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Soltis, P. S.

Publications and source records attributed to Soltis, P. S..

At least 19 recordsLinked to original sources

All detectable ancient whole-genome duplications involve hybridization

Whole-genome duplication (WGD), or polyploidy, is a major evolutionary force throughout the tree of life. Ancient WGDs are commonly inferred from the distribution of synonymous substitutions per synonymous site () between duplicated genes. Here, we argue that the standard interpretation of these distributions is incomplete. Using haplotype-phased genome assemblies spanning canonical autopolyploid and allopolyploid systems, we find that accumulates primarily between gene copies on non-recombining chromosomes. Thus, -based WGD detection depends not simply on WGD, but on whether duplicated copies evolve independently. This distinction reframes many inferences of ancient WGD as signatures of hybridization and the evolution of meiotic isolation and alters how we interpret the origin, detectability, and evolutionary consequences of polyploidy across the tree of life.

evolutionary biology↗

Regional trait-threat interactions determine extinction risk in plants.

Global plant biodiversity and associated ecosystem services are being severely threatened by human activities and land-use change. This has led to an immense effort to assess the extinction risk of individual species and associated drivers to inform conservation actions and priorities. However, we lack a more general understanding of the processes that determine variation in vulnerability and resilience among plant taxa facing the same threats in the same or similar ecological conditions and geographic regions. This research helps identify these generalities and determines species and traits that are at disproportionate risk of extinction. Given Floridas high levels of biodiversity and endemism, coupled with ongoing rapid and extensive human development, we use the states native flora as our model system. By combining data on extinction risk, human-induced threats, and plant functional traits, our results show that species threatened with extinction cluster within trait space, with smaller herbaceous species at greater risk than larger woody species. We also find that all categories of threat considered in our study (Development and Infrastructure; Environmental Change and Modification; Natural Hazards and Climate Change; and Resource Extraction) increase extinction risk except for the Invasive Species, Pests, and Diseases threat category. Generalised linear mixed-effect models show differing responses of species to environmental change, habitat loss, and fragmentation, driven by differences in life-history strategies and dispersal capabilities and mechanisms. The varied responses of species facing the same threats uncovered here highlight that plant functional traits in the context of regional ecosystem processes can be used to predict species-specific responses to threats and land-use change, providing a valuable resource for conservation management and prioritisation. Article impact statementPlant functional traits can be used to estimate species-specific responses to human-induced threats and predict overall extinction risk.

ecology↗

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

Carya glabra (2n = 4x = 64), also known as pignut hickory, is a widely distributed species in the walnut family (Juglandaceae). Native to the central and eastern United States and southeastern Canada, C. glabra plays an important ecological role as a common upland forest species; it is closely related to several economically valuable nut trees, including C. illinoinensis (pecan). A deeper understanding of the genetics of C. glabra is essential for studying its evolutionary history and biology, with potential implications for agricultural improvement of pecan. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased, representing the first assembled polyploid genome in the genus Carya. A total of 64 pseudochromosomes were assembled and phased into four haplotypes. The haplotype A assembly spans 600.4 Mb, comprises 55.0% repetitive sequences, and contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Functional annotation assigned 94.3% of haplotype A genes to gene families, and 79.7% and 86.3% of genes were annotated with Gene Ontology terms and protein domains, respectively; 635 putative plant disease resistance genes were found in haplotype A. The other three haplotypes exhibited similarly high-quality annotation metrics. Our genomic analyses also suggest that C. glabra is an autotetraploid. Comparative genomic analyses revealed high collinearity among the four haplotypes of C. glabra and the published genomes of three other Carya species, although structural variation among the genomes of these species was identified. In addition, we provide an improved chloroplast genome assembly and the first mitochondrial genome for C. glabra. Importantly, most members of the research team are undergraduate students; the sequenced individual is located in McCarty Woods, a Conservation Area on the University of Florida campus. This work highlights the value of genome assembly efforts as powerful tools for teaching genomics and supporting conservation initiatives. This first high-quality reference genome for C. glabra provides a valuable resource for studying Carya, a genus of significant ecological and economic importance. Article summaryCarya glabra (pignut hickory) is a common upland forest species in North America. This species is a member of the walnut family (Juglandaceae), which includes many economically important nut trees. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased. The haplotype A assembly contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Our genomic analyses suggest that C. glabra is an autopolyploid. We also provide chloroplast and mitochondrial genome assemblies. This nuclear genome provides a valuable resource for studying Carya, a genus of significant ecological and economic importance.

