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Understanding the causes of the morphological diversity among organisms is a topic of great interest to evolutionary developmental biologists. Although developmental biologists have had great success in identifying the developmental mechanisms and molecular processes that specify organ size and shape within species, only relatively recently have the molecular tools become available to study how variation in these mechanisms gives rise to the phenotypic differences that are observed among closely related species. In addition to these technological advances, researchers interested in understanding how molecular variation gives rise to phenotypic variation have used three primary strategies to identify the molecular differences underlying species-specific traits: the candidate gene approach, differential gene expression screens, and between-species genetic mapping experiments. In this review, we discuss how these approaches have been successful in identifying the genes and the cellular mechanisms by which they specify variation in one of the most recognizable examples of the evolution of organ size, the adaptive variation in beak morphology among Darwin’s finches. We also discuss insect reproductive structures as a model with great potential to advance our understanding of the specification and evolution of organ size and shape differences among species. The results from these two examples, and those from other species, show that species-specific variation in organ size and shape typically evolves via changes in the timing, location, and amount of gene/protein expression that act on tissue growth processes.

The model organism

The model organism Drosophila melanogaster has become a focal system for investigations of rapidly evolving genital morphology as well as the development and functions of insect reproductive structures. To follow up on a previous paper outlining unifying terminology for the structures of the male terminalia in this species, we offer here a detailed description of the female terminalia of D. melanogaster. Informative diagrams and micrographs are presented to provide a comprehensive overview of the external and internal reproductive structures of females. We propose a collection of terms and definitions to standardize the terminology associated with the female terminalia in D. melanogaster and we provide a correspondence table with the terms previously used. Unifying terminology for both males and females in this species will help to facilitate communication between various disciplines, as well as aid in synthesizing research across publications within a discipline that has historically focused principally on male features. Our efforts to refine and standardize the terminology should expand the utility of this important model system for addressing questions related to the development and evolution of animal genitalia, and morphology in general.

The model organism Drosophila melanogaster has become a focal system for investigations of rapidly evolving genital morphology as well as the development and functions of insect reproductive structures. To follow up on a previous paper outlining unifying terminology for the structures of the male terminalia in this species, we offer here a detailed description of the female terminalia of D. melanogaster. Informative diagrams and micrographs are presented to provide a comprehensive overview of the external and internal reproductive structures of females. We propose a collection of terms and definitions to standardize the terminology associated with the female terminalia in D. melanogaster and we provide a correspondence table with the terms previously used. Unifying terminology for both males and females in this species will help to facilitate communication between various disciplines, as well as aid in synthesizing research across publications within a discipline that has historically focused principally on male features. Our efforts to refine and standardize the terminology should expand the utility of this important model system for addressing questions related to the development and evolution of animal genitalia, and morphology in general.

The model organism Drosophila melanogaster has become a focal system for investigations of rapidly evolving genital morphology as well as the development and functions of insect reproductive structures. To follow up on a previous paper outlining unifying terminology for the structures of the male terminalia in this species, we offer here a detailed description of the female terminalia of D. melanogaster. Informative diagrams and micrographs are presented to provide a comprehensive overview of the external and internal reproductive structures of females. We propose a collection of terms and definitions to standardize the terminology associated with the female terminalia in D. melanogaster and we provide a correspondence table with the terms previously used. Unifying terminology for both males and females in this species will help to facilitate communication between various disciplines, as well as aid in synthesizing research across publications within a discipline that has historically focused principally on male features. Our efforts to refine and standardize the terminology should expand the utility of this important model system for addressing questions related to the development and evolution of animal genitalia, and morphology in general.

