Adaptive Divergence in Sunflowers

Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans-species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non-native ancestry in an endangered native salamander, are examined.

We developed a Bayesian genomic cline model to study the genetic architecture of adaptive divergence and reproductive isolation between hybridizing lineages. This model quantifies locus-specific patterns of introgression with two cline parameters that describe the probability of locus-specific ancestry as a function of genome-wide admixture. 'Outlier' loci with extreme patterns of introgression relative to most of the genome can be identified. These loci are potentially associated with adaptive divergence or reproductive isolation. We simulated genetic data for admixed populations that included neutral introgression, as well as loci that were subject to directional, epistatic or underdominant selection, and analysed these data using the Bayesian genomic cline model. Under many demographic conditions, underdominance or directional selection had detectable and predictable effects on cline parameters, and 'outlier' loci were greatly enriched for genetic regions affected by selection. We also analysed previously published genetic data from two transects through a hybrid zone between Mus domesticus and M.musculus. We found considerable variation in rates of introgression across the genome and particularly low rates of introgression for two X-linked markers. There were similarities and differences in patterns of introgression between the two transects, which likely reflects a combination of stochastic variability because of genetic drift and geographic variation in the genetic architecture of reproductive isolation. By providing a robust framework to quantify and compare patterns of introgression among genetic regions and populations, the Bayesian genomic cline model will advance our understanding of the genetics of reproductive isolation and the speciation process.

Adaptive divergence is widely accepted as a contributor to speciation and the maintenance of species integrity. However, the mechanisms leading to reproductive isolation, the genes involved in adaptive divergence, and the traits that shape the adaptation of wild species to changes in climate are still largely unknown. In studying the role of ecological interactions and environment-driven selection, trees have emerged as potential model organisms because of their longevity and large genetic diversity, especially in natural habitats. Due to recurrent gene flow among species with different ecological preferences, oaks arose as early as the 1970s as a model for understanding how speciation can occur in the face of interspecific gene flow, and what we mean by “species” when geographically and genomically heterogeneous introgression seems to undermine species’ genetic coherence. In this review, we provide an overview of recent research into the genomic underpinnings of adaptive divergence and maintenance of species integrity in oaks in the face of gene flow. We review genomic and analytical tools instrumental to better understanding mechanisms leading to reproductive isolation and environment-driven adaptive introgression in oaks. We review evidence that oak species are genomically coherent entities, focusing on sympatric populations with ongoing gene flow, and discuss evidence for and hypotheses regarding genetic mechanisms linking adaptive divergence and reproductive isolation. As the evolution of drought- and freezing-tolerance have been key to the parallel diversification of oaks, we investigate the question of whether the same or a similar set of genes are involved in adaptive divergence for drought and stress tolerance across different taxa and sections. Finally, we propose potential future research directions on the role of hybridization and adaptive introgression in adaptation to climate change.

Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.

The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene–space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution.

Hybridisation between genetically divergent populations may lead to the formation of new evolutionary lineages. This may occur via duplication of a hybrid's chromosome complement (allopolyploid speciation) or by stabilisation of a fertile hybrid segregant (homoploid hybrid speciation). Although more common in plants, both modes of hybrid speciation also occur in fungi and in animals, including fish, amphibians and insects. The successful origin and establishment of hybrid species is highly dependent on an ability to occupy novel and/or spatially isolated habitats, in order to escape the effects of competition and gene flow from parental species. This ability is favoured by the generation of genetic novelty resulting from the dramatic effects that hybridisation (and genome duplication in allopolyploids) have on modifying genome structure and gene expression. Examples of recently originated allopolyploid and homoploid hybrid species are important models for investigating processes involved in hybrid speciation and establishment.Key ConceptsHybridisation between genetically divergent populations is promoted by habitat disturbance and may lead to the formation of new evolutionary lineages.Hybrid speciation may occur via the duplication of a hybrid's chromosome complement (allopolyploid speciation) or by the stabilisation of a reproductively isolated, fertile hybrid segregant (homoploid hybrid speciation).Allopolyploidy leads to instantaneous reproductive isolation between the allopolyploid neospecies and its parents and is therefore an example of very rapid speciation.Allopolyploidy is very common in higher plants but less common in animals, although examples are known in insects, crustaceans, molluscs, fish, amphibians, reptiles and mammals.Homoploid hybrid speciation is thought to be relatively rare, although an increasing number of homoploid hybrid species of animals, plants and fungi are being recognised using molecular markers.Homoploid hybrid speciation can be completed within a few generations, although several hundred generations may be required before the genome of the hybrid neospecies is fully stabilised.Considerable genetic novelty is generated in the early stages of allopolyploidy and homoploid hybrid speciation due to the marked effects that hybridisation (and genome duplication in the case of allopolyploidy) have on modifying genome structure and gene expression.Such genetic novelty aids the establishment of hybrid neospecies in ecologically divergent habitats, thus reducing the likelihood of competition and crossing with parents.Several examples are known of new allopolyploid and homoploid hybrid species originating within the past 250 years, and these have become important models for investigating processes involved in hybrid speciation and establishment.

