Ilik J. Saccheri

Summary: The extent to which adaptation to environmental change occurs via single or multiple advantageous mutations remains an open question, which we examined by studying the spread of melanic forms of the peppered moth in Britain and continental Europe, in response to industrial coal pollution. In Britain, the darkest melanic form is due to the insertion of a transposable element ( carb-TE ) into a genomic region called ivory . Here, we characterize the spread of melanic forms in continental Europe from historical records and uncover the genetic basis of European melanism using genomic analyses of modern and museum specimens. We show that European melanism is also associated with variants at ivory , but with multiple alleles featuring structural variants, including several transposable elements, though not carb-TE . The primary central European melanic allele is a genetically dominant 805 base pair deletion ( sollichau ). Interestingly, melanic individuals with either sollichau (deletion) or carb-TE (insertion) alleles show elevated expression of ivory and its effector micro-RNA ( mir-193 ) compared to non-melanic ( typica ) individuals, suggesting that contrasting structural variants in ivory have similar regulatory effects. A functional role for sollichau was corroborated, serendipitously, by its presence in a typica individual which also contains a linked deletion of mir-193 , which is predicted to cancel the melanizing effect of the sollichau deletion. Our results support the idea that there can be many genetic origins of the same adaptive trait within a species, particularly one with a large effective population size and heterogeneous natural habitat, and when many mutations can give rise to the same phenotype.

Genetic factors can have a major influence on both short‐ and long‐term success of reintroductions. Genomic monitoring can give a range of insights into the early life of a reintroduced population and ultimately can help to avoid wasting limited conservation resources. In this study, we characterise the genetic diversity of a reintroduced Carterocephalus palaemon (Chequered Skipper butterfly) population in England with respect to the spatial genetic structure and diversity of the source populations in south Belgium. We aim to evaluate the success of the reintroduction, including the effectiveness of the donor sampling strategy, and assess genetic vulnerabilities that may affect the population's future. We also use an isolation‐by‐distance approach to make quantitative inferences about dispersal, and we explore covariance between host mitochondrial and Wolbachia genomes. We find that, four generations following the initial release, the reintroduced population, founded by 66 wild‐caught adults, has an effective size of c. 33, yet has retained similar levels of genomic heterozygosity to those in the source subpopulations in Belgium and shows low levels of inbreeding. However, the restricted number of founders and variance in reproductive success among the surviving families have resulted in a higher level of kinship, likely to result in somewhat higher rates of inbreeding in the future. Furthermore, there is a distinct split between two source landscapes in Belgium, and all genomic evidence suggests that the reintroduced population is descended from only one of these landscapes (called Fagne). We discuss potential causes behind these results, including whether Wolbachia strains are causing genetic incompatibility between clades. We conclude that a conservative strategy for any further translocations would prefer Fagne sites as sources because of the strong evidence of their ability to survive. However, our results warrant further investigation into the reasons for the divergence found in Belgium.

Nature has devised many ways of producing males and females. Here, we report on a previously undescribed mechanism for Lepidoptera that functions without a female-specific gene. The number of alleles or allele heterozygosity in a single Z-linked gene ( BaMasc ) is the primary sex-determining switch in Bicyclus anynana butterflies. Embryos carrying a single BaMasc allele develop into WZ (or Z0) females, those carrying two distinct alleles develop into ZZ males, while (ZZ) homozygotes initiate female development, have mismatched dosage compensation, and die as embryos. Consequently, selection against homozygotes has favored the evolution of spectacular allelic diversity: 205 different coding sequences of BaMasc were detected in a sample of 246 females. The structural similarity of a hypervariable region (HVR) in BaMasc to the HVR in Apis mellifera csd suggests molecular convergence between deeply diverged insect lineages. Our discovery of this primary switch highlights the fascinating diversity of sex-determining mechanisms and underlying evolutionary drivers.

We present a genome assembly from an individual female Miltochrista miniata (the Rosy Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 1057.0 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.93 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,879 protein coding genes.

We present a genome assembly from an individual female Hipparchia semele (the Rock Grayling; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 403.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,540 protein coding genes.

We present a genome assembly from an individual male Carterocephalus palaemon (the Arctic Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 394.5 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.78 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,032 protein coding genes.

We present a genome assembly from an individual female Bicyclus anynana (the Squinting Bush Brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 457.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length.

We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.

The assembly of divergent haplotypes using noisy long-read data presents a challenge to the reconstruction of haploid genome assemblies, due to overlapping distributions of technical sequencing error, intralocus genetic variation, and interlocus similarity within these data. Here, we present a comparative analysis of assembly algorithms representing overlap-layout-consensus, repeat graph, and de Bruijn graph methods. We examine how postprocessing strategies attempting to reduce redundant heterozygosity interact with the choice of initial assembly algorithm and ultimately produce a series of chromosome-level assemblies for an agricultural pest, the diamondback moth, Plutella xylostella (L.). We compare evaluation methods and show that BUSCO analyses may overestimate haplotig removal processing in long-read draft genomes, in comparison to a k-mer method. We discuss the trade-offs inherent in assembly algorithm and curation choices and suggest that “best practice” is research question dependent. We demonstrate a link between allelic divergence and allele-derived contig redundancy in final genome assemblies and document the patterns of coding and noncoding diversity between redundant sequences. We also document a link between an excess of nonsynonymous polymorphism and haplotigs that are unresolved by assembly or postassembly algorithms. Finally, we discuss how this phenomenon may have relevance for the usage of noisy long-read genome assemblies in comparative genomics.

We present a genome assembly based on an individual female Aphantopus hyperantus, also known as Maniola hyperantus (the ringlet butterfly; Arthropoda; Insecta; Lepidoptera, Nymphalidae), scaffolded using data from a second, unrelated specimen. The genome sequence is 411 megabases in span. The majority of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the Z sex chromosome.