Massive haplotypes underlie ecotypic differentiation in sunflowers.

Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation.

Influence of a climatic gradient on genetic exchange between two oak species.

PREMISE: In plant groups with limited intrinsic barriers to gene flow, it is thought that environmental conditions can modulate interspecific genetic exchange. Oaks are known for limited barriers to gene flow among closely related species. Here, we use Quercus as a living laboratory in which to pursue a fundamental question in plant evolution: Do environmental gradients restrict or promote genetic exchange between species? METHODS: We focused on two North American oaks, the rare Quercus dumosa and the widespread Q. berberidifolia. We sampled intensively along a contact zone in California, USA. We sequenced restriction site-associated DNA markers and measured vegetative phenotype. We tested for genetic exchange, the association with climate, and the effect on phenotype. RESULTS: There is evidence for genetic exchange between the species. Admixed plants are found in areas of intermediate climate, while less admixed plants are found at the extremes of the climatic gradient. Genetic and phenotypic patterns are out of phase in the contact zone; some plants display the phenotype of one species but are genetically associated with another. CONCLUSIONS: Our results support the hypothesis that a strong climatic gradient can promote genetic exchange between species. The overall weak correlation between genotype and phenotype in the contact zone between the species suggests that genetic exchange can lead to the breakdown of trait combinations used to define species. This incongruency predicts ongoing problems for conservation of Q. dumosa, with implications for conservation of other oaks.

Evolution of leaf structure and drought tolerance in species of Californian Ceanothus.

PREMISE OF THE STUDY: Studies across diverse species have established theory for the contribution of leaf traits to plant drought tolerance. For example, species in more arid climates tend to have smaller leaves of higher vein density, higher leaf mass per area, and more negative osmotic potential at turgor loss point (πTLP ). However, few studies have tested these associations for species within a given lineage that have diversified across an aridity gradient. METHODS: We analyzed the anatomy and physiology of 10 Ceanothus (Rhamnaceae) species grown in a common garden for variation between and within "wet" and "dry" subgenera (Ceanothus and Cerastes, respectively) and analyzed a database for 35 species for leaf size and leaf mass per area (LMA). We used a phylogenetic generalized least squares approach to test hypothesized relationships among traits, and of traits with climatic aridity in the native range. We also tested for allometric relationships among anatomical traits. KEY RESULTS: Leaf form, anatomy, and drought tolerance varied strongly among species within and between subgenera. Cerastes species had specialized anatomy including hypodermis and encrypted stomata that may confer superior water storage and retention. The osmotic potentials at turgor loss point (πTLP ) and full turgor (πo ) showed evolutionary correlations with the aridity index (AI) and precipitation of the 10 species' native distributions, and LMA with potential evapotranspiration for the 35 species in the larger database. We found an allometric correlation between upper and lower epidermal cell wall thicknesses, but other anatomical traits diversified independently. CONCLUSIONS: Leaf traits and drought tolerance evolved within and across lineages of Ceanothus consistently with climatic distributions. The πTLP has signal to indicate the evolution of drought tolerance within small clades.

Leaf adaptations and species boundaries in North American Cercis: implications for the evolution of dry floras.

PREMISE OF THE STUDY: The North American Cercis clade spans dry to mesic climates and exhibits complex morphological variation. We tested various proposed species classifications of this group and whether aspects of leaf morphology, particularly the "drip-tip" in some regional populations, are adaptive and/or linked with phylogeny. METHODS: We made measurements on over 1100 herbarium specimens from throughout North America and analyzed the data with univariate and multivariate approaches. We analyzed phylogenetically DNA sequence data from nuclear ITS and three plastid regions from 40 samples, and estimated divergence times with a relaxed-clock Bayesian analysis. We used climate and geographic position data to predict the variation observed in leaf size and shape by using stepwise multiple linear regressions. KEY RESULTS: Morphometric analyses yielded a pattern of continuous and often clinal character variation across North America, without correlated gaps in character states. Conversely, phylogenetic and divergence time analyses yielded distinct clades from California, the interior west, and eastern North America separated by between ~12 and 16 million years. Multiple regressions yielded highly significant correlations between leaf apex shape and precipitation of the warmest quarter. CONCLUSIONS: Despite a pattern of continuous morphological character variation, the long period of geographic and presumably genetic isolation warrants the delimitation of three species. Predictive modeling supports the adaptive value of acuminate apices or "drip-tips" in mesic habitats. This suggests that Cercis leaves change more rapidly than inferred from parsimony reconstruction, which has implications for the evolution of the dry floras of North America and Eurasia.

