Biology subjects

Folk, R. A.

Publications and source records attributed to Folk, R. A..

At least 19 recordsLinked to original sources

bioRxiv2026

Multidomain triple target capture for navigating complex symbioses

Amplicon sequencing remains the benchmark technique for characterizing microbial communities, but the limitations of PCR bias and single-locus targets conspire to limit conclusions. Metagenomics, the primary alternative, shares with amplicon sequencing challenges of economic scaling at adequate sequencing depth. Targeted enrichment strategies can improve the data resolution and economics of sequencing efforts while reducing methodological bias. Here, we develop a target capture strategy for metagenomic characterization of eukaryotic ribosomal DNA and root nodule symbiosis genes and test it in the metagenomes of plant root nodules. We utilize biotinylated RNA probes to selectively capture genomic regions of interest from complex environmental DNA samples, avoiding forms of PCR bias that can undermine community characterization and overcoming the need for conserved priming sites often lacking in functional genes. We designed custom probe sets targeting conserved flanking regions of eukaryotic ITS and known root nodule symbiosis (RNS)-related genes and tested them on diverse root nodule metagenomes and a mock community. We observed high recovery of target loci from samples, very high on-target read proportions, and enhanced detection of low-abundance taxa compared to amplicon sequencing, including stronger alignment with known mock community compositions. This approach will enable deeper insights into the phylogenetic diversity of eukaryotic symbionts, their genomic adaptations, and the functional potential of symbiotic interactions in a cost-effective manner suitable for large-scale projects. This strategy advances our understanding of microbial community dynamics and symbiotic relationships in natural and anthropogenic ecosystems.

ecology↗

bioRxiv2026

"Fuzzy specificity" shapes diazotroph diversity and composition in nodulating plants of the Southeastern USA

Nitrogen-fixing symbioses, particularly those occurring in root nodules, are among the most consequential mutualisms in natural and agricultural systems and represent a globally important source of bioavailable nitrogen. Despite their importance, patterns of diversity and composition among diazotrophic symbionts--and the processes structuring those patterns in natural systems--remain poorly resolved, with competing hypotheses emphasizing ecological, or phylogenetic constraints on host-symbiont associations. Here, using a broad survey of nodulating plants from the southeastern United States, we examine how diazotrophic symbiont communities vary across host plant phylogeny, habitat context, and geographic origin. We find that host phylogeny is the primary determinant of symbiont composition, outweighing effects of fine-scale taxonomic identity. Symbiont associations are therefore structured mainly at deeper phylogenetic levels, consistent with phylogenetically constrained, or "fuzzy," host specificity. Likewise, nodule community diversity--potentially reflecting variation in host control over infection--differs primarily among higher-level clades rather than among closely related taxa. Habitat context also shapes nodule communities, but its influence is secondary and most evident in undisturbed environments. As well, nonnative legumes harbor distinct symbiont assemblages despite occupying similar habitats, whereas distantly related legume clades share symbionts across habitats, highlighting interactions among phylogeny, ecology, and geographic history. Overall, our results show that host phylogeny exerts the strongest influence on nodule microbial communities, likely reflecting evolutionary divergence in symbiotic function across major host lineages.

ecology↗

bioRxiv2026

Phosphorus-laden Mg/Fe Layered Double Hydroxide Dispersed on Douglas fir Biochar as a Controlled Release Fertilizer and its effect on the growth of bush beans (Phaseolus vurlagris).

