Rafael F. Guerrero

Speciation as a sieve for ancestral polymorphism

Because they are considered rare, balanced polymorphisms are often discounted as crucial constituents of genome‐wide variation in sequence diversity. Despite its perceived rarity, however, long‐term balancing selection can elevate genetic diversity and significantly affect observed divergence between species. Here, we discuss how ancestral balanced polymorphisms can be “sieved” by the speciation process, which sorts them unequally across descendant lineages. After speciation, ancestral balancing selection is revealed by genomic regions of high divergence between species. This signature, which resembles that of other evolutionary processes, can potentially confound genomic studies of population divergence and inferences of “islands of speciation.”

Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis

Little is known about the physiological responses and genetic mutations associated with reproductive isolation between species, especially for postmating prezygotic isolating barriers. Here, we examine changes in gene expression that accompany the expression of ‘unilateral incompatibility’ (UI)—a postmating prezygotic barrier in which fertilization is prevented by gamete rejection in the reproductive tract [in this case of pollen tubes (male gametophytes)] in one direction of a species cross, but is successful in the reciprocal crossing direction. We use whole‐transcriptome sequencing of multiple developmental stages of male and female tissues in two Solanum species that exhibit UI to: (i) identify transcript differences between UI‐competent and UI noncompetent tissues; (ii) characterize transcriptional changes specifically associated with the phenotypic expression of UI; and (iii) using these comparisons, evaluate the behaviour of a priori candidate loci for UI and identify new candidates for future manipulative work. In addition to describing transcriptome‐wide changes in gene expression that accompany this isolating barrier, we identify at least five strong candidates for involvement in postmating prezygotic incompatibility between species. These include three novel candidates and two candidates that are strongly supported by prior developmental, functional, and quantitative trait locus mapping studies. These latter genes are known molecular players in the intraspecific expression of mate choice via genetic self‐incompatibility, and our study supports prior evidence that these inter‐ and intraspecific postmating prezygotic reproductive behaviours share specific genetic and molecular mechanisms.

Pervasive antagonistic interactions among hybrid incompatibility loci

Species barriers, expressed as hybrid inviability and sterility, are often due to epistatic interactions between divergent loci from two lineages. Theoretical models indicate that the strength, direction, and complexity of these genetic interactions can strongly affect the expression of interspecific reproductive isolation and the rates at which new species evolve. Nonetheless, empirical analyses have not quantified the frequency with which loci are involved in interactions affecting hybrid fitness, and whether these loci predominantly interact synergistically or antagonistically, or preferentially involve loci that have strong individual effects on hybrid fitness. We systematically examined the prevalence of interactions between pairs of short chromosomal regions from one species (Solanum habrochaites) co-introgressed into a heterospecific genetic background (Solanum lycopersicum), using lines containing pairwise combinations of 15 chromosomal segments from S. habrochaites in the background of S. lycopersicum (i.e., 95 double introgression lines). We compared the strength of hybrid incompatibility (either pollen sterility or seed sterility) expressed in each double introgression line to the expected additive effect of its two component single introgressions. We found that epistasis was common among co-introgressed regions. Interactions for hybrid dysfunction were substantially more prevalent in pollen fertility compared to seed fertility phenotypes, and were overwhelmingly antagonistic (i.e., double hybrids were less unfit than expected from additive single introgression effects). This pervasive antagonism is expected to attenuate the rate at which hybrid infertility accumulates among lineages over time (i.e., giving diminishing returns as more reproductive isolation loci accumulate), as well as decouple patterns of accumulation of sterility loci and hybrid incompatibility phenotypes. This decoupling effect might explain observed differences between pollen and seed fertility in their fit to theoretical predictions of the accumulation of isolation loci, including the ‘snowball’ effect.

Genome-wide patterns of regulatory divergence revealed by introgression lines.

