Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar).

Abstract:

:As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 single nucleotide polymorphisms (SNPs) and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and the processes shaping them. We found evidence of high (mean FST  = 0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3 Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16 and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium, despite no significant reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near-fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.

journal_name

Mol Ecol

journal_title

Molecular ecology

authors

Lehnert SJ,Kess T,Bentzen P,Clément M,Bradbury IR

doi

10.1111/mec.15480

subject

Has Abstract

pub_date

2020-06-01 00:00:00

pages

2160-2175

issue

12

eissn

0962-1083

issn

1365-294X

journal_volume

29

pub_type

杂志文章
  • Anthropogenic and natural barriers affect genetic connectivity in an Alpine butterfly.

    abstract::Dispersal is a key biological process serving several functions including connectivity among populations. Habitat fragmentation caused by natural or anthropogenic structures may hamper dispersal, thereby disrupting genetic connectivity. Investigating factors affecting dispersal and gene flow is important in the curren...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15707

    authors: Trense D,Schmidt TL,Yang Q,Chung J,Hoffmann AA,Fischer K

    更新日期:2020-10-27 00:00:00

  • Complex sociogenetic organization and reproductive skew in a primitively eusocial sweat bee, Lasioglossum malachurum, as revealed by microsatellites.

    abstract::The sweat bees (Family Halictidae) are a socially diverse taxon in which eusociality has arisen independently numerous times. The obligate, primitively eusocial Lasioglossum malachurum, distributed widely throughout Europe, has been considered the zenith of sociality within halictids. A single queen heads a colony of ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2002.01620.x

    authors: Paxton RJ,Ayasse M,Field J,Soro A

    更新日期:2002-11-01 00:00:00

  • A tale of two flatties: different responses of two terrestrial flatworms to past environmental climatic fluctuations at Tallaganda in montane southeastern Australia.

    abstract::Comparative phylogeographic studies of animals with low mobility and/or high habitat specificity remain rare, yet such organisms may hold fine-grained palaeoecological signal. Comparisons of multiple, codistributed species can elucidate major historical events. As part of a multitaxon programme, mitochondrial cytochro...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2006.03107.x

    authors: Sunnucks P,Blacket MJ,Taylor JM,Sands CJ,Ciavaglia SA,Garrick RC,Tait NN,Rowell DM,Pavlova A

    更新日期:2006-12-01 00:00:00

  • Timing strains of the marine insect Clunio marinus diverged and persist with gene flow.

    abstract::Genetic divergence of populations in the presence of gene flow is a central theme in speciation research. Theory predicts that divergence can happen with full range overlap - in sympatry - driven by ecological factors, but there are few empirical examples of how ecologically divergent selection can overcome gene flow ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15791

    authors: Kaiser TS,von Haeseler A,Tessmar-Raible K,Heckel DG

    更新日期:2021-01-07 00:00:00

  • Coyote movements and social structure along a cryptic population genetic subdivision.

    abstract::A recent region-wide study determined that the central California coyote (Canis latrans) population was genetically subdivided according to habitat bioregions, supporting the hypothesis that coyotes exhibit a dispersal bias toward their natal habitat type. Here, we further investigated this hypothesis using radio-coll...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2005.02473.x

    authors: Sacks BN,Mitchell BR,Williams CL,Ernest HB

    更新日期:2005-04-01 00:00:00

  • Spreading introgression in the wake of a moving contact zone.

    abstract::An increasing number of studies describe moving hybrid zones. This raises the issue of their actual frequency and emphasizes the need for methods that enable the detection of zone movements without historical records. Asymmetric introgression, usually considered as a signature of geographical shift, might be misleadin...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2006.02948.x

    authors: Secondi J,Faivre B,Bensch S

    更新日期:2006-08-01 00:00:00

  • Suppression of randomly primed polymerase chain reaction products (random amplified polymorphic DNA) in heterozygous diploids.

    abstract::In a study of genetic polymorphism in the gypsy moth Lymantria dispar we observed the aberrant inheritance of a random amplified polymorphic DNA (RAPD) fragment designated H11-589. This fragment was present in amplification products of F1 progeny of different crosses although it was not amplified from either parental ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.1999.00714.x

    authors: Reineke A,Karlovsky P,Zebitz CP

    更新日期:1999-09-01 00:00:00

  • A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level.

    abstract::Abstract Microsatellites are powerful molecular markers, used commonly to estimate intraspecific genetic distances. With the exception of band sharing similarity index, available distance measures were developed specifically for diploid organisms and are unsuited for comparisons of polyploids. Here, we present a simpl...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2004.02209.x

    authors: Bruvo R,Michiels NK,D'Souza TG,Schulenburg H

    更新日期:2004-07-01 00:00:00

  • Independent evolution of sexual dimorphism and female-limited mimicry in swallowtail butterflies (Papilio dardanus and Papilio phorcas).

