Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges

Publication type:
Journal article
Metadata:
Autoren
  • Hanno Schmidt
  • Bastian Greshake
  • Barbara Feldmeyer
  • Thomas Hankeln
  • Markus Pfenninger
Sammlungen
  • metadata
ISSN
1471-2164
Zeitschrift
BMC genomics
Schlüsselwörter
  • 570 Biowissenschaften
  • 570 Life sciences
Sprache
eng
Paginierung
Art. 384
Datum der Veröffentlichung
2013
Herausgeber
BioMed Central
Herausgeber URL
http://dx.doi.org/10.1186/1471-2164-14-384
Datum der Datenerfassung
2020
Datum, an dem der Datensatz öffentlich gemacht wurde
2020
Zugang
Public
Titel
Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges
Ausgabe der Zeitschrift
14

Data source: METADATA.UB

Other metadata sources:
Autoren
  • Hanno Schmidt
  • Bastian Greshake
  • Barbara Feldmeyer
  • Thomas Hankeln
  • Markus Pfenninger
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000320535800001&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1186/1471-2164-14-384
Externe Identifier
  • Clarivate Analytics Document Solution ID: 166DW
  • PubMed Identifier: 23758757
ISSN
1471-2164
Zeitschrift
BMC GENOMICS
Schlüsselwörter
  • Adaptive sequence evolution
  • Positive selection
  • McDonald-Kreitman test
  • Chironomus riparius
  • Chironomus piger
Artikelnummer
ARTN 384
Datum der Veröffentlichung
2013
Status
Published
Titel
Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges
Sub types
  • Article
Ausgabe der Zeitschrift
14

Data source: Web of Science (Lite)

Abstract
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (<jats:italic>Chironomus riparius</jats:italic>and<jats:italic>C. piger</jats:italic>).</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>More than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Three candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species’ ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution.</jats:p></jats:sec>
Autoren
  • Hanno Schmidt
  • Bastian Greshake
  • Barbara Feldmeyer
  • Thomas Hankeln
  • Markus Pfenninger
DOI
10.1186/1471-2164-14-384
eISSN
1471-2164
Ausgabe der Veröffentlichung
1
Zeitschrift
BMC Genomics
Sprache
en
Artikelnummer
384
Online publication date
2013
Datum der Veröffentlichung
2013
Status
Published
Herausgeber
Springer Science and Business Media LLC
Herausgeber URL
http://dx.doi.org/10.1186/1471-2164-14-384
Datum der Datenerfassung
2022
Titel
Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges
Ausgabe der Zeitschrift
14

Data source: Crossref

Abstract
<h4>Background</h4>There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (Chironomus riparius and C. piger).<h4>Results</h4>More than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection.<h4>Conclusions</h4>Three candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species' ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution.
Addresses
  • Molecular Ecology Group, Biodiversity and Climate Research Centre (BiK-F) by Senckenberg Gesellschaft für Naturforschung and Goethe University, Biocampus Siesmayerstraße, Frankfurt am Main, 60054, Germany.
Autoren
  • Hanno Schmidt
  • Bastian Greshake
  • Barbara Feldmeyer
  • Thomas Hankeln
  • Markus Pfenninger
DOI
10.1186/1471-2164-14-384
eISSN
1471-2164
Externe Identifier
  • PubMed Identifier: 23758757
  • PubMed Central ID: PMC3685581
Open access
true
ISSN
1471-2164
Zeitschrift
BMC genomics
Schlüsselwörter
  • Animals
  • Chironomidae
  • Gene Expression Profiling
  • Sequence Alignment
  • Sequence Analysis
  • Genomics
  • Evolution, Molecular
  • Phylogeny
  • Polymorphism, Genetic
  • Ecological and Environmental Phenomena
  • Selection, Genetic
  • Molecular Sequence Annotation
Sprache
eng
Medium
Electronic
Online publication date
2013
Open access status
Open Access
Paginierung
384
Datum der Veröffentlichung
2013
Status
Published
Publisher licence
CC BY
Datum der Datenerfassung
2013
Titel
Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges.
Sub types
  • Research Support, Non-U.S. Gov't
  • research-article
  • Journal Article
Ausgabe der Zeitschrift
14

Files

https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-14-384 https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23758757/pdf/?tool=EBI https://europepmc.org/articles/PMC3685581?pdf=render

Data source: Europe PubMed Central

Abstract
BACKGROUND: There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (Chironomus riparius and C. piger). RESULTS: More than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection. CONCLUSIONS: Three candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species' ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution.
Date of acceptance
2013
Autoren
  • Hanno Schmidt
  • Bastian Greshake
  • Barbara Feldmeyer
  • Thomas Hankeln
  • Markus Pfenninger
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/23758757
DOI
10.1186/1471-2164-14-384
eISSN
1471-2164
Externe Identifier
  • PubMed Central ID: PMC3685581
Zeitschrift
BMC Genomics
Schlüsselwörter
  • Animals
  • Chironomidae
  • Ecological and Environmental Phenomena
  • Evolution, Molecular
  • Gene Expression Profiling
  • Genomics
  • Molecular Sequence Annotation
  • Phylogeny
  • Polymorphism, Genetic
  • Selection, Genetic
  • Sequence Alignment
  • Sequence Analysis
Sprache
eng
Country
England
Paginierung
384
PII
1471-2164-14-384
Datum der Veröffentlichung
2013
Status
Published online
Datum, an dem der Datensatz öffentlich gemacht wurde
2013
Titel
Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges.
Sub types
  • Journal Article
  • Research Support, Non-U.S. Gov't
Ausgabe der Zeitschrift
14

Data source: PubMed

Author's licence
CC-BY
Autoren
  • Hanno Schmidt
  • Bastian Greshake
  • Barbara Feldmeyer
  • Thomas Hankeln
  • Markus Pfenninger
Hosting institution
Universitätsbibliothek Mainz
Sammlungen
  • DFG-OA-Publizieren (2012 - 2017)
Resource version
Published version
DOI
10.1186/1471-2164-14-384
Funding acknowledgements
  • DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin
File(s) embargoed
false
Open access
true
ISSN
1471-2164
Zeitschrift
BMC genomics
Schlüsselwörter
  • 570 Biowissenschaften
  • 570 Life sciences
Sprache
eng
Open access status
Open Access
Paginierung
Art. 384
Datum der Veröffentlichung
2013
Public URL
https://openscience.ub.uni-mainz.de/handle/20.500.12030/7989
Herausgeber
BioMed Central
Herausgeber URL
http://dx.doi.org/10.1186/1471-2164-14-384
Datum der Datenerfassung
2022
Datum, an dem der Datensatz öffentlich gemacht wurde
2022
Zugang
Public
Titel
Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges
Ausgabe der Zeitschrift
14

Files

genomic_basis_of_ecological_n-20220925155415616.pdf

Data source: OPENSCIENCE.UB

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