Modes and Mechanisms of Speciation PDF

60 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation Hannes Schuler1 , Glen R. Hood1 , Scott P. Egan2 , and Jeffrey L. Feder1 1 Univer...

60 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation Hannes Schuler1 , Glen R. Hood1 , Scott P. Egan2 , and Jeffrey L. Feder1 1 University of Notre Dame, Department of Biological Sciences, 291 Galvin Life Sciences Building, Notre Dame, Indiana 46556, USA , 2 Rice University, Department of Biosciences, 6100 Main Street, Houston Texas, 77088 USA 1 Introduction 62 2 What Are Species? 62 3 Classifying Barriers to Gene Flow 66 3.1 Prezygotic Isolation 66 3.1.1 Temporal isolation 67 3.1.2 Mating isolation 67 3.1.3 Habitat isolation 67 3.1.4 Behavioral isolation 67 3.1.5 Pollination in plants 68 3.1.6 Mechanical isolation 69 3.1.7 Gametic isolation 69 3.2 Postzygotic Isolation 69 3.2.1 Intrinsic postzygotic isolation 70 3.2.2 Extrinsic postzygotic isolation 70 4 Modes of Speciation 71 4.1 Allopatric Speciation 72 4.1.1 Peripatric speciation 73 4.2 Sympatric Speciation 73 4.3 Parapatric Speciation 74 4.4 A Plurality of Modes 74 5 Evolutionary Mechanisms Causing Population Divergence 75 5.1 Natural Selection and Ecology 75 5.2 Sexual Selection 77 5.3 Hybrid, Polyploid, and Homoploid Speciation 78 Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 61 5.4 Reinforcement 79 5.5 The Role of Endosymbionts in Speciation 81 6 Next-Generation DNA Sequencing and the Genetics of Speciation 83 6.1 Next-Generation Sequencing and the Speciation Continuum 83 6.2 Combining Genomic and Experimental Approaches 84 7 Final Thoughts 84 References 85 Keywords Speciation Process where an inbreeding population diverges into different reproductively isolated groups. Genomics Discipline that applies DNA sequencing methods and bioinformatics to analyze the genetic structure of organisms. Gene flow The movement of alleles between different populations. Reproductive isolation Barriers of reproduction and gene exchange between different incipient species. Symbiosis Two or more dissimilar organisms living in close association. In The Origin of Species, Charles Darwin described the formation of new species as the “mystery of mysteries”. More than 150 years after Darwin first posed the problem much progress has been made in discerning what creates the great diversity of life. Spe- ciation is the evolutionary process where a group of inbreeding populations diverges into two or more reproductively isolated groups. In this chapter, we summarize the current understanding of speciation in sexually reproductive organisms. In particular, we describe how barriers to gene flow evolve and focus on the most important fac- tors promoting speciation. Further, we integrate different perspectives by describing recent progress from many different model systems for the study of speciation. Build- ing on this work, we emphasize new genomic approaches to the study of speciation and how advances in DNA sequencing methods will revolutionize our understanding of the genetic basis of the speciation process. We conclude by summarizing our cur- rent understanding of speciation and show that although much of Darwin’s mystery is solved, many important questions remain. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 62 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine 1 further insights and addition information Introduction about the subject [5–13]. It is estimated that there are about 8.7 million eukaryotic species on Earth 2 , with some assessments being as high What Are Species? as 100 million. But what exactly are species, and what evolutionary processes Species are the fundamental units of bio- are responsible for generating this great diversity. It therefore seems logical and diversity of life? Charles Darwin once important to have a working definition of described the formation of new species as what constitutes a species if the process the “mystery of mysteries”. While spe- of speciation is to be studied. Indeed, ciation may be one of the least understood how could the origins of new species be features of evolution , since Darwin’s understood if we had no idea how to define time much progress has been made in a species or what separates one species discerning how speciation occurs. In par- from another? ticular, the mystery of how genetic barriers There is still ongoing debate about what to gene flow can evolve to reproductively a species is and whether Darwin himself isolate formerly interbreeding populations defined species. While there are some who to generate new sexual species is solved insist that, in The Origin of Species Darwin in large part, although many important failed to define species, he did in fact questions still remain. describe species as groups of individuals In this chapter, the current understand- that maintain observable discontinuities ing of speciation in sexually reproducing when and where they co-occur. In other organisms is summarized and some of the words, species can be defined by gaps that more important factors and mechanisms exist in the distribution of the diversity of involved in speciation are highlighted. life. One of Darwin’s great contributions to First, an investigation is made into how biology and natural history was seeing that species are defined, after which an outline species were not static. Rather, the gaps is provided of what constitutes the barri- are dynamic due to species being contin- ers to gene flow and the nature of traits ually created and changing through time. causing reproductive isolation (hereafter Ultimately, if the gaps among species were abbreviated RI). Next, different modes of traced further and further back into the speciation (largely geographically defined) past, they would disappear and converge are examined and the different mechanisms into nested sets of shared common ances- that can underlie the evolution of RI and tors. Life is therefore a tree of diversity, the formation of new species are elaborated with species being the various discernible on. Finally, future avenues of research are branches (evolutionary lineages) hierar- discussed, with attention focused on how chically connected to one another through technical advances in DNA sequencing can time by shared ancestry. Broadly speaking, accelerate the understanding of the genetic species could be conceptualized as lineages basis for speciation. The reader is also that have different evolutionary trajectories referred to several excellent recent reviews branching from one another on the tree of and books on speciation that provide life. Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 63 The existence of RI is now generally con- hybridization occurs and some regions sidered the critical criterion for recognizing of the genome may move (introgress) different evolutionary lineages as species, between populations, while others do not. epitomized by the conceptualization of As speciation is usually not a singular sexual species as groups of actually or event in time but rather is a continuous potentially interbreeding natural popula- process that unfolds over thousands, tens tions, which are reproductively isolated of thousands, hundreds of thousands, or from other such groups. This view millions of generations, where should the was termed the Biological Species Concept line be drawn along this continuum of (BSC) by Mayr [15, 16], and it roots can population divergence and decreasing gene be traced back further to other biologists flow to designate species (Fig. 1)? Clearly, including Theodosius Dobzhansky , there may not be a demarcation that all Eduard B. Poulton , Benjamin Walsh agree on. As a result, some have argued that and John Ray. Thus, the BSC holds species represent arbitrary and artificial that species will not exchange genes often constructs of the human mind stemming enough with other species through sexual from a need to define and organize entities reproduction to lose their distinction, if and into different categories. when they were to co-occur. This criterion Furthermore, what specifically is being can be problematic for asexual organisms referred to by gene flow? Is the metric of such as bacteria that, like sexual species, gene flow a measure of the overall level of can form distinct units of biodiversity, hybridization, or a mean rate of genetic but unlike sexual organisms, reproduce introgression for all genes in the genome (divide) by binary fission. Nevertheless, between populations – is RI a property the BSC is useful because it defines the of the entire genome? Or, alternatively, central problem of studying speciation is reference being made to those genes for sexual organisms as an understanding showing the lowest or highest degree of of how heritable barriers to gene flow exchange between populations – is RI a evolve that separate formally interbreeding genic characteristic of individual genes [23, populations into reproductively isolated 24]? During speciation, populations may species. show great heterogeneity in the porousness So why is there still a problem defining of different regions of the genome to intro- species? Much of the reason stems from gression. It is therefore not always clear the difficulty in determining at what level how a summary statistic such as the gross of RI (reduced gene flow) populations migration rate or frequency of hybridiza- should be considered varieties or races tion effectively translates into species versus species. Obviously, elephants and status. Of course, the same consideration mice represent “good species” that do not applies to estimates for individual genes. hybridize where they co-occur and, thus, do Nevertheless, during speciation the effects not exchange genes through sexual repro- of individual traits and genes on RI can duction and remain