The contribution of multiple barriers to reproduction between edaphically divergent lineages in the Amazonian tree \u3cem\u3eProtium subserratum\u3c/em\u3e (Burseraceae)

Disentangling the strength and importance of barriers to reproduction that arise between diverging lineages is central to our understanding of species origin and maintenance. To date, the vast majority of studies investigating the importance of different barriers to reproduction in plants have focused on short-lived temperate taxa while studies of reproductive isolation in trees and tropical taxa are rare. Here, we systematically examine multiple barriers to reproduction in an Amazonian tree, Protium subserratum (Burseraceae) with diverging lineages of soil specialist ecotypes. Using observational, molecular, distributional, and experimental data, we aimed to quantify the contributions of individual prezygotic and postzygotic barriers including ecogeographic isolation, flowering phenology, pollinator assemblage, pollen adhesion, pollen germination, pollen tube growth, seed development, and hybrid fitness to total reproductive isolation between the ecotypes. We were able to identify five potential barriers to reproduction including ecogeographic isolation, phenological differences, differences in pollinator assemblages, differential pollen adhesion, and low levels of hybrid seed development. We demonstrate that ecogeographic isolation is a strong and that a combination of intrinsic and extrinsic prezygotic and postzygotic barriers may be acting to maintain near complete reproductive isolation between edaphically divergent populations of the tropical tree, P. subserratum

Bird nests as botanical time capsules: DNA barcoding identifies the contents of contemporary and historical nests

Bird nests in natural history collections are an abundant yet vastly underutilized source of genetic information. We sequenced the nuclear ribosomal internal transcribed spacer to identify plant species used as nest material in two contemporary (2003 and 2018) and two historical (both 1915) nest specimens constructed by Song Sparrows (Melospiza melodia) and Savannah Sparrows (Passerculus sandwichensis). A total of 13 (22%) samples yielded single, strong bands that could be identified using GenBank resources: six plants (Angiospermae), six green algae (Chlorophyta), and one ciliate (Ciliophora). Two native plant species identified in the nests included Festuca microstachys, which was introduced to the nest collection site by restoration practitioners, and Rosa californica, identified in a nest collected from a lost habitat that existed about 100 years ago. Successful sequencing was correlated with higher sample mass and DNA quality, suggesting future studies should select larger pieces of contiguous material from nests and materials that appear to have been fresh when incorporated into the nest. This molecular approach was used to distinguish plant species that were not visually identifiable, and did not require disassembling the nest specimens as is a traditional practice with nest material studies. The many thousands of nest specimens in natural history collections hold great promise as sources of genetic information to address myriad ecological questions

Exploring the links between secondary metabolites and leaf spectral reflectance in a diverse genus of Amazonian trees

Plant defense chemistry is often hypothesized to drive ecological and evolutionary success in diverse tropical forests, yet detailed characterizations of plant secondary metabolites in tropical plants are logistically challenging. Here, we explore a new integrative approach that combines visible-to-shortwave infrared (VSWIR) spectral reflectance data with detailed plant metabolomics data from 19 Protium (Burseraceae) tree species. Building on the discovery that different Protium species have unique chemistries yet share many secondary metabolites, we devised a method to test for associations between metabolites and VSWIR spectral data. Given species-level variation in metabolite abundance, we correlated the concentration of particular chemicals with the reflectance of the spectral bands in a wavelength band per secondary metabolite matrix. We included 45 metabolites that were shared by at least 5 Protium species and correlated their per-species foliar abundances against each one of 210 wavelength bands of field-measured VSWIR spectra. Finally, we tested whether classes of similar metabolites showed similar relationships with spectral patterns. We found that many secondary metabolites yielded strong correlations with VSWIR spectra of Protium. Furthermore, important Protium metabolite classes such as procyanidins (condensed tannins) and phytosterols were grouped together in a hierarchical clustering analysis (Ward’s algorithm), confirming similarity in their associations with plant spectral patterns. We also found a significant correlation in the phenolics content between juvenile and canopy trees of the same species, suggesting that species-level variation in defense chemistry is consistent across life stages and geographic distribution. We conclude that the integration of spectral and metabolic approaches could represent a powerful and economical method to characterize important aspects of tropical plant defense chemistry

