A pipeline for the rapid collection of color data from photographs.

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.

Parallel evolution and cryptic diversification in a common and widespread Amazonian tree, Protium subserratum.

The lowland Amazon rainforest houses some of the greatest tree diversity on Earth. While the vast majority of these species are rare, a small number are common and widespread and thus considered to play a disproportionate role in many of the global ecosystem services provided by the Amazon. However, the extent to which dominant Amazonian tree species actually include multiple clades, each on their own unique evolutionary trajectory, is unknown. Here we investigate the extent to which lineage divergence may be occurring within Protium subserratum (Burseraceae), a common and widespread tree species that is monophyletic with populations exhibiting genotypic and phenotypic differences associated with soil and geography. Utilizing a combination of phylogenomic and population genomic methods with sampling from across the range, we found that P. subserratum contains at least eight distinct clades. Specialization onto white-sand soils has evolved independently at least twice within the species; however, phenotype is not correlated with soil type. Finally, cryptic diversity at the base of the Andes is associated with elevational shifts. Together these results lend support to the hypothesis that common and widespread Amazon tree species may not represent evolutionary cohesive units. Instead, these dominant species may more commonly represent species complexes, undergoing evolutionary transitions on a trajectory to become multiple range-restricted, specialist species.

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.

The roles of dispersal limitation, climatic niches and glacial history in endemism of the North American bryophyte flora.

PREMISE: Bryophytes (mosses, liverworts, and hornworts) tend to have very large geographic ranges, which impedes progress toward understanding the drivers of diversification and extinction. This study aimed to investigate whether North American endemics differ geographically from more widespread species and whether differences in climatic niche or traits related to dispersal and establishment differ between endemics and more widespread species. METHODS: All available herbarium records of bryophytes from North America north of Mexico (106 collections) were used. Traits related to dispersal were obtained from the literature. Analyses tested whether range sizes and extents differed between endemics and nonendemics, and whether trait differences were associated with endemism. Climate data were used to determine whether differences in niche breadth are present between endemics and nonendemics, and whether suitable climate for endemics occurs outside North America. RESULTS: Nonendemics have range sizes twice as large as endemics and they occur farther north and have greater longitudinal extents. However, they do not have the widest niche breadths and do not differ in spore size (with few exceptions) or sexual condition. Asexual propagules are more prevalent among nonendemics. Climatic models indicate that substantial areas of climate suitable for endemics exist outside of North America. CONCLUSIONS: Distributions of endemics and nonendemics are consistent with an important role of glaciation in shaping the North American bryophyte flora. Endemics are not limited to the continent based on a lack of suitable climate elsewhere or by spore size or sexual condition.

Range change evolution of peat mosses (Sphagnum) within and between climate zones.

Peat mosses (Sphagnum) hold exceptional importance in the control of global carbon fluxes and climate because of the vast stores of carbon bound up in partially decomposed biomass (peat). This study tests the hypothesis that the early diversification of Sphagnum was in the Northern Hemisphere, with subsequent range expansions to tropical latitudes and the Southern Hemisphere. A phylogenetic analysis of 192 accessions representing the moss class Sphagnopsida based on four plastid loci was conducted in conjunction with biogeographic analyses using BioGeoBEARS to investigate the tempo and mode of geographic range evolution. Analyses support the hypothesis that the major intrageneric clades of peat-forming species accounting for >90% of peat moss diversity originated and diversified at northern latitudes. The genus underwent multiple range expansions into tropical and Southern Hemisphere regions. Range evolution in peat mosses was most common within latitudinal zones, attesting to the relative difficulty of successfully invading new climate zones. Allopolyploidy in Sphagnum (inferred from microsatellite heterozygosity) does not appear to be biased with regard to geographic region nor intrageneric clade. The inference that Sphagnum diversified in cool-or cold-climate regions and repeatedly expanded its range into tropical regions makes the genus an excellent model for studying morphological, physiological, and genomic traits associated with adaptation to warming climates.

Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta).

Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.

Endemism in the moss flora of North America.

