Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut.


:Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole-genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin-resistant strain 536, in the digestive tract of streptomycin-treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that 'evolve and sequence' approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.


Mol Ecol


Molecular ecology


Lescat M,Launay A,Ghalayini M,Magnan M,Glodt J,Pintard C,Dion S,Denamur E,Tenaillon O




Has Abstract


2017-04-01 00:00:00












  • Variation for neutral markers is correlated with variation for quantitative traits in the plant pathogenic fungus Mycosphaerella graminicola.

    abstract::We compared genetic variation and population differentiation at RFLP marker loci with seven quantitative characters including fungicide resistance, temperature sensitivity, pycnidial size, pycnidial density, colony size, percentage of leaves covered by pycnidia (PLACP) and percentage of leaves covered by lesions (PLAC...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Zhan J,Linde CC,Jürgens T,Merz U,Steinebrunner F,McDonald BA

    更新日期:2005-08-01 00:00:00

  • Local adaptation at higher trophic levels: contrasting hyperparasite-pathogen infection dynamics in the field and laboratory.

    abstract::Predicting and controlling infectious disease epidemics is a major challenge facing the management of agriculture, human and wildlife health. Co-evolutionarily derived patterns of local adaptation among pathogen populations have the potential to generate variation in disease epidemiology; however, studies of local ada...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Parratt SR,Barrès B,Penczykowski RM,Laine AL

    更新日期:2017-04-01 00:00:00

  • Genetic structure in the Mediterranean seagrass Posidonia oceanica: disentangling past vicariance events from contemporary patterns of gene flow.

    abstract::The Mediterranean Sea is a two-basin system, with the boundary zone restricted to the Strait of Sicily and the narrow Strait of Messina. Two main population groups are recognized in the Mediterranean endemic seagrass Posidonia oceanica, corresponding to the Western and the Eastern basins. To address the nature of the ...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Serra IA,Innocenti AM,Di Maida G,Calvo S,Migliaccio M,Zambianchi E,Pizzigalli C,Arnaud-Haond S,Duarte CM,Serrao EA,Procaccini G

    更新日期:2010-02-01 00:00:00

  • SNP analyses reveal a diverse pool of potential colonists to earthquake-uplifted coastlines.

    abstract::In species that form dense populations, major disturbance events are expected to increase the chance of establishment for immigrant lineages. Real-time tests of the impact of disturbance on patterns of genetic structure are, however, scarce. Central to testing these concepts is determining the pool of potential immigr...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Peters JC,Waters JM,Dutoit L,Fraser CI

    更新日期:2020-01-01 00:00:00

  • MHC diversity and the association to nematode parasitism in the yellow-necked mouse (Apodemus flavicollis).

    abstract::In vertebrates, the genes of the major histocompatibility complex (MHC) are among the most debated candidates accounting for co-evolutionary processes of host-parasite interaction at the molecular level. The exceptionally high allelic polymorphism found in MHC loci is believed to be maintained by pathogen-driven selec...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Meyer-Lucht Y,Sommer S

    更新日期:2005-06-01 00:00:00

  • Genomic evidence for gene flow between monarchs with divergent migratory phenotypes and flight performance.

    abstract::Monarch butterflies are known for their spectacular annual migration in eastern North America, with millions of monarchs flying up to 4,500 km to overwintering sites in central Mexico. Monarchs also live west of the Rocky Mountains, where they travel shorter distances to overwinter along the Pacific Coast. It is often...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Talla V,Pierce AA,Adams KL,de Man TJB,Nallu S,Villablanca FX,Kronforst MR,de Roode JC

    更新日期:2020-07-01 00:00:00

  • Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex.

    abstract::Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome-wide loci are analysed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next-generation platform to sequence thousands of barcoded P...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: O'Neill EM,Schwartz R,Bullock CT,Williams JS,Shaffer HB,Aguilar-Miguel X,Parra-Olea G,Weisrock DW

    更新日期:2013-01-01 00:00:00

  • Long-distance gene flow and cross-Andean dispersal of lowland rainforest bees (Apidae: Euglossini) revealed by comparative mitochondrial DNA phylogeography.

    abstract::Euglossine bees (Apidae; Euglossini) exclusively pollinate hundreds of orchid species and comprise up to 25% of bee species richness in neotropical rainforests. As one of the first studies of comparative phylogeography in a neotropical insect group, we performed a mitochondrial DNA (mtDNA)-based analysis of 14 eugloss...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Dick CW,Roubik DW,Gruber KF,Bermingham E

    更新日期:2004-12-01 00:00:00

  • Unearthing the impact of human disturbance on a notorious weed.

    abstract::Large-scale anthropogenic changes in the environment are reshaping global biodiversity and the evolutionary trajectory of many species. Evolutionary mechanisms that allow organisms to thrive in this rapidly changing environment are just beginning to be investigated (Hoffmann & Sgrò 2011; Colautti & Barrett 2013). Weed...