The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist tree species of Protium (Burseraceae) across the Amazon Basin

ABSTRACT Aim Edaphic heterogeneity may be an important driver of population differentiation in the Amazon but remains to be investigated in trees. We compared the phylogeographic structure across the geographic distribution of two Protium (Burseraceae) species with different degrees of edaphic specialization: Protium alvarezianum, an edaphic specialist of white-sand habitat islands; and Protium subserratum, an edaphic generalist found in white sand as well as in more widespread soil types. We predicted that in the edaphic specialist, geographic distance would structure populations more strongly than in the edaphic generalist, and that soil type would not structure populations in the edaphic generalist unless habitat acts as a barrier promoting population differentiation. Location Tropical rain forests of the Peruvian and Brazilian Amazon, Guyana and French Guiana. Methods We sequenced 1209-1211 bp of non-coding nuclear ribosomal DNA (internal transcribed spacer and external transcribed spacer) and a neutral lowcopy nuclear gene (phytochrome C) from P. subserratum (n = 65, 10 populations) and P. alvarezianum (n = 19, three populations). We conducted a Bayesian phylogenetic analysis, constructed maximum parsimony haplotype networks and assessed population differentiation among groups (soil type or geographic locality) using analysis of molecular variance and spatial analysis of molecular variance. Results The edaphic specialist exhibited considerable genetic differentiation among geographically distant populations. The edaphic generalist showed significant genetic differentiation between the Guianan and Amazon Basin populations. Within Peru, soil type and not geographic distance explained most of the variation among populations. Non-white-sand populations in Peru exhibited lower haplotype/nucleotide diversity than white-sand populations, were each other's close relatives, and formed an unresolved clade derived from within the white-sand populations. Main conclusions Geographic distance is a stronger driver of population differentiation in the edaphic specialist than in the generalist. However, this difference did not appear to be related to edaphic generalism per se as adjacent populations from both soil types in the edaphic generalist did not share many haplotypes. Populations of the edaphic generalist in white-sand habitats exhibite

Data from: Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree: Protium subserratum (Burseraceae)

Soil gradients are known to be an important driver of divergent natural selection in plant populations. Neotropical trees have the highest diversity on earth and it is not uncommon to find soil specialist congeners distributed parapatrically. Nevertheless very little is known about the role that edaphic heterogeneity plays in the origin and maintenance of tropical tree diversity. We predict that the mosaic of different soils in the lowland Amazon rainforest play a major role in generating and maintaining genetic variation in tropical tree populations through ecological divergence. This study examines genetic and morphological differentiation in the tropical tree Protium subserratum populations growing on the mosaic of white-sand, brown-sand and clay soil types distributed parapatrically throughout the western Amazon basin. We use nuclear microsatellites and vegetative characters to answer four major questions: (1) Are populations phenotypically and genetically differentiated across all three habitat types? (2) Can we detect a signature of natural selection over drift divergence among populations on different soil types? (3) What is the extent of hybridization and introgression across habitat types? (4) What is the relative importance of spatial distance and soil type in structuring P. subserratum tree populations and influencing migration rates among populations? We found significant morphological variation in populations across the three soil types. Higher levels of genetic differentiation and lower levels of gene flow were observed between adjacent populations found on different soil types than between geographically distant populations on the same soil type. Comparisons of phenotypic and neutral genetic variation among soil specialist populations suggest a role for natural selection in population divergence and a small number of hybrid individuals were detected between soil ecotypes showing that gene flow among populations may be occurring at a low frequency. Our results suggest that edaphic specialization in P. subserratum populations has occurred across multiple soil boundaries. While we cannot discern which factors caused initial divergence our results do suggest that natural selection is plays an important role in maintaining the integrity of populations across ecological boundaries and that edaphic specialization may be a general mechanism that promotes and maintains Amazonian tree diversity

Morphology_dataset

All morphological measurements use

Microsatellite primers for an Amazonian lowland tropical tree, Protium subserratum (Burseraceae)