distinct evolutionary become coupled, synergistically reducing lineages. Hence, there is no ambiguity gene flow, and elevating divergence more when RI is complete. However, often taxa uniformly across the genome [25–31]. that many biologists would recognize Thus, it is possible that marked increases in as different species are not separated by RI may be observed as lineages diverge. absolute genetic barriers to gene flow: some If this were true, then it may be possible © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 64 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine Reproductive isolation Genotypic clustering Lineage sorting Geographic or ecological clines Genetic divergence Weak Strong Fig. 1 Overview of different stages of popula- according to their genotypes and what a genetic tion divergence along the speciation continuum cline might look like between the populations if from races or biotypes (on left) to completely iso- they were to have a parapatric distribution due lated taxa (on right). Shown are how idealized to primary or secondary contact. Modified from populations of individuals are expected to cluster Ref.. to compare metrics of RI between pairs of or absolute, RI considered alone from a populations at different stages of divergence practical standpoint can be difficult to along the “continuum of speciation” from interpret as a metric for delineating species. freely interbreeding populations, to races, In this spirit, a number of ideas have been to subspecies, to completely isolated taxa, proposed to operationally define species as and associate the transitionary phase of distinct genotypic clusters of individuals, accelerate RI to species formation. as groups of related individuals sharing a However, such a scenario requires further common genealogy, and as distinct phy- testing to determine its generality and may logenetic clades whose members can be be difficult to apply in a uniform manner to distinguished by their possessing a uniquely all groups, especially those lacking several evolutionarily derived trait(s) (termed populations at varying stages of divergence. autapomorphies) [23, 32–34]. These The key point is that while conceptually various definitions can be thought of as rep- appealing as a framework for understand- resenting different stages of divergence for ing speciation, unless essentially absent lineages along the speciation continuum on Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 65 the tree of life, from varieties to completely an autapomorphy under a phylogentic or reproductively isolated taxa (genotypic cladistic species concept would suggest clusters < shared genealogy < clades) (see no gene flow and complete RI (although it Fig. 1). Moreover, when applied to is possible that very strong selection on a sexually reproducing organisms, genotypic specific trait could produce the appearance clusters, shared genealogy and the presence of near fixation with gene flow), which of autapomorphies are all the result of heri- would put us back in the same quandary table barriers to gene flow evolving between that was faced before with the BSC. Only sexually reproducing populations. Conse- taxa that are completely isolated could be quently, at their core, all the definitions are easily identified as species. conceptually linked to the BSC and, thus, The take-home message with respect to they all share potentially the same difficulty the question of defining species is therefore of imposing a biologically arbitrary divide that it is easy to become quickly lost and on the continuous process of speciation. not see the forest through the trees. All For example, when are genotypic clusters paths eventually lead back, however, to the distinct enough to be considered species crucial problem of speciation highlighted versus representing intraspecific poly- by the BSC for sexually reproducing organ- morphisms? With gene flow, there will be isms: discerning the nature and origins of some individuals of parental and/or mixed heritable barriers to gene flow that evolve ancestry in both populations. So where to separate populations. As a result, there should the divide be set? Is it sufficient may not be universal agreement on when that genotypic clusters just be observed at two populations (lineages) have diverged local “sympatric” (i.e., complete geographic to the point of being considered different overlap of populations) sites to consider species (Fig. 1). However, this does not two populations as species, or must all necessarily mean that species are not real local populations cluster distinctly from and natural entities. As populations diverge, one another across the entire range of “gaps” will evolve that distinguish taxa as geographic overlap to designate species differentiated genotypic clusters, groups of status? Certainly geographic variation individuals sharing a common genealogy, within taxa (e.g., clines or drift in local or phylogenetic clades possessing uniquely populations) could potentially play havoc derived traits. However, drawing a hard with the global clustering of populations line demarking species is problematic across the landscape. Similar questions and, in this regard, named species may also arise with respect to the genealogical be considered somewhat arbitrary human definition, unless gene flow has ceased constructs of convenience. Nevertheless, it for a period of time between populations. is clear that the central issue of speciation Moreover, with a heterogeneous pattern is the same no matter what one’s favorite of divergence, longstanding polymorphism definition of a species: to understand (genetic variation) and/or a degree of gene speciation requires identifying the traits flow, alleles within an individual can have and factors causing RI among populations differing genealogies, with some variants of sexually reproducing organisms and more closely related to genes in the alter- their genetic bases and historical origins. nate population. What then is the genealogy This pursuit is at the heart of the BSC and of these individuals? Is the decision made unites all the various definitions of species. by majority rule? Finally, the presence of Similar considerations may actually apply © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 66 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine to most asexual organisms (e.g., bacteria occur before mating by restricting indi- can exchange parts of their genomes dur- viduals from different populations from ing conjugation). However, the issues of copulating with each other. It can also whether asexual species exist, what consti- occur after mating by impeding the union tutes an asexual species, and how they may of gametes (fertilization) to form a zygote. form are beyond the scope of this review. Because prezygotic isolation acts earlier in the life cycle of sexually reproducing organisms than postzygotic barriers, it can 3 have a relatively greater effect on reducing Classifying Barriers to Gene Flow gene flow between populations [7, 39]. For example, consider two factors – one prezy- After pondering what sexual species are gotic and the other postzygotic – that each and, in the process, defining the seminal cause a 50% reduction in gene flow. If two taxa come into contact, the first prezygotic issue driving speciation research, the dif- factor reduces the net rate of effective gene ferent ways in which populations can be flow between the taxa by 50%. However, the reproductively isolated from one another second postzygotic factor only reduces the can now be discussed. Two pioneers in this net rate of gene flow by 25% (= 0.5 × 0.5), area were Poulton and Dobzhansky because the prezygotic factor already , who recognized the importance of acted to restrict genetic exchange between two major divisions of RI constituting the taxa by half. In addition, prezygotic prezygotic and postzygotic barriers to gene isolation (in the form of mate choice) can flow (see Table 1). directly affect who mates with whom. Thus, prezygotic isolation can generate assor- 3.1 tative mating for traits under divergent Prezygotic Isolation selection, increasing the effectiveness of selection in differentiating populations Prezygotic isolation refers to RI that occurs and reducing gene flow beyond the direct prior to zygote formation [8, 38]. It can effects of prezygotic isolation alone. Finally, Tab. 1 Outline of heritable barriers to gene flow between population causing RI. Geographic isolation Geographic barriers prevent gene flow Premating Behavioral isolation “Sexual isolation” different mate signals prevent populations from mating Prezygotic Ecological isolation Adaptation to different habitats and/or different activity or breeding time can inhibit gene flow Mechanical isolation Different genitalia structures impede successful transfer of sperm despite attempted mating (copulation) Gametic isolation Transferred gametes cannot effect fertilization Postmating Extrinsic Ecological inviability: hybrids fall between parental ecological niches Behavioral sterility: hybrids are less attractive (and successful) in Postzygotic obtaining mates Intrinsic Hybrid inviability: hybrids suffer developmental problems Hybrid sterility: hybrids suffer reproductive problems and produce fewer number or no functional gametes Modified from Ref.. Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 67 by preventing the formation of zygotes, species complex (Fig. 2), where different prezygotic isolation can potentially impact species such as the two host races of R. the entire genome. This may or may not pomonella, the blueberry maggot Rhago- be the case for postzygotic isolation when letis mendax, the snowberry fly Rhagoletis hybrids form and are partly viable and zephyria and the undescribed flowering fertile. dogwood fly have diverged, in part, due to There are several different types of prezy- preferring to mate on different host plants gotic isolation, as highlighted below. [41, 47, 48]. Other cases of divergence associated with habitat choice involve pea 3.1.1 Temporal isolation aphids , walking sticks in the genus Differences in the time of tissue availability Timema [50, 51] (Fig. 2), and three-spine of plants (e.g., flowering time) or in the sticklebacks (Fig. 2). mating time of animals are ways that individuals in different populations can 3.1.3 Habitat isolation become seasonally or temporally isolated Prezygotic isolation can also stem not only from one another. Examples of this type from habitat choice but may also be due to of “temporal” or “allochronic” prezygotic differential performance or adaptation to isolation include the apple maggot fly, alternate habitats. For example, migrants Rhagoletis pomonella, where apple and from different populations may not survive hawthorn host races of the fly are isolated well in non-natal habitats, and thus not by a difference in the fruiting times of their mate and be prezygotically isolated from respective host plants [40, 41], members of resident individuals. Adaptation to the Enchenopa binotata species complex of different environments may also change treehoppers that are adapted to differences the behavior and appearance of organ- in when the phloem of their host trees flow isms in different habitats that can result [42, 43], periodical cicada that differ in their in individuals avoiding mating with one emergence times (14 years versus 17 years), another. and the pine processionary moth, Thaume- topoea pityocampa, that has summer and 3.1.4 Behavioral isolation winter populations that are behaviorally Behavioral differences in mate preferences and genetically differentiated. can also reduce crossbreeding between populations. This can occur through 3.1.2 Mating isolation “sexual isolation” in which individuals Individuals from different populations may from different populations prefer different behaviorally prefer to mate in or on their signals or courtship displays to mate. Such natal home turf [45, 46]. Such differences in differences have been proposed to evolve habitat choice can translate directly to mate by a number of different means of sexual choice, and establish systems of positive selection including runaway, chase away assortative mating in which individuals (sexual conflict), good genes and sensory tend to mate with other individuals of like drive (for reviews, see Refs [27, 53]). Several preferences and traits. Thus, differences in examples exist in which differences in where organisms prefer to mate can also mating cues result in prezygotic isolation. result in prezygotic RI and be important In birds , amphibians [55, 56] and catalysts for speciation. Examples of habitat insects there are many cases in which or host choice include the R. pomonella females do not respond to the acoustic © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 68 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine (a) (b) (c) (d) (e) (f) Fig. 2 Model organisms of speciation. (a) The of the genus Heliconius (© Montse Poch); (e) apple maggot fly, Rhagoletis pomonella (© Hannes the cichlid Pundamilia nyererei (© Greg and Lee Schuler); (b) the three-spined stickleback, Gasteros- Ann Stevens); (f ) a Timema stick insect (© Moritz teus aculeatus (© Ingo Seiel); (c) the annual phlox, Muschik). Phlox drummondii (© Gertrud Kanu); (d) butterfly signals produced by heterospecific males As a consequence of these behavioral. Chemical signals where males do differences, pollinators can affect the not respond to pheromones produced evolution of floral morphology and the by females of different species represent movement of pollen (gene flow) among chemosensory prezygotic barriers. For plants, which potentially leads to speciation instance, chemoreception plays a major. Phylogenetic studies have suggested role in mate detection in different moth that plant speciation is not uncommonly species, and this may lead to behavioral accompanied by changes in the pollination isolation. Finally, visual signals where system. Genetic studies have shown females respond to a conspecific color or that changes of a few genes can influence pattern in males play a significant role in floral differences and affect pollinator behavioral isolation in butterflies and birds. activity , whereas RI due to hybrid Species of the neotropical butterfly genus sterility can have a more complex genetic Heliconius differ in wing pattern, and males basis [65–67]. It is therefore possible that prefer to mate with females with the same shifts in traits affecting pollination and wing pattern [60, 61]. pollination systems leading to RI have the 3.1.5 Pollination in plants potential to occur more rapidly or readily In contrast to animals, behavioral prezy- than other forms of isolation in plants. It gotic isolation in plants is often caused should be noted, however, that additional by differences in the animals or insects forms of prezygotic isolation in plants pollinating the plants. Pollinators often associated with pollen tube growth and vary in their preferences for visiting flow- egg/sperm compatibility also have the ers of different size, shape, and color. potential to evolve rapidly and be major Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 69 factors underlying RI and speciation in or cross-attraction between gametes, plants. failure of fertilization at gametic contact, or a reduced rate of oviposition. 3.1.6 Mechanical isolation Competitive isolation: This results when Mechanical isolation due to incompatibil- sperm of different taxa are present in the ities between the reproductive structures reproductive tract of a female at the same of organisms is another form of prezygotic time and conspecific sperm are favored isolation. In animals, different species can over and fertilize a disproportion number evolve different-shaped sex organs that do of eggs than heterospecific sperm. In not fit properly between males and females. the absence of conspecific sperm, het- Dufour was the first to describe such erospecific sperm alone may not show a a “lock-and-key” mechanism where the dramatic reduction in fertility compared male genitalia (the key) in one taxa evolves to conspecific sperm. Sperm competition in a species-specific manner due to sexual has been documented in ground crickets, selection that eventually does not fit with where multiple mating of a female with the organ (the lock) of interspecific females. a conspecific and a heterospecific male One of the best-studied examples is the resulted in the fertilization of the majority sympatrically overlapping Japanese carabid of the eggs by the conspecific male and beetles Carabus maiyasanus and Carabus between conspecific pollen grains in the iwakianus that show low hybridization stigma of plants. because of mismatching genitals between males and females of different species The take-home message with respect to. In plants, mechanical isolation can prezygotic isolation is that there are many occur if structures of the flowers hinder different ways, both prior to and after mat- the capture of pollen from other species ing, that the gametes of different taxa can. Moreover, an analogous form of RI be prevented from fusing to form zygotes. to mechanical isolation can occur if key Given that prezygotic RI impedes gene flow features of pollinators, such as the beak of a before postzygotic RI in the life cycle, it bird versus the proboscis of a moth, vary in can generate assortative mating for traits a manner such that they differentially fit in under divergent selection, and can also the flowers to different plants and, thereby, affect pollen transfer. potentially affect the whole genome. Thus prezygotic RI may often be an important 3.1.7 Gametic isolation component to speciation, particularly in Gametic isolation (postmating prezygotic cases of speciation with gene flow. isolation) can occur if gametes of different species fail to unite. Coyne and Orr 3.2 Postzygotic Isolation defined two different types of gametic isolation: Postzygotic isolation occurs when zygotes Noncompetitive isolation: This is due (offspring) produced from “hybrid” mat- to the poor transfer of sperm between ings are inviable or sterile. Postzygotic different taxa, the inviability of gametes RI can be due to negative interactions in the reproductive tract of females of the of hybrids with external environmental opposite taxon, poor movement of sperm conditions (extrinsic), or due to internal © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 70 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine genomic incompatibilities independent of the effects of recessive mutations differing the environment (intrinsic). between species can be exposed. Haldane’s rule will result when in a hemizygous state 3.2.1 Intrinsic postzygotic isolation in the heterogametic sex (i.e., when an Intrinsic genomic hybrid incompatibility individual has only one copy of a sex-linked was first postulated by Bateson in 1909 gene instead of the usual two copies in , and elaborated upon and empirically diploids), these mutations have greater studied by Dobzhansky and Muller negative consequences on fitness (more in different Drosophila species. Under than twice) than in a heterozygous state in the Bateson–Dobzhansky–Muller (D-M) the homogametic sex. There is generally model, populations initially become geo- widespread adherence to Haldane’s rule graphically isolated and independently in different mammal, bird, and insect evolve different mutations. Following sub- species , regardless of which sex is sequent secondary contact, when hybrids heterogametic. form, they will possess mutations from