Here we critically review the scale and extent of adaptive genetic variation in Atlantic salmon (Salmo salar L.), an important model system in evolutionary and conservation biology that provides fundamental insights into population persistence, adaptive response and the effects of anthropogenic change. We consider the process of adaptation as the end product of natural selection, one that can best be viewed as the degree of matching between phenotype and environment. We recognise three potential sources of adaptive variation: heritable variation in phenotypic traits related to fitness, variation at the molecular level in genes influenced by selection, and variation in the way genes interact with the environment to produce phenotypes of varying plasticity. Of all phenotypic traits examined, variation in body size (or in correlated characters such as growth rates, age of seaward migration or age at sexual maturity) generally shows the highest heritability, as well as a strong effect on fitness. Thus, body size in Atlantic salmon tends to be positively correlated with freshwater and marine survival, as well as with fecundity, egg size, reproductive success, and offspring survival. By contrast, the fitness implications of variation in behavioural traits such as aggression, sheltering behaviour, or timing of migration are largely unknown. The adaptive significance of molecular variation in salmonids is also scant and largely circumstantial, despite extensive molecular screening on these species. Adaptive variation can result in local adaptations (LA) when, among other necessary conditions, populations live in patchy environments, exchange few or no migrants, and are subjected to differential selective pressures. Evidence for LA in Atlantic salmon is indirect and comes mostly from ecological correlates in fitness-related traits, the failure of many translocations, the poor performance of domesticated stocks, results of a few common-garden experiments (where different populations were raised in a common environment in an attempt to dissociate heritable from environmentally induced phenotypic variation), and the pattern of inherited resistance to some parasites and diseases. Genotype x environment interactions occurr for many fitness traits, suggesting that LA might be important. However, the scale and extent of adaptive variation remains poorly understood and probably varies, depending on habitat heterogeneity, environmental stability and the relative roles of selection and drift. As maladaptation often results from phenotype-environment mismatch, we argue that acting as if populations are not locally adapted carries a much greater risk of mismanagement than acting under the assumption for local adaptations when there are none. As such, an evolutionary approach to salmon conservation is required, aimed at maintaining the conditions necessary for natural selection to operate most efficiently and unhindered. This may require minimising alterations to native genotypes and habitats to which populations have likely become adapted, but also allowing for population size to reach or extend beyond carrying capacity to encourage competition and other sources of natural mortality.

BackgroundThe haplochromine cichlid species assemblages of Lake Malawi and Victoria represent some of the most important study systems in evolutionary biology. Identifying adaptive divergence between closely-related species can provide important insights into the processes that may have contributed to these spectacular radiations. Here, we studied a pair of sympatric Lake Malawi species, Pseudotropheus fainzilberi and P. emmiltos, whose reproductive isolation depends on olfactory communication. We tested the hypothesis that these species have undergone divergent selection at MHC class II genes, which are known to contribute to olfactory-based mate choice in other taxa.Methodology/Principal FindingsDivergent selection on functional alleles was inferred from the higher genetic divergence at putative antigen binding sites (ABS) amino acid sequences than at putatively neutrally evolving sites at intron 1, exon 2 synonymous sequences and exon 2 amino acid residues outside the putative ABS. In addition, sympatric populations of these fish species differed significantly in communities of eukaryotic parasites.Conclusions/SignificanceWe propose that local host-parasite coevolutionary dynamics may have driven adaptive divergence in MHC alleles, influencing odor-mediated mate choice and leading to reproductive isolation. These results provide the first evidence for a novel mechanism of adaptive speciation and the first evidence of adaptive divergence at the MHC in closely related African cichlid fishes.