Understanding the genetic basis for changes in transcriptional regulation is an important aspect of understanding phenotypic evolution. Using interspecific introgression lines, we infer the mechanisms of divergence in genome‐wide patterns of gene expression between the nightshades Solanum pennellii and S. lycopersicum (domesticated tomato). We find that cis‐ and trans‐regulatory changes have had qualitatively similar contributions to divergence in this clade, unlike results from other systems. Additionally, expression data from four tissues (shoot apex, ripe fruit, pollen, and seed) suggest that introgressed regions in these hybrid lines tend to be downregulated, while background (nonintrogressed) genes tend to be upregulated. Finally, we find no evidence for an association between the magnitude of differential expression in NILs and previously determined sterility phenotypes. Our results contradict previous predictions of the predominant role of cis‐ over trans‐regulatory divergence between species, and do not support a major role for gross genome‐wide misregulation in reproductive isolation between these species.

Topological features of a gene co-expression network predict patterns of natural diversity in environmental response

Molecular interactions affect the evolution of complex traits. For instance, adaptation may be constrained by pleiotropic or epistatic effects, both of which can be reflected in the structure of molecular interaction networks. To date, empirical studies investigating the role of molecular interactions in phenotypic evolution have been idiosyncratic, offering no clear patterns. Here, we investigated the network topology of genes putatively involved in local adaptation to two abiotic stressors—drought and cold—in Arabidopsis thaliana. Our findings suggest that the gene-interaction topologies for both cold and drought stress response are non-random, with genes that show genetic variation in drought expression response (eGxE) being significantly more peripheral and cold response genes being significantly more central than genes which do not show GxE. We suggest that the observed topologies reflect different constraints on the genetic pathways involved in environmental response. The approach presented here may inform predictive models linking genetic variation in molecular signalling networks with phenotypic variation, specifically traits involved in environmental response.

Transcriptomic analysis links gene expression to unilateral pollen-pistil reproductive barriers

BackgroundUnilateral incompatibility (UI) is an asymmetric reproductive barrier that unidirectionally prevents gene flow between species and/or populations. UI is characterized by a compatible interaction between partners in one direction, but in the reciprocal cross fertilization fails, generally due to pollen tube rejection by the pistil. Although UI has long been observed in crosses between different species, the underlying molecular mechanisms are only beginning to be characterized. The wild tomato relative Solanum habrochaites provides a unique study system to investigate the molecular basis of this reproductive barrier, as populations within the species exhibit both interspecific and interpopulation UI. Here we utilized a transcriptomic approach to identify genes in both pollen and pistil tissues that may be key players in UI.ResultsWe confirmed UI at the pollen-pistil level between a self-incompatible population and a self-compatible population of S. habrochaites. A comparison of gene expression between pollinated styles exhibiting the incompatibility response and unpollinated controls revealed only a small number of differentially expressed transcripts. Many more differences in transcript profiles were identified between UI-competent versus UI-compromised reproductive tissues. A number of intriguing candidate genes were highly differentially expressed, including a putative pollen arabinogalactan protein, a stylar Kunitz family protease inhibitor, and a stylar peptide hormone Rapid ALkalinization Factor. Our data also provide transcriptomic evidence that fundamental processes including reactive oxygen species (ROS) signaling are likely key in UI pollen-pistil interactions between both populations and species.ConclusionsGene expression analysis of reproductive tissues allowed us to better understand the molecular basis of interpopulation incompatibility at the level of pollen-pistil interactions. Our transcriptomic analysis highlighted specific genes, including those in ROS signaling pathways that warrant further study in investigations of UI. To our knowledge, this is the first report to identify candidate genes involved in unilateral barriers between populations within a species.

Genotypic context modulates fitness landscapes: Effects on the speed and direction of evolution for antimicrobial resistance

