Uncovering cryptic asexuality in Daphnia magna by RAD sequencing

The breeding systems of many organisms are cryptic and difficult to investigate with observational data, yet they have profound effects on a species’ ecology, evolution, and genome organization. Genomic approaches offer a novel, indirect way to investigate breeding systems, specifically by studying the transmission of genetic information from parents to offspring. Here we exemplify this method through an assessment of self-fertilization vs. automictic parthenogenesis in Daphnia magna. Self-fertilization reduces heterozygosity by 50% compared to the parents, but under automixis, whereby two haploid products from a single meiosis fuse, the expected heterozygosity reduction depends on whether the two meiotic products are separated during meiosis I or II (i.e., central vs. terminal fusion). Reviewing the existing literature and incorporating recombination interference, we derive an interchromosomal and an intrachromosomal prediction of how to distinguish various forms of automixis from self-fertilization using offspring heterozygosity data. We then test these predictions using RAD-sequencing data on presumed automictic diapause offspring of so-called nonmale producing strains and compare them with “self-fertilized” offspring produced by within-clone mating. The results unequivocally show that these offspring were produced by automixis, mostly, but not exclusively, through terminal fusion. However, the results also show that this conclusion was only possible owing to genome-wide heterozygosity data, with phenotypic data as well as data from microsatellite markers yielding inconclusive or even misleading results. Our study thus demonstrates how to use the power of genomic approaches for elucidating breeding systems, and it provides the first demonstration of automictic parthenogenesis in Daphnia

Effects of environmental Bisphenol A exposures on germ cell development and Leydig cell function in the human fetal testis

<div><p>Background</p><p>Using an organotypic culture system termed human Fetal Testis Assay (hFeTA) we previously showed that 0.01 μM BPA decreases basal, but not LH-stimulated, testosterone secreted by the first trimester human fetal testis. The present study was conducted to determine the potential for a long-term antiandrogenic effect of BPA using a xenograft model, and also to study the effect of BPA on germ cell development using both the hFETA and xenograft models.</p><p>Methods</p><p>Using the hFeTA system, first trimester testes were cultured for 3 days with 0.01 to 10 μM BPA. For xenografts, adult castrate male nude mice were injected with hCG and grafted with first trimester testes. Host mice received 10 μM BPA (~ 500 μg/kg/day) in their drinking water for 5 weeks. Plasma levels of total and unconjugated BPA were 0.10 μM and 0.038 μM respectively. Mice grafted with second trimester testes received 0.5 and 50 μg/kg/day BPA by oral gavage for 5 weeks.</p><p>Results</p><p>With first trimester human testes, using the hFeTA model, 10 μM BPA increased germ cell apoptosis. In xenografts, germ cell density was also reduced by BPA exposure. Importantly, BPA exposure significantly decreased the percentage of germ cells expressing the pluripotency marker AP-2γ, whilst the percentage of those expressing the pre-spermatogonial marker MAGE-A4 significantly increased. BPA exposure did not affect hCG-stimulated androgen production in first and second trimester xenografts as evaluated by both plasma testosterone level and seminal vesicle weight in host mice.</p><p>Conclusions</p><p>Exposure to BPA at environmentally relevant concentrations impairs germ cell development in first trimester human fetal testis, whilst gonadotrophin-stimulated testosterone production was unaffected in both first and second trimester testis. Studies using first trimester human fetal testis demonstrate the complementarity of the FeTA and xenograft models for determining the respective short-term and long term effects of environmental exposures.</p></div

Complexity vs linearity: relations between functional traits in a heterotrophic protist

Abstract Background Functional traits are phenotypic traits that affect an organism’s performance and shape ecosystem-level processes. The main challenge when using functional traits to quantify biodiversity is to choose which ones to measure since effort and money are limited. As one way of dealing with this, Hodgson et al. (Oikos 85:282, 1999) introduced the idea of two types of traits, with soft traits that are easy and quick to quantify, and hard traits that are directly linked to ecosystem functioning but difficult to measure. If a link exists between the two types of traits, then one could use soft traits as a proxy for hard traits for a quick but meaningful assessment of biodiversity. However, this framework is based on two assumptions: (1) hard and soft traits must be tightly connected to allow reliable prediction of one using the other; (2) the relationship between traits must be monotonic and linear to be detected by the most common statistical techniques (e.g. linear model, PCA). Results Here we addressed those two assumptions by focusing on six functional traits of the protist species Tetrahymena thermophila, which vary both in their measurement difficulty and functional meaningfulness. They were classified as: easy traits (morphological traits), intermediate traits (movement traits) and hard traits (oxygen consumption and population growth rate). We detected a high number (> 60%) of non-linear relations between the traits, which can explain the low number of significant relations found using linear models and PCA analysis. Overall, these analyses did not detect any relationship strong enough to predict one trait using another, but that does not imply there are none. Conclusions Our results highlighted the need to critically assess the relations among the functional traits used as proxies and those functional traits which they aim to reflect. A thorough assessment of whether such relations exist across species and communities is a necessary next step to evaluate whether it is possible to take a shortcut in quantifying functional diversity by collecting the data on easily measurable traits

No evidence for large differences in genomic methylation between wild and hatchery steelhead (Oncorhynchus mykiss)

When salmonid fish that have been raised in hatcheries spawn in the wild, they often produce fewer surviving adult offspring than wild fish. Recent data from steelhead (Oncorhynchus mykiss) in the Hood River (Oregon, USA) show that even one or two generations of hatchery culture can result in dramatic declines in fitness. Although intense domestication selection could cause such declines, it is worth considering alternative explanations. One possibility is heritable epigenetic changes induced by the hatchery environment. Here, we show, using methylation-sensitive amplified fragment length polymorphism, that hatchery and wild adult steelhead from the Hood River do not appear to differ substantially in overall levels of genomic methylation. Thus, although altered methylation of specific DNA sites or other epigenetic processes could still be important, the hatchery environment does not appear to cause a global hypo- or hypermethylation of the genome or create a large number of sites that are differentially methylated

A multidimensional approach to the expression of phenotypic plasticity

Phenotypic plasticity is increasingly recognized as a key element of eco‐evolutionary dynamics, but it remains challenging to assess because of its multidimensional nature. Indeed, organisms live in complex environments where numerous factors can impact the phenotypic expression of traits (inter‐environment axis), possess multiple traits that can influence each other's expression (inter‐trait axis) and differ in their genetic background (inter‐genotype axis), which can not only impact the traits' values but also their plasticity. We addressed six questions related to phenotypic plasticity: (a) do different environmental gradients show similar effects on a given trait? (b) Are the effects of two environmental gradients on a trait additive? (c) Do different traits show similar plastic response to a given environmental gradient? (d) Do the (co)variances between traits vary across environmental gradients? (e) Do genotypes differ in their plastic response to a given environmental gradient? (f) Are some genotypes more plastic than others across all traits? We designed a microcosm experiment using the protist Tetrahymena thermophila aimed at encompassing all these aspects of phenotypic plasticity. We exposed 15 distinct genotypes to 25 combinations of temperature and nutrient availability and assessed the plasticity of five phenotypic traits. Our results show strong differences in the plastic response depending on the environmental gradient, not only regarding the shape of the reaction norm of the different traits tested, but also in the overall plasticity of the organisms. We did not find any covariance between traits that was consistent across all environments. Overall, our results suggest independent impacts of the environmental dimension considered on the observed plastic response. These results underline potential difficulties in generalizing findings about plasticity to all environments and all traits

Sensitivity of tropical stratospheric ozone to short term solar variability

International audienceSolar variability. Solar influences on climate. The solar UV/ozone relatio

Transition from Environmental to Partial Genetic Sex Determination in Daphnia through the Evolution of a Female-Determining Incipient W Chromosome

Sex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species of Daphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, including transformer2 and sox9. Taken together, the region determining the genetic females shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes. D. magna is a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution

Dynamic transcriptomic analysis of ischemic injury in a porcine pre-clinical model mimicking donors deceased after circulatory death

Due to organ shortage, clinicians are prone to consider alternative type of organ donors among them donors deceased after circulatory death (DCD). However, especially using these organs which are more prone to graft dysfunction, there is a need to better understand mechanistic events ocuring during ischemia phase and leading to ischemia/reperfusion injuries (IRI). The aim of this study is to provide a dynamic transcriptomic analysis of preclinical porcine model kidneys subjected to ischemic stress mimicking DCD donor. We compared cortex and corticomedullary junction (CMJ) tissues from porcine kidneys submitted to 60 min warm ischemia (WI) followed by 0, 6 or 24 hours of cold storage in University of Wisconsin solution versus control non-ischemic kidneys (n=5 per group). 29 cortex genes and 113 CMJ genes were significantly up or down-regulated after WI versus healthy kidneys, and up to 400 genes were regulated after WI followed by 6 or 24 hours of cold storage (p < 0.05). Functionnal enrichment analysis (home selected gene kinetic classification, Gene-ontology-biological processes and Gene-ontology-molecular-function) revealed relevant genes implication during WI and cold storage. We uncovered targets which we will further validate as biomarkers and new therapeutic targets to optimize graft kidney quality before transplantation and improve whole transplantation outcome