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Although theory has demonstrated rather low levels of gene flow are sufficient to counteract opposing mutation, drift, and selection, widespread recognition of the evolutionary importance of gene flow has come slowly. The perceived role of gene flow as an evolutionary force has vacillated over the last century. In the last few decades, new methods and analyses have demonstrated that plant gene flow rates vary tremendously-from nil to very high-depending on the species and specific populations involved, and sometimes over time for individual populations. In many cases, the measured gene flow rates are evolutionarily significant at distances of hundreds and sometimes thousands of meters, occurring at levels sufficient to counteract drift, spread advantageous alleles, or thwart moderate levels of opposing local selection. Gene flow in plants is likely to often act as a cohesive force, uniting individual plant species into real evolutionary units. Also, gene flow can evolve under natural selection, decreasing or increasing. The fact of frequent, but variable, plant gene flow has important consequences for applied issues in which the presence or absence of gene flow might influence the outcome of a policy, regulatory, or management decision. Examples include the unintended spread of engineered genes, the evolution of invasiveness, and conservation. New data-rich genomic techniques allow closer scrutiny of the role of gene flow in plant evolution. Most plant evolutionists now recognize the importance of gene flow, and it is receiving increased recognition from other areas of plant biology as well., (© 2014 Botanical Society of America, Inc.)

Debate over what is a species was already considered old hat when Darwin wrote his seminal abstract (as he called it) more than 150 years ago.(1) Endless papers, workshops, and symposia have been presented in an effort to "solve" the species problem. Yet, here we are, at it again. Has there been any progress? I believe that there has been, and that among the many advances enabled by the genomics revolution, progress on species concepts and species recognition is among them. To quote Feder and colleagues,(2) we are on the brink of a "unified theory of speciation genomics.", (Copyright © 2014 Wiley Periodicals, Inc.)

Brachionus calyciflorus is a species complex consisting of four recently described species. Although several lines of evidence support their species status, hybridization between two of the sibling species B. calyciflorus s.s. and B. elevatus has been inferred from both field and laboratory studies. In this study, we tested for the existence of prezygotic barriers between these species by performing two types of cross-fertilization experiments. In a 'mate competition' experiment we exposed mictic females to equal numbers of conspecific and allospecific males and demonstrate that intraspecific fertilizations occur at much higher frequencies than interspecific fertilizations, providing evidence for a strong prezygotic reproductive barrier. This result was consistent across numerous combinations of parental genotypes. In addition, by creating interspecific combinations of mictic females and males in a 'no choice' experiment, we found that interspecific fertilization success is independent of fertilization direction while it does seem to depend on maternal genotype. Our results demonstrate the existence of a strong prezygotic barrier that may play an important role in the maintenance of species boundaries. Yet, the observation of hybrids also shows a potential for gene flow between the species through hybridization. [ABSTRACT FROM AUTHOR]

The process of speciation remains poorly understood and hence definitions of species continue to be a focus of sharp debate. A key unresolved issue in speciation debates is whether local populations that are somewhat distinct from a parent population in morphology or genotype but that remain connected to the parent population via gene flow should be recognized as species. The species status of the Cassia crossbill Loxia sinesciuris, as well as other distinctive populations in the red crossbill Loxia curvirostra clade including the parrot crossbill L. pytyopsittacus and the Scottish crossbill L. scotica, are test cases for whether the hundreds of other avian ecomorphs should be taxonomically elevated to full species. We argue that these regional populations of red crossbills do not meet stated criteria for species designation under the Biological Species Concept and, regardless of species concept, fail as species simply following logic, parsimony, and consistency. There are no diagnostic morphological characteristics that definitively separate birds in the Cassia crossbill, parrot crossbill, or Scottish crossbill populations from birds in other sympatric crossbill populations. Call type, the behavioral characteristic that is proposed to distinguish Cassia crossbills, parrot crossbills and Scottish crossbills from other populations of crossbills, is learned and can change within the life of an individual. There is evidence of substantial on‐going gene flow between Cassia crossbills, parrot crossbills, and Scottish crossbill and other populations of red crossbills, and there is no divergence in mitochondrial genotype. Instead, there exist few fixed genetic differences in nuclear genotype between individuals from these local crossbill populations and individuals from other red crossbill populations. We propose that the recognition of the Cassia crossbill, parrot crossbill and Scottish crossbill as species sets a poor precedent in avian taxonomy and muddles understanding of the process of speciation. [ABSTRACT FROM AUTHOR]

