Leonie C. Moyle

Asymmetrical crossing barriers in angiosperms.

Patterns of reproductive isolation between species may provide insight into the mechanisms and evolution of barriers to interspecific gene exchange. We used data from published interspecific hybridization experiments from 14 genera of angiosperms in order to test for the presence of asymmetrical barriers to gene exchange. Reproductive isolation was examined at three life–history stages: the ability of interspecific crosses to produce seeds, the viability of F1 hybrids, and the fertility of F1 hybrids. Statistically significant asymmetries in the strength of reproductive isolation between species were detected in all genera and at each of the three life–history stages. Asymmetries in seed production may be caused by a variety of mechanisms including differences in stigma/style lengths, self compatibility and differential fruit abortion. Asymmetries in post–zygotic isolation are probably caused by nuclear—cytoplasmic interactions. Asymmetrical reproductive isolation between plant taxa may have important implications for the dynamics of hybrid zones, the direction of genetic introgression and the probability of reinforcement.

Asymmetric Postmating Isolation: Darwin's Corollary to Haldane's Rule

Asymmetric postmating isolation, where reciprocal interspecific crosses produce different levels of fertilization success or hybrid sterility/inviability, is very common. Darwin emphasized its pervasiveness in plants, but it occurs in all taxa assayed. This asymmetry often results from Dobzhansky–Muller incompatibilities (DMIs) involving uniparentally inherited genetic factors (e.g., gametophyte–sporophyte interactions in plants or cytoplasmic–nuclear interactions). Typically, unidirectional (U) DMIs act simultaneously with bidirectional (B) DMIs between autosomal loci that affect reciprocal crosses equally. We model both classes of two-locus DMIs to make quantitative and qualitative predictions concerning patterns of isolation asymmetry in parental species crosses and in the hybrid F1 generation. First, we find conditions that produce expected differences. Second, we present a stochastic analysis of DMI accumulation to predict probable levels of asymmetry as divergence time increases. We find that systematic interspecific differences in relative rates of evolution for autosomal vs. nonautosomal loci can lead to different expected F1 fitnesses from reciprocal crosses, but asymmetries are more simply explained by stochastic differences in the accumulation of U DMIs. The magnitude of asymmetry depends primarily on the cumulative effects of U vs. B DMIs (which depend on heterozygous effects of DMIs), the average number of DMIs required to produce complete reproductive isolation (more asymmetry occurs when fewer DMIs are required), and the shape of the function describing how fitness declines as DMIs accumulate. Comparing our predictions to data from diverse taxa indicates that unidirectional DMIs, specifically involving sex chromosomes, cytoplasmic elements, and maternal effects, are likely to play an important role in postmating isolation.

PATTERNS OF REPRODUCTIVE ISOLATION IN THREE ANGIOSPERM GENERA

Abstract Analyses among animal species have found that reproductive isolation increases monotonically with genetic distance, evolves more quickly for prezygotic than postzygotic traits, and is stronger among sympatric than allopatric species pairs. The latter pattern is consistent with expectations under the reinforcement hypothesis. To determine whether similar trends are found among plant species, patterns of reproductive isolation (postpollination prezygotic, postzygotic, and “total” isolation) in three plant genera (Glycine, Silene, Streptanthus) were examined using data from previously published artificial hybridization experiments. In Silene, all measures of reproductive isolation were positively correlated with genetic distance. In contrast, in Glycine and Streptanthus, correlations between reproductive isolation and genetic distance were weak or nonsignificant, possibly due to the influence of biologically unusual taxa, variable evolutionary forces acting in different lineages, or insufficient time to accumulate reproductive isolation. There was no evidence that postpollination prezygotic reproductive isolation evolved faster than postzygotic isolation in Glycine or Silene. We also detected no evidence for faster accumulation of postmating prezygotic isolation between sympatric than allopatric species pairs; thus we found no evidence for the operation of speciation via reinforcement. In Silene, which included six polyploid species, results suggest that changes in ploidy disrupt a simple monotonic relationship between isolation and genetic distance.

What can patterns of differentiation across plant genomes tell us about adaptation and speciation

Genome scans have become a common approach to identify genomic signatures of natural selection and reproductive isolation, as well as the genomic bases of ecologically relevant phenotypes, based on patterns of polymorphism and differentiation among populations or species. Here, we review the results of studies taking genome scan approaches in plants, consider the patterns of genomic differentiation documented and their possible causes, discuss the results in light of recent models of genomic differentiation during divergent adaptation and speciation, and consider assumptions and caveats in their interpretation. We find that genomic regions of high divergence generally appear quite small in comparisons of both closely and more distantly related populations, and for the most part, these differentiated regions are spread throughout the genome rather than strongly clustered. Thus, the genome scan approach appears well-suited for identifying genomic regions or even candidate genes that underlie adaptive divergence and/or reproductive barriers. We consider other methodologies that may be used in conjunction with genome scan approaches, and suggest further developments that would be valuable. These include broader use of sequence-based markers of known genomic location, greater attention to sampling strategies to make use of parallel environmental or phenotypic transitions, more integration with approaches such as quantitative trait loci mapping and measures of gene flow across the genome, and additional theoretical and simulation work on processes related to divergent adaptation and speciation.

