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Wyethia reticulata Greene is a rare perennial herb found only on gabbro-derived soils of the Pine Hill formation in the Sierra Nevada foothills of El Dorado County, CA. Wyethia reticulata is capable of both vegetative (clonal) and sexual reproduction, although the former is thought to be more common than the latter, with sexual reproduction tied to fire. The potential dominance of vegetative reproduction has conservation implications for W. reticulata, as populations could appear healthy in terms of stand density, while losing genetic diversity due to a lack of sexual recruitment. Past genetic assessments of W. reticulata relied on low-resolution markers from a small number of populations and did not directly address conservation issues. Here, double-digest random amplified DNA (ddRAD) sequencing was used to develop a high-resolution genomic dataset for a sample of 168 W. reticulata samples from seven locations that represent every known population center of the species. The data was used to 1) calculate the frequency of asexual reproduction, 2) determine which populations contain unique genetic variation, and 3) test whether there are any ecological correlates of genetic patterns. In contrast to past genetic research, the results presented here indicate that clonality is not common; less than 2% of plants were identified as being derived from asexual reproduction. Nevertheless, some locations seem to be more affected by asexuality than others; the index of association varied from 4.4 to 19.4 (M = 10.9). Genetic differentiation among locations was low (Fst = 0.03-0.04). However, clustering identified three distinct population segments that were not previously recognized. Elevation was the only environmental variable significantly associated with genetic differentiation. Based on these results, it is recommended that conservation effort be focused on genetically isolated population segments.

El Dorado bedstraw (Galium californicumsubsp.sierrae) is a federally endangered dioecious, octoploid, perennial herb found only in the Pine Hill region of El Dorado County, CA, USA. Like many species ofGalium, El Dorado bedstraw is capable of both sexual and asexual reproduction, spreading via stem-layering as well as seeds. El Dorado bedstraw is also dioecious, and thus dependent on pollinators to transfer pollen from male to female stems. The capacity for asexual reproduction has conservation implications for this plant, due to the potential for populations to become dominated by a small number of clones in the absence of recruitment from seeds. No previous work has examined either the population genetics or pollination biology of this plant. Here, double-digest restriction site-associated DNA sequencing was used to develop a genetic dataset for a sample of El Dorado bedstraw (12 individuals from each of seven locations). Genomic data was used to calculate population genetic statistics and quantify the degree to which clonality affects the sampled populations. Visual observation of insect visitors at every sampling location was used to assess the potential for pollen transfer within and among locations. A total of 23 clonal colonies were detected across 82 successfully sequenced stems, consisting of an average of 2.4 individuals (range: 2–6). Significant isolation by distance among locations was detected using a Mantel test. Insect pollinators were from eleven families, consisting mainly of small species with weak flight. It is recommended that clonality and small-scale population differentiation be taken into account in conservation measures.

Species often include multiple ecotypes that are adapted to different environments 1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations 2-4. 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. Local adaptation is common in species that experience different environments across their range, often resulting in the formation of ecotypes-ecological races with distinct morphological and/or physiological characteristics that provide an environment-specific fitness advantage. Despite the prevalence of ecotypic differentiation, much remains to be understood about the genetic basis and evolutionary mechanisms that underlie its establishment and maintenance. In particular , a longstanding evolutionary question-dating to criticisms of Darwin's theories by his contemporaries 4-concerns how such ecological divergence can occur when challenged by hybridization with non-adapted populations 2. Local adaptation typically requires alleles at multiple loci that contribute to increased fitness in the same environment ; however, different ecotypes are often geographically close and interfertile, and hybridization between them should break up adaptive allelic combinations 3. To better understand the genetic basis of local adaptation and ecotypic differentiation, we conducted an in-depth study of genetic, phenotypic and environmental variation in three annual sunflower species, each of which includes multiple reproductively compatible ecotypes. Two species (H. annuus and H. petiolaris) have broad, overlapping distributions across North America. Helianthus annuus, the common sunflower, is generally found on mesic soils, but can grow in a variety of disturbed or extreme habitats, including semi-desert or frequently flooded areas. An especially well-characterized ecotype (formally known as H. annuus subsp. texanus) is adapted to the higher temperatures and herbivore pressures in Texas (USA) 5. Helianthus petiolaris, the prairie sunflower, prefers sandier soils; ecotypes of this species are adapted to sand sheets and dunes 6. The third species-H. argophyllus, the silverleaf sunflower-is endemic to southern Texas and includes both an early-flowering, coastal-island ecotype and a late-flowering inland ecotype 7. Population structure of wild sunflowers In a common garden experiment, we grew 10 plants from each of 151 populations of the 3 species, selected from across their native range (Fig. 1a); for each of these populations, we collected corresponding soil samples. We generated extensive records of developmental and morphological traits, and resequenced the genomes of 1,401 individual plants. We resequenced an additional 105 H. annuus plants to fill gaps in geographical coverage, as well as 12 outgroup taxa (Supplementary Table 1). Sunflower genomes are relatively large (H. annuus, 3.5 Gbp; https://doi.