    journal_title:Molecular ecology

    pub_type: 评论,杂志文章


    authors: Hodgins K

    更新日期:2014-05-01 00:00:00

  • Plant dispersal in the sub-Antarctic inferred from anisotropic genetic structure.

    abstract::Climatic conditions and landscape features often strongly affect species' local distribution patterns, dispersal, reproduction and survival and may therefore have considerable impacts on species' fine-scale spatial genetic structure (SGS). In this study, we demonstrate the efficacy of combining fine-scale SGS analyses...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Born C,Le Roux PC,Spohr C,McGeoch MA,Van Vuuren BJ

    更新日期:2012-01-01 00:00:00

  • Rabbit haemorrhagic disease: applying Occam's razor to competing hypotheses.

    abstract::Rabbit haemorrhagic disease virus (RHDV) is a highly virulent lagovirus endemic in Europe and Australasian populations of the European rabbit, Oryctolagus cuniculus. It has also caused several unexplained disease outbreaks in domestic European rabbits in North America. Non-pathogenic spread of RHDV leading to persiste...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Peacock D,Mutze G,Sinclair R,Kovaliski J,Cooke B

    更新日期:2012-03-01 00:00:00

  • Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.

    abstract::Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resis...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Eoche-Bosy D,Gautier M,Esquibet M,Legeai F,Bretaudeau A,Bouchez O,Fournet S,Grenier E,Montarry J

    更新日期:2017-09-01 00:00:00

  • Natural hybridization between Senecio jacobaea and Senecio aquaticus: molecular and chemical evidence.

    abstract::Hybridization is known to be involved in a number of evolutionary processes, including species formation, and the generation of novel defence characteristics in plants. The genus Senecio of the Asteraceae family is highly speciose and has historically demonstrated significant levels of interspecific hybridization. The...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Kirk H,Macel M,Klinkhamer PG,Vrieling K

    更新日期:2004-08-01 00:00:00

  • Hares on ice: phylogeography and historical demographics of Lepus arcticus, L. othus, and L. timidus (Mammalia: Lagomorpha).

    abstract::Phylogeographical investigations of arctic organisms provide spatial and temporal frameworks for interpreting the role of climate change on biotic diversity in high-latitude ecosystems. Phylogenetic analyses were conducted on 473 base pairs of the mitochondrial control region in 192 arctic hares (Lepus arcticus, Lepus...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Waltari E,Cook JA

    更新日期:2005-09-01 00:00:00

  • Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae).

    abstract::Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics o...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Trénel P,Hansen MM,Normand S,Borchsenius F

    更新日期:2008-08-01 00:00:00

  • A gene for resistance to the Varroa mite (Acari) in honey bee (Apis mellifera) pupae.

    abstract::Social insect colonies possess a range of defences which protect them against highly virulent parasites and colony collapse. The host-parasite interaction between honey bees (Apis mellifera) and the mite Varroa destructor is unusual, as honey bee colonies are relatively poorly defended against this parasite. The inter...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Conlon BH,Aurori A,Giurgiu AI,Kefuss J,Dezmirean DS,Moritz RFA,Routtu J

    更新日期:2019-06-01 00:00:00

  • Phylogeography of a high-dispersal New Zealand sea-star: does upwelling block gene-flow?

    abstract::New Zealand's (NZ) geographical isolation, extensive coastline and well-characterized oceanography offer a valuable system for marine biogeographical research. Here we use mtDNA control region sequences in the abundant endemic sea-star Patiriella regularis to test the following literature-based predictions: that coast...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Waters JM,Roy MS

    更新日期:2004-09-01 00:00:00

  • Expression of olfactory receptors in different life stages and life histories of wild Atlantic salmon (Salmo salar).

    abstract::It has been hypothesized that salmonids use olfactory cues to return to their natal rivers and streams. However, the key components of the molecular pathway involved in imprinting and homing are still unknown. If odorants are involved in salmon homing migration, then olfactory receptors should play a critical role in ...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Johnstone KA,Lubieniecki KP,Koop BF,Davidson WS

    更新日期:2011-10-01 00:00:00

  • Parent and offspring genotypes influence gene expression in early life.

    abstract::Parents can have profound effects on offspring fitness. Little, however, is known about the mechanisms through which parental genetic variation influences offspring physiology in natural systems. White-throated sparrows (Zonotrichia albicollis, WTSP) exist in two genetic morphs, tan and white, controlled by a large po...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Newhouse DJ,Barcelo-Serra M,Tuttle EM,Gonser RA,Balakrishnan CN

    更新日期:2019-09-01 00:00:00

  • Association between Wolbachia and Spiroplasma within Drosophila neotestacea: an emerging symbiotic mutualism?

    abstract::Interspecific mutualism can evolve when specific lineages of different species tend to be associated with each other from one generation to the next. Different maternally transmitted endosymbionts occurring within the same cytoplasmic lineage fulfil this requirement. Drosophila neotestacea is infected with maternally ...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Jaenike J,Stahlhut JK,Boelio LM,Unckless RL

