John Stanton-Geddes

Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula.

Genome-wide association study (GWAS) has revolutionized the search for the genetic basis of complex traits. To date, GWAS have generally relied on relatively sparse sampling of nucleotide diversity, which is likely to bias results by preferentially sampling high-frequency SNPs not in complete linkage disequilibrium (LD) with causative SNPs. To avoid these limitations we conducted GWAS with >6 million SNPs identified by sequencing the genomes of 226 accessions of the model legume Medicago truncatula. We used these data to identify candidate genes and the genetic architecture underlying phenotypic variation in plant height, trichome density, flowering time, and nodulation. The characteristics of candidate SNPs differed among traits, with candidates for flowering time and trichome density in distinct clusters of high linkage disequilibrium (LD) and the minor allele frequencies (MAF) of candidates underlying variation in flowering time and height significantly greater than MAF of candidates underlying variation in other traits. Candidate SNPs tagged several characterized genes including nodulation related genes SERK2, MtnodGRP3, MtMMPL1, NFP, CaML3, MtnodGRP3A and flowering time gene MtFD as well as uncharacterized genes that become candidates for further molecular characterization. By comparing sequence-based candidates to candidates identified by in silico 250K SNP arrays, we provide an empirical example of how reliance on even high-density reduced representation genomic makers can bias GWAS results. Depending on the trait, only 30–70% of the top 20 in silico array candidates were within 1 kb of sequence-based candidates. Moreover, the sequence-based candidates tagged by array candidates were heavily biased towards common variants; these comparisons underscore the need for caution when interpreting results from GWAS conducted with sparsely covered genomes.

Genomic Signature of Adaptation to Climate in Medicago truncatula

Local adaptation and adaptive clines are pervasive in natural plant populations, yet the effects of these types of adaptation on genomic diversity are not well understood. With a data set of 202 accessions of Medicago truncatula genotyped at almost 2 million single nucleotide polymorphisms, we used mixed linear models to identify candidate loci responsible for adaptation to three climatic gradients—annual mean temperature (AMT), precipitation in the wettest month (PWM), and isothermality (ITH)—representing the major axes of climate variation across the species’ range. Loci with the strongest association to these climate gradients tagged genome regions with high sequence similarity to genes with functional roles in thermal tolerance, drought tolerance, or resistance to herbivores of pathogens. Genotypes at these candidate loci also predicted the performance of an independent sample of plant accessions grown in climate-controlled conditions. Compared to a genome-wide sample of randomly drawn reference SNPs, candidates for two climate gradients, AMT and PWM, were significantly enriched for genic regions, and genome segments flanking genic AMT and PWM candidates harbored less nucleotide diversity, elevated differentiation between haplotypes carrying alternate alleles, and an overrepresentation of the most common haplotypes. These patterns of diversity are consistent with a history of soft selective sweeps acting on loci underlying adaptation to climate, but not with a history of long-term balancing selection.

Role of climate and competitors in limiting fitness across range edges of an annual plant

It is often assumed that the geographic distributions of species match their climatic tolerances, but this assumption is not frequently tested. Moreover, few studies examine the relative importance of abiotic and biotic factors for limiting species ranges. We combined multiple approaches to assess the extent to which fitness of a widespread native annual legume, Chamaecrista fasciculata, decreases at and beyond its northern and western range edges, and how this is influenced by the presence of neighbors. First, we examined plant fitness and the effect of neighbors in natural populations at different geographic range locations for three years. Fitness decreased toward the northern range edge, but not the western edge. Neighbor removal had a consistently positive effect on seedpod production across all years and sites. Second, we established experimental populations at sites within the range, and at and beyond the northern and western range edges. We tracked individual fitness and recorded seedling recruitment in the following year (a complete generation) to estimate population growth rate. Individual fitness and population growth declined to near zero beyond both range edges, indicating that C. fasciculata with its present genetic composition will not establish in these regions, given conditions currently. We also carried out a neighbor removal treatment. Consistent with the natural populations, neighbors reduced seedpod production of reproductive adults. However, neighbors also increased early-season survival, and this positive effect early in life history resulted in a net positive effect of neighbors on lifetime fitness at most range locations. Our data show that the population growth rate of C. fasciculata includes values above replacement, and populations are well adapted to conditions up to the edge of the range, whereas the severely compromised fitness at sites beyond the edge precludes immediate establishment of populations and thereby impedes adaptation to these conditions.

