scholarly journals The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Alvaro Martinez Barrio ◽  
Sangeet Lamichhaney ◽  
Guangyi Fan ◽  
Nima Rafati ◽  
Mats Pettersson ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Genetic Factors ◽  
Geographic Origin ◽  
Natural Populations ◽  
Ecological Adaptation ◽  
Timing Of Reproduction ◽  
Haplotype Blocks ◽  
Subdivided Populations

Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

scholarly journals The genetic architecture underlying ecological adaptation in Atlantic herring is not consistent with the infinitesimal model

2020 ◽  
Author(s):  
Fan Han ◽  
Minal Jamsandekar ◽  
Mats E. Pettersson ◽  
Leyi Su ◽  
Angela Fuentes-Pardo ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
North Atlantic ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Allele Frequencies ◽  
Ecological Adaptation ◽  
Genetic Adaptation ◽  
Atlantic Herring ◽  
Long Read

AbstractAtlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in the herring is in conflict with the infinitesimal model for complex traits because of the large shifts in allele frequencies at hundreds of loci under selection.

The potential for rapid speciation in plants

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 203-210 ◽  
Author(s):  
Mark R. Macnair
Keyword(s):  
Reproductive Isolation ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Natural Populations ◽  
Direct Result ◽  
Epistatic Interactions ◽  
Genetic Changes ◽  
Rapid Speciation ◽  
Genetic Revolution ◽  
Self Fertilization

Speciation involves both ecological adaptation and reproductive isolation. This paper reviews various ways in which plants could achieve reproductive isolation as a direct result of adaptation to prevailing conditions, particularly through changes in flowering time, the adoption of self-fertilization, and changes in flower morphology so that different pollinators are attracted. These characters are likely to have a relatively simple genetic architecture, and there must frequently be genetic variance for them in natural populations. It is argued that speciation could thus be initiated swiftly in plants, without any need for a "genetic revolution" or the fixation of genes with strongly epistatic interactions. Postmating barriers also often have a simple genetic basis in plants, and so could also evolve swiftly if associated with an adaptive response. The nature of the genetic changes associated with speciation in a number of recent speciation events in Layia, Stephanomeria, and Mimulus is reviewed.Key words: Speciation, adaptation, reproductive isolation.

scholarly journals Genetic architecture of a feeding adaptation: garter snake ( Thamnophis ) resistance to tetrodotoxin bearing prey

2010 ◽  
Vol 277 (1698) ◽  
pp. 3317-3325 ◽  
Author(s):  
Chris R. Feldman ◽  
Edmund D. Brodie ◽  
Edmund D. Brodie ◽  
Michael E. Pfrender
Keyword(s):  
Genetic Architecture ◽  
Genetic Basis ◽  
Allelic Variation ◽  
Natural Populations ◽  
Major Effect ◽  
Garter Snake ◽  
Thamnophis Sirtalis ◽  
Ecological Context ◽  
Garter Snakes ◽  
Genetic Level

Detailing the genetic basis of adaptive variation in natural populations is a first step towards understanding the process of adaptive evolution, yet few ecologically relevant traits have been characterized at the genetic level in wild populations. Traits that mediate coevolutionary interactions between species are ideal for studying adaptation because of the intensity of selection and the well-characterized ecological context. We have previously described the ecological context, evolutionary history and partial genetic basis of tetrodotoxin (TTX) resistance in garter snakes ( Thamnophis ). Derived mutations in a voltage-gated sodium channel gene (Na v 1.4) in three garter snake species are associated with resistance to TTX, the lethal neurotoxin found in their newt prey ( Taricha ). Here we evaluate the contribution of Na v 1.4 alleles to TTX resistance in two of those species from central coastal California. We measured the phenotypes (TTX resistance) and genotypes (Na v 1.4 and microsatellites) in a local sample of Thamnophis atratus and Thamnophis sirtalis . Allelic variation in Na v 1.4 explains 23 per cent of the variation in TTX resistance in T. atratus while variation in a haphazard sample of the genome (neutral microsatellite markers) shows no association with the phenotype. Similarly, allelic variation in Na v 1.4 correlates almost perfectly with TTX resistance in T. sirtalis , but neutral variation does not. These strong correlations suggest that Na v 1.4 is a major effect locus. The simple genetic architecture of TTX resistance in garter snakes may significantly impact the dynamics of phenotypic coevolution. Fixation of a few alleles of major effect in some garter snake populations may have led to the evolution of extreme phenotypes and an ‘escape’ from the arms race with newts.