    abstract::Several species of swallowtail butterflies (genus Papilio) are Batesian mimics that express multiple mimetic female forms, while the males are monomorphic and nonmimetic. The evolution of such sex-limited mimicry may involve sexual dimorphism arising first and mimicry subsequently. Such a stepwise scenario through a n...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14012

    authors: Timmermans MJ,Thompson MJ,Collins S,Vogler AP

    更新日期:2017-03-01 00:00:00

  • Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes.

    abstract::Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic 'barcode' for an objec...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2003.02070.x

    authors: Thalmann O,Hebler J,Poinar HN,Pääbo S,Vigilant L

    更新日期:2004-02-01 00:00:00

  • Rapid acclimation of juvenile corals to CO2 -mediated acidification by upregulation of heat shock protein and Bcl-2 genes.

    abstract::Corals play a key role in ocean ecosystems and carbonate balance, but their molecular response to ocean acidification remains unclear. The only previous whole-transcriptome study (Moya et al. Molecular Ecology, 2012; 21, 2440) documented extensive disruption of gene expression, particularly of genes encoding skeletal ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13021

    authors: Moya A,Huisman L,Forêt S,Gattuso JP,Hayward DC,Ball EE,Miller DJ

    更新日期:2015-01-01 00:00:00

  • Age-specific mating strategies and reproductive senescence.

    abstract::While males gain obvious direct advantages from multiple mating, the reproductive capacity of females is more constrained. The reason why polyandry evolved in females is therefore open to many conjectures. One hypothesis postulates that females gain indirect benefits by increasing the probability of siring young from ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2005.02662.x

    authors: Richard M,Lecomte J,de Fraipont M,Clobert J

    更新日期:2005-09-01 00:00:00

  • Microsatellite analysis of kinkajou social organization.

    abstract::Kinkajou social groups generally consist of one adult female, two males, one subadult and one juvenile. Based on analysis of variation in 11 microsatellite loci, we assess the degree of kinship within and between four social groups totaling 25 kinkajous. We use exclusion and likelihood analyses to assign parents for s...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2000.00921.x

    authors: Kays RW,Gittleman JL,Wayne RK

    更新日期:2000-06-01 00:00:00

  • One gene, multiple alleles: insights into the microevolution of pigmentation polymorphisms.

    abstract::Understanding how phenotypic variation is generated and maintained, and the evolutionary forces that shape these processes is the main goal of evolutionary biology. Great progress has been made in uncovering the genetic basis of morphological diversity, yet little is known about both the genetics and developmental bas...

    journal_title:Molecular ecology

    pub_type: 评论,新闻

    doi:10.1111/mec.14099

    authors: Santos ME

    更新日期:2017-05-01 00:00:00

  • Environmental filtering structures fungal endophyte communities in tree bark.

    abstract::The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tre...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15237

    authors: Pellitier PT,Zak DR,Salley SO

    更新日期:2019-12-01 00:00:00

  • Phylogeography and Pleistocene refugia of the adder (Vipera berus) as inferred from mitochondrial DNA sequence data.

    abstract::In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2006.03031.x

    authors: Ursenbacher S,Carlsson M,Helfer V,Tegelström H,Fumagalli L

    更新日期:2006-10-01 00:00:00

  • Isolation by distance among California sea lion populations in Mexico: redefining management stocks.

    abstract::Understanding the spatial structure of a population is critical for effective assessment and management. However, direct observation of spatial dynamics is generally difficult, particularly for marine mammals. California sea lions (Zalophus californianus) are polygynous pinnipeds distributed along the Pacific coast of...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04093.x

    authors: González-Suárez M,Flatz R,Aurioles-Gamboa D,Hedrick PW,Gerber LR

    更新日期:2009-03-01 00:00:00

  • Colony kin structure and host-parasite relatedness in the barnacle goose.

    abstract::Conspecific brood parasitism (CBP), females laying eggs in the nest of other 'host' females of the same species, is a common alternative reproductive tactic among birds. For hosts there are likely costs of incubating and rearing foreign offspring, but costs may be low in species with precocial chicks such as waterfowl...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04397.x

    authors: Anderholm S,Waldeck P,VAN DER Jeugd HP,Marshall RC,Larsson K,Andersson M

    更新日期:2009-12-01 00:00:00

  • Sex-specific genetic structure in Schistosoma mansoni: evolutionary and epidemiological implications.

    abstract::We studied the population genetic structure of 360 and 1247 adult Schistosoma mansoni using seven microsatellite and seven random amplified polymorphic DNA (RAPD) markers, respectively. Parasites were collected from their natural definitive host Rattus rattus in Guadeloupe (West Indies). We found a sex-specific geneti...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2002.01518.x

    authors: Prugnolle F,De Meeûs T,Durand P,Sire C,Théron A

    更新日期:2002-07-01 00:00:00

  • Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of a Choristoneura budworm.

