Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation.

Abstract:

:Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulation (Muller's ratchet). Here, we analyse genomic effects of hybridity, polyploidy and allelic divergence in apomictic plants, and identify loci under divergent selection among sexual/apomictic lineages. RNAseq was used to sequence the flower-specific transcriptomes of five genotypes of the Ranunculus auricomus complex, representing three sexual and two apomictic reproductive biotypes. The five sequence libraries were pooled and de novo assembly performed, and the resultant assembly was used as a backbone for a subsequent alignment of each separate library. High-quality single-nucleotide (SNP) and insertion-deletion (indel) polymorphisms were mined from each library. Annotated genes for which open reading frames (ORF) could be determined were analysed for signatures of divergent versus stabilizing selection. A comparison between all genotypes supports the hypothesis of Pleistocene hybrid origin of both apomictic genotypes from R. carpaticola and R. cassubicifolius, with subsequent allelic divergence of apomictic lineages (Meselson effect). Pairwise comparisons of nonsynonymous (dN) to synonymous (dS) substitution rate ratios between apomictic and sexual genotypes for 1231 genes demonstrated similar distributions for all comparisons, although 324 genes demonstrated outlier (i.e. elevated) dN/dS ratios. Gene ontology analyses of these outliers revealed significant enrichment of genes associated with reproduction including meiosis and gametogenesis, following predictions of divergent selection between sexual and apomictic reproduction, although no significant signal of genome-wide mutation accumulation could be identified. The results suggest that gene function should be considered in order to understand effects of mutation accumulation in asexual lineages.

journal_name

Mol Ecol

journal_title

Molecular ecology

authors

Pellino M,Hojsgaard D,Schmutzer T,Scholz U,Hörandl E,Vogel H,Sharbel TF

doi

10.1111/mec.12533

subject

Has Abstract

pub_date

2013-12-01 00:00:00

pages

5908-21

issue

23

eissn

0962-1083

issn

1365-294X

journal_volume

22

pub_type

杂志文章
  • Host and geographical factors influence the thermal niche of enteric bacteria isolated from native Australian mammals.

    abstract::The thermal profiles of 118 bacterial strains, representing six species of the family Enterobacteriaceae, isolated from a variety of native Australian mammals were determined under in vitro conditions. Each of the bacterial species had a unique thermal profile and differed in their minimum or maximum temperature for g...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.0962-1083.2001.01384.x

    authors: Okada S,Gordon DM

    更新日期:2001-10-01 00:00:00

  • Molecular biodiversity and population structure in common ash (Fraxinus excelsior L.) in Britain: implications for conservation.

    abstract::Current forestry policy promotes the use of local seed for new plantings, on the assumption that local material may be better adapted to local conditions. However, landscape-scale genetic studies which are necessary to underpin conservation and breeding strategies are often lacking. We investigated molecular diversity...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04376.x

    authors: Sutherland BG,Belaj A,Nier S,Cottrell JE,P Vaughan S,Hubert J,Russell K

    更新日期:2010-06-01 00:00:00

  • Ecological patterns and genetic analysis of post-dispersal seed predation in sunflower (Helianthus annuus) crop-wild hybrids.

    abstract::Crop-wild hybridization has been documented in many cultivated species, but the ecological and genetic factors that influence the likelihood or rate that cultivar alleles will introgress into wild populations are poorly understood. Seed predation is one factor that could mitigate the spread of otherwise advantageous c...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2010.04740.x

    authors: Dechaine JM,Burger JC,Burke JM

    更新日期:2010-08-01 00:00:00

  • High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice.

    abstract::Small population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15471

    authors: Stervander M,Dierickx EG,Thorley J,Brooke ML,Westerdahl H

    更新日期:2020-05-16 00:00:00

  • Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific.

    abstract::The population structure of variation in a nuclear actin intron and the control region of mitochondrial DNA is described for humpback whales from eight regions in the North Pacific Ocean: central California, Baja Peninsula, nearshore Mexico (Bahia Banderas), offshore Mexico (Socorro Island), southeastern Alaska, centr...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.1998.00384.x

    authors: Baker CS,Medrano-Gonzalez L,Calambokidis J,Perry A,Pichler F,Rosenbaum H,Straley JM,Urban-Ramirez J,Yamaguchi M,von Ziegesar O

