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 captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM(©) , we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals' diet to generate tissue correction factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected) to 14 ± 9% (TCF-corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate digestion correction factors (DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.

journal_name

Mol Ecol

journal_title

Molecular ecology

authors

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

doi

10.1111/mec.12523

subject

Has Abstract

pub_date

2014-08-01 00:00:00

pages

3706-18

issue

15

eissn

0962-1083

issn

1365-294X

journal_volume

23

pub_type

杂志文章
  • A comparison of genomic islands of differentiation across three young avian species pairs.

    abstract::Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in FST ), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of different...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14858

    authors: Irwin DE,Milá B,Toews DPL,Brelsford A,Kenyon HL,Porter AN,Grossen C,Delmore KE,Alcaide M,Irwin JH

    更新日期:2018-12-01 00:00:00

  • Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs.

    abstract::Digital gene expression (DGE) analysis offers a route to gene discovery which by-passes the need to develop bespoke arrays for nonmodel species, and is therefore a potentially valuable tool for molecular ecologists. Scottish blackface sheep, which vary in resistance to the common abomasal parasitic nematode Teladorsag...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2010.04992.x

    authors: Pemberton JM,Beraldi D,Craig BH,Hopkins J

    更新日期:2011-03-01 00:00:00

  • Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil.

    abstract::Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Q...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14239

    authors: Gehara M,Garda AA,Werneck FP,Oliveira EF,da Fonseca EM,Camurugi F,Magalhães FM,Lanna FM,Sites JW Jr,Marques R,Silveira-Filho R,São Pedro VA,Colli GR,Costa GC,Burbrink FT

    更新日期:2017-09-01 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

  • A range-wide genetic bottleneck overwhelms contemporary landscape factors and local abundance in shaping genetic patterns of an alpine butterfly (Lepidoptera: Pieridae: Colias behrii).

    abstract::Spatial and environmental heterogeneity are major factors in structuring species distributions in alpine landscapes. These landscapes have also been affected by glacial advances and retreats, causing alpine taxa to undergo range shifts and demographic changes. These nonequilibrium population dynamics have the potentia...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2012.05696.x

    authors: Schoville SD,Lam AW,Roderick GK

    更新日期:2012-09-01 00:00:00

  • Molecular and quantitative trait variation across the native range of the invasive species Hypericum canariense: evidence for ancient patterns of colonization via pre-adaptation?

    abstract::To understand the success of invasive species, it is important to know whether colonization events are facilitated by adaptive evolution or are limited to sites where a species is pre-adapted to thrive. Studies of the ancient colonization patterns of an invader in its native range provide an opportunity to examine its...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2007.03508.x

    authors: Dlugosch KM,Parker IM

    更新日期:2007-10-01 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

  • 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

  • Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

    abstract::Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throu...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14396

    authors: Chen YL,Deng Y,Ding JZ,Hu HW,Xu TL,Li F,Yang GB,Yang YH

    更新日期:2017-12-01 00:00:00

  • Postglacial climate changes and rise of three ecotypes of harbour porpoises, Phocoena phocoena, in western Palearctic waters.

    abstract::Despite no obvious barriers to gene flow in the marine realm, environmental variation and ecological specializations can lead to genetic differentiation in highly mobile predators. Here, we investigated the genetic structure of the harbour porpoise over the entire species distribution range in western Palearctic water...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12817

    authors: Fontaine MC,Roland K,Calves I,Austerlitz F,Palstra FP,Tolley KA,Ryan S,Ferreira M,Jauniaux T,Llavona A,Öztürk B,Öztürk AA,Ridoux V,Rogan E,Sequeira M,Siebert U,Vikingsson GA,Borrell A,Michaux JR,Aguilar A

    更新日期:2014-07-01 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

  • Genetic structure and distinctness of Apis mellifera L. populations from the Canary Islands.

    abstract::The genetic structure of Apis mellifera populations from the Canary Islands has been assessed by mitochondrial (restriction fragment length polymorphisms of the intergenic transfer RNAleu-COII region) and nuclear (microsatellites) studies. These populations show a low level of genetic variation in terms of average num...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2001.01303.x

    authors: De la Rúa P,Galián J,Serrano J,Moritz RF

    更新日期:2001-07-01 00:00:00

  • Fungal host specificity is not a bottleneck for the germination of Pyroleae species (Ericaceae) in a Bavarian forest.

    abstract::Plants that produce dust seeds can recruit fungi to meet their earliest requirements for carbon and other nutrients. This germination strategy, termed initial mycoheterotrophy, has been well investigated among the orchid family, but there are numerous other plant lineages that have independently evolved mycoheterotrop...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12180

    authors: Hynson NA,Weiß M,Preiss K,Gebauer G,Treseder KK

    更新日期:2013-03-01 00:00:00

  • Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios.

    abstract::The application of spatially explicit models of population dynamics to fisheries management and the design marine reserve network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity u...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04109.x

    authors: Saenz-Agudelo P,Jones GP,Thorrold SR,Planes S

    更新日期:2009-04-01 00:00:00

  • The coup de grâce for the nested clade phylogeographic analysis?

    abstract::Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the history of populations across species ranges. Ever since its invention in 1995, criticisms have been formulated, but the method, which has been regularly updated, continues to attract investigators. Molecular Ecology has pu...

    journal_title:Molecular ecology

    pub_type: 新闻

    doi:10.1111/j.1365-294X.2007.03589.x

    authors: Petit RJ

    更新日期:2008-01-01 00:00:00

  • DNA from soil mirrors plant taxonomic and growth form diversity.