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.

Del Mar manzanita (Arctostaphylos glandulosa Eastw. subsp. crassifolia (Jeps.) P.V. Wells) is a federally listed endangered shrub found in San Diego County, California and Baja California, Mexico. This manzanita forms part of the imperiled southern maritime chaparral of southwestern California and adjacent Baja California, Mexico. Del Mar manzanita is problematic to identify because of morphological intergradation with other subspecies of A. glandulosa. Such intergradation could result from biological phenomena, such as gene flow among subspecies. Alternatively, it could be that the current circumscription of the Del Mar manzanita is not correct, and that the morphological characters used to diagnose this subspecies are inaccurate indicators of underlying genetics. This situation leads to problems for conservation planning, where accurate identification of individual plants is essential. Here, we used high-throughput sequencing of restriction-site associated DNA markers (RADseq) to develop single nucleotide polymorphism (SNP) data for a large sample of putative Del Mar manzanita, and a small sample of closely related subspecies of A. glandulosa. We analyzed genetic relationships using a total of 65,964 SNPs, with the aim of testing whether morphological traits used to identify Del Mar manzanita are an accurate reflection of underlying genetic patterns. We conclude that vegetative morphology is a poor predictor of genetic patterns, and that the current morphology-based circumscription of Del Mar manzanita is probably in need of some change. However, due to the limited sampling of A. glandulosa subspecies in this study, it is not possible to determine the taxonomic limits of Del Mar manzanita using our SNP data.

Common persimmon (Diospyros virginiana L.) is a deciduous tree occurring widely in eastern North America, as far west as Texas. The species is known for producing relatively large, edible fruits that were consumed by Native Americans and by the European colonists who arrived in North America more recently. Because of its fruit production, D. virginiana is broadly planted outside its natural range. Here, I report on five naturalized occurrences of D. virginiana found in the state of California, where the species is not native. In 2016 and 2017, these populations were surveyed and monitored for fruit production. In all populations, mature fruits were found in the autumn, and these fruits were observed to produce viable seeds with filled embryos. Two of the populations have greater than 70 individuals and contain trees at varying levels of maturity. It is not yet known if these populations are the result of asexual reproduction via root sprouting or sexual reproduction via diaspores. However, the production of viable diaspores in all surveyed populations indicates that sexual seed set is occurring. The large size of two stands, one along a creek in Butte County and the other on a river flood plain in Tulare County, suggests that some areas of California might be susceptible to invasion by this species. Future research should try to determine whether recruitment via diaspores is occurring, and whether these seeds are the product of selfing in perfect-flowered plants, or cross fertilization in a population containing both male and female plants, as this would have important implications for the potential invasiveness of this species in the state.