The evolution of plastic responses to external cues allows species to maintain fitness in response to the environmental variations they regularly experience. However, it remains unclear how plasticity evolves during adaptation. To test whether distinct patterns of plasticity are associated with adaptive divergence, we quantified plasticity for two closely related but ecologically divergent Sicilian daisy species (Senecio, Asteraceae). We sampled 40 representative genotypes of each species from their native range on Mt. Etna and then reciprocally transplanted multiple clones of each genotype into four field sites along an elevational gradient that included the native elevational range of each species, and two intermediate elevations. At each elevation, we quantified survival and measured leaf traits that included investment (specific leaf area), morphology, chlorophyll fluorescence, pigment content, and gene expression. Traits and differentially expressed genes that changed with elevation in one species often showed little changes in the other species, or changed in the opposite direction. As evidence of adaptive divergence, both species performed better at their native site and better than the species from the other habitat. Adaptive divergence is, therefore, associated with the evolution of distinct plastic responses to environmental variation, despite these two species sharing a recent common ancestor.

Homoploid hybrid speciation occurs when a stable, fertile and reproductively isolated lineage results from hybridization between two distinct species, without a change in ploidy level. Reproductive isolation between a homoploid hybrid species and its parents is generally attained by chromosomal rearrangements, ecological divergence and/or spatial isolation from the parental species; these factors prevent the incipient hybrid species from being genetically swamped through mating with the parental species, and allow it to evolve as an independent lineage (Gross and Rieseberg, 2005). Homoploid hybrid species are useful for speciation studies because the parental (hybridizing) species are often extant, and provide a baseline against which the changes that accompany the speciation process are measured. In this issue, Brennan et al. (2012) quantify the degree of molecular and phenotypic divergence between a hybrid species and its progenitors. The results suggest that molecular and phenotypic divergence can each follow very different trajectories during the development of a new species, and raises the question of whether quantitative trait divergence is always higher than neutral marker divergence between a homoploid hybrid species and its parents.

Homoploid hybrid speciation is the origin of a hybrid species without change in chromosome number. Although currently thought to be a rare form of speciation, especially relative to the more common allopolyploid hybrid speciation, it is feasible that many examples of homoploid hybrid species will be discovered in the future now that genetic resources are readily available for testing their occurrence. In this review, we focus on the speed of homoploid hybrid speciation, the importance of ecological and spatial isolation in the process, and the nature of genetic changes that occur in a new hybrid during its origin and establishment in the wild. With reference mainly to the extensive work carried out on homoploid hybrid species of Helianthus, and to our own work on the very recently originated diploid hybrid species Senecio squalidus, we review evidence showing: (1) that new fertile homoploid hybrid species can originate very quickly, although a longer period is likely to be required before the species becomes fully stabilized both genomically and phenotypically; (2) ecological divergence of the hybrid species from its parents is key to successful establishment, and that this can occur even in the absence of post­zygotic isolation caused by chromosomal and/or genetic sterility barriers; (3) transgressive changes in phenotypic traits and gene expression are of great importance in adapting homoploid hybrid species to habitats that are ecologically and spatially divergent from those of the parents; (4) adaptive differences distinguishing a homoploid hybrid species from its parental species are likely to be maintained in the face of parental gene flow, and evolve in concert across populations representing multiple origins of the species; (5) in the absence of parental gene flow, i.e., under conditions of geographical isolation, rapid genetic divergence of the hybrid species is likely to be enhanced due to the combined effects of founder events, genetic drift and selection.

The origin of new diploid, or homoploid, hybrid species is associated with rapid genomic restructuring in the hybrid neospecies. This mode of speciation has been best characterized in wild sunflower species in the genus Helianthus, where three homoploid hybrid species (H. anomalus, H. deserticola, and H. paradoxus) have independently arisen via ancient hybridization events between the same two parental species (H. annuus and H. petiolaris). Most previous work examining genomic restructuring in these sunflower hybrid species has focused on chromosomal rearrangements. However, the origin of all three homoploid hybrid sunflower species also is associated with massive proliferation events of Ty3/gypsy-like retrotransposons in the hybrid species' genomes. We compared the genomic organization of these elements in the parent species and two of the homoploid hybrid species using fluorescence in situ hybridization (FISH). We found a significant expansion of Ty3/gypsy-like retrotransposons confined to the pericentromeric regions of two hybrid sunflower species, H. deserticola and H. paradoxus. In contrast, we detected no significant increase in the frequency or extent of dispersed retrotransposon populations in the hybrid species within the resolution limits of our assay. We discuss the potential role that transposable element proliferation and localization plays in the evolution of homoploid hybrid species.

Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.

We are pleased to report that Molecular Ecology continues to rank among the top journals in evolution and ecology. According to the 2017 Journal Citation Reports, Molecular Ecology's Impact Factor rose slightly to 6.13, ranking 6th among 49 journals in evolutionary biology and 10th of 158 journals in ecology. Molecular Ecology ranks second among ecology journals in total impact over the past five years as measured by Google Scholar's h5 index, which rates journals according to their cumulative h-index. Managing Editor Karen Chambers has continued to streamline the editorial and production process for Molecular Ecology, increasing the speed with which manuscripts are reviewed and published. The average time from submission to first decision is now less than a month (29 days). Once accepted manuscripts are received by Wiley, they are published on Early View in circa 25 days on average. Time to online issue publication takes, on average, slightly more than two months. We also have established a junior editorial board, with the goal of obtaining advice from early career researchers on changing research and dissemination needs in molecular ecology. The junior editorial board is comprised of the winners and runners-up for the Harry Smith Prize (see below). The founding members are Luke Browne (University of California, Los Angeles, USA), Nick Fountain-Jones (University of Minnesota USA) and Megan L. Smith (Ohio State University, USA). The Molecular Ecology Prize is awarded annually to “an outstanding scientist who has made significant contributions to molecular ecology,” as selected by an independent award committee. It is considered to be the most prestigious award in our discipline. The 2018 Molecular Ecology Prize has been awarded to Dr. Robin Waples, a senior scientist at the Northwest Fisheries Science Center of the National Marine Fisheries Service in Seattle, USA. The prize recognized Robin's extensive contributions in the use of molecular genetic data to estimate effective population size, gene flow and population subdivision in natural populations and complex life-history scenarios. A biography of Robin and his contributions to the field of molecular ecology can be found on pages XX–XX of this issue. Our editorial board recently established a new prize that recognizes the best paper published in Molecular Ecology by early career scholars. The prize is named after Professor Harry Smith FRS, who founded the journal and served as both its Chief and Managing Editor during the journal's critical early years. He continued as the journal's Managing Editor until 2008, and he went out of his way to encourage early career scholars. As with the Molecular Ecology Prize, the winner of this annual prize is selected by an independent award committee. This inaugural Harry Smith Prize has been awarded to Dr. Nick Fountain-Jones (University of Minnesota, USA) for his paper “Urban landscapes can change virus gene flow and evolution in a fragmentation-sensitive carnivore” (Fountain-Jones et al., 2017). Fountain-Jones et al. addressed the impact of urbanization on disease epidemiology in native carnivores. The study paired molecular epidemiology of feline immunodeficiency virus with genetic analysis of a native host, the bobcat (Lynx rufus). Despite working across systems, and in organisms that are inherently difficult to sample, the study describes an innovative and rigorous application of molecular tools to extract valuable practical insights into disease dynamics in human-altered landscapes. We want to take this opportunity to thank Professor Louis Bernatchez for 15 years of exceptional service as the Reviews Editor for Molecular Ecology! While Louis is stepping down as Reviews Editor because of other commitments, he will continue to serve as one of our valued Senior Editors, albeit with a reduced workload. Professor Pierre Taberlet, another Senior Editor, will replace Louis as Reviews Editor. There also will be a change in the commissioning of special issues. Over last few years, this role was handled by News and Views Editor, Armando Geraldes, who did an outstanding job of not only identifying topics that were of interest to our readers, but also convincing leaders in these research areas to serve as guest editors. In the future, Managing Editor, Karen Chambers, along with our new Junior Editorial Board, will take over responsibility for identifying special issues, as well as commissioning editors and authors. Armando will continue as the News and Views Editor for both Molecular Ecology and Molecular Ecology Resources and will spearhead a new “target reviews” category. Lastly, we wish to express our gratitude to our many referees, who are listed at the end of this editorial, for the donation of their time to the journal and to the discipline of molecular ecology. Molecular Ecology serves as the intellectual home for the community of molecular ecologists through the Molecular Ecologist blog (http://www.molecularecologist.com/), symposia, our News and Views section, special issues, and so forth. Below, we briefly discuss some of the scientific highlights from the