Many agricultural soils are deficient in key macronutrients needed for healthy plant development. Relying on highly water-soluble commercial fertilizers for long durations can be costly and environmentally harmful. This study investigates a phosphorus-loaded Mg/Fe layered double hydroxide (LDH) dispersed on Douglas fir biochar (Mg/Fe-LDH biochar) as a controlled-release fertilizer and evaluates its impact on bush bean (Phaseolus vulgaris L.) growth. Emphasizing sustainability, the work integrates controlled-release fertilizers, biochar, and LDH modification to enhance nutrient use efficiency and mitigate environmental runoff. Mg/Fe-LDH was directly synthesized on biochar via a co-precipitation approach, loaded the composite with phosphate by anion exchange, and characterized the material using elemental analysis, N2 Brunauer-Emmett-Teller (BET) determinations surface area analysis, and x-ray photoelectron spectroscopy to confirm successful LDH modification on Douglas fir biochar, and high surface area with accessible active sites. The synthesis yielded a stable P-Mg/Fe-LDH biochar with enhanced dispersibility and phosphate-buffering capacity, enabling controlled-release fertilization. In greenhouse experiments, bush beans grown with the P-Mg/Fe-LDH biochar exhibited improved growth metrics, including increased yield (beans fresh weight of 31.7 g), biomass (plant dry weight of 6.3 g), plant height (32.8 cm), and improved nutrient uptakes (1.88 mg (P) g-1) at 100.88 kg (P2O5) ha-1 compared with unfertilized controls and conventional P fertilizers, indicating efficient, controlled-release phosphate delivery and sustained nutrient availability. The results demonstrate that integrating LDH-modified biochar can enhance P uptake and plant growth while reducing leaching losses. Overall, this study highlights the strategic significance of combining biochar, layered double hydroxides, and controlled-release formulations to advance sustainable nutrient management and improve crop performance in agroecosystems. The findings offer a promising pathway for environmentally conscious fertilizer design and soil amendment strategies that align with global goals for resource efficiency and food security. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/727001v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@2ab2aforg.highwire.dtl.DTLVardef@139014corg.highwire.dtl.DTLVardef@1842c62org.highwire.dtl.DTLVardef@7e0b06_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2026

THE GEOGRAPHIC STRUCTRUE OF CHLOROPLAST CAPTURE IN A HYBRID ZONE

The frequency of hybridization differs strongly across different taxa and areas of Earth, yet the environmental drivers of this variation remain poorly understood. Areas strongly influenced by Pleistocene glaciation have long been hypothesized to be rich in hybrid taxa through forcing previously allopatric species into contact and interrupting ecological barriers. Here, we revisit naturally occurring Heuchera americana x H. richardsonii in North America using deep population level sampling of nuclear and plastid genomes to re-evaluate the long-standing hypothesis that Pleistocene climate dynamics promoted hybridization in this system. An extensive population-level sampling scheme involving nuclear and plastid genetic data (729 individuals across 455 populations) reveals a more complex hybridization history than implied by previous representative phylogenetic sampling. Our analyses identify multiple independent chloroplast capture events since diversification within this complex, rather than a previously hypothesized single ancestral event. Strong geographic structure at higher-level plastid clades but little structure within subclades, together with the rarity of ancestral plastid genomes, suggests a unidirectional inheritance of the introgressed plastid genome rather than a simple geographic distribution of plastid haplotypes. Ancestral niche projections indicate that Pleistocene glacial maxima created a shared narrow eastern refugium east of the Mississippi River, enabling localized hybridization, while western refugia were larger and taxa probably allopatric. This contrast led to an east-west gradient in cytonuclear discord. Our results corroborate and refine a 90-year-old hypothesis of climate-mediated hybridization by demonstrating that historical gene flow was spatially restricted but hybrid genotypes now command a larger geographic area. Our study highlights the importance of deep population-level sampling for accurately reconstructing hybridization histories and underscores the catalytic role of climatic instability in general as a driver of hybridization in Heuchera, and likely many other taxa across the tree of life.

