Tight Genetic Linkage Research Articles

Genetic Coupling of Mate Recognition Systems in the Genomic Era.

The concept of "genetic coupling" in mate recognition systems arose in the 1960s as a potential mechanism to maintain coordination between signals and receivers during evolutionary divergence. At its most basic it proposed that the same genes might influence trait and preference, and therefore mutations could result in coordinated changes in both traits. Since then, the concept has expanded in scope and is often used to include linkage or genetic correlation between recognition system components. Here we review evidence for genetic coupling, concentrating on proposed examples of a common genetic basis for signals and preferences. Mapping studies have identified several examples of tight genetic linkage between genomic regions influencing signals and preferences, or assortative mating. Whether this extends as far as demonstrating pleiotropy remains a more open question. Some studies, notably of Drosophila, have identified genes in the sex determination pathway and in pheromonal communication where single loci can influence both signals and preferences. This may be based on isoform divergence, in which sex- and tissue-specific effects are facilitated by alternative spicing, or on regulatory divergence. Hence it is not clear that such examples provide compelling evidence of pleiotropy in the sense that "magic mutations" could maintain trait coordination. Rather, coevolution may be facilitated by regulatory divergence but require different mutations or coevolution across isoforms. Reconsidering the logic of genetic coupling, it may be that pleiotropy could actually be less effective than linkage if distinct but associated variants allow molecular coevolution to occur more readily than potentially "unbalanced" mutations in single genes. Genetic manipulation or studies of mutation order effects during divergence are challenging but perhaps the only way to disentangle the role of pleiotropy versus close linkage in coordinated trait divergence.

Divergent amplifications of CYP9A cytochrome P450 genes provide two noctuid pests with differential protection against xenobiotics

Here, we provide mechanistic support for the involvement of the CYP9A subfamily of cytochrome P450 monooxygenases in the detoxification of host plant defense compounds and chemical insecticides in Spodoptera exigua and Spodoptera frugiperda. Our comparative genomics shows that a large cluster of CYP9A genes occurs in the two species but with significant differences in its contents, including several species-specific duplicates and substantial sequence divergence, both between orthologs and between duplicates. Bioassays of CRISPR-Cas9 knockouts of the clusters show that, collectively, the CYP9As can detoxify two furanocoumarin plant defense compounds (imperatorin and xanthotoxin) and insecticides representing three different chemotypes (pyrethroids, avermectins, and oxadiazines). However, in vitro metabolic assays of heterologously expressed products of individual genes show several differences between the species in the particular CYP9As with activities against these compounds. We also find that the clusters show tight genetic linkage with high levels of pyrethroid resistance in field strains of the two species. We propose that their divergent amplifications of the CYP9A subfamily have not only contributed to the development of the broad host ranges of these species over long evolutionary timeframes but also supplied them with diverse genetic options for evolving resistance to chemical insecticides in the very recent past.

Tight genetic linkage of genes causing hybrid necrosis and pollinator isolation between young species

The mechanisms of reproductive isolation that cause phenotypic diversification and eventually speciation are a major topic of evolutionary research. Hybrid necrosis is a post-zygotic isolation mechanism in which cell death develops in the absence of pathogens. It is often due to the incompatibility between proteins from two parents. Here we describe a unique case of hybrid necrosis due to an incompatibility between loci on chromosomes 2 and 7 between two pollinator-isolated Petunia species. Typical immune responses as well as endoplasmic reticulum stress responses are induced in the necrotic line. The locus on chromosome 2 encodes ChiA1, a bifunctional GH18 chitinase/lysozyme. The enzymatic activity of ChiA1 is dispensable for the development of necrosis. We propose that the extremely high expression of ChiA1 involves a positive feedback loop between the loci on chromosomes 2 and 7. ChiA1 is tightly linked to major genes involved in the adaptation to different pollinators, a form of pre-zygotic isolation. This linkage of pre- and post-zygotic barriers strengthens reproductive isolation and probably contributes to rapid diversification and speciation.