    abstract::Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughpu...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2012.05545.x

    authors: Yoccoz NG,Bråthen KA,Gielly L,Haile J,Edwards ME,Goslar T,Von Stedingk H,Brysting AK,Coissac E,Pompanon F,Sønstebø JH,Miquel C,Valentini A,De Bello F,Chave J,Thuiller W,Wincker P,Cruaud C,Gavory F,Rasmussen M,Gilb

    更新日期:2012-08-01 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

  • New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations.

    abstract::Seagrass meadows are among the most important coastal ecosystems in terms of both spatial extent and ecosystem services, but they are also declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for designing sound management, conservation and restoration strategies. However, poor knowl...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15532

    authors: Arnaud-Haond S,Stoeckel S,Bailleul D

    更新日期:2020-09-01 00:00:00

  • Amassing diversity in an ancient lake: evolution of a morphologically diverse parthenogenetic gastropod assemblage in Lake Malawi.

    abstract::Exceptional ecological niche diversity, clear waters and unique divergent selection pressures have often been invoked to explain high morphological and genetic diversity of taxa within ancient lakes. However, it is possible that in some ancient lake taxa high diversity has arisen because these historically stable envi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2006.03171.x

    authors: Genner MJ,Todd JA,Michel E,Erpenbeck D,Jimoh A,Joyce DA,Piechocki A,Pointier JP

    更新日期:2007-02-01 00:00:00

  • Macrogeographic population structuring in the cosmopolitan agricultural pest Bactrocera cucurbitae (Diptera: Tephritidae).

    abstract::The macrogeographic population structure of the agricultural pest Bactrocera cucurbitae (Diptera: Tephritidae) was investigated in order to identify the geographic origin of the species and reconstruct its range expansion. Individuals of B. cucurbitae were collected from 25 worldwide-distributed localities (n = 570) a...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2010.04662.x

    authors: Virgilio M,Delatte H,Backeljau T,De Meyer M

    更新日期:2010-07-01 00:00:00

  • Did the pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers.

    abstract::There is a long-standing debate over whether or not the Pleistocene glaciations promoted speciation. While some models predict that extensive mixing of populations during interglacial expansion would have inhibited divergence, others postulate that divergence among allopatric glacial refuges or founder events during r...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2001.01206.x

    authors: Knowles LL

    更新日期:2001-03-01 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

  • 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

  • Past and future demographic dynamics of alpine species: limited genetic consequences despite dramatic range contraction in a plant from the Spanish Sierra Nevada.

    abstract::Anthropogenic global climate change is expected to cause severe range contractions among alpine plants. Alpine areas in the Mediterranean region are of special concern because of the high abundance of endemic species with narrow ranges. This study combined species distribution models, population structure analyses and...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12383

    authors: Blanco-Pastor JL,Fernández-Mazuecos M,Vargas P

    更新日期:2013-08-01 00:00:00

  • Gynodioecy in structured populations: understanding fine-scale sex ratio variation in Beta vulgaris ssp. maritima.

    abstract::Natural selection, random processes and gene flow are known to generate sex ratio variations among sexually polymorphic plant populations. In gynodioecious species, in which hermaphrodites and females coexist, the relative effect of these processes on the maintenance of sex polymorphism is still up for debate. The aim...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2011.05414.x

    authors: De Cauwer I,Dufay M,Hornoy B,Courseaux A,Arnaud JF

    更新日期:2012-02-01 00:00:00

  • Evidence for selective sweeps by Wolbachia infections: phylogeny of Altica leaf beetles and their reproductive parasites.

    abstract::Infections with maternally inherited Wolbachia bacteria may have dramatic influences on reproductive traits and speciation patterns of their hosts. We here show that in the beetle genus Altica, infection has influenced phylogenetic patterns of the host's mtDNA and different strains led to repeated selective sweeps. By...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12389

    authors: Jäckel R,Mora D,Dobler S

    更新日期:2013-08-01 00:00:00

  • Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana).

    abstract::Replicated ecological gradients are prime systems to study processes of molecular evolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H2 S) and compared two population pairs of sulphide-adapt...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13397

    authors: Pfenninger M,Patel S,Arias-Rodriguez L,Feldmeyer B,Riesch R,Plath M

    更新日期:2015-11-01 00:00:00

  • Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline.

    abstract::This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo-Pacific. If mixing o...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12754

    authors: Vignaud TM,Maynard JA,Leblois R,Meekan MG,Vázquez-Juárez R,Ramírez-Macías D,Pierce SJ,Rowat D,Berumen ML,Beeravolu C,Baksay S,Planes S

    更新日期:2014-05-01 00:00:00

  • Fire coral clones demonstrate phenotypic plasticity among reef habitats.

    abstract::Clonal populations are often characterized by reduced levels of genotypic diversity, which can translate into lower numbers of functional phenotypes, both of which impede adaptation. Study of partially clonal animals enables examination of the environmental settings under which clonal reproduction is favoured. Here, w...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.14165

    authors: Dubé CE,Boissin E,Maynard JA,Planes S

    更新日期:2017-08-01 00:00:00

  • Genetic monitoring to assess the success of restoring rare plant populations with mixed gene pools.

    abstract::Increasing genetic diversity and maintaining evolutionary processes are primary goals of conservation translocations, which involve the intentional movement of an at-risk species to establish new populations or augment existing populations, with the ultimate goal of reversing declines. Much debate has focused on how t...

    journal_title:Molecular ecology

    pub_type: 评论,杂志文章

    doi:10.1111/mec.15658

    authors: Albrecht MA,Edwards CE

    更新日期:2020-11-01 00:00:00