American Journal of Botany

PREMISE OF THE STUDYLife history is an important predictor of population genetic variation, although this link remains unexplored in numerous important plant lineages. One such lineage is the legume genus Strophostyles, which contains both annual and herbaceous perennial vines native to eastern North America. Specifically, it remains to be determined whether Strophostyles species with different life histories show different patterns of genetic differentiation and diversity, as well as if these species hybridize across their range. METHODSHere we sampled the perennial Strophostyles helvola and annual S. leiosperma in five sites across a latitudinal transect in the central United States, including three sites where the species occur in sympatry. Using genotyping-by-sequencing, we identified 5556 polymorphic SNPs across 166 individuals. KEY RESULTSThere is no evidence that Strophostyles helvola and S. leiosperma hybridize in the populations examined. Within species, Strophostyles helvola (perennial) displays admixture among populations, while S. leiosperma (annual) does not, although both species show more genetic diversity among rather than within populations. Patterns of genetic diversity are varied across populations of both species, with both heterozygote excess and deficiency. CONCLUSIONSThe complex patterns of genetic differentiation and diversity warrant further investigation of life history and population dynamics in Strophostyles, particularly mating system and modes of gene flow. This study exemplifies the diversity of population genetic patterns even within a small genus, and it reinforces the need to characterize such diversity in non-model systems to gain a more complete understanding of how life history contributes to population genetics.

Alpine areas are host to diverse plant communities that support ecosystems through structural and floral resources and persist through specialized adaptations to harsh high-elevation conditions. An ongoing question in these plant communities is whether composition is shaped by stochastic processes (e.g., dispersal limitations) or by deterministic processes (e.g., climate, geology), and if those processes select for common phylogenetic clades across space. This study evaluates the drivers of dissimilarity in alpine vascular plant communities across 32 peaks in the Cascade Mountain Range of Washington State and examines the effects of incorporating phylogenetic relatedness to these conclusions. We documented an average of 54 species per peak and used our overall inventory of 307 taxa to construct a phylogenetic tree for the entire mountain range plant community sampled. We used multivariate techniques to quantify the phylogenetic and taxonomic differences between alpine plant communities and to relate those differences to each peaks climate, geology, and topography. Our models indicate that the age of each peaks parent material formation, precipitation, latitude, and temperature had the largest role in shaping alpine plant communities relative to the baseline effects of distance between peaks and time of sampling. A unique result was a distinct plant community in peaks with ultramafic geologic parent material formed in the Paleozoic Era, which has an extreme geochemistry that we found to form evolutionarily distinct lineages compared to all other peaks. With changing climate conditions and disturbance regimes, understanding facets of alpine plant communities like species turnover, geologic endemism, and responses to precipitation changes are vital to conserving these ecosystems.

Premise of the ResearchThe prevalence of sexual dimorphisms, which evolve due to contrasting strategies to maximize reproductive success in males and females, is variable among dioecious plant species. In the Salicaceae, many traits have been assessed across many studies, but direct or indirect associations between these traits and reproductive allocation are often neglected. Given the dynamic evolution of sex determination systems and the strong interest in wood production in the family, we wondered whether sexual dimorphisms related to reproduction may have gone unreported. Here, we assess sexual dimorphism in reproductive traits in two species of Salix. Recognition of reproductive sexually dimorphic traits will contribute to understanding the evolution of sex determination systems in the Salicaceae. MethodologyWe conducted observational studies in natural populations to assess the presence of sexual dimorphisms in early spring bud density, catkin number, and flower number per catkin across four sampling periods in Salix exigua. We also analyzed flower number and catkin number per flower in Salix nigra. Pivotal ResultsWe observed no sexual dimorphism in pre-season buds per branch in S. exigua but did find that males produced more flowers per catkin and more catkins per branch than females in both S. exigua and S. nigra. ConclusionsHigher flower numbers in males compared to females is consistent with expectations from intra-sexual selection among males. The presence of reproductive sexual dimorphisms in Salix suggests that sexual selection may affect the evolution of mating strategies in Salix species, and the evolution of the sex determination system within this genus.

Background & AimsPollinators play a crucial role in the evolution and diversification of flowering plants. Intraspecific variation in floral traits occurs frequently and likely reflects variable biotic and abiotic selection pressures. The hummingbird-pollinated monkeyflower Mimulus cardinalis occurs across western North America, where geographic mosaics of selection have likely influenced its natural history, due to this wide species range. Processes driving early stages of divergence and speciation remain poorly understood, though theory predicts that trait divergence will be most likely at range edges. Within M. cardinalis, which is usually red-flowered and hummingbird-pollinated, two independent shifts to yellow flowers have occurred at the northern and southern range edges, including a population found on Cedros Island, off the coast of Baja California, Mexico. MethodsThis study characterises the local climatic variables of five accessions of M. cardinalis derived from locations across a latitudinal geographic gradient. Highly integrative methods in metabolomics and morphological analyses were used to characterise a suite of pollinator-relevant floral traits across the range of M. cardinalis species variation. We use transcriptomics and whole genome sequencing to study underlying genetic variation in two yellow-coloured, range-edge accessions. Key ResultsThis study uncovers high levels of variation in morphology, nectar properties, pigmentation and scent profile across geographically diverse Mimulus cardinalis accessions, in addition to profiling how these accessions are perceived by potential pollinators. We find high levels of phenotypic variation across M. cardinalis, particularly in the biochemistry of pigment and scent, where inflorescences that appear to be the same shade of red have completely different anthocyanin profiles. Floral trait-underlying genetic differences between different M. cardinalis lines were also investigated, revealing potential mechanisms underlying floral diversification. ConclusionsThis work highlights the importance of interplay between floral trait diversification, pollinator perception and climate. This work also highlights the importance of considering suites of floral traits in a quantitative fashion when studying intraspecific variation in relation to species range. This study also provides genetic insight into changes in these traits and provides many future directions to study the early stages of pollinator-mediated trait differentiation across a species range.

Premise of the studyPaternal diversity and its distribution within maternal plants is governed by various factors, including frequency of pollinator visits, patterns of pollinator movement and pollen carryover. Floral display size may have opposite effects on fruit and plant-level paternal diversity, because plants with large displays should receive more pollinator visits but also more sequential probes per visit. MethodsTo investigate the effect of floral display size on the distribution of paternal diversity in Silene dioica, we genotyped and assigned paternity for 1320 seeds sampled in several fruits per plant in control and manipulated females, whose flower number was artificially increased. We estimated within-fruit paternal diversity and sire profile dissimilarity among fruits and compared these metrics between control and manipulated plants. We then studied pollen carryover using controlled pollinator visits and pollen counts. Key resultsMost fruits were multiply sired, but we found no effect of flower supplementation on within-fruit paternal diversity. Sire profiles were more similar between fruits located on the same than on different females, but sire profile similarity was not higher within manipulated than within control plants. The pollen deposition curve was steep, with an increasing carryover fraction throughout the visitation sequence. ConclusionsOur results suggest that the effect of floral display size on pollinator foraging behaviour is too weak to affect paternal diversity and its distribution in S. dioica, or that other processes, such as limited pollen carryover and spatially restricted pollen dispersal, blur the effect of pollinator visit frequency and movements on sire profiles.