Breaking the tight genetic linkage between the a1 and sh2 genes led to the development of anthocyanin-rich purple-pericarp super-sweetcorn

The existence of purple-pericarp super-sweetcorn based on the supersweet mutation, shrunken2 (sh2), has not been previously reported, due to its extremely tight genetic linkage to a non-functional anthocyanin biosynthesis gene, anthocyaninless1 (a1). Generally, pericarp-pigmented starchy purple corn contains significantly higher anthocyanin. The development of purple-pericarp super-sweetcorn is dependent on breaking the a1–sh2 tight genetic linkage, which occurs at a very low frequency of < 1 in 1000 meiotic crossovers. Here, to develop purple-pericarp super-sweetcorn, an initial cross between a male purple-pericarp maize, ‘Costa Rica’ (A1Sh2.A1Sh2) and a female white shrunken2 super-sweetcorn, ‘Tims-white’ (a1sh2.a1sh2), was conducted. Subsequent self-pollination based on purple-pericarp-shrunken kernels identified a small frequency (0.08%) of initial heterozygous F3 segregants (A1a1.sh2sh2) producing a fully sh2 cob with a purple-pericarp phenotype, enabled by breaking the close genetic linkage between the a1 and sh2 genes. Resulting rounds of self-pollination generated a F6 homozygous purple-pericarp super-sweetcorn (A1A1.sh2sh2) line, ‘Tim1’. Genome sequencing revealed a recombination break between the a1 and yz1 genes of the a1–yz1-x1–sh2 multigenic interval. The novel purple-pericarp super-sweetcorn produced a similar concentration of anthocyanin and sugar as in its purple-pericarp maize and white super-sweetcorn parents, respectively, potentially adding a broader range of health benefits than currently exists with standard yellow/white sweetcorn.

Post-translational regulation and proteolytic activity of the metalloproteinase ADAMTS8

A disintegrin-like and metalloprotease domain with thrombospondin type 1 motifs (ADAMTS)8 is a secreted protease, which was recently implicated in pathogenesis of pulmonary arterial hypertension (PAH). However, the substrate repertoire of ADAMTS8 and regulation of its activity are incompletely understood. Although considered a proteoglycanase because of high sequence similarity and close phylogenetic relationship to the proteoglycan-degrading proteases ADAMTS1, 4, 5, and 15, as well as tight genetic linkage with ADAMTS15 on human chromosome 11, its aggrecanase activity was reportedly weak. Several post-translational factors are known to regulate ADAMTS proteases such as autolysis, inhibition by endogenous inhibitors, and receptor-mediated endocytosis, but their impacts on ADAMTS8 are unknown. Here, we show that ADAMTS8 undergoes autolysis at six different sites within its spacer domain. We also found that in contrast to ADAMTS4 and 5, ADAMTS8 levels were not regulated through low-density lipoprotein receptor-related protein 1 (LRP1)-mediated endocytosis. Additionally, ADAMTS8 lacked significant activity against the proteoglycans aggrecan, versican, and biglycan. Instead, we found that ADAMTS8 cleaved osteopontin, a phosphoprotein whose expression is upregulated in PAH. Multiple ADAMTS8 cleavage sites were identified using liquid chromatography–tandem mass spectrometry. Osteopontin cleavage by ADAMTS8 was efficiently inhibited by TIMP-3, an endogenous inhibitor of ADAMTS1, 4, and 5, as well as by TIMP-2, which has no previously reported inhibitory activity against other ADAMTS proteases. These differences in post-translational regulation and substrate repertoire differentiate ADAMTS8 from other family members and may help to elucidate its role in PAH.