scholarly journals On the genetic architecture of rapidly adapting and convergent life history traits in guppies

2021 ◽  
Author(s):  
James R Whiting ◽  
Josephine R Paris ◽  
Paul J Parsons ◽  
Sophie Matthews ◽  
Yuridia Reynoso ◽  
...  
Keyword(s):  
Life History ◽  
Life Histories ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Natural Populations ◽  
Female Size ◽  
Size At Maturity ◽  
Sequencing Data ◽  
Genome Wide ◽  
Polygenic Traits

The genetic basis of traits can shape and constrain how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, whereas polygenic traits may restrict re-use of the same genes in adaptation (genetic convergence). The rapidly evolving life histories of guppies in response to predation risk provide an opportunity to test this proposition. Guppies adapted to high- (HP) and low-predation (LP) environments in northern Trinidad evolve rapidly and convergently among natural populations. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use an F2 QTL design to examine the genetic basis of seven (five female, two male) guppy life history phenotypes. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many-loci of small effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but these may restrict gene-reuse across populations, in agreement with an absence of strong signatures of genetic convergence from recent population genomic analyses of wild HP-LP guppies.

scholarly journals Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Fan Han ◽  
Minal Jamsandekar ◽  
Mats E Pettersson ◽  
Leyi Su ◽  
Angela P Fuentes-Pardo ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
North Atlantic ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Allele Frequencies ◽  
Ecological Adaptation ◽  
Genetic Adaptation ◽  
Atlantic Herring ◽  
Long Read

Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.

scholarly journals Genetic Variants of the NF-κB Pathway: Unraveling the Genetic Architecture of Psoriatic Disease

2021 ◽  
Vol 22 (23) ◽  
pp. 13004
Author(s):  
Rubén Queiro ◽  
Pablo Coto-Segura ◽  
Leire González-Lara ◽  
Eliecer Coto
Keyword(s):  
Genetic Variants ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Genetic Factors ◽  
Disease Susceptibility ◽  
Cell Types ◽  
Psoriatic Disease ◽  
Pharmacological Response ◽  
Light Chain Enhancer ◽  
Shared Genetic

Psoriasis is a multifactorial genetic disease for which the genetic factors explain about 70% of disease susceptibility. Up to 30–40% of psoriasis patients develop psoriatic arthritis (PsA). However, PsA can be considered as a “disease within a disease”, since in most cases psoriasis is already present when joint complaints begin. This has made studies that attempt to unravel the genetic basis for both components of psoriatic disease enormously difficult. Psoriatic disease is also accompanied by a high burden of comorbid conditions, mainly of the cardiometabolic type. It is currently unclear whether these comorbidities and psoriatic disease have a shared genetic basis or not. The nuclear factor of kappa light chain enhancer of activated B cells (NF-κB) is a transcription factor that regulates a plethora of genes in response to infection, inflammation, and a wide variety of stimuli on several cell types. This mini-review is focused on recent findings that highlight the importance of this pathway both in the susceptibility and in the determinism of some features of psoriatic disease. We also briefly review the importance of genetic variants of this pathway as biomarkers of pharmacological response. All the above may help to better understand the etiopathogenesis of this complex entity.

scholarly journals Genetic control of male cuticular hydrocarbons in Drosophila melanogaster