plant biology↗

bioRxiv2026

SPECIES DELIMITATION IN AN INTRACTABLE SYNGAMEON: BRINGING ORDER TO THE POLYPHYLETIC HEUCHERA AMERICANA GROUP

Species are the fundamental analytical units of evolutionary processes; thus evidence-based species delimitation is a crucial step for understanding species radiations. However, the task of delimiting species is particularly challenging in the context of a syngameon--a group of distinct, but closely related species that have incomplete reproductive isolation and frequently hybridize in nature. This problem is further exacerbated by the presence of cryptic species--species that are phenotypically distinct, though difficult to distinguish with gross morphology alone. Heuchera subsect. Heuchera comprises both clear and cryptic species within a syngameon that has seen study from morphological, experimental, and phylogenetic aspects. This group has long been recognized for its taxonomic complexity, namely two recognized hybrid zones with extreme morphological variation and persistent non-monophyly among parental populations. Here, we reassess species limits within Heuchera subsect. Heuchera, focusing on the hybrid complex between H. americana and H. richardsonii and adjacent H. americana populations. We use a multipronged approach with deep population-level sampling to 1) assess the genetic structure of 655 individuals across the geographic range of the H. americana group to identify genetic lineages and 2) assess the phenotypic diagnosability of these lineages. Despite extensive admixture and gene tree conflict, we find multiple cohesive lineages with diagnosable phenotypes. We recognize five species and three varieties within the H. americana group, one new and four resurrected. Our results demonstrate that even highly reticulate syngameons can be partitioned into meaningful taxonomic units with multiple lines of evidence.

plant biology↗

bioRxiv2026

Investigating the landscape of plant-pollinator interactions in a hybrid zone

Little is known about environmental drivers of opportunities for hybridization, but its phylogenetic distribution across species and areas is heterogeneous, suggesting that ecological traits may play an important role in concert with postzygotic isolation. Because plant-pollinator interactions are responsible for gene flow in most plant species, differences in the mosaic landscape of plant-pollinator interactions could explain why some plants are particularly prone to hybridization. Prezygotic isolation is mediated by sometimes complex pollen presentation; conversely, conserved pollination strategies would lead to evolutionary constraints on pollinator assemblage divergence in the speciation process and therefore predict higher opportunities for gene flow, although this hypothesis has yet to be tested. The plant taxonomic tribe Heuchereae (Saxifragaceae) is a well-characterized system for pollinator interactions and particularly for floral scent, the primary pollinator attractant in the group. Floral volatile organic compounds (VOCs) in this clade are hypervariable at the population level and are thought to be responsible for pollination selectivity, leading to divergent pollinator assemblages. Observing a contrast of hybridizing and non-hybridizing species, the levels of attractant divergence may therefore predict levels of hybridization. We investigated pollination biology in the plant genus Heuchera, notable for frequent interspecific gene flow compared to tribal relatives, asking whether high rates of hybridization may be associated with low interspecific divergence of VOCs and the pollinator assemblages they shape, using as our system the hybrid zone between H. americana var. americana and H. richardsonii in the midwestern USA. We optimized a closed-space collection and GC-MS (gas chromatography-mass spectrometry) protocol to characterize VOCs in Heuchera flowers. To identify floral visitation and effective pollinators we conducted pollination observations at 40 Heuchera populations over the span of two field seasons. GC-MS data from 89 Heuchera specimens representing 69 populations suggests that classes of VOCs, and to a large extent individual compounds, are shared within the hybrid complex while other Heuchera that are not thought to hybridize with these species have distinct species-specific compounds. Pollination observations and metabarcoding of pollinator pollen loads confirm shared effective pollinators in the hybrid zone and between adjacent parental populations. Attractant and visitation data considered together suggest that conservatism of pollinator interactions may be a typical feature associated with frequent hybridizers, perhaps arising from developmental or biochemical constraints on prezygotic isolation, and more broadly that the macroevolution of isolation mechanisms may be predictive of natural hybridization rate.

plant biology↗

bioRxiv2023

Phylogenetic diversity and regionalization in the temperate arid zone

Astragalus (Fabaceae) is astoundingly diverse in temperate, cold arid regions of Earth, positioning this group as a model clade for investigating the distribution of plant diversity in the face of climatic challenge. Here we identify the spatial distribution of diversity and endemism in Astragalus, using species distribution models for 752 species and a phylogenetic tree comprising 847 species. We integrated these to map centers of species richness (SR) and relative phylogenetic diversity (RPD), and used grid cell randomizations to investigate centers of endemism. We also used clustering methods to identify phylogenetic regionalizations. We then assembled predictor variables of current climate conditions to test environmental factors predicting these phylogenetic diversity results, especially temperature and precipitation seasonality. We find that SR centers are distributed globally at temperate middle latitudes in arid regions, but the Mediterranean Basin is the most important center of RPD. Endemism centers also occur globally, but Iran represents a key endemic area with a concentration of both paleo- and neoendemism. Phylogenetic regionalization recovered an east-west gradient in Eurasia and an amphitropical disjunction across North and South America; American phyloregions are overall most closely related to east and central Asia. SR, RPD, and lineage turnover are driven mostly by precipitation and seasonality, but endemism is driven primarily by diurnal temperature variation. Endemism and regionalization results point to western Asia and especially Iran as a biogeographic gateway between Europe and Asia. RPD and endemism highlight the importance of temperature and drought stress in determining plant diversity and endemism centers.

plant biology↗

bioRxiv2023

Phylogenetic diversity and regionalization of root nodule symbiosis

AimHere we determine centers of species richness (SR), relative phylogenetic diversity (RPD) and centers of paleo- and neo-endemism, and regionalizations of phylogenetic diversity in the mimosoid clade of the legumes to understand the distribution and environmental associates of mimosoids lacking RNS (root nodule symbiosis). LocationGlobal. Time periodPresent. Major taxa studiedMimosoid legumes. MethodsWe built a phylogenetic tree of 1313 species and high-quality species distribution models for 1128 species representing the phylogenetic breadth of the mimosoid clade to identify the geographic distribution of RNS. Centers of significant RPD and endemism were identified using a randomization approach, the latter using CANAPE. Phylogenetic regionalization used a distance-based phylogenetic beta-diversity approach. ResultsWe recognized nine areas of contiguous high SR as distinct SR hotspots. Non-RNS species occur mainly outside hotspots but are closely correlated with high RPD. Absence of RNS was best predicted by high precipitation, and represents multiple independent phylogenetic assemblages in different biogeographic areas. Main conclusionsSR hotspots are partly incongruent with centers of RPD and phylogenetic endemism. Lineages lacking RNS are distributed in SR hotspots in Africa and the Americas, belong to biogeographically separate species assemblages, and are, in most cases, associated with relatively moist tropical environments with low temperature seasonality and high available soil nitrogen.

ecology↗

bioRxiv2023

Rapid in-situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

O_LIThe macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. C_LIO_LIWe integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. C_LIO_LIOur results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in-situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. C_LIO_LIThe proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in-situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in-situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales. C_LI

evolutionary biology↗

bioRxiv2023

Climatic and biogeographic processes underlying the diversification of the pantropical and early divergent angiosperm family Annonaceae

AimTropical rainforests harbour the richest biodiversity among terrestrial ecosystems, but few studies have addressed underlying processes of species diversification in these ecosystems. We use the pantropical and early divergent flowering plant family Annonaceae as a model system to investigate how abiotic factors such as climate and biogeographic events contribute to the diversification process and lead to its high diversity across a long evolutionary history. LocationTropics and subtropics TaxonAnnonaceae MethodsA super-matrix was constructed for 835 taxa (34% of Annonaceae species), based on eight chloroplast regions. To understand the patterns of diversification, we reconstructed climatic niche evolution and historical biogeographical events, and tested their association with diversification rates. ResultsThe analysis of temperature-dependent models in Annonaceae lineages provides strong support for the significant influence of global temperature on net diversification and accumulation of species diversity. The pattern of lineage accumulation in the initial radiation is better aligned with the "museum model," followed by later accumulation consistent with the "recent cradle model" from the late Oligocene to the present. The increase in the diversification rate of the family (around 25 Ma) lags behind the accumulation of niche divergences (around 15 Ma). Biogeographic events are related to only two of the five diversification rate shifts detected. While no direct relationship to shifts in the diversification rate was uncovered, shifts in niche evolution appear to be associated with increasingly seasonal environments. Main ConclusionsGlobal temperature plays a crucial role in driving recent rapid diversification in the Annonaceae. Our study challenges the prevailing assumption of the "museum model" alone and proposes instead a transition from the "museum model" to the "recent cradle model" during the diversification history of the family. However, our findings do not support the direct correlation of any particular climatic niche shifts or historical biogeographical events with shifts in diversification rate. Instead, Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. The evolutionary direction of niche shifts furthermore provides insight into the future expansion of Annonaceae into temperate regions. Our results highlight the complexity of the diversification process in taxa with long evolutionary histories, indicating that identifying isolated driving factors is simplistic and inadequate for explaining the observed patterns. Further comprehensive analyses of range evolution are necessary to delve deeper into the interplay among key opportunities, key innovation, and species diversification.

