A guide to the genomics of ecological speciation in natural animal populations

Ecological speciation, the origin of new species via divergent natural selection, is one of the most fundamental and unresolved processes in evolution. Although the evidence for adaptation of organisms to their environment is abundant, the role of ecological selection in mediating species formation remains controversial. This knowledge-gap arises in part from a scarcity of experimental evidence linking environmental selection to the creation of reproductive barriers that ultimately lead to species formation. An experimental framework to investigate ecological speciation consists in studying the genetic architecture of adaptive traits and reproductive isolation in interbreeding populations adapted to contrasting environments. In my thesis I explored the genomics of ecological speciation in plants using the Senecio lautus species complex, a diverse group of plants that have adapted to a broad array of environment across Australia. It has been suggested that local adaptation to different environments will lead to genetic divergence and speciation only if genomic regions controlling adaptive traits are not exchanged between organisms adapted to different niches. This will happen if adaptive genes also mediate reproductive isolation, thus making migration between environments difficult, or leading to poor survival of recombinants. This model of ecological speciation creates testable predictions on the genomic architecture of adaptation: Firstly, genomic divergence between incipient species is expected to be heterogeneous, where a few genomic regions display outlier differentiation. Secondly one expects divergent regions to contain genes affecting fitness in natural environments. Thirdly, these “genomic islands of speciation” will also contain loci controlling adaptive traits and reproduction. In my thesis I tested these predictions using divergent populations of plants from the S. lautus species complex. I used a combination of genomic and ecological approaches to: (i) Describe patterns of genomic differentiation between natural populations across Australia and made inferences about the forces that generated these patterns. Specifically, I tested the repeated and independent evolution of forms to coastal environments and analyzed whether genomic divergence was more heterogeneous between parapatric than allopatric populations. (ii) Demonstrate experimentally that divergent genomic regions contain genes controlling differential survivorship between environments. (iii) Detect QTLs associated to environmentally selected traits and associate their location to genomic regions of high differentiation between parapatric populations. In combination, these experiments were used to test the role of ecology in creating and maintaining the reproductive barriers that ultimately lead to plant speciation. A phylogenomic study of a continental collection of S. lautus populations showed that these plants have a monophyletic origin and evolved rapidly colonizing a broad array of environments. Importantly, populations adapted to adjacent but contrasting coastal environments, appeared as sister groups in phylogenetic analyses of thousands of loci, which suggests that these environments have been colonized repeatedly, and possibly in the presence of gene flow. To explore this hypothesis in further detail I analysed genetic differentiation between the genomes of populations. Our results revealed that genomic divergence was less heterogeneous between allopatric than parapatric populations, where a few genomic regions showed high differentiation while the rest of the genome was very similar. Additionally, genomic differentiation between some of these adjacent populations was related the magnitude of the differences between the environments that they inhabit, suggesting that divergence between them occurred in the face of gene flow. I investigated the evolutionary role of highly differentiated genomic regions through a combination of techniques that allowed us to connect genotype, phenotype and fitness. Firstly, I showed that these regions are enriched in coding mutations and associations to environmental variables, which suggest that they contain functionally important genes. However, patterns of divergence varied considerably across natural populations indicating that genomic divergence followed complex and divergent trajectories. Interestingly, functional analyses of divergent genes suggest that natural selection could have targeted different genes participating in the similar processes. By mapping loci involved in the control of fitness and convergent morphological traits across replicate populations I was able to demonstrate that divergent genomic regions contain adaptive and reproductive genes. Additionally I showed that genomic regions involved in adaptive trade-offs, have diverged repeatedly between environments, which supports their importance in mediating parapatric divergence. Overall my results provide genomic and functional evidence for a model of ecological speciation where natural selection creates divergence between the genomes of locally adapted organisms. These results also show that natural selection can have a complex genetic basis but create predictable patterns, especially at higher scales of biological organization.