1996 ◽  
Vol 67 (3) ◽  
pp. 211-218 ◽  
Author(s):  
Jean-François Ferveur ◽  
Jean-Marc Jallon
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Control ◽  
Cuticular Hydrocarbons ◽  
Genetic Basis ◽  
Genetic Factors ◽  
Geographic Origin ◽  
Courtship Behaviour ◽  
Functional Implication ◽  
Chromosome Iii ◽  
Chromosome Ii

Summary7-tricosene (7-T) and 7-pentacosene (7-P) are the two main hydrocarbons on the cuticle of male Drosophila melanogaster. These two substances might play a pheromonal role during courtship behaviour. We investigated the genetic basis of the quantitative polymorphism observed in the production of 7-T and 7-P. Strains of different geographic origin, with males producing either predominantly 7-T or predominantly 7-P, were hybridized with strains carrying genetic markers. We found that chromosome II changes the balance between 7-T and 7-P while chromosome III regulates the overall quantity of both 7-monoenes. We have also characterized and roughly mapped sept and smoq, two genetic factors on chromosome II that act additively on the production of both cuticular hydrocarbons. The genetic control of the variation in 7-T and 7-P varies between D. melanogaster strains and between D. melanogaster and its sibling species D.simulans. The possible evolutionary and physiological causes of this variation as well as its functional implication for courtship behaviour are discussed.

scholarly journals Genetic diversity of Simao pine in China revealed by SRAP markers

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6529 ◽  
Author(s):  
Dawei Wang ◽  
Bingqi Shen ◽  
Hede Gong
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Geographic Origin ◽  
Natural Populations ◽  
Molecular Data ◽  
Mantel Test ◽  
Management Program ◽  
Group Method ◽  
Srap Markers ◽  
High Level

Background Simao pine (Pinus kesiya Royle ex Gordon var. langbianensis (A. Chev.) Gaussen) is one of the most important tree species in the production of timber and resin in China. However, the genetic diversity of the natural populations has not been assessed to date. In this study, sequence related amplified polymorphism (SRAP) markers were used to investigate the genetic composition of natural Simao pine populations. Method The SRAP markers were applied and their efficiency was compared using various statistical multivariate methods, including analysis molecular of variance (AMOVA), the unweighted pair group method with arithmetic mean (UPGMA), and Principal coordinate analysis (PCoA). Results The 11 populations revealed a high level of genetic diversity (PPB = 95.45%, H = 0.4567, I = 0.6484) at the species level. A moderately low level of genetic differentiation (Gst = 0.1701), and a slightly high level of gene flow (Nm = 2.4403) were observed among populations using AMOVA. Eleven populations of Simao pine were gathered into four distinct clusters based on molecular data, and the results of UPGMA and PCoA also illustrated that assignment of populations is not completely consistent with geographic origin. The Mantel test revealed there was no significant correlation between geographic and genetic distance (r = 0.241, p = 0.090). Discussion The SRAP markers were very effective in the assessment of genetic diversity in Simao pine. Simao pine populations display high levels of genetic diversity and low or moderate levels of genetic differentiation due to frequent gene exchange among populations. The low genetic differentiation among populations implied that conservation efforts should aim to preserve all remaining natural populations of this species. The information derived from this study is useful when identifying populations and categorizing their population origins, making possible the design of long term management program such as genetic improvement by selective breeding.

scholarly journals GENETIC DIFFERENTIATION BETWEEN GEOGRAPHICALLY DISTANT POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽  
1982 ◽  
Vol 101 (2) ◽  
pp. 235-256
Author(s):  
Rama S Singh ◽  
Donal A Hickey ◽  
Jean David
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Differentiation ◽  
Gene Frequency ◽  
Natural Populations ◽  
Allozyme Variation ◽  
Clinal Variation ◽  
Significant Genetic Differentiation ◽  
African Populations ◽  
Latitudinal Clines ◽  
North And South

ABSTRACT We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and south. These differences arise mainly from seven loci that show gene-frequency patterns suggestive of latitudinal clines in allele frequencies. The clinal variation is such that subtropical populations are more heterozygous than temperate populations. These results are discussed in relation to the selectionist and neutralist hypotheses of genetic variation in natural populations.

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