Understanding the forces that drive the dynamics of adaptive evolution is a goal of many subfields within evolutionary biology. The fitness landscape analogy has served as a useful abstraction for addressing these topics across many systems, and recent treatments have revealed how different environments can frame the particulars of adaptive evolution by changing the topography of fitness landscapes. In this study, we examine how the larger, ambient genotypic context in which the fitness landscape being modeled is embedded affects fitness landscape topography and subsequent evolution. Using simulations on empirical fitness landscapes, we discover that genotypic context, defined by genetic variability in regions outside of the locus under study (in this case, an essential bacterial enzyme target of antibiotics), influences the speed and direction of evolution in several surprising ways. These findings have implications for how we study the evolution of drug resistance in nature, and for presumptions about how biological evolution might be expected to occur in genetically-modified organisms. More generally, the findings speak to theory surrounding how “difference can beget difference” in adaptive evolution: that small genetic differences between organisms can greatly alter the specifics of how evolution occurs, which can rapidly drive even slightly diverged populations further apart. Author summary Technological advances enable scientists to engineer individual mutations at specific sites within an organism’s genome with increasing ease. These breakthroughs have provided scientists with tools to study how different engineered mutations affect the function of a given gene or protein, yielding useful insight into genotype-phenotype mapping and evolution. In this study, we use engineered strains of bacteria to show how the dynamics (speed and direction) of evolution of drug resistance in an enzyme depends on the species-type of that bacterial enzyme, and on the presence/absence of mutations in other genes in the bacterial genome. These findings have broad implications for public health, genetic engineering, and theories of speciation. In the context of public health and biomedicine, our results suggest that future efforts in managing antimicrobial resistance must consider genetic makeup of different pathogen populations before predicting how resistance will occur, rather than assuming that the same resistance pathways will appear in different pathogen populations. With regard to broader theory in evolutionary biology, our results show how even small genetic differences between organisms can alter how future evolution occurs, potentially causing closely-related populations to quickly diverge.

Quantifying the risk of hemiplasy in phylogenetic inference

Convergent evolution is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely— or more likely—than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a new method to calculate the ratio of these two probabilities (the “hemiplasy risk factor”) along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree in order to identify when and where incongruent traits may be more likely to be due to hemiplasy than homoplasy.

Linking gene expression to unilateral pollen-pistil reproductive barriers

Unilateral incompatibility (UI) is an asymmetric reproductive barrier that unidirectionally prevents gene flow between species and/or populations. UI is characterized by a compatible interaction between partners in one direction, but in the reciprocal cross fertilization fails, generally due to pollen tube rejection by the pistil. Although UI has long been observed in crosses between different species, the underlying molecular mechanisms are only beginning to be characterized. The wild tomato relative Solanum habrochaites provides a unique study system to investigate the molecular basis of this reproductive barrier, as populations within the species exhibit both interspecific and interpopulation UI. Here we used a transcriptomic approach to identify genes in both pollen and pistil tissues that may be probable key players in UI. We confirmed UI at the pollen-pistil level between a self-incompatible population and a self-compatible population of S. habrochaites. A comparison of gene expression between pollinated styles exhibiting the incompatibility response and unpollinated controls revealed only a small number of differentially expressed transcripts. Many more differences in transcript profiles were identified between UI-competent versus UI-compromised reproductive tissues. A number of intriguing candidate genes were highly differentially expressed, including a putative pollen arabinogalactan protein, a stylar Kunitz family protease inhibitor, and a stylar peptide hormone Rapid Alkalinization Factor. Our data also provide transcriptomic evidence that fundamental processes including reactive oxygen species signaling are likely key in UI pollen-pistil interactions between both populations and species. Our transcriptomic analysis highlighted specific genes, including those in ROS signaling pathways that warrant further study in investigations of UI. To our knowledge, this is the first report to identify candidate genes involved in unilateral barriers between populations of the same species.

The Moose of Isle Royale: An Unnatural Condition?

The now iconic moose of Isle Royale National Park arrived on the island sometime between 1910 and 1915 (Hickie, 1936; Murie, 1934). Prior to that period there is no evidence of moose in either naturalist reports or in the archaeological history of the island (Murie, 1934; Scarpino, 2011). Early naturalists–while observing the moose during their first 20 years on the island—noted both their dramatic expansion, and equally dramatic population crash in the 1930s, see Figure 1. Around 1950, and just as the moose were rebounding, wolves crossed a frozen Lake Superior and began what is now one of our most emblematic predator/prey systems (Peterson, 1995). Recently, the wolves on Isle Royale appear headed for local extinction (Mlot, 2015). Calls to repopulate the island have renewed the vigorous debate surrounding what is and what is not wild about Isle Royale (Scarpino, 2011; Cronon, 1996; Nelson & Callicott, 2008; Cronon, 2003; Peterson, 1999).