3,803 research outputs found
Ancient tree genomes for old questions
No full textMost foundational work on the evolution and migration of plant species relies on genomic data from contemporary samples. Ancient plant samples can give us access to allele sequences and distributions on the landscape dating back to the mid Holocene or earlier (Gugerli et al., 2005). Nuclear DNA from ancient wood, however, has been mostly inaccessible until now. In a From the Cover article in this issue of
Molecular Ecology
, Wagner et al. (2023) present the first resequenced nuclear genomes from ancient oak wood, including two samples dated to the 15th century and one that dates to more than 3500 years ago. These ancient tree genomes open the possibility for investigating species adaptation, migration, divergence, and hybridisation in the deep past. They pave the way for what we hope will be a new era in the use of paleogenomics to study Holocene tree histories.Division of Environmental Biology https://doi.org/10.13039/10000015
Sharing of chloroplast haplotypes among red oak species suggests interspecific gene flow between neighboring populations
No full textThe North American red oak speciesThe accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author
Use of Genomic Resources to Assess Adaptive Divergence and Introgression in Oaks
No full textAdaptive divergence is widely accepted as a contributor to speciation and the maintenance of species integrity. However, the mechanisms leading to reproductive isolation, the genes involved in adaptive divergence, and the traits that shape the adaptation of wild species to changes in climate are still largely unknown. In studying the role of ecological interactions and environment-driven selection, trees have emerged as potential model organisms because of their longevity and large genetic diversity, especially in natural habitats. Due to recurrent gene flow among species with different ecological preferences, oaks arose as early as the 1970s as a model for understanding how speciation can occur in the face of interspecific gene flow, and what we mean by “species” when geographically and genomically heterogeneous introgression seems to undermine species’ genetic coherence. In this review, we provide an overview of recent research into the genomic underpinnings of adaptive divergence and maintenance of species integrity in oaks in the face of gene flow. We review genomic and analytical tools instrumental to better understanding mechanisms leading to reproductive isolation and environment-driven adaptive introgression in oaks. We review evidence that oak species are genomically coherent entities, focusing on sympatric populations with ongoing gene flow, and discuss evidence for and hypotheses regarding genetic mechanisms linking adaptive divergence and reproductive isolation. As the evolution of drought- and freezing-tolerance have been key to the parallel diversification of oaks, we investigate the question of whether the same or a similar set of genes are involved in adaptive divergence for drought and stress tolerance across different taxa and sections. Finally, we propose potential future research directions on the role of hybridization and adaptive introgression in adaptation to climate change
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Rcode_Pearse_Hipp_2014
No full textcode (R programming language) for analyses in Pearse & Hipp 2014. Some data on site-level characteristics within code
Effective shear speed in two-dimensional phononic crystals
No full textThe quasistatic limit of the antiplane shear-wave speed ('effective speed') c in 2D periodic lattices is studied. Two new closed-form estimates of c are derived by employing two different analytical approaches. The first proceeds from a standard background of the plane wave expansion (PWE). The second is a new approach, which resides in x-space and centers on the monodromy matrix (MM) introduced in the 2D case as the multiplicative integral, taken in one coordinate, of a matrix with components being the operators with respect to the other coordinate. On the numerical side, an efficient PWE-based scheme for computing c is proposed and implemented. The analytical and numerical findings are applied to several examples of 2D square lattices with two and three high contrast components, for which the new PWE and MM estimates are compared with the numerical data and with some known approximations. It is demonstrated that the PWE estimate is most efficient in the case of densely packed stiff inclusions, especially when they form a symmetric lattice, while in general it is the MM estimate that provides the best overall fitting accuracy.Peer reviewe
best_quercus_phylogeny
No full textA supertree of oaks (Quercus and Notholithocarpus). The backbone of the phylogeny was a published AFLP phylogeny (Pearse & Hipp 2009). Oak species were placed on the phylogeny based on various evidence (listed in Table S1)
Oak morphology dataset from Iturrarán Botanical Garden and supplementary files.
No full text<p>Files in this folder include raw data as well as supplementary files corresponding to the paper: "Oak leaf morphology may be more strongly shaped by climate than by phylogeny" Rubén Martín-Sánchez, Domingo Sancho-Knapik, David Alonso-Forn, Ana López-Ballesteros, Juan Pedro Ferrio, Andrew L. Hipp, José Javier Peguero-Pina, Eustaquio Gil-Pelegrín. Annals of Forest Science. 2024. https://doi.org/10.1186/s13595-024-01232-z</p>
<p>In addition, you can also find the five supplementary tables generated for the same paper. </p>
<p>Corresponding author: Rubén Martín Sánchez ([email protected])</p>
<p>-Morphological data.xlsx: Mean values of each species for the four quantitative traits (LA, LW, ILB and LMA) and the five qualitative traits (Leaf Habit, Pubescence, Shape, Apex, Margin) LA: Leaf Area, expressed in cm2. LW: Lenght-Width ratio, dimensionless. ILB: Index of Lobulation, expressed as (Perimeter/square root of Area), dimensionless. LMA: dry Leaf Mass per Area, expresed as (dry weight/leaf area), expressed in g/m2. Leaf Habit: Deciduous or Evergreen Pubescence: Glabrous, Pubescent or Densely Pubescent Shape: Elliptic, Obovate, Oblong, Lanceolate, Ovate or Circular. Apex: Acute, Acuminate, Rounded or Straight Margin: Entire, Lobated, Serrate, Dentate, Undulate, Spinose or Crenate.</p>
<p>-Climatic data.csv: Average Worldclim variables for each species used in the climatic PCA. See https://www.worldclim.org/data/bioclim.html for further details. "bio20" was calculated ex profeso for the paper as a result of BIO16 minus BIO17.</p>
<p>-Supplementary Tables.xlsx: Supplementary material containing the five supplementary tables for the main manuscript.</p>
alternate_quercus_phylogenies
No full textAlternate Quercus phylogenies that either collapse species relationships to polytomies within established clades, force even branching times, or move the placement of the old world white oaks, based on recent phylogenetic treatments (Hipp et al 2014). Multiple Newick tree files. Descriptions of which file is which phylogeny can be found in the R code
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