Summary Climate change poses an unprecedented challenge to agriculture. While growers have always struggled with year-to-year variation in climate – early rains or unusually hot summers – climate change provides a major directional shift in mean climate. Across the globe, growing regions are warming and plants are shifting in both time and space. Current and future shifts pose a major challenge to researchers and growers alike, yet they also highlight a major avenue to adapt crops to climate change – by understanding and exploiting phenological diversity. Using winegrapes (Vitis vinifera subsp. vinifera) as a case study, we review the phenological diversity present within one crop and its underlying environmental and genetic drivers. In winegrapes, harvest dates are strongly tied to temperature, but this sensitivity varies greatly, with different cultivars (or ‘varieties’) of grapes ripening much more or less for the same amount of warming. Synthesis. This phenological diversity provides a mechanism to help growers adapt winegrapes to shifting climates – by planting different varieties that will grow well under current and future climate regimes. More generally, understanding phenological diversity – including its environmental vs. genetic components – offers a major avenue to use ecological knowledge to advance adaptation for winegrapes, and many other crops, to climate change.

Pebble plains are a unique edaphic environment known only from the high valleys of the San Bernardino Mountains, California. The pebble plains have long been celebrated for the high vascular plant diversity they support, including at least six taxa endemic to the San Bernardino Mountains. Past research has shown that pebble plains soils differ most notably from nearby non-pebble plains soils in terms of their high clay content and loose, stony structure, especially in their upper-most horizon and on the soil surface. The stony upper horizon is probably the result of frost-heaving and erosion of soil particles by wind; the resulting accumulation of stone fragments at the soil surface is what inspired the name “pebble plains.” The combined effects of a friable, rocky surface, heavy lower horizons, frost heaving, high solar insolation, and desiccating winds are thought to limit recruitment of shrubs and trees and foster the persistence of a unique pebble plains flora consisting of herbaceous annuals...

Species often include multiple ecotypes that are adapted to different environments. But how do ecotypes arise, and how are their distinctive combinations of adaptive alleles maintained despite hybridization with non-adapted populations? Re-sequencing of 1506 wild sunflowers from three species identified 37 large (1-100 Mbp), non-recombining haplotype blocks associated with numerous ecologically relevant traits, and soil and climate characteristics. Limited recombination in these regions keeps adaptive alleles together, and we find that they differentiate several sunflower ecotypes; for example, they control a 77 day difference in flowering between ecotypes of silverleaf sunflower (likely through deletion of a FLOWERING LOCUS T homolog), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, associated with polymorphic structural variants, and often appear to represent introgressions from other, possibly extinct, congeners. This work highlights a pervasive role of structural variation in maintaining complex ecotypic adaptation.

PREMISE Collecting and characterizing the genetic diversity of wild relatives of crops can contribute importantly to sustainable crop production and food security. Wild sunflower, Helianthus niveus, occurs in arid regions in western North America and is partially cross-compatible with the cultivated sunflower (H. annuus). We assessed phylogenetic relationships and patterns of genetic divergence among three previously described subspecies (subsp. niveus, subsp. canescens, and subsp. tephrodes) as well as two new morphotypes of H. niveus recently discovered in extreme drought and dune habitats in Baja California, Mexico. METHODS We measured 50 plants growing in a common garden for 27 morphological traits and conducted principal component analysis to assess patterns of phenotypic variation. Genome size of each accession was determined using flow cytometry. Pollen viability of first generation hybrids between taxa was tested to infer the strength of intrinsic postzygotic reproductive barriers. Finally, genotyping-by-sequencing data were used to investigate the genetic structure and phylogenetic relationships among the previously described subspecies and new morphotypes. RESULTS The intraspecific genetic and phenotypic divergence of H. niveus populations closely tracks their geographical distribution. Subspecies niveus is phenotypically, genetically, and reproductively distinct from the other two subspecies and has a larger genome. Therefore, H. niveus as currently circumscribed should be considered to contain two distinct species, H. niveus and H. tephrodes. ABBA-BABA tests revealed substantial introgression between subsp. canescens and its sympatric congener H. petiolaris, which might contribute to their morphological similarities. The two new morphotypes collected in Mexico represent local ecotypes of subsp. niveus that occur in extreme drought and dune environments. Mantel tests showed a strong positive correlation between genetic and geographic distances. CONCLUSIONS We conclude that geographic isolation is primarily responsible for intraspecific genomic divergence within H. niveus, while patterns of phenotypic variation appear to have been shaped by ecological selection and interspecific introgression.

