Exploration of community traits as ecological markers in microbial metagenomes.

Abstract:

:The rate of information collection generated by metagenomics is uncoupled with its meaningful ecological interpretation. New analytical approaches based on functional trait-based ecology may help to bridge this gap and extend the trait approach to the community level in vast and complex environmental genetic data sets. Here, we explored a set of community traits that range from nucleotidic to genomic properties in 53 metagenomic aquatic samples from the Global Ocean Sampling (GOS) expedition. We found significant differences between the community profile derived from the commonly used 16S rRNA gene and from the functional trait set. The traits proved to be valuable ecological markers by discriminating between marine ecosystems (coastal vs. open ocean) and between oceans (Atlantic vs. Indian vs. Pacific). Intertrait relationships were also assessed, and we propose some that could be further used as habitat descriptors or indicators of artefacts during sample processing. Overall, the approach presented here may help to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework.

journal_name

Mol Ecol

journal_title

Molecular ecology

authors

Barberán A,Fernández-Guerra A,Bohannan BJ,Casamayor EO

doi

10.1111/j.1365-294X.2011.05383.x

subject

Has Abstract

pub_date

2012-04-01 00:00:00

pages

1909-17

issue

8

eissn

0962-1083

issn

1365-294X

journal_volume

21

pub_type

杂志文章
  • Inclusive fitness of 'kissing cousins': new evidence of a role for kin selection in the evolution of extra-pair mating in birds.

    abstract::Social monogamy is nearly ubiquitous across avian taxa,but evidence from a proliferation of studies utilizing molecular paternity analysis suggests that sexual monogamy is the rare exception rather than the rule (Griffith et al. 2002). Efforts to explain the prevalence of extra-pair paternity (EPP) have largely focuse...

    journal_title:Molecular ecology

    pub_type: 评论,杂志文章

    doi:10.1111/j.1365-294x.2011.05118.x

    authors: Oh KP

    更新日期:2011-07-01 00:00:00

  • Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss.

    abstract::Divergent life history strategies occur in steelhead or rainbow trout Oncorhynchus mykiss, and many populations produce both migrant (anadromous fish that move to the ocean after rearing) and resident (do not migrate and remain in fresh water) individuals. Mechanisms leading to each type are only partially understood;...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12713

    authors: Sutherland BJ,Hanson KC,Jantzen JR,Koop BF,Smith CT

    更新日期:2014-04-01 00:00:00

  • The demographic history of the New Zealand short-tailed bat Mystacina tuberculata inferred from modified control region sequences.

    abstract::Short-tailed bats Mystacina tuberculata were widespread throughout the forest that dominated prehuman New Zealand, but extensive deforestation has restricted them to scattered populations in forest fragments. In a previous study, the species' intraspecific phylogeny was investigated using multiple mitochondrial gene s...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2003.01879.x

    authors: Lloyd BD

    更新日期:2003-07-01 00:00:00

  • No evidence of inbreeding avoidance despite demonstrated survival costs in a polygynous rodent.

    abstract::Individuals are generally predicted to avoid inbreeding because of detrimental fitness effects. However, several recent studies have shown that limited inbreeding is tolerated by some vertebrate species. Here, we examine the costs and benefits of inbreeding in a largely polygynous rodent, the yellow-bellied marmot (Ma...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2011.05389.x

    authors: Olson LE,Blumstein DT,Pollinger JR,Wayne RK

    更新日期:2012-02-01 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

  • Spawning success in Atlantic salmon (Salmo salar L.): a long-term DNA profiling-based study conducted in a natural stream.

    abstract::Spawning success of Atlantic salmon (Salmo salar L.) was investigated, under near-natural conditions, in the Girnock Burn, an 8-km long tributary of the River Dee in Scotland. Employing minisatellite-based DNA profiling, mating outcomes were resolved over three spawning seasons by assigning parentage to progeny sample...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2001.01254.x

    authors: Taggart JB,McLaren IS,Hay DW,Webb JH,Youngson AF

    更新日期:2001-04-01 00:00:00

  • Estimation of gene flow in the tropical-rainforest tree Neobalanocarpus heimii (Dipterocarpaceae), inferred from paternity analysis.

    abstract::Pollen flow and population genetic structure among 30 potentially flowering individuals of Neobalanocarpus heimii, a tropical emergent tree, were investigated in a lowland tropical rainforest of Malaysia using microsatellite polymorphism. The 248 offspring in the vicinity of five reproductive trees of the 30 potential...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2000.01081.x

    authors: Konuma A,Tsumura Y,Lee CT,Lee SL,Okuda T

    更新日期:2000-11-01 00:00:00

  • Cytonuclear evidence for hybridogenetic reproduction in natural populations of the Australian carp gudgeon (Hypseleotris: Eleotridae).

