Evolutionary integration and modularity in the archosaur cranium

Complex structures, like the vertebrate skull, are composed of numerous elements or traits that must develop and evolve in a coordinated manner to achieve multiple functions. The strength of association among phenotypic traits (i.e., integration), and their organization into highly-correlated, semi-independent subunits termed modules, is a result of the pleiotropic and genetic correlations that generate traits. As such, patterns of integration and modularity are thought to be key factors constraining or facilitating the evolution of phenotypic disparity by influencing the patterns of variation upon which selection can act. It is often hypothesized that selection can reshape patterns of integration, parceling single structures into multiple modules or merging ancestrally semi-independent traits into a strongly correlated unit. However, evolutionary shifts in patterns of trait integration are seldom assessed in a unified quantitative framework. Here, we quantify patterns of evolutionary integration among regions of the archosaur skull to investigate whether patterns of cranial integration are conserved or variable across this diverse group. Using high-dimensional geometric morphometric data from 3D surface scans and CT scans of modern birds (n = 352), fossil non-avian dinosaurs (n = 27), and modern and fossil mesoeucrocodylians (n = 38), we demonstrate that some aspects of cranial integration are conserved across these taxonomic groups, despite their major differences in cranial form, function, and development. All three groups are highly modular and consistently exhibit high integration within the occipital region. However, there are also substantial divergences in correlation patterns. Birds uniquely exhibit high correlation between the pterygoid and quadrate, components of the cranial kinesis apparatus, whereas the non-avian dinosaur quadrate is more closely associated with the jugal and quadratojugal. Mesoeucrocodylians exhibit a slightly more integrated facial skeleton overall than the other grades. Overall, patterns of trait integration are shown to be stable among archosaurs, which is surprising given the cranial diversity exhibited by the clade. At the same time, evolutionary innovations such as cranial kinesis that reorganize the structure and function of complex traits can result in modifications of trait correlations and modularity

Forum. Stratigraphic Fit to Phylogenies: A Proposed Solution

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73634/1/j.1096-0031.1998.tb00333.x.pd

Parsing and reflective printing, bidirectionally

Language designers usually need to implement parsers and printers. Despite being two intimately related programs, in practice they are often designed separately, and then need to be revised and kept consistent as the language evolves. It will be more convenient if the parser and printer can be unified and developed in one single program, with their consistency guaranteed automatically.Furthermore, in certain scenarios (like showing compiler optimisation results to the programmer), it is desirable to have a more powerful reflective printer that, when an abstract syntax tree corresponding to a piece of program text is modified, can reflect the modification to the program text while preserving layouts, comments, and syntactic sugar.To address these needs, we propose a domain-specific language BIYACC, whose programs denote both a parser and a reflective printer for an unambiguous context-free grammar. BIYACC is based on the theory of bidirectional transformations, which helps to guarantee by construction that the pairs of parsers and reflective printers generated by BIYACC are consistent. We show that BIYACC is capable of facilitating many tasks such as Pombrio and Krishnamurthi's "resugaring", simple refactoring, and language evolution.We would like to thank reviewers for their valuable comments. This work was partially supported by the Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Scientific Research (A) No. 25240009

W(h)ither Fossils? Studying Morphological Character Evolution in the Age of Molecular Sequences

A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these phylogenetic hypotheses be effectively applied to the study of morphological character evolution. At least two analytical approaches to solving this problem have been utilized: (1) simultaneous analysis of molecular sequence and morphological data with fossil taxa included as terminals in the analysis, and (2) the molecular scaffold approach, in which morphological data are analyzed over a molecular backbone (with constraints that force extant taxa into positions suggested by sequence data). The perceived obstacles to including fossil taxa directly in simultaneous analyses of morphological and molecular sequence data with extant taxa include: (1) that fossil taxa are missing the molecular sequence portion of the character data; (2) that morphological characters might be misleading due to convergence; and (3) character weighting, specifically how and whether to weight characters in the morphological partition relative to characters in the molecular sequence data partition. The molecular scaffold has been put forward as a potential solution to at least some of these problems. Using examples of simultaneous analyses from the literature, as well as new analyses of previously published morphological and molecular sequence data matrices for extant and fossil Chiroptera (bats), we argue that the simultaneous analysis approach is superior to the molecular scaffold approach, specifically addressing the problems to which the molecular scaffold has been suggested as a solution. Finally, the application of phylogenetic hypotheses including fossil taxa (whatever their derivation) to the study of morphological character evolution is discussed, with special emphasis on scenarios in which fossil taxa are likely to be most enlightening: (1) in determining the sequence of character evolution; (2) in determining the timing of character evolution; and (3) in making inferences about the presence or absence of characteristics in fossil taxa that may not be directly observable in the fossil record. Published By: Missouri Botanical Garde

Parametricity and Dependent Types

Reynolds' abstraction theorem shows how a typing judgement in System F can be translated into a relational statement (in second order predicate logic) about inhabitants of the type. We (in second order predicate logic) about inhabitants of the type. We obtain a similar result for a single lambda calculus (a pure type system), in which terms, types and their relations are expressed. Working within a single system dispenses with the need for an interpretation layer, allowing for an unusually simple presentation. While the unification puts some constraints on the type system (which we spell out), the result applies to many interesting cases, including dependently-typed ones

The nature of frontier orbitals under systematic ligand exchange in pseudo octahedral Fe II complexes

Understanding and controlling properties of transition metal complexes is a crucial step towards tailoring materials for sustainable energy applications. In a systematic approach, we use resonant inelastic X ray scattering to study the influence of ligand substitution on the valence electronic structure around an aqueous iron II center. Exchanging cyanide with 2 20 bipyridine ligands reshapes frontier orbitals in a way that reduces metal 3d charge delocalization onto the ligands. This net decrease of metal ligand covalency results in lower metal centered excited state energies in agreement with previously reported excited state dynamics. Furthermore, traces of solvent effects were found indicating a varying interaction strength of the solvent with ligands of different character. Our results demonstrate how ligand exchange can be exploited to shape frontier orbitals of transition metal complexes in solution phase chemistry; insights upon which future efforts can built when tailoring the functionality of photoactive systems for light harvesting application