The California Floristic Province (CFP) is an area of high biodiversity and endemism corresponding roughly to the portion of western North America having a Mediterranean-type climate. High levels of diversity and endemism in the CFP are attributed to the unique geo-climatic setting of the region. In recent years, much has been learned about the origins of plant diversity in western North America. This work, however, has been hindered by a focus on political rather than biotic regions, such that much more is known about diversity and endemism in the state of California than the natural biotic region represented by the CFP. Here we present a preliminary list of native land plants (vascular plants and bryophytes) found in the CFP, as well as an analysis of diversity and endemism patterns at the level of both species and minimum rank taxa (MRT; species and infraspecific taxa). A total of 6,927 MRT are native to the CFP, including 6,143 vascular plants and 784 bryophytes. Of these, 2,612 vascular plan...

The diverse New World shrub genus Ceanothus (Rhamnaceae) is made up of two deeply divergent, reciprocally monophyletic groups that are treated as subgenera in most recent systematic and flora treatments, Ceanothus subgenus Cerastes, and Ceanothus subgenus Ceanothus. The two groups are phylogenetically divergent and appear to have simultaneously diversified in western North America, particularly the California Floristic Province. Ceanothus subgenus Cerastes is easily distinguished from Ceanothus subgenus Ceanothus by its sclerophyllous (versus thin) leaves, stomata sequestered in pits (versus on the leaf surface), and swollen (versus papery) stipules. Low levels of genetic divergence among species, combined with highly variable, intergrading morphology makes taxonomic work in Ceanothus subgenus Cerastes difficult. To aid research in this diverse and ecologically important group of plants, we present a taxonomic conspectus of Ceanothus subgenus Cerastes, including formal recognition of Cerastes at ...

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.

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.

Premise of the study Pachypodium (Apocynaceae) is a genus of iconic stem-succulent and poisonous plants endemic to Madagascar and southern Africa. We tested hypotheses about the mode of action and macroevolution of toxicity in this group. We further hypothesized that while monarch butterflies are highly resistant to cardenolide toxins (a type of cardiac glycoside) from American Asclepias, they may be negatively affected by Pachypodium defenses, which evolved independently. Methods We grew 16 of 21 known Pachypodium spp. and quantified putative cardenolides by HPLC and also by inhibition of animal Na+ /K+ -ATPase (the physiological target of cardiac glycosides) using an in vitro assay. Pachypodium extracts were tested against monarch caterpillars in a feeding bioassay. We also tested four Asclepias spp. and five Pachypodium spp. extracts, contrasting inhibition of the cardenolide-sensitive porcine Na+ /K+ -ATPase to the monarch's resistant form. Key results We found evidence for low cardenolides by HPLC, but substantial toxicity when extracts were assayed on Na+ /K+ -ATPases. Toxicity showed phylogenetic signal, and taller species showed greater toxicity (this was marginal after phylogenetic correction). Application of Pachypodium extracts to milkweed leaves reduced monarch growth, and this was predicted by inhibition of the sensitive Na+ /K+ -ATPase in phylogenetic analyses. Asclepias extracts were 100-fold less potent against the monarch compared to the porcine Na+ /K+ -ATPase, but this difference was absent for Pachypodium extracts. Conclusions Pachypodium contains potent toxicity capable of inhibiting sensitive and cardenolide-adapted Na+ /K+ -ATPases. Given the monarch's sensitivity to Pachypodium, we suggest that these plants contain novel cardiac glycosides or other compounds that facilitate toxicity by binding to Na+ /K+ -ATPases.

3 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 fibroad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35 877 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 fi nd 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 concat- enated 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.