past year. The Molecular Ecologist has had a quieter year, averaging about 13,000 visitors in 20,000 sessions per month from July 2017 to August 2018. This represents a decline of circa 11% (visitors) and 13% (sessions) over the equivalent previous period. This appears to result from changes in site policy and user behaviour on the big social networks rather than a decline in interest in the Blog. Indeed, Blog Editor, Jeremy Yoder, recruited a new cohort of regular contributors in early 2018, who have provided highly viewed coverage of topics that were not as well represented before. Especially, popular posts addressed speciation and species delimitation, evolutionary simulation methods and next-generation sequencing techniques. A second series of "How molecular ecologists work" interviews was also very popular. In 2018, Molecular Ecology continued to host a diverse and vibrant community of researchers studying a wide range of topics. A total of 14 Perspectives highlighted some noteworthy contributions, including the divergence of genes underlying pheromones leading to reproductive isolation (Pelletier & Denton, 2018), and, similarly, evolution of olfaction genes facilitating sympatric speciation (Brock & Wagner, 2018). Other studies looked at the genetic architecture of reproductive isolation more broadly (Hamilton & Miller, 2018), or (on the flip side) the genetic signature of hybridization (Vallejo-Marin, 2018). Genetic shifts associated with abiotic adaptation were a topic of quite a few studies, including the combined effects of phenotypic plasticity and local adaption in allowing lizard adaptation to new climatic regimes (Card, Schield, & Castoe, 2018), local adaptation in abalone (Lampert, 2018) and adaptive evolution following species introductions (Seeb, McKinney, & Seeb, 2018). Microbial communities are clearly an emerging area of interest, with papers examining the genetic basis of host–fungal symbiont interactions, particularly relating to the evolution of host specialization (Gladieux, 2018), and the transcriptomics of biofilms (Veach & Griffiths, 2018). Other Perspectives discussed the predictability of evolutionary genetic changes (Linnen, 2018), the maintenance of diversity because of selection driven by sexual conflict (Meisel, 2018), the value of improved annotation of gene functions by analysing expression responses to environmental conditions (Stanford & Rogers, 2018), gene expression differences in brain tissue from females, territorial and sneaker male peacock blennies (Böhne, 2018) and the potential importance of crop–wild hybrids in weedy populations in maintaining important crop allelic diversity (Ellstrand, 2018). Opinion papers discussed the best practices for effective SNP filtering for use in population genetic analyses (O'Leary, Puritz, Willis, Hollenbeck, & Portnoy, 2018) and argued for more consistent use of COI as the community DNA metabarcode for metazoans (Andujar, Arribas, Yu, Vogler, & Emerson, 2018). One Comment and its Reply debated whether high levels of observed hybridization and recombination challenges the "predominant clonal evolution" model of Trypanosoma congolense, which is the major pathogen responsible for nagana (sleeping sickness), a disease of cattle and other animals in Africa transmitted by the tsetse fly (Van den Broeck, Tavernier, Vermeiren, Dujardin, & Abbeele, 2018; Tibayrenc & Ayala, 2018). Other News and Views discussions included whether a very recent origin, assuming an unusually high mutation rate (Martin & Höhna, 2018) or an ancient origin, along with a more typical mutation rate (Saglam et al., 2018), is more likely for the endangered Devil's Hole pupfish. A meeting review of a symposium on "Detecting the Genomic Signal of Polygenic Adaptation and the Role of Epistasis in Evolution" (Csilléry, Rodriguez-Verdugo, Rellstab, & Guillaume, 2018) highlighted the often-complex genetic underpinnings of evolution. Two other meeting reviews also highlighted the important role of genomic data in unifying previously distinct and diverse fields of study, including an international meeting on Littorinid evolution (Ravinet, 2018) and the Wild Animal Models Bi-Annual Meeting in Quebec (Morrissey et al., 2018). This unifying feature of DNA sequence data is being discussed more and more frequently, suggesting that the field of Molecular Ecology is becoming increasingly successful as an interdisciplinary approach. Special Issues are an important component of the journal. They allow us to highlight leading research in areas of special interest to our readership and to call attention to developing subjects that we believe are slated for considerable growth in the future. This year we published two special issues. The Special Issue “The host associated microbiome: pattern, process and function,” edited by Laura Wegener Parfrey, Corrie S. Moreau and Jacob A. Russell, was our third special issue in the past four years with a focus on microbiology (the others being “Nature's microbiome” in 2014 and “Microbial local adaptation” in 2017) and furthered our quest to highlight the role of microorganisms in ecology and evolution. The issue featured a wide diversity of