a novel alliance of tail and forelimb use during aerial locomotion. We suggest that there is evidence of anatomical and functional decoupling of the tail from adjacent hindlimb and trunk muscles during avian evolution to facilitate its specialization for rectricial control in flight.

scholarly journals High-throughput sequencing is revealing genetic associations with avian plumage color

The Auk ◽  
2019 ◽  
Vol 136 (4) ◽  
Author(s):  
Erik R Funk ◽  
Scott A Taylor
Keyword(s):  
High Throughput Sequencing ◽  
Large Body ◽  
Bird Species ◽  
Genetic Associations ◽  
Plumage Color ◽  
Protein Coding ◽  
Avian Evolution ◽  
Color Changes ◽  
Coding Regions ◽  
Color Differences

Abstract Avian evolution has generated an impressive array of patterns and colors in the ~10,000 bird species that exist on Earth. Recently, a number of exciting studies have utilized whole-genome sequencing to reveal new details on the genetics of avian plumage color. These findings provide compelling evidence for genes that underlie plumage variation across a wide variety of bird species (e.g., juncos, warblers, seedeaters, and estrildid finches). While much is known about large, body-wide color changes, these species exhibit discrete color differences across small plumage patches. Many genetic differences appear to be located in regulatory regions of genes rather than in protein-coding regions, suggesting gene expression is playing a large role in the control of these color patches. Taken together, these studies have the potential to broadly facilitate further research of sexual selection and evolution in these charismatic taxa.

scholarly journals Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

2019 ◽  
Vol 68 (5) ◽  
pp. 698-716 ◽  
Author(s):  
Sergei Tarasov
Keyword(s):  
Regulatory Networks ◽  
Markov Models ◽  
Phylogenetic Inference ◽  
Phenotypic Traits ◽  
Character State ◽  
Body Parts ◽  
Ancestral Character State ◽  
State Models ◽  
Hidden States ◽  
New Framework

Abstract Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes—hierarchical and hidden—which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks (GRNs) underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models (SMM) equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of SMM with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of GRNs and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing “tail color problem,” in which the trait is scored for species with tails of different colors or no tails. It also presents a previously unknown issue called the “two-scientist paradox,” in which the nature of coding the trait and the hidden processes driving the trait’s evolution are confounded; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This article gives practical examples of using the new framework for phylogenetic inference and comparative analysis.

scholarly journals Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Claudio G. Ametrano ◽  
Felix Grewe ◽  
Pedro W. Crous ◽  
Stephen B. Goodwin ◽  
Chen Liang ◽  
...  
Keyword(s):  
Character State ◽  
Ancestral Character State ◽  
Wide Range ◽  
Tree Inference ◽  
Ancestral Character State Reconstruction ◽  
Inference Methods ◽  
Genome Scale ◽  
The Impact ◽  
Rock Inhabiting Fungi ◽  
Scale Data

Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

Convergence to the tiniest detail: vocal sac structure in torrent-dwelling frogs

2019 ◽  
Author(s):  
Agustín J Elias-Costa ◽  
Julián Faivovich
Keyword(s):  
Background Noise ◽  
Evolutionary History ◽  
Visual Display ◽  
Character State ◽  
Visual Displays ◽  
State Reconstruction ◽  
Ancestral Character State ◽  
History Of ◽  
Ancestral Character State Reconstruction ◽  
Detection And Recognition

Abstract Cascades and fast-flowing streams impose severe restrictions on acoustic communication, with loud broadband background noise hampering signal detection and recognition. In this context, diverse behavioural features, such as ultrasound production and visual displays, have arisen in the evolutionary history of torrent-dwelling amphibians. The importance of the vocal sac in multimodal communication is being increasingly recognized, and recently a new vocal sac visual display has been discovered: unilateral inflation of paired vocal sacs. In the diurnal stream-breeding Hylodidae from the Atlantic forest, where it was first described, this behaviour is likely to be enabled by a unique anatomical configuration of the vocal sacs. To assess whether other taxa share this exceptional structure, we surveyed torrent-dwelling species with paired vocal sacs across the anuran tree of life and examined the vocal sac anatomy of exemplar species across 18 families. We found striking anatomical convergence among hylodids and species of the distantly related basal ranid genera Staurois, Huia, Meristogenys and Amolops. Ancestral character state reconstruction identified three new synapomorphies for Ranidae. Furthermore, we surveyed the vocal sac configuration of other anuran species that perform visual displays and report observations on what appears to be unilateral inflation of paired vocal sacs, in Staurois guttatus – an extremely rare behaviour in anurans.

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