D-M incompatibilities are not the only the two populations that, when brought causes of intrinsic hybrid sterility. Meiotic together for the first time in individuals drive that occurs when one gene or hap- of mixed ancestry, can interact negatively lotype is inherited by more than half of with one another and cause sterility or invi- the progeny, generating a segregation ratio ability. RI is considered intrinsic because differing Mendelian expectations can also the developmental irregularities occur and cause intrinsic hybrid sterility. In this are consistent regardless of environmental case, different selfish meiotic drive systems conditions , which is not the case for and their “suppressors” can independently extrinsic isolation. evolve in allopatric populations. When One important characteristic of intrinsic brought together in hybrids the different RI is that, under certain circumstances suppressor systems may not act properly, depending upon the nature of interac- and the drive systems can become active, tions in developmental and physiological resulting in reduced gamete production pathways, the number of loci contributing in hybrids and leading to their sterility. to D-M genomic incompatibilities can Similar considerations can also apply to exponentially increase (“snowball”) through transposable elements, where active ele- time. If individual incompatibilities ments in hybrids can result in both intrinsic have roughly equivalent effects on fitness, sterility and inviability. then the increase in contributing loci can result in a corresponding nonlinear increase 3.2.2 Extrinsic postzygotic isolation in the rate that intrinsic RI evolves between In contrast to intrinsic isolation, extrinsic populations. postzygotic isolation can evolve both in Another feature of intrinsic RI is that allopatry and in cases of speciation with it may evolve at different rates between gene flow (see below). Another distinction sexes. Haldane’s rule states that when is that extrinsic postzygotic isolation is eco- hybrids of one sex are disproportionately logically context-dependent. Thus, hybrids sterile or inviable, it will most often be may not suffer any inherent loss of fitness the heterogametic sex (i.e., the sex of a when reared, for example, under benign species in which the sex chromosomes are conditions in the laboratory, but they fare not the same). In the heterogametic sex, poorly in Nature. Thus, extrinsic RI is Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 71 not due to inherent negative interactions Indeed, in cases of allopatric (geographic) among genes per se, but results from the speciation (see below), when there is no way in which these genes interact with chance for hybridization between diverging the environment to cause hybrids to have populations, there is no reason to assume reduced fitness in the wild. In general, it that postzygotic isolation should not evolve appears that extrinsic postzygotic isolation at the same rate as prezygotic RI. often evolves before intrinsic isolation , suggesting that divergent ecological adaptation may often play a critical role in 4 initiating speciation. Modes of Speciation One study examining the role that extrinsic postzygotic RI plays in population Modes of speciation are usually defined on divergence involves populations of the the basis of the geographic distribution of stickleback fish, Gasterosteus aculeatus populations during the speciation process (Fig. 2), which is endemic to lakes in British (i.e., the degree and pattern of spatial Columbia. Here, the fish have evolved overlap of diverging populations as RI repeatedly and in parallel into two different evolves). Major geographic modes include ecomorphs: one living in the limnetic zone allopatric (complete physical separation of (open water area lakes), and the other in populations), parapatric (partial geographic the benthic zone (deeper level). Although overlap of populations) and sympatric crosses between the two morphs result in speciation (complete geographic overlap of viable offspring in the laboratory, hybrids populations). Parapatric speciation can be perform poorly in Nature and grow more further divided into instances of primary slowly than the parental morphs [79–81]. versus secondary contact. In cases of Hybrids have phenotypes generally less primary contact, the diverging populations well-suited for utilizing benthic and lim- were always connected by a region of netic niches than their parents and, thus, geographic overlap where gene flow was suffer decreased fitness and viability [79, occurring as they evolved into different 81]. A similar example comes from ecologi- species. In contrast, in secondary contact, cally divergent, host-associated populations populations were initially geographically of Neochlamisus bebbianae leaf beetles, separated and diverged in allopatry before where F1 and backcross hybrids grow expanding their range(s) to geographically slower on both host plants than do the overlap and hybridize. Distinguishing parental forms [82, 83]. between these two possibilities is important The take-home message with respect to because it bears on the question of whether postzygotic isolation is that, like prezygotic speciation is possible without the complete RI, there are many different ways that fol- geographic isolation of populations at lowing zygote formation, hybrid offspring some stage of the process (see Refs [4, 38, can suffer reduced fitness and fail to sur- 84–86] for further discussions of differ- vive, produce viable gametes, and/or mate. ent geographic modes of speciation and Given that prezygotic RI is not expected to controversy surrounding them). be complete early in speciation, postzygotic In addition to geography, different modes RI is also likely to evolve and be an impor- of divergence can also be defined based on tant contributor to reducing gene flow the mechanism(s) causing divergence. For during the speciation process for most taxa. example, in ecological speciation, RI results © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 72 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine from populations differentially adapting to between the populations, whether due different environments or habitats due to to genetic drift or directional and diver- divergence selection. Adaptations advan- gent selection, can potentially generate tageous in one habitat may be detrimental RI by any of the means discussed above in others, resulting in the reduced viability (D-M incompatibilities, ecological fitness or fertility of migrants and hybrids causing tradeoffs, sexual selection, polyploidy, fitness tradeoffs [4, 5, 8]. In contrast, in translocations, etc.). Indeed, certain types mutation order speciation, genes under of RI, like those due to intrinsic D-M directional selection to similar ecological incompatibilities, are more likely to evolve conditions or experiencing drift can differ- via a geographic than non-geographic entiate between two geographically isolated mode. The reason for this is that mutations populations [5, 87]. When brought back causing genomic incompatibilities which together for the first time, these loci can result in reduced fitness will normally be negatively interact and cause postzygotic RI eliminated by selection in populations. and D-M incompatibilities. Various other However, in allopatric populations these chromosomal modes of speciation have mutations may not cause incompatibilities also been proposed in which differences in and could, in fact, be favored by natural ploidy levels (the number of complete sets selection. It is only when the mutations of chromosomes individuals possess) or that have accumulated independently in structural features of chromosomes (e.g., isolates are brought together for the first inversions, translocations, or chromosomal time in hybrids that they interact negatively fusions or fissions) disrupt proper meiosis and inadvertently causing sterility and in hybrids and generate RI. inviability. Thus, geographic isolation may be a common precursor to speciation for 4.1 many organisms, especially those that Allopatric Speciation primarily display strong intrinsic RI. One indication of the importance The important role that geographic isola- of geography in population divergence tion can play in facilitating speciation was and speciation is the observation of first emphasized by Poulton and under- reproductive isolation-by distance (RIBD) scored by Mayr [15, 16]. Speciation could [89, 90]. In RIBD, the degree to which be thought of as a “tug of war” between pairs of populations are genetically dif- evolutionary processes causing populations ferentiated and reproductively isolated to diverge from one another, and migration from one another is correlated with the and gene flow causing them to homoge- geographic distance separating them. Thus, nize. Whichever force is stronger will win increased geographic separation – and, by out. When populations are allopatric and implication, reduced migration and homog- geographically isolated, then the homoge- enization due to gene flow – equates with nizing effects of gene flow can be removed increased divergence and RI between popu- from the speciation equation due to the lations. Ring species are classic examples of lack of migration between populations. RIBD: Populations are distributed in a spa- Essentially, a state of complete prezygotic tially arrayed circle such that, starting at the RI exists between allopatric populations, middle of the ring ever more-differentiated allowing them to evolve independently. populations can be found moving in oppo- Subsequently, any genetic change occurring site directions around the circumference Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 73 until they eventually meet as fully isolated as a prerequisite for speciation in animals. species when they come into contact at However, with the increasing study of its end [15, 91, 92]. Possible examples of the role of ecology and sexual selection ring species include the greenish warbler in speciation over the past few decades (Phylloscopus trochiloides) encircling the [98–102], sympatric speciation has gained inhospitable Tibetan plateau [91, 93], and greater acceptance among evolutionary the Ensatina eschscholtzii salamanders biologists as being possible and occurring encircling the inhospitable central valley of at least part of the time in Nature [46, California. 