host–microbiome interactions and was organized in four sections that probed different aspects of these relationships. The first section focused on the mechanistic underpinnings of host–microbe interactions, all the way from obligate symbioses where nutritional codependence is common (Beinart, Beaudoin, Bernhard, & Edgcomb, 2018; Feng, Wang, Wuchty, & Wilson, 2018; Thairu, Cheng, & Hansen, 2018), to more transient ones where benefits can include defence, growth and development, and tolerance to abiotic stress (Bost et al., 2018; Haney et al., 2018; Hudson, Gardiner, Deshpande, & Egan, 2018; Kessler, Weiss, Kuegler, Hermes, & Wichard, 2018; Palakurty, Stinchcombe, & Afkhami, 2018). The second section featured a number of manuscripts that investigated the structure of the microbiome in an attempt to understand the drivers of microbiota community assembly and turnover. Some contributions weighed in on the role of host phylogeny vs. ecology (Erlandson, Savage, Wei, Cavender-Bares, & Peay, 2018; Ivens, Gadau, Kiers, & Kronauer, 2018; Hernandez-Gomez, Briggler, & Williams, 2018; Kohl, Dearing, & Bordenstein, 2018; Nishida & Ochman, 2018; Roth-Schulze et al.., 2018; Schuelke, Pereira, Hardy, & Bik, 2018), others probed how the presence of hosts themselves alters the microbiota around them (Chen & Parfrey, 2018; Shukla, Vogel, Heckel, Vilcinskas, & Kaltenpoth, 2018), one investigated patterns of co-infection (Rock et al., 2018) and one documented changes in microbiota during development (Prest, Kimball, Kueneman, & McKenzie, 2018). A few studies in this section studied the structure of the microbiome with manipulative experiments (e.g., Chen & Parfrey, 2018; Erlandson et al., 2018; Morella, Gomez, Wang, Leung, & Koskella, 2018; Raymann, Bobay, & Moran, 2018). The third section probed the evolution of symbiotic relationships and how they shape host adaptation (Engl et al., 2018; Gauthier et al.., 2018; Vanderpool, Bracewell, & McCutcheon, 2018) and the fourth section looked into the resilience of these relationships in the changing environment of the Anthropocene (Deveautour, Donn, Power, Bennett, & Powell, 2018; Doremus et al., 2018; Ramsby, Hoogenboom, Whalan, & Webster, 2018). The issue concluded with a theoretical and conceptual framework that highlighted how symbioses can be viewed within an ecosystem services framework (McKenney, Koelle, Dunn, & Yoder, 2018). The editors of the issue conclude that “the deeper understanding of the ecology, evolution and function of the microbiome—gained by studying a multitude of hosts and symbionts—promises tangible benefits to the welfare of humans and the ecosystems surrounding us” and suggest that “as the tools for manipulation become further honed, we are finally realizing the translational potential of innovative, multifaceted microbiome science” (Parfrey, Moreau, & Russell, 2018). The second Special Issue of 2018 titled “Sex chromosomes and speciation” was edited by Bret A. Payseur, Daven C. Presgraves and Dmitry A. Filatov and compiles an exciting array of studies that represent a fascinating fresh look at the idea that sex chromosomes play an outsized role in speciation. As the editors point out in the introduction (Payseur, Presgraves, & Filatov, 2018) to the issue, “the most widespread and convincing evidence for this conclusion stems from two empirical patterns that characterize reproductive isolation between nascent species pairs […]. These “two rules of speciation” (Coyne & Orr, 1989) excite biologists because they raise the possibility of general mechanisms responsible for the birth of new species. The first is Haldane's rule, where reduced hybrid fitness is first detected in the heterogametic sex (males in XY and females in ZW systems), and the second is the large X effect, where hybrid dysfunction disproportionately maps to the X or Z chromosomes. A personal essay from Jerry Coyne (Coyne, 2018) in this issue gives an historical sketch of his seminal contribution to the field as well as some insightful discussion on the leading hypotheses to explain the pattern. The rest of the issue is a healthy mix of theory (e.g., Charlesworth, Campos, & Jackson, 2018; Ghenu, Blanckaert, Butlin, Kulmuni, & Bank, 2018; Patten, 2018), review (Cutter, 2018; Irwin, 2018; O'Neill & O'Neill, 2018; Presgraves, 2018), methods development (Steinrücken, Spence, Kamm, Wieczorek, & Song, 2018) and empirical papers, some focusing on comparing patterns of differentiation and gene flow between incipient species at autosomes and sex chromosomes (Van Belleghem et al., 2018; Moran et al., 2018; Steinrücken et al., 2018), others looking at sequence and expression evolution of sex-linked genes (Filatov, 2018; Llopart, 2018), some mapping the genomic architecture of reproductive isolation (Liu & Karrenberg, 2018) or even using comparative phylogenetic approaches (Pennell, Mank, & Peichel, 2018). Of significance, the issue included systems that have not been studied very commonly in this context such as plants (Filatov, 2018; Liu & Karrenberg, 2018) and worms (Cutter, 2018). In the end, the issue will likely disappoint those expecting a final verdict on the ultimate causes of the large role of sex