    abstract::Populations are often exposed to multiple sources of gene flow, but accounts are lacking of the population genetic dynamics that result from these interactions or their effects on local evolution. Using a genomic clines framework applied to 1,195 single nucleotide polymorphisms, we documented genomewide, locus-specifi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14386

    authors: Blackburn GS,Brunet BMT,Muirhead K,Cusson M,Béliveau C,Levesque RC,Lumley LM,Sperling FAH

    更新日期:2017-12-01 00:00:00

  • Evolutionary history of a dispersal-associated locus across sympatric and allopatric divergent populations of a wing-polymorphic beetle across Atlantic Europe.

    abstract::Studying the evolutionary history of trait divergence, in particular those related to dispersal capacity, is of major interest for the process of local adaptation and metapopulation dynamics. Here, we reconstruct the evolution of different alleles at the nuclear-encoded mitochondrial NADP(+)-dependent isocitrate dehyd...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13031

    authors: Van Belleghem SM,Roelofs D,Hendrickx F

    更新日期:2015-02-01 00:00:00

  • Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations.

    abstract::Breeding indigenous African taurine cattle tolerant to trypanosomosis is a straightforward approach to control costs generated by this disease. A recent study identified quantitative trait loci (QTL) underlying trypanotolerance traits in experimental crosses between tolerant N'Dama and susceptible Boran zebu cattle. A...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04141.x

    authors: Dayo GK,Thevenon S,Berthier D,Moazami-Goudarzi K,Denis C,Cuny G,Eggen A,Gautier M

    更新日期:2009-04-01 00:00:00

  • Marine genetic swamping: hybrids replace an obligately estuarine fish.

    abstract::Populations of obligately estuarine taxa are potentially small and isolated and may lack genetic variation and display regional differentiation as a result of drift and inbreeding. Hybridization with a wide-ranging marine congener should introduce genetic variation and reduce the effects of inbreeding depression and g...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04501.x

    authors: Roberts DG,Gray CA,West RJ,Ayre DJ

    更新日期:2010-02-01 00:00:00

  • Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations.

    abstract::We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global p...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12341

    authors: Iacchei M,Ben-Horin T,Selkoe KA,Bird CE,García-Rodríguez FJ,Toonen RJ

    更新日期:2013-07-01 00:00:00

  • A landscape genetics approach for quantifying the relative influence of historic and contemporary habitat heterogeneity on the genetic connectivity of a rainforest bird.

    abstract::Landscape genetics is an important framework for investigating the influence of spatial pattern on ecological process. Nevertheless, the standard analytic frameworks in landscape genetics have difficulty evaluating hypotheses about spatial processes in dynamic landscapes. We use a predictive hypothesis-driven approach...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04226.x

    authors: Pavlacky DC Jr,Goldizen AW,Prentis PJ,Nicholls JA,Lowe AJ

    更新日期:2009-07-01 00:00:00

  • Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.

    abstract::The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13358

    authors: Ingram CM,Troendle NJ,Gill CA,Braude S,Honeycutt RL

    更新日期:2015-10-01 00:00:00

  • Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation.

    abstract::Effective population size (N(e)) is a key parameter to understand evolutionary processes and the viability of endangered populations as it determines the rate of genetic drift and inbreeding. Low Ne can lead to inbreeding depression and reduced population adaptability. In this study, we estimated contemporary N(e) usi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12770

    authors: Baalsrud HT,Saether BE,Hagen IJ,Myhre AM,Ringsby TH,Pärn H,Jensen H

    更新日期:2014-06-01 00:00:00

  • The Leptynia hispanica species complex (Insecta Phasmida): polyploidy, parthenogenesis, hybridization and more.

    abstract::The Leptynia hispanica stick insect species complex includes bisexuals, triploid and tetraploid parthenogenetic populations, suggesting that polyploidy has played a central role in the evolution of this complex. An analysis of karyotype, mitochondrial DNA (cox2) and nuclear DNA (ef1-alpha) markers was carried out to c...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2007.03471.x

    authors: Ghiselli F,Milani L,Scali V,Passamonti M

    更新日期:2007-10-01 00:00:00

  • Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer.

    abstract::What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical,...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15162

    authors: Bourgeois Y,Boissinot S

    更新日期:2019-08-01 00:00:00

  • Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera.

    abstract::We developed genetic markers for three microsatellite loci in the tropical tree Symphonia globulifera and used them to examine the demographic genetic consequences of forest fragmentation. High levels of genetic variation were revealed in samples of adults, saplings, and seedlings. The more-variable loci exhibited les...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.1998.00396.x

    authors: Aldrich PR,Hamrick JL,Chavarriaga P,Kochert G

    更新日期:1998-08-01 00:00:00