Editorial and Retrospective 2007

Imagine a hypothetical scenario. Imagine you are traveling through space and come across Earth for the first time ... what would you be most struck by? Would it be the water that gives our planet the nickname ‘blue-marble’? I doubt it. We’ve now found water on the moon (Saal et al., 2008), on several other planets in our own solar system (Carr et al., 1998; Malin and Edgett, 2000), and a single survey of the Milky Way found >270 planets in the so-called “habitable zone,” warm enough for liquid water (Borucki et al., 2011). Would you instead be struck by the mountains, canyons and other geological features that are most visible from space? Again, it’s doubtful. Geologists tell us there are few, if any, landforms that are wholly unique to Earth (Baker, 2008; Dietrich and Perron, 2006), and you probably would have seen them all before. Based on our current understanding of the universe, the only thing a space-traveler is likely to be struck by, and the one thing that appears to be fundamentally unique to Earth, is its remarkable variety of life. Ever since the first prokaryotic cells evolved more than 3 billion years ago, the diversity of life on Earth has steadily increased, punctuated by only a handful of extinction events. Our best guess is there are perhaps 9 million forms of eukaryotic organisms on this planet (Mora et al., 2011). The number of prokaryotic organisms is largely unknown, but a single hydrothermal vent on the bottom of the ocean can harbor an astounding 37,000 unique types of microbes (Huber et al., 2007). While the great variety of life is perhaps the most striking feature of Earth, loss of this biodiversity is one of the most striking forms of environmental change in the Anthopocene. The percentage of species that have gone extinct ranges from just < 1% to 13% of described taxa depending on the group considered (Barnosky et al., 2011). But rates of extinction are occurring orders of magnitude faster than what is ‘normal’ in the fossil record. Projections suggest that if these high rates of extinction continue, biodiversity loss could equal or exceed the five prior mass extinctions (loss of 75% or more of known taxa) in 240 to 540 years (Barnosky et al., 2011). So what? What does it matter if we lose 75% of all life forms on the planet over the next few centuries? Will Earth become any less hospitable for humans? Will this planet still be able provide people with the food, water, air, and other goods and services needed to survive and prosper? Won’t evolution simply replace all of that lost diversity with life forms that are more fit for a human dominated planet? And if evolution does compensate for extinctions in the Anthropocene, what ecological roles will those newly evolved species play? These are pressing questions as we ponder what future Earth will be like. The variety of life that has evolved over 3.6-billion years is a catalog of biological resources from which we produce nearly all of the goods and services needed for humanity to prosper (Daily et al., 1997; MEA, 2005; Cardinale et al., 2012). If we are to have any hope of predicting how human domination of the planet will impact our own prosperity in an era that will have fewer biological options, we must develop a general theory of Earth’s biodiversity that can predict both the causes as well as the consequences of biological variation. Fortunately, biologists have made great strides on developing models that simultaneously explain three dimensions of biodiversity: (a) the evolutionary origin of biodiversity, (b) the ecological maintenance of biodiversity, and (c) the ecosystem-level function of biodiversity. Below I describe one set of evolutionary and ecological models that are beginning to show remarkably consistency in form. These models are by no means the only descriptions of how diversity originates, why species coexist, or how diversity influences ecosystem function. But the particular models discussed here do have a common thread that suggests biologists from different sub-disciplines are, in some instances, converging on a suite of equations, all with similar terms that collectively predict the origin, maintenance, and function of biodiversity. Domain Editor-in-Chief Donald R. Zak, University of Michigan

Speciation Associated with Shifts in Migratory Behavior in an Avian Radiation.

Gradients of variation--or clines--have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait. A third neutral process, surfing of a newly arisen mutation during the colonization of a new habitat, is more difficult to test. Here, we designed a spatially explicit approximate Bayesian computation (ABC) simulation framework to evaluate whether the strong cline in the genetically based reddish coloration observed in the European barn owl (Tyto alba) arose as a by-product of a range expansion or whether selection has to be invoked to explain this colour cline, for which we have previously ruled out the actions of IBD or secondary contact. Using ABC simulations and genetic data on 390 individuals from 20 locations genotyped at 22 microsatellites loci, we first determined how barn owls colonized Europe after the last glaciation. Using these results in new simulations on the evolution of the colour phenotype, and assuming various genetic architectures for the colour trait, we demonstrate that the observed colour cline cannot be due to the surfing of a neutral mutation. Taking advantage of spatially explicit ABC, which proved to be a powerful method to disentangle the respective roles of selection and drift in range expansions, we conclude that the formation of the colour cline observed in the barn owl must be due to natural selection.

Ecological speciation occurs when local adaptation generates reproductive isolation as a by-product of natural selection. Although ecological speciation is a fundamental source of diversification, the mechanistic link between natural selection and reproductive isolation remains poorly understood, especially in natural populations. Here, we show that experimental evolution of parasite body size over 4 y (approximately 60 generations) leads to reproductive isolation in natural populations of feather lice on birds. When lice are transferred to pigeons of different sizes, they rapidly evolve differences in body size that are correlated with host size. These differences in size trigger mechanical mating isolation between lice that are locally adapted to the different sized hosts. Size differences among lice also influence the outcome of competition between males for access to females. Thus, body size directly mediates reproductive isolation through its influence on both intersexual compatibility and intrasexual competition. Our results confirm that divergent natural selection acting on a single phenotypic trait can cause reproductive isolation to emerge from a single natural population in real time.

