Pamela S Soltis

Pamela S Soltis
University of Florida | UF

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805
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Publications

Publications (805)
Article
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While flowering plants have diversified in virtually every terrestrial clime, climate constrains the distribution of individual lineages. Overcoming climatic constraints may be associated with diverse evolutionary phenomena including whole genome duplication (WGD), gene‐tree conflict, and life‐history changes. Climatic shifts may also have facilita...
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Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic...
Preprint
The identity of the diploid progenitors of octoploid cultivated strawberry ( Fragaria × 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...
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Polyploidy is a cellular state containing more than two complete chromosome sets. It has largely been studied as a discrete phenomenon in either organismal, tissue, or disease contexts. Increasingly, however, investigation of polyploidy across disciplines is coalescing around common principles. For example, the recent Polyploidy Across the Tree of...
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The southeastward extrusion of Indochina along the Ailao Shan–Red River shear zone (ARSZ) is one of two of the most prominent consequences of the India–Asia collision. This plate-scale extrusion has greatly changed Southeast Asian topography and drainage patterns and effected regional climate and biotic evolution. However, little is known about how...
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Du et al. (2023) produced a phylogeny of Cornus L. using three sets of genomic data, proposed a classification within the clade, and phylogenetically defined 13 clade names following the International Code of Phylogenetic Nomenclature (PhyloCode). However, the clade names were not fully established because no registration numbers were cited in the...
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The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated 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 through gametophytes due to the complex characteristics of fern genomes, genetics and physiology. Here, we es...
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Agalinis (Orobanchaceae, tribe Pedicularideae) consists of approximately 70 hemiparasitic species distributed among North, Central, and South America. Previous phylogenetic studies did not include tropical species nor comprehensive sampling for closely allied genera, limiting our systematic understanding of these lineages. We generated an updated p...
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Premise Traditional methods of ploidal‐level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site‐based heterozygosity have been developed. However, these approaches may require high‐coverage sequence data, use in...
Article
Whole-genome duplication (WGD; i.e., polyploidy) and chromosomal rearrangement (i.e., genome shuffling) significantly influence genome structure and organization. Many polyploids show extensive genome shuffling relative to their pre-WGD ancestors. No reference genome is currently available for Platanaceae (Proteales), one of the sister groups to th...
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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...
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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 environmental challenges. Here, we identify the spatial distribution of diversity and endemism in Astragalus using species distribution models for 752 sp...
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How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the di...
Preprint
Full-text available
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...
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Full-text available
Despite experimental and observational studies demonstrating that biodiversity enhances primary productivity, the best metric for predicting productivity at broad geographic extents—functional trait diversity, phylogenetic diversity, or species richness—remains unknown. Using >1.8 million tree measurements from across eastern US forests, we quantif...
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Premise Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs). Method...
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Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and...
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Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome‐wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids. The naturally occurrin...
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Premise Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant 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‐a...
Preprint
Full-text available
Premise: Traditional 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,...
Article
Phylogenetic placement of Hydrostachys (Hydrostachyaceae) has long been enigmatic, the highly divergent morphology of Hydrostachys having prevented its confident placement in any clade of angiosperms. Phylogenetic placements using DNA sequence data have varied, with most studies suggesting a placement within Cornales. We conducted a large‐scale phy...
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Societal Impact Statement It is important to recognize how our current understanding of plants has been shaped by diverse cultural contexts, as this underscores the importance of valuing and incorporating contributions from all knowledge systems in scientific pursuits. This approach emphasizes the ongoing bias, including within scientific practices...
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The 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. We integrated phylogenomic, environmental ordination, and macroevo...
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Objectives Escallonia (Escalloniaceae) belongs to the Escalloniales, a diverse clade of flowering plants with unclear placement in the tree of life. Escallonia species show impressive morphological and ecological diversity and are widely distributed across three hotspots of biodiversity in the Neotropics. To shed light on the genomic substrate of t...
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Each year, SARS-CoV-2 is infecting an increasingly unprecedented number of species. In the present article, we combine mammalian phylogeny with the genetic characteristics of isolates found in mammals to elaborate on the host-range potential of SARS-CoV-2. Infections in nonhuman mammals mirror those of contemporary viral strains circulating in huma...
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Objectives Lavandula angustifolia (English lavender) is commercially important not only as an ornamental species but also as a major source of fragrances. To better understand the genomic basis of chemical diversity in lavender, we sequenced, assembled, and annotated the ‘Munstead’ cultivar of L. angustifolia. Data description A total of 80 Gb of...
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Introduction The well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages is...
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iNaturalist has the potential to be an extremely rich source of organismal occurrence data. Launched in 2008, it now contains over 150 million uploaded observations as of May 2023. Based on the findings of a limited number of past studies assessing the taxonomic accuracy of participatory science-driven sources of occurrence data such as iNaturalist...
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Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and...
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Although originating from a common Gondwanan flora, the diversity and composition of the floras of Africa and South America have greatly diverged since continental breakup of Africa from South America now having much higher plant species richness. However, the phylogenetic diversity of the floras and what this tells us about their evolution remaine...
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Allopolyploidy is a major force in evolution. It is often assumed that if two congeneric species hybridize, there is the potential for allopolyploid formation. We propose a “compatibility hypothesis” which may play a major role in allopolyploidization—that is, only a subset of the many constituent genotypes of two congeners (referred to here as com...
Preprint
Full-text available
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...
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Thanks to substantial support for biodiversity data mobilization in recent decades, billions of occurrence records are openly available, documenting life on Earth and enabling timely research, awareness raising, and policy-making. Initiatives across local to global scales have been separately funded to serve different, yet often overlapping audienc...