• Premise of the study: The first microsatellite primers were developed for Protium subserratum, a widespread Amazonian tree, to investigate genetic differentiation between populations found on clay, brown-sand, and white-sand soils. • Methods and Results: Seventeen primer pairs were identified from two individuals of P. subserratum found on white-sand and brown-sand soil types. Polymorphism was analyzed in 63 individuals from a total of three populations, each found on a different soil type. The primers amplified tetra-, tri-, and dinucleotide repeats with three to 24 alleles per locus. Excluding monomorphic loci, observed and expected heterozygosities ranged from 0 to 0.852 and 0.036 to 0.901, respectively. • Conclusions: These new microsatellite markers will be useful in studies of genetic diversity, population differentiation, and gene flow across habitat types in P. subserratum. © 2012 Botanical Society of America

A pipeline for the rapid collection of color data from photographs

Abstract Premise There are relatively few studies of flower color at landscape scales that can address the relative importance of competing mechanisms (e.g., biotic: pollinators; abiotic: ultraviolet radiation, drought stress) at landscape scales. Methods We developed an R shiny pipeline to sample color from images that were automatically downloaded using query results from a search using iNaturalist or the Global Biodiversity Information Facility (GBIF). The pipeline was used to sample ca. 4800 North American wallflower (Erysimum, Brassicaceae) images from iNaturalist. We tested whether flower color was distributed non‐randomly across the landscape and whether spatial patterns were correlated with climate. We also used images including ColorCheckers to compare analyses of raw images to color‐calibrated images. Results Flower color was strongly non‐randomly distributed spatially, but did not correlate strongly with climate, with most of the variation explained instead by spatial autocorrelation. However, finer‐scale patterns including local correlations between elevation and color were observed. Analyses using color‐calibrated and raw images revealed similar results. Discussion This pipeline provides users the ability to rapidly capture color data from iNaturalist images and can be a useful tool in detecting spatial or temporal changes in color using citizen science data

Population Genetic Structure of California Hazelnut, An Important Food Source for People in Quiroste Valley in the Late Holocene

Abstract California hazelnuts (Corylus cornuta var. californica) are abundant in the archaeological record of site CA-SMA-113 in Quiroste Valley Cultural Preserve, and hazel management on the Central Coast was recorded in late 18th century Spanish accounts. However, this species is currently absent from Quiroste Valley proper and rare in the watershed, though it is locally common elsewhere in the Santa Cruz Mountains. Because high California hazelnut abundance is associated with frequent fire regimes, we believe that its current low abundance could be due to fire suppression enforced in the region for the past two hundred years. We sequenced nuclear microsatellites from ten populations of California hazelnuts to test the hypothesis that this species has experienced demographic changes in response to changing climate and land management practices. We found that all populations exhibited high levels of genetic variation and negative population growth consistent with large population sizes in the past with some decline over time. We also found subtle patterns of geographic structure suggesting that Quiroste Valley and neighboring Butano may have been important refugia habitats during past climate warming events. These results provide an important foundation demonstrating tha

Population Genetic Structure of California Hazelnut, An Important Food Source for People in Quiroste Valley in the Late Holocene

Abstract California hazelnuts (Corylus cornuta var. californica) are abundant in the archaeological record of site CA-SMA-113 in Quiroste Valley Cultural Preserve, and hazel management on the Central Coast was recorded in late 18th century Spanish accounts. However, this species is currently absent from Quiroste Valley proper and rare in the watershed, though it is locally common elsewhere in the Santa Cruz Mountains. Because high California hazelnut abundance is associated with frequent fire regimes, we believe that its current low abundance could be due to fire suppression enforced in the region for the past two hundred years. We sequenced nuclear microsatellites from ten populations of California hazelnuts to test the hypothesis that this species has experienced demographic changes in response to changing climate and land management practices. We found that all populations exhibited high levels of genetic variation and negative population growth consistent with large population sizes in the past with some decline over time. We also found subtle patterns of geographic structure suggesting that Quiroste Valley and neighboring Butano may have been important refugia habitats during past climate warming events. These results provide an important foundation demonstrating tha