103]. In contrast to allopatric speciation, where 4.1.1 Peripatric speciation speciation is initiated in the absence of gene Peripatric speciation is a type of allopatric flow, sympatric speciation occurs between divergence where small satellite popula- geographically overlapping populations in tions become geographically isolated on the face of continuous gene flow. A the fringes of the distribution of what central tenet of many sympatric speciation usually is a larger central population. models is that strong fitness tradeoffs Often, these peripheral populations pass exist, resulting in host or habitat specialist through a genetic bottleneck and experi- populations evolving that are reproduc- ence founder effects when they colonize tively isolated from other populations by areas at the boundaries and beyond of the ecological barriers to gene flow [45, 46]. species range. They can also expe- Sympatric speciation is generally thought rience strong selection due to differing to be difficult since gene flow will prevent environmental conditions at the edge of the evolution of specialization and RI [16, the range, as well as be subject to extensive 38]. However, both theoretical models genetic drift due to their smaller effective [104–106] and empirical studies [47, 100, population sizes. All of these factors 101, 107] have shown that, under certain can contribute to rapid genetic change in circumstances, speciation with ongoing peripatric populations that may result in the gene flow can occur. “Magic traits” in which origin of a new species. The colonization the same traits or loci under divergent of oceanic islands or archipelagoes may ecological selection also are involved in present conditions potentially conducive to mate choice and positive assortative mating peripatric speciation. One possible example can also facilitate speciation with gene involves the radiation of a myriad of differ- flow , as can frequency-dependent ent Drosophila species that are endemic to selection on resource use generated by different islands in the Hawaiian chain. competition (adaptive dynamics) [108, 109]. 4.2 One of the best-studied examples of Sympatric Speciation sympatric speciation is the apple maggot R. pomonella, a major economic pest of While allopatry is a widely accepted and apples in North America [47, 100, 110, common mode of speciation , sym- 111]. The native ancestral host for R. patric speciation in the absence of complete pomonella is hawthorn (Crataegus sp.). geographic isolation and in the face of After introduction of the domesticated continuous gene flow is more controversial. apple Malus domestica to North Amer- Indeed, Mayr [16, 97] considered allopatry ica about 400 years ago, a portion of the © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 74 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine hawthorn-infesting population shifted parapatric divergence via the evolution of to and started to attack sympatrically different opsin genes that enable them to occurring apples [47, 112]. Within less than see at different water depths. 150 years this led to the formation of eco- logically and genetically differentiated apple 4.4 host race of the fly [47, 100, 111]. A number A Plurality of Modes of other closely related and morphologically similar sibling species are sympatric with The strict geographically based division of R. pomonella and attack different host speciation into purely allopatric, sympatric plants native to North America. These or parapatric modes may not always reflect considerations led Bush to propose the reality of speciation [110, 118]. During that the whole R. pomonella sibling species speciation, the geographic distribution of group arose via sympatric host shifts. In this populations may change over time, and case, fly taxa attacking flowering dogwood, RI may evolve at times when populations blueberries, snowberries and silky dogwood were alternately in allopatry, parapatry, and plants are in varying stages of ecological sympatry. Indeed, the genetic bases for divergence along the speciation continuum speciation may often have originated at a ranging from host races to morphologically different place and time than the proximate distinct species [113–116]. selection pressures causing population divergence. For instance, secondary contact 4.3 of geographically isolated R. pomonella Parapatric Speciation populations in the past appears to have led to the introgression of raw genetic Populations are partially geographically iso- material that affected diapause traits and lated during parapatric speciation (Fig. 2). contributed to the genetic shift of host races Parapatric speciation can occur when in sympatry [110, 119]. Similar examples of populations adapt to different ecological “transporter” speciation involving standing habitats or accumulate different mutations genetic variation “recycled” to contribute by selection or drift in different portions of to independent adaptive divergence have their ranges, but still at least partially over- been documented for stickleback fishes lap in their distributions such that gene flow and Heliconius butterfly hybridization is ongoing. Thus, the overall rate of gene. Moreover, different types of RI may flow is higher than in allopatric speciation, have evolved and contributed to popula- but lower compared to sympatric speci- tion divergence at different stages of the ation. Although, in principle, parapatric speciation process. Thus, Dieckmann et al. speciation may be common it is perhaps have classified different “routes” to the most difficult mode to verify. His- speciation, involving varying combinations torical data of past species ranges are often of factors, modes and mechanisms of missing, making it difficult to determine if population divergence through time. In currently overlapping taxa represent cases addition, several authors (e.g., Refs [123, of parapatric divergence versus secondary 124]) have advocated for a reclassification contact of taxa that already completed of RI models from the current framework the speciation process in allopatry prior dominated by geographic context to one to their present overlap. Certain cichlid that includes mechanisms of speciation. fish in Africa may represent examples of The take-home message is that one size Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 75 does not fit all, and that speciation may process when hybridization is common. often involve a plurality of different modes The reason for this is that alleles and new and mechanisms through time and space. mutations that cause intrinsic reductions in fitness in hybrids in all habitats will usually be quickly eliminated from populations. 5 However, under certain circumstances, Evolutionary Mechanisms Causing Population as populations progress further along in Divergence speciation and effective gene flow rates become significantly reduced, it is possible As discussed above, a number of factors for new mutations that cause both fitness and mechanisms interact to cause popula- tradeoffs and intrinsic genomic incompat- tions to evolve and become reproductively ibilities between populations to establish isolated from one another and eventually in sympatry or parapatry, as long as the speciate. Some of these processes are negative pleiotropic consequences of the examined in more depth in the following mutations are comparatively less than the sections. survival advantage they confer in favorable habitats. 5.1 Allopatric populations can also evolve Natural Selection and Ecology intrinsic RI when adapting to the same environmental conditions. Here, allopatric Natural selection may be the most impor- populations can independently accumu- tant single factor responsible for the late different sets of beneficial mutations origin of new species. Divergent ecological that are universally favored across all selection can generate extrinsic RI and populations. However, these mutations facilitate speciation between populations in may pleiotropically cause genomic D-M allopatry, parapatry, or sympatry. In effect, incompatibilities in hybrids. Thus while traits adapting individuals to one habitat beneficial, they may not spread between result in reduce fitness in the alternative populations following secondary contact, habitat (tradeoffs) such that migrants and remain diverged, and contribute to RI, individuals of mixed hybrid ancestry have leading to speciation (termed “mutation lower survivorship, fertility and ability to order” speciation [5, 87]). In sympatry, attract mates than parental types. Divergent it is difficult for intrinsic RI to evolve ecological selection pressures can include due to adaptation to the same ecological abiotic and biotic factors such as food conditions. Any new universally favored resources or climatic conditions, as well as mutation will quickly spread between pop- interspecies interactions such as diseases, ulations, and any allele(s) causing intrinsic competition, and behavioral interference reductions in fitness will be selectively [5, 123]. removed from populations. Similarly, in Divergently selected genes can also the overlapping portion of the range of inadvertently cause D-M incompatibilities parapatric populations it is also difficult for in hybrids. This indirect effect of divergent D-M incompatibilities to evolve via adapta- selection in generating intrinsic RI will tion to similar ecology. However, they can generally be more common in cases of still evolve if the mutations contributing to allopatry than parapatry or sympatry, at intrinsic RI arise in the non-overlapping least early in the speciation with gene flow portions of the population ranges. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 76 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine Empirical evidence for a role of selection about them can be complicated. Not only in allopatric speciation can be seen in the are mapping and functional studies needed molecular patterns of evolution displayed to identify candidate loci, but also details by several putative “speciation genes” that of the natural history of populations must have been associated with D-M incompat- be discerned to establish the evolutionary ibilities. In these cases, statistically high chronology of RI. As discussed above, levels of replacement substitutions in cod- several potential speciation genes affecting ing regions of loci, particularly in relation intrinsic postzygotic RI have been char- to levels of standing non-synonymous poly- acterized, many in Drosophila (Table 2). morphism, imply past episodes of positive For the most part, however, the epistatic natural selection [126, 127]. However, not partners interacting with these genes to all genes under selection and contribut- cause D-M incompatibilities and the nature ing to intrinsic RI are speciation genes. of these interactions still largely remain to Strictly speaking, only genes that diverged be resolved. and increased RI prior to taxa speciating Evidence for a role of divergent natural (or becoming completely isolated) are selection in speciation is most easily doc- truly “speciation genes”. Differences umented in cases of speciation with gene that evolved afterward represent post- flow. Here, the logic is that genes and traits speciation divergence. As a result, verifying not under selection or not closely physically speciation genes and drawing inferences linked to such genes will be homogenized Tab. 2 Selected overview of “speciation genes” causing intrinsic RI hybrid inviability and sterility. Gene Organism Details References Hybrid inviability cytc Tigriopus californicus A mitochondrial gene [128, 129] that interacts with nuclear genes Lhr, D. simulans, Two functionally Hmr D. melanogaster divergent genes that cause hybrid lethality NB-LRR Arabidopsis thaliana Disease resistance gene Nup69, D. simulans, Interaction of different Nup160 D. melanogaster nuclear pore complex proteins Hybrid sterility Aep2 S. bayanus, Incompatibility of S. cerevisiae mitochondrial and nuclear genome OdsH D. simulans, Homebox gene that [134, 135] D. mauritiana causes enhancement of sperm production Overdrive D. pseudoobscura Causes RI and segregation distortion in F1 hybrids Prdm9 Mus musculus Encodes a histone H3 methyltransferase Modified from Ref.. Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 77 by gene flow. Hence, genome scans of the speciation of different plant taxa (e.g., genetic markers between populations can Helianthus, Mimulus, Phlox, reviewed in reveal loci showing exceptional divergence Ref. ; see Fig. 2), amphibians (e.g., (outlier loci) that can be inferred to be Bombina ), fishes (e.g., Poecilia ; under divergent selection. Such studies see Fig. 2), and insects (e.g., Heliconius have identified putative “islands of speci- ). ation” containing genes under divergent selection contributing to RI in the genomes 5.2 of several organisms including mosquitoes, Sexual Selection Timema walking sticks, Heliconius butter- flies, flycatchers, whitefish, and sticklebacks In species in which individuals differ in [139–144]. A stronger case for divergent characters that influence mating preference selection can be made if migration and gene and success, sexual isolation can be a factor flow is occurring between populations, causing prezygotic RI. Darwin as it is possible that populations evolved observed that species that have elabo- RI in the absence of gene flow. Under rated sexual characters tend to be more certain conditions, this could result in species-rich than those that do not and, patterns of genomic divergence similar to thus, suggested that the evolution of sexual those predicted in sympatric and para- characters may cause sexual selection and patric speciation [145, 146]. In addition, be involved in speciation. divergent selection may be differentiation Sexual selection can occur between populations if the markers in genomic individuals of the same sex, or involve regions displaying significant divergence interactions between individuals of dif- are associated with different traits or ferent sexes. Intrasexual selection environmental/ecological conditions. The involves competition between individuals latter can be accomplished through genetic within a given sex (usually males) to gain mapping studies involving test crosses reproductive access to the opposite sex of individuals with differing phenotypes, (usually females). Intrasexual selection can through genome wide association studies lead to the evolution of sexual dimorphism (GWASs) genotyping individuals sampled (phenotypic differences between males and from natural populations that vary in females) that can involve traits associated their phenotypes, and through selection with physical combat, such us antlers in experiments in which key environmental deer or horns in beetles. In contrast, variables are manipulated in the laboratory intersexual selection occurs when individ- or field (i.e., by transplant experiments uals (usually males) compete to be chosen moving individuals between habitats) to by the opposite sex (usually females). Inter- test for a genetic response in predicted sexual selection can lead to the evolution of directions at the speciation islands. Such sexual characters such as the elongated tail a strategy has been used to confirm the of the red-collared widowbird, Euplectes action of divergent ecological selection for ardens or the span between eyes of Timema walking sticks [144, 147] and host the stalk-eyed fly, Cyrtodiopsis dalmanni races of Rhagoletis fruit flies attacking apple. and hawthorn host plants. Several Following up on Darwin’s lead, recent additional studies have described the role comparative studies have confirmed that that natural selection and ecology play in sexually selected taxa are generally more © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 78 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine species-rich , implying that assortative a particular environment , or due mating caused by divergent sexual selection to sensory drive in which males evolve may facilitate speciation. In passer- exaggerated displays taking advantage of an ine birds, for example, clades with more adaptive change in perception associated sexually dichromatic taxa contained more with higher survivorship in a habitat. For species. Sexual selection also appears example, if seeing a particular color is to be an important factor in the radiation of advantageous, males showing this color in cichlid fishes, especially in the lakes of the abundance could gain a mating advantage African Rift Valley (Fig. 2).. In the case of stickleback fish and Although sexual selection can be an African cichlids, traits involved in ecolog- important contributor to RI and speciation ical niche specialization also contribute , major questions remain concern- to positive assortative mating [164, 165]. ing the mechanism(s) responsible for its Empirical and theoretical studies suggest evolution. One central issue is whether that sexual selection may therefore often sexual selection primarily originates due go hand-in-hand with ecological differen- to mating preference differences alone or tiation, forming the basis for “magic traits” is the consequence of ecological selection. facilitating speciation [12, 105]. However, In the former instance, individuals may differences in mating traits can also form choose to mate with the opposite sex based prezygotic isolation without ecological on traits that initially have no inherent differentiation. Moreover, a recent theo- fitness effects on their bearers in and of retical study showed that sexual selection themselves. This represents sexual selection alone enables the overlapping coexistence in the classic Fisherian “run away” sense, of ecologically equivalent species. where peacock females, for example, may Determining whether sexual selection prefer to mate with males possessing a alone plays a direct role in speciation and large tail feather simply because it catches the process responsible for sexual selection their fancy and their sons will, thus, tend (runaway, chase away, good genes, sensory to have large tail feathers too and gain drive, etc.) remain areas requiring much a mating advantage. (Note: “chase further study to verify. away” selection can also occur in which males evolve certain traits that confer 5.3 increased fertility but have detrimental Hybrid, Polyploid, and Homoploid Speciation consequences for females, resulting in a battle between the sexes in which females Hybridization and polyploidization are evolve measures to counteract the effects two – sometimes interrelated – processes of the male traits.) In contrast to that can facilitate speciation. In hybrid the classic Fisher model, sexual selection speciation, interbreeding between two could also be dependent on traits under differentiated populations generates new ecological selection. In this case, adapta- genotypic and phenotypic variation that tion to different environments or