Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade

Wing patterning in Heliconius butterflies is a longstanding example of both Müllerian mimicry and phenotypic radiation under strong natural selection. The loci controlling such patterns are “hotspots” for adaptive evolution with great allelic diversity across different species in the genus. We characterise nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium, and candidate gene expression at two loci and across multiple hybrid zones in Heliconius melpomene and relatives. Alleles at HmB control the presence or absence of the red forewing band, while alleles at HmYb control the yellow hindwing bar. Across HmYb two regions, separated by ∼100 kb, show significant genotype-by-phenotype associations that are replicated across independent hybrid zones. In contrast, at HmB a single peak of association indicates the likely position of functional sites at three genes, encoding a kinesin, a G-protein coupled receptor, and an mRNA splicing factor. At both HmYb and HmB there is evidence for enhanced linkage disequilibrium (LD) between associated sites separated by up to 14 kb, suggesting that multiple sites are under selection. However, there was no evidence for reduced variation or deviations from neutrality that might indicate a recent selective sweep, consistent with these alleles being relatively old. Of the three genes showing an association with the HmB locus, the kinesin shows differences in wing disc expression between races that are replicated in the co-mimic, Heliconius erato, providing striking evidence for parallel changes in gene expression between Müllerian co-mimics. Wing patterning loci in Heliconius melpomene therefore show a haplotype structure maintained by selection, but no evidence for a recent selective sweep. The complex genetic pattern contrasts with the simple genetic basis of many adaptive traits studied previously, but may provide a better model for most adaptation in natural populations that has arisen over millions rather than tens of years

Challenge clusters facing LCA in environmental decision-making—what we can learn from biofuels

Purpose Bioenergy is increasingly used to help meet greenhouse gas (GHG) and renewable energy targets. However, bioenergy’s sustainability has been questioned, resulting in increasing use of life cycle assessment (LCA). Bioenergy systems are global and complex, and market forces can result in significant changes, relevant to LCA and policy. The goal of this paper is to illustrate the complexities associated with LCA, with particular focus on bioenergy and associated policy development, so that its use can more effectively inform policymakers. Methods The review is based on the results from a series of workshops focused on bioenergy life cycle assessment. Expert submissions were compiled and categorized within the first two workshops. Over 100 issues emerged. Accounting for redundancies and close similarities in the list, this reduced to around 60 challenges, many of which are deeply interrelated. Some of these issues were then explored further at a policyfacing workshop in London, UK. The authors applied a rigorous approach to categorize the challenges identified to be at the intersection of biofuels/bioenergy LCA and policy. Results and discussion The credibility of LCA is core to its use in policy. Even LCAs that comply with ISO standards and policy and regulatory instruments leave a great deal of scope for interpretation and flexibility. Within the bioenergy sector, this has led to frustration and at times a lack of obvious direction. This paper identifies the main challenge clusters: overarching issues, application and practice and value and ethical judgments. Many of these are reflective of the transition from application of LCA to assess individual products or systems to the wider approach that is becoming more common. Uncertainty in impact assessment strongly influences planning and compliance due to challenges in assigning accountability, and communicating the inherent complexity and uncertainty within bioenergy is becoming of greater importance. Conclusions The emergence of LCA in bioenergy governance is particularly significant because other sectors are likely to transition to similar governance models. LCA is being stretched to accommodate complex and broad policy-relevant questions, seeking to incorporate externalities that have major implications for long-term sustainability. As policy increasingly relies on LCA, the strains placed on the methodology are becoming both clearer and impedimentary. The implications for energy policy, and in particular bioenergy, are large

Structure of MHC class I-like MILL2 reveals heparan-sulfate binding and interdomain flexibility

