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Speciation Genetics: Evolving Approaches

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Speciation Genetics: Evolving Approaches REVIEWS Speciation genetics: evolving approaches Mohamed A. F. Noor* and Jeffrey L. Feder‡ Abstract | Much progress has been made in the past two decades in understanding Darwin’s mystery of the origins of species. Applying genomic techniques to the analysis of laboratory crosses and natural populations has helped to determine the genetic basis of barriers to gene flow which create new species. Although new methodologies have not changed the prevailing hypotheses about how species form, they have accelerated the pace of data collection. By facilitating the compilation of case studies, advances in genetic techniques will help to provide answers to the next generation of questions concerning the relative frequency and importance of different processes that cause speciation. Gene flow What types of genetic change bring about speciation is sophisticated methods has led to finer dissection of the The movement of alleles one of the most basic questions in biology. Speciation is a genetic origins of species down to the level of the indi- between local populations that fundamental outcome of life. Given metabolism, repro- vidual loci and eventually nucleotides. Technical and is due to the migration of duction, mutation, heredity, and the spatial–temporal statistical advances are also extending laboratory-based individuals. subdivision of the environment and of individuals into discovery to natural populations, allowing researchers Hybrid zone populations, new species form through time, increasing to investigate barriers to gene flow, genomic interactions A location where the hybrid biodiversity. The evolution of this biodiversity can only and the genetic permeability of species boundaries in offspring of two divergent, be fully explained if we identify the heritable underpin- hybrid zones where differentiated taxa overlap and inter- partially geographically nings of species formation and the forces responsible breed. Whole-genome surveys can provide representative overlapping groups are prevalent. Hybrid zones are for their origins. snapshots of differentiation across the entire genomes sometimes stable for many Here, we review how recent advances in molecular of model genetic systems. Ultimately this progress is generations and there is often and genomic techniques are helping to achieve a greater leading to large-scale comparative genomic analysis variation in the fitness of understanding of the genetics of speciation. For the of entire taxonomic groups (model and emerging- hybrids within the zone. purpose of this review, we focus on technical advances model systems alike) from which general patterns and Genomic conflict rather than theoretical concepts, which are discussed rules might emerge. Competition within a genome extensively elsewhere1. We define speciation for sexually We conclude by discussing what the new methods for transmission to or success reproducing organisms as the transformation of within- have and potentially will reveal about the genetics of of gametes. population variation into taxonomic differences through speciation. We argue that the new technology is not the evolution of inherent barriers to gene flow. This necessarily providing results that are inherently dif- definition is not universally accepted, but it remains the ferent from those of earlier studies. Rather, the new *DCMB Group/ Biology Department, Duke University, most commonly used by students of speciation and is of methodology is adding detail by accelerating the rate BOX 91000, Durham, North the greatest utility to dissecting the genetics of the proc- and ease of data collection on a genome-wide scale. Carolina 27708, USA. ess1. We discuss whether and how molecular techniques We contend that this aspect of technology will have the ‡Department of Biological are helping to discern the genetic bases and evolutionary greatest immediate impact — it will allow us to move Sciences, University of Notre origins of barriers that contribute to population diver- from isolated case studies to compilations of results Dame, Galvin Life Science Center, PO BOX 369, Notre gence. We present some recent discoveries from labora- for representative groups to answer relative frequency Dame, Indiana 46556-0369, tory and field studies that apply molecular and genomics questions about processes and factors that contrib- USA. techniques to the speciation question. Our examples are ute to speciation. For example, how often do natural e-mails: [email protected]; chosen to illustrate some of the breadth of approaches selection, sexual selection, genomic conflict and eco- [email protected] doi:10.1038/nrg1968 that are used to tackle this exciting question. logical interactions drive divergence? What proportion Published online We begin by framing the problem from a historical of genetic change is regulatory versus functional? 3 October 2006 perspective, tracing how the development of ever-more- How important is chromosomal change in speciation? NATURE REVIEWS | GENETICS VOLUME 7 | NOVEMBER 2006 | 851 © 2006 Nature Publishing Group REVIEWS How often does speciation occur in the face of peri- Classical approaches odic or regular gene flow, generating mosaic patterns Descriptive and conceptual. Although he entitled his of genomic differentiation? It is not clear that the new famous book On the Origin of Species, Darwin2 had only methodology will lead to a major shift in our think- vague insights into the speciation process itself, viewing ing about the ways in which speciation can occur. We it as a later stage in a continuum from adaptive diver- propose that this limitation is not technical, but mostly gence among ‘varieties’ within species. The Russian rests in the imagination of students in the field. geneticist Theodosius Dobzhansky and the German systematist Ernst Mayr instilled broader excitement in the field of speciation genetics with three conceptual advances in the 1930s and 1940s. First, Dobzhansky3 Box 1 | Classical approaches to the study of speciation genetics and Mayr4 compiled lists of traits that prevent gene H G F E D C B A flow between species, such as habitat divergence and hybrid sterility (here, we refer to them collectively as Inverted in AR barriers). They noted that some of these barriers pre- vent the formation of hybrid offspring, whereas others prevent the success and propagation of hybrid offspring once formed. Second, Dobzhansky and Mayr argued AR ST A that species can be defined in the context of these traits. A A This second advance identified a means for the study of speciation genetics: the genetics of barriers acting to reduce gene flow in nature indicates the genetics B of speciation itself. Third, they studied these barriers B B directly: Mayr defined which ones operate in nature and Dobzhansky determined their genetic basis in C H the laboratory through controlled crosses (BOX 1). The D C implications of this last endeavour were profound, dem- C onstrating that barriers are traits that can be genetically H G D D mapped and that species boundaries can be quantified F E H genetically. G Despite the dramatic advances in molecular and E genomic techniques, the ‘old-school’ approaches of F G E Dobzhansky and Mayr for studying the genetics of spe- F ciation still apply today5 (BOX 1). Since that time, simi- Genetic studies of speciation, which date back to the early twentieth century, lar laboratory and field studies have become plentiful attempt to identify the number, distribution and type of genes that contribute to enough for elegant meta-analyses of broader taxonomic phenotypes that prevent gene flow between species. They also examine patterns of data sets to be carried out. These meta-analyses have differentiation between the genomes of diverging taxa. found, unsurprisingly, that barriers between long- Laboratory or garden hybridization studies diverged species are typically much stronger or more Laboratory or garden hybridization studies have traditionally had a central role in effective than barriers between very recently diverged understanding the genetic basis of barrier (speciation-related) traits. Examining species (for example, see REFS 6–11). Therefore, genetic the distribution of phenotypes over one or two generations of controlled crosses divergence is associated with the accumulation of more has been used to infer the contributions of the sex chromosomes versus autosomes, (and/or stronger) barriers, irrespective of how genetic identify patterns of dominance and provide estimates of the minimum number of genes that affect the speciation-related traits. An advance was made with the first divergence is measured. true genetic mapping efforts, when associations were assessed between genetic Echoing the differences in Dobzhansky’s and Mayr’s approaches, a slight divide has nonetheless emerged (now, often molecular) markers and barrier traits in F2 or other hybrids. For example, Dobzhansky133 correlated hybrid testis size (a proxy for fertility) with within the speciation community. At one extreme are genotype at seven mutant markers in a cross between races of Drosophila the researchers who investigate barriers to gene flow pseudoobscura (now, described as separate species). In principle, this is no different using laboratory crosses of well-established model from modern QTL mapping studies. species, often focusing on easily scored phenotypes Genetic diversity within and between species such as hybrid sterility or inviability. They have been Speciation genetics has also been explored using studies of genetic diversity successful in identifying
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