AO_SCPLOWBSTRACTC_SCPLOWPhylogenomic discordance is pervasive and cannot always be resolved by increasing the amount of sequencing data alone. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are major contributors to discordance and must be accounted for to avoid misleading evolutionary interpretations. To better understand how these processes influence phylogenetic reconstruction, we conducted a comprehensive phylogenomic study in the complex genus Packera. With over 90 species and varieties, 40% of which exhibit polyploidy, aneuploidy, or other cytological complexities, Packera presents significant challenges for phylogenetic reconstruction. Given these complexities, we assessed different published paralog processing methods on the resulting evolutionary relationships and phylogenetic support of this group. We then applied three of these methods to evaluate their impact on tree topology and our understanding of Packeras evolutionary history by constructing a time-calibrated phylogeny, reconstructing historical biogeography, and testing for ancient reticulation. Phylogenetic outcomes varied based on the paralog processing method used, with no method performing the best over others. Our findings highlight the large impact of orthology inference and paralog processing on phylogenomic analyses, particularly in polyploid-rich groups such as Packera, and we offer guidance on methodological impacts along with practical recommendations. We note that gaining a robust understanding of Packeras evolutionary history requires more than computational approaches alone. While technological advancements have greatly expanded our ability to analyze genomic data, effective phylogenomic research still relies on strong taxon sampling and detailed species knowledge. Without careful attention to the biological context, such as reproductive boundaries, cytological variation, ecological interactions, and historical biogeographic processes, phylogenomic studies risk misinterpreting evolutionary history and processes. By accounting for these factors, we can begin to improve the accuracy of evolutionary reconstructions and gain deeper insights into the complex history of plant diversification.

Population genetic analysis of species of conservation concern provides information to devise management plans to effectively conserve the genetic variation of endangered species. One such endangered plant, Physaria globosa is a federally endangered species in the mustard family with a geographically restricted range that occurs in four disjunct locations in Indiana, Kentucky, and Tennessee (i.e., Highland Rim and Nashville Basin regions) and along the Wabash, Kentucky, and Cumberland Rivers. In this study, we sampled populations from throughout the range of P. globosa, genotyped them using 20 microsatellite loci, and assessed genetic diversity and structure within and among populations. The goals of the study were to understand: 1) levels of genetic diversity in P. globosa and whether populations show evidence of having experienced reductions in genetic diversity as the result of genetic bottlenecks, genetic drift, or inbreeding, 2) rangewide genetic diversity and structure in P. globosa and how genetic structure is affected by the disjunctions in the species range, and 3) implications for prioritization of in-situ and ex-situ conservation efforts. On average, P. globosa showed comparable levels of genetic diversity to other species of Physaria. However, some populations showed evidence of inbreeding, genetic bottlenecks, or decreases in genetic diversity, possibly due to anthropogenic or climate-related pressures and decreases in population size due to competition with invasive bush honeysuckle. Genetic variation was strongly structured into two main geographic groups, one in the northern part of the species range (KY and IN), and the other in the southern part of the species range (TN), but some populations likely originated via long-distance dispersal. We also found significant isolation by distance, likely due to both life history characteristics and physical barriers associated with the complex topological structure of the landscape occupied by P. globosa, limiting population connectivity. Given the strong genetic structure found in P. globosa, several populations should be protected and managed within each geographic region to conserve genetic variation. Ex situ conservation will also be important to protect genetic diversity, particularly for populations that are difficult to access and manage.

Reticulate evolutionary events are hallmarks of plant phylogeny, and are increasingly recognized as common occurrences in other branches of the Tree of Life. However, inferring the evolutionary history of admixed lineages presents a difficult challenge for systematists due to genealogical discordance caused by both incomplete lineage sorting (ILS) and hybridization. Methods that accommodate both of these processes are continuing to be developed, but they often do not scale well to larger numbers of species. An additional complicating factor for many plant species is the occurrence of whole genome duplication (WGD), which can have various outcomes on the genealogical history of haplotypes sampled from the genome. In this study, we sought to investigate patterns of hybridization and WGD in two subsections from the genus Penstemon (Plantaginaceae; subsect. Humiles and Proceri), a speciose group of angiosperms that has rapidly radiated across North America. Species in subsect. Humiles and Proceri occur primarily in the Pacific Northwest of the United States, occupying habitats such as mesic, subalpine meadows, as well as more well-drained substrates at varying elevations. Ploidy levels in the subsections range from diploid to hexaploid, and it is hypothesized that most of the polyploids are hybrids (i.e., allopolyploids). To estimate phylogeny in these groups, we first developed a method for estimating quartet concordance factors (QCFs) from multiple sequences sampled per lineage, allowing us to model all haplotypes from a polyploid. QCFs represent the proportion of gene trees that support a particular species quartet relationship, and are used for species network estimation in the program SNaQ (Solis-Lemus & Ane. 2016. PLoS Genet. 12:e1005896). Using phased haplotypes for nuclear amplicons, we inferred species trees and networks for 38 taxa from P. subsect. Humiles and Proceri. Our phylogenetic analyses recovered two clades comprising a mix of taxa from both subsections, indicating that the current taxonomy for these groups is inconsistent with our estimates of phylogeny. In addition, there was little support for hypotheses regarding the formation of putative allopolyploid lineages. Overall, we found evidence for the effects of both ILS and admixture on the evolutionary history of these species, but were able to evaluate our taxonomic hypotheses despite high levels of gene tree discordance. Our method for estimating QCFs from multiple haplotypes also allowed us to include species of varying ploidy levels in our analyses, which we anticipate will help to facilitate estimation of species networks in other plant groups as well.