Rapid divergence in genital structures among nascent species has been posited to be an early-evolving cause of reproductive isolation, although evidence supporting this idea as a widespread phenomenon remains mixed. Using a collection of interspecific introgression lines between twoDrosophilaspecies that diverged ∼240,000 years ago, we tested the hypothesis that even modest divergence in genital morphology can result in substantial fitness losses. We studied the reproductive consequences of variation in the male epandrial posterior lobes betweenDrosophila mauritianaandD. sechelliaand found that divergence in posterior lobe morphology has significant fitness costs on several pre-fertilization and post-copulatory reproductive measures. Males with divergent posterior lobe morphology also significantly reduced the life span of their mates. Interestingly, one of the consequences of genital divergence was decreased oviposition and fertilization, which suggests that a sensory bias for posterior lobe morphology could exist in females, and thus posterior lobe morphology may be the target of cryptic female choice in these species. Our results provide evidence that divergence in genitalia can in fact give rise to substantial reproductive isolation early during species divergence, and they also reveal novel reproductive functions of the external male genitalia inDrosophila.

Animal terminalia represent some of the most diverse and rapidly evolving structures in the animal kingdom, and for this reason have been a mainstay in the taxonomic description of species. The terminalia of Drosophila melanogaster, with its wide range of experimental tools, have recently become the focus of increased interest in the fields of development, evolution, and behavior. However, studies from different disciplines have often used discrepant terminologies for the same anatomical structures. Consequently, the terminology of genital parts has become a barrier to integrating results from different fields, rendering it difficult to determine what parts are being referenced. We formed a consortium of researchers studying the genitalia of D. melanogaster to help establish a set of naming conventions. Here, we present a detailed visual anatomy of male genital parts, including a list of synonymous terms, and suggest practices to avoid confusion when referring to anatomical parts in future studies. The goal of this effort is to facilitate interdisciplinary communication and help newcomers orient themselves within the exciting field of Drosophila genitalia.

Males and females transmit and receive signals prior to mating that convey information such as sex, species identity, or individual condition. In some animals, tactile signals relayed during physical contact between males and females before and during mating appear to be important for mate choice or reproductive isolation. This is common among odonates, when a male grasps a female's thorax with his terminal appendages prior to copulation, and the female subsequently controls whether copulation occurs by bending her abdomen to complete intromission. It has been hypothesized that mechanosensory sensilla on the female thoracic plates mediate mating decisions, but is has been difficult to test this idea. Here, we use North American damselflies in the genus Enallagma (Odonata: Coenagrionidae) to test the hypothesis that variation in female sensilla traits is important for species recognition. Enallagma anna and E. carunculatum hybridize in nature, but experience strong reproductive isolation as a consequence of divergence in male terminal appendage morphology. We quantified several mechanosensory sensilla phenotypes on the female thorax among multiple populations of both species and compared divergence in these traits in sympatry versus allopatry. Although these species differed in features of sensilla distribution within the thoracic plates, we found no strong evidence of reproductive character displacement among the sensilla traits we measured in regions of sympatry. Our results suggest that species‐specific placement of female mechanoreceptors may be sufficient for species recognition, although other female sensory phenotypes might have diverged in sympatry to reduce interspecific hybridization.

Drosophila imaginal discs provide an ideal model to study processes important for cell signaling and cell specification, tissue differentiation, and cell competition during development. One challenge to understanding genetic control of cellular processes and cell interactions is the difficulty in effectively targeting a defined subset of cells in developing tissues in gene manipulation experiments. A recently developed Flippase-induced intersectional GAL80/GAL4 repression method incorporates several gene manipulation technologies in Drosophila to enable such fine-scale dissection in neural tissues. In particular, this approach brings together existing GAL4 transgenes, newly developed enhancer-trap flippase transgenes, and GAL80 transgenes flanked by Flippase recognition target sites. The combination of these tools enables gene activation/repression in particular subsets of cells within a GAL4 expression pattern. Here, we expand the utility of a large collection of these enhancer-trap flippase transgenic insertion lines by characterizing their expression patterns in third larval instar imaginal discs. We screened 521 different enhancer-trap flippase lines and identified 28 that are expressed in imaginal tissues, including two transgenes that show sex-specific expression patterns. Using a line that expresses Flippase in the wing imaginal disc, we demonstrate the utility of this intersectional approach for studying development by knocking down gene expression of a key member of the planar cell polarity pathway. The results of our experiments show that these enhancer-trap flippase lines enable fine-scale manipulation in imaginal discs.

The genitalia of internally fertilizing taxa represent a striking example of rapid morphological evolution. Although sexual selection can shape variation in genital morphology, it has been difficult to test whether multiple sexual selection pressures combine to drive the rapid evolution of individual genital structures. Here, we test the hypothesis that both pre‐ and postcopulatory sexual selection can act in concert to shape complex structural variation in secondary genital morphology. We genetically modified the size and shape of the posterior lobes of Drosophila melanogaster males and tested the consequences of morphological variation on several reproductive measures. We found that the posterior lobes are necessary for genital coupling and that they are also the targets of multiple postcopulatory processes that shape quantitative variation in morphology, even though these structures make no direct contact with the external female genitalia or internal reproductive organs during mating. We also found that males with smaller and less structurally complex posterior lobes suffer substantial fitness costs in competitive fertilization experiments. Our results show that sexual selection mechanisms can combine to shape the morphology of a single genital structure and that the posterior lobes of D. melanogaster are the targets of multiple postcopulatory selection pressures.

External male reproductive structures have received considerable attention as a cause of reproductive isolation (RI), because the morphology of these structures often evolves rapidly between populations. This rapid evolution presents the potential for mechanical incompatibilities with heterospecific female structures during mating and could thus prevent interbreeding between nascent species. Although such mechanical incompatibilities have received little empirical support as a common cause of RI, the potential for mismatch of reproductive structures to cause RI due to incompatible species-specific tactile cues has not been tested. We tested the importance of mechanical and tactile incompatibilities in RI between Enallagma anna and E. carunculatum, two damselfly species that diverged within the past ∼250,000 years and currently hybridize in a sympatric region. We quantified 19 prezygotic and postzygotic RI barriers using both naturally occurring and laboratory-reared damselflies. We found incomplete mechanical isolation between the two pure species and between hybrid males and pure species females. Interestingly, in mating pairs for which mechanical isolation was incomplete, females showed greater resistance and refusal to mate with hybrid or heterospecific males compared to conspecific males. This observation suggests that tactile incompatibilities involving male reproductive structures can influence female mating decisions and form a strong barrier to gene flow in early stages of speciation.

The divergent genital morphology observed among closely related animal species has long been posited as a mechanism of reproductive isolation. Despite the intuitive appeal that rapidly evolving genitalia might cause speciation, evidence for its importance—or even its potential—in reproductive isolation is mixed. Most tests of genital structural isolation between species often fail to find convincing evidence that differences in morphology prevent copulation or insemination between species. However, recent work suggests that differences in genital morphology might contribute to reproductive isolation in less obvious ways through interactions with sensory mechanisms that result in lowered reproductive fitness in heterospecific matings. In this paper, I present a brief history of the “lock-and-key” hypothesis, summarize the evidence for the involvement of genital morphology in different mechanisms of reproductive isolation, discuss progress in identifying the molecular and genetic bases of species differences in genital morphology, and discuss prospects for future work on the role of genitalia in speciation. L'armure copulatrice est un organe ou mieux un instrument ingénieusement compliqué, destiné à s'adapter aux parties sexuelles externes de la femelle pour l'accomplissement de l'acte copulatif; elle est la garantie de la conservation des types, la sauvegarde de la légitimité de l'espèce. [The copulation armor is an organ or better an instrument ingeniously complicated, destined to adapt to sexual parts external to the female for the completion of copulation; it is the guarantee of the preservation of the standards, the safeguard of the legitimacy of the species.] L. Dufour, 1844