    更新日期:1998-06-01 00:00:00

  • Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence.

    abstract::The evolutionary origin of extant species in the Neotropics, one of the most biodiverse regions of the world, has been widely debated. One hypothesis is that neotropical species emerged primarily during the Quaternary (the last approximately 2 million years), favoured by alternating glacial/interglacial climates. An o...

    journal_title:Molecular ecology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1365-294X.2008.03789.x

    authors: Rull V

    更新日期:2008-06-01 00:00:00

  • Detecting the signature of selection on immune genes in highly structured populations of wild sheep (Ovis dalli).

    abstract::The confounding effects of population structure complicate efforts to identify regions of the genome under the influence of selection in natural populations. Here we test for evidence of selection in three genes involved in vertebrate immune function - the major histocompatibility complex (MHC), interferon gamma (IFNG...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2006.02829.x

    authors: Worley K,Carey J,Veitch A,Coltman DW

    更新日期:2006-03-01 00:00:00

  • Temporal change in the genetic structure between and within cohorts of a marine fish, Diplodus sargus, induced by a large variance in individual reproductive success.

    abstract::Temporal changes at 16 allozyme loci in the Diplodus sargus population of Banyuls-sur-Mer (Mediterranean Sea, France) were monitored. Temporal genetic variation within a single population was examined over two temporal scales: (i) among three year-classes sampled at the same age, and (ii) within a single year-class sa...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2002.01521.x

    authors: Planes S,Lenfant P

    更新日期:2002-08-01 00:00:00

  • The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB.

    abstract::Variation in social behaviour is common, yet little is known about the genetic architectures underpinning its evolution. A rare exception is in the fire ant Solenopsis invicta: Alternative variants of a supergene region determine whether a colony will have exactly one or up to dozens of queens. The two variants of thi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14054

    authors: Pracana R,Priyam A,Levantis I,Nichols RA,Wurm Y

    更新日期:2017-06-01 00:00:00

  • Molecular phylogenies reveal host-specific divergence of Ophiocordyceps unilateralis sensu lato following its host ants.

    abstract::Ophiocordyceps unilateralis (Hypocreales, Ascomycetes) is an entomopathogenic fungus specific to formicine ants (Formicinae, Hymenoptera). Previous works have shown that the carpenter ant Camponotus leonardi acts as the principal host with occasional infections of ants from the genus Polyrhachis (sister genus of Campo...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2012.05574.x

    authors: Kobmoo N,Mongkolsamrit S,Tasanathai K,Thanakitpipattana D,Luangsa-Ard JJ

    更新日期:2012-06-01 00:00:00

  • Sexual conflict and the maintenance of genetic variation in natural populations.

    abstract::Understanding the factors that maintain genetic variation in natural populations is a foundational goal of evolutionary biology. To this end, population geneticists have developed a variety of models that can produce stable polymorphisms. In one of the earliest models, Owen () demonstrated that differences in selectio...

    journal_title:Molecular ecology

    pub_type: 评论,新闻

    doi:10.1111/mec.14787

    authors: Meisel RP

    更新日期:2018-09-01 00:00:00

  • Connectivity, small islands and large distances: the Cellana strigilis limpet complex in the Southern Ocean.

    abstract::The Southern Ocean contains some of the most isolated islands on Earth, and fundamental questions remain regarding their colonization and the connectivity of their coastal biotas. Here, we conduct a genetic investigation into the Cellana strigilis (limpet) complex that was originally classified based on morphological ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2011.05185.x

    authors: Reisser CM,Wood AR,Bell JJ,Gardner JP

    更新日期:2011-08-01 00:00:00

  • Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias.

    abstract::Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that capt...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12523

    authors: Thomas AC,Jarman SN,Haman KH,Trites AW,Deagle BE

    更新日期:2014-08-01 00:00:00

  • Similarities in temperature-dependent gene expression plasticity across timescales in threespine stickleback (Gasterosteus aculeatus).