The MILL family, composed of MILL1 and MILL2, is a group of nonclassical MHC class I molecules that occur in some orders of mammals. It has been reported that mouse MILL2 is involved in wound healing; however, the molecular mechanisms remain unknown. Here, we determine the crystal structure of MILL2 at 2.15 Å resolution, revealing an organization similar to classical MHC class I. However, the α1-α2 domains are not tightly fixed on the α3-β2m domains, indicating unusual interdomain flexibility. The groove between the two helices in the α1-α2 domains is too narrow to permit ligand binding. Notably, an unusual basic patch on the α3 domain is involved in the binding to heparan sulfate which is essential for MILL2 interactions with fibroblasts. These findings suggest that MILL2 has a unique structural architecture and physiological role, with binding to heparan sulfate proteoglycans on fibroblasts possibly regulating cellular recruitment in biological events

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Water use implications of bioenergy cropping systems in Eastern England

Food and fuel security in the face of population growth and climate change represent key societal challenges. Extending an arable farm-level bio-economic optimisation model ‘MEETA’ to include dedicated energy crops (DECs) and water metrics, we quantify water use implications and trade-offs between greenhouse gas emissions, net energy and farm profitability. Drawing upon the limited available water use data for arable and energy crops applicable for East Anglia in the UK, six different farm scenarios were investigated. Profit maximisation produces a conventional crop mix, while maximising net energy and minimising greenhouse gas emissions result in crop mixes which impose financial penalties and lower water use in comparison to conventional cropping; average financial impacts of the associated reduced water use under these respective scenarios range from £0.12 to £0.28 per m3 of water. Confidence in these results and work on water use and management more generally would be improved through better data on inter-annual crop-water needs, temporal water availability relationships and water response functions. Water availability for UK crop production is largely perceived to be a non-limiting resource; however climate change predictions demonstrate that availability of water for UK crop production is of increasing concern for both farmers and society as a whole

Potential for Second Generation Biofuel Feedstock from English Arable Farms

Meeting the EU renewable fuel targets for 2020 will require a large increase in bioenergy feedstocks. To date, first generation biofuels have been the major response to meeting these targets. However, second generation biofuels from dedicated energy crops (e.g. miscanthus) or crop residues (e.g. straw) offer potential. Based on an on-farm survey of Farm Business Survey arable farmers in England and aggregated to national levels, we estimate that 5.27 Mt of cereal straw is produced annually on these farm types, of which farmers indicated that they would be willing to sell 2.5 Mt for bioenergy purposes, provided appropriate contractual conditions meet their needs. However, only 555Kt-840Kt would be obtained from straw currently incorporated into the soil. Timeliness of crop operations and benefits to soil were cited as key reasons for incorporating straw. A ‘good price’ represents the key incentive to encourage straw baling. With respect to dedicated energy crops, 81.6% (87.7%) would not consider growing miscanthus (SRC), while respectively, 17.2% (11.9%) would consider growing and 1.2% (0.4%) were currently growing these crops. Assuming 9.29% (average percentage of arable land set-aside between 1996-2005) of their utilised agricultural area to these crops, 89,900 ha (50,700 ha) of miscanthus (SRC) would be grown on English arable farms. Land quality issues, profitability and committing land for a long period of time were cited as both negative and positive reasons for farmer decisions about their level of willingness to grow these crops. Food and fuel policies must increasingly be integrated in order to meet societal goals without generating unintended consequences

Discovery of CD8+ T cell epitopes in Chlamydia trachomatis infection through use of caged class I MHC tetramers

Class I MHC tetramers allow direct phenotypic identification of CD8+ T cell populations, but their production remains laborious. A peptide exchange strategy that employs class I MHC products loaded with conditional ligands (caged MHC molecules) provides a fast and straightforward method to obtain diverse arrays of class I MHC tetramers and facilitates CD8+ T cell epitope discovery. Here, we describe the development of photocleavable analogs of the FAPGNYPAL (SV9) epitope that bind H-2Kb and H-2Db with full retention of their structural and functional integrity. We ranked all possible H-2Kb octameric and H-2Db nonameric epitopes that span the genome of Chlamydia trachomatis and prepared MHC tetramers from ≈2,000 of the highest scoring peptides by replacement of the SV9 analog with the peptide of choice. The resulting 2,000-member class I MHC tetramer array allowed the discovery of two variants of an epitope derived from polymorphic membrane protein I (PmpI) and an assessment of the kinetics of emergence and the effector function of the corresponding CD8+ T cells