High-temperature wheat leaf rust resistance gene Lr13 exhibits pleiotropic effects on hybrid necrosis

High-temperature wheat leaf rust resistance gene Lr13 exhibits pleiotropic effects on hybrid necrosis

Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm

BackgroundThe process of speciation involves differentiation of whole genome sequences between a pair of diverging taxa. In the absence of a geographic barrier and in the presence of gene flow, genomic differentiation may occur when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host–plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that genomic differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for genomic differentiation in the fall armyworm.ResultsThese two strains exhibit a low level of genomic differentiation (FST = 0.0174), while 99.2% of 200 kb windows have genetically differentiated sequences (FST > 0). We found that the combined effect of mild positive selection and genetic linkage to selectively targeted loci are responsible for the genomic differentiation. However, a single event of very strong positive selection appears not to be responsible for genomic differentiation. The contribution of chromosomal inversions or tight genetic linkage among positively selected loci causing reproductive barriers is not supported by our data. Phylogenetic analysis shows that the genomic differentiation occurred by sub-setting of genetic variants in one strain from the other.ConclusionsFrom these results, we concluded that genomic differentiation may occur at the early stage of a speciation process in the fall armyworm and that mild positive selection targeting many loci alone is sufficient evolutionary force for generating the pattern of genomic differentiation. This genomic differentiation may provide a condition for accelerated genomic differentiation by synergistic effects among linkage disequilibrium generated by following events of positive selection. Our study highlights genomic differentiation as a key evolutionary factor connecting positive selection to divergent selection.

Adaptation via pleiotropy and linkage: Association mapping reveals a complex genetic architecture within the stickleback Eda locus.

Genomic mapping of the loci associated with phenotypic evolution has revealed genomic “hotspots,” or regions of the genome that control multiple phenotypic traits. This clustering of loci has important implications for the speed and maintenance of adaptation and could be due to pleiotropic effects of a single mutation or tight genetic linkage of multiple causative mutations affecting different traits. The threespine stickleback (Gasterosteus aculeatus) is a powerful model for the study of adaptive evolution because the marine ecotype has repeatedly adapted to freshwater environments across the northern hemisphere in the last 12,000 years. Freshwater ecotypes have repeatedly fixed a 16 kilobase haplotype on chromosome IV that contains Ectodysplasin (Eda), a gene known to affect multiple traits, including defensive armor plates, lateral line sensory hair cells, and schooling behavior. Many additional traits have previously been mapped to a larger region of chromosome IV that encompasses the Eda freshwater haplotype. To identify which of these traits specifically map to this adaptive haplotype, we made crosses of rare marine fish heterozygous for the freshwater haplotype in an otherwise marine genetic background. Further, we performed fine‐scale association mapping in a fully interbreeding, polymorphic population of freshwater stickleback to disentangle the effects of pleiotropy and linkage on the phenotypes affected by this haplotype. Although we find evidence that linked mutations have small effects on a few phenotypes, a small 1.4‐kb region within the first intron of Eda has large effects on three phenotypic traits: lateral plate count, and both the number and patterning of the posterior lateral line neuromasts. Thus, the Eda haplotype is a hotspot of adaptation in stickleback due to both a small, pleiotropic region affecting multiple traits as well as multiple linked mutations affecting additional traits.

MiR156f integrates panicle architecture through genetic modulation of branch number and pedicel length pathways

BackgroundRice (Oryza sativa) panicle architecture is the major determinant of the ideal plant architecture that directly influence yield potential. Many genes influencing development of primary branches, secondary branches, spikelet and pedicel would also influence panicle architecture, which is thus a complex trait regulated by genes from various aspects. miR156, an extensively studied miRNA, has recently emerged as promising target for crop improvement because of its role in plant architecture regulation, such as the number of tillers, plant height and the panicle architecture. Increasing evidence suggests that miR156 might play an important role in panicle architecture regulation.Main bodyTo study the detailed function of miR156 in rice panicle architecture regulation, we examined the genetic interaction or transcriptional regulation of miR156/OsSPL to other panicle regulating genes. Our results revealed that expression of many panicle related genes were influenced by miR156. Through biochemical analysis, we further proved that miR156 directly regulated the axillary meristem regulating gene, LAX1, at the transcription level. And the intimate relations between miR156 and LAX1, and miR156 and LAX2 were also uncovered by genetic analysis. On the other hand, a tight genetic linkage between miR156 and RCN2, the panicle branch promoting gene, was also detected, which suggested a buffering mechanism for the miR156 mediated panicle architecture regulation. Furthermore, genetic analysis also demonstrated that miR156 functioned in the same pathway with OsRA2 to regulate pedicel length.Short conclusionAltogether, miR156 integrates several genetic pathways mediated by genes such as LAX1, LAX2, RCN2 and OsRA2, and comprehensively regulates panicle development in rice. Based on these analysis, we concluded that miR156 acts as an important regulator for panicle architecture through influencing various aspects of panicle development.

