Conspecific pollen precedence (CPP) is a major component of reproductive isolation between many flowering plant taxa and may reveal mechanisms of gametophytic evolution within species, but little is known about the genetic basis and evolutionary history of CPP. We systematically investigated the genetic architecture of CPP using patterns of transmission ratio distortion (TRD) in F2 and backcross hybrids between closely related species of Mimulus (Phrymaceae) with divergent mating systems. We found that CPP in Mimulus hybrids was polygenic and was the majority source of interspecific TRD genome-wide, with at least eight genomic regions contributing to the transmission advantage of M. guttatus pollen grains on M. guttatus styles. In aggregate, these male-specific transmission ratio distorting loci (TRDLs) were more than sufficient to account for the 100% precedence of pure M. guttatus pollen over M. nasutus pollen in mixed pollinations of M. guttatus. All but one of these pollen TRDLs were style-dependent; that is, we observed pollen TRD in F₁ and/or M. guttatus styles, but not in M. nasutus styles. These findings suggest that species-specific differences in pollen tube performance accumulate gradually and may have been driven by coevolution between pollen and style in the predominantly outcrossing M. guttatus.

Using seasonal cues to time reproduction appropriately is crucial for many organisms. Plants in particular often use photoperiod to signal the time to transition to flowering. Because seasonality varies latitudinally, adaptation to local climate is expected to result in corresponding clines in photoperiod-related traits. By experimentally manipulating photoperiod cues and measuring the flowering responses and photoperiod plasticity of 138 Eurasian accessions of Arabidopsis thaliana, we detected strong longitudinal but not latitudinal clines in flowering responses. The presence of longitudinal clines suggests that critical photoperiod cues vary among populations occurring at similar latitudes. Haplotypes at PHYC, a locus hypothesized to play a role in adaptation to light cues, were also longitudinally differentiated. Controlling for neutral population structure revealed that PHYC haplotype influenced flowering time; however, the distribution of PHYC haplotypes occurred in the opposite direction to the phenotypic cline, suggesting that loci other than PHYC are responsible for the longitudinal pattern in photoperiod response. Our results provide previously missing empirical support for the importance of PHYC in mediating photoperiod sensitivity in natural populations of A. thaliana. However, they also suggest that other loci and epistatic interactions likely play a role in the determination of flowering time and that the environmental factors influencing photoperiod in plants vary longitudinally as well as latitudinally.

Rapid and inexpensive sequencing technologies are making it possible to collect whole genome sequence data on multiple individuals from a population. This type of data can be used to quickly identify genes that control important ecological and evolutionary phenotypes by finding the targets of adaptive natural selection, and we therefore refer to such approaches as “reverse ecology.” To quantify the power gained in detecting positive selection using population genomic data, we compare three statistical methods for identifying targets of selection: the McDonald–Kreitman test, the mkprf method, and a likelihood implementation for detecting d_N/d_S > 1. Because the first two methods use polymorphism data we expect them to have more power to detect selection. However, when applied to population genomic datasets from human, fly, and yeast, the tests using polymorphism data were actually weaker in two of the three datasets. We explore reasons why the simpler comparative method has identified more genes under selection, and suggest that the different methods may really be detecting different signals from the same sequence data. Finally, we find several statistical anomalies associated with the mkprf method, including an almost linear dependence between the number of positively selected genes identified and the prior distributions used. We conclude that interpreting the results produced by this method should be done with some caution.

The plant group Solanum section Lycopersicon (the clade containing the domesticated tomato and its wild relatives) is ideal for integrating genomic tools and approaches into ecological and evolutionary research. Wild species within Lycopersicon span broad morphological, physiological, life history, mating system, and biochemical variation, and are separated by substantial, but incomplete postmating reproductive barriers, making this an ideal system for genetic analyses of these traits. This ecological and evolutionary diversity is matched by many logistical advantages, including extensive historical occurrence records for all species in the group, publicly available germplasm for hundreds of known wild accessions, demonstrated experimental tractability, and extensive genetic, genomic, and functional tools and information from the tomato research community. Here I introduce the numerous advantages of this system for Ecological and Evolutionary Functional Genomics (EEFG), and outline several ecological and evolutionary phenotypes and questions that can be fruitfully tackled in this system. These include biotic and abiotic adaptation, reproductive trait evolution, and the genetic basis of speciation. With the modest enhancement of some research strengths, this system is poised to join the best of our currently available model EEFG systems.