genomics↗

'Dispersification' of Agalinis (Orobanchaceae) into South America is associated with hummingbird pollination and perennial life history shifts

AimSeveral mechanisms contribute to the plant biodiversity of the Neotropics, with the highlands of South America serving as important hotspots of diversity. In particular, the Brazilian highlands exhibit high biodiversity due to complex diversification dynamics and a mixture of contributions from different biomes. In this study, we reconstruct the timing and potential triggers of diversification of Agalinis, hemiparasitic plants that inhabit open grassland habitats, to investigate their biogeographic history and migration patterns across the Americas. LocationNorth, Central, and South America TaxonAgalinis. MethodsWe reconstructed dated phylogenies of Agalinis using a secondary calibration approach, sampling 73% of the known species, including multiple species from the Andes and Brazilian highlands. We inferred ancestral distributions to understand migration patterns between North and South America and within South America. Additionally, we investigated shifts in diversification rates within the genus and reconstructed ancestral pollination syndrome and life history strategy states. All analyses were performed across a distribution of trees to account for phylogenetic uncertainty. ResultsAgalinis likely originated in southeastern North America during the early Miocene and rapidly diversified, followed by movement into South America in the Late Miocene or Early Pliocene. We propose two possible routes for Agalinis movement into South America: either through the Andes or via the South American lowland grasslands (e.g., Chaco, Pampas, Cerrado, Caatinga, Llanos), using grassland corridors for dispersal within the continent. After its arrival in South American highlands, the clade underwent rapid diversification. State reconstructions indicated that the genus had a bee-pollinated ancestor and that hummingbird pollination evolved only once, with many transitions back to bee pollination. In contrast, the perennial life strategy evolved multiple times within the genus, including at least once in the ancestor of all South American species and twice in the North American species. Main ConclusionsAgalinis likely originated in North America and later migrated to South America, followed by rapid diversification (i.e., dispersification). Thus, Agalinis is a clade that refutes the tropical conservatism hypothesis and the out-of-the-tropics model. Moreover, the dispersal to the Brazilian highlands was from nearby species pools and not from other highland habitats such as the Andes, followed by several in situ speciation events. These high diversification rates were partly associated with Quaternary climatic oscillations, and perennial and hummingbird-pollinated species exhibited higher turnover rates.

plant biology↗

Homoploid Hybridization Resolves the Origin of Octoploid Strawberries

The identity of the diploid progenitors of octoploid cultivated strawberry (Fragaria x ananassa) has been subject to much debate. Past work identified four subgenomes and consistent evidence for F. californica (previously named F. vesca subsp. bracteata) and F. iinumae as donors for subgenomes A and B, respectively, with conflicting results for the origins of subgenomes C and D. Here, reticulate phylogeny and admixture analysis support hybridization between F. viridis and F. vesca in the ancestry of subgenome A, and between F. nipponica and F. iinumae in the ancestry of subgenome B. Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports of F. viridis and F. nipponica as donors of the C and D subgenomes and unify conflicting hypotheses about the evolutionary origin of octoploid Fragaria.

genetics↗

ZW sex chromosome structure in Amborella trichopoda

Sex chromosomes have evolved hundreds of times, and their recent origins in flowering plants can shed light on the early consequences of suppressed recombination. Amborella trichopoda, the sole species on a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly-contiguous assemblies of the Z and W chromosomes. We identify a [~]3-Megabase sex-determination region (SDR) captured in two strata that includes a [~]300-Kilobase inversion that is enriched with repetitive sequence and contains a homolog of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, like repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is recently derived in Amborella and the sex chromosome pair has not significantly degenerated.

