Genetic analyses of nickel tolerance in a North American serpentine endemic plant, Caulanthus amplexicaulis var. barbarae (Brassicaceae)

Genomic basis and phenotypic manifestation of (non-)parallel serpentine adaptation in Arabidopsis arenosa

Parallel evolution is common in nature and provides one of the most compelling examples of rapid environmental adaptation. In contrast to the recent burst of studies addressing genomic basis of parallel evolution, integrative studies linking genomic and phenotypic parallelism are scarce. Edaphic islands of toxic serpentine soils provide ideal systems for studying rapid parallel adaptation in plants, imposing strong, spatially replicated selection on recently diverged populations. We leveraged threefold independent serpentine adaptation of Arabidopsis arenosa and combined reciprocal transplants, ion uptake phenotyping, and available genome-wide polymorphisms to test if parallelism is manifested to a similar extent at both genomic and phenotypic levels. We found pervasive phenotypic parallelism in functional traits yet with varying magnitude of fitness differences that was congruent with neutral genetic differentiation between populations. Limited costs of serpentine adaptation suggest absence of soil-driven trade-offs. On the other hand, the genomic parallelism at the gene level was significant, although relatively minor. Therefore, the similarly modified phenotypes, for example, of ion uptake arose possibly by selection on different loci in similar functional pathways. In summary, we bring evidence for the important role of genetic redundancy in rapid adaptation involving traits with polygenic architecture.

The Evolutionary Genomics of Serpentine Adaptation

Serpentine barrens are among the most challenging settings for plant life. Representing a perfect storm of hazards, serpentines consist of broadly skewed elemental profiles, including abundant toxic metals and low nutrient contents on drought-prone, patchily distributed substrates. Accordingly, plants that can tolerate the challenges of serpentine have fascinated biologists for decades, yielding important insights into adaptation to novel ecologies through physiological change. Here we highlight recent progress from studies which demonstrate the power of serpentine as a model for the genomics of adaptation. Given the moderate - but still tractable - complexity presented by the mix of hazards on serpentine, these venues are well-suited for the experimental inquiry of adaptation both in natural and manipulated conditions. Moreover, the island-like distribution of serpentines across landscapes provides abundant natural replicates, offering power to evolutionary genomic inference. Exciting recent insights into the genomic basis of serpentine adaptation point to a partly shared basis that involves sampling from common allele pools available from retained ancestral polymorphism or via gene flow. However, a lack of integrated studies deconstructing complex adaptations and linking candidate alleles with fitness consequences leaves room for much deeper exploration. Thus, we still seek the crucial direct link between the phenotypic effect of candidate alleles and their measured adaptive value - a prize that is exceedingly rare to achieve in any study of adaptation. We expect that closing this gap is not far off using the promising model systems described here.

Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)

Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., >1 km), possibly via zoochory.

Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant

Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.

Fitness consequences of short- and long-distance pollinations in Phlox hirsuta, an endangered species

PREMISE OF THE STUDY

The persistence of rare and endangered plant species may depend on the distance pollinators travel when dispersing pollen. Pollinations between adjacent plants, which are often genetically similar, can decrease seed set, germination, and/or progeny vigor due to shared S-alleles or inbreeding depression. Interpopulation pollen dispersal is often suggested as a management tool to increase genetic diversity; however, long-distance pollinations also have the potential to decrease fitness.

METHODS

We performed experimental hand pollinations in the field and germination experiments in a growth chamber to determine the effect of intrapopulation pollination distance (1 m, 10 m, and 100 m) on seed set, seed germination, progeny growth, and progeny reproduction in Phlox hirsuta. In addition, we included interpopulation pollinations (6740 m) to determine whether artificial gene flow is a viable management option for this endangered species.

KEY RESULTS

Although pollination distance did not affect the number of healthy seeds produced or the likelihood of radicle emergence, it did significantly affect the ability of germinating seeds to successfully produce cotyledons. Outbreeding depression was observed during seed germination and early seedling development. Seedlings resulting from interpopulation pollinations developed more slowly and were less likely to survive to produce cotyledons than seedlings resulting from all three intrapopulation pollination distances.