Despite compelling evidence that adaptation to local climate is common in plant populations, little is known about the evolutionary genetics of traits that contribute to climatic adaptation. A screen of natural accessions of Arabidopsis thaliana revealed Tsu-1 and Kas-1 to be opposite extremes for water-use efficiency and climate at collection sites for these accessions differs greatly. To provide a tool to understand the genetic basis of this putative adaptation, Kas-1 and Tsu-1 were reciprocally crossed to create a new mapping population. Analysis of F₃ families showed segregating variation in both δ¹³C and transpiration rate, and as expected these traits had a negative genetic correlation (r_g=− 0.3). 346 RILs, 148 with Kas-1 cytoplasm and 198 with Tsu-1 cytoplasm, were advanced to the F₉ and genotyped using 48 microsatellites and 55 SNPs for a total of 103 markers. This mapping population was used for QTL analysis of δ¹³C using F₉ RIL means. Analysis of this reciprocal cross showed a large effect of cytoplasmic background, as well as two QTL for δ¹³C. The Kas-1 × Tsu-1 mapping population provides a powerful new resource for mapping QTL underlying natural variation and for dissecting the genetic basis of water-use efficiency differences.

Few studies have investigated the roles that plant hybridization and individual plant genotype play in promoting population divergence within arthropod species. Using nrDNA sequence information and reciprocal transfer experiments, we examined how tree cross type (i.e., pure Populus angustifolia and P. angustifolia × P. fremontii F₁ type hybrids) and individual tree genotype influence host race formation in the bud-galling mite Aceria parapopuli. Three main findings emerged: (1) Strong genetic differentiation of mite populations found on pure P. angustifolia and F₁ type hybrids indicates that these mites represent morphologically cryptic species. (2) Within the F₁ type hybrids, population genetic analyses indicate migration among individual trees; however, (3) transfer experiments show that the mites found on heavily infested F₁ type trees perform best on their natal host genotype, suggesting that genetic interactions between mites and their host trees drive population structure, local adaptation, and host race formation. These findings argue that hybridization and genotypic differences in foundation tree species may drive herbivore population structure, and have evolutionary consequences for dependent arthropod species.

Although there are theoretical reasons to suspect that gametic incompatibility may develop readily among populations of broadcast spawning marine invertebrates, there have been very few studies documenting geographic patterns of interpopulation incompatibility for any species. To address this we determined how successfully individuals of the intertidal serpulid polychaete, Galeolaria caespitosa, can cross-fertilize within and among populations from across temperate Australia. Fertilization assays revealed asymmetrical differences between very distantly located populations from different coasts, with near-complete incompatibility between eggs from Sydney with sperm from Adelaide, but the reverse cross (Adelaide eggs, Sydney sperm) was reasonably compatible. Although that pattern was congruent with a clear difference in Cytochrome B sequences between worms on the south and east coasts of Australia, we also detected some indication of interpopulation incompatibility within the genetic grouping on east coast, between two populations separated by only 220 km. We then assessed whether commonly proposed gametic compatibility arms-races could account for these patterns. Our results suggest reduced gametic compatibility may reduce a female's maximum fertilization potential, resulting in a cost to this potential mechanism for reducing polyspermy. Consequently, the apparently rapid development of reproductive barriers here seems unlikely to have been driven by arms-races involving sexual conflict over fertilization rate.

Measuring reproductive isolation across multiple generations and environments is a key endeavor in speciation research because it indicates which isolating barriers currently prevent introgression and the extent to which they are intrinsic versus environmentally dependent. Here, I present data from several crosses (parental crosses, F1s, F2s, back-crosses) between two species of killifish (Lucania goodei and L. parva) that have diverged along a salinity gradient (L. goodei—freshwater, L. parva—euryhaline). Offspring were raised under high and low salinity to test for (1) extrinsic isolation, (2) intrinsic isolation manifested through genetic incompatibilities, and (3) environmentally dependent genetic incompatibilities. I found evidence for both intrinsic and extrinsic isolation, but no evidence for environmentally dependent genetic incompatibilities. The presence of extrinsic and intrinsic isolation varied among fitness measures, and all forms of reproductive isolation were asymmetric. Early egg survival was independent of salinity, but demonstrated pronounced intrinsic isolation. Both extrinsic and intrinsic isolation existed for egg hatching and survival of fry to the eating stage. Unfortunately, the order in which extrinsic and intrinsic isolation arose is unresolved. Understanding the extent to which adaptation to salinity creates multiple forms of reproductive isolation is critical for understanding diversification in many fish taxa.

