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Species can be defined as populations that are diagnosably distinct, reproductively isolated, cohesive, or exclusive groups of organisms. Boundaries between species in sympatry are maintained by intrinsic barriers to gene exchange; these boundaries may not be uniform in space, in time, or across the genome. Here, we explore the nature of the species boundary, defined as the phenotypes/genes/genome regions that remain differentiated in the face of potential hybridization and introgression. We emphasize that species boundaries are semipermeable, with permeability (gene exchange) being a function of genome region. The early evidence for semipermeable species boundaries came from data on differential introgression in hybrid zones. This "genic view" of species was common in the hybrid zone literature even when few molecular markers were available to characterize genome-wide patterns of variation. Now, molecular tools allow detailed characterization of differentiation between diverging lineages and patterns of variation across natural hybrid zones, but the questions being asked by evolutionary biologists have remained much the same. Recent data (from DNA sequences and genotypes) reinforce earlier conclusions about the semipermeable nature of most species boundaries. However, debate persists over the nature and extent of genome divergence that accompanies speciation.

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Speciation involves the origin of trait differences that limit or prevent gene exchange and ultimately results in daughter populations that form monophyletic or exclusive genetic groups. However, for recently diverged populations or species between which reproductive isolation is often incomplete, gene genealogies will be discordant, and most regions of the genome will display nonexclusive genealogical patterns. In these situations, genome regions for which one or both species are exclusive groups may mark the footprint of recent selective sweeps. Alternatively, such regions may include or be closely linked to ''speciation genes,'' genes involved in reproductive isolation. Therefore, comparisons of gene genealogies allow inferences about the genetic architectures of both reproductive isolation and adaptation. Contrasting genealogical relationships in sexually isolated pheromone strains of the European corn borer moth (Ostrinia nubilalis) demonstrate the relevance of this approach. Genealogies for five gene regions are discordant, and only one molecular marker, the sex-linked gene Tpi, has evidence for pheromone strain exclusivity. Tpi maps to a position on the sex chromosome that is indistinguishable from a major factor (Pdd) affecting differences in postdiapause development time. The major factor (Resp) determining male behavioral response to pheromone is also sex-linked, but maps 20 -30 cM away. Exclusivity at Tpi may be a consequence of these linkage relationships because evidence from phenotypic variation in natural populations implicates both Pdd and Resp as candidates for genes involved in recent sweeps and͞or reproductive isolation between strains.genealogy ͉ genetic linkage map ͉ introgression ͉ selective sweep ͉ speciation

This paper examines variation in morphology and allozymes in a hybrid zone between two closely related eastern North American species of field cricket (genus Gryllus). I show that patterns of variation across the zone do not conform to a simple model of monotonic clinal variation. In fact, the hybrid zone is a mosaic of populations. Pockets of "pure" parental forms are found within the hybrid zone, and striking reversals in mean character index score occur along transects across the zone. Treating hybrid zones as mosaics has important consequences for thinking about the dynamics of such zones.Patterns of variation in morphology and allozymes are not concordant across the hybrid zone. Rather, there is strong evidence for differential and asymmetric introgression, with morphological integrity maintained despite considerable introgression of alleles at allozyme loci. Species boundaries must be thought of as semipermeable, the permeability varying with he genetic marker used.I also show that there is strong positive assortative mating at one site within the hybrid zone and that assortative mating persists despite introgression at allozyme loci. Habitat isolation and behavioural differences may both affect the extent of assortative mating.

Recent essays on the species problem have emphasized the commonality that many species concepts have with basic evolutionary theory. Although true, such consensus fails to address the nature of the ambiguity that is associated with species-related research. We argue that biologists who endure the species problem can benefit from a synthesis in which individual taxonomic species are used as hypotheses of evolutionary entities. We discuss two sources of species uncertainty: one that is a semantic confusion, and a second that is caused by the inherent uncertainty of evolutionary entities. The former can be dispelled with careful communication, whereas the latter is a conventional scientific uncertainty that can only be mitigated by research. This scientific uncertainty cannot be 'solved' or stamped out, but neither need it be ignored or feared.For researchers, few ideals are as sought after as those of the independent observer; preferably, a scientist should discover and transmit his or her story, and not be a part of it. But what if that cannot be arranged? In some fields, most notably quantum physics and human behavioral research, observation per se can have a direct effect on outcomes, so that studies must be designed to incorporate those effects. Of course, research in these fields does not come to a halt. Neither does research halt in other fields where the impact of the observer cannot be avoided or ignored safely, but rather is addressed directly as part of the research program. Here, we argue that biological research on species will benefit from an explicit recognition of the inherent limitations that biologists experience as investigators of species.Many evolutionary biologists, systematists and ecologists struggle with the related questions of how to identify species and how to define the word 'species'. These persistent questions constitute what is known as the 'species problem'. The problem is not new. Indeed, Darwin drew upon the persistence of wide taxonomic disagreements to support his arguments for the evolution of species, but the problem endures with a steadily increasing literature on how to define 'species'. A recent listing of species concepts found 24 in the modern literature [1] and new books appear steadily [2 -4].

This manuscript gives an up-to-date and comprehensive overview of the effects of energetic particle precipitation (EPP) onto the whole atmosphere, from the lower thermosphere/mesosphere through the stratosphere and troposphere, to the surface. The paper summarizes the different sources and energies of particles, principally galactic cosmic rays (GCRs), solar energetic particles (SEPs) and energetic electron precipitation (EEP). All the proposed mechanisms by which EPP can affect the atmosphere are discussed, including chemical changes in the upper atmosphere and lower thermosphere, chemistry-dynamics feedbacks, the global electric circuit and cloud formation. The role of energetic particles in Earth's atmosphere is a multi-disciplinary problem that requires expertise from a range of scientific backgrounds. To assist with this synergy, summary tables are provided, which are intended to evaluate the level of current knowledge of the effects of energetic particles on processes in the entire atmosphere.

Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genome-wide scale, and recent genome scans have focused on the presence of “islands” of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness, and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the “same” species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations.