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Valérie Ducret, Michael Schaub, Jérôme Goudet, Alexandre Roulin
Non-random gene flow is a widely neglected force in evolution and ecology. This genotype-dependent dispersal is difficult to assess, yet can impact the genetic variation of natural populations and their fitness. In this work, we demonstrate a high immigration rate of barn owls (Tyto alba) inside a Swiss population surveyed during 15 years. Using ten microsatellite loci as an indirect method to characterize dispersal, two-third of the genetic tests failed to detect a female-biased dispersal, and Monte Carlo simulations confirmed a low statistical power to detect sex-biased dispersal in case of high dispersal rate of both sexes...
July 13, 2018: Heredity
Luca Ferretti, Daniel Weinreich, Fumio Tajima, Guillaume Achaz
In the last years, several genotypic fitness landscapes-combinations of a small number of mutations-have been experimentally resolved. To learn about the general properties of "real" fitness landscapes, it is key to characterize these experimental landscapes via simple measures of their structure, related to evolutionary features. Some of the most relevant measures are based on the selectively acessible paths and their properties. In this paper, we present some measures of evolutionary constraints based on (i) the similarity between accessible paths and (ii) the abundance and characteristics of "chains" of obligatory mutations, that are paths going through genotypes with a single fitter neighbor...
July 11, 2018: Heredity
Mari Suontama, Jaroslav Klápště, Emily Telfer, Natalie Graham, Toby Stovold, Charlie Low, Russell McKinley, Heidi Dungey
Genomic selection is expected to enhance the genetic improvement of forest tree species by providing more accurate estimates of breeding values through marker-based relationship matrices compared with pedigree-based methodologies. When adequately robust genomic prediction models are available, an additional increase in genetic gains can be made possible with the shortening of the breeding cycle through elimination of the progeny testing phase and early selection of parental candidates. The potential of genomic selection was investigated in an advanced Eucalyptus nitens breeding population focused on improvement for solid wood production...
July 6, 2018: Heredity
Joshua A Banta, Christina L Richards
Epigenetics refers to chemical modifications of chromatin or transcribed DNA that can influence gene activity and expression without changes in DNA sequence. The last 20 years have yielded breakthroughs in our understanding of epigenetic processes that impact many fields of biology. In this review, we discuss how epigenetics relates to quantitative genetics and evolution. We argue that epigenetics is important for quantitative genetics because: (1) quantitative genetics is increasingly being combined with genomics, and therefore we should expand our thinking to include cellular-level mechanisms that can account for phenotypic variance and heritability besides just those that are hard-coded in the DNA sequence; and (2) epigenetic mechanisms change how phenotypic variance is partitioned, and can thereby change the heritability of traits and how those traits are inherited...
July 6, 2018: Heredity
Martin I Lind, Foteini Spagopoulou
No abstract text is available yet for this article.
July 5, 2018: Heredity
Tristan Cumer, François Pompanon, Frédéric Boyer
Sheep, the Jaagsiekte sheep retrovirus (JSRV) and its endogenous forms (enJSRVs) are a good model to study long-time relationships between retroviruses and their hosts. Taking advantage of 76 whole genome resequencing data of wild and domestic Ovis, we investigated the evolution of this relationship. An innovative analysis of re-sequencing data allowed characterizing 462 enJSRVs insertion sites (including 435 newly described insertions) in the Ovis genus. We focused our study on endogenous copies inserted in the q13 locus of chromosome 6 (6q13)...
July 5, 2018: Heredity
Diego F Alvarado-Serrano, Megan L Van Etten, Shu-Mei Chang, Regina S Baucom
Examining how the landscape may influence gene flow is at the forefront of understanding population differentiation and adaptation. Such understanding is crucial in light of ongoing environmental changes and the elevated risk of ecosystems alteration. In particular, knowledge of how humans may influence population structure is imperative to allow for informed decisions in management and conservation as well as to gain a better understanding of anthropogenic impacts on the interplay between gene flow, genetic drift, and selection...
July 2, 2018: Heredity
Mark P Zwart, Martijn F Schenk, Sungmin Hwang, Bertha Koopmanschap, Niek de Lange, Lion van de Pol, Tran Thi Thuy Nga, Ivan G Szendro, Joachim Krug, J Arjan G M de Visser
While synonymous mutations were long thought to be without phenotypic consequences, there is growing evidence they can affect gene expression, protein folding, and ultimately the fitness of an organism. In only a few cases have the mechanisms by which synonymous mutations affect the phenotype been elucidated. We previously identified 48 mutations in TEM-1 β-lactamase that increased resistance of Escherichia coli to cefotaxime, 10 of which were synonymous. To better understand the molecular mechanisms underlying the beneficial effect of these synonymous mutations, we made a series of measurements for a panel containing the 10 synonymous together with 10 non-synonymous mutations as a reference...
July 2, 2018: Heredity
Arnaud Sentis, Raphaël Bertram, Nathalie Dardenne, Felipe Ramon-Portugal, Gilles Espinasse, Ines Louit, Lucie Negri, Elena Haeler, Thomas Ashkar, Théo Pannetier, James L Cunningham, Christoph Grunau, Gaël Le Trionnaire, Jean-Christophe Simon, Alexandra Magro, Benoit Pujol, Jean-Louis Hemptinne, Etienne Danchin
Transgenerational phenotypic plasticity is a fast non-genetic response to environmental modifications that can buffer the effects of environmental stresses on populations. However, little is known about the evolution of plasticity in the absence of standing genetic variation although several non-genetic inheritance mechanisms have now been identified. Here we monitored the pea aphid transgenerational phenotypic response to ladybird predators (production of winged offspring) during 27 generations of experimental evolution in the absence of initial genetic variation (clonal multiplication starting from a single individual)...
June 29, 2018: Heredity
Simone Immler
The fact that sperm carry more than the paternal DNA has only been discovered just over a decade ago. With this discovery, the idea that the paternal condition may have direct implications for the fitness of the offspring had to be revisited. While this idea is still highly debated, empirical evidence for paternal effects is accumulating. Male condition not only affects male fertility but also offspring early development and performance later in life. Several factors have been identified as possible carriers of non-genetic information, but we still know little about their origin and function and even less about their causation...
June 29, 2018: Heredity
Shamshidin Abduriyim, Yoshinori Nishita, Pavel A Kosintsev, Evgeniy Raichev, Risto Väinölä, Alexey P Kryukov, Alexei V Abramov, Yayoi Kaneko, Ryuichi Masuda
Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci...
June 29, 2018: Heredity
Marlene Jahnke, Daniela D'Esposito, Luigi Orrù, Antonella Lamontanara, Emanuela Dattolo, Fabio Badalamenti, Silvia Mazzuca, Gabriele Procaccini, Luisa Orsini
Seagrass meadows provide important ecosystem services and are critical for the survival of the associated invertebrate community. However, they are threatened worldwide by human-driven environmental change. Understanding the seagrasses' potential for adaptation is critical to assess not only their ability to persist under future global change scenarios, but also to assess the persistence of the associated communities. Here we screened a wild population of Posidonia oceanica, an endemic long-lived seagrass in the Mediterranean Sea, for genes that may be target of environmental selection, using an outlier and a genome-wide transcriptome analysis...
June 28, 2018: Heredity
Danelle K Seymour, Eunyoung Chae, Burak I Arioz, Daniel Koenig, Detlef Weigel
The equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. The preferential transmission of alleles or genotypes is termed transmission ratio distortion (TRD). Examples of TRD have been identified in many species, implying that they are universal, but the resolution of species-wide studies of TRD are limited. We have performed a species-wide screen for TRD in over 500 segregating F2 populations of Arabidopsis thaliana using pooled reduced-representation genome sequencing...
June 28, 2018: Heredity
Luís Felipe Ventorim Ferrão, Romário Gava Ferrão, Maria Amélia Gava Ferrão, Aymbiré Fonseca, Peter Carbonetto, Matthew Stephens, Antonio Augusto Franco Garcia
Genomic selection has been proposed as the standard method to predict breeding values in animal and plant breeding. Although some crops have benefited from this methodology, studies in Coffea are still emerging. To date, there have been no studies describing how well genomic prediction models work across populations and environments for different complex traits in coffee. Considering that predictive models are based on biological and statistical assumptions, it is expected that their performance vary depending on how well these assumptions align with the true genetic architecture of the phenotype...
June 25, 2018: Heredity
Evan McCartney-Melstad, Müge Gidiş, H Bradley Shaffer
Genomic data have the potential to inform high resolution landscape genetic and biological conservation studies that go far beyond recent mitochondrial and microsatellite analyses. We characterize the relationships of populations of the foothill yellow-legged frog, Rana boylii, a declining, "sentinel" species for stream ecosystems throughout its range in California and Oregon. We generated RADseq data and applied phylogenetic methods, hierarchical Bayesian clustering, PCA and population differentiation with admixture analyses to characterize spatial genetic structure across the species range...
June 25, 2018: Heredity
Hailan Liu, Guo-Bo Chen
In our previous work, we proposed a genomic prediction method combing identical-by-state-based Haseman-Elston regression and best linear prediction with additive variance component only (HEBLP|A herein), the most essential component of genetic variation. Since the dominance effects contribute significantly in heterosis, it is desirable to incorporate the HEBLP with dominance variance component that is expected to enhance the predictive accuracy as we move to the further development: HEBLP|AD, a paralleled implementation of genomic prediction compared with genomic best linear unbiased prediction (GBLUP)...
June 20, 2018: Heredity
Olivia Roth, Anne Beemelmanns, Seth M Barribeau, Ben M Sadd
Parental experience with parasites and pathogens can lead to increased offspring resistance to infection, through a process known as transgenerational immune priming (TGIP). Broadly defined, TGIP occurs across a wide range of taxa, and can be viewed as a type of phenotypic plasticity, with hosts responding to the pressures of relevant local infection risk by altering their offspring's immune defenses. There are ever increasing examples of both invertebrate and vertebrate TGIP, which go beyond classical examples of maternal antibody transfer...
June 18, 2018: Heredity
Mériam Ben Romdhane, Leila Riahi, Badra Bouamama, Hela Houissa, Abdelwahed Ghorbel, Néjia Zoghlami
The increasing anthropologic pressure and the modernization of agriculture have led to a forsaking of pearl millet traditional cultivars, inducing a progressive loss of the genetic variability encompassed in this locally adapted germplasm. Imperatively, national efforts based on robust data gleaned from genetic surveys have to be undertaken in order to set up suitable conservation priorities. In this study, in addition to the assessment of the genetic diversity and population structure among and within a set of seven pearl millet landrace populations from coastal North Africa, demographic and phylogenetic data, conservation priority scores were calculated according to Vane-Wright et al...
June 14, 2018: Heredity
Rocío Pérez-Portela, Owen S Wangensteen, Alex Garcia-Cisneros, Claudio Valero-Jiménez, Cruz Palacín, Xavier Turon
The genetic structure of 13 populations of the amphiatlantic sea urchin Arbacia lixula, as well as temporal genetic changes in three of these localities, were assessed using ten hypervariable microsatellite loci. This thermophilous sea urchin is an important engineer species triggering the formation of barren grounds through its grazing activity. Its abundance seems to be increasing in most parts of the Mediterranean, probably favoured by warming conditions. Significant genetic differentiation was found both spatially and temporally...
June 14, 2018: Heredity
Erin L Macartney, Angela J Crean, Russell Bonduriansky
It is now recognized that post-copulatory traits, such as sperm and ejaculate production can impose metabolic costs, and such traits are therefore expected to exhibit condition-dependent expression, whereby, low condition individuals experience a greater marginal cost of investment compared to high condition individuals. Ejaculates are especially costly in species where males invest in offspring quality through nutrient-rich spermatophores or other seminal nuptial gifts. However, recent evidence shows that, in species where males do not provision females or offspring, males can still influence offspring development through paternal effects mediated by epigenetic factors, such as non-coding RNAs, DNA methylation and chromatin structure...
June 14, 2018: Heredity
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