Something Old and Something New: Wedding Recombinant Inbred Lines with Traditional Line Cross Analysis Increases Power to Describe Gene Interactions

In this paper we present a novel approach to quantifying genetic architecture that combines recombinant inbred lines (RIL) with line cross analysis (LCA). LCA is a method of quantifying directional genetic effects (i.e. summed effects of all loci) that differentiate two parental lines. Directional genetic effects are thought to be critical components of genetic architecture for the long term response to selection and as a cause of inbreeding depression. LCA typically begins with two inbred parental lines that are crossed to produce several generations such as F1, F2, and backcrosses to each parent. When a RIL population (founded from the same P1 and P2 as was used to found the line cross population) is added to the LCA, the sampling variance of several nonadditive genetic effect estimates is greatly reduced. Specifically, estimates of directional dominance, additive x additive, and dominance x dominance epistatic effects are reduced by 92%, 94%, and 56% respectively. The RIL population can be simultaneously used for QTL identification, thus uncovering the effects of specific loci or genomic regions as elements of genetic architecture. LCA and QTL mapping with RIL provide two qualitatively different measures of genetic architecture with the potential to overcome weaknesses of each approach alone. This approach provides cross-validation of the estimates of additive and additive x additive effects, much smaller confidence intervals on dominance, additive x additive and dominance x dominance estimates, qualitatively different measures of genetic architecture, and the potential when used together to balance the weaknesses of LCA or RIL QTL analyses when used alone

Evolutionary Time for Dispersal Limits the Extent but Not the Occupancy of Species’ Potential Ranges in the Tropical Plant Genus Psychotria (Rubiaceae)

Explaining the diversity in geographic range sizes among species is a central goal of ecological and evolutionary studies. We tested species age as an explanation of range size variation within a group of understory shrubs in the Neotropics (Psychotria subgenus Psychotria, Rubiaceae). We distinguish between range occupancy (filling an occupied area) and range extent (maximum distances dispersed). We used Bayesian relaxed-clock dating of molecular sequence data to estimate the relative age of species, and we used species distribution modeling to predict species\u27 potential ranges. If the range sizes of species are limited by time for dispersal, we hypothesize that older species should have (1) larger realized range occupancies and realized range extents than younger species, (2) filled a greater proportion of their potential range occupancies, and (3) colonized a greater proportion of their potential range extents. We found (1) a significant but weak positive relationship between species age versus both realized range occupancy and realized range extent, (2) no relationship between species age and filling of potential range occupancies, but (3) that older species had colonized a significantly greater proportion of their potential range extents than younger species. Our results indicate that a time-for-dispersal effect can limit the extent of ranges of species but not necessarily their occupancies

Family‐ and population‐level responses to atmospheric CO2 concentration: gas exchange and the allocation of C, N, and biomass in Plantago lanceolata (Plantaginaceae)

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142197/1/ajb21080.pd

Demographic and Genetic Patterns of Variation among Populations of Arabidopsis thaliana from Contrasting Native Environments

Background: Understanding the relationship between environment and genetics requires the integration of knowledge on the demographic behavior of natural populations. However, the demographic performance and genetic composition of Arabidopsis thaliana populations in the species' native environments remain largely uncharacterized. This information, in combination with the advances on the study of gene function, will improve our understanding on the genetic mechanisms underlying adaptive evolution in A. thaliana. Methodology/Principal Findings: We report the extent of environmental, demographic, and genetic variation among 10 A. thaliana populations from Mediterranean (coastal) and Pyrenean (montane) native environments in northeast Spain. Geographic, climatic, landscape, and soil data were compared. Demographic traits, including the dynamics of the soil seed bank and the attributes of aboveground individuals followed over a complete season, were also analyzed. Genetic data based on genome-wide SNP markers were used to describe genetic diversity, differentiation, and structure. Coastal and montane populations significantly differed in terms of environmental, demographic, and genetic characteristics. Montane populations, at higher altitude and farther from the sea, are exposed to colder winters and prolonged spring moisture compared to coastal populations. Montane populations showed stronger secondary seed dormancy, higher seedling/juvenile mortality in winter, and initiated flowering later than coastal populations. Montane and coastal regions were genetically differentiated, montane populations bearing lower genetic diversity than coastal ones. No significant isolation-by-distance pattern and no shared multilocus genotypes among populations were detected. Conclusions/Significance: Between-region variation in climatic patterns can account for differences in demographic traits, such as secondary seed dormancy, plant mortality, and recruitment, between coastal and montane A. thaliana populations. In addition, differences in plant mortality can partly account for differences in the genetic composition of coastal and montane populations. This study shows how the interplay between variation in environmental, demographic, and genetic parameters may operate in natural A. thaliana populations. © 2009 Montesinos et al

Dataset S1

Dataset of literature citations with abstracts included in topic models

Data from: The changing uses of herbarium data in an era of global change: an overview using automated content analysis

Widespread specimen digitization has greatly enhanced the use of herbarium data in scientific research. Publications using herbarium data have increased exponentially over the last century. Here, we review changing uses of herbaria through time with a computational text analysis of 13,702 articles from 1923 to 2017 that quantitatively complements traditional review approaches. Although maintaining its core contribution to taxonomic knowledge, herbarium use has diversified from a few dominant research topics a century ago (e.g., taxonomic notes, botanical history, local observations), with many topics only recently emerging (e.g., biodiversity informatics, global change biology, DNA analyses). Specimens are now appreciated as temporally and spatially extensive sources of genotypic, phenotypic, and biogeographic data. Specimens are increasingly used in ways that influence our ability to steward future biodiversity. As we enter the Anthropocene, herbaria have likewise entered a new era with enhanced scientific, educational, and societal relevance

Source and hybridity indicies and coefficients of directional genetic effects.

<p>Source and hybridity indices and the resulting coefficients for the genetic effects in line cross equations, including all two-way epistatic interactions, after (Lynch and Walsh 1998, Chapter 9). Lines are created by crossing inbred parent 1 (P1) with inbred parent 2 (P2) to produce the F1 and F2 generations as well as reciprocal backcrosses to P1 (B1) and P2 (B2). Recombinant inbred lines (RIL) are formed by repeatedly selfing the F2s. The meaning of the columns: S = proportion of genome from P1; H = proportion of heterozygous loci; θ_S = source index, indicating the relative contributions of P1 and P2 to the generation genome; θ_H = hybridity index, indicating expected heterozygosity of the generation's genome on a scale of 1 to −1. μ = the mean phenotype of the F2 generation. The values in the remaining columns indicate expected contribution of the column's genetic effect to the phenotype of the row's generation. The effect types: A = additive; D = dominance; AA = dominance by dominance interaction; AD = additive by dominance interaction; DD = dominance by dominance interaction.</p

Data from: Developmental instability is genetically correlated with phenotypic plasticity, constraining heritability, and fitness

Although adaptive plasticity would seem always to be favored by selection, it occurs less often than expected. This lack of ubiquity suggests that there must be trade-offs, costs, or limitations associated with plasticity. Yet, few costs have been found. We explore one type of limitation, a correlation between plasticity and developmental instability, and use quantitative genetic theory to show why one should expect a genetic correlation. We test that hypothesis using the Landsberg erecta × Cape Verde Islands recombinant inbred lines (RILs) of Arabidopsis thaliana. RILs were grown at four different nitrogen (N) supply levels that span the range of N availabilities previously documented in North American field populations. We found a significant multivariate relationship between the cross-environment trait plasticity and the within-environment, within-RIL developmental instability across 13 traits. This genetic covariation between plasticity and developmental instability has two costs. First, theory predicts diminished fitness for highly plastic lines under stabilizing selection, because their developmental instability and variance around the optimum phenotype will be greater compared to nonplastic genotypes. Second, empirically the most plastic traits exhibited heritabilities reduced by 57% on average compared to nonplastic traits. This demonstration of potential costs in inclusive fitness and heritability provoke a rethinking of the evolutionary role of plasticity