    abstract::Phenotypic plasticity occurs at a variety of timescales, but little is known about the degree to which plastic responses at different timescales are associated with similar underlying molecular processes, which is critical for assessing the effects of plasticity on evolutionary trajectories. To address this issue, we ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14591

    authors: Metzger DCH,Schulte PM

    更新日期:2018-05-01 00:00:00

  • Differential threshold effects of habitat fragmentation on gene flow in two widespread species of bush crickets.

    abstract::Effects of habitat fragmentation on genetic diversity vary among species. This may be attributed to the interacting effects of species traits and landscape structure. While widely distributed and abundant species are often considered less susceptible to fragmentation, this may be different if they are small sized and ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2010.04877.x

    authors: Lange R,Durka W,Holzhauer SI,Wolters V,Diekötter T

    更新日期:2010-11-01 00:00:00

  • Differential gene expression in narrow- and broad-headed European glass eels (Anguilla anguilla) points to a transcriptomic link of head shape dimorphism with growth rate and chemotaxis.

    abstract::One of the major challenges in evolutionary biology is to understand the mechanisms underlying morphological dimorphism and plasticity, including the genomic basis of traits and links to ecology. At the yellow eel stage of the European eel (Anguilla anguilla), two morphotypes are found: broad- and narrow-heads. This d...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14155

    authors: De Meyer J,Maes GE,Dirks RP,Adriaens D

    更新日期:2017-08-01 00:00:00

  • Population genetics of wolf spiders of fragmented habitat in the wheat belt of New South Wales.

    abstract::Possible effects of habitat fragmentation on the population genetics of a species of wolf spider (Lycosidae) from remnant Callitris woodland in the wheat belt of central western New South Wales in Australia are examined. Single-strand conformational analysis of mitochondrial cytochrome oxidase (subunit 1) was used to ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2002.01626.x

    authors: Colgan DJ,Brown S,Major RE,Christie F,Gray MR,Cassis G

    更新日期:2002-11-01 00:00:00

  • Magadi tilapia ecological specialization: filling the early gap in the speciation continuum.

    abstract::Cichlid fish are well known for their high speciation rates, which are usually accompanied by spectacular and rapid diversification in eco-morphological and secondary sexual traits. This is best illustrated by the famous repeated explosive radiations in the African Great Lakes Tanganyika, Malawi and Victoria, each lak...

    journal_title:Molecular ecology

    pub_type: 评论,杂志文章

    doi:10.1111/mec.13598

    authors: Pinho C,Faria R

    更新日期:2016-04-01 00:00:00

  • Changes in melanocyte RNA and DNA methylation favour pheomelanin synthesis and may avoid systemic oxidative stress after dietary cysteine supplementation in birds.

    abstract::Cysteine plays essential biological roles, but excessive amounts produce cellular oxidative stress. Cysteine metabolism is mainly mediated by the enzymes cysteine dioxygenase and γ-glutamylcysteine synthetase, respectively coded by the genes CDO1 and GCLC. Here we test a new hypothesis posing that the synthesis of the...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15024

    authors: Rodríguez-Martínez S,Márquez R,Inácio Â,Galván I

    更新日期:2019-03-01 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

  • Can assignment tests measure dispersal?

    abstract::Individual-based assignment tests are now standard tools in molecular ecology and have several applications, including the study of dispersal. The measurement of natal dispersal is vital to understanding the ecology of many species, yet the accuracy of assignment tests in situations where natal dispersal is common rem...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2004.2081.x

    authors: Berry O,Tocher MD,Sarre SD

    更新日期:2004-03-01 00:00:00

  • Population dynamics of the sudden oak death pathogen Phytophthora ramorum in Oregon from 2001 to 2004.

    abstract::Phytophthora ramorum (Oomycetes) is an emerging plant pathogen in forests in southwestern Oregon (Curry County). Moreover, since 2003 it has been repeatedly isolated from plants in Oregon nurseries. In this study, we analysed the genetic diversity of the P. ramorum population in Oregon from 2001 to 2004 by using micro...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2007.03343.x

    authors: Prospero S,Hansen EM,Grünwald NJ,Winton LM

    更新日期:2007-07-01 00:00:00

  • Climate and habitat barriers to dispersal in the highly mobile grey wolf.