Premise of the StudyRecent studies of floral disparity in the asterid order Ericales have shown that flowers vary strongly among families and that disparity is unequally distributed between the three flower modules (perianth, androecium, gynoecium). However, it remains unknown whether these patterns are driven by heterogeneous rates of morphological evolution or other factors. MethodsHere, we compiled a dataset of 33 floral characters scored for 414 extant ericalean species sampled from 346 genera and all 22 families. We conducted ancestral state reconstructions using an equal rates Markov models for each trait. We used the rates estimated during the ancestral state reconstruction for comparing evolutionary rates between flower modules, creating a "rate profile" of ericalean flowers. Key ResultsThe androecium exhibits the highest evolutionary rates across most characters, whereas most perianth and gynoecium characters evolve slower. High and low rates of morphological evolution can result in high floral disparity in Ericales. Analyses of an angiosperm-wide floral dataset reveal that this pattern appears to be conserved across most major angiosperm clades. ConclusionsElevated rates of morphological evolution in the androecium of Ericales may explain the higher disparity reported for this floral module. We discuss the implications of heterogenous morphological rates of evolution among floral modules from a functional perspective. Comparing rates of morphological evolution through rate profiles proves to be a powerful tool in understanding floral evolution.

>Mixed-cytotype populations are ideal to understand polyploid establishment and diversification. We used the orchid Zygopetalum mackayi to understand how facultative apomictic reproduction relates to polyploidy. Sexual diploids and facultative apomictic tetraploids occur under distinct niches, with a contact zone where triploids occur. We hypothesized that facultative apomictic reproduction increases the fitness of tetraploids through reproductive interference between cytotypes. We predict patterns of genetic diversity of allopatric tetraploid populations to be significantly different from contact zone populations as a result of dominant apomictic reproduction in the later. We also describe the contact nature of diploids and tetraploids and the role of the intermediate triploids based on patterns of genetic structure within and among pure and mixed-cytotype populations.\n>We designed eight microsatellite markers and genotyped 155 individuals from six populations resulting in 237 alleles. We described patterns of genetic diversity and structure within and among populations and cytotypes.\n>Genotypic diversity is similarly high among all populations and cytotypes. Each cytotype emerged as a genetically cluster, combining individuals from different populations. Triploids clustered in an intermediate position between diploids andtetraploids.\n>We rejected the hypothesis of reproductive interference between cytotypes of Z. mackayi. Patterns of genetic diversity are incongruent with the occurrence of apomict reproduction in tetraploids. Mixed-cytotype populations originate from secondary contact and triploids are hybrids between diploids and tetraploids and act as a reproductive barrier. We suggest polyploidy rather than facultative apomixis explains higher fitness of tetraploids in this species and, therefore, eco-geographical patterns of distribution.