evolutionary biology↗

bioRxiv2023

Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus

Astragalus (Fabaceae), with more than 3,000 species, represents a successful radiation of morphologically highly similar species found across the Northern Hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness. Here, for the first time using extensive taxonomic sampling in a phylogenetic analysis, we ask whether (1) Astragalus is uniquely characterized by bursts of radiation or is instead similar to related taxa. Then we test whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats or (3) particular soils. Finally, we test (4) whether Astragalus originated in central Asia as proposed and (5) whether niche evolutionary shifts were associated with the colonization of other continents. Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but attributable to no abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. We find strong evidence for a central Asian origin and direct dispersals from this region responsible for much of the present-day distribution, highlighting the importance of central Asia as a biogeographic gateway. In contrast to diversification shifts, biogeographic shifts have a strong association with the abiotic environment. Our most important result was a fundamental divide in soil types and diurnal temperature variation between the Eastern and Western Hemisphere species; this divergence does not reflect differences in available habitat among these biogeographic domains but may reflect unique local gains of edaphic and abiotic stress adaptations. While large clades are logistically difficult to tackle, our investigation shows the importance of phylogenetic and evolutionary studies of "mega-radiations." Our findings reject any simple key innovation behind the dominance and richness of Astragalus and underline the often nuanced, multifactorial processes leading to species-rich clades.

plant biology↗

bioRxiv2023

FloraTraiter: Automated parsing of traits from descriptive biodiversity literature

Premise--Plant trait data are essential for quantifying biodiversity and function across Earth, but these data are challenging to acquire for large studies. Diverse strategies are needed, including the liberation of heritage data locked within specialist literature such as floras and taxonomic monographs. Here we report FloraTraiter, a novel approach using rule-based natural language processing (NLP) to parse computable trait data from biodiversity literature. Methods and Results--FloraTraiter was implemented through collaborative work between programmers and botanical experts, and customized for both online floras and scanned literature. We report a strategy spanning OCR, recognition of taxa, iterative building of traits, and establishing linkages among all of these, as well as curational tools and code for turning these results into standard morphological matrices. Over 95% of treatment content was successfully parsed for traits with < 1% error. Data for more than 700 taxa are reported including a demonstration of common downstream uses. Conclusions--We identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open-source trait datasets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale.

plant biology↗

bioRxiv2023

Phylogenetic and spatial determinants of leaf endophyte microbiomes in the flowering plant genus Heuchera (Saxifragaceae)