Does a facultative mutualism limit species range expansion

The availability and quality of mutualists beyond a species’ range edge may limit range expansion. With the legume Chamaecrista fasciculata, we asked to what extent the availability and quality of rhizobia beyond the range edge limits host range expansion. We tested the effect of rhizobia availability on plant growth by transplanting seed from three locations into five sites spanning C. fasciculata’s range (interior, at the northern and western range edges, and beyond the range edges), and inoculating half the seeds with rhizobia. We recorded growth of all surviving plants, and, for the uninoculated plants, whether they had formed nodules or not. We isolated rhizobia from nodules collected on the uninoculated plants, and cross-inoculated seed from four populations (both range edge and interior populations) in the greenhouse to determine whether the quality of rhizobia differed between regions. We found that seeds transplanted beyond the range edge were less likely to be nodulated when they were not experimentally inoculated, and there was benefit to inoculation at all sites. In the greenhouse, the three inocula that formed nodules on plants, from the range interior, northern edge and beyond the northern edge, did not detectably differ in their effect on plant growth. These results suggest that low densities of suitable rhizobia beyond the range edge may limit range expansion of legume species.

Do trade-offs have explanatory power for the evolution of organismal interactions?

The concept of a trade‐off has long played a prominent role in understanding the evolution of organismal interactions such as mutualism, parasitism, and competition. Given the complexity inherent to interactions between different evolutionary entities, ecological factors may especially limit the power of trade‐off models to predict evolutionary change. Here, we use four case studies to examine the importance of ecological context for the study of trade‐offs in organismal interactions: (1) resource‐based mutualisms, (2) parasite transmission and virulence, (3) plant biological invasions, and (4) host range evolution in parasites and parasitoids. In the first two case studies, mechanistic trade‐off models have long provided a strong theoretical framework but face the challenge of testing assumptions under ecologically realistic conditions. Work under the second two case studies often has a strong ecological grounding, but faces challenges in identifying or quantifying the underlying genetic mechanism of the trade‐off. Attention is given to recent studies that have bridged the gap between evolutionary mechanism and ecological realism. Finally, we explore the distinction between ecological factors that mask the underlying evolutionary trade‐offs, and factors that actually change the trade‐off relationship between fitness‐related traits important to organismal interactions.

Genome-wide association of drought-related and biomass traits with HapMap SNPs in Medicago truncatula

Improving drought tolerance of crop plants is a major goal of plant breeders. In this study, we characterized biomass and drought-related traits of 220 Medicago truncatula HapMap accessions. Characterized traits included shoot biomass, maximum leaf size, specific leaf weight, stomatal density, trichome density and shoot carbon-13 isotope discrimination (δ(13) C) of well-watered M. truncatula plants, and leaf performance in vitro under dehydration stress. Genome-wide association analyses were carried out using the general linear model (GLM), the standard mixed linear model (MLM) and compressed MLM (CMLM) in TASSEL, which revealed significant overestimation of P-values by CMLM. For each trait, candidate genes and chromosome regions containing SNP markers were found that are in significant association with the trait. For plant biomass, a 0.5 Mbp region on chromosome 2 harbouring a plasma membrane intrinsic protein, PIP2, was discovered that could potentially be targeted to increase dry matter yield. A protein disulfide isomerase-like protein was found to be tightly associated with both shoot biomass and leaf size. A glutamate-cysteine ligase and an aldehyde dehydrogenase family protein with Arabidopsis homologs strongly expressed in the guard cells were two of the top genes identified by stomata density genome-wide association studies analysis.