Gene flow to marginal populations at a species range edge can facilitate rapid adaptation by increasing genetic diversity, reducing inbreeding depression, and introducing novel alleles. In highly inbred populations, hybrid vigor is often observed in the first generation (F1), but hybrid breakdown may diminish fitness in subsequent generations. Thus, benefits of gene flow may be overestimated when only F1 performance is assessed. We tested whether gene flow among populations of the annual plant Erythranthe laciniata (A. Gray) G.L. Nesom, from similar and contrasting environments, confers persistent fitness advantages across F1 and F2 generations at the high-elevation edge of its range in the California Sierra Nevada. Gene flow was experimentally introduced through pollen transfer between cold-edge populations, between cold edge and central populations, and within local cold edge populations, and compared to self-fertilized offspring, the predominant mating strategy of E. laciniata. For F1 progeny, we measured morphological, phenological, and fitness traits in a common garden located near the cold-climate range limit during 2008-2009, a relatively average year, and for F2 progeny in 2009-2010, a relatively wet year. Although F1 crosses showed no initial performance advantage measured in the previous year, F2 progeny from center-to-edge and edge-to-edge crosses significantly outperformed selfed and locally outcrossed lines in fruit mass, total pedicels, biomass, and height. Our findings demonstrate that gene flow can confer long-term fitness benefits, especially among populations adapted to similar selective pressures, and highlight the potential of assisted gene flow to bolster or rescue peripheral populations facing climate change. SIGNIFICANCE STATEMENTSpecies living at the edges of their geographic ranges often have small, isolated populations with limited genetic diversity, which can restrict their ability to adapt to environmental change. Gene flow from other populations may increase adaptive potential, but its long-term consequences remain uncertain because most studies evaluate only first-generation hybrids. Using experimental crosses in the mountain wildflower Erythranthe laciniata, we show that gene flow can produce stronger fitness benefits in second-generation hybrids than in the first generation at a high-elevation range edge. These results suggest that recombination among populations can generate advantageous genetic combinations that emerge over multiple generations. Our findings highlight the potential for assisted gene flow to enhance adaptation and persistence of range-edge populations under climate change.

Premise of researchHermaphroditic plants reproduce as females by maturing seeds from fertilized ovules and as males by fertilizing the ovules of other plants. Sex allocation theory predicts a trade-off between investment in male and female function. Thus, to maximize fitness, selection should favor plasticity in resource allocation among individuals or flowers of the same plant in response to environmental conditions. As female reproduction is typically more costly while male reproduction is mate-limited, we predict greater investment in female function when resources are plentiful and in male function when pollination is limited. MethodologyWe investigated plasticity in sex allocation in the rapid cycling lineage of the hermaphroditic mustard species, Brassica rapa, in response to resource availability (altered pot size) and the pollination environment (unpollinated or fully pollinated). We assess investment in male function (anther length) and female function (ovary length) in flower buds produced at the onset of reproduction and in buds produced approximately 15 days later. We also measured traits often correlated with increased allocation to female (plant size) and male (flower size) function. Pivotal ResultsLarger plants had longer anthers, longer ovaries, and larger flowers at the onset of reproduction, resulting in similar anther:ovary length ratios across plants of different sizes. Independent of plant-size, plants produced smaller anthers at the onset of reproduction in the low resource treatment and larger flowers over the course of reproduction in the pollen-absent treatment. Furthermore, larger plants produced increasingly longer ovaries over the course of reproduction compared to smaller plants. ConclusionsOur findings underscore the influence of condition on changes in sex allocation and correlated traits over time. Furthermore, we provide some additional supporting evidence that resource availability and the pollination environment can influence sex allocation and contribute cautionary advice on effective methods for experimentally eliciting and measuring sex allocation plasticity.

PremiseIsolated populations at the southern range edge of aspen (Populus tremuloides Michx.) offer a unique opportunity to study ploidy, clonality and distribution of sex under arid, high-elevation conditions. We aimed to characterize such traits, including potential sex biases and associations with ploidy, investigating previously unexamined Texan populations in a range-wide genomic framework of genetic structure and demographic history of this keystone species. MethodsWe combined new genotypic data from western Texas (Davis Mountains, Big Bend, Guadalupe Mountains) with preexisting datasets, assessing range-wide genetic diversity, clonality, ploidy, and sex. We further conducted ADMIXTURE and phylogenetic analyses, reconstructed historical effective population sizes (Ne) with Stairway Plot 2. ResultsTexan stands revealed high clonality, with diploid and triploid genets. Most Davis and Guadalupe Mountain individuals clustered with a southwestern U.S. lineage of aspen, whereas Big Bend individuals grouped with a Mexican, demonstrating for the first time the continuous northward geographic distributions of allele frequencies in aspen coherent with phylogenetics. The significant male bias in sex ratios, particularly among triploids, suggests dimorphism in survival or reproduction. No effect of elevation on sex was identified. Demographic inference indicated an ancient bottleneck ([~]1-2 Mya) common to all six lineages, but more recent historical Ne trajectories differ between the northern and southern regions. ConclusionsThese findings shed light on how clonality, ploidy, and sex have interacted in shaping dioecious plant species, highlighting the importance of incorporating such information into projections of how climate change and habitat loss will affect their distribution, abundance, and the extinction risk of their marginal populations.

Background and AimsThe study of morphological diversity (i.e., disparity) offers unique opportunities to understand evolutionary patterns and processes. Plant disparity studies reveal that morphological disparification can be related to factors such as secondary woodiness or to pollination niche, for example. Similarly, some pollen traits are known to be shaped by environmental pressures, but this influence has only been evaluated in monads, never in multi-grained dispersal units. In this study, we investigated the disparity of aggregated dispersal units in two lineages of Neotropical mimosoid legumes. The Mimosa and Stryphnodendron clades are independent lineages that share similarities in pollen morphology and biome shifts. In this context, we asked: What are the patterns of pollen disparity in these lineages, and are these patterns similar between lineages occurring in the same biomes? MethodsTo answer these questions, we compiled data from the literature on pollen morphology and biomes of occurrence for a phylogenetically representative set of taxa in the Mimosa and Stryphnodendron clades. With these data, we calculated morphospaces and disparity metrics, and tested whether the pollen morphology of distinct lineages occurring in the same biome differs significantly. Key ResultsOur results show that Mimosa and Stryphnodendron clades exhibit distinct patterns of pollen disparity, as do independent lineages occurring in the same biomes. Additionally, we observed that certain biomes support greater or lesser levels of morphological disparity. ConclusionsWe conclude that (1) the Mimosa clade has greater disparity, possibly due to evolution of novel pollen morphologies in the genus Mimosa, (2) there is a maintenance of similarities in the pollen of the Stryphnodendron clade, Adenopodia and Piptadenia, and (3) the evolution of pollen grains in these groups appears to be primarily shaped by phylogeny and developmental constraints, with environmental pressures playing a comparatively smaller role.

Plants with large geographic distributions experience varying biotic and abiotic conditions across their geographic range that can influence plant defense traits among plant populations. It is often the case that more productive regions support higher herbivore numbers. Yet whether this results in greater herbivore pressure and stronger plant defenses in these populations compared to populations inhabiting less productive regions is uncertain. Here we quantified defense traits and herbivory of Solanum carolinense L. across a large productivity gradient that spans its entire north-south range (29-44{degrees} N), using both field observations (33 populations; [~]14 plants per population) and a common garden experiment (15 populations; [~]4 plants per population). We examined the effects of productivity on 1) plant defense traits (specific leaf area, trichome density and glycoalkaloid concentration), 2) herbivory, and 3) the correlation among traits and herbivory in field and common garden plants. Trichome density and herbivory were higher for S. carolinense at the center of its range, while glycoalkaloid concentrations were negatively associated with productivity both in the field and in the common garden. In the field, plants with higher glycoalkaloid production experienced reduced herbivory, but there was no association with plant defense traits and herbivory in the common garden. Overall, these findings suggest that different types of defensive traits within a single species may follow different ecological and evolutionary trends and highlight the need for trait-specific considerations when applying plant defense hypotheses at the intraspecific level.

