Phasing Hyb-Seq loci from two combined bait sets to investigate phylogenetic patterns of hybridization within Boechera s.s. (Brassicaceae).

Background And Aims: The complex landscape of hybridization and apomixis that characterizes the genus Boechera (Brassicaceae) is only beginning to be understood. Boechera, with over 80 recognized sexual species predominantly in North America, has emerged as a key model system for studying apomixis, primarily because of its remarkable capacity to form apomictic hybrids. This study builds on recent Hyb-Seq analyses by incorporating seven phased apomictic taxa into an existing topology of 108 sexual samples, thereby enhancing the existing phylogenetic framework and refining our understanding of the taxonomy of Boechera.

Genome structure and molecular phylogeny of the only Eurasian Boechera species, Boechera falcata (Brassicaceae).

Boechera falcata (Turcz.) Al-Shehbaz, previously known as Arabis turczaninowii Ledeb., is a herbaceous perennial of the East Siberian, boreal-steppe ecotype.

The PteridoPortal: A publicly accessible collection of over three million records of extant and extinct pteridophytes.

Premise: Pteridophytes-vascular land plants that disperse by spores-are a powerful system for studying plant evolution, particularly with respect to the impact of abiotic factors on evolutionary trajectories through deep time. However, our ability to use pteridophytes to investigate such questions-or to capitalize on the ecological and conservation-related applications of the group-has been impaired by the relative isolation of the neo- and paleobotanical research communities and by the absence of large-scale biodiversity data sources.

Methods: Here we present the Pteridophyte Collections Consortium (PCC), an interdisciplinary community uniting neo- and paleobotanists, and the associated PteridoPortal, a publicly accessible online portal that serves over three million pteridophyte records, including herbarium specimens, paleontological museum specimens, and iNaturalist observations.

Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset.

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data.

A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets.

Premise: Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae.

Methods: To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family.

An in-depth investigation of cryptic taxonomic diversity in the rare endemic mustard Draba maguirei.

Premise: Previously published evidence suggests that Draba maguirei, a mustard endemic to a few localities in the Bear River, Wellsville, and Wasatch Mountains of northern Utah, may represent a cryptic species complex rather than a single species. Conservation concerns prompted an in-depth systematic study of this taxon and its putative relatives.

Methods: Sampling most known populations of D.

Once more unto the breach, dear friends: Resolving the origins and relationships of the Pellaea wrightiana hybrid complex.

Premise: The taxonomic status of Wright's cliff brake fern, Pellaea wrightiana, has been in dispute ever since it was first described by Hooker in 1858. Previously published evidence suggested that this "taxon" may represent a polyploid complex rather than a single discrete species, a hypothesis tested here using a multifaceted analytical approach.

Methods: Data derived from cytogenetics, spore analyses, leaf morphometrics, enzyme electrophoresis, and phylogenetic analyses of plastid and nuclear DNA sequences are used to elucidate the origin, relationships, and taxonomic circumscription of P.

When it only takes one to tango: assessing the impact of apomixis in the fern genus Pteris.

Premise: Apomixis (asexual reproduction by seed, spore, or egg) has evolved repeatedly across the tree of life. Studies of animals and angiosperms show that apomictic lineages are often evolutionarily short-lived and frequently exhibit different distributions than their sexual relatives. However, apomixis is rare in these groups.

The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.

Premise: Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort.

Methods And Results: Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets.

A drought-driven model for the evolution of obligate apomixis in ferns: evidence from pellaeids (Pteridaceae).

Premise: Xeric environments impose major constraints on the fern life cycle, yet many lineages overcome these limitations by evolving apomixis. Here, we synthesize studies of apomixis in ferns and present an evidence-based model for the evolution and establishment of this reproductive strategy, focusing on genetic and environmental factors associated with its two defining traits: the production of "unreduced" spores (n = 2n) and the initiation of sporophytes from gametophyte tissue (i.e.

Using computer vision on herbarium specimen images to discriminate among closely related horsetails ().

Premise: is a distinctive vascular plant genus with 15 extant species worldwide. Species identification is complicated by morphological plasticity and frequent hybridization events, leading to a disproportionately high number of misidentified specimens. These may be correctly identified by applying appropriate computer vision tools.

Chromosomal Evolution and Apomixis in the Cruciferous Tribe Boechereae.

The mustard family (Brassicaceae) comprises several dozen monophyletic clades usually ranked as tribes. The tribe Boechereae plays a prominent role in plant research due to the incidence of apomixis and its close relationship to . This tribe, largely confined to western North America, harbors nine genera and c.

A basic ddRADseq two-enzyme protocol performs well with herbarium and silica-dried tissues across four genera.

Premise: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double-digest restriction site-associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica-dried and herbarium tissue.