Hybrid Incompatibility “Snowballs” Between Solanum Species

Rolling Snowballs The genetic incompatibilities that separate ongoing speciation events have been hypothesized by the Dobzhansky-Muller model of speciation to snowball—that is, accumulate mutations causing postzygotic isolation at a faster rate than the linear accumulation of mutations. This occurs because of potential deleterious epistatic interactions in hybrids involving two or more interacting genes. Testing QTLs (quantitative trait loci) in seed and pollen sterility between multiple species pairs in the plant group Solanum, Moyle and Nakazato (p. 1521) show that hybrid female (seed) sterility accumulates exponentially between increasingly distant species pairs, although not for hybrid male (pollen) sterility. In contrast, loci contributing to differences in other traits show no evidence for nonlinear accumulation over time. Matute et al. (p. 1518) come to similar conclusions through the use of deletion mapping in comparisons between two pairs of species of Drosophila. The number of genes causing postzygotic isolation grows as fast as the square of the number of substitutions between two species. Thus, a hybrid snowball effect is found in both plants and animals. Two studies support the theory that the number of genes involved in hybrid incompatibility increases faster than linearly. Among the reproductive barriers that can isolate species, hybrid sterility is frequently due to dysfunctional interactions between loci that accumulate between differentiating lineages. Theory describing the evolution of these incompatibilities has generated the prediction, still empirically untested, that loci underlying hybrid incompatibility should accumulate faster than linearly with time—the “snowball effect.” We evaluated the accumulation of quantitative trait loci (QTL) between species in the plant group Solanum and found evidence for a faster-than-linear accumulation of hybrid seed sterility QTL, thus empirically evaluating and confirming this theoretical prediction. In comparison, loci underlying traits unrelated to hybrid sterility show no evidence for an accelerating rate of accumulation between species.

POPULATION VIABILITY ANALYSIS IN ENDANGERED SPECIES RECOVERY PLANS: PAST USE AND FUTURE IMPROVEMENTS

Using the results of a survey of recovery plans for threatened and endangered species, we evaluated the role that Population Viability Analysis (PVA) has played in recovery planning and management of rare species in the United States. Although there was a significant increase over time in the percentage of plans presenting information on PVA and assigning recovery tasks to collect more such information, the use of PVA was still called for in less than half of the plans approved since 1991. Because scarcity of data for rare species may be limiting the application of PVA to endangered species, we also assessed how often recovery plans proposed to collect the full complement of data required to perform four general types of PVA. For most of the species in the database, proposed monitoring data would allow the simplest type of PVA method (i.e., analysis of total population counts) to be applied, but more complex PVAs would be possible for <25% of the species. We conclude with brief recommendations for how the use of PVA in endangered species recovery planning might be improved in the future.

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a “PhyloGWAS” approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

ENVIRONMENTAL FACTORS PREDICT ADAPTIVE PHENOTYPIC DIFFERENTIATION WITHIN AND BETWEEN TWO WILD ANDEAN TOMATOES

Abstract Environmental variation is widely viewed as a major force driving morphological change and speciation. Although many environmental attributes are potentially critical for adaptive responses within and between species, the individual and relative importance of these diverse attributes remain poorly understood. Here we combine a geographical information systems (GIS)-based analysis of environmental variation with a multipopulation analysis of phenotypic, physiological, and genetic variation, to generate and test hypotheses of environmental factors likely driving adaptive divergence within and between two wild Andean plant species. First, we document large environmental differences between population locations of the two species, and among regions within species. Second, we show evidence for inter- and intraspecific differences in genetically based phenotypic and physiological variation. Third, combining these data, we report evidence for trait–environment associations both among populations within species, and between species, that are strongly indicative of recent and rapid adaptive responses. Finally, we show that these trait–environment associations cannot be simply explained by genetic relatedness within species, reinforcing our inference that local, regional, and species-wide environmental conditions are responsible for phenotypic and physiological diversification. The strongest trait–environment associations involve temperature and precipitation gradients, suggesting these climatic factors are predominant drivers of adaptive diversification in these species.

Ecological and Evolutionary Genomics in the Wild Tomatoes (Solanum Sect. Lycopersicon)

Abstract 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.

Interspecific reproductive barriers in the tomato clade: opportunities to decipher mechanisms of reproductive isolation

The tomato clade within the genus Solanum has numerous advantages for mechanistic studies of reproductive isolation. Its thirteen closely related species, along with four closely allied Solanum species, provide a defined group with diverse mating systems that display complex interspecific reproductive barriers. Several kinds of pre- and postzygotic barriers have already been identified within this clade. Well-developed genetic maps, introgression lines, interspecific bridging lines, and the newly available draft genome sequence of the domesticated tomato (Solanum lycopersicum) are valuable tools for the genetic analysis of interspecific reproductive barriers. The excellent chromosome morphology of these diploid species allows detailed cytological analysis of interspecific hybrids. Transgenic methodologies, well developed in the Solanaceae, allow the functional testing of candidate reproductive barrier genes as well as live imaging of pollen rejection events through the use of fluorescently tagged proteins. Proteomic and transcriptomics approaches are also providing new insights into the molecular nature of interspecific barriers. Recent progress toward understanding reproductive isolation mechanisms using these molecular and genetic tools is assessed in this review.