Genetic Diversity of Three Indigenous Cattle Breeds Reared in Benin

Livestock production is an important component of the Benin economy contributing an upward of 25% of the agricultural Gross Domestic Products (GDP). Indigenoues cattle sector contributes more to the GDP compared to other livestock species. Despite the economic role played by the sector, there has been little or no efforts to genetically improve the indigenous cattle in the country. Recently, the government and other development partners have embarked on projects to improve the sector performance. The first step would be to morphologically and genetically characterize the cattle populations so as to match them with the available resources for optimal conservation and utilization. There exist no genetic diversity information for the different cattle types in Benin. The objective of this study was thus to determine the genetic diversity of the three most abundant indigenous cattle types. A total of 86 cattle from all three breeds were genotyped at the 14 loci. High levels of allelic and gene diversity were observed with an overall mean of 8.67 and 0.76 respectively. The mean inbreeding estimate within breeds was found to be negative at -0.124, -0.111 and -0.146 in Azawak, Borgou and Somba cattle breeds respectively. The global F statistics and AMOVA resulted in low genetic differentiation among the breeds with 1.14% of total variation being attributed to between-breed differences. Neighbor-joining tree revealed Azawak and Borgou clustered together while Somba breed being relatively distinct from the aforementioned. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances. Besides, the STRUCTURE analysis confirmed the tight genetic linkage between the breeds. High genetic diversity and poor genetic structure among the cattle breeds investigated could be due to historic zebu–taurine admixture and unstructured breeding practices. This results will aid in design of sustainable indigenous cattle genetic improvement programmes.

A20 suppresses canonical Smad-dependent fibroblast activation: novel function for an endogenous inflammatory modulator.

BackgroundThe ubiquitin-editing cytosolic enzyme A20, the major negative regulator of toll-like receptor (TLR)-mediated cellular inflammatory responses, has tight genetic linkage with systemic sclerosis (SSc). Because recent studies implicate endogenous ligand-driven TLR signaling in SSc pathogenesis, we sought to investigate the regulation, role and mechanism of action of A20 in skin fibroblasts.MethodA20 expression and the effects of forced A20 expression or siRNA-mediated A20 knockdown on fibrotic responses induced by transforming growth factor-ß (TGF-ß) were evaluated was evaluated in explanted human skin fibroblasts. Additionally, A20 regulation by TGF-ß, and by adiponectin, a pleiotropic adipokine with anti-fibrotic activity, was evaluated.ResultsIn normal fibroblasts, TGF-ß induced sustained downregulation of A20, and abrogated its TLR4-dependent induction. Forced expression of A20 aborted the stimulation of collagen gene expression and myofibroblast transformation induced by TGF-ß, and disrupted canonical Smad signaling and Smad-dependent transcriptional responses. Conversely, siRNA-mediated knockdown of A20 enhanced the amplitude of fibrotic responses elicited by TGF-ß. Adiponectin, previously shown to block TLR-dependent fibrotic responses, elicited rapid and sustained increase in A20 accumulation in fibroblasts.ConclusionThese results identify the ubiquitin-editing enzyme A20 as a novel endogenous mechanism for negative regulation of fibrotic response intensity. Systemic sclerosis-associated genetic variants of A20 that cause impaired A20 expression or function, combined with direct suppression of A20 by TGF-ß within the fibrotic milieu, might play a significant functional role in persistence of fibrotic responses, while pharmacological augmentation of A20 inhibitory pathway activity might represent a novel therapeutic strategy.Electronic supplementary materialThe online version of this article (doi:10.1186/s13075-016-1118-7) contains supplementary material, which is available to authorized users.

