Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher.
Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?
Some links on this page may take you to non-federal websites. Their policies may differ from this site.
-
Nielsen, Rasmus (Ed.)
Abstract An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.
-
The hallmark of highly frustrated systems is the presence of many states close in energy to the ground state. Fluctuations between these states can preclude the emergence of any form of order and lead to the appearance of spin liquids. Even on the classical level, spin liquids are not all alike: they may have algebraic or exponential correlation decay, and various forms of long wavelength description, including vector or tensor gauge theories. Here, we introduce a classification scheme, allowing us to fit the diversity of classical spin liquids (CSLs) into a general framework as well as predict and construct new kinds. CSLs with either algebraic or exponential correlation-decay can be classified via the properties of the bottom flat band(s) in their soft-spin Hamiltonians. The classification of the former is based on the algebraic structures of gapless points in the spectra, which relate directly to the emergent generalized Gauss's laws that control the low temperature physics. The second category of CSLs, meanwhile, are classified by the fragile topology of the gapped bottom band(s). Utilizing the classification scheme we construct new models realizing exotic CSLs, including one with anisotropic generalized Gauss's laws and charges with subdimensional mobility, one with a network of pinch-line singularities in its correlation functions, and a series of fragile topological CSLs connected by zero-temperature transitions.more » « less
-
Classical spin liquids (CSL) lack long-range magnetic order and are characterized by an extensive ground state degeneracy. We propose a classification scheme of CSLs based on the structure of the flat bands of their Hamiltonians. Depending on absence or presence of the gap from the flat band, the CSL are classified as algebraic or fragile topological, respectively. Each category is further classified: the algebraic case by the nature of the emergent Gauss's law at the gap-closing point(s), and the fragile topological case by the homotopy of the eigenvector winding around the Brillouin zone. Previously identified instances of CSLs fit snugly into our scheme, which finds a landscape where algebraic CSLs are located at transitions between fragile topological ones. It also allows us to present a new, simple family of models illustrating that landscape, which hosts both fragile topological and algebraic CSLs, as well as transitions between themmore » « less
-
Electronic spins can form long-range entangled phases of condensed matter named quantum spin liquids. Their existence is conceptualized in models of two- or three-dimensional frustrated magnets that evade symmetry-breaking order down to zero temperature. Quantum spin ice (QSI) is a theoretically well-established example described by an emergent quantum electrodynamics, with excitations behaving like photon and matter quasiparticles. The latter are fractionally charged and equivalent to the `spinons' emerging from coherent phases of singlets in one dimension, where clear experimental proofs of fractionalization exist. However, in frustrated magnets it remains difficult to establish consensual evidence for quantum spin liquid ground states and their fractional excitations. Here, we use backscattering neutron spectroscopy to achieve extremely high resolution of the time-dependent magnetic response of the candidate QSI material Ce2Sn2O7. We find a gapped spectrum featuring a threshold and peaks that match theories for pair production and propagation of fractional matter excitations (spinons) strongly coupled to a background gauge field. The observed peaks provide evidence for a QSI through spectroscopic signatures of space-time symmetry fractionalization, while the threshold behavior corroborates the regime of strong light-matter interaction predicted for the emergent universe in a QSI.more » « less
-
We investigate the correlated state of Ce2Hf2O7 using neutron scattering, finding signatures of correlations of both dipolar and octupolar character. A dipolar inelastic signal is also observed, as expected for spinons in a quantum spin ice (QSI). Fits of thermodynamic data using exact diagonalization methods indicate that the largest interaction is an octupolar exchange, with a strength roughly twice as large as other terms. This hierarchy of exchange interactions - far from a perturbative regime but still in the octupolar QSI phase - rationalises observations in neutron scattering, which illustrate the multipolar nature of degrees of freedom in Ce3+ pyrochlores.more » « less