Discerning Oriental from European beech by leaf spectroscopy: Operational and physiological implications

European beech (Fagus sylvatica L.) forests have recently experienced severe diebacks that are expected to increase in future. Oriental beech (Fagus sylvatica spp. orientalis (Lipsky) Greut. & Burd) is a potential candidate for assisted migration (AM) in European forests due to its greater genetic diversity and potentially higher drought resistance. Yet AM entails not only benefits, but also risks, and it is therefore important to monitor the progression of introduced (sub)species. Here, we demonstrate the potential of leaf spectroscopy to replace resourceintensive genetic analysis and field phenotyping for the discrimination and characterization of these two beech subspecies. We studied two European beech forests, one in France and one in Switzerland, where Oriental beech from the Greater Caucasus was introduced over 100 years ago. During two summers (2021, 2022), we measured leaf spectral reflectance, leaf morphological and biochemical traits from genotyped adult trees. Subspecies prediction models were developed separately for top-of-canopy leaves (amenable to remote sensing) and bottom-of-canopy leaves (easier to harvest) using partial least squares discriminant analysis (PLS-DA) and different sets of spectral predictors. Morphological, biochemical and spectra-derived leaf traits indicated that Oriental beech trees at the sites studied were characterized by higher lignin and nitrogen per unit leaf area than European beech, suggesting more protein-rich leaves on a per-area basis. The model based on top-of-canopy leaf reflectance spectra in the short-wave-infrared region (SWIR I: 1450–1750 nm) most accurately distinguished Oriental from European beech (BA = 0.86 ± 0.08, k = 0.72 ± 0.15), closely followed by models based on SWIR II, and on spectra-derived traits (BA ≥ 0.84, k ≥ 0.67). This study provides a proof-of-principle for the development of spectroscopy-based approaches when monitoring introduced species, subspecies or provenances. Our findings hold promise for upscaling to large forest areas using airborne remote sensing

Contrasting signatures of genomic divergence during sympatric speciation

Population genomic analyses of Midas cichlid fishes in young Nicaraguan crater lakes suggest that sympatric speciation is promoted by polygenic architectures. The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin(1,2). Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process(3). Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs(4), but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories(5). Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.Peer reviewe

Discerning Oriental from European beech by leaf spectroscopy : operational and physiological implications

European beech (Fagus sylvatica L.) forests have recently experienced severe diebacks that are expected to increase in future. Oriental beech (Fagus sylvatica spp. orientalis (Lipsky) Greut. & Burd) is a potential candidate for assisted migration (AM) in European forests due to its greater genetic diversity and potentially higher drought resistance. Yet AM entails not only benefits, but also risks, and it is therefore important to monitor the progression of introduced (sub)species. Here, we demonstrate the potential of leaf spectroscopy to replace resource-intensive genetic analysis and field phenotyping for the discrimination and characterization of these two beech subspecies. We studied two European beech forests, one in France and one in Switzerland, where Oriental beech from the Greater Caucasus was introduced over 100 years ago. During two summers (2021, 2022), we measured leaf spectral reflectance, leaf morphological and biochemical traits from genotyped adult trees. Subspecies prediction models were developed separately for top-of-canopy leaves (amenable to remote sensing) and bottom-of-canopy leaves (easier to harvest) using partial least squares discriminant analysis (PLS-DA) and different sets of spectral predictors. Morphological, biochemical and spectra-derived leaf traits indicated that Oriental beech trees at the sites studied were characterized by higher lignin and nitrogen per unit leaf area than European beech, suggesting more protein-rich leaves on a per-area basis. The model based on top-of-canopy leaf reflectance spectra in the short-wave-infrared region (SWIR I: 1450–1750 nm) most accurately distinguished Oriental from European beech (BA = 0.86 ± 0.08, k = 0.72 ± 0.15), closely followed by models based on SWIR II, and on spectra-derived traits (BA ≥ 0.84, k ≥ 0.67). This study provides a proof-of-principle for the development of spectroscopy-based approaches when monitoring introduced species, subspecies or provenances. Our findings hold promise for upscaling to large forest areas using airborne remote sensing

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Disambiguation of Researcher Careers: Shifting the Perspective from Documents to Authors

The thesis describes an algorithm that disambiguates the namespaces of inventors and researchers, spawned by their patents and publications, into career paths. A probabilistic theory to assess the risk of erroneously linking documents of namesakes, different individuals with a mutual name, into one career bypasses the need for training datasets, thereby avoiding a namesake bias caused by the inherent underestimation of namesakes in training/benchmark data. The economic relevance of identified careers is illustrated by two applications. The first one outlines the impact of inter-regional inventor mobility in Italy on the total factor productivity of the sending and receiving regions. We show that an inflow of high skilled labor has a significant positive effect on TFP, while outflow decreases it. We further separate mobility in firm-internal relocation and job switches to find a more pronounced effect for the latter mobility. The second application observes the reaction of German university researchers to an exogenous change in federal law pertaining the property rights of their inventions equivalent to the Bayh Dole Act. Being able to trace their careers along with the careers of an unaffected control group allows us to evaluate the efficacy of technology transfer offices replacing the former informal activities of the university professors in regard of academic entrepreneurship. We find that an overall decrease of university patenting neutralizes any institutionalized efforts of spurring entrepreneurship at the expense of informal faculty-firm networks as channels for knowledge transfer

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Reading the biomineralized book of life: expanding otolith biogeochemical research and applications for fisheries and ecosystem-based management

Chemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle responses to environmental stressors, linking these to ecological, physiological, and life-history processes. Here, we review emerging approaches and innovative research directions in otolith chemistry, as well as in the chemistry of other archival tissues, outlining their value for fisheries and ecosystem-based management, turning the spotlight on areas where such biomarkers can support decision making. We summarise recent milestones and the challenges that lie ahead to using otoliths and archival tissues as biomarkers, grouped into seven, rapidly expanding and application-oriented research areas that apply chemical analysis in a variety of contexts, namely: (1) supporting fish age estimation; (2) evaluating environmental stress, ecophysiology and individual performance; (3) confirming seafood provenance; (4) resolving connectivity and movement pathways; (5) characterising food webs and trophic interactions; (6) reconstructing reproductive life histories; and (7) tracing stock enhancement efforts. Emerging research directions that apply hard part chemistry to combat seafood fraud, quantify past food webs, as well as to reconcile growth, movement, thermal, metabolic, stress and reproductive life-histories provide opportunities to examine how harvesting and global change impact fish health and fisheries productivity. Ultimately, improved appreciation of the many practical benefits of archival tissue chemistry to fisheries and ecosystem-based management will support their increased implementation into routine monitoring.[GRAPHICS]

Statistical Population Genomics

This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions

Genomics of adaptation revealed in threespine stickleback

Natural selection is the ultimate, but not only force underlying organismal diversity. Despite this general biological insight, our understanding of how selection targets and shapes the genome during adaptation remains incomplete and is the central quest of this thesis. My main model organism is the threespine stickleback fish (Gasterosteus aculeatus). Stickleback provide an outstanding opportunity to study adaptive evolutionary change, because marine ancestors have repeatedly colonized and adapted to different freshwater environments all over the northern hemisphere since the last glacial retreat about 12,000 years ago. Besides wild populations, I also make use of lab-raised stickleback hybrids from controlled crosses for this thesis work. Thousands of genome-wide genetic polymorphisms (i.e., genetic markers) called in marine, but predominantly in distinct lake and stream stickleback populations from different geographic locations allow me to decipher the number and position of genomic targets of selection in the early phase of adaptive divergence. I find that selection acts on many loci distributed widely across the genome. On a genomic scale, the recombination landscape along chromosomes proves to be - in concert with selection - an important factor in driving heterogeneous genetic differentiation among populations. To investigate the rate of recombination across the stickleback's genome in more detail, I use an artificially crossed second-generation (F2) population. This reveals constraints in the frequency and location of detectable recombination events (i.e., cross-overs) within the genome. For example, cross-overs prove to be more frequent in chromosome peripheries than centers. This, together with selection, results in decreased within-population genetic diversity and increased between-population differentiation in the centers of chromosomes as opposed to the peripheries. Furthermore, I show that the cessation of recombination between the heterogametic sex chromosomes occurred in independent bouts. As a consequence, I find extended genomic regions distinct in their degree of degeneration between the X and Y chromosome, so called evolutionary strata. Finally, recombination reveals to be an important determinant of other aspects of a genome, such as its nucleotide composition. Integrating theoretical modeling with targeted and genome-wide sequencing, my research further demonstrates that the inference and interpretation of genomic regions exhibiting particularly high and low population differentiation is not as straightforward as commonly believed. This is because the type of genetic variation available to selection (i.e., pre-existing vs. de novo variation) as well as the mode of adaptation (i.e., divergent vs. parallel adaptation) influence the way neutral variation is shaped by selection across the genome. I demonstrate that a genomic region of high differentiation may not necessarily be indicative of divergent selection when populations adapt in parallel to similar environments from a shared pool of genetic variation. Based on several hundreds of F2 specimens reared under standardized conditions in the laboratory, I also link variation in heritable phenotypic traits to genetic variation, a research program generally referred to as quantitative trait locus (QTL) mapping. Corroborating with the results from my genome scans within and between wild populations (indicating that adaptive divergence involves many loci widespread across the genome), QTL mapping reveals that most phenotypic traits are controlled by numerous genetic loci. In general, each of these loci explains a small fraction of the entire phenotypic trait variation. I also use high resolution SNP data to infer the demographic history of several lake and stream stickleback populations from the Lake Constance watershed (Central Europe) and demonstrate that the repeated occurrence of similar stream phenotypes are, in this particular system, better explained by an evolutionary scenario of 'ecological vicariance' rather than repeated parallel divergence. I then show how selection has shaped local and broad-scale linkage, diversity and differentiation across the genome in these populations. Interestingly, I find evidence for strong divergent selection acting on large chromosomal rearrangements I had previously detected to be important for marine vs. freshwater adaptation. This finding provides a strong case for the re-use of pre-existing genetic variation in stickleback and demonstrates that the same genomic regions can be involved in adaptive divergence between disparate ecotype pairs. Overall, I come to conclude that signatures of selection are - at various physical scales - frequent within the stickleback genome. Stickleback repeatedly use pre-existing genetic variation, shared across various geographic ranges, to adapt to similar or disparate environments. Yet, there is a substantial degree of genetic non-parallelism - at least at the level of neutral markers - that goes along with parallel phenotypic evolution. My thesis emphasizes that the reliable detection and interpretation of genomic signatures of selection requires integrating many replicate study populations within a clear-cut ecological and demographic framework, as well as complementary analytical approaches. Controlled crossing experiments and theoretical modeling are key to deriving predictions about the genomics of adaptation in the wild and to facilitate our understanding of complex biological processes and patterns