Premise of StudyThe parentage of a widespread member of the carnivorous sundew genus Drosera, the allopolyploid Drosera anglica, remains uncertain despite over 100 years of morphological, cytological, and, more recently, molecular study. MethodsUsing transcriptomic and genomic data from 12 species Drosera sect. Drosera including four D. anglica populations and a disjunct Idaho population of D. intermedia, we assembled genes in HybPiper and phased sequences in HybPhaser. We estimated heterozygosity and generated flow cytometry data to assess ploidy levels. We estimated species relationships with phylogenetic and pairwise genetic distance methods. Additionally, we assembled rbcL and ITS reads to compare to previous data. Key ResultsSequences from phased subgenomes highly supported D. anglica as sister to D. rotundifolia and D. linearis, differing from previous analyses based on chromosome pairing and Sanger sequencing with limited taxon sampling. Both ITS and rbcL sequences of D. anglica were the most similar to D. linearis. Drosera anglica is intermediate between both parents in leaf shape and microhabitat; however, across D. sect. Drosera, neither leaf shape nor biogeographic distribution were reliable indicators of phylogenetic relationships. Despite a range-wide sampling, we did not find evidence for multiple origins of D. anglica. Additionally, we confirmed that the Idaho population previously identified as D. intermedia is D. anglica. ConclusionsDrosera anglica arose from allopolyploidy between D. linearis (the chloroplast donor) and D. rotundifolia. Our study demonstrates the importance of taxon sampling and careful examining complex phylogenomic data, and presents an exemplar of analyzing allopolyploid relationships in plant lineages.

Biologists have long pondered species geographical distributions and sought to understand what factors drive dispersal and determine species ranges. In considering plant species with large ranges, a question that has remained underexplored is whether large ranges are attained primarily through many instances of short scale dispersal or whether instead widespread ranges are attained by propagules with increased dispersal distances. Ferns provide an ideal system to explore this question as their propagules are very small spores, which have been theorised can be carried by wind to essentially anywhere on the planet. Unfortunately, population-level genetic data in ferns is relatively uncommon, limiting our ability to answer this and related questions. For this work, I focus on Cheilanthes distans (Pteridaceae) as a study system, a widespread fern with extensive spore variation that occurs over Australia and into New Zealand/Aotearoa, New Caledonia, and other Pacific islands. I sampled widely across the species range, in addition to across Australasian Cheilanthes (as a robust tree for the genus does not exist), ultimately building a phylogeny based on the GoFlag 451 bait set. With these data, we can investigate additional questions, including whether reproductive mode, polyploidy, or lineage influence dispersal, as well as whether movement is occurring randomly or is instead asymmetrical. I explored the relationships between sexual and apomictic specimens to understand whether the former are the parental lineages to apomictic plants and whether we find evidence for apomictic plants dispersing out of a small parental range. I investigated how many times polyploid lineages have arisen in C. distans and whether they are each limited geographically, perhaps forming isolated ranges that collectively result in C. distans larger range. Additionally, I generated estimates for ancestral ranges and dispersal between populations to understand whether certain lineages are limited to particular geographic regions, to explore the directionality of dispersal, and to assess whether most movement is happening over short or long distances. Particularly interestingly, I find that most dispersal in this species appears to occur over smaller steps rather than longer jumps, underscoring how short movement can nevertheless allow for establishment of large ranges; this dispersal is not limited phylogenetically and seems to occur equally for all lineages. What is more, I find evidence for asymmetrical dispersal directionality, apparently most frequently tracking trade winds. These findings demonstrate the importance of population-level data, and provide concrete results that add nuance to long-standing dispersibility hypotheses in the fern community that have, until now, lacked empirical data.

PremiseLeafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. Yet, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants. MethodsWe sequenced and analyzed the plastome of Degranvillea dermaptera, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities. Key ResultsWe revealed the most reduced plastome sequenced to date among the orchid subfamily Orchidoideae. Degranvillea has lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement of Degranvillea within the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and correlations among substitution rates and several other "traits" of the plastome among leafless members of orchid subfamily Orchidoideae. ConclusionsOur findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern.

Species are often regarded as basic units of study in biology, following the presumption that they are real and discrete natural entities. But several biologists wonder if species are arbitrary divisions that do not correspond to discrete natural groups of organisms. Two issues must be addressed to solve this controversy, but few studies seem to do so. The first is whether organisms form sympatric and synchronic groups that are distinct in terms of phenotypes and genome-wide allele frequencies, often called "good species." Alternatives to "good species" include "cryptic species," syngameons and, more generally, cases in which phenotypes and genome-wide allele frequencies reflect contrasting evolutionary histories. The second issue is the degree to which species taxa (i.e., taxonomic classification at the species level) reflect natural groups of organisms or constitute arbitrary divisions of biological diversity. Here, we empirically addressed both issues by studying plants of the Andean genus Espeletia (Asteraceae). We collected a geographically dense sample of 538 specimens from the paramo de Sumapaz, in the Cordillera Oriental of Colombia. Additionally, we examined 165 herbarium specimens previously collected by other researchers in this region, or from taxa known to occur there. We tested for the existence of phenotypic groups using normal mixture models and data on 13 quantitative characters. Among 307 specimens with all 13 measurements, we found six distinct phenotypic groups in sympatry. We also tested for the existence of groups defined by genome-wide allele frequencies, using ancestry models and data on 2,098 single nucleotide polymorphisms. Among 77 specimens with complete genomic data, we found three groups in sympatry, with high levels of admixture. Concordance between groups defined by phenotype and genome-wide allele frequencies was low, suggesting that phenotypes and genome-wide allele frequencies reflect contrasting evolutionary histories. Moreover, the high levels of admixture suggest that Espeletia plants form a syngameon in the paramo de Sumapaz. To determine the extent to which species taxa corresponded to phenotypic and genomic groups, we used data on 12 phenotypic characters to assign 307 specimens to species taxa, according to descriptions of species taxa in the most recent monograph of Espeletia. This sample included 27 specimens cited in the monograph. Remarkably, only one out of 307 specimens in our sample fell inside any of the phenotypic ranges reported in the monograph for the species taxa known to occur in the paramo de Sumapaz. These results show that species taxa in Espeletia are delineations of largely empty phenotypic space that miss biological diversity.

PremiseAdaptive radiation in ecologically and morphologically diverse plant lineages presents an opportunity to investigate the rapid evolution of novel floral traits. While some types of floral traits, such as flower color, are well-characterized, other types of complex morphologies remain understudied. One example is occluded personate flowers, dorso-ventrally compressed flowers with obstructed floral passageways, which have evolved in multiple genera, but have only been characterized from snapdragon. MethodsOur study examined the morphological basis and evolutionary history of personate flowers in a clade of Penstemon species that includes three personate-flowered species. We characterized floral morphology and inferred phylogenomic relationships for 13 species in this group in order to examine the evolutionary history of personate flowers. We used phylogenomic tests for introgression to examine whether personate-flowered lineages have a history of introgression. ResultsUnlike the personate flowers of snapdragon, personate flowers in Penstemon are produced by deep pleats in the ventral petal tissue that curve the ventral petal surface upwards, obstructing the floral tube opening. Our phylogenetic tree suggests that personate flowers evolved in two separate lineages. Phylogenomic analyses indicate incomplete lineage sorting and introgression between certain taxa have contributed to phylogenomic discordance, however we found little evidence of recent introgression between the two personate-flowered lineages. ConclusionsThe evolution of personate flowers in Penstemon involves a distinct morphological basis than snapdragon. Personate flowers have evolved multiple times in Penstemon on a rapid evolutionary timescale. The source of genetic variation for repeated shifts may be de novo mutations or pre-existing variants.