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Monoterpenes are the main component in essential oils of Lippia alba. In this species, the chemical composition of essential oils varies with genome size: citral (geraniol and neral) is dominant in diploids and tetraploids, and linalool in triploids. Because environmental stress impacts various metabolic pathways, we hypothesized that stress respon...
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Aim Quantifying niche shifts of non‐native species and their interactions with natives is vital in evaluating invasion risk yet remains difficult. Climate filtering and competition with native congeners are two important processes impacting niche changes and yielding contradictory predictions for the coexistence of non‐native and native species. Cl...
Preprint
The 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. We integrated phylogenomic, environmental ordination, and macroevo...
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This article is a Commentary on Halabi et al. (2023), 240: 918–927.
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The mulberry genus, Morus L. (Moraceae), has long been taxonomically difficult, and its species circumscription has only been defined recently. This genus comprises ca. 16 species distributed across Asia and the Americas, yet its biogeographic history remains poorly understood. In this study, we reconstructed the phylogeny and explored the biogeogr...
Preprint
Driven by the national conversation on systemic racism, ongoing inequities, appeals to decolonize science, and the many recent calls for diversity, equity, accessibility, and inclusion, we use stories of plants to discuss the history of bias and exclusionary practices in scientific botany, particularly regarding access to scientific spaces, and the...
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The Arctic tundra is a relatively young and new type of biome and is especially sensitive to the impacts of global warming. However, little is known about how the Arctic flora was shaped over time. Here we investigate the origin and evolutionary dynamics of the Arctic flora by sampling 32 angiosperm clades that together encompass 3626 species. We s...
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Premise: Developing an effective and easy-to-use high-molecular-weight (HMW) DNA extraction method is essential for genomic research, especially in the era of third-generation sequencing. To efficiently use technologies capable of generating long-read sequences, it is important to maximize both the length and purity of the extracted DNA; however,...
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Tragopogon (Asteraceae) includes two recently and repeatedly formed allopolyploids, T. mirus and T. miscellus, both of which formed in western North America following the human-mediated introduction of three diploids from Europe: T. dubius, T. porrifolius, and T. pratensis. We recently investigated the genetics of the introduction history to North...
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Distribution models are widely used to understand landscape biodiversity patterns, facilitate evolutionary and ecological studies, and for making informed conservation decisions. While it is common to examine consequences of climate change, impacts of land use on distributions, a major factor in limiting ranges and corridors between populations, ar...
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Premise: Recently formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. The allopolyploid species have also been resynthesized, allowing comparisons between the youngest possible allopolyploid...
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Butterflies are a diverse and charismatic insect group that are thought to have evolved with plants and dispersed throughout the world in response to key geological events. However, these hypotheses have not been extensively tested because a comprehensive phylogenetic framework and datasets for butterfly larval hosts and global distributions are la...
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Oaks (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 phylogen...
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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 invoke...
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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...
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Societal Impact Statement: Given the rapidly increasing drought and temperature stresses associated with climate change, innovative approaches for food security are imperative. One understudied opportunity is using feral crops—plants that have escaped and persisted without cultivation—as a source of genetic diversity, which could build resilience...
Preprint
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 today's freezing terrestrial environments. The angiosperm order Fagales, comprising iconic compo...
Article
Hybridization has long been recognized as a fundamental evolutionary process in plants, but our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure-until recently. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybr...
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Full-text available
The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological and biogeographic transitions within the clade. We used target capture sequencing with the Angiosperms353 probes, taxon-sampling encompassing nearly all genera of t...
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Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modelle...
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The genetic consequences following polyploidy (i.e., whole-genome duplication; WGD) vary greatly across organisms and through time since polyploidization. At the gene level in allopolyploids, changes include loss/retention of both parental gene copies, function/expression divergence between the two parental copies, and silencing of one parental cop...
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Premise: A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s. l.), reconstruct the biogeographic history of the clade, and...
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Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody...
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Aim The North American Coastal Plain is currently recognized as a global biodiversity hotspot. However, the mechanisms driving high levels of species richness in a region with relatively low topographic relief and homogeneous climate are unclear. We investigated the evolutionary processes driving ancestral area evolution and diversification in a bi...
Preprint
Full-text available
Hybridization has long been recognized as a fundamental evolutionary process in plants, but our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure—until recently. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybr...
Article
Full-text available
The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia–eastern North America (EA−ENA disjuncts) and their associ...
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Rapid climate change is threatening biodiversity via habitat loss, range shifts, increases in invasive species, novel species interactions, and other unforeseen changes. Coastal and estuarine species are especially vulnerable to the impacts of climate change due to sea level rise and may be severely impacted in the next several decades. Species dis...
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The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii . The asse...
Preprint
Full-text available
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 invoke...
Article
Full-text available
Caves are home to unique and fragile biotas with high levels of endemism. However, little is known about how the biotic colonization of caves has developed over time, especially in caves from middle and low latitudes. Subtropical East Asia holds the world's largest karst landform with numerous ancient caves, which harbor a high diversity of cave-dw...
Preprint
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Root nodule symbiosis (RNS) allows plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. RNS is a complex trait requiring coordination from both the plant host and the bacterial symbiont, and pinpointing the evolutionary origins of root nodules is critical for understanding the gene...
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Eastern Asia (EA) and North America north of Mexico (NA) have comparable latitude, land area, and climate, but the overall plant diversity is much higher in EA than in NA. Despite intensive studies on disjunct taxa of the two regions, the temporal and spatial diversity patterns between the two floras remain unclear. Here we explore the floristic di...