    abstract::Although most vertebrates reproduce sexually, a small number of fishes, amphibians and reptiles are known in which reproduction is asexual, i.e. without meiotic recombination. In fishes, these so-called unisexual lineages usually comprise only females and utilize co-occurring males of a related sexual species to repro...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2011.05206.x

    authors: Schmidt DJ,Bond NR,Adams M,Hughes JM

    更新日期:2011-08-01 00:00:00

  • Exploring population genetic structure in three species of Lesser Antillean bats.

    abstract::We explore population genetic structure in phyllostomid bats (Ardops nichollsi, Brachyphylla cavernarum and Artibeus jamaicensis) from the northern Lesser Antilles by investigating the degree to which island populations are genetically differentiated. Our hypothesis, that the island populations are genetically distinc...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2004.02250.x

    authors: Carstens BC,Sullivan J,Davalos LM,Larsen PA,Pedersen SC

    更新日期:2004-09-01 00:00:00

  • Sex-specific genetic differentiation and coalescence times: estimating sex-biased dispersal rates.

    abstract::I derive the equilibrium values of sex-specific FST parameters, in an island model for a dioecious species with sex-biased dispersal and binomial distribution of family size before dispersal (as assumed in a Wright-Fisher population). I show that FST may take different values among males and among females whenever dis...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.0962-1083.2001.01414.x

    authors: Vitalis R

    更新日期:2002-01-01 00:00:00

  • Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae).

    abstract::Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal abili...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2004.02357.x

    authors: Schweiger O,Frenzel M,Durka W

    更新日期:2004-12-01 00:00:00

  • Interspecific hybridization and restricted trans-Pacific gene flow in the Tropical Eastern Pacific Pocillopora.

    abstract::Coral reefs in the Tropical Eastern Pacific (TEP) are among the most isolated in the world. This isolation has resulted in relatively low species diversity but comparatively high endemism. The dominant reef-building corals of the TEP are the Pocillopora corals, a ubiquitous Indo-Pacific genus commonly regarded as infe...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2007.03672.x

    authors: Combosch DJ,Guzman HM,Schuhmacher H,Vollmer SV

    更新日期:2008-03-01 00:00:00

  • Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes.

    abstract::Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographical features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13471

    authors: Saenz-Agudelo P,Dibattista JD,Piatek MJ,Gaither MR,Harrison HB,Nanninga GB,Berumen ML

    更新日期:2015-12-01 00:00:00

  • Gene network architecture as a canvas for the interpretation of ecological genomics investigations.

    abstract::New technologies promise to revolutionize the field of molecular ecology. This technological progress comes with its own set of challenges. Among the most important ones is the analysis and interpretation of the data in a way that tells us about the molecular causes of the phenotype of interest and its consequences. I...

    journal_title:Molecular ecology

    pub_type: 评论,杂志文章

    doi:10.1111/j.1365-294X.2010.04830.x

    authors: Landry CR,Aubin-Horth N

    更新日期:2010-12-01 00:00:00

  • Genomic footprints of a biological invasion: Introduction from Asia and dispersal in Europe of the topmouth gudgeon (Pseudorasbora parva).

    abstract::Facilitated by the intensification of global trading, the introduction and dispersal of species to areas in which they are historically non-native is nowadays common. From an evolutionary standpoint, invasions are paradoxical: not only non-native environments could be different from native ones for which introduced in...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15313

    authors: Baltazar-Soares M,Blanchet S,Cote J,Tarkan AS,Záhorská E,Gozlan RE,Eizaguirre C

    更新日期:2020-01-01 00:00:00

  • Paternal effects in a wild-type zebrafish implicate a role of sperm-derived small RNAs.

    abstract::While the importance of maternal effects has long been appreciated, a growing body of evidence now points to the paternal environment having an important influence on offspring phenotype. Indeed, research on rodent models suggests that paternal stress leaves an imprint on the behaviour and physiology of offspring via ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15505

    authors: Ord J,Heath PR,Fazeli A,Watt PJ

    更新日期:2020-07-01 00:00:00

  • Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks.

    abstract::Linear and heterogeneous habitat makes headwater stream networks an ideal ecosystem in which to test the influence of environmental factors on spatial genetic patterns of obligatory aquatic species. We investigated fine-scale population structure and influence of stream habitat on individual-level genetic differentiat...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2011.05210.x

    authors: Kanno Y,Vokoun JC,Letcher BH

    更新日期:2011-09-01 00:00:00

  • Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae).

    abstract::Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's successional history, we studi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2007.03361.x

    authors: Chung MY,Nason JD,Chung MG

    更新日期:2007-07-01 00:00:00

  • Diversity, distribution and exchange of blood parasites meeting at an avian moving contact zone.

    abstract::Research on contact zones has paid relatively little attention to host-parasite interactions, although these situations have important but different implications depending on whether one considers the host or the parasite's perspective. We investigated both the role of a host contact zone in parasite expansion and whe...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2005.02826.x

    authors: Reullier J,Pérez-Tris J,Bensch S,Secondi J

    更新日期:2006-03-01 00:00:00

  • Evolution rampant: house mice on Madeira.

