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  1. AU="Stephen R. Palumbi"
  2. AU="Rosmarin, David H."
  3. AU="Dahal, Jeebika"
  4. AU="Ahanfeshar-Adams, Mozhdeh"
  5. AU="Rosa Pérez, Ana" AU="Rosa Pérez, Ana"
  6. AU="Snaith, Henry J"
  7. AU="Mao, Yimin"
  8. AU="Exel, Tim K"
  9. AU="Nelson, Noah T"
  10. AU="Surana, Amit"
  11. AU="Praetzel-Wunder, Silke"
  12. AU="Nabil, Fatima Mohamed"
  13. AU="Lindh, Christian"
  14. AU="Vetkas, Artur"
  15. AU="Gorelick, Root"
  16. AU="Mezdari, Zaineb"
  17. AU=Wilkinson Beverley
  18. AU=Halbower Ann C AU=Halbower Ann C
  19. AU="Ghosh, Ananya"
  20. AU="Spoletini, Gabriele"
  21. AU="Gracefo, Sara"
  22. AU="Works, Kaitlyn R"
  23. AU="LIU Lei"
  24. AU="McLennan, John D"
  25. AU=Dickinson Gordon M AU=Dickinson Gordon M
  26. AU=Hertzler Dean A 2nd
  27. AU="Yan, Xinrui"
  28. AU="Seal, M L"
  29. AU="Seka, Devin J"
  30. AU="Nguyen, Phuong T B"

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  1. Artikel ; Online: Rapid Adaptation to Temperature via a Potential Genomic Island of Divergence in the Invasive Green Crab, Carcinus maenas

    Carolyn K. Tepolt / Stephen R. Palumbi

    Frontiers in Ecology and Evolution, Vol

    2020  Band 8

    Abstract: Widespread species often adapt easily to novel conditions – both those found in new habitats and those generated by climate change. However, rapid adaptation may be hindered in the marine realm, where long-distance dispersal and consequently high gene ... ...

    Abstract Widespread species often adapt easily to novel conditions – both those found in new habitats and those generated by climate change. However, rapid adaptation may be hindered in the marine realm, where long-distance dispersal and consequently high gene flow are predicted to limit potential for local adaptation. Here, we use a highly dispersive invasive marine crab to test the nature and speed of adaptation to temperature in the sea. Using single nucleotide polymorphisms (SNPs) generated from cardiac transcriptome sequencing, we characterized six populations of the European green crab (Carcinus maenas) located across parallel thermal gradients in their native and invasive ranges. We compared SNP frequencies with local temperatures and previously generated data on cardiac heat and cold tolerance to identify candidate markers associated with population-level differences in thermal physiology. Of 10,790 SNPs, 104 were identified as frequency outliers, a signal that was strongly driven by association with temperature and/or cold tolerance. Seventy-two of these outlier markers, representing 28 different genes, were in a cluster of SNPs identified as a potential inversion polymorphism using linkage disequilibrium network analysis. This SNP cluster was unique in the data set, which was otherwise characterized by low levels of linkage disequilibrium, and markers in this cluster showed a significant enrichment of coding substitutions relative to the full SNP set. These 72 outlier SNPs appear to be transmitted as a unit, and represent a putative genomic island of divergence which varied in frequency with organismal cold tolerance. This relationship was strikingly similar across both native and invasive populations, all of which showed a very strong correlation with cold tolerance (R2 = 0.96 over all six populations). Notably, three of these populations have diverged recently (<100 years) and show little to no neutral divergence, suggesting that this genomic region may be responding to temperature on a relatively short time scale. This relationship indicates adaptation to temperature based on the action of a putative genomic island of divergence, perhaps partially explaining the extraordinary invasive ability of this species.
    Schlagwörter rapid adaptation ; supergene ; thermal adaptation ; gene flow ; invasive species ; balanced polymorphism ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
    Thema/Rubrik (Code) 333
    Sprache Englisch
    Erscheinungsdatum 2020-11-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Widespread variation in heat tolerance and symbiont load are associated with growth tradeoffs in the coral Acropora hyacinthus in Palau

    Brendan Cornwell / Katrina Armstrong / Nia S Walker / Marilla Lippert / Victor Nestor / Yimnang Golbuu / Stephen R Palumbi

    eLife, Vol

    2021  Band 10

    Abstract: Climate change is dramatically changing ecosystem composition and productivity, leading scientists to consider the best approaches to map natural resistance and foster ecosystem resilience in the face of these changes. Here, we present results from a ... ...