As it has presently become evident, reproductive isolation can no longer be considered as the leading criterion for estimating the species limits, but it is still used for determining the status of the majority of morphs. The presence/absence of hybridization between individuals is not directly related to the degree of their evolutionary insularity. Hybridization can result in the origin of new morphs including those that have species status. The application of phylogenetic methods is justified in reconstructing the relation links within complex groups including the morphs of various evolutionary levels (from geographical races to "good" species), the relationships between which are exacerbated by hybridogenous polymorphism and/or the hybridization origins of their populations. Taking into account both new data and new conceptions, we suggest genuine interrelated definitions of concepts such as species, subspecies, and semispecies in birds. The definitions are based on two main criteria: biological, i.e., an evaluation of the reproductive relations of the particular morphs with each other, and phylogenetic, i.e., an evaluation of their evolutionary age and kinship. The main feature of a species as an evolutionary entity should be considered through its stability in time even when its reproductive isolation is periodically broken. Geographic intraspecies races show sustainable variations of different degrees, but they have no reproductive isolation; they breed upon contact and form intergradation zones. They are taxonomically denoted as subspecies. Descriptions of new subspecies are viable to the limits that reflect the species' natural geographic structure to the fullest extent. For the young morphs that have reached the level of species insularity in the course of evolution, it seems appropriate to restore a semispecies category. Semispecies show significant morphological differences and distinguished ecological particularities, as a rule, but they are connected to closely related morphs by gene flows in contact zones. Distinguishing this category is not regulated by the International Code of Zoological Nomenclature and, as splitter tendencies prevail in modern systematics, semispecies are more often equated to species; i.e., they have binominal names. We propose to denote the attribution of a semispecies to a particular species group (superspecies) in parentheses between genus and species names. Thus, it would become possible to outline natural complexes and avoid a groundless increase in the taxonomic statuses of morphs in the stage of development. Representatives of distant phylogenetic lines (morphs that separated historically long ago) are not to be considered as semispecies even in the cases of their reproductive isolation being broken and a steady hybridization existing between them. [ABSTRACT FROM AUTHOR]

Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms. [ABSTRACT FROM AUTHOR]

Delineation of species is fundamental to organizing and understanding biological diversity. The most widely applied criterion for distinguishing species is the Biological Species Concept (BSC), which defines species as groups of interbreeding individuals that remain reproductively isolated fromother suchgroups. The BSC has broad appeal; however, many organisms, most notably asexual lineages, cannot be classified according to the BSC. Despite their exclusively asexual mode of reproduction, Bacteria and Archaea can transfer and exchange genes though homologous recombination. Here we show that barriers to homologous gene exchange define biological species in prokaryotes with the same efficacy as in sexual eukaryotes. By analyzing the impact of recombination on the polymorphisms in thousands of genome sequences, we find that over half of named bacterial species undergo continuous recombination among sequenced constituents, indicative of true biological species. However, nearly a quarter of named bacterial species show sharp discontinuities and comprise multiple biological species. These interruptions of gene flow are not a simple function of genome identity, indicating that bacterial speciation does not uniformly proceed by the gradual divergence of genome sequences. The same genomic approach based on recombinant polymorphisms retrieves known species boundaries in sexually reproducing eukaryotes. Thus, a single biological species definition based on gene flow, once thought to be limited only to sexually reproducing organisms, is applicable to all cellular lifeforms. [ABSTRACT FROM AUTHOR]