Adam C. Schneider

We used genome skimming to improve the phylogenetic resolution of tribe Orobancheae. Most importantly, we show that the previously unplaced Eremitilla is sister to Kopsiopsis, and a new, brilliantly coloured species from Baja California that parasitizes Arctostaphylos, described here as Kopsiopsis rosea, is sister to but deeply divergent from the rest of the genus. Among the distinguishing features of this new species is a pentacarpellate ovary, which is present in just one other species of Orobanchaceae, Eremitilla mexicana. Phylogenetic and morphological analysis further support the demotion of K. strobilacea to subspecific rank under K. hookeri.

Conopholis americana (American cancer-root) and Epifagus virginiana (beechdrops) are sister genera of holoparasitic plants (Orobanchaceae) native to eastern North America, parasitizing oaks and American beech, respectively. Both have served as models for plastid genome reduction, yet no nuclear genomes exist for either genus or any New World holoparasitic Orobanchaceae. Here we present the first nuclear genome assemblies for both species using PacBio HiFi sequencing. The C. americana assembly totals 1.82 Gb and E. virginiana totals 440 Mb, representing an approximately 4-fold difference in genome size between these sister genera. We observed a BUSCO completeness of 79% to 80% in both species, which is typical of holoparasites. While gene prediction identified 33,889 genes in C. americana and 21,031 in E. virginiana, repeat annotation revealed that LTR retrotransposons account for 78% of the genome size difference. These assemblies reveal contrasting mechanisms of genome evolution in sister holoparasitic genera and provide foundational resources for comparative genomics of parasitic plants.

We present a uniform atmospheric retrieval analysis of 22 late-T and Y-type brown dwarfs within 20 pc, observed with the James Webb Space Telescope NIRSpec PRISM and MIRI low-resolution spectrometer. This dataset provides the first continuous ∼0.95–12 μ m spectroscopic coverage of late-T and Y-type brown dwarfs, which in turn enables precise constraints on their thermal structures and volume mixing ratios (VMRs) of H ₂ O, CH ₄ , CO, CO ₂ , NH ₃ , H ₂ S, K, Na, and PH ₃ . We find positive correlations between the VMR of H ₂ O and CH ₄ , and CO and CO ₂ , consistent with thermochemical equilibrium chemistry. Using the VMRs, we derive atmospheric metallicity, which is positively correlated with H ₂ O and CH ₄ , showing H ₂ O and CH ₄ trace oxygen and carbon content, respectively, allowing us to effectively measure (O/H) _bulk and (C/H) _bulk . We also report tentative PH ₃ detections in roughly half the sample, suggesting potential vertical mixing or nonequilibrium chemistry. Apart from chemical properties, we retrieve masses and radii spanning ∼6–77 M Jup N and ∼0.66–1.53 R Jup N , respectively. We compare the derived log 10 ( g ) (∼4–5.5 (cm s ⁻² )) and T _eff (∼350–1100 K) with Sonora Bobcat evolutionary models and find an age range of 0.4 to 10 Gyr amongst the sample. Comparing our retrieved thermal profiles with the Elf-Owl forward model thermal profiles, we find a systematic difference between the two, likely arising due to the difference in chemistry treatment.

Castilleja lassenensis, a species of root-parasitic plants endemic to the Mt. Lassen region in northern California, has been subject to taxonomic debate since its first description in 1940. While morphological and ecological distinctions from its close relative Castilleja lemmonii have been documented, many regional floras do not list C. lassenensis or treat it as a synonym of C. lemmonii. We sequenced the nuclear genomes of C. lassenensis and C. lemmonii and performed comparative genomic analyses including gene content, functional enrichment, and phylogenetic placement. The genome of C. lassenensis, although slightly smaller than that of C. lemmonii, shows higher gene content, with different patterns of gene duplication. Functional genomic analysis revealed distinct enrichment patterns in the two species, with metabolic and transport functions enriched in C. lassenensis versus cellular organization in C. lemmonii. The taxa also show divergence in peptidase and CAZyme distributions, as well as in KAI2d proteins involved in strigolactone perception. Population-level validation using diagnostic gene markers across multiple individuals from geographically separate populations confirmed stable genomic differences. Our results support the recognition of C. lassenensis as a distinct species and underscore the need for measures to ensure its conservation.

