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Search Results: 1 - 10 of 32446 matches for " John Gatesy "
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Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution
Michelle Spaulding, Maureen A. O'Leary, John Gatesy
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0007062
Abstract: Background Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. Methodology/Principal Findings We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, ?Creodonta, Lipotyphla, and the ?raoellid artiodactylan ?Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to ?Indohyus, with ?Mesonychia outside of Artiodactyla. The relationships of ?Mesonychia and ?Indohyus are highly unstable, however - in trees only two steps longer than minimum length, ?Mesonychia falls inside Artiodactyla and displaces ?Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. Conclusions/Significance Integration of new fossil material of ?Indohyus impacts placement of another extinct clade ?Mesonychia, pushing it much farther down the tree. The phylogenetic position of ?Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales + hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.
A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea
Jonathan H Geisler, Michael R McGowen, Guang Yang, John Gatesy
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-112
Abstract: We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses.The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti and crown Odontoceti, suggesting that these two clades radiated in the late Oligocene or later, contra some recent molecular clock studies. Our trees also imply that many character states shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats.It has been 12 years since the publication of Messenger and McGuire [1], the first major effort to develop a phylogenetic hypothesis for crown Cetacea (Neoceti) based on a combined phylogenetic analysis of morphological and molecular charact
Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans
Michael R McGowen, Stephen H Montgomery, Clay Clark, John Gatesy
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-98
Abstract: We sequenced ~1240 basepairs of the brain development gene microcephalin (MCPH1) in 38 cetacean species. Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution) using site and branch models of molecular evolution. We also tested the hypothesis that selection on MCPH1 was correlated with brain size in cetaceans using a continuous regression analysis that accounted for phylogenetic history. Our analyses revealed widespread signals of adaptive evolution in the MCPH1 of Cetacea and in other subclades of Mammalia, however, there was not a significant positive association between ω and brain size within Cetacea.In conjunction with a recent study of Primates, we find no evidence to support an association between MCPH1 evolution and the evolution of brain size in highly encephalized mammalian species. Our finding of significant positive selection in MCPH1 may be linked to other functions of the gene.The human brain is arguably one of the most remarkable adaptations in the history of life. Compared to other mammals, the human lineage has undergone a massive expansion in relative brain and forebrain size, cortical surface area, and overall cognitive ability [1]. However, many other vertebrates exhibit increased relative brain and forebrain sizes, as well as complex social and cognitive behaviours. For example, odontocete cetaceans (toothed whales) have some of the largest brains relative to their body mass among extant mammals [2]. Relative brain size in some odontocete species is greater than non-human primates [3], and in absolute terms, the giant sperm whale (Physeter macrocephalus) has the largest brain of any living organism at a maximum of 10 kg [4]. According to some researchers, high relative brain or forebrain sizes are positively correlated with indices of cognition or "intelligence" [1,5], althou
Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes
Meredith Robert W,Gatesy John,Springer Mark S
BMC Evolutionary Biology , 2013, DOI: 10.1186/1471-2148-13-20
Abstract: Background Secondary edentulism (toothlessness) has evolved on multiple occasions in amniotes including several mammalian lineages (pangolins, anteaters, baleen whales), birds, and turtles. All edentulous amniote clades have evolved from ancestors with enamel-capped teeth. Previous studies have documented the molecular decay of tooth-specific genes in edentulous mammals, all of which lost their teeth in the Cenozoic, and birds, which lost their teeth in the Cretaceous. By contrast with mammals and birds, tooth loss in turtles occurred in the Jurassic (201.6-145.5 Ma), providing an extended time window for tooth gene degradation in this clade. The release of the painted turtle and Chinese softshell turtle genomes provides an opportunity to recover the decayed remains of tooth-specific genes in Testudines. Results We queried available genomes of Testudines (Chrysemys picta [painted turtle], Pelodiscus sinensis [Chinese softshell turtle]), Aves (Anas platyrhynchos [duck], Gallus gallus [chicken], Meleagris gallopavo [turkey], Melopsittacus undulatus [budgerigar], Taeniopygia guttata [zebra finch]), and enamelless mammals (Orycteropus afer [aardvark], Choloepus hoffmanni [Hoffmann’s two-toed sloth], Dasypus novemcinctus [nine-banded armadillo]) for remnants of three enamel matrix protein (EMP) genes with putative enamel-specific functions. Remnants of the AMBN and ENAM genes were recovered in Chrysemys and retain their original synteny. Remnants of AMEL were recovered in both testudines, although there are no shared frameshifts. We also show that there are inactivated copies of AMBN, AMEL and ENAM in representatives of divergent avian lineages including Galloanserae, Passeriformes, and Psittaciformes, and that there are shared frameshift mutations in all three genes that predate the basal split in Neognathae. Among enamelless mammals, all three EMP genes exhibit inactivating mutations in Orycteropus and Choloepus. Conclusions Our results highlight the power of combining fossil and genomic evidence to decipher macroevolutionary transitions and characterize the functional range of different loci involved in tooth development. The fossil record and phylogenetics combine to predict the occurrence of molecular fossils of tooth-specific genes in the genomes of edentulous amniotes, and in every case these molecular fossils have been discovered. The widespread occurrence of EMP pseudogenes in turtles, birds, and edentulous/enamelless mammals also provides compelling evidence that in amniotes, the only unique, non-redundant function of these genes is in ena
Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals
Robert W. Meredith,John Gatesy,William J. Murphy,Oliver A. Ryder,Mark S. Springer
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000634
Abstract: Vestigial structures occur at both the anatomical and molecular levels, but studies documenting the co-occurrence of morphological degeneration in the fossil record and molecular decay in the genome are rare. Here, we use morphology, the fossil record, and phylogenetics to predict the occurrence of “molecular fossils” of the enamelin (ENAM) gene in four different orders of placental mammals (Tubulidentata, Pholidota, Cetacea, Xenarthra) with toothless and/or enamelless taxa. Our results support the “molecular fossil” hypothesis and demonstrate the occurrence of frameshift mutations and/or stop codons in all toothless and enamelless taxa. We then use a novel method based on selection intensity estimates for codons (ω) to calculate the timing of iterated enamel loss in the fossil record of aardvarks and pangolins, and further show that the molecular evolutionary history of ENAM predicts the occurrence of enamel in basal representatives of Xenarthra (sloths, anteaters, armadillos) even though frameshift mutations are ubiquitous in ENAM sequences of living xenarthrans. The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin's theory.
Rod Monochromacy and the Coevolution of Cetacean Retinal Opsins
Robert W. Meredith,John Gatesy,Christopher A. Emerling,Vincent M. York,Mark S. Springer
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003432
Abstract: Cetaceans have a long history of commitment to a fully aquatic lifestyle that extends back to the Eocene. Extant species have evolved a spectacular array of adaptations in conjunction with their deployment into a diverse array of aquatic habitats. Sensory systems are among those that have experienced radical transformations in the evolutionary history of this clade. In the case of vision, previous studies have demonstrated important changes in the genes encoding rod opsin (RH1), short-wavelength sensitive opsin 1 (SWS1), and long-wavelength sensitive opsin (LWS) in selected cetaceans, but have not examined the full complement of opsin genes across the complete range of cetacean families. Here, we report protein-coding sequences for RH1 and both color opsin genes (SWS1, LWS) from representatives of all extant cetacean families. We examine competing hypotheses pertaining to the timing of blue shifts in RH1 relative to SWS1 inactivation in the early history of Cetacea, and we test the hypothesis that some cetaceans are rod monochomats. Molecular evolutionary analyses contradict the “coastal” hypothesis, wherein SWS1 was pseudogenized in the common ancestor of Cetacea, and instead suggest that RH1 was blue-shifted in the common ancestor of Cetacea before SWS1 was independently knocked out in baleen whales (Mysticeti) and in toothed whales (Odontoceti). Further, molecular evidence implies that LWS was inactivated convergently on at least five occasions in Cetacea: (1) Balaenidae (bowhead and right whales), (2) Balaenopteroidea (rorquals plus gray whale), (3) Mesoplodon bidens (Sowerby's beaked whale), (4) Physeter macrocephalus (giant sperm whale), and (5) Kogia breviceps (pygmy sperm whale). All of these cetaceans are known to dive to depths of at least 100 m where the underwater light field is dim and dominated by blue light. The knockout of both SWS1 and LWS in multiple cetacean lineages renders these taxa rod monochromats, a condition previously unknown among mammalian species.
Shake a Tail Feather: The Evolution of the Theropod Tail into a Stiff Aerodynamic Surface
Michael Pittman, Stephen M. Gatesy, Paul Upchurch, Anjali Goswami, John R. Hutchinson
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0063115
Abstract: Theropod dinosaurs show striking morphological and functional tail variation; e.g., a long, robust, basal theropod tail used for counterbalance, or a short, modern avian tail used as an aerodynamic surface. We used a quantitative morphological and functional analysis to reconstruct intervertebral joint stiffness in the tail along the theropod lineage to extant birds. This provides new details of the tail’s morphological transformation, and for the first time quantitatively evaluates its biomechanical consequences. We observe that both dorsoventral and lateral joint stiffness decreased along the non-avian theropod lineage (between nodes Theropoda and Paraves). Our results show how the tail structure of non-avian theropods was mechanically appropriate for holding itself up against gravity and maintaining passive balance. However, as dorsoventral and lateral joint stiffness decreased, the tail may have become more effective for dynamically maintaining balance. This supports our hypothesis of a reduction of dorsoventral and lateral joint stiffness in shorter tails. Along the avian theropod lineage (Avialae to crown group birds), dorsoventral and lateral joint stiffness increased overall, which appears to contradict our null expectation. We infer that this departure in joint stiffness is specific to the tail’s aerodynamic role and the functional constraints imposed by it. Increased dorsoventral and lateral joint stiffness may have facilitated a gradually improved capacity to lift, depress, and swing the tail. The associated morphological changes should have resulted in a tail capable of producing larger muscular forces to utilise larger lift forces in flight. Improved joint mobility in neornithine birds potentially permitted an increase in the range of lift force vector orientations, which might have improved flight proficiency and manoeuvrability. The tail morphology of modern birds with tail fanning capabilities originated in early ornithuromorph birds. Hence, these capabilities should have been present in the early Cretaceous, with incipient tail-fanning capacity in the earliest pygostylian birds.
Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix
Mark S. Springer, Robert W. Meredith, John Gatesy, Christopher A. Emerling, Jong Park, Daniel L. Rabosky, Tanja Stadler, Cynthia Steiner, Oliver A. Ryder, Jan E. Jane?ka, Colleen A. Fisher, William J. Murphy
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049521
Abstract: Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.
Three-Dimensional, High-Resolution Skeletal Kinematics of the Avian Wing and Shoulder during Ascending Flapping Flight and Uphill Flap-Running
David B. Baier, Stephen M. Gatesy, Kenneth P. Dial
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0063982
Abstract: Past studies have shown that birds use their wings not only for flight, but also when ascending steep inclines. Uphill flap-running or wing-assisted incline running (WAIR) is used by both flight-incapable fledglings and flight-capable adults to retreat to an elevated refuge. Despite the broadly varying direction of travel during WAIR, level, and descending flight, recent studies have found that the basic wing path remains relatively invariant with reference to gravity. If so, joints undergo disparate motions to maintain a consistent wing path during those specific flapping modes. The underlying skeletal motions, however, are masked by feathers and skin. To improve our understanding of the form-functional relationship of the skeletal apparatus and joint morphology with a corresponding locomotor behavior, we used XROMM (X-ray Reconstruction of Moving Morphology) to quantify 3-D skeletal kinematics in chukars (Alectoris chukar) during WAIR (ascending with legs and wings) and ascending flight (AF, ascending with wings only) along comparable trajectories. Evidence here from the wing joints demonstrates that the glenohumeral joint controls the vast majority of wing movements. More distal joints are primarily involved in modifying wing shape. All bones are in relatively similar orientations at the top of upstroke during both behaviors, but then diverge through downstroke. Total excursion of the wing is much smaller during WAIR and the tip of the manus follows a more vertical path. The WAIR stroke appears “truncated” relative to ascending flight, primarily stemming from ca. 50% reduction in humeral depression. Additionally, the elbow and wrist exhibit reduced ranges of angular excursions during WAIR. The glenohumeral joint moves in a pattern congruent with being constrained by the acrocoracohumeral ligament. Finally, we found pronounced lateral bending of the furcula during the wingbeat cycle during ascending flight only, though the phasic pattern in chukars is opposite of that observed in starlings (Sturnus vulgaris).
Evaluating the Use of Role Playing Simulations in Teaching Negotation Skills to University Students  [PDF]
John Andrew, John Meligrana
Creative Education (CE) , 2012, DOI: 10.4236/ce.2012.36104
Abstract: This paper critically evaluates the use of role-playing simulations in a negotiation course taught to graduate students. The course consisted primarily of a series of simulations involving the alternative dispute resolution (ADR) processes of negotiation, facilitation and mediation. Data were obtained from two sets of questionnaires completed by 41 students before and after the course. A review of previous research reveals that despite the widespread use of role-playing simulations in education, there has been very little empirical evaluation of their effectiveness, especially in conflict resolution and planning. Comparison of the data acquired from the two surveys generated findings regarding student understanding of ADR processes and key issues in conflict resolution; the educational value of simulations; the amenability of types of planning and planning goals to ADR; appropriate learning objectives; the importance of negotiation skills in planning; challenges in conducting effective simulations; the value of simulations in resolving real conflicts; the utility of negotiation theory; and obstacles to applying ADR to planning disputes. More generally, the paper concludes that role-playing simulations are very effective for teaching negotiation skills to students, and preparing them to manage actual conflicts skillfully and to participate effectively in real ADR processes. However, this technique is somewhat less valuable for teaching aspects of planning other than conflict resolution. Surprisingly, prior experience with simulations had no significant influence on the responses to the pre-course survey. Also surprising was the lack of a significant correlation between final exam scores and responses to relevant questions on the post-course survey.
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