    abstract::House mice are extra-ordinary animals -extra-ordinary in the literal sense of that word. They are pests - but also a valued laboratory animal. They are generalized rodents - and successful in habitats from tundra to tropics and from sea-level to high altitudes. They have differentiated into a perplexity of taxa, yet d...

    journal_title:Molecular ecology

    pub_type: 评论,杂志文章

    doi:10.1111/j.1365-294X.2009.04345.x

    authors: Berry RJ

    更新日期:2009-11-01 00:00:00

  • Phylogeography of the barbel (Barbus barbus) assessed by mitochondrial DNA variation.

    abstract::Using the phylogeographic framework, we assessed the DNA sequence variation at the mitochondrial cytochrome b gene across the distribution range of the barbel Barbus barbus, a widely distributed European cyprinid. Reciprocal monophyly of non-Mediterranean European and Balkan/Anatolian populations is taken as evidence ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.0962-1083.2001.01344.x

    authors: Kotlík P,Berrebi P

    更新日期:2001-09-01 00:00:00

  • Fine-scale diversity and specificity in the most prevalent lineage of symbiotic dinoflagellates (Symbiodinium, Dinophyceae) of the Caribbean.

    abstract::The success of coral reefs is due to obligate mutualistic symbioses involving invertebrates and photosynthetic dinoflagellate symbionts belonging to the genus Symbiodinium. In the Caribbean, the vast majority of octocorals and other invertebrate hosts associate with Symbiodinium clade B, and more selectively, with a s...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2003.02058.x

    authors: Santos SR,Shearer TL,Hannes AR,Coffroth MA

    更新日期:2004-02-01 00:00:00

  • The impact of stocking on the genetic integrity of Arctic charr (Salvelinus) populations from the Alpine region.

    abstract::There is a long tradition of artificially stocking lakes and rivers with fish in the hope to increase the quality and amount of fish that can be harvested. The animals used for stocking often originate in distant hatcheries or hatcheries that breed fish from remote regions. This stocking practice could have effects on...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2002.01498.x

    authors: Englbrecht CC,Schliewen U,Tautz D

    更新日期:2002-06-01 00:00:00

  • Molecular analysis of predation: a review of best practice for DNA-based approaches.

    abstract::Molecular analysis of predation, through polymerase chain reaction amplification of prey remains within the faeces or digestive systems of predators, is a rapidly growing field, impeded by a lack of readily accessible advice on best practice. Here, we review the techniques used to date and provide guidelines accessibl...

    journal_title:Molecular ecology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1365-294X.2007.03613.x

    authors: King RA,Read DS,Traugott M,Symondson WO

    更新日期:2008-02-01 00:00:00

  • 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...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15480

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

    更新日期:2020-06-01 00:00:00

  • Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs.

    abstract::Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional method...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13604

    authors: Hotaling S,Foley ME,Lawrence NM,Bocanegra J,Blanco MB,Rasoloarison R,Kappeler PM,Barrett MA,Yoder AD,Weisrock DW

    更新日期:2016-05-01 00:00:00

  • Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus).

    abstract::Investigating how environmental features shape the genetic structure of populations is crucial for understanding how they are potentially adapted to their habitats, as well as for sound management. In this study, we assessed the relative importance of spatial distribution, ocean currents and sea surface temperature (S...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13811

    authors: Benestan L,Quinn BK,Maaroufi H,Laporte M,Clark FK,Greenwood SJ,Rochette R,Bernatchez L

    更新日期:2016-10-01 00:00:00

  • Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations.

    abstract::Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in differ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13452

    authors: Santure AW,Poissant J,De Cauwer I,van Oers K,Robinson MR,Quinn JL,Groenen MA,Visser ME,Sheldon BC,Slate J

    更新日期:2015-12-01 00:00:00

  • Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin.

    abstract::Hybridization among conspecifics in native and introduced habitats has important implications for biological invasions in new ecosystems. Bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are genetically isolated and occur in sympatry within their native range. Following their introduction to North Am...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13285

    authors: Lamer JT,Ruebush BC,Arbieva ZH,McClelland MA,Epifanio JM,Sass GG

    更新日期:2015-08-01 00:00:00

  • Does genetic distance between parental species influence outcomes of hybridization among coral reef butterflyfishes?

    abstract::Christmas Island is located at the overlap of the Indian and Pacific Ocean marine provinces and is a hot spot for marine hybridization. Here, we evaluate the ecological framework and genetic consequences of hybridization between butterflyfishes Chaetodon guttatissimus and Chaetodon punctatofasciatus. Further, we compa...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12762

    authors: Montanari SR,Hobbs JP,Pratchett MS,Bay LK,Van Herwerden L

    更新日期:2014-06-01 00:00:00