Ceanothus otayensis McMinn (Rhamnaceae) was previously known only from metavolcanic-derived soils of the northern Peninsular Ranges—predominantly the San Ysidro Mountains—in San Diego County, California, and adjacent Baja California, Mexico. Recently, a new population of C. otayensis was discovered on sedimentary soils at Marine Corps Air Station Miramar, 25 km northwest of the next nearest known population. Sedimentary deposits at the new locality are thought to produce unusual soils. It is possible that the disjunct distribution of C. otayensis is a response to soil conditions, a phenomenon frequently seen in other members of Ceanothus, for instance on serpentine. The present study uses soil chemistry data for seven populations and subpopulations of C. otayensis (metavolcanic: n = 5; sedimentary: n = 2), as well as 22 populations of closely related Ceanothus, to determine whether soils of C. otayensis are chemically distinct from those of closely related Ceanothus, and answer the following ...

Carnivorous wasps of the family Vespidae are known to seek out and disperse the diaspores of at least two North American and two Asian plant species. Attraction of the wasps to the diaspores is likely due to the release of volatile compounds that signal availability of an eliaiosome rich in protein and fat, which the wasps remove before releasing the diaspore. It is thought that this interaction between carnivorous wasps and plants is rare, occurring in just a few plant species. Here, we present our findings on dispersal of spicebush (Calycanthus occidentalis Hook. & Arn.) achenes by carnivorous wasps of the genus Vespula. Observations and experiments were performed with the goals of discovering: how geographically widespread this interaction is; what the reward system is, if any; and, how wasps detect the achenes. Eight populations of C. occidentalis in northern California were used to observe wasps and plants, and to perform experiments on wasp attraction to the achenes. In all examined populations, workers of western yellowjacket (Vespula pensylvanica [de Saussure, 1857]) were observed entering mature Calycanthus receptacles, removing achenes, taking flight with them, and successfully transporting achenes through the air. Receptacles were found to open upward at an average angle of 45° (SD = 29°), preventing the achenes from falling to the ground when mature. No animals other than wasps were observed visiting the receptacles during the observations. Experiments suggest that wasps are attracted to an elaiosome-like organ of the achene. Nutritional analysis shows that this organ is high in fat and protein. Further experiments using solvent extracts of the achenes suggest that the attraction is likely mediated by volatile compounds.

QUESTION: Soil properties are known to have a profound effect on the geographic distribution of plants. Unusual soils seem to allow species to occur outside their "typical" (realized) climatic niche. However, the generality of this pattern, and the mechanisms that drive it, are poorly known. Here, we focus on the tendency for some plant species to occur at unusually low elevations on infertile substrates, especially serpentine soils. We ask whether there is a flora-wide trend in the state of California toward lower elevations and warmer thermal limits on infertile serpentine soils than on other soils. LOCATION: State of California, USA. METHODS: We used herbarium data from 19 institutions. We only used species collected from both serpentine and non-serpentine soils. To focus on plant response to recent climate, we discarded records from before 1979. Finally, we discarded records that did not report latitude and longitude. The final data set consisted of 36 045 specimens representing 814 species. Latitude and longitude were used to infer elevation, temperature and soil type. We then developed a simulation modelling approach to test for significant differences in elevational and thermal distribution between serpentine and non-serpentine soils. RESULTS: Serpentine populations are found at lower elevations than non-serpentine populations, at both the low and high ends of elevation distributions (two tailed t-test, P

UNLABELLED 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.

The Ceanothus vestitus complex comprises three closely-related shrub species restricted to the southwestern United States and northern Mexico: C. paucifloms, C. perplexans, and C. vestitus. These plants are an ecologically important component of shrubland habitats at moderate to high elevations over a large portion of North America, and are strongly represented in herbaria. However, taxonomy in the C. vestitus complex is complicated by highly variable, intergrading morphology, leading to identification problems. We use multivariate morphometries to explore variation, test circumscriptions, and search for diagnostic traits. Analyses are based on a suite of nine characters scored for 248 specimens. Results show that only C. perplexans is significantly divergent from other members of the complex. Furthermore, variation is continuous among species for all nine characters. Cluster analyses suggest alternative groupings, but none are discrete. Given the lack of significant divergence between C. vestitu...

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.

