Academic literature on the topic 'Avian evolution; Phylogenic tree shape'

Adaptation is the fundamental driver of functional and biomechanical evolution. Accordingly, the states of biomechanical traits (absolute or relative trait values) have long been used as proxies for adaptations in response to direct selection. However, ignoring evolutionary history, in particular ancestry, passage of time and the rate of evolution, can be misleading. Here, we apply a recently developed phylogenetic statistical approach using significant rate shifts to detect instances of exceptional rates of adaptive changes in bite force in a large group of terrestrial vertebrates, the amniotes. Our results show that bite force in amniotes evolved through multiple bursts of exceptional rates of adaptive changes, whereby whole groups—including Darwin's finches, maniraptoran dinosaurs (group of non-avian dinosaurs including birds), anthropoids and hominins (fossil and modern humans)—experienced significant rate increases compared to the background rate. However, in most parts of the amniote tree of life, we find no exceptional rate increases, indicating that coevolution with body size was primarily responsible for the patterns observed in bite force. Our approach represents a template for future studies in functional morphology and biomechanics, where exceptional rates of adaptive changes can be quantified and potentially linked to specific ecological factors underpinning major evolutionary radiations.

Mass media and popular science journals commonly report that new fossil discoveries have ‘rewritten evolutionary history’. Is this merely journalistic hyperbole or is our sampling of systematic diversity so limited that attempts to derive evolutionary history from these datasets are premature? We use two exemplars—catarrhine primates (Old World monkeys and apes) and non-avian dinosaurs—to investigate how the maturity of datasets can be assessed. Both groups have been intensively studied over the past 200 years and so should represent pinnacles in our knowledge of vertebrate systematic diversity. We test the maturity of these datasets by assessing the completeness of their fossil records, their susceptibility to changes in macroevolutionary hypotheses and the balance of their phylogenies through study time. Catarrhines have shown prolonged stability, with discoveries of new species being evenly distributed across the phylogeny, and thus have had little impact on our understanding of their fossil record, diversification and evolution. The reverse is true for dinosaurs, where the addition of new species has been non-random and, consequentially, their fossil record, tree shape and our understanding of their diversification is rapidly changing. The conclusions derived from these analyses are relevant more generally: the maturity of systematic datasets can and should be assessed before they are exploited to derive grand macroevolutionary hypotheses.

Toll-like receptors (TLRs) play important role in the innate immune system. TLR15 is reported to have a unique role in defense against pathogens, but its structural and evolution characterizations are still poorly understood. In this study, we identified 57 completed TLR15 genes from avian and reptilian genomes. TLR15 clustered into an individual clade and was closely related to family 1 on the phylogenetic tree. Unlike the TLRs in family 1 with the broken asparagine ladders in the middle, TLR15 ectodomain had an intact asparagine ladder that is critical to maintain the overall shape of ectodomain. The conservation analysis found that TLR15 ectodomain had a highly evolutionarily conserved region on the convex surface of LRR11 module, which is probably involved in TLR15 activation process. Furthermore, the protein–protein docking analysis indicated that TLR15 TIR domains have the potential to form homodimers, the predicted interaction interface of TIR dimer was formed mainly by residues from the BB-loops andαC-helixes. Although TLR15 mainly underwent purifying selection, we detected 27 sites under positive selection for TLR15, 24 of which are located on its ectodomain. Our observations suggest the structural features of TLR15 which may be relevant to its function, but which requires further experimental validation.

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.]