habitats serves as the basis for creating new forms can lead to divergence in morphological reproductively isolated from parental pop- characters that influence mate choice ulations. In polyploid speciation, changes. This could be due to sexual selection in the number of whole sets of chromo- for mates advertising their possession of somes in the genome in derived versus “good genes” conferring higher fitness to parental populations can cause problems Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 79 in development or in meiosis in hybrids, sunflowers also appear to have originated generating RI. Polyploid speciation appears by hybridization and inhabit novel, often to be much more common in plants marginal, habitats to which they are diver- than in animals. gently adapted. In contrast to the Hybrid speciation can occur by either butterflies, many genomic components an allopolyploid or homoploid route. from both parental taxa are present in In allopolyploid speciation, hybridization hybrid sunflower species. between different taxa is a trigger for Hybrid and polyploid speciation are polyploidization [170, 171]. The new hybrid now generally accepted as occurring not polyploid, having a different chromosomal uncommonly in Nature. The major question constitution, is immediately reproductively here concerns how frequently homoploid isolated from the parental populations. hybrid speciation occurs, although recent Subsequent ecological adaptation of the studies have suggested that it may be more allopolyploid populations to novel envi- common than previously thought [9, 174, ronmental conditions is often required for 179–181]. the new species to persist and not be dis- placed by parental forms. It is also possible, 5.4 however, for polyploidy to occur without Reinforcement hybridization conspecifically in a process termed autopolyploidy and generate RI When hybridization generates offspring leading to speciation [172, 173]. of lower fitness than parental matings, Homoploid hybrid speciation does not any trait or behavior that causes indi- involve ploidy changes. Instead, hybridiza- viduals to be more discriminant in their tion produces novel combinations of genes choice of partners and mate only with that can adapt hybrids to new habitats those of like kind can be favored. Such or biotic conditions that cause them to circumstances represent one of the few be reproductively isolated from parental cases in which natural selection may populations [174, 175]. Divergent ecolog- directly favor the evolution of increased ical adaptation is thought to be crucial prezygotic isolation between populations in order for hybrid populations to avoid to further the speciation process. being swamped by gene flow from parental This process is termed “reinforcement,” species or being competitively excluded and was first proposed by Alfred Russel. A case study in tephritid flies showed Wallace and later more extensively that hybridization of Rhagoletis mendax and accurately described by Theodosius (that infests blueberries) with R. zephyria Dobzhansky. (that infests snowberries) formed a new There are several important considera- hybrid population that attacks Lonicera tions with regard to reinforcement. First, (honeysuckle). As a consequence of populations must be hybridizing with at infesting and ecologically specializing on least some gene flow occurring for the honeysuckle, the hybrid fly population can evolution of increased prezygotic RI to persist sympatrically with both parental constitute reinforcement. If hybrids populations. Many Heliconius butterflies are completely inviable or sterile, then this may have been formed by hybridization represents “character displacement.” The , involving changes in just a few genes difference may seem semantic, but if gene affecting mimicry. Certain Helianthus flow has ceased altogether between taxa, © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 80 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine then they have already speciated and the selection will generate a degree of dise- evolution of increased prezygotic isolation quilibrium (the nonrandom association of through character displacement is not alleles at different loci) between habitat contributing to the speciation process. choice and performance genes, even for Second, early theoretical studies sug- physically unlinked loci. The reason gested that it was difficult for increased for this is that individuals which survive in prezygotic isolation to evolve in the face a particular environment will tend to return of moderate to high gene flow , as to the same environment to mate (termed it would be difficult for alleles causing “habitat” or “host fidelity” ), creating assortative mating to be maintained in the a system of positive assortative mating correct linkage phase with those causing for choice and performance genes that postzygotic RI. Recombination would break can mitigate the selection–recombination up favored combinations of genes that antagonism and allow speciation with are responsible for mate choice, thereby gene flow to progress. Essentially, a feed- affecting assortative mating and genes back mechanism is established in which causing D-M incompatibilities. Similar increased survival creates stronger selec- arguments pertaining to the antagonism tion pressures for increased reinforcement between selection and recombination were by favoring stronger habitat fidelity and made concerning sympatric speciation sexual selection against hybridization [28,. However, the theory applies only 104]. to two-allele systems, where a polymor- Third, reinforcement is also believed to phism exists for individuals possessing be difficult in circumstances not only when one allele to cause assortative mating and gene flow was moderate to high but also individuals possessing the alternative allele when it was low. Here, selection pressures to do likewise. In one-allele systems, in favoring assortative mating would be which a mutation causes assortative mating reduced because very few hybrid matings between individuals of like phenotypes, would occur. Moreover, in situations of linkage and selection–recombination parapatry, the migration of conspecifics antagonism are not issues. The same from areas outside of the contact zone is true for magic traits, in which the trait (where there would be no selection for responsible for divergent adaptation also assortative mating) could swamp out the directly affects mating and, thus, gen- evolution of any prezygotic RI in the area erates prezygotic RI. For example, of geographic overlap and hybridization. populations adapted to resources that are However, unless there is significant cost to present at different times of the year, such being overly choosy, increased prezygotic as the apple and hawthorn host races of isolation would eventually evolve between R. pomonella, can have different timing postzygotically isolated populations, pro- of life histories matching these resources. vided that the populations maintained their As a result, individuals using the alter- isolation and did not fuse. In addition, nate resources will be temporally offset divergent sexual selection occurring in the from one another, and variations in life allopatric ranges of the populations could history timing will directly affect mate also spill over to the region of contact. choice and result in allochronic mating Here, sexual selection could help further isolation. Moreover, when individuals mate reduce hybridization (for a review, see in preferred habitats, divergent ecological Ref. ). Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 81 A fourth important consideration with and the pioneering work on the regard to reinforcement is that the concept genetics of speciation by Dobzhansky was originally developed for scenarios of led to a focus on the phenotypic effects secondary contact, in which populations of mutations in the genome as being evolved postzygotic isolation in allopa- the ultimate source of RI. As a result, try prior to re-establishing contact and Wallin’s idea sank into oblivion. hybridizing in sympatry or parapatry. However, technical progress in profil- However, as selection against hybrids is a ing microbial symbionts during the past requisite for sympatric speciation , two decades have provided new insights reinforcement can also occur in instances of into the impacts that endosymbionts primary contact in sympatry or parapatry, have on the biology of their hosts and provided that fitness tradeoffs have evolved have rekindled interest in the question between populations. of the involvement of endosymbionts in As discussed above, the role of reinforce- speciation. ment in speciation has been controversial One common endosymbiont is Wol-. However, during the past few decades bachia , which infects a broad range theoretical studies , as well as empiri- of arthropod and nematode hosts. cal evidence in Drosophila fruit flies [189, Wolbachia are maternally inherited, and 190], rainforest frogs , stickleback consequently can increase their trans- fishes , Timema walking sticks mission rate by skewing the reproduction (Fig. 2), the Texas wildflower Phlox drum- of their hosts toward females through mondii (Fig. 2), and birds , have cytoplasmic incompatibility (CI ), bolstered the case for the process. Today, male killing , feminization and it is generally assumed that reinforcement induced parthenogenesis. Recipro- can sometimes be an important contributor cal CI caused by populations possessing to speciation in sympatry, parapatry, and different strains of Wolbachia has been allopatry [4, 196]. a focus of interest because it can gener- 5.5 ate RI contributing to speciation. The Role of Endosymbionts in Speciation When Wolbachia-infected males mate with uninfected females (unidirectional An unexpected and novel mechanism infection), no or few offspring are pro- driving speciation comes from the micro- duced, and all other crosses are fertile bial communities associated with sexually (Fig. 3). As a result, once infection levels reproducing organisms. Endosymbiont have passed a threshold, Wolbachia can bacteria are ubiquitous in animal hosts sweep through a host population [212, and have important consequences for their 213]. When both partners are infected with host’s nutrition , behavior , and different strains of Wolbachia, however, defense against natural enemies , CI also occurs and matings are infertile, including protection against viruses. but now in both directions (Fig. 3). It is The diverse effects of microorganisms on this aspect of CI, where populations have their hosts led Wallin to hypothesize acquired different strains of the bacteria that microorganisms may play a role in (bidirectional infection), that has peaked speciation. The development of modern interest in the possible role of Wolbachia in genetics and gene mapping by Morgan speciation. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 82 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine (a) (b) Fig. 3 Schematic representation of cytoplas- infected with one Wolbachia strain (red dot) mates mic incompatibility. (a) Unidirectional CI occurs with a female infected with a different strain (blue if an infected male (red dot) mates with an unin- dot), and vice versa. fected female; (b) Bidirectional CI occurs if a male One of the first examples that implied a larvae reared on different diets acquired role for Wolbachia in speciation involved different symbionts and displayed strong parasitic wasps of the genus Nasonia. mate discrimination. However, the Nasonia giraulti and Nasonia longicor- prezygotic RI was lost when the flies were nis are infected with different strains of treated with antibiotics, eliminating their Wolbachia, and crosses between these symbionts. Gene-microbe interac- two closely related sister species of wasps tions may also cause postzygotic RI. The resulted in no offspring. However, after beneficial gut community of closely related antibiotic curing, hybrids between the Nasonia species is linked to the phylogeny Nasonia species were completely viable of their hosts , and crosses between and fertile, which suggested that Wolbachia wasps possessing different gut bacteria have had induced bidirectional CI caused RI in resulted in hybrid lethality dying during the early stages of wasp speciation. larval development. However, antibiotic Theoretical studies have confirmed that curing of the gut bacteria showed near nor- high levels of bidirectional CI can reduce mal fitness in the hybrid larvae, implying gene flow and help facilitate speciation that the gut microbiota was responsible for. hybrid lethality. However, CI is not the only mechanism The overall contribution that endosym- by which endosymbionts can cause RI. bionts make to speciation is still contro- Interactions between beneficial bacterial versial , and they may not often be communities and their hosts can influence the primary factor initiating or driving host behavior and cause prezygotic RI. population divergence. However, recent For example, Drosophila melanogaster results have suggested that endosymbionts Vol 2 | No 3 | 2016 © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Rev. Cell Biol. Mol. Medicine Modes and Mechanisms of Speciation 83 can be involved in speciation, and the RI expectation (outlier loci) that represent they cause can make them potential agents candidates for being (or containing) speci- facilitating the evolution of reinforcement ation genes contributing to RI. In addition,. Therefore, it seems reasonable to the pattern of differentiation across the include considerations of symbionts and genome can provide insights into the CI into classic models of nuclear-based genetic architecture of speciation and pos- speciation. sible mechanisms facilitating population divergence. For example, it is becoming increasingly 6 possible to assess whether genes contribut- Next-Generation DNA Sequencing and the ing to RI generally have large or small Genetics of Speciation effect sizes. That is, do just a few genes that have major effects on traits associated with Advances in next-generation (Next-Gen) RI underlie speciation, or are most traits DNA sequencing are quickly changing the responsible for RI polygenic and encoded ability to determine the identity, nature, by many loci of small effect ? Similarly, interactions, and genomic architecture questions concerning whether selection of genes underlying RI and speciation. acting directly on individual genes to cause The ability to sequence the genomes of population divergence (genic speciation), model and non-model genetic organisms or processes involving genetic coupling is accelerating the analysis of the genet- and hitchhiking in which the combined ics of speciation. The new methods are effects of multiple loci together overcome providing an immense number of vari- gene flow to allow speciation to progress able markers that help to answer many (genomic speciation ), can also be different biological questions such as addressed. mapping the location of speciation genes Genome scans may also help resolve in greater detail in the genome, or finding issues concerning the involvement of struc- differentiated genomic regions across tural features of the genome (e.g., inversions the genome of different populations or that locally reduce recombination rates and species. enhance linkage disequilibrium) in facil- itating population divergence [11, 220]. 6.1 Moreover, the ability to survey entire Next-Generation Sequencing and the genomes will allow a more comprehensive Speciation Continuum determination of whether taxa can be distinguished on the basis of: (i) forming Next-generation DNA sequencing tech- distinct genetic clusters; (ii) sharing most niques are allowing genome scans to common recent ancestry; and (iii) possess- be performed between pairs of taxa at ing diagnostically fixed autapomorphies. varying stages of divergence along the In other words, the taxonomic status of speciation continuum. In cases of primary populations can be assessed in reference or secondary contact, in which gene flow to different current genetic definitions of is occurring between populations, such species. In addition, if the coupling of loci genome scans can identify genes (or gene of smaller effect occurs during speciation regions) showing significant differentia- to cumulatively enhance RI genome-wide, tion between taxa above baseline neutral then a marked acceleration in the rate of © 2016 Wiley-VCH Verlag GmbH & Co. KGaA Vol 2 | No 3 | 2016 84 Modes and Mechanisms of Speciation Rev. Cell Biol. Mol. Medicine genomic divergence may be observed as their natal and non-natal host plant envi- populations reach this stage in speciation ronments in Nature and high-throughput [29–31]. sequenced to characterize the genomic Finally, advances in next-generation architecture of early stages of speciation. sequencing enable the comparison of Similarly, Chenoweth et al. released genomes of different species. Having an 12 populations of Drosophila serrata in a annotated genome for an organism in which novel environment and characterized the the locations of protein-coding regions, influence of sexual and natural selection on regulatory regions affecting gene expres- different regions of the genome. sion, and other transcribed sequences are known, can be useful for determining the identities of specific candidate genes or 7 sequences causing RI. With this knowl- Final Thoughts edge, transplant experiments and genetic introgression studies involving repeated In conclusion, students of speciation now live in an era of high-throughput genomics, backcrossing of hybrids to one or the other enabling a greater push to understanding parental types can be conducted to confirm the genetic basis of speciation. However, the involvement of candidate speciation the answers to the mystery of speciation genes in population divergence, and to still rest on combining what can be learned study the nature of their interactions with from DNA sequences with experiments, other loci in causing RI. crosses in the laboratory, and studies of the natural history of organisms in the 6.2 wild. Genomics provides one means (and a Combining Genomic and Experimental powerful one at that!) to help understand Approaches the natural history of the “how and why” of speciation. Genomics will quicken the One of the classic examples of experimental pace of discovery, lead to a wealth of new evolution is the study of Rice and Salt information on the molecular and genetic , who designed a maze with extreme bases of gene flow barriers, and will hasten environments in which individuals of the compilation of comparative data sets D. melanogaster could choose different for meta-analyses to test for broad patterns habitats. These authors showed that, by and possible rules of speciation. How- crossing just individuals from the extreme ever, this information loses significance habitats, selection on extreme habitats when divorced from the proper ecological, caused prezygotic isolation. Combining historical, and phylogenetic context of manipulative laboratory and field trans- speciation. In this chapter, a broad outline plant experiments with Next-Gen DNA has been presented of the current concept sequencing offers a particularly powerful of what species are and how they form. means of characterizing the effects of Yet, it must be highlighted that despite divergent selection on population diver- all of these technical advances, it is still gence and RI. One example involves a necessary to climb back into Darwin’s “tree recent