Premise: Endophytic plant-microbe interactions range from mutualistic relationships that confer important ecological and agricultural traits to neutral or quasi-parasitic relationships. In contrast to root-associated endophytes, the role of environmental and host-related factors for acquiring leaf endophyte communities remains relatively unexplored. Here we assess leaf endophyte diversity to test the hypothesis that membership of these microbial communities is driven primarily by abiotic environment and host phylogeny. Methods: We used a broad geographic coverage of North America in the genus, Heuchera (Saxifragaceae). Bacterial and fungal communities were characterized with 16S and ITS amplicon sequencing, using QIIME2 to call operational taxonomic units and calculate species richness, Shannon diversity, and phylogenetic diversity. We assembled environmental predictors for microbial diversity at collection sites including latitude, elevation, temperature, precipitation, and soil parameters. Results: We find differing assembly patterns for bacterial and fungal endophytes; we found that only host phylogeny is significantly associated with bacteria, while geographic distance alone was the best predictor of fungal community composition. Species richness and phylogenetic diversity are very similar across sites and species, with only fungi showing a response to aridity and precipitation for some metrics. Unlike what has been observed with root-associated microbial communities, in this system microbes show no relationship with pH or other soil factors. Conclusions: Host phylogeny and geographic distance independently influence different microbial communities, while aridity and precipitation determine fungal diversity within leaves of Heuchera. Our results indicate the importance of detailed clade-based investigation of microbiomes and the complexity of microbiome assembly within specific plant organs.

ecology↗

bioRxiv2023

Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae)

AO_SCPLOWBSTRACTC_SCPLOWOaks (Quercus), one of the most species-rich and ecologically dominant woody plant clades in the Northern Hemisphere, are well known for their propensity to hybridize and form syngameons, complexes where alleles are readily exchanged among closely related species. While hybridization has been extensively studied towards the tips of the oak phylogeny, the extent, timeline, and evolutionary scenarios of hybridization during the early radiation of oaks and related genera (Quercoideae) remain poorly known. Using an expansive new dataset of nuclear and chloroplast sequences (including up to 431 spp.), we conducted a multifaceted phylogenomic investigation of Quercus aimed at characterizing gene-tree and cytonuclear (chloroplast-nuclear) discordance and identifying ancient reticulation in the early evolution of the group. We document extensive nuclear gene-tree and cytonuclear discordance at deep nodes in Quercus and Quercoideae, with Quercus recovered as non-monophyletic in the chloroplast phylogeny. Analyses recovered clear signatures of gene flow against a backdrop of incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and Quercoideae during their initial radiation, dated to the early-middle Eocene. Ancestral reconstructions including fossil data suggest that the ancestors of Castanea+Castanopsis, Lithocarpus, and the Old World oak clade co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Following this initial phase of radiation and reticulation, we detected multiple niche shifts in Quercus and other Quercoideae genera that likely facilitated their expansion into new habitats arising from post-Eocene climatic changes. Our study shows that hybridization--perhaps in the form of ancient syngameons similar to those seen today--has been a common and important process throughout the evolutionary history of oaks and their close relatives.

evolutionary biology↗

bioRxiv2023

Spatial phylogenetics of Fagales: Investigating the history of temperate forests

AimQuantifying the phylogenetic diversity of temperate trees is essential for understanding what processes are implicated in shaping the modern distribution of temperate broadleaf forest and other major forest biomes. Here we focus on Fagales, an iconic member of forests worldwide, to uncover global diversity and endemism patterns and investigate potential drivers responsible for the spatial distribution of fagalean forest communities. LocationGlobal. TaxonFagales. MethodsWe combined phylogenetic data covering 60.2% of living species, fine-scale distribution models covering 90% of species, and nodulation data covering all species to investigate the distribution of species richness at fine spatial scales and compare this to relative phylogenetic diversity (RPD) and phylogenetic endemism. Further, we quantify phylogenetic betadiversity and bioregionalization of Fagales and determine hotspots of Fagales species engaging in root nodule symbiosis (RNS) with nitrogen-fixing actinomycetes. ResultsWe find the highest richness in temperate east Asia, eastern North America, and equatorial montane regions of Asia and Central America. By contrast, RPD is highest at higher latitudes, where RNS also predominates. We found a strong spatial structuring of regionalizations of Fagales floras as defined by phylogeny and traits related to RNS, reflecting distinct Northern and Southern Hemisphere floras (with the exception of a unique Afro-Boreal region) and highly distinct tropical montane communities. Main conclusionsSpecies richness and phylogenetic regionalization accord well with traditional biogeographic concepts for temperate forests, but RPD does not. This may reflect ecological filtering specific to Fagales, as RNS strategies are almost universal in the highest RPD regions. Our results highlight the importance of global-scale, clade-specific spatial phylogenetics and its utility for understanding the history behind temperate forest diversity.