PREMISE OF THE STUDY: Identifying regions of high endemism is a critical step toward understanding the mechanisms underlying diversification and establishing conservation priorities. Here, we identified regions of high moss endemism across North America. We also identified lineages that contribute disproportionately to endemism and document the progress of efforts to inventory the endemic flora. METHODS: To understand the documentation of endemic moss diversity in North America, we tabulated species publication dates to document the progress of species discovery across the continent. We analyzed herbarium specimen data and distribution data from the Flora of North America project to delineate major regions of moss endemism. Finally, we surveyed the literature to assess the importance of intercontinental vs. within-continent diversification for generating endemic species. KEY RESULTS: Three primary regions of endemism were identified and two of these were further divided into a total of nine subregions. Overall endemic richness has two peaks, one in northern California and the Pacific Northwest, and the other in the southern Appalachians. Description of new endemic species has risen steeply over the last few decades, especially in western North America. Among the few studies documenting sister species relationships of endemics, recent diversification appears to have played a larger role in western North America, than in the east. CONCLUSIONS: Our understanding of bryophyte endemism continues to grow rapidly. Large continent-wide data sets confirm early views on hotspots of endemic bryophyte richness and indicate a high rate of ongoing species discovery in North America.

Soil nutrients trump intraspecific effects on understory plant communities.

Understanding the links between intraspecific genetic variation and patterns of diversity in associated communities has been the primary focus of community genetics or 'genes-to-ecosystem' research in ecology. While other ecological factors, such as the abiotic environment, have well-documented influences on communities, the relative contributions of genetic variation versus the environment to species interactions remains poorly explored. In this study, we use a common garden experiment to study a coastal dune plant community dominated by the shrub, Baccharis pilularis, which displays a morphological dimorphism in plant architecture. We found the differences in the understory plant community between erect and prostrate morphs of Baccharis to be statistically significant, but small relative to the impacts of nutrient additions (NPK and C additions), for the richness, cover, and biomass of the understory plant community. There were no significant interactions between Baccharis morphology and nutrient-addition treatments, suggesting the influence of nutrient addition was consistent between erect and prostrate morphs. Moreover, we found no difference in overall plant community composition between Baccharis morphs, while NPK additions led to shifts in understory community composition compared to unfertilized shrubs. In sum, our results indicate that nutrients are the more important factor governing understory plant community structure in a coastal dunes ecosystem followed by intraspecific variation in dominant shrub architecture. Our results address a growing call to understand the extended consequences of intraspecific variation across heterogeneous environments in terrestrial ecosystems.

Species delimitation and cryptic diversity in the moss genus Scleropodium (Brachytheciaceae).

Cryptic lineage diversification is an important component of global biodiversity, but it presents challenges to our ability to catalog and understand that diversity. Because of their relative morphological simplicity and broad geographic distributions, bryophytes are an ideal study group for investigating this phenomenon. This study generated molecular data from 109 ingroup individuals to test morphological species circumscriptions and examine patterns of cryptic lineage diversification within the small north temperate moss genus Scleropodium (Brachytheciaceae). Maximum Parsimony and Bayesian phylogenetic analyses and statistical parsimony network analyses of ITS and chloroplast rps4, psbA2 and trnG regions indicate that the genus comprises six distinct molecular groups. Five of these molecular groups correspond to previously recognized species: S. californicum (Lesq.) Kindb., S. cespitans (Müll.) Koch, S. julaceum Lawton, S. obtusifolium (Mitt.) Kindb. in Macoun and S. touretii Brid. (Koch). However, the sixth group does not correspond to any existing species. Maximum parsimony and Bayesian posterior probability support for the monophyly of species varied widely and depended on both the dataset (ITS, chloroplast, combined) and the analysis method (Parsimony/Bayesian). Low phylogenetic resolution of species is attributable to the lack of informative DNA sequence vaiation and incongruent placements of three accessions in the chloroplast and ITS gene trees, both suggesting recent divergence within the genus. Re-examination of the herbarium vouchers for the sixth molecular group reveals that they form a group nested within the morphological circumscription of S. obtusifolium. One subtle morphological character (relative frequency of a costa spine) was identified that has utility in discriminating these two genetically distinct but morphologically very similar species.

Climate change and the future of California's endemic flora.

The flora of California, a global biodiversity hotspot, includes 2387 endemic plant taxa. With anticipated climate change, we project that up to 66% will experience >80% reductions in range size within a century. These results are comparable with other studies of fewer species or just samples of a region's endemics. Projected reductions depend on the magnitude of future emissions and on the ability of species to disperse from their current locations. California's varied terrain could cause species to move in very different directions, breaking up present-day floras. However, our projections also identify regions where species undergoing severe range reductions may persist. Protecting these potential future refugia and facilitating species dispersal will be essential to maintain biodiversity in the face of climate change.