Editorial: Polar genomics in a changing world

Polar regions play critical roles in the function of the Earth’s climate system, many of which are underpinned by their endemic biota. Whilst being home to some of the world’s best-known charismatic megafauna such as polar bears, whales, penguins, seals and albatrosses, polar regions also harbour some of the most poorly explored and least understood biodiversity on the planet (https://www.ipcc.ch/reports, accessed on 9 June 2023). Moreover, these regions are amongst those areas of our planet experiencing the most rapid rates of warming [1,2], resulting in severe threats to their unique ecosystems [3]. With regional warming, the organisms living in these frozen ecosystems will have to adapt if they are to survive, yet we currently have a very limited understanding of polar biodiversity, or indeed of the future resilience of polar organisms in our changing world. To generate a priori predictions of biodiversity change in these regions, it is imperative to understand the true extent of polar biodiversity, including how organisms interact (for example, in food webs), the biological mechanisms by which they have adapted to polar environments, their levels of phenotypic plasticity, and how these attributes may impact their abilities to respond to change. Critical to this understanding are “genomics” approaches that exploit the high-throughput sequencing of genetic material. With the costs of sequencing DNA and RNA having decreased dramatically over recent years, our abilities to probe the genetic code of polar organisms have expanded immeasurably, such that we are now able to answer ecological and evolutionary questions that were intractable even a few years ago, as exemplified by the contributions in this Special Issue on polar genomics

No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals

Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background. We addressed this issue in Antarctic fur seals by analysing skin swabs together with full-length MHC DQB II exon 2 sequences and data from 41 genome-wide distributed microsatellites. We did not find any effects of MHC relatedness on chemical similarity and there was also no relationship between MHC heterozygosity and chemical diversity. However, multilocus heterozygosity showed a significant positive association with chemical diversity, even after controlling for MHC heterozygosity. Our results appear to rule out a dominant role of the MHC in the chemical encoding of genetic information in a wild vertebrate population and highlight the need for genome-wide approaches to elucidate the mechanism(s) and specific genes underlying genotype-odour associations

Vortex structure in d-density wave scenario of pseudogap

We investigate the vortex structure assuming the d-density wave scenario of the pseudogap. We discuss the profiles of the order parameters in the vicinity of the vortex, effective vortex charge and the local density of states. We find a pronounced modification of these quantities when compared to a purely superconducting case. Results have been obtained for a clean system as well as in the presence of a nonmagnetic impurity. We show that the competition between superconductivity and the density wave may explain some experimental data recently obtained for high-temperature superconductors. In particular, we show that the d-density wave scenario explains the asymmetry of the gap observed in the vicinity of the vortex core.Comment: 8 pages, 10 figure

A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them

Custom genotyping arrays provide a flexible and accurate means of genotyping single nucleotide polymorphisms (SNPs) in a large number of individuals of essentially any organism. However, validation rates, defined as the proportion of putative SNPs that are verified to be polymorphic in a population, are often very low. A number of potential causes of assay failure have been identified, but none have been explored systematically. In particular, as SNPs are often developed from transcriptomes, parameters relating to the genomic context are rarely taken into account. Here, we assembled a draft Antarctic fur seal (Arctocephalus gazella) genome (assembly size: 2.41Gb; scaffold/contig N50: 3.1Mb/27.5kb). We then used this resource to map the probe sequences of 144 putative SNPs genotyped in 480 individuals. The number of probe-to-genome mappings and alignment length together explained almost a third of the variation in validation success, indicating that sequence uniqueness and proximity to intron-exon boundaries play an important role. The same pattern was found after mapping the probe sequences to the Walrus and Weddell seal genomes, suggesting that the genomes of species divergent by as much as 23 million years can hold information relevant to SNP validation outcomes. Additionally, re-analysis of genotyping data from seven previous studies found the same two variables to be significantly associated with SNP validation success across a variety of taxa. Finally, our study reveals considerable scope for validation rates to be improved, either by simply filtering for SNPs whose flanking sequences align uniquely and completely to a reference genome, or through predictive modeling

Critical Currents and Vortex States at Fractional Matching Fields in Superconductors with Periodic Pinning

We study vortex states and dynamics in 2D superconductors with periodic pinning at fractional sub-matching fields using numerical simulations. For square pinning arrays we show that ordered states form at 1/1, 1/2, and 1/4 filling fractions while only partially ordered states form at other filling fractions, such as 1/3 and 1/5, in agreement with recent imaging experiments. For triangular pinning arrays we observe matching effects at filling fractions of 1/1, 6/7, 2/3, 1/3, 1/4, 1/6, and 1/7. For both square and triangular pinning arrays we also find that, for certian sub-matching fillings, vortex configurations depend on pinning strength. For weak pinning, ordering in which a portion of the vortices are positioned between pinning sites can occur. Depinning of the vortices at the matching fields, where the vortices are ordered, is elastic while at the incommensurate fields the motion is plastic. At the incommensurate fields, as the applied driving force is increased, there can be a transition to elastic flow where the vortices move along the pinning sites in 1D channels and a reordering transition to a triangular or distorted triangular lattice. We also discuss the current-voltage curves and how they relate to the vortex ordering at commensurate and incommensurate fields.Comment: 14 figure

