Symmetry witnesses

A symmetry witness is a suitable subset of the space of selfadjoint trace class operators that allows one to determine whether a linear map is a symmetry transformation, in the sense of Wigner. More precisely, such a set is invariant with respect to an injective densely defined linear operator in the Banach space of selfadjoint trace class operators (if and) only if this operator is a symmetry transformation. According to a linear version of Wigner's theorem, the set of pure states, the rank-one projections, is a symmetry witness. We show that an analogous result holds for the set of projections with a fixed rank (with some mild constraint on this rank, in the finite-dimensional case). It turns out that this result provides a complete classification of the set of projections with a fixed rank that are symmetry witnesses. These particular symmetry witnesses are projectable; i.e., reasoning in terms of quantum states, the sets of uniform density operators of corresponding fixed rank are symmetry witnesses too.Comment: 15 page

The genome sequence of the silver-studded blue, Plebejus argus (Linnaeus, 1758)

We present a genome assembly from an individual male Plebejus argus (silver-studded blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 382 megabases in span. The entire assembly (100%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 27.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,693 protein coding genes.This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194, https://doi.org/10.35802/206194) and the Darwin Tree of Life Discretionary Award (218328, https://doi.org/10.35802/218328). AH is supported by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/N020146/1). KL and DL are supported by an ERC grant (ModelGenomLand 757648) which also supported the fieldwork. KL was also supported by a NERC fellowship (NE/L011522/1). RV is supported by Grant PID2019-107078GB-I00 funded by Ministerio de Ciencia e Innovación and Agencia Estatal de Investigación (MCIN/AEI/10.13039/ 501100011033).Peer reviewe

Massive encapsulation of larval Anguillicoloides crassus in the intestinal wall of Japanese eels

<p>Abstract</p> <p>Background</p> <p>Within the last 25 years, after the introduction of the swimbladder nematode <it>Anguillicoloides </it>crassus from East-Asia to Europe, a body of work has aggregated on the host parasite interactions in the acquired host <it>Anguilla anguilla</it>. Despite the emerging evolutionary interest there is still a lack of knowledge about host parasite relations of <it>A. crassus </it>in its natural host <it>Anguilla japonica</it>. We examined the <it>Anguillicoloides </it>infections of wild-caught Japanese eels as well as from aquacultured specimens in Taiwan with respect to the fate of migratory L3 larvae and performed infection experiments with Japanese eels.</p> <p>Results</p> <p>Inside the intestinal wall of cultured eels, where the infective pressure was higher than among wild eels, we found large numbers of granuloma-like cysts. In a few eels these cysts contained nematodes still recognizable as L3 larvae of <it>A. crassus</it>, while in most cases the content of these capsules was degraded to amorphous matter. Occurrence of these objects was correlated with the number of encapsulated larvae in the swimbladder wall. We were able to show, that the cysts contained disintegrated L3 larvae by amplification and subsequent sequencing of large subunit ribosomal rRNA. Furthermore we identified repeated infections with high doses of larvae as prerequisites for the processes of encapsulation in infection experiments.</p> <p>Conclusion</p> <p>Under high infective pressure a large percentage of L3 larvae of <it>A. crassus </it>coming from the gut lumen are eliminated by the natural host within its intestinal tissue. It is possible to reproduce this condition in infection experiments. We provide a fast, easy and reliable PCR-based method for identification of encapsulated swimbladder parasites.</p

The phylogenetics of Anguillicolidae (Nematoda: Anguillicolidea), swimbladder parasites of eels

BACKGROUND: Anguillicolidae Yamaguti, 1935 is a family of parasitic nematode infecting fresh-water eels of the genus Anguilla, comprising five species in the genera Anguillicola and Anguillicoloides. Anguillicoloides crassus is of particular importance, as it has recently spread from its endemic range in the Eastern Pacific to Europe and North America, where it poses a significant threat to new, naïve hosts such as the economic important eel species Anguilla anguilla and Anguilla rostrata. The Anguillicolidae are therefore all potentially invasive taxa, but the relationships of the described species remain unclear. Anguillicolidae is part of Spirurina, a diverse clade made up of only animal parasites, but placement of the family within Spirurina is based on limited data. RESULTS: We generated an extensive DNA sequence dataset from three loci (the 5' one-third of the nuclear small subunit ribosomal RNA, the D2-D3 region of the nuclear large subunit ribosomal RNA and the 5' half of the mitochondrial cytochrome c oxidase I gene) for the five species of Anguillicolidae and used this to investigate specific and generic boundaries within the family, and the relationship of Anguillicolidae to other spirurine nematodes. Neither nuclear nor mitochondrial sequences supported monophyly of Anguillicoloides. Genetic diversity within the African species Anguillicoloides papernai was suggestive of cryptic taxa, as was the finding of distinct lineages of Anguillicoloides novaezelandiae in New Zealand and Tasmania. Phylogenetic analysis of the Spirurina grouped the Anguillicolidae together with members of the Gnathostomatidae and Seuratidae. CONCLUSIONS: The Anguillicolidae is part of a complex radiation of parasitic nematodes of vertebrates with wide host diversity (chondrichthyes, teleosts, squamates and mammals), most closely related to other marine vertebrate parasites that also have complex life cycles. Molecular analyses do not support the recent division of Anguillicolidae into two genera. The described species may hide cryptic taxa, identified here by DNA taxonomy, and this DNA barcoding approach may assist in tracking species invasions. The propensity for host switching, and thus the potential for invasive behaviour, is found in A. crassus, A. novaezelandiae and A. papernai, and thus may be common to the group