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.

The evolutionary history of ferns inferred from 25 low-copy nuclear genes.

UNLABELLED: • PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.

Limited hybridization across an edaphic disjunction between the gabbro-endemic shrub Ceanothus roderickii (Rhamnaceae) and the soil-generalist Ceanothus cuneatus.

PREMISE OF THE STUDY: Hybridization is thought to have played an important role in diversification of the speciose shrub genus Ceanothus; putative hybrid species have been described, and data suggest that intrinsic barriers may not exist among closely related species. However, the extent to which hybridization occurs in the wild is not known, and little is understood about how extrinsic factors such as soil chemistry may influence the process. The present research focuses on the gabbro-endemic C. roderickii and the closely related soil-generalist C. cuneatus. Though the species occur peripatrically, they remain distinct across an edaphic disjunction. • METHODS: AFLP was used to quantify hybridization and introgression. Biological data and experiments were used to test for prezygotic isolation. Growth trials were used to test for local adaptation and selection against hybrids. • KEY RESULTS: Ceanothus cuneatus and C. roderickii were strongly differentiated morphologically and genetically, despite a lack of evidence for prezygotic barriers. Hybrids and back-crosses were present but infrequent. Finally, there was selection against hybrids in nonnative soil. • CONCLUSIONS: There is little genetic exchange between the focal species across an edaphic disjunction, despite the absence of prezygotic barriers. This result implies that soil conditions, as well as other extrinsic factors, should be considered as forces that may restrict hybridization and gene flow in Ceanothus, influencing local adaptation and speciation. Findings presented here are significant because they imply that exchange of genetic material between plants may be limited directly by the abiotic environment, rather than by the biology of the plants.

Microsatellite markers from Ceanothus roderickii (Rhamnaceae) using next-generation sequencing technology.

PREMISE OF THE STUDY: Ceanothus roderickii is an endangered shrub endemic to California. To investigate the population genetics of this species, including the genetic consequences of population fragmentation and hybridization, 10 microsatellite markers were developed. METHODS AND RESULTS: Using next-generation sequencing (454) data from a single C. roderickii individual, 10 microsatellite markers were developed. A group of 12 individuals representing all of the major C. roderickii populations were analyzed. All loci were found to be polymorphic, with a range from two to 12 alleles per locus. Observed heterozygosity ranged from 0.08 to 0.83 across loci. All 10 loci were also amplifiable in at least one other Ceanothus species. CONCLUSIONS: Results presented here indicate the utility of our new microsatellite primers in ongoing and future studies concerning population genetics and gene flow in C. roderickii, as well as the potential applicability of these primers in similar studies on other Ceanothus species.

Phylogeny of the plant genus Pachypodium (Apocynaceae).

Background. The genus Pachypodium contains 21 species of succulent, generally spinescent shrubs and trees found in southern Africa and Madagascar. Pachypodium has diversified mostly into arid and semi-arid habitats of Madagascar, and has been cited as an example of a plant group that links the highly diverse arid-adapted floras of Africa and Madagascar. However, a lack of knowledge about phylogenetic relationships within the genus has prevented testing of this and other hypotheses about the group. Methodology/Principal Findings. We use DNA sequence data from the nuclear ribosomal ITS and chloroplast trnL-F region for all 21 Pachypodium species to reconstruct evolutionary relationships within the genus. We compare phylogenetic results to previous taxonomic classifications and geography. Results support three infrageneric taxa from the most recent classification of Pachypodium, and suggest that a group of African species (P. namaquanum, P. succulentum and P. bispinosum) may deserve taxonomic recognition as an infrageneric taxon. However, our results do not resolve relationships among major African and Malagasy lineages of the genus. Conclusions/Significance. We present the first molecular phylogenetic analysis of Pachypodium. Our work has revealed five distinct lineages, most of which correspond to groups recognized in past taxonomic classifications. Our work also suggests that there is a complex biogeographic relationship between Pachypodium of Africa and Madagascar.

Transcriptome-mining for single-copy nuclear markers in ferns.

BACKGROUND: Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. PRINCIPAL FINDINGS: We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. CONCLUSIONS: The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.