    Abstract Climate change is dramatically changing ecosystem composition and productivity, leading scientists to consider the best approaches to map natural resistance and foster ecosystem resilience in the face of these changes. Here, we present results from a large-scale experimental assessment of coral bleaching resistance, a critical trait for coral population persistence as oceans warm, in 221 colonies of the coral Acropora hyacinthus across 37 reefs in Palau. We find that bleaching-resistant individuals inhabit most reefs but are found more often in warmer microhabitats. Our survey also found wide variation in symbiont concentration among colonies, and that colonies with lower symbiont load tended to be more bleaching-resistant. By contrast, our data show that low symbiont load comes at the cost of lower growth rate, a tradeoff that may operate widely among corals across environments. Corals with high bleaching resistance have been suggested as a source for habitat restoration or selective breeding in order to increase coral reef resilience to climate change. Our maps show where these resistant corals can be found, but the existence of tradeoffs with heat resistance may suggest caution in unilateral use of this one trait in restoration.
    Schlagwörter Acropora hyacinthus ; bleaching resistance ; fitness tradeoffs ; local adaptation ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 612 ; 551
    Sprache Englisch
    Erscheinungsdatum 2021-08-01T00:00:00Z
    Verlag eLife Sciences Publications Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Forschungsdaten: (mit Forschungsdaten) Practical low‐coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

    Therkildsen, Nina Overgaard / Stephen R. Palumbi

    Molecular ecology resources. 2017 Mar., v. 17, no. 2

    2017  

    Abstract: Today most population genomic studies of nonmodel organisms either sequence a subset of the genome deeply in each individual or sequence pools of unlabelled individuals. With a step‐by‐step workflow, we illustrate how low‐coverage whole‐genome ... ...

    Abstract Today most population genomic studies of nonmodel organisms either sequence a subset of the genome deeply in each individual or sequence pools of unlabelled individuals. With a step‐by‐step workflow, we illustrate how low‐coverage whole‐genome sequencing of hundreds of individually barcoded samples is now a practical alternative strategy for obtaining genomewide data on a population scale. We used a highly efficient protocol to generate high‐quality libraries for ~6.5 USD from each of 876 Atlantic silversides (a teleost fish with a genome size ~730 Mb) that we sequenced to 1–4× genome coverage. In the absence of a reference genome, we developed a bioinformatic pipeline for mapping the genomic reads to a de novo assembled reference transcriptome. This provides an ‘in silico’ method for exome capture that avoids the complexities and expenses of using wet chemistry for target isolation. Using novel tools for analysis of low‐coverage data, we extracted population allele frequencies, individual genotype likelihoods and polymorphism data for 2 504 335 SNPs across the exome for the 876 fish. To illustrate the use of the resulting data, we present a preliminary analysis of geographical patterns in the exome data and a comparison of complete mitochondrial genome sequences for each individual (constructed from the low‐coverage data) that show population colonization patterns along the US east coast. With a total cost per sample of less than 50 USD (including sequencing) and ability to prepare 96 libraries in only 5 h, our approach adds a viable new option to the population genomics toolbox.
    Schlagwörter bioinformatics ; coasts ; DNA barcoding ; fish ; gene frequency ; genotype ; metagenomics ; mitochondrial genome ; single nucleotide polymorphism ; transcriptome ; United States
    Sprache Englisch
    Erscheinungsverlauf 2017-03
    Umfang p. 194-208.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel ; Forschungsdaten
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 2406816-0
    ISSN 1471-8286 ; 1755-098X ; 1755-098X
    ISSN (online) 1471-8286
    ISSN 1755-098X
    DOI 10.1111/1755-0998.12593
    Datenquelle NAL Katalog (AGRICOLA)

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  4. Artikel: Uncovering hidden worlds of ocean biodiversity

    Armbrust, E. Virginia / Stephen R. Palumbi

    Science. 2015 May 22, v. 348, no. 6237

    2015  

    Abstract: A bewildering swirl of tiny creatures dominates life in the oceans. More numerous than the stars in the universe, these organisms serve as the foundation of all marine food webs, recycling major elements and producing and consuming about half the organic ...

    Abstract A bewildering swirl of tiny creatures dominates life in the oceans. More numerous than the stars in the universe, these organisms serve as the foundation of all marine food webs, recycling major elements and producing and consuming about half the organic matter generated on Earth each year (1). In this issue, five research articles from the Tara Oceans expedition (2 – 6) provide a vivid, potentially transformative view of the genetic diversity and interconnectivity of these unseen marine communities of viruses, bacteria, archaea, single-celled eukaryotes, and small planktonic animals (see the figure). Together, these studies deliver compelling evidence for extensive networks of previously hidden biological interactions in the sea.
    Schlagwörter animals ; Archaea ; bacteria ; biodiversity ; eukaryotic cells ; food webs ; genetic variation ; oceans ; organic matter ; plankton ; viruses
    Sprache Englisch
    Erscheinungsverlauf 2015-0522
    Umfang p. 865-867.
    Erscheinungsort American Association for the Advancement of Science
    Dokumenttyp Artikel
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.aaa7378
    Datenquelle NAL Katalog (AGRICOLA)

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  5. Artikel ; Online: Bacterial community dynamics are linked to patterns of coral heat tolerance

    Maren Ziegler / Francois O. Seneca / Lauren K. Yum / Stephen R. Palumbi / Christian R. Voolstra

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Band 8

    Abstract: Coral-associated microbes could enhance the capacity of their host organism to respond to environmental change. Ziegler and colleagues use a reciprocal transplant experiment to show that microbiomes of heat-tolerant corals are more resilient to change ... ...

    Abstract Coral-associated microbes could enhance the capacity of their host organism to respond to environmental change. Ziegler and colleagues use a reciprocal transplant experiment to show that microbiomes of heat-tolerant corals are more resilient to change than those of heat-sensitive corals.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2017-02-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel: Transcriptomic responses to seawater acidification among sea urchin populations inhabiting a natural pH mosaic

    Evans, Tyler G / Eric Sanford / Gretchen E. Hofmann / Melissa H. Pespeni / Stephen R. Palumbi

    Molecular ecology. 2017 Apr., v. 26, no. 8

    2017  

    Abstract: Increasing awareness of spatial and temporal variation in ocean pH suggests some marine populations may be adapted to local pH regimes and will therefore respond differently to present‐day pH variation and to long‐term ocean acidification. In the ... ...

    Abstract Increasing awareness of spatial and temporal variation in ocean pH suggests some marine populations may be adapted to local pH regimes and will therefore respond differently to present‐day pH variation and to long‐term ocean acidification. In the Northeast Pacific Ocean, differences in the strength of coastal upwelling cause latitudinal variation in prevailing pH regimes that are hypothesized to promote local adaptation and unequal pH tolerance among resident populations. In this study, responses to experimental seawater acidification were compared among embryos and larvae from six populations of purple sea urchins (Strongylocentrotus purpuratus) inhabiting areas that differ in their frequency of low pH exposure and that prior research suggests are locally adapted to seawater pH. Transcriptomic analyses demonstrate urchin populations most frequently exposed to low pH seawater responded to experimental acidification by expressing genes within major ATP‐producing pathways at greater levels than populations encountering low pH less often. Multiple genes within the tricarboxylic acid cycle, electron transport chain and fatty acid beta oxidation pathways were upregulated in urchin populations experiencing low pH conditions most frequently. These same metabolic pathways were significantly over‐represented among genes both expressed in a population‐specific manner and putatively under selection to enhance low pH tolerance. Collectively, these data suggest natural selection is acting on metabolic gene networks to redirect ATP toward maintaining acid–base homeostasis and enhance tolerance of seawater acidification. As a trade‐off, marine populations more tolerant of low pH may have less energy to put towards other aspects of fitness and to respond to additional ocean change.
    Schlagwörter acid tolerance ; acidification ; adenosine triphosphate ; beta oxidation ; electron transport chain ; energy ; fatty acids ; gene expression regulation ; gene regulatory networks ; genes ; homeostasis ; larvae ; natural selection ; ocean acidification ; pH ; seawater ; Strongylocentrotus purpuratus ; temporal variation ; transcriptomics ; tricarboxylic acid cycle ; Pacific Ocean
    Sprache Englisch
    Erscheinungsverlauf 2017-04
    Umfang p. 2257-2275.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.14038
    Datenquelle NAL Katalog (AGRICOLA)

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  7. Artikel ; Online: Mechanisms of Thermal Tolerance in Reef-Building Corals across a Fine-Grained Environmental Mosaic

    Luke Thomas / Noah H. Rose / Rachael A. Bay / Elora H. López / Megan K. Morikawa / Lupita Ruiz-Jones / Stephen R. Palumbi

    Frontiers in Marine Science, Vol

    Lessons from Ofu, American Samoa

    2018  Band 4

    Abstract: Environmental heterogeneity gives rise to phenotypic variation through a combination of phenotypic plasticity and fixed genetic effects. For reef-building corals, understanding the relative roles of acclimatization and adaptation in generating thermal ... ...

    Abstract Environmental heterogeneity gives rise to phenotypic variation through a combination of phenotypic plasticity and fixed genetic effects. For reef-building corals, understanding the relative roles of acclimatization and adaptation in generating thermal tolerance is fundamental to predicting the response of coral populations to future climate change. The temperature mosaic in the lagoon of Ofu, American Samoa, represents an ideal natural laboratory for studying thermal tolerance in corals. Two adjacent back-reef pools approximately 500 m apart have different temperature profiles: the highly variable (HV) pool experiences temperatures that range from 24.5 to 35°C, whereas the moderately variable (MV) pool ranges from 25 to 32°C. Standardized heat stress tests have shown that corals native to the HV pool have consistently higher levels of bleaching resistance than those in the MV pool. In this review, we summarize research into the mechanisms underlying this variation in bleaching resistance, focusing on the important reef-building genus Acropora. Both acclimatization and adaptation occur strongly and define thermal tolerance differences between pools. Most individual corals shift physiology to become more heat resistant when moved into the warmer pool. Lab based tests show that these shifts begin in as little as a week and are equally sparked by exposure to periodic high temperatures as constant high temperatures. Transcriptome-wide data on gene expression show that a wide variety of genes are co-regulated in expression modules that change expression after experimental heat stress, after acclimatization, and even after short term environmental fluctuations. Population genetic scans show associations between a corals' thermal environment and its alleles at 100s to 1000s of nuclear genes and no single gene confers strong environmental effects within or between species. Symbionts also tend to differ between pools and species, and the thermal tolerance of a coral is a reflection of individual host genotype and specific ...
    Schlagwörter phenotypic plasticity ; polygenic adaptation ; coral reefs ; thermal tolerance ; acclimatization ; Acropora ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
    Thema/Rubrik (Code) 333
    Sprache Englisch
    Erscheinungsdatum 2018-02-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: Genetic structure among 50 species of the northeastern Pacific rocky intertidal community.

    Ryan P Kelly / Stephen R Palumbi

    PLoS ONE, Vol 5, Iss 1, p e

    2010  Band 8594

    Abstract: Comparing many species' population genetic patterns across the same seascape can identify species with different levels of structure, and suggest hypotheses about the processes that cause such variation for species in the same ecosystem. This comparative ...

    Abstract Comparing many species' population genetic patterns across the same seascape can identify species with different levels of structure, and suggest hypotheses about the processes that cause such variation for species in the same ecosystem. This comparative approach helps focus on geographic barriers and selective or demographic processes that define genetic connectivity on an ecosystem scale, the understanding of which is particularly important for large-scale management efforts. Moreover, a multispecies dataset has great statistical advantages over single-species studies, lending explanatory power in an effort to uncover the mechanisms driving population structure. Here, we analyze a 50-species dataset of Pacific nearshore invertebrates with the aim of discovering the most influential structuring factors along the Pacific coast of North America. We collected cytochrome c oxidase I (COI) mtDNA data from populations of 34 species of marine invertebrates sampled coarsely at four coastal locations in California, Oregon, and Alaska, and added published data from 16 additional species. All nine species with non-pelagic development have strong genetic structure. For the 41 species with pelagic development, 13 show significant genetic differentiation, nine of which show striking FST levels of 0.1-0.6. Finer scale geographic investigations show unexpected regional patterns of genetic change near Cape Mendocino in northern California for five of the six species tested. The region between Oregon and Alaska is a second focus of intraspecific genetic change, showing differentiation in half the species tested. Across regions, strong genetic subdivision occurs more often than expected in mid-to-high intertidal species, a result that may reflect reduced gene flow due to natural selection along coastal environmental gradients. Finally, the results highlight the importance of making primary research accessible to policymakers, as unexpected barriers to marine dispersal break the coast into separate demographic zones that may ...
    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2010-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales

    S Elizabeth Alter / Seth D Newsome / Stephen R Palumbi

    PLoS ONE, Vol 7, Iss 5, p e

    insights from ancient DNA and stable isotopes.

    2012  Band 35039

    Abstract: Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population ... ...

    Abstract Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 333
    Sprache Englisch
    Erscheinungsdatum 2012-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel ; Online: Correction

    Vanessa K. Michelou / J. Gregory Caporaso / Rob Knight / Stephen R. Palumbi

    PLoS ONE, Vol 8, Iss

    The Ecology of Microbial Communities Associated with Macrocystis pyrifera.

    2013  Band 12

    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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