    abstract::We reanalysed published data to evaluate whether climate and habitat are barriers to dispersal in one of the most mobile and widely distributed mammals, the grey wolf (Canis lupus). Distance-based redundancy analysis (dbRDA) was used to examine the amount of variation in genetic distances that could be explained by an...

    journal_title:Molecular ecology

    pub_type: 杂志文章,meta分析

    doi:10.1111/j.1365-294X.2004.02244.x

    authors: Geffen E,Anderson MJ,Wayne RK

    更新日期:2004-08-01 00:00:00

  • Masculinized dominant females in a cooperatively breeding species.

    abstract::The molecular mechanisms underlying complex social behaviours such as dominance are largely unknown. Studying the cooperatively breeding African cichlid Neolamprologus pulcher, we show that dominant females were similar to dominant males in dominance behaviour, high testosterone levels and brain arginine vasotocin exp...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2007.03249.x

    authors: Aubin-Horth N,Desjardins JK,Martei YM,Balshine S,Hofmann HA

    更新日期:2007-04-01 00:00:00

  • Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus).

    abstract::Noninvasive samples are useful for molecular genetic analyses of wild animal populations. However, the low DNA content of such samples makes DNA amplification difficult, and there is the potential for erroneous results when one of two alleles at heterozygous microsatellite loci fails to be amplified. In this study we ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.0962-1083.2001.01308.x

    authors: Morin PA,Chambers KE,Boesch C,Vigilant L

    更新日期:2001-07-01 00:00:00

  • Comparison of gene expression in segregating families identifies genes and genomic regions involved in a novel adaptation, zinc hyperaccumulation.

    abstract::One of the challenges of comparative genomics is to identify specific genetic changes associated with the evolution of a novel adaptation or trait. We need to be able to disassociate the genes involved with a particular character from all the other genetic changes that take place as lineages diverge. Here we show that...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2006.02981.x

    authors: Filatov V,Dowdle J,Smirnoff N,Ford-Lloyd B,Newbury HJ,Macnair MR

    更新日期:2006-09-01 00:00:00

  • Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses.

    abstract::Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses a...

    journal_title:Molecular ecology

    pub_type: 杂志文章,评审

    doi:10.1111/mec.13029

    authors: Prunier JG,Colyn M,Legendre X,Nimon KF,Flamand MC

    更新日期:2015-01-01 00:00:00

  • Cryptic invasions of the crab Carcinus detected by molecular phylogeography.

    abstract::Coastal marine ecosystems world-wide are threatened by invasions of nonindigenous species. The ubiquity of marine sibling species identifiable only by genetic analysis suggests that many invasions are cryptic and therefore undetected, causing an underestimation of the actual number and impacts of invading species. We ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.1997.00256.x

    authors: Geller JB,Walton ED,Grosholz ED,Ruiz GM

    更新日期:1997-10-01 00:00:00

  • Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae).

    abstract::Genetic variation is often arrayed in latitudinal or altitudinal clines, reflecting either adaptation along environmental gradients, migratory routes, or both. For forest trees, climate is one of the most important drivers of adaptive phenotypic traits. Correlations of single and multilocus genotypes with environmenta...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2010.04698.x

    authors: Eckert AJ,Bower AD,González-Martínez SC,Wegrzyn JL,Coop G,Neale DB

    更新日期:2010-09-01 00:00:00

  • Evolutionary insight from whole-genome sequencing of experimentally evolved microbes.

    abstract::Experimental evolution (EE) combined with whole-genome sequencing (WGS) has become a compelling approach to study the fundamental mechanisms and processes that drive evolution. Most EE-WGS studies published to date have used microbes, owing to their ease of propagation and manipulation in the laboratory and relatively...

    journal_title:Molecular ecology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1365-294X.2012.05484.x

    authors: Dettman JR,Rodrigue N,Melnyk AH,Wong A,Bailey SF,Kassen R

    更新日期:2012-05-01 00:00:00