Natural selection imposed by interacting species frequently varies among geographic locations and can lead to local adaptation, where alternative phenotypes are found in different populations. Little is known, however, about whether geographically variable selection acting on traits that mediate species interactions is consistent or strong enough to influence patterns of nucleotide variation at individual loci. To investigate this question, we examined patterns of nucleotide diversity and population structure at 16 plant innate immunity genes, with putative functions in defending plants against pathogens or herbivores, from six populations of teosinte (Zea mays ssp. parviglumis). Specifically, we tested whether patterns of population structure and within-population diversity at immunity genes differed from patterns found at nonimmunity (reference) loci and from neutral expectations derived from coalescent simulations of structured populations. For the majority of genes, we detected no strong evidence of geographically variable selection. However, in the wound-induced serine protease inhibitor (wip1), which inhibits the hydrolysis of dietary proteins in insect herbivores, one population showed unusually high levels of genetic differentiation, very low levels of nucleotide polymorphism, and was fixed for a novel replacement substitution in the active site of the protein. Taken together, these data suggest that wip1 experienced a recent selective sweep in one geographic region; this pattern may reflect local adaptation or an ongoing species-wide sweep. Overall, our results indicate that a signature of local adaptation at the molecular level may be uncommon—particularly for traits that are under complex genetic control.

Chromosomal rearrangements may play an important role in how populations adapt to a local environment. The gene arrangement polymorphism on the third chromosome of Drosophila pseudoobscura is a model system to help determine the role that inversions play in the evolution of this species. The gene arrangements are the likely target of strong selection because they form classical clines across diverse geographic habitats, they cycle in frequency over seasons, and they form stable equilibria in population cages. A numerical approach was developed to estimate the fitness sets for 15 gene arrangement karyotypes in six niches based on a model of selection–migration balance. Gene arrangement frequencies in the six different niches were able to reach a stable meta-population equilibrium that matched the observed gene arrangement frequencies when recursions used the estimated fitnesses with a variety of initial inversion frequencies. These analyses show that a complex pattern of selection is operating in the six niches to maintain the D. pseudoobscura gene arrangement polymorphism. Models of local adaptation predict that the new inversion mutations were able to invade populations because they held combinations of two to 13 local adaptation loci together.

We study victim–exploiter coevolution in a spatially heterogeneous island model. In each species, fitness consequences of between-species interactions are controlled by a single haploid diallelic locus. Our emphasis is on the conditions for the maintenance of genetic variation, the dynamic patterns observed, the extent of local adaptation and genetic differentiation between different demes, and on how different parameters (such as the strength and heterogeneity in selection, migration rates, and the number of sites) affect the dynamic and static behavior of the system. We show that under spatially homogeneous selection the maintenance of genetic variation is possible through asynchronous nonlinear dynamics where the allele frequencies in a majority of demes quickly synchronize but the rest do not. Spatially heterogeneous selection can maintain genetic variation even if migration rates are maximal. This happens in an oscillatory way. Genetic variation is most likely to be maintained at high levels if the heterogeneity in selection is large. If there are some restrictions on migration, genetic variation can be maintained at a stable equilibrium. This behavior is most likely at intermediate migration rates. In this case, the system can exhibit high spatial subdivision as measured by F_ST values but relatively low local adaptation.

Multilocus analysis of phylogeography and population history is a powerful tool for understanding the origin, dispersal, and geographic structure of species over time and space. Using 36 genetic markers (29 newly developed anonymous nuclear loci, six introns and one from mitochondrial DNA, amounting to over 15 kb per individual), we studied population structure and demographic history of the red-backed fairy wren Malurus melanocephalus, a small passerine distributed in the northern and eastern part of Australia across the Carpentarian barrier. Analysis of anonymous loci markers revealed large amounts of genetic diversity (π= 0.016 ± 0.01; average number of SNPs per locus = 48; total number of SNPs = 1395), and neither nuclear nor mitochondrial gene trees showed evidence of reciprocal monophyly among Cape York (CY), Eastern Forest (EF), and Top End (TE) populations. Despite traditional taxonomy linking TE and CY populations to the exclusion of EF, we found that the CY population is genetically closer to the EF population, consistent with predicted area cladograms in this region. Multilocus coalescent analysis suggests that the CY population was separated from the other two regions approximately 0.27 million years ago, and that significant gene flow between the ER and the CY populations (∼2 migrants per generation) suggests geographic continuity in eastern Australia. By contrast, gene flow between the CY and the TE populations has been dampened by divergence across the Carpentarian barrier.