Methods: DNAs from , , , and were processed with a ddRADseq protocol.

Infraspecific diversification of the star cloak fern (Notholaena standleyi) in the deserts of the United States and Mexico.

Premise: Not all ferns grow in moist and shaded habitats. One well-known example is Notholaena standleyi, a species that thrives in deserts of the southwestern United States and Mexico. This species exhibits several "chemotypes" that differ in farina (flavonoid exudates) color and chemistry.

Apospory and Diplospory in Diploid (Brassicaceae) May Facilitate Speciation by Recombination-Driven Apomixis-to-Sex Reversals.

Apomixis (asexual seed formation) in angiosperms occurs either sporophytically, through adventitious embryony, or gametophytically, where an unreduced female gametophyte (embryo sac) forms and produces an unreduced egg that develops into an embryo parthenogenetically. Multiple types of gametophytic apomixis occur, and these are differentiated based on where and when the unreduced gametophyte forms, a process referred to as apomeiosis. Apomeiotic gametophytes form directly from ameiotic megasporocytes, as in Antennaria-type diplospory, from unreduced spores derived from 1st division meiotic restitutions, as in Taraxacum-type diplospory, or from cells of the ovule wall, as in Hieracium-type apospory.

Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae).

Notholaenids are an unusual group of ferns that have adapted to, and diversified within, the deserts of Mexico and the southwestern United States. With approximately 40 species, this group is noted for being desiccation-tolerant and having "farina"-powdery exudates of lipophilic flavonoid aglycones-that occur on both the gametophytic and sporophytic phases of their life cycle. The most recent circumscription of notholaenids based on plastid markers surprisingly suggests that several morphological characters, including the expression of farina, are homoplasious.

Ecological differentiation facilitates fine-scale coexistence of sexual and asexual Boechera.

Premise Of The Study: Ecological differentiation (ED) between sexual and asexual organisms may permit the maintenance of reproductive polymorphism. Several studies of sexual/asexual ED in plants have shown that the geographic ranges of asexuals extend beyond those of sexuals, often in areas of higher latitude or elevation. But very little is known about ED at fine scales, wherein coexistence of sexuals and asexuals may be permitted by differential niche occupation.

Deciphering the sexual diploid members of the complex (Brassicaceae, Boechereae).

is a model genus that is of particular interest for understanding apomixis due to the presence of numerous apomictic diploid lineages that are tightly correlated with hybridisation events. includes many narrowly distributed endemics and apomictic hybrid lineages that obscure morphological boundaries amongst taxa. In this study, we focus on the complex, a phylogenetically well-supported but taxonomically complex north-western United States clade whose diploid species currently include the widespread and two narrowly distributed serpentine endemics, and .

Admixture, evolution, and variation in reproductive isolation in the Boechera puberula clade.

Background: Hybridization is very common in plants, and the incorporation of new alleles into existing lineages (i.e. admixture) can blur species boundaries.

Can asexuality confer a short-term advantage? Investigating apparent biogeographic success in the apomictic triploid fern Myriopteris gracilis.

Premise Of The Study: Although asexual taxa are generally seen as evolutionary dead ends, asexuality appears to provide a short-term benefit in some taxa, including a wider geographic distribution compared to sexual relatives. However, this may be an illusion created by multiple, morphologically cryptic, asexual lineages, each occupying a relatively small area. In this study we investigate the role of multiple lineages in the biogeography of Myriopteris gracilis Fée (Pteridaceae), a North American apomictic triploid fern species with a particularly large range.

Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage.

Unlabelled: Boechera (Brassicaceae) has many features to recommend it as a model genus for ecological and evolutionary research, including species richness, ecological diversity, experimental tractability and close phylogenetic proximity to Arabidopsis . However, efforts to realize the full potential of this model system have been thwarted by the frequent inability of researchers to identify their samples and place them in a broader evolutionary context. Here we present the Boechera Microsatellite Website (BMW), a portal that archives over 55 000 microsatellite allele calls from 4471 specimens (including 133 nomenclatural types).

Natural hybridization between genera that diverged from each other approximately 60 million years ago.

A fern from the French Pyrenees-×Cystocarpium roskamianum-is a recently formed intergeneric hybrid between parental lineages that diverged from each other approximately 60 million years ago (mya; 95% highest posterior density: 40.2-76.2 mya).

Evidence for reciprocal origins in Polypodium hesperium (Polypodiaceae): a fern model system for investigating how multiple origins shape allopolyploid genomes.

Unlabelled: •

Premise Of The Study: Many polyploid species are composed of distinct lineages originating from multiple, independent polyploidization events. In the case of allopolyploids, reciprocal crosses between the same progenitor species can yield lineages with different uniparentally inherited plastid genomes. While likely common, there are few well-documented examples of such reciprocal origins.

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery.