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Pedigree and phenotypic variables used for estimation of heritability of sand lizard badge size and condition

Sexual selection on fitness-determining traits should theoretically erode genetic variance and lead to low heritability. However, many sexually selected traits maintain significant phenotypic and additive genetic variance, with explanations for this "lek paradox" including genic capture due to condition-dependence, and breaks on directional selection due to environmental sources of variance including maternal effects. Here we investigate genetic and environmental sources of variance in the intrasexually selected green badge of the sand lizard (Lacerta agilis). The badge functions as a cue to male fighting ability in this species, and male-male interactions determine mate acquisition. Using animal models on a pedigree including three generations of males measured over an extensive nine year field study, we partition phenotypic variance in both badge size and body condition into additive genetic, maternal, and permanent environmental effects experienced by an individual over its lifespan. Heritability of badge size was 0.33 with a significant estimate of underlying additive genetic variance. Body condition was strongly environmentally determined in this species and does not show either significant additive genetic variance or heritability. Neither badge size nor body condition were responsive to maternal effects. We propose that the lack of additive genetic variance and heritability of body condition makes it unlikely that genic capture mechanisms maintains additive genetic variance for badge size. That said, genic capture was originally proposed for male traits under female choice, not agonistic selection. If developmental pathways generating variance in body condition, and/or the covarying secondary sex trait, differ between inter- and intrasexual selection, or the rate at which their additive genetic variance or covariance is depleted, future work may show whether genic capture is largely restricted to intersexual selection processes.

Data from: Intra-specific variation in responses to habitat restoration: Could artificial reefs increase spatiotemporal segregation between migratory phenotypes of lake sturgeon?

Habitat restoration is an important tool used to conserve biodiversity and restore species, but its effects are notoriously difficult to predict. Although outcomes of restoration projects are usually assessed using indices of species abundance and diversity, phenotypic differences among individuals within species are likely associated with differing responses to restored habitats. Here, we use lake sturgeon (Acipenser fulvescens) as a case study to illustrate how responses to habitat restoration can differ between phenotypes and potentially lead to unanticipated effects on populations. North America's St. Clair River supports one of the largest remaining populations of lake sturgeon but has lost much spawning habitat due to its role as a major industrial corridor between the Laurentian Great Lakes Erie and Huron. Two artificial reefs were recently built in the lower and middle segments of the river to increase the available sturgeon spawning habitat. Interestingly, lake sturgeon in the St. Clair River express different migratory phenotypes that may be associated with different likelihoods of colonizing artificial reefs. Acoustic telemetry revealed that artificial reefs were more likely to be used by sturgeon that migrated downstream to overwinter in Lake St. Clair than those that migrated upstream to overwinter in Lake Huron. Furthermore, increasing time spent at the artificial reefs by Lake St. Clair migrants was associated with later arrival to and shorter occupancy of the river's only natural spawning site, the primary location where the two phenotypes have opportunity to interbreed. Additional research is necessary to determine the ultimate impacts of the artificial reefs on lake sturgeon populations; nevertheless, our study showed phenotype-specific opportunity to colonize restored habitat and a mechanism through which this could lead to changes in gene flow. Our results illustrate the importance of considering intra-specific diversity when planning restoration projects and assessing the effects on populations.

opencc-by-4.0Mar 2023View details →

Phenotypes for Setaria pan-genome study

This is the 226 phenotypes for foxtail millet GWAS and GS studies. These can be used in gene identification, marker assisted breeding, genomic selection and/or genome editing to accelerate crop improvement under different climatic conditions.

Phenotypic screening using waveform analysis of synchronized calcium oscillations in primary cortical cultures

At present, in vitro phenotypic screening methods are widely used for drug discovery. In the field of epilepsy research, measurements of neuronal activities have been utilized for predicting efficacy of anti-epileptic drugs (AEDs). Fluorescence measurements of calcium oscillations in neurons are commonly used for measurement of neuronal activities, and some anti-epileptic drugs have been evaluated using this assay technique. However, changes in waveforms were not quantified in previous reports. Here, we have developed a high-throughput screening system containing a new analysis method for quantifying waveforms, and our method has successfully enabled simultaneous measurement of calcium oscillations in a 96-well plate. Features of waveforms were extracted automatically and allowed the characterization of some anti-epileptic drugs using principal component analysis. Moreover, we have shown that trajectories in accordance with the concentrations of compounds in principal component analysis plots were unique to the mechanism of anti-epileptic drugs. We believe that an approach that focuses on the features of calcium oscillations will lead to better understanding of the characteristics of existing anti-epileptic drugs and allow prediction of the mechanism of action (MoA) of novel drug candidates.

Data from: Spatiotemporal segregation by migratory phenotype indicates potential for assortative mating in lake sturgeon

Migratory diversity can promote population differentiation if sympatric phenotypes become temporally, spatially, or behaviorally segregated during breeding. In this study, the potential for spatiotemporal segregation was tested among three migratory phenotypes of lake sturgeon (Acipenser fulvescens) that spawn in the St. Clair River of North America's Laurentian Great Lakes but differ in how often they migrate into the river and in which direction they move after spawning. Acoustic telemetry over nine years monitored use of two major spawning sites by lake sturgeon that moved north to overwinter in Lake Huron or south to overwinter in Lake St. Clair. Lake St. Clair migrants were further distinguished by whether they migrated into the St. Clair River each year (annual migrants) or intermittently (intermittent migrants). Social network analyses indicated lake sturgeon generally co-occurred with individuals of the same migratory phenotype more often than with different migratory phenotypes. A direct test for differences in space use revealed one site was almost exclusively visited by Lake St. Clair migrants whereas the other site was visited by Lake Huron migrants, intermittent Lake St. Clair migrants, and, to a lesser extent, annual Lake St. Clair migrants. Analysis of arrival and departure dates indicated an opportunity for co-occurrence at the site visited by all phenotypes but showed Lake Huron migrants arrived approximately two weeks before Lake St. Clair migrants. Taken together, our results indicated partial spatiotemporal segregation of migratory phenotypes that may generate assortative mating and promote population differentiation.

opencc-zeroApr 2023View details →

Phenotypic selection in natural populations: what have we learned in 40 years?

In 1983, Russell Lande and Stevan Arnold published "The measurement of selection on correlated characters," which became a highly influential citation classic in evolutionary biology. This paper stimulated a cottage industry of field studies of natural and sexual selection in nature and resulted in several large-scale meta-analyses, statistical developments and methods papers. The statistical tools in their paper contributed to a breakdown of the traditional dichotomy between ecological and evolutionary time scales and stimulated later developments such as "eco-evolutionary dynamics". However, regression-based selection analyses also became criticized from philosophical, methodological and statistical viewpoints and stimulated some still ongoing debates about causality in evolutionary biology. Here I return to this landmark paper by Lande and Arnold, analyse the controversies and debates it gave rise to and discuss the past, present and future of selection analyses in natural populations. A remaining legacy of Lande and Arnold (1983) is that studies of selection and inheritance can fruitfully be decoupled and be studied separately, since selection acts on phenotypes regardless of their genetic basis, and hence selection and evolutionary responses to selection are distinct processes.

opencc-zeroApr 2023View details →

Sorghum leaf blight phenotypes for two recombinant inbred line populations

Sorghum leaf blight and northern corn leaf blight, both caused by Exserohilum turcicum, are major diseases of sorghum and maize, respectively. Examining the genetic architecture of resistance in sorghum will lead to a better understanding of the relationship between resistance in sorghum and maize, which can ultimately enhance management options in both crops. In 2018 and 2019 we evaluated two sorghum recombinant inbred line (RIL) populations for resistance to E. turcicum. The BTx623 x IS3620C and BTx623 x SC155 populations consisted of 235 and 81 RILs, respectively. Resistance in both populations was moderately to highly heritable. We identified a total of six quantitative trait loci (QTL) across the two populations. Three QTL with small to moderate effect sizes were identified in the BTx623 x IS3620C population. Three QTL, including a large-effect QTL on chromosome three that explained 24% of the variation, were identified in the BTx623 x SC155 population. We compared the identified QTL with the position of northern corn leaf blight candidate genes and found eight candidate resistance gene orthologs that colocalize with the sorghum leaf blight QTL. There were also several nucleotide-binding leucine rich repeat encoding genes within the candidate intervals. Understanding host resistance in multiple species furthers our understanding of the Exserohilum turcicum pathosystem.

opencc-by-4.0Apr 2023View details →

Data for "Bootstrapping outperforms community-weighted approaches for estimating the shapes of phenotypic distributions"

This repository contains datasets used in the manuscript entitled "Bootstrapping outperforms community-weighted approaches for estimating the shapes of phenotypic distributions" by Maitner et al.  For details of these datasets, see https://www.authorea.com/users/244803/articles/523535-on-estimating-the-shape-and-dynamics-of-phenotypic-distributions-in-ecology-and-evolution. All datasets contain individual (and in some cases, organ-level) trait measurements. The dataset "all_traits_unscaled_RMBL.rds" was compiled by  Christine Lamanna, Lindsey L Sloat, Andrew J. Kerkhoff, and Brian J. Enquist, Full details in https://www.authorea.com/users/244803/articles/523535-on-estimating-the-shape-and-dynamics-of-phenotypic-distributions-in-ecology-and-evolution The dataset "Julies_panama_data.xlsx" was compiled by Julie Messier and collaborators, full details here: https://doi.org/10.1111/j.1461-0248.2010.01476.x The dataset "TreefrogTadpoles.xlsx" was compiled by Nick Rasmussen, full details here: https://www.jstor.org/stable/44082203  The dataset "zooplankton_2019.zip" was compiled by Ewa Merz and Francesco Pomati. For more details, see www.aquascope.ch , <a href="https://github.com/mbaityje/plankifier">https://github.com/mbaityje/plankifier</a>, <a href="https://github.com/tooploox/SPCConvert">https://github.com/tooploox/SPCConvert</a>, and https://www.authorea.com/users/244803/articles/523535-on-estimating-the-shape-and-dynamics-of-phenotypic-distributions-in-ecology-and-evolution .

opencc-zeroMay 2023View details →

Data for: Phenotypic outcomes of predator-prey coevolution are predicted by landscape variation in climate and community composition

<ol> <li>Landscape patterns of phenotypic coevolution are determined by variation in the outcome of predator-prey interactions. These outcomes may depend not only on the functional phenotypes that mediate species interactions but also on aspects of the environment that enable encounters between coevolutionary partners.</li> <li>Exploring the relationship between coevolutionary traits and the environment requires extensive sampling across the range of the interaction to determine the relationship between local ecological variation and coevolution.</li> <li>In this study, we synthesized >30 years of data on predator-prey interactions between toxic newts (Taricha granulosa) and their snake predators (Thamnophis sirtalis) to explore the environmental predictors of arms race escalation.</li> <li>We found that geographic variation in phenotypes at the interface of coevolution was best predicted by a combination of community and climatic variation. Coevolutionary phenotypes were greatest in environments with climate favorable for newt-snake overlap. We found prey toxicity was elevated in regions with more predator species, and predator resistance was higher in regions with more prey species.</li> <li>Our results suggest specific environmental conditions reinforce the process of coevolution, signifying the phenotypic outcomes of coevolutionary arms races are sensitive to local ecological contexts that vary across the landscape. </li> </ol>

opencc-by-4.0May 2023View details →

Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes

Data relevant to Wu et al. "Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes".

opencc-zeroMay 2023View details →

Mismatches between phenotype and environment shape fitness at hyperlocal scales (Agama atra)

In the era of human-driven climate change, understanding whether behavioural buffering of temperature change is linked with organismal fitness is essential. According to the "cost-benefit" model of thermoregulation, animals that live in environments with high frequencies of favourable thermal microclimates should incur lower thermoregulatory costs, thermoregulate more efficiently and shunt the associated savings in time and energy towards other vital tasks such as feeding, territory defence, and mate acquisition, increasing fitness. Here, we explore how thermal landscapes at the scale of individual territories, physiological performance, and behaviour interact and shape fitness in the southern rock agama lizard (Agama atra). We integrated laboratory assays of whole organism performance with behavioural observations in the field, fine-scale estimates of environmental temperature, and paternity assignment of offspring to test whether fitness is predicted by territory thermal quality (i.e., the number of hours that operative temperatures in a territory fall within individual's performance breadth). Male lizards that occupied territories of low thermal quality spent more time behaviourally compensating for suboptimal temperatures and displayed less. Further, display rate was positively associated with lizard fitness, suggesting that there is an opportunity cost to engaging in thermoregulatory behaviour that will increase as climate change progresses.

opencc-by-2.0May 2023View details →

Datasets for "The Case for Retaining Natural Language Descriptions of Phenotypes in Plant Databases and a Web Application as Proof of Concept", 2023

The collection of a dataset that organized information about plant genes, phenotypes, and annotations from a variety of data sources

opencc-zeroMay 2023View details →

50 shades of greenbeard: Robust evolution of altruism based on similarity of complex phenotypes

We study the evolution of altruistic behavior under a model where individuals choose to cooperate by comparing a set of continuous phenotype tags. Individuals play a donation game and only donate to other individuals that are sufficiently similar to themselves in a multidimensional phenotype space. We find the generic maintenance of robust altruism when phenotypes are multidimensional. Selection for altruism is driven by the coevolution of individual strategy and phenotype; altruism levels shape the distribution of individuals in phenotype space. Low donation rates induce a phenotype distribution that renders the population vulnerable to the invasion of altruists, whereas high donation rates prime a population for cheater invasion, resulting in cyclic dynamics that maintain substantial levels of altruism. Altruism is therefore robust to invasion by cheaters in the long term in this model. Furthermore, the shape of the phenotype distribution in high phenotype dimension allows altruists to better resist the invasion by cheaters, and as a result, the amount of donation increases with increasing phenotype dimension. We also generalize previous results in the regime of weak selection to two competing strategies in continuous phenotype space, and show that success under weak selection is crucial to success under strong selection in our model. Our results support the viability of a simple similarity-based mechanism for altruism in a well-mixed population.

FIGURE 4 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia

FIGURE 4. An unrooted Neighbor Joining tree of Lake Tana Labeobarbus species constructed by APE (an R-package) using pair-wise genetic distances among individuals based on analysis of 10 microsatellite loci. Bootstrap percentage values shown at nodes are from 100 pseudo-replicates and indicate the level of support for each group; only bootstrap values higher than 50% are indicated.

FIGURE 3 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia

FIGURE 3. Scatter plot from Discriminant analysis of Principal Components (DPC; Jombart et al. 2010) of microsatellite data from 161 Lake Tana Labeobarbus individuals. The 95% confidence ellipses of each group based on the common covariance matrix assumption for the multivariate normal distribution are presented. Points represent individual genotypes and symbols represent species (A) or spawning populations (B). A. Using species as grouping factor with asterisks representing the estimated means for each population: Pop A = L. acutirostris, Pop B = L. brevicephalus, Pop C = L. crassibarbus, Pop D = L. gorgorensis, Pop E = L. gorguari, Pop F = L. intermedius, Pop G = L. longissimus, Pop H = L. macrophtalmus, Pop I = L. megastoma, Pop J = L. nedgia, Pop K = L. platydorsus, Pop L = L. surkis, Pop M = L. tsanensis, Pop N = L. truttiformis. B. Using spawning strategy as grouping criteria: ▲riverine spawning population, ●lacustrine spawning population.

FIGURE 2 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia

FIGURE 2. Bayesian clustering assignment of individuals based on Structure analysis of 10 microsatellite loci of Labeobarbus populations from Lake Tana and adjacent water bodies. A. Analysis of whole dataset without a priori population definitions (K=1–15). B. Lake Tana Labeobarbus populations only with K = 2 inferred clusters. 1. L. acitirostris, 2. L. brevicephalus, 3. L. crassibarbus, 4. L. gorgorensis, 5. L. gorguari, 6. L. longissimus, 7. L. macrophtalmus, 8. L. megastoma, 9. L. nedgia, 10. L. platydorsus, 11. L. surkis, 12. L. truttiformis, 13. L. tsanensis, 14. L. intermedius, 15. L. beso.

FIGURE 1. A in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia

FIGURE 1. A. Map showing major river drainages of Ethiopia; B. Map of Lake Tana. All samples of Lake Tana were drawn from sites (area lying within the red rectangle) located in the Bahir Dar Gulf.

opennotspecifiedMay 2023View details →

Fig. 1 Vitis arizonica sampling and phenotypes. A in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 1 Vitis arizonica sampling and phenotypes. A map of the Southwestern United States and Northern Mexico indicates sampling locations of the n = 167 V. arizonica accessions used in this study. The color of sample locations (circles) are colored according to their resistance phenotype, as measured by bacterial load (CFU/mL). The histogram of phenotypes (in CFU/mL) is to the right of the map. Map generation relied on information from GADM, a publicly available database (http:gadm.org).

opencc-by-4.0Jun 2023View details →

Dataset: Bridging Time-series Image Phenotyping and Functional-Structural Plant Modeling to Predict Adventitious Root System Architecture

Dataset for Bridging Time-series Image Phenotyping and Functional-Structural Plant Modeling to Predict Adventitious Root System Architecture manuscript submitted to Plant Phenomics. The dataset contains raw and processed root architecture images, RhizoVision trait outputs, and the associated R scripts for statistical analysis and model parameterization.