Understanding how and why certain clades diversify greatly in morphology whereas others do not remains a major theme in evolutionary biology. Projecting families of phylogenies into multivariate morphospaces can distinguish two scenarios potentially leading to unequal morphological diversification: unequal magnitude of change per phylogenetic branch, and unequal efficiency in morphological innovation. This approach is demonstrated using a case study of skulls in sister clades within the South American fish superfamily Anostomoidea. Unequal morphological diversification in this system resulted not from the morphologically diverse clade changing more on each phylogenetic branch, but from that clade distributing an equal amount of change more widely through morphospace and innovating continually. Although substantial morphological evolution occurred throughout the less diverse clade's history, most of that clade's expansion in morphospace occurred in the most basal branches, and more derived portions of that radiation oscillated within previously explored limits. Because simulations revealed that there is a maximum 2.7% probability of generating two clades that differ so greatly in the density of lineages within morphospace under a null Brownian model, the observed difference in pattern likely reflects a difference in the underlying evolutionary process. Clade–specific factors that may have promoted or arrested morphological diversification are discussed.

Brain size is under many opposing selection pressures. Estimating their relative influence and reconstructing the brain's evolutionary history have, however, proved difficult. Here, we confirm the suggestion that the brain of brood parasitic cuckoos is smaller in relation to their body weight than that of nonparasitic cuckoo species. Two hypotheses explaining reductions in brain size are tested, using phylogenetically controlled correlations and evolutionary pathway analyses. In a novel approach, the pathway models are combined to build the most likely evolutionary sequence of trait changes correlating with changes in brain size. Brain size changed before brood parasitism, followed by a shift toward less-productive habitats and an increase in migration. This sequence shows that brain size was not reduced as a consequence of a loss of cognitive skills related to chick provisioning, and it offers no support for the hypothesis that an increase in energetic demands or a reduction in energy availability selected for a reduction of brain size. Instead, the sequence suggests that the reduction in energetic demands due to the smaller brain size and parasitic breeding strategy may have enabled parasitic cuckoos to colonize new niches.

Explanations for the maintenance of variation in reproductive traits influenced by seminal fluid accessory gland proteins (Acps) in male Drosophila melanogaster include nontransitivity in the outcome of sperm competition and/or condition dependence of the traits involved. We investigated the effects of adult male nutrition (five diets) on the expression of Acp- and sperm- mediated traits. We found novel, nonlinear effects, with females showing lower levels of refractoriness to remating after mating with males held on the lowest and highest yeast diets. There were no significant effects of adult male nutrition on male paternity share, but there was a striking, nonlinear effect on second male progeny production, with males kept on intermediate yeast diets fathering the highest number of offspring. Such “bell shaped” responses of life-history traits to nutrition have only previously been reported for longevity. Consistent with previous reports, males maintained on low protein diets had lower premating success and gained fewer rematings with nonvirgins. We show novel and body size independent effects of adult male nutrition on traits influenced by Acps and sperm, which do not fit current condition-dependent handicap models and can affect the strength of sexual selection acting upon such fitness-related traits.

Recent research has shown the potential for nonallopatric speciation, but we lack an adequate understanding of the mechanisms of prezygotic barriers and how these evolve in the presence of gene flow. The marine snail Littorina saxatilis has distinct ecotypes in different shore microhabitats. Ecotypes hybridize in contact zones, but gene flow is impeded by assortative mating. Earlier studies have shown that males and females of the same ecotype copulate for longer than mates of different ecotype. Here we report a new mechanism that further contributes to reproductive isolation between ecotypes in the presence of gene flow. This mechanism is linked to the ability of males to track potential partners by following their mucous trail. We show that cliff ecotype males follow the trails of females of the same ecotype for longer than females of the alternate (boulder) ecotype. In addition, cliff males are more likely to follow the mucous trail in the correct direction if the trail is laid by a cliff-female. The capacity to discriminate the ecotype of female mucous trails combined with differential copulation times creates a strong prezygotic reproductive barrier between ecotypes of L. saxatilis that reduces gene flow from cliff to boulder ecotypes by ≥80%.

Many of the greatest challenges in medicine and public health involve the evolution of drug resistance by pathogens. Recent advances in the theory of natural selection suggest that there are two broad classes of pathogen traits that can be targeted by drugs or vaccines. The first class, consisting of traits that benefit the individual organisms bearing them, causes a strong evolutionary response and the rapid emergence of drug resistance. The second class, consisting of traits that benefit groups of pathogen organisms including the individual provider, causes a weaker evolutionary response and less drug resistance. Although most previous drug development has targeted the first class, it would be advantageous to focus on the second class as targets for drug and vaccine development. Specific examples and test cases are discussed.