Background and Aims: Photosynthesis is central to plant function, yet it has been repeatedly lost or diminished in parasitic angiosperm lineages. This variation raises questions about how photosynthetic function is retained, modified or repurposed in the evolutionary context of parasitism. Cuscuta species, as a model system for studying parasitism, exhibit varying degrees of plastid functionality and photosynthetic ability, based on genomic and ultrastructure studies. However, few direct physiological studies exist, and none that span multiple developmental stages of autotrophic, mixotrophic and non-photosynthetic species in a phylogenetic framework. Methods: To address this gap, we paired photosynthetic activity measurements from fluorometry with quantitative analysis of chlorophylls and carotenoids from multiple developmental stages in 14 Cuscuta species, representing the phylogenetic breadth of the genus, and a closely related autotrophic species. Multivariate data were analysed using non-parametric hypothesis tests, and comparative phylogenetic patterns were explored through Bayesian model testing. Key Results: Photosynthetic activity and chlorophyll and carotenoid content were highest in meristematic regions (e.g. shoot tips and developing seeds) and lowest in older stems or haustoria. Neoxanthin, a carotenoid typically highly conserved in plants, appears to have been lost once in Cuscuta and subsequently re-gained in certain lineages. Complex relationships between photosynthetic activity and lutein epoxide concentration suggest differing roles in developmental stages with high and low energetic needs. Conclusions: These findings provide substantial evidence that photosynthesis in Cuscuta is not vestigial but rather modulated based on developmental stage and across phylogenetic history, revealing a dynamic interplay between parasitism and photosynthetic function.

Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small “many analyst” study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.

Premise: Phelipanche ramosa is an economically damaging parasitic plant that has been reported in North America since the late 1800s. While this species comprises a variety of genetically distinct host races in its native range, the genetic composition of adventive populations in the New World remains unexplored. On the basis of morphological and ecological variation, some have suggested that the closely related P. nana may also be present.Methods: Genome skimming was used to assess the relationships of 30 populations of Phelipanche spanning the geographic and host ranges in North and South America, plus one P. nana reference population from Lebanon.Results: Phylogenetic analysis indicated four distinct genetic groups, though plastome and nrDNA data supported conflicting signals of relationships among them. First, specimens from Chilean tomato fields were nearly indistinguishable genetically from the reference P. nana. Second, a pair of samples from Virginia showed similar nrDNA as the first group, but divergent plastomes. The remaining 24 samples sorted into two groups, one which parasitizes cultivated plants, especially tomato, and the other on roadside weeds in different parts of the United States.Conclusions: The geographic and ecological cohesiveness of four distinct genetic groups supports a hypothesis of multiple introductions to the Americas, presumably from Eurasia, followed by little to no subsequent gene flow among them. However, such groups do not align with existing morphological or ecological species concepts for P. ramosa and P. nana. In practice, threat assessment of Phelipanche populations to agricultural settings should be evaluated regionally given the phylogeographic and ecological heterogeneity.

Rapid adaptation during invasion has historically been considered limited and unpredictable. We leverage whole-genome sequencing of >2600 plants across six continents to investigate the relative roles of colonization history and adaptation during the worldwide invasion of Trifolium repens. Introduced populations contain high levels of genetic variation with independent colonization histories evident on different continents. Five large structural variants on three chromosomes exist as standing genetic variation within the native range, and exhibit strong signatures of parallel climate-associated adaptation across continents. Common gardens in the native and introduced ranges demonstrate that three structural variants exhibit patterns of selection consistent with local adaptation across each range. Our results provide strong evidence that rapid and parallel adaptation during invasion is caused by large-effect structural variants introduced throughout the world. Significance Statement Biological invasions occur over short timescales and introductions are often hypothesized to include limited genetic diversity, making the role of adaptation in invasion success controversial. We demonstrate that the invasion of a human-commensal species, Trifolium repens, likely stems from multiple, diverse introductions with significant evidence of climate-associated adaptation following introduction. The genetic basis of adaptation is most strongly linked to five chromosomal rearrangements that each span hundreds of genes – matching theoretical predictions that large-effect variants are key to the initial stages of adaptation to novel environments. Chromosomal rearrangements have remarkably parallel signatures of adaptation across different introductions despite initial colonization from different areas of Europe. Our study highlights the impact of globalization and rapid adaptation for the invasion success of human commensal species.

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established by the Parasite Microbiome Project (PMP) consortium, in collaboration with the Genomics Standard Consortium. The SA was built upon the host-associated MIxS standard, but reflects the nestedness of symbiont-associated microbiota within and across host-symbiont-microbe interactions. This package is designed to facilitate the collection and reporting of a broad range of metadata information that apply to symbionts such as life history traits, association with one or multiple host organisms, or the nature of host-symbiont interactions along the mutualism-parasitism continuum. To better reflect the inherent nestedness of all biological systems, we present a novel feature that allows users to co-localize samples, to nest a package within another package, and to identify replicates. Adoption of the MIxS-SA and of the new terms will facilitate reports of complex sampling design from a myriad of environments.