genomics↗

Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes

Southwest China is characterized by high plateaus, large mountain systems, and deeply incised dry valleys formed by major rivers and their tributaries. Despite the considerable attention given to alpine plant radiations in this region, the timing and mode of the diversification of the numerous plant lineages in the dry valley habitat remains unknown. To address this knowledge gap, we investigate the macroevolution of Isodon (Lamiaceae), a lineage commonly distributed in the dry valleys in southwest China and wetter areas of Asia and Africa. We reconstructed a robust phylogeny encompassing nearly 90% of the approximately 140 extant Isodon species using transcriptome and genome-resequencing data. Our results suggest a rapid radiation of Isodon during the Pliocene that coincided with a habit shift from herbs to shrubs and a habitat shift from humid areas to dry valleys. The shrubby growth form likely acted as a preadaptation allowing for the movement of Isodon species into these valleys. Ecological analysis highlighted aridity and precipitation as key factors influencing the niche preferences of different growth forms and species richness of Isodon. Integrating our results with insights from tectonic movements in the Tibetan Plateau and adjacent regions, we infer that the interplay between topography and the evolution of the East Asian monsoon since the middle Miocene likely contributed to the formation of the dry valley biome in southwest China. This study enhances our understanding of evolutionary dynamics and ecological drivers shaping the distinctive flora of this region.

evolutionary biology↗

Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-related nuclease (Cas) system allows precise and easy editing of genes in many plant species. However, this system has not yet been applied to any fern species due to the complex characteristics of fern genomes, genetics and physiology. Here, we established, for the first time, a protocol for gametophyte-based screening single-guide RNAs (sgRNAs) with high efficiency for CRISPR/Cas-mediated gene editing in a model fern species, Ceratopteris richardii. We utilized the C. richardii Actin promoter to drive sgRNA expression and enhanced CaMV 35S promoter to drive the expression of Streptococcus pyogenes Cas9 in this CRISPR-mediated editing system, which was employed to successfully edit a few genes (e.g., nucleotidase/phosphatase 1, CrSAL1; Cryptochrome 4, CRY4) and CrPDS, encoding a phytoene desaturase protein that resulted in an albino phenotype in C. richardii. Knockout of CrSAL1 resulted in significantly reduced stomatal conductance (gs), leaf transpiration rate (E), stomatal/pore length, and abscisic acid (ABA)-induced reactive oxygen species (ROS) accumulation in guard cells. Moreover, CrSAL1 overexpressing plants showed significantly increased net photosynthetic rate (A), gs, E and intrinsic water use efficiency (iWUE) as well as most of the stomatal traits and ROS production in guard cells compared to those in the wild-type (WT) plants. Taken together, the optimized CRISPR/Cas9 system provides a useful tool for functional genomics in a model fern species, allowing the exploration of fern gene functions for evolutionary biology, herbal medicine discovery and agricultural applications.

plant biology↗

nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity

PremiseTraditional methods of ploidal level estimation are tedious; leveraging sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage DNA sequence data for ploidy prediction based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use improper probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package, that addresses the main shortcomings of current methods. Methods and ResultsnQuack performs model selection for improved ploidy predictions. Here, we implement expected maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack. ConclusionInferring ploidal level based on site-based heterozygosity alone is discouraged due to the low accuracy of pattern-based inference.

bioinformatics↗

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↗

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↗

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↗

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↗

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↗

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↗

Dynamics of mixed-ploidy populations under demographic and environmental stochasticities

The theoretical population dynamics of autopolyploids - organisms with more than two genome copies of a single ancestral species - and their diploid progenitors have been extensively studied. The acquisition of multiple genome copies, being in essence a stochastic process, strongly suggests a probabilistic approach to examine the long-term dynamics of a population with multiple cytotypes. Yet, our current understanding of empirical evidence on the dynamics of autopolyploid populations has not incorporated stochastic population dynamics. To investigate the factors contributing to the probability and stability of coexisting cytotypes, we designed a new population dynamics model with demographic and environmental stochasticities to simulate the formation, establishment, and persistence of diploids, triploids, and autotetraploids over time when gene flow is allowed among cytotypes. Contrary to previous research, increased selfing rates and pronounced reproductive isolation stabilized the long-run coexistence of multiple cyto-types. In stressful environments, these dynamics become much more complex, and our stochastic modeling approach helped reveal the resulting intricacies that give tetraploids competitive advantage over their diploid progenitors. Our work is fundamental to a better understanding of the dynamics of coexistence of multiple cytotypes and is a necessary step for further work modeling the dynamics between an autopolyploid and its diploid progenitor.

evolutionary biology↗

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↗

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↗