CONCLUSIONS

Our results suggest that the success of P. hirsuta does not depend on the distance pollinators travel within populations and that conservation strategies that involve transporting genes between populations can be counterproductive.

Nickel accumulation in leaves, floral organs and rewards varies by serpentine soil affinity

Serpentine soils are edaphically stressful environments that host many endemic plant species. In particular, serpentine soils are high in several heavy metals (e.g. nickel, cobalt and chromium) and these high heavy metal concentrations are thought, in part, to lead to varying levels of plant adaptation and soil affinities (i.e. endemic vs. non-endemic plant species). It is unclear, however, whether serpentine endemics vs. non-endemics differ with respect to heavy metal uptake into either vegetative or reproductive organs. Here, we use nickel as a model to determine whether plant heavy metal uptake varies with the level of endemism in several non-hyperaccumulating species. Under controlled greenhouse conditions, we grew seven plant species from the Brassicaceae family that vary in their degrees of affinity to serpentine soil from low (indifferent) to medium (indicator) and high (endemic) in soil that was nickel supplemented or not. We quantified nickel concentrations in leaves, pistils, anthers, pollen and nectar. While nickel concentrations did not vary across organs or affinities when grown in control soils, under conditions of nickel supplementation endemic species had the lowest tissue concentrations of nickel, particularly when considering leaves and pistils, compared with indifferent/indicator species. Species indifferent to serpentines incorporated higher concentrations of nickel into reproductive organs relative to leaves, but this was not the case for indicator species and endemics where nickel concentration was similar in these organs. Our findings suggest that endemic species possess the ability to limit nickel uptake into above-ground tissues, particularly in reproductive organs where it may interfere with survival and reproduction. Indifferent species accumulated significantly more nickel into reproductive organs compared with leaves, which may limit their reproductive potential relative to endemic species when growing on serpentine soils. Additional work determining the fitness consequences of these differences will further our understanding of edaphic endemism.

Novel nuclear markers inform the systematics and the evolution of serpentine use in Streptanthus and allies (Thelypodieae, Brassicaceae)

Streptanthus is a genus of ca. 35 species in the tribe Thelypodieae (Brassicaceae) that has remarkable morphological and ecological diversity, a large number of species in the group being edaphic specialists endemic to unusual soils such as serpentine. While ecological research has shed some light on adaptation to serpentine in Streptanthus, there have been few insights on the origins and evolution of serpentine tolerance in this group, largely due to limited success in resolving the phylogenetic relationships among Streptanthus and allied genera of the Thelypodieae (Streptanthoid complex). We present a well-resolved phylogenetic hypothesis for the Streptanthoid complex, based on three newly identified and highly variable single copy nuclear regions (AT4G34700, AT1G61620, and AT1G56590, and three others that are widely used (ITS, phyA, and PEPC). We also include data for two chloroplast regions (trnL and trnH-psbA). Collectively, our new markers provide 75% of the nuclear parsimony informative characters in our data. Taxonomically, our sampling is the most inclusive of any study of the Streptanthoid Complex to date, including 46 out of the 53 species of Streptanthus and Caulanthus, as well as representatives of several closely allied genera in the Thelypodieae. Our results reveal that Streptanthus, Caulanthus, and Thelypodium are not reciprocally monophyletic as currently defined. The species of Streptanthus form two rather distantly related clades. One clade (SC-I) is comprised of species with bilateral flowers and urn-shaped calyces that occur mainly within the California Floristic Province (CFP) hotspot; the other clade (SC-II) is composed of species with extant ranges mainly outside the CFP. Our data indicate that serpentine tolerance has evolved between eight and ten times in this group, of which between four and five have resulted in endemism. While serpentine endemism has been rarely lost, large and diverse clades composed mainly of serpentine endemics indicate that serpentine endemics in this group are more than mere 'dead-ends'.