We use an individual-based numerical simulation to study the effects of phenotypic plasticity on ecological speciation. We find that adaptive plasticity evolves readily in the presence of dispersal between populations from different ecological environments. This plasticity promotes the colonization of new environments but reduces genetic divergence between them. We also find that the evolution of plasticity can either enhance or degrade the potential for divergent selection to form reproductive barriers. Of particular importance here is the timing of plasticity in relation to the timing of dispersal. If plasticity is expressed after dispersal, reproductive barriers are generally weaker because plasticity allows migrants to be better suited for their new environment. If plasticity is expressed before dispersal, reproductive barriers are either unaffected or enhanced. Among the potential reproductive barriers we considered, natural selection against migrants was the most important, primarily because it was the earliest-acting barrier. Accordingly, plasticity had a much greater effect on natural selection against migrants than on sexual selection against migrants or on natural and sexual selection against hybrids. In general, phenotypic plasticity can strongly alter the process of ecological speciation and should be considered when studying the evolution of reproductive barriers.

The origin of species

Adaptation to different environments is thought to play a key role in speciation. However, speciation typically begins in allopatry, where reproductive isolation can also arise through neutral processes or selection unrelated to ecological differences. Disentangling the role of adaptive ecological divergence in the early stages of speciation therefore remains an important challenge in understanding the origin of new species. Here, we study threespine stickleback populations that have recently evolved in isolated postglacial lakes either in the presence or absence of prickly sculpin-a resource competitor that also shares ubiquitous trout predators with stickleback. We simulated secondary contact between several stickleback populations from these two ecological contexts in large, seminatural ponds, and genotyped offspring from 411 mating events to assess the strength of premating isolation associated with this biotic factor. Assortative mating between populations of the same ecological type (i.e., both sculpin-sympatric or both solitary) was moderate on average but ranged from weak to complete. Strikingly, and in line with a central premise of ecological speciation, the strength of premating isolation increased with increasing morphological and genomic population divergence shaped by sculpin-mediated selection. In contrast, overall phenotypic and genomic population divergence agnostic to sculpin presence/absence only poorly explained premating isolation, highlighting how ecological speciation in allopatry can be obscured by other sources of divergence. More broadly, our findings demonstrate how interactions with other ecologically similar species can play a major role in initiating and driving evolutionary trajectories toward new species, even in allopatry.

INTRODUCTION Understanding the genetic basis of complex adaptive traits is key to understanding how natural and anthropomorphic factors have influenced and will influence the shape of genetic diversity and trajectory of evolution in natural populations. Complex adaptive traits are quantitative traits – those that vary on a continuous scale, and even more generally, are sometimes defined as traits that are expressed as a function of products from multiple genes (Falconer & MacKay 1996; Roff 1997; Lynch & Walsh 1998). Although classical quantitative genetics has revealed the genetic basis to numerous morphological, physiological, and life history traits in plants and animals, the actual genes (loci) and allelic variation with loci underlying key functional differences among organisms remain unknown. Understanding the genes involved in species- and population-level diversity can provide important tools (i.e., genetic markers) for resource managers that are charged with conservation, management, and restoration of natural populations. In this chapter, our examples and review are focused on non-model, non-domesticated organisms as it is the diversity in natural populations, shaped by the natural processes of evolution, with which natural resource managers are most concerned. Population genetics has undoubtedly been one of the most important fields in the conservation, management, and restoration of native plant and animal species. Together with ecological and life history information, “neutral” genetic markers, or those mirroring the neutral demographic processes of natural populations, are important tools for the delineation of management units or evolutionary significant units for conservation and management. Loci that have been shaped by natural selection, in the process of adaptive population divergence, can however exhibit levels of differentiation markedly different than neutral loci (Leinonen et al. 2008; Vali et al. 2008; Nosil et al. 2009).

Phenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally-mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.