chromosomes on the origin of species, instead, as the editors highlight in the last section of their introduction, it is likely that there is no unifying reason why sex chromosomes have a large role in speciation. We are excited to announce that two special issues will be coming out in the first few months of 2019. The first will be titled “Species interactions, ecological networks and community dynamics” and the second “The role of genomic structural variants in adaptation and diversification.” We would like to thank all the editors and authors who make these special issues an integral part of the journal. We are grateful for the continued support of the molecular ecology community, as well as the many excellent contributions of our authors, reviewers and editors. Publication of this journal would not be possible without you, and we are open to suggestions on how to serve you better. We thank the large number of individuals who have contributed to the field of molecular ecology by reviewing manuscripts for the journal. The following list contains people who reviewed articles for Molecular Ecology between 1 October 2017 and 30 September 2018. Duur Aanen Matthew Aardema Marco Abbiati Patrick Abbot Pedro Abellán Nerea Abrego Karina Acevedo-Whitehouse Karen Adair Sarah Adamowicz Rachelle Adams Eric Adetutu Elizabeth Adkins-Regan Sina Adl Lynn Adler Irene Adrian-Kalchhauser Jeffrey Adrion Simon Aeschbacher Matthias Affenzeller Michelle Afkhami Ingi Agnarsson Hélène Agogué Aneil Agrawal Annie Agrawal Anurag Agrawal Jon Ågren Montserrat Aguadé Andres Aguilar Felipe Aguilera Julio Aguirre Windsor Aguirre Nuria Agusti Freed Ahmad Dag Ahrén Collin Ahrens Bin Ai Tracy Ainsworth Tania Aires Sally Aitken Tuomas Aivelo Ostaizka Aizpurua Mikael Akesson Melis Akman Serap Aksoy Outi Ala-Honkola Aitor Albaina Antton Alberdi Caroline Albertin Filipe Alberto Florian Alberto Craig Albertson Miguel Alcaide Fernando Alda Pau Aleixandre Alana Alexander Harriet Alexander Mhairi E. Alexander Soren Alexandersen Robin Allaby Brandon Allen Geraldine Allen Richard M. Allen Scott Allen Simon Allen Fred Allendorf Pedro Almeida Conchita Alonso Suzanne Alonzo Maria Alp Benjamin Alric S. Elizabeth Alter Florian Altermatt David Althoff Ianina Altshuler Diego Alvarado-Serrano Mariano Alvarez Joel Alves Marta Alves Linda Amaral-Zettler George Amato Katherine Amato Jon Amberg Anthony Amend Stephen Amish Antonio Amorim Nevil Amos William Amos Oivind Andersen Eric Anderson James Anderson Jill Anderson Kirk Anderson Anders Andersson Dan Andersson Martin Andersson Staffan Andersson Haruko Ando Peter Andolfatto Krikor Andonian Adrien Andre Alyson Andreasen Rune Andreassen Aida Andres Rose Andrew Rose L. Andrew Samuel Andrew Kimberly Andrews Matthew Andrews Robin M. Andrews Tommy Andriollo Carmelo Andujar Cecile Ane Put O. Ang Jr. Roey Angel Fred Angelier Frédéric Angelier Lisa Angeloni Bernard Angers Amy Angert Spinello Antinori Agostinho Antunes Rachael Antwis Yahya Anvar Joseph Apodaca Amy Apprill Manuel Aranda Lastra Elizabeth Archie Lina Arcila Hernandez William Ardren Arjona Yurena Cristina Armas W. Scott Armbruster John Armstrong Karen Armstrong Einar Árnason Sophie Arnaud-Haond Matt Arnegard Elizabeth Arnold Sarah Arnold J. W. (Pim) Arntzen Serge Aron Jigyasa Arora Paula Arribas Marie-Claire Arrieta Aitor Arrizabalaga Escudero Defne Arslan Wes Arson Joan Artigas Ines Aschenbrenner Sassan Asgari Muhammad Asghar Alyson Ashe Oliver Ashford Mary Ashley Noah Ashley Jouni Aspi Jana Asselman Raquel Assis Ana Assuncao Carter Atkinson Shannon Atkinson Catherine Attard Nadia Aubin-Horth Michelle Audsley Asta Audzijonyte Marc D. Auffret Stuart Auld Didier Aurelle Jeremy Austin Robert Austin Brian Avery Teresa Cristina Avila-Pires John Avise Zoya Avramova Amaury Avril David Ayre Eric Baack Matt Baber Wieslaw Babik Evelyne Bachere Doris Bachtrog Kyoungwhan Back Niclas Backstrom Cecile Bacles Amy Baco Christine Bacon Badouin Hélène Helene Badouin Alexander Badyaev Jin-Woo Bae Boris C. Elizabeth A. Joseph Anthony John Amy Andrew Scott William Matthew David Laura James William Matt J. D. A. Matthew Ana Matthew Richard E. Sarah Marta Diego Felipe Craig A. Andres David Felipe Scott Scott Stuart Jeremy Matthew Elizabeth David A. Pedro Lisa James Karen Anthony J. Andres Laura Scott Shannon Andrew John Marco Miguel Peter David E. C. Jeremy David Laura E. James John Martin Sarah A. David Caroline David Alberto Andrew Andrew Linda Mary David S. Dan C. Andrew Benjamin Jeremy Martin Oliver Sarah Florian Didier Elizabeth Andrew Sarah Brian W. Bret Laura W. Joseph Benjamin Sophie Jon Marine Jon J. Richard Luke Browne Robert Patrick Nadia Robert W. Katherine Marc Richard Katherine Scott C. Catherine W. David Joseph Peter Maria Armando Marc Scott J. J. Eric C. Pedro Karen Matthew Craig John Ana Miguel David L. L. Andre Scott M. Paula E. Alberto Samuel Scott A. James David Brian Sophie Andrew Chen Chen Chen Chen Chen Chen Chen Chen Chen Pierre John Elizabeth Elizabeth L. J. John David Katherine Andrew Maria Robert John David J. Peter Ana Richard Matthew C. James Joseph Elizabeth Scott David Richard Robert Miguel A. Joan Stephen George James L. Eric Peter Dan Bernard D. Karen