Demographically explicit scans for barriers to gene flow using gIMble

Identifying regions of the genome that act as barriers to gene flow between recently diverged taxa has remained challenging given the many evolutionary forces that generate variation in genetic diversity and divergence along the genome, and the stochastic nature of this variation. Progress has been impeded by a conceptual and methodological divide between analyses that infer the demographic history of speciation and genome scans aimed at identifying locally maladaptive alleles i.e. genomic barriers to gene flow. Here we implement genomewide IM blockwise likelihood estimation (), a composite likelihood approach for the quantification of barriers, that bridges this divide. This analytic framework captures background selection and selection against barriers in a model of isolation with migration (IM) as heterogeneity in effective population size (N$_{e}$) and effective migration rate (m$_{e}$), respectively. Variation in both effective demographic parameters is estimated in sliding windows via pre-computed likelihood grids. includes modules for pre-processing/filtering of genomic data and performing parametric bootstraps using coalescent simulations. To demonstrate the new approach, we analyse data from a well-studied pair of sister species of tropical butterflies with a known history of post-divergence gene flow: Heliconius melpomene and H. cydno. Our analyses uncover both large-effect barrier loci (including well-known wing-pattern genes) and a genome-wide signal of a polygenic barrier architecture

Chromosome fissions and fusions act as barriers to gene flow between Brenthis fritillary butterflies

Includes supplementary materials for the online appendix.Chromosome rearrangements are thought to promote reproductive isolation between incipient species. However, it is unclear how often, and under what conditions, fission and fusion rearrangements act as barriers to gene flow. Here we investigate speciation between two largely sympatric fritillary butterflies, Brenthis daphne and Brenthis ino. We use a composite likelihood approach to infer the demographic history of these species from whole-genome sequence data. We then compare chromosome-level genome assemblies of individuals from each species and identify a total of nine chromosome fissions and fusions. Finally, we fit a demographic model where effective population sizes and effective migration rate vary across the genome, allowing us to quantify the effects of chromosome rearrangements on reproductive isolation. We show that chromosomes involved in rearrangements experienced less effective migration since the onset of species divergence and that genomic regions near rearrangement points have a further reduction in effective migration rate. Our results suggest that the evolution of multiple rearrangements in the B. daphne and B. ino populations, including alternative fusions of the same chromosomes, have resulted in a reduction in gene flow. Although fission and fusion of chromosomes are unlikely to be the only processes that have led to speciation between these butterflies, this study shows that these rearrangements can directly promote reproductive isolation and may be involved in speciation when karyotypes evolve quickly.We would like to thank Marian Thompson and Robert Foster (both Edinburgh Genomics) for preparing Pacbio and HiC sequencing libraries and Katy MacDonald for help in the molecular lab. We also thank Maria Jesus Cañal Villanueva and Luis Valledor (Universidad de Orviedo) for help with fieldwork logistics, as well as Vlad Dincă, Raluca Vodă, and Sabina Vila for contributing samples. We would like to thank Staffan Bensch and Deborah Charlesworth for insightful comments on an earlier version of the manuscript and Sam Ebdon for helping to improve figure 1. A.M. is supported by an E4 PhD studentship from the Natural Environment Research Council (NE/S007407/1). K.L. is supported by a fellowship from the Natural Environment Research Council (NERC, NE/L011522/1). R.V. is supported by Grant PID2019-107078GB-I00 funded by Ministerio de Ciencia e Innovación and Agencia Estatal de Investigación (MCIN/AEI/10.13039/501100011033). S.H.M. is supported by a Royal Society University Research Fellowship (URF/R1/180682). This work was supported by a European Research Council starting grant (ModelGenomLand 757648) to K.L. and a David Phillips Fellowship (BB/N020146/1) by the Biotechnology and Biological Sciences Research Council (BBSRC) to A.H