A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal

Evaluating how populations are connected by migration is important for understanding species resilience because gene flow can facilitate recovery from demographic declines. We therefore investigated the extent to which migration may have contributed to the global recovery of the Antarctic fur seal (Arctocephalus gazella), a circumpolar distributed marine mammal that was brought to the brink of extinction by the sealing industry in the eighteenth and nineteenth centuries. It is widely believed that animals emigrating from South Georgia, where a relict population escaped sealing, contributed to the re-establishment of formerly occupied breeding colonies across the geographical range of the species. To investigate this, we interrogated a genetic polymorphism (S291F) in the melanocortin 1 receptor gene, which is responsible for a cream-coloured phenotype that is relatively abundant at South Georgia and which appears to have recently spread to localities as far afield as Marion Island in the sub-Antarctic Indian Ocean. By sequencing a short region of this gene in 1492 pups from eight breeding colonies, we showed that S291F frequency rapidly declines with increasing geographical distance from South Georgia, consistent with locally restricted gene flow from South Georgia mainly to the South Shetland Islands and Bouvetøya. The S291F allele was not detected farther afield, suggesting that although emigrants from South Georgia may have been locally important, they are unlikely to have played a major role in the recovery of geographically more distant populations

Competing orders in a magnetic field: spin and charge order in the cuprate superconductors

We describe two-dimensional quantum spin fluctuations in a superconducting Abrikosov flux lattice induced by a magnetic field applied to a doped Mott insulator. Complete numerical solutions of a self-consistent large N theory provide detailed information on the phase diagram and on the spatial structure of the dynamic spin spectrum. Our results apply to phases with and without long-range spin density wave order and to the magnetic quantum critical point separating these phases. We discuss the relationship of our results to a number of recent neutron scattering measurements on the cuprate superconductors in the presence of an applied field. We compute the pinning of static charge order by the vortex cores in the `spin gap' phase where the spin order remains dynamically fluctuating, and argue that these results apply to recent scanning tunnelling microscopy (STM) measurements. We show that with a single typical set of values for the coupling constants, our model describes the field dependence of the elastic neutron scattering intensities, the absence of satellite Bragg peaks associated with the vortex lattice in existing neutron scattering observations, and the spatial extent of charge order in STM observations. We mention implications of our theory for NMR experiments. We also present a theoretical discussion of more exotic states that can be built out of the spin and charge order parameters, including spin nematics and phases with `exciton fractionalization'.Comment: 36 pages, 33 figures; for a popular introduction, see http://onsager.physics.yale.edu/superflow.html; (v2) Added reference to new work of Chen and Ting; (v3) reorganized presentation for improved clarity, and added new appendix on microscopic origin; (v4) final published version with minor change

A dynamic neural field approach to natural and efficient human-robot collaboration

A major challenge in modern robotics is the design of autonomous robots that are able to cooperate with people in their daily tasks in a human-like way. We address the challenge of natural human-robot interactions by using the theoretical framework of dynamic neural fields (DNFs) to develop processing architectures that are based on neuro-cognitive mechanisms supporting human joint action. By explaining the emergence of self-stabilized activity in neuronal populations, dynamic field theory provides a systematic way to endow a robot with crucial cognitive functions such as working memory, prediction and decision making . The DNF architecture for joint action is organized as a large scale network of reciprocally connected neuronal populations that encode in their firing patterns specific motor behaviors, action goals, contextual cues and shared task knowledge. Ultimately, it implements a context-dependent mapping from observed actions of the human onto adequate complementary behaviors that takes into account the inferred goal of the co-actor. We present results of flexible and fluent human-robot cooperation in a task in which the team has to assemble a toy object from its components.The present research was conducted in the context of the fp6-IST2 EU-IP Project JAST (proj. nr. 003747) and partly financed by the FCT grants POCI/V.5/A0119/2005 and CONC-REEQ/17/2001. We would like to thank Luis Louro, Emanuel Sousa, Flora Ferreira, Eliana Costa e Silva, Rui Silva and Toni Machado for their assistance during the robotic experiment

A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal

Evaluating how populations are connected by migration is important for understanding species resilience because gene flow can facilitate recovery from demographic declines. We therefore investigated the extent to which migration may have contributed to the global recovery of the Antarctic fur seal (Arctocephalus gazella), a circumpolar distributed marine mammal that was brought to the brink of extinction by the sealing industry in the eighteenth and nineteenth centuries. It is widely believed that animals emigrating from South Georgia, where a relict population escaped sealing, contributed to the re-establishment of formerly occupied breeding colonies across the geographical range of the species. To investigate this, we interrogated a genetic polymorphism (S291F) in the melanocortin 1 receptor gene, which is responsible for a cream-coloured phenotype that is relatively abundant at South Georgia and which appears to have recently spread to localities as far afield as Marion Island in the sub-Antarctic Indian Ocean. By sequencing a short region of this gene in 1492 pups from eight breeding colonies, we showed that S291F frequency rapidly declines with increasing geographical distance from South Georgia, consistent with locally restricted gene flow from South Georgia mainly to the South Shetland Islands and Bouvetøya. The S291F allele was not detected farther afield, suggesting that although emigrants from South Georgia may have been locally important, they are unlikely to have played a major role in the recovery of geographically more distant populations.J.I.H., E.B., A.J.P., E.H., L.M.B., C.K., F.C., N.K., B.F. and A.M. were funded by Deutsche Forschungsgemeinschaft (DFG) standard grant no. (HO 5122/3-1) and this research was also partly funded by the DFG as part of the SFB TRR 212 (NC3, project A01). A.C.C., C.L., K.M.K. and A.L. were funded by projects from the Norwegian Antarctic Research Expeditions. The Department of Science and Technology of South Africa provided funding through the National Research Foundation (NRF) for Marion Island research. Support for the publication fee was provided by the DFG and the Open Access Publication Funds of Bielefeld University.http://rsos.royalsocietypublishing.orgam2019Mammal Research InstituteZoology and Entomolog