Interactions between Soil Habitat and Geographic Range Location Affect Plant Fitness

Populations are often found on different habitats at different geographic locations. This habitat shift may be due to biased dispersal, physiological tolerances or biotic interactions. To explore how fitness of the native plant Chamaecrista fasciculata depends on habitat within, at and beyond its range edge, we planted seeds from five populations in two soil substrates at these geographic locations. We found that with reduced competition, lifetime fitness was always greater or equivalent in one habitat type, loam soils, though early-season survival was greater on sand soils. At the range edge, natural populations are typically found on sand soil habitats, which are also less competitive environments. Early-season survival and fitness differed among source populations, and when transplanted beyond the range edge, range edge populations had greater fitness than interior populations. Our results indicate that even when the optimal soil substrate for a species does not change with geographic range location, the realized niche of a species may be restricted to sub-optimal habitats at the range edge because of the combined effects of differences in abiotic and biotic effects (e.g. competitors) between substrates.

Modulation of the heat shock response is associated with acclimation to novel temperatures but not adaptation to climatic variation in the ants Aphaenogaster picea and A. rudis

Ecological diversification into thermally divergent habitats can push species toward their physiological limits, requiring them to accommodate temperature extremes through plastic or evolutionary changes that increase persistence under the local thermal regime. One way to withstand thermal stress is to increase production of heat shock proteins, either by maintaining higher baseline abundance within cells or by increasing the magnitude of induction in response to heat stress. We evaluated whether environmental variation was associated with expression of three heat shock protein genes in two closely-related species of woodland ant, Aphaenogaster picea and A. rudis. We compared adult workers from colonies collected from 25 sites across their geographic ranges. Colonies were maintained at two different laboratory temperatures, and tested for the independent effects of environment, phylogeny, and acclimation temperature on baseline and heat-induced gene expression. The annual maximum temperature at each collection site (Tmax) was not a significant predictor of either baseline expression or magnitude of induction of any of the heat shock protein genes tested. A phylogenetic effect was detected only for basal expression of Hsp40, which was lower in the most southern populations of A. rudis and higher in a mid-range population of possible hybrid ancestry. In contrast, a higher acclimation temperature significantly increased baseline expression of Hsc70-4, and increased induction of Hsp40 and Hsp83. Thus, physiological acclimation to temperature variation appears to involve modulation of the heat shock response, whereas other mechanisms are likely to be responsible for evolutionary shifts in thermal performance associated with large-scale climate gradients.

The Effect of Plant Inbreeding and Stoichiometry on Interactions with Herbivores in Nature: Echinacea angustifolia and Its Specialist Aphid

Fragmentation of once widespread communities may alter interspecific interactions by changing genetic composition of interacting populations as well as their abundances and spatial distributions. In a long-term study of a fragmented population of Echinacea angustifolia, a perennial plant native to the North American prairie, we investigated influences on its interaction with a specialist aphid and tending ants. We grew plant progeny of sib-matings (I), and of random pairings within (W) and between (B) seven remnants in a common field within 8 km of the source remnants. During the fifth growing season, we determined each plants burden of aphids and ants, as well as its size and foliar elemental composition (C, N, P). We also assayed composition (C, N) of aphids and ants. Early in the season, progeny from genotypic classes B and I were twice as likely to harbor aphids, and in greater abundance, than genotypic class W; aphid loads were inversely related to foliar concentration of P and positively related to leaf N and plant size. At the end of the season, aphid loads were indistinguishable among genotypic classes. Ant abundance tracked aphid abundance throughout the season but showed no direct relationship with plant traits. Through its potential to alter the genotypic composition of remnant populations of Echinacea, fragmentation can increase Echinaceas susceptibility to herbivory by its specialist aphid and, in turn, perturb the abundance and distribution of aphids.

In defense of P values: comment on the statistical methods actually used by ecologists.

In recent years, a persuasive argument has been made for the use of information criterion (IC) model selection in place of null hypothesis significance testing (NHST) based on P values (Johnson 1999, Burnham and Anderson 2002, Johnson and Omland 2004). In this issue, Murtaugh (2014) questions the basis for this argument. We comment on this paper from the perspective of early-career ecologists and present the results of an informal survey of our colleagues on their choice of statistical methods. Specifically, we ask to what extent the IC approach has supplanted traditional hypothesis testing. Finally, we address issues related to the use and interpretation of P values, the Akaike information criterion (AIC), and effect sizes in ecological studies.