New species may arise via hybridization and without a change in ploidy. This process, termed homoploid hybrid speciation, is theoretically difficult because it requires the development of reproductive barriers in sympatry or parapatry. Theory suggests that isolation may arise through rapid karyotypic evolution and/or ecological divergence of hybrid neospecies. Here, we investigate the role of karyotypic change in homoploid hybrid speciation by generating detailed genetic linkage maps for three hybrid sunflower species, Helianthus anomalus, H. deserticola, and H. paradoxus, and comparing these maps to those previously generated for the parental species, H. annuus and H. petiolaris. We also conduct a quantitative trait locus (QTL) analysis of pollen fertility in a BC2 population between the parental species and assess levels of pollen and seed fertility in all cross-combinations of the hybrid and parental species. The three hybrid species are massively divergent from their parental species in karyotype; gene order differences were observed for between 9 and 11 linkage groups (of 17 total), depending on the comparison. About one-third of the karyoypic differences arose through the sorting of chromosomal rearrangements that differentiate the parental species, but the remainder appear to have arisen de novo (six breakages/six fusions in H. anomalus, four breakages/three fusions in H. deserticola, and five breakages/five fusions in H. paradoxus). QTL analyses indicate that the karyotypic differences contribute to reproductive isolation. Nine of 11 pollen viability QTL occur on rearranged chromosomes and all but one map close to a rearrangement breakpoint. Finally, pollen and seed fertility estimates for F1's between the hybrid and parental species fall below 11%, which is sufficient for evolutionary independence of the hybrid neospecies.