Chromosomal speciation is one of the major modes of the origin of new species through the splitting of preexisting species. New species may originate by gene speciation, and also by the establishment of post‐mating reproductive isolation through structural chromosome rearrangements. The latter may induce low‐hybrid fitness, generated by macromutations, and even by micromutations, that is, molecular changes causing meiotic disturbances (e.g. GC incompatibilities), although the latter awaits empirical support. Criticism against the traditional model of chromosomal speciation led to renewed theoretical models arguing that chromosomal rearrangements can generate reproductive isolation between species by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to reproductive isolation and adaptive divergence and radiation. Likewise, coding and noncoding genomes, and novel chromosomal breakpoint regions can generate novel combinations of genes and regulatory elements that contribute to both adaptive radiation and ecological speciation. Chromosomal speciation is certainly an important speciation mode across life, although we cannot yet quantify it in relation to other modes. The spalacid example of blind subterranean mole rats in the East Mediterranean is presented as a widely studied case of chromosomal ecological speciation. The proportion of chromosomal speciation in nature, particularly in animals, remains a future challenge. Key Concepts: Speciation – the evolutionary process leading to the multiplication of species and generating biodiversity. Chromosomal speciation – the theory asserting that chromosomal rearrangements cause reproductive isolation between populations and lead to speciation. Peripatric speciation – the origin of a new species by budding from a parental species established beyond the periphery of the parental species range. Sympatric speciation – speciation without geographic (spatial) isolation; the origin of a new species within a deme. Polyploidy – the condition in which the number of chromosomes is an integral greater than two of the haploid numbers. Biological species concept (BSC) – defines species as groups of interbreeding natural populations that are reproductively (genetically) isolated from other such groups. Allopatric speciation – the evolution of a population into a separate species involving a period of geographic isolation. The evolutionary divergence of a single phyletic line into different niches or adaptive zones.

Natural selection commonly drives the origin of species, as Darwin initially claimed. Mechanisms of speciation by selection fall into two broad categories: ecological and mutation-order. Under ecological speciation, divergence is driven by divergent natural selection between environments, whereas under mutation-order speciation, divergence occurs when different mutations arise and are fixed in separate populations adapting to similar selection pressures. Tests of parallel evolution of reproductive isolation, trait-based assortative mating, and reproductive isolation by active selection have demonstrated that ecological speciation is a common means by which new species arise. Evidence for mutation-order speciation by natural selection is more limited and has been best documented by instances of reproductive isolation resulting from intragenomic conflict. However, we still have not identified all aspects of selection, and identifying the underlying genes for reproductive isolation remains challenging.

Evolutionary biologists continue to disagree about the relative importance of natural selection, drift and phylogenetic constraint in determining characteristics of an organism1. Because of the difficulty of identifying examples of selection in nature there are few rigorous field studies of selection2–6. We have been studying selection on flower colour in the small perennial larkspur Delphinium nelsonii, a native to mountains of the western USA. Previously we showed that white-flowered forms, which are very rare in natural populations, produce fewer seeds than their common blue-flowered conspecifics, and that this selective disadvantage results from partial discrimination against white flowers by bumblebee and hummingbird pollinators7. Here we present evidence that discrimination occurs because white flowers have inferior ‘nectar guides’ and therefore require longer handling times than blue flowers. Pollinators may thus experience lower net rates of energy intake on white flowers, a sufficient reason for undervisitation by optimally-foraging animals.

Since Darwin published the "Origin," great progress has been made in our understanding of speciation mechanisms. The early investigations by Mayr and Dobzhansky linked Darwin's view of speciation by adaptive divergence to the evolution of reproductive isolation, and thus provided a framework for studying the origin of species. However, major controversies and questions remain, including: When is speciation nonecological? Under what conditions does geographic isolation constitute a reproductive isolating barrier? and How do we estimate the "importance" of different isolating barriers? Here, we address these questions, providing historical background and offering some new perspectives. A topic of great recent interest is the role of ecology in speciation. "Ecological speciation" is defined as the case in which divergent selection leads to reproductive isolation, with speciation under uniform selection, polyploid speciation, and speciation by genetic drift defined as "nonecological." We review these proposed cases of nonecological speciation and conclude that speciation by uniform selection and polyploidy normally involve ecological processes. Furthermore, because selection can impart reproductive isolation both directly through traits under selection and indirectly through pleiotropy and linkage, it is much more effective in producing isolation than genetic drift. We thus argue that natural selection is a ubiquitous part of speciation, and given the many ways in which stochastic and deterministic factors may interact during divergence, we question whether the ecological speciation concept is useful. We also suggest that geographic isolation caused by adaptation to different habitats plays a major, and largely neglected, role in speciation. We thus provide a framework for incorporating geographic isolation into the biological species concept (BSC) by separating ecological from historical processes that govern species distributions, allowing for an estimate of geographic isolation based upon genetic differences between taxa. Finally, we suggest that the individual and relative contributions of all potential barriers be estimated for species pairs that have recently achieved species status under the criteria of the BSC. Only in this way will it be possible to distinguish those barriers that have actually contributed to speciation from those that have accumulated after speciation is complete. We conclude that ecological adaptation is the major driver of reproductive isolation, and that the term "biology of speciation," as proposed by Mayr, remains an accurate and useful characterization of the diversity of speciation mechanisms.