Ploidy level and genome size variation in the homosporous ferns Botrychium

Recent cytological and molecular studies have investigated genome size variation and evolution in the homosporous ferns, but representatives of the Ophioglossaceae were largely overlooked, despite their evolutionary singularity. Flow cytometry analysis was performed on 41 individuals of eight species of the genera Botrychium (B.), Botrypus, and Sceptridium to estimate their ploidy level variation. In a subset of individuals, we also estimated the absolute genome size and corresponding C values. Additionally, a classical chromosome count was made on the recently described species B. alaskense. Ploidy level and new genome size records were determined for Botrychium alaskense, B. boreale, B. lanceolatum, B. “neolunaria” ined., B. pinnatum, Botrypus virginianus and Sceptridium multifidum. In addition, we confirmed the genome size of B. matricariifolium, B. minganense and B. lunaria. Two of the three major sub-clades of Botrychium differ slightly in their averaged homoploid genome size (subclade Lanceolatum, 24.72 ± 0.40 pg; subclade Lunaria, 27.51 ± 0.47 pg). Flow cytometry and chromosome counting confirmed that B. alaskense is a tetraploid. A new hexaploid cytotype, putatively formed through an autopolyploidization from the sympatric tetraploid cytotype, was detected in a single individual of B. boreale. This is only the second report of hexaploidy in the genus Botrychium and our data highlight the potential to find other ploidy levels within other Botrychium species. Interestingly, no difference within the monoploid genome sizes was detected between ploidy levels, thus supporting the hypothesis of genome size stability after polyploidization and rejecting the scenario of genome downsizing

Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure

Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within-species studies based on high-resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about ~19.0-23.7 Gb. We assembled 25,677 high-quality transcripts with an average length of 1,333 bp based on deep RNA-sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome-wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High-quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations

A range‐wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence

Aim: Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming. We infer the hitherto unresolved postglacial history of Pinus cembra. Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re‐colonisation routes. Location: European Alps and Carpathians. Taxa: Pinus cembra. Methods: We genotyped nuclear and chloroplast microsatellite markers in nearly 3000 individuals from 147 locations across the entire natural range of P. cembra. Spatial genetic structure (Bayesian modelling) and demographic history (approximate Bayesian computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re‐colonisation of the current range. Results: We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial c. 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during postglacial re‐colonisation. Main Conclusions: Combining genetic and palaeoecological evidence suggests that P. cembra primarily survived the LGM in ‘cold period’ refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene ‘warm period’ refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographical break in the European Alps also found in herbaceous alpine plant species

The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

Are Women Happier When Their Spouse is Teleworker?

© 2017 Springer Science+Business Media Dordrecht. This study explores the household production allocation and happiness of women when their spouse is teleworker using data from the British Household Panel Survey over the years 1991–2009. The study aims to answer whether the women spend additional time on housework and are happier when they or their partner is teleworker. Also, we explore whether are happier when they share the household–domestic production with their partners. Fixed effects estimates take place, and we consider a Bayesian Network framework and a directed acyclic graph for causal inference. The results show that women are more likely to state that the household allocation, such as cooking, cleaning, ironing and childcare is shared when their partner teleworks. Shopping is an exception which can be regarded as an outdoor activity while one partner may be mainly responsible for this chore. In addition, women are happier when they or their spouse is teleworker, and they report higher levels of happiness when the household production allocation is a shared process. This may indicate men teleworkers may contribute extra to the household production releasing a burden for the partners and improving their well-being

The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available

Between but not within species variation in the distribution of fitness effects

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is therefore of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence and genetic background. We find statistical support for there being variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and that evolutionarily recent events, such as demographic changes and local adaptation, have little impact