Key residues at the membrane-distal surface of KACL, but not glycosylation, determine the functional interaction of the keratinocyte-specific C-type lectin-like receptor KACL with its high-affinity receptor NKp65.

Keratinocyte-associated C-type lectin (KACL) is a peculiar C-type lectin-like receptor (CTLR) due to its selective expression by human keratinocytes and cognate interaction with the genetically coupled CTLR NKp65. KACL and NKp65 are members of the CLEC2 and NKRP1 subfamilies of natural killer gene complex (NKC)-encoded CTLR, respectively. Most NKRP1 molecules are expressed on NK cells and T cells and act as receptors of CLEC2 glycoproteins with their genes being intermingled in a certain sub-region of the mammalian NKC. The reasons for the tight genetic linkage of these dedicated receptor/ligand pairs are unknown, as is the physiological expression of NKp65. Recently, we reported that the CTLR NKp65 and KACL interact with high affinity, resulting in activation of NKp65-expressing NK-92MI cells. Here, we address the molecular basis of this high-affinity interaction by analysing KACL mutants with KACL-specific monoclonal antibodies (mAb), soluble NKp65 (sNKp65) and NK-92MI-NKp65 cells. We find that none of the three N-linked carbohydrates of KACL glycoproteins significantly contributes to KACL surface expression and NKp65 interaction. However, KACL mutants with non-conservative amino acid substitutions of arginine 158 or isoleucine 161 abrogated binding of both KACL-specific mAb OMA1 and sNKp65, well in line with the blockade of NKp65-KACL interaction by OMA1. Accordingly, functional recognition of these KACL mutants by NK-92M-NKp65 cells was completely abolished. Arginine 158 and isoleucine 161 located at the membrane-distal surface of KACL were defined as residues, decisively determining functional KACL-NKp65 interaction that is independent of KACL glycosylation.

Mis-splicing of the ABCC2 gene linked with Bt toxin resistance in Helicoverpa armigera.

Toxins from the bacterium Bacillus thuringiensis (Bt) are used widely for insect control in sprays and transgenic plants, but their efficacy is reduced when pests evolve resistance. Previous work showed that mutations in a gene encoding the transporter protein ABCC2 are linked with resistance to Bt toxins Cry1Ab, Cry1Ac or both in four species of Lepidoptera. Here we compared the ABCC2 gene of Helicoverpa armigera (HaABCC2) between susceptible strains and a laboratory-selected strain with >1,000-fold resistance to Cry1Ac relative its susceptible parent strain. We discovered a 73-base pair (bp) insertion in the cDNA of the resistant strain that generates a premature stop codon expected to yield a truncated ABCC2 protein. Sequencing of genomic DNA revealed that this insertion is an intron that is not spliced out because of a 6-bp deletion at its splicing site. Analysis of progeny from crosses revealed tight genetic linkage between HaABCC2 and resistance to Cry1Ac. These results provide the first evidence that mis-splicing of a gene encoding an ABCC2 protein confers resistance to a Bt toxin.

Supergenes and their role in evolution

Adaptation is commonly a multidimensional problem, with changes in multiple traits required to match a complex environment. This is epitomized by balanced polymorphisms in which multiple phenotypes co-exist and are maintained in a population by a balance of selective forces. Consideration of such polymorphisms led to the concept of the supergene, where alternative phenotypes in a balanced polymorphism segregate as if controlled by a single genetic locus, resulting from tight genetic linkage between multiple functional loci. Recently, the molecular basis for several supergenes has been resolved. Thus, major chromosomal inversions have been shown to be associated with polymorphisms in butterflies, ants and birds, offering a mechanism for localised reduction in recombination. In several examples of plant self-incompatibility, the functional role of multiple elements within the supergene architecture has been demonstrated, conclusively showing that balanced polymorphism can be maintained at multiple coadapted and tightly linked elements. Despite recent criticism, we argue that the supergene concept remains relevant and is more testable than ever with modern molecular methods.

An experimental study of strong reciprocity in bacteria

Strong reciprocity, whereby cooperators punish non-cooperators, may help to explain the evolutionary success of cooperative behaviours. However, theory suggests that selection for strong reciprocity can depend upon tight genetic linkage between cooperation and punishment, to avoid the strategy being outcompeted by non-punishing cooperators. We tested this hypothesis using experimental populations of the bacterium Pseudomonas aeruginosa, which cooperate by producing iron-scavenging siderophores and, in this context, punish non-cooperators with toxins. Consistent with theory, we show that cooperative punishers can indeed invade cheats, but only when the traits are tightly linked. These results emphasize that punishment is only likely to be favoured when the punishment itself leads to a direct or indirect fitness benefit to the actor.

Genetically coupled receptor–ligand pair NKp80-AICL enables autonomous control of human NK cell responses

AbstractNKp80 is a C-type lectin-like receptor broadly expressed on human natural killer (NK) cells, triggering cytotoxicity via an atypical cytoplasmic hemi-immunoreceptor tyrosine-based activation motif. As with other lectin-like NK receptors, NKp80 is encoded in the natural killer gene complex, but unlike most of these, adjacent to its ligand, ie, activation-induced C-type lectin (AICL). The reasons for the tight genetic linkage of this receptor–ligand pair remain elusive. Previous studies showed that NKp80 augments NK cell responses toward malignant and nonmalignant myeloid cells. Here, we report that resting human NK cells not only express NKp80 but also contain intracellular stores of AICL colocalizing with the Golgi complex. Domain-swapping experiments revealed that intracellular localization of AICL is determined by its C-type lectin-like ectodomain. Exposure of NK cells to monokines associated with conversion into memorylike cells induces substantial AICL cell surface expression, whereas NKp80 is downregulated, and NK cells become refractory to NKp80-mediated stimulation. AICL on monokine-exposed NK cells elicits NKp80-dependent effector responses by autologous NK cells and, hence, renders monokine-activated NK cells susceptible to NKp80-mediated cytolysis. Altogether, our data report a previously unrecognized regulatory circuit enabling autonomous control of human NK cell responses via the NKp80–AICL axis.

Chimeric Exchange of Coronavirus nsp5 Proteases (3CLpro) Identifies Common and Divergent Regulatory Determinants of Protease Activity

Human coronaviruses (CoVs) such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) cause epidemics of severe human respiratory disease. A conserved step of CoV replication is the translation and processing of replicase polyproteins containing 16 nonstructural protein domains (nsp's 1 to 16). The CoV nsp5 protease (3CLpro; Mpro) processes nsp's at 11 cleavage sites and is essential for virus replication. CoV nsp5 has a conserved 3-domain structure and catalytic residues. However, the intra- and intermolecular determinants of nsp5 activity and their conservation across divergent CoVs are unknown, in part due to challenges in cultivating many human and zoonotic CoVs. To test for conservation of nsp5 structure-function determinants, we engineered chimeric betacoronavirus murine hepatitis virus (MHV) genomes encoding nsp5 proteases of human and bat alphacoronaviruses and betacoronaviruses. Exchange of nsp5 proteases from HCoV-HKU1 and HCoV-OC43, which share the same genogroup, genogroup 2a, with MHV, allowed for immediate viral recovery with efficient replication albeit with impaired fitness in direct competition with wild-type MHV. Introduction of MHV nsp5 temperature-sensitive mutations into chimeric HKU1 and OC43 nsp5 proteases resulted in clear differences in viability and temperature-sensitive phenotypes compared with MHV nsp5. These data indicate tight genetic linkage and coevolution between nsp5 protease and the genomic background and identify differences in intramolecular networks regulating nsp5 function. Our results also provide evidence that chimeric viruses within coronavirus genogroups can be used to test nsp5 determinants of function and inhibition in common isogenic backgrounds and cell types.

Tight Genetic Linkage of Prezygotic Barrier Loci Creates a Multifunctional Speciation Island in Petunia

Most flowering plants depend on animal vectors for pollination and seed dispersal. Differential pollinator preferences lead to premating isolation and thus reduced gene flow between interbreeding plant populations. Sets of floral traits, adapted to attract specific pollinator guilds, are called pollination syndromes. Shifts in pollination syndromes have occurred surprisingly frequently, considering that they must involve coordinated changes in multiple genes affecting multiple floral traits. Although the identification of individual genes specifying single pollination syndrome traits is in progress in many species, little is known about the genetic architecture of coadapted pollination syndrome traits and how they are embedded within the genome. Here we describe the tight genetic linkage of loci specifying five major pollination syndrome traits in the genus Petunia: visible color, UV absorption, floral scent production, pistil length, and stamen length. Comparison with other Solanaceae indicates that, in P. exserta and P. axillaris, loci specifying these floral traits have specifically become clustered into a multifunctional "speciation island". Such an arrangement promotes linkage disequilibrium and avoids the dissolution of pollination syndromes by recombination. We suggest that tight genetic linkage provides a mechanism for rapid switches between distinct pollination syndromes in response to changes in pollinator availabilities.

Indirect evolution of hybrid lethality due to linkage with selected locus in Mimulus guttatus.

Author SummaryAdaptive evolution by natural selection is the primary force generating biological diversity. A critical question is whether the evolution of hybrid incompatibility, which is essential for the maintenance of species diversity, is caused by adaptive evolution. In this article, we investigate one of the most widely cited examples of ecological divergence driving the evolution of reproductive incompatibility, the strong association between hybrid lethality and copper tolerance in a copper mine population of the wildflower Mimulus guttatus. Hybrid lethality and tolerance of high levels of copper co-segregate as a single Mendelian locus. While copper tolerance and hybrid lethality are nearly universal in the mine population at Copperopolis, California, they are absent from adjacent off-mine populations, suggesting that reproductive isolation evolved rapidly as a pleiotropic by-product of recent adaptation to the mine environment. We find that copper tolerance and hybrid lethality are controlled by distinct loci, in tight genetic linkage. We also demonstrate that this genomic region has experienced strong recent selection and conclude that ecological selection for copper tolerance indirectly caused the neighboring hybrid lethality allele to hitchhike to high frequency. To our knowledge, this is the first case to demonstrate that reproductive isolation factors can evolve as an incidental by-product of adaptation to novel environments through genetic hitchhiking.

Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data.

Genome-wide association studies (GWASs) identify single nucleotide polymorphisms (SNPs) that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer phenotype or function; moreover, many SNPs are in tight genetic linkage, so that a SNP identified as associated with a particular disease may not itself be causal, but rather signify the presence of a linked SNP that is functionally relevant to disease pathogenesis. Here, we present an analysis method that takes advantage of the recent rapid accumulation of epigenomics data to address these problems for some SNPs. Using asthma as a prototypic example; we show that non-coding disease-associated SNPs are enriched in genomic regions that function as regulators of transcription, such as enhancers and promoters. Identifying enhancers based on the presence of the histone modification marks such as H3K4me1 in different cell types, we show that the location of enhancers is highly cell-type specific. We use these findings to predict which SNPs are likely to be directly contributing to disease based on their presence in regulatory regions, and in which cell types their effect is expected to be detectable. Moreover, we can also predict which cell types contribute to a disease based on overlap of the disease-associated SNPs with the locations of enhancers present in a given cell type. Finally, we suggest that it will be possible to re-analyze GWAS studies with much higher power by limiting the SNPs considered to those in coding or regulatory regions of cell types relevant to a given disease.