evolutionary biology↗

bioRxiv2023

Fagalean phylogeny in a nutshell: Chronicling the diversification history of Fagales

Reconstructing the biogeographical history and timing of the diversification of temperate forests is essential for understanding their history and resolving uncertainties about how flowering plants emerged from their deep tropical origins to dominate in todays freezing terrestrial environments. The angiosperm order Fagales, comprising iconic components of temperate forests worldwide with an extensive fossil record, are an excellent plant system in which to apply a fossil-aware paradigm, such as the fossilized birth-death (FBD) process, for investigating the macroevolution of temperate forest biomes. Here, we improve upon previous efforts to resolve phylogeny and incorporate fossils in Fagales using low-copy nuclear loci and an expanded morphological matrix to reevaluate the Fagales fossil record and: (1) infer the phylogenetic relationships and the time of origin of the clade using the FBD model as implemented in RevBayes, (2) provide a framework for evaluating the climatic and biogeographic history of Fagales, and (3) investigate how the inclusion of fossils via the FBD method influences ancestral reconstruction and diversification estimation. The phylogenetic relationships we recovered are conventional except for the position of Nothofagaceae, while our inferred ages support older timelines than previously proposed, with a mid-Cretaceous date for the most recent common ancestor (MRCA) of the order. Biogeographical analysis shows an origin of Fagales consistent with an ancestral circumboreal temperate distribution corroborated by ancestral niche reconstructions. While distributions today largely reflect the general conservatism of temperate forests, we identified two episodes of high diversification, one at the mid-Cretaceous origin of the clade and the other continuing from the Miocene to the present. Removing fossil taxa from the tree reveals a different story, shifting the origin of extant families from North America to East Asia, reflecting refugial distributions in this biodiversity "museum" and implying a general bias towards low extinction areas in biogeographic reconstruction. Likewise, without fossil data, diversification estimates were higher and unable to detect an early diversification burst. Based on our analyses, we close with recommendations regarding the interpretation of estimates of diversification and ancestral state reconstruction using phylogenetic trees with only extant species as tips.

plant biology↗

bioRxiv2022

Testing the evolutionary drivers of nitrogen-fixing symbioses in challenging soil environments

O_LIWhile the importance of root nodular symbioses (RNS) in plants has long been recognized, the ecological and evolutionary factors maintaining RNS remain obscure. RNS is associated with environmental stressors such as aridity and nitrogen-poor soils; the ability to tolerate harsh environments may provide ecological opportunities for diversification, yet, nodulators are also diverse outside these environments. C_LIO_LIWe test several environmental determinants of increased survival and enhanced diversification of RNS species, using an explicitly phylogenetic approach for the first time. We assembled the largest phylogeny of the nitrogen-fixing clade to date and a comprehensive set of abiotic niche estimates and nodulation data. We used comparative phylogenetic tools to test environmental and diversification associations. C_LIO_LIWe found that RNS is associated with warm, arid, and nitrogen-poor habitats. However, RNS was gained long before lineages entered these habitats. RNS is associated with accelerated diversification, but diversification rates are heterogeneous among nodulators, and non-legume nodulators do not show elevated diversification. C_LIO_LIOur findings undermine the interpretation that RNS directly drove the invasion of challenging habitats, and do not support a direct relationship between soil or climate and the diversity of nodulators. Still, RNS may have been an important exaptation allowing further niche evolution. C_LI

plant biology↗

bioRxiv2022

Identifying climatic drivers of hybridization in Heuchereae (Saxifragaceae)

Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and ultimately confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization.

evolutionary biology↗