The hedgehog signaling pathway plays a vital role in human and animal patterning and cell proliferation during the developmental process. The hedgehog gene family of vertebrate species includes three genes, Shh, Dhh, and Ihh, which possess different functions and expression patterns. Despite the importance of hedgehog genes, genomic evidence of this gene family in reptiles is lacking. In this study, the available genomes of a number of representative reptile species were explored by utilizing adaptive evolutionary analysis methods to characterize the evolutionary patterns of the hedgehog gene family. Altogether, 33 sonic hedgehog (Shh), 25 desert hedgehog (Dhh), and 20 Indian hedgehog (Ihh) genes were obtained from reptiles, and six avian and five mammalian sequences were added to the analysis. The phylogenetic maximum likelihood (ML) tree of the Shh, Dhh, and Ihh genes revealed a similar topology, which is approximately consistent with the traditional taxonomic group. No shared positive selection site was identified by the PAML site model or the three methods in the Data Monkey Server. Branch model and Clade model C analyses revealed that the Dhh and Ihh genes experienced different evolutionary forces in reptiles and other vertebrates, while the Shh gene was not significantly different in terms of selection pressure. The different evolutionary rates of the Dhh and Ihh genes suggest that these genes may be potential contributors to the discrepant sperm and body development of different clades. The different adaptive evolutionary history of the Shh, Dhh, and Ihh genes among reptiles may be due to their different functions in regulating cellular events of development from the embryonic stages to adulthood. Overall, this study has provided meaningful information regarding the evolution of the hedgehog gene family in reptiles and a theoretical foundation for further analyses on the functional and molecular mechanisms that have shaped the reptilian hedgehog genes.

Vegetation characteristics are commonly invoked to explain differential nesting success, but few studies have identified how habitat attributes may be associated with specific predator groups responsible for nest losses. We measured vegetation characteristics at artificial songbird nests deployed on and above the ground in mixedwood forest in west-central Alberta, to discriminate characteristics of successful nests from those of nests destroyed by mice and voles, squirrels, and birds. Successful nests, and those depredated by mice and voles, tended to be on the ground and were well concealed by dense shrubs. Squirrels and birds usually raided aboveground nests at sites with few shrubs and high tree densities. These results suggest that nest visibility is a major factor influencing risk of predation, but the relative importance of concealment varies according to the types of predators and their behavior. The characteristics of nests from which eggs were removed, leaving no egg remains to identify predators, closely resembled those of nests visited by squirrels and birds. Our findings have implications for how individual songbird species cope with selection pressures imposed by nest predators associated with vegetation characteristics of birds' nest patches and, ultimately, how predators may shape the structure of avian communities.

AbstractMaximizing biodiversity persistence in heterogeneous human-modified landscapes is hindered by the complex interactions between habitat quality and configuration of native and non-native habitats. Here we examined these complex interactions considering avian diversity across 26 sampling sites, each of which comprised of three sampling points located across a gradient of disturbance: core native habitat fragment, fragment edge, and non-native adjacent matrix. The 78 sampling points were further nested within three neotropical biomes—Amazonia, Cerrado and Pantanal—in central-western Brazil. Matrix type consisted of cattle pastures in the Amazon and teak plantations in the Pantanal and Cerrado. We considered the interactive effects of (1) disturbance-context: fragment core, edge and adjacent matrix, (2) matrix type: tree plantation or cattle pastures, both subject to varying land-use intensity, and (3) native habitat configuration (fragment size, shape and isolation) on bird species richness, abundance and composition. Based on point-count surveys, we recorded 210 bird species. Bird species richness and abundance declined across the disturbance gradient, while genus composition only differed within the adjacent matrix, particularly cattle-pastures. The effect of native habitat area was positive but only detected at fragment edges. Overall bird diversity increased at sites characterized by higher availability of either relict trees within pasture landscapes or old-growth trees within teak plantation landscapes. The core of native fragments played a primary role in ensuring the persistence of bird diversity, regardless of fragment size. In contrast to pastures, tree plantations likely harbour a higher proportion of forest-dependent species while bird diversity can be further enhanced by reduced management intensity in both matrix types. Strategies to maximize avian persistence should not only include retaining native habitats, but also maximizing the size of core native habitats. Likewise, more structurally complex matrix types should be encouraged while maintaining low levels of land-use intensity.