High diversity and endemism in the California Floristic Province (CFP) are an alleged response to the late Cenozoic advent of Mediterranean-type climate in this region. Ceanothus comprises two divergent subgenera with centers of diversity in the CFP. We reconstruct the evolution of Ceanothus by using DNA sequence data from the nuclear gene nitrate reductase. We find that the timing of diversification events is related to geological and climatic history. In both subgenera, diversification is characterized by recent divergence of extant taxa and geographically structured phylogenetic relationships. A strong north-south divergence of subgenus Cerastes across the Transverse Ranges indicates that phylogenetic relationships may be structured by climatically divergent regions of the CFP. Divergence-time estimation suggests that the age of extant diversification in both subgenera is ∼6 Ma. This agrees with the fossil record but predates the hypothesized Quaternary (2-Ma) origin of Mediterranean-type climate in th...

Garrya (Garryaceae) comprises 15 species of shrubs and small trees restricted to the Americas. Garrya is taxonomically divided into two subgenera, Garrya and Fadyenia, which differ in morphology, secondary chemistry, and geographic distribution. The present work uses nuclear ribosomal DNA (ITS) sequence data from 11 Garrya species to elucidate phylogenetic relationships within the genus and test the monophyly of the subgenera. Results strongly support subgenus Fadyenia as monophyletic, while monophyly of subgenus Garrya is supported only by maximum parsimony analyses. ITS data do not provide evidence for genetic admixture between the two subgenera of Garrya in spite of broad geographic overlap.

Edaphic-endemic plant taxa are often interpreted as recently derived entities that evolved in situ, with genetic divergence driven by substrate specialization. However, little is known about the evolution of specific edaphic-endemic taxa, particularly the role that soil conditions may play in their initial divergence and continued persistence. Our study focuses on Ceanothus roderickii, a strict specialist on soils derived from a single outcrop of the geological material gabbro located in south-western El Dorado County, California. In order to elucidate the evolutionary history of C. roderickii we sequenced the third intron of the low-copy nuclear gene nitrate reductase (NIA) for individuals representing four populations of C. roderickii and a wide taxonomic and geographic sampling of closely related plants, including 37 populations of Ceanothus cuneatus and a single representative from 16 other taxa. Analysis of NIA shows that C. roderickii is closely related to C. cuneatus var. cuneatus, a widel...

The genus Paliurus, recognized by its distinctive orbicular‐winged fruit, is well represented in the fossil record of the Northern Hemisphere. Fruits assignable to Paliurus are known from the Tertiary of North America, Europe, and Asia, while extant species are limited to Eurasia. We examined variation in fruit morphology among extant species as a basis for interpreting fossil fruits. Although Paliurus fruits are diverse in size, shape, and sculpture, there are few consistent criteria for demarcating species. On the basis of morphometric analysis, we recommend synonymy of most fossil fruits under the name Paliurus favonii. New records for this species are reported from the Eocene and Miocene of North America, and a distinctive new species from the Middle Eocene of North America, Paliurus clarnensis, is introduced. The genus ranges from the Middle Eocene to Late Miocene in North America, the Late Eocene to Pleistocene in Asia, and from the Oligocene to Pliocene in Europe. The fossil record indicates range ...

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.

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.

To elucidate the evolutionary origin of nickel (Ni) hyperaccumulation by the Australian serpentinite-endemic plant Stackhousia tryonii Bailey, phylogenetic analyses of chloroplast and nuclear DNA for Stackhousia and its close relatives were combined with assays of plant-tissue Ni concentrations. Thirty-five plants from 20 taxa were analysed by sequencing nuclear rDNA (ITS) and the plastid trnL–F region. Phylogenetic analysis of sequence data was conducted under maximum parsimony and Bayesian search criteria. In all, 100 plants from 39 taxa, including all 33 Stackhousia species, were analysed for Ni concentration by radial inductively coupled plasma atomic-emission spectrometry (ICP–AES). In phylogenetic analyses, S. tryonii was monophyletic, nested within a monophyletic Stackhousia. Only S. tryonii contained concentrations of Ni above the hyperaccumulation threshold (0.1%; 1000 ppm), containing between 0.25% (2500 ppm) and 4.1% (41 000 ppm) Ni by dry weight. Nickel-hyperaccumulation ability appears to have been acquired once during diversification of Stackhousia, by S. tryonii.