    更新日期:2010-01-01 00:00:00

  • Gene expression under thermal stress varies across a geographical range expansion front.

    abstract::Many ectothermic species are currently expanding their distributions polewards due to anthropogenic global warming. Molecular genetic mechanisms facilitating range expansion under these conditions are largely unknown, but understanding these could help mitigate expanding pests and disease vectors, or help explain why ...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Lancaster LT,Dudaniec RY,Chauhan P,Wellenreuther M,Svensson EI,Hansson B

    更新日期:2016-03-01 00:00:00

  • A molecular analysis of relationships and biogeography within a species complex of Holarctic fish (genus Osmerus).

    abstract::Episodes of trans-Arctic faunal exchange and isolation between the north Pacific and Atlantic ocean basins have been implicated as important historic geological events contributing to extant patterns of genetic diversity and structure in Holarctic faunas. We made a further test of the significance of such biogeographi...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Taylor EB,Dodson JJ

    更新日期:1994-06-01 00:00:00

  • Host use evolution in Chrysochus milkweed beetles: evidence from behaviour, population genetics and phylogeny.

    abstract::In two sister species of leaf beetles with overlapping host associations, Chrysochus auratus and C. cobaltinus, we established diet breadth and food preference of local populations for evaluation together with genetic differentiation between populations. While C. auratus turned out to be monophagous on the same plant ...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Dobler S,Farrell BD

    更新日期:1999-08-01 00:00:00

  • Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago.

    abstract::We present a study of the genetic diversity and structure of a tropical tree in an insular system. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. A total of 431 individuals over 17 populations were analysed for eight polymorphic microsatell...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Bottin L,Verhaegen D,Tassin J,Olivieri I,Vaillant A,Bouvet JM

    更新日期:2005-06-01 00:00:00

  • A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research.

    abstract::Despite much discussion of the importance of quantifying and reporting genotyping error in molecular studies, it is still not standard practice in the literature. This is particularly a concern for amplified fragment length polymorphism (AFLP) studies, where differences in laboratory, peak-calling and locus-selection ...

    journal_title:Molecular ecology

    pub_type: 杂志文章,评审


    authors: Crawford LA,Koscinski D,Keyghobadi N

    更新日期:2012-12-01 00:00:00

  • Noninvasive genome sampling in chimpanzees.

    abstract::The inevitable has happened: genomic technologies have been added to our noninvasive genetic sampling repertoire. In this issue of Molecular Ecology, Perry et al. (2010) demonstrate how DNA extraction from chimpanzee faeces, followed by a series of steps to enrich for target loci, can be coupled with next-generation s...

    journal_title:Molecular ecology

    pub_type: 评论,杂志文章


    authors: Kohn MH

    更新日期:2010-12-01 00:00:00

  • Leveraging eDNA to expand the study of hybrid zones.

    abstract::Hybrid zones are important windows into ecological and evolutionary processes. Our understanding of the significance and prevalence of hybridization in nature has expanded with the generation and analysis of genome-spanning data sets. That said, most hybridization research still has restricted temporal and spatial res...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Stewart KA,Taylor SA

    更新日期:2020-08-01 00:00:00

  • The role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica).

    abstract::Landscape genomics promises to provide novel insights into how neutral and adaptive processes shape genome-wide variation within and among populations. However, there has been little emphasis on examining whether individual-based phenotype-genotype relationships derived from approaches such as genome-wide association ...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Wenzel MA,Douglas A,James MC,Redpath SM,Piertney SB

    更新日期:2016-01-01 00:00:00

  • Genetic consequences of plant edaphic specialization to solfatara fields: Phylogenetic and population genetic analysis of Carex angustisquama (Cyperaceae).

    abstract::Edaphic specialization is one of the main drivers of plant diversification and has multifaceted effects on population dynamics. Carex angustisquama is a sedge plant growing only on heavily acidified soil in solfatara fields, where only extremophytes can survive. Because of the lack of closely related species in simila...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Nagasawa K,Setoguchi H,Maki M,Goto H,Fukushima K,Isagi Y,Suyama Y,Matsuo A,Tsunamoto Y,Sawa K,Sakaguchi S

    更新日期:2020-09-01 00:00:00

  • A 6.5-kb intergenic structural variation enhances P450-mediated resistance to pyrethroids in malaria vectors lowering bed net efficacy.

    abstract::Elucidating the complex evolutionary armory that mosquitoes deploy against insecticides is crucial to maintain the effectiveness of insecticide-based interventions. Here, we deciphered the role of a 6.5-kb structural variation (SV) in driving cytochrome P450-mediated pyrethroid resistance in the malaria vector, Anophe...

    journal_title:Molecular ecology

    pub_type: 杂志文章


    authors: Mugenzi LMJ,Menze BD,Tchouakui M,Wondji MJ,Irving H,Tchoupo M,Hearn J,Weedall GD,Riveron JM,Cho-Ngwa F,Wondji CS

    更新日期:2020-11-01 00:00:00