The external genitalia are some of the most rapidly evolving morphological structures in insects. The posterior lobe of the male genital arch shows striking differences in both size and shape among closely related species of the Drosophila melanogaster species subgroup. Here, we dissect the genetic basis of posterior lobe morphology between D. mauritiana and D. sechellia, two island endemic species that last shared a common ancestor ∼300,000 years ago. We test a large collection of genome-wide homozygous D. mauritiana genetic introgressions, which collectively cover ∼50% of the genome, for their morphological effects when placed in a D. sechellia genetic background. We find several introgressions that have large effects on posterior lobe morphology and that posterior lobe size and posterior lobe shape can be separated genetically for some of the loci that specify morphology. Using next generation sequencing technology, we perform whole transcriptome gene expression analyses of the larval genital imaginal disc of D. mauritiana, D. sechellia, and two D. mauritiana–D. sechellia hybrid introgression genotypes that each have large effects on either posterior lobe size or posterior lobe shape. Many of the genes we identify as differentially expressed are expressed at levels similar to D. mauritiana in one introgression hybrid, but are expressed at levels similar to D. sechellia in the other introgression hybrid. However, we also find that both introgression hybrids express some of the same genes at levels similar to D. mauritiana, and notably, that both introgression hybrids possess genes in the insulin receptor signaling pathway, which are expressed at D. mauritiana expression levels. These results suggest the possibility that the insulin signaling pathway might integrate size and shape genetic inputs to establish differences in overall posterior lobe morphology between D. mauritiana and D. sechellia.

Study of the genetics of speciation--and especially of the genetics of intrinsic postzygotic isolation-has enjoyed remarkable progress over the last 2 decades. Indeed progress has been so rapid that one might be tempted to ask if the genetics of postzygotic isolation is now wrapped up. Here we argue that the genetics of speciation is far from complete. In particular, we review 2 topics where recent work has revealed major surprises: 1) the role of meiotic drive in hybrid sterility and 2) the role of gene transposition in speciation. These surprises, and others like them, suggest that evolutionary biologists may understand less about the genetic basis of speciation than seemed likely a few years ago.

Until recently, the genes that cause reproductive isolation remained black boxes. Consequently, evolutionary biologists were unable to answer several questions about the identities and characteristics of "speciation genes". Over the past few years, however, evolutionary geneticists have finally succeeded in isolating several such genes, providing our first glimpse at factors that are thought to be representative of those underlying the origin of species. Evolutionary analysis of these genes suggests that speciation results from positive Darwinian selection within species. Molecular evolutionary study of the genes causing reproductive isolation may represent an important new phase in the study of speciation.

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes, and anal plates exhibit striking differences between Drosophila mauritiana and D. simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.

Although several evolutionary forces have been proposed to contribute to genital morphological diversification, it is unclear which might act early during the evolution of novel structural traits. We test the hypothesis that mismatch between interacting male and female secondary sexual structures gives rise to increased harm to females, consistent with the outcome predicted from a history of sexual conflict. We mate Drosophila sechellia females to males from a collection of D. mauritiana-D. sechellia interspecific genetic introgression lines that possess quantitative morphological variation in the posterior lobe of the genital arch, an external genital structure that can cause wounds to the female abdomen during mating. We find that males with smaller posterior lobes, and those that possess lobes with similarities in shape to D. mauritiana, cause more severe wounding compared to either D. sechellia males with strain-specific morphologies or introgression males that possess larger lobes or lobes with more pronounced D. sechellia features. These results suggest a possible history of sexual conflict during the evolution of the posterior lobe in D. sechellia, but also suggest a potential contribution of divergence in sensory recognition mechanisms to posterior lobe evolution.

Although several evolutionary forces have been proposed to contribute to genital morphological diversification, it is unclear which might act early during the evolution of novel structural traits. We test the hypothesis that mismatch between interacting male and female secondary sexual structures gives rise to increased harm to females, consistent with the outcome predicted from a history of sexual conflict. We mate Drosophila sechellia females to males from a collection of D. mauritiana-D. sechellia interspecific genetic introgression lines that possess quantitative morphological variation in the posterior lobe of the genital arch, an external genital structure that can cause wounds to the female abdomen during mating. We find that males with smaller posterior lobes, and those that possess lobes with similarities in shape to D. mauritiana, cause more severe wounding compared to either D. sechellia males with strain-specific morphologies or introgression males that possess larger lobes or lobes with more pronounced D. sechellia features. These results suggest a possible history of sexual conflict during the evolution of the posterior lobe in D. sechellia, but also suggest a potential contribution of divergence in sensory recognition mechanisms to posterior lobe evolution.

Postzygotic reproductive isolation is characterized by two striking empirical patterns. The first is Haldane's rule—the preferential inviability or sterility of species hybrids of the heterogametic (XY) sex. The second is the so-called large X effect—substitution of one species's X chromosome for another's has a disproportionately large effect on hybrid fitness compared to similar substitution of an autosome. Although the first rule has been well-established, the second rule remains controversial. Here, we dissect the genetic causes of these two rules using a genome-wide introgression analysis of Drosophila mauritiana chromosome segments in an otherwise D. sechellia genetic background. We find that recessive hybrid incompatibilities outnumber dominant ones and that hybrid male steriles outnumber all other types of incompatibility, consistent with the dominance and faster-male theories of Haldane's rule, respectively. We also find that, although X-linked and autosomal introgressions are of similar size, most X-linked introgressions cause hybrid male sterility (60%) whereas few autosomal introgressions do (18%). Our results thus confirm the large X effect and identify its proximate cause: incompatibilities causing hybrid male sterility have a higher density on the X chromosome than on the autosomes. We evaluate several hypotheses for the evolutionary cause of this excess of X-linked hybrid male sterility., Author Summary The evolution of reproductive isolation is a fundamental step in the origin of species. One kind of reproductive isolation, the sterility and inviability of species hybrids, is characterized by two of the strongest rules in evolutionary biology. The first is Haldane's rule: for species crosses in which just one hybrid sex is sterile or inviable, it tends to be the sex defined by having a pair of dissimilar sex chromosomes (e.g., the “XY” of males in humans). The second rule is the large X effect: the X chromosome has a disproportionately large effect on hybrid fitness. We dissected the genetic causes of these two rules of speciation by replacing many small chromosomal segments of the fruit fly Drosophila sechellia with those of a closely related species, D. mauritiana. Together, these segments cover 70% of the genome. We found that virtually all segments causing hybrid sterility or inviability act recessively and that hybrid male sterility is by far the most common type of hybrid incompatibility, confirming two leading theories about the causes of Haldane's rule. We also found that X-linked segments are more likely to cause hybrid male sterility than similarly sized autosomal segments. These results show that the large X effect is caused by a higher density of hybrid incompatibilities on the X chromosome., A genome-wide introgression analysis of Drosophila mauritiana chromosome segments in an otherwise D. sechellia genetic background confirms the large X effect, a cornerstone of speciation theory, and reveals its cause.

We describe reproductive isolation caused by a gene transposition. In certain Drosophila melanogaster – D. simulans hybrids, hybrid male sterility is caused by the lack of a single-copy gene essential for male fertility, JYAlpha . This gene is located on the fourth chromosome of D. melanogaster but on the third chromosome of D. simulans . Genomic and molecular analyses show that JYAlpha transposed to the third chromosome during the evolutionary history of the D. simulans lineage. Because of this transposition, a fraction of hybrids completely lack JYAlpha and are sterile, representing reproductive isolation without sequence evolution.

Many evolutionary studies use comparisons across species to detect evidence of natural selection and to examine the rate of character evolution. Statistical analyses in these studies are usually performed by means of a species phylogeny to accommodate the effects of shared evolutionary history. The phylogeny is usually treated as known without error; this assumption is problematic because inferred phylogenies are subject to both stochastic and systematic errors. We describe methods for accommodating phylogenetic uncertainty in evolutionary studies by means of Bayesian inference. The methods are computationally intensive but general enough to be applied in most comparative evolutionary studies.