Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers

Population genetic studies provide insights into the evolutionary processes that influence the distribution of sequence variants within and among wild populations. FST is among the most widely used measures for genetic differentiation and plays a central role in ecological and evolutionary genetic studies. It is commonly thought that large sample sizes are required in order to precisely infer FST and that small sample sizes lead to overestimation of genetic differentiation. Until recently, studies in ecological model organisms incorporated a limited number of genetic markers, but since the emergence of next generation sequencing, the panel size of genetic markers available even in non-reference organisms has rapidly increased. In this study we examine whether a large number of genetic markers can substitute for small sample sizes when estimating FST. We tested the behavior of three different estimators that infer FST and that are commonly used in population genetic studies. By simulating populations, we assessed the effects of sample size and the number of markers on the various estimates of genetic differentiation. Furthermore, we tested the effect of ascertainment bias on these estimates. We show that the population sample size can be significantly reduced (as small as n = 4–6) when using an appropriate estimator and a large number of bi-allelic genetic markers (k.1,000). Therefore, conservation genetic studies can now obtain almost the same statistical power as studies performed on model organisms using markers developed with next-generation sequencing

ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata

<p>Abstract</p> <p>Background</p> <p>The guppy, <it>Poecilia reticulata</it>, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available.</p> <p>Results</p> <p>With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes.</p> <p>Conclusion</p> <p>Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.</p

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

This document is the Accepted Manuscript version, made available in accordance to Springer Nature Terms of reuse of archived manuscripts.Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 .Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.Peer reviewe

Populationsgenomik der nächsten Generation im Guppy (Poecilia reticulata)

Population genetic studies estimate allele frequency distributions and the change of these frequencies over time in order to infer the demographic history of natural populations. Such studies aim to explain how adaptation and speciation have occurred. Until recently, inferences in non-reference taxa have been based on very few loci due to the high cost of developing a large set of markers de-novo. Only in established model organisms with a known reference genome was it possible to study genome-wide patterns of sequence variation. However, the advent of Next Generation Sequencing (NGS) technologies has revolutionized the field of whole genome research, and facilitated the development of genome-wide genetic markers. The guppy (Poecilia reticulata) is an important model organism in ecological genetics. Adaptation of guppies to contrasting upland and lowland habitats has been extensively studied with respect to behavior, morphology and life history. Guppy populations are able to adapt rapidly to new environments, presumably due to their high level of standing natural variation. However, it was previously not possible to deduce a genome-wide picture of genetic variability and to scan for the causative genomic regions under selection. In this thesis, I will describe our efforts to move from population genetics to population genomics in the guppy. This was achieved by first using a genome-wide set of genetically mapped single nucleotide polymorphism (SNP) markers for the analysis of population history and then, for the first time, to check for regions under selection in the guppy genome. By simulating populations, I assessed the effects of sample size and marker number on the various estimates of genetic differentiation. I will show how NGS can be used to identify genes in genomic regions of interest without an available reference genome and, finally, I will describe how restriction associated DNA sequencing (RAD-seq) facilitates the development of genome wide SNP markers in the guppy.Populationsgenetische Studien beschreiben die Verteilung von Allelfrequenzen mit dem Ziel, deren Veränderung über die Zeit abzuleiten, woraus wiederum auf den demographischen Werdegang natürlicher Populationen rückgeschlossen werden kann. Darüber hinaus versuchen sie das Phänomen der Adaptation und der Artenbildung zu erklären. Bis vor kurzem basierten Studien in Nicht-Referenzorganismen auf nur wenigen genotypisierten Loci, da die Neuentwicklung einer großen Anzahl von Markern sehr kostspielig war und darum außerhalb der Möglichkeiten der meisten Forschungsprojekte lag. Bisher waren nur in etablierten Modelorganismen mit bekanntem Referenzgenom „populationsgenomische“ Studien, die das genomweite Muster von Sequenzvariationen innerhalb und zwischen nahverwandten Populationen und Spezies untersuchen, möglich. Die Verfügbarkeit von neuen Sequenziertechnologien der nächsten Generation (NGS) hat nicht nur grosse Fortschritte in der Genomforschung ermöglicht, sondern auch die Entwicklung genomweiter Marker erleichtert. Der Guppy (Poecilia reticulata) ist ein wichtiger Modelorganismus in der ökologischen Genetik. Die Anpassung von Guppies in Hinblick auf Verhalten, Morphologie und Lebensweg in gegensätzlichen oberen und unteren Flussläufen wurde ausführlich untersucht. Guppies sind in der Lage sich schnell an eine neue Umgebung anzupassen, was vermutlich an der hohen natürlichen Variation liegt. Bisher war es unmöglich genomweite Analysen genetischer Variabilität durchzuführen oder nach Regionen im Genom, die einen Selektionsvorteil aufweisen, zu suchen. Diese Arbeit beschreibt den Übergang von Populationsgenetik zu Poplationgenomik im Guppy. Zuerst untersuchen wir die Populationsstruktur in einer Auswahl natürlicher Populationen und suchen zum ersten Mal nach Regionen mit Selektionsvorteil mittels eines genomweiten Satzes von genetisch kartierten Single Nukleotid Polymorphismus (SNP) Markern. Durch die Simulation von Populationen konnte ich abschätzen welchen Einfluss die Stichprobengröße einer Population und die Anzahl der Marker auf unterschiedliche Schätzer von genetischer Differenzierung haben. Ich demonstriere wie NGS genutzt werden kann, um die Gene in Regionen von Interesse, auch ohne Referenzgenom, zu identifizieren und am Ende zeige ich wie Sequenzierung von DNA Abschnitten neben Restriktionsschnittstellen (RAD-seq) die genomweite Entwicklung von SNP Markern im Guppy ermöglicht

Reasons for the invasive success of a guppy (Poecilia reticulata) population in Trinidad

The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype.Publisher PDFPeer reviewe

Estimated F_ST values changed allele frequency distributions, n = 50, k = 1000.

<p>Estimated F_ST values changed allele frequency distributions, n = 50, k = 1000.</p

Effect of increasing the number of markers.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042649#s2" target="_blank">Results</a> are shown for the simulations where allele frequencies were equally distributed from 0.05 to 0.95. The number of individuals was fixed at n = 4 (left column) and n = 20 (right column). Each row contains (like in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042649#pone-0042649-g001" target="_blank">Figure 1</a>) a different level of genetic differentiation (F_ST = 0, 0.01, 0.05, 0.1, 0.2, 0.4). The results (average F_ST and 95% CI) of each estimator are depicted in the different graphs: F_ST^W (blue circles), F_ST^C&W (purple squares) and F_ST^R (green triangles). The dashed red line indicates the actual F_ST for the simulated population.</p