GLORIA

GEOMAR Library Ocean Research Information Access

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    In: Ecology and Evolution, Wiley, Vol. 13, No. 10 ( 2023-10)
    Abstract: A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei , a noneusocial hymenopteran and exemplar of a pine‐specialized lineage evolved from angiosperm‐feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high‐quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under‐sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2635675-2
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 2
    In: Molecular Ecology, Wiley, Vol. 24, No. 11 ( 2015-06), p. 2759-2776
    Abstract: Host race formation, the establishment of new populations using novel resources, is a major hypothesized mechanism of ecological speciation, especially in plant‐feeding insects. The initial stages of host race formation will often involve phenotypic plasticity on the novel resource, with subsequent genetically based adaptations enhancing host‐associated fitness differences. Several studies have explored the physiology of the plastic responses of insects to novel host environments. However, the mechanisms underlying evolved differences among host races and species remain poorly understood. Here, we demonstrate a reciprocal larval performance difference between two closely related species of R hagoletis flies, R . pomonella and R . zephyria , specialized for feeding in apple and snowberry fruit, respectively. Microarray analysis of fly larvae feeding in apples versus snowberries revealed patterns of transcriptome‐wide differential gene expression consistent with both plastic and evolved responses to the different fruit resources, most notably for detoxification‐related genes such as cytochrome p450s. Transcripts exhibiting evolved expression differences between species tended to also demonstrate plastic responses to fruit environment. The observed pattern suggests that R hagoletis larvae exhibit extensive plasticity in gene expression in response to novel fruit that may potentiate shifts to new hosts. Subsequent selection, particularly selection to suppress initially costly plastic responses, could account for the evolved expression differences observed between R . pomonella and R . zephyria , creating specialized races and new fly species. Thus, genetically based ecological adaptations generating new biodiversity may often evolve from initial plastic responses in gene expression to the challenges posed by novel environments.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 3
    In: Molecular Ecology, Wiley, Vol. 30, No. 18 ( 2021-09), p. 4551-4566
    Abstract: Though seemingly bizarre, the dramatic morphological and ecological transformation that occurs when immature life stages metamorphose into reproductive adults is one of the most successful developmental strategies on the planet. The adaptive decoupling hypothesis (ADH) proposes that metamorphosis is an adaptation for breaking developmental links between traits expressed in different life stages, thereby facilitating their independent evolution when exposed to opposing selection pressures. Here, we draw inspiration from the ADH to develop a conceptual framework for understanding changes in gene expression across ontogeny. We hypothesized that patterns of stage‐biased and sex‐biased gene expression are the product of both decoupling mechanisms and selection history. To test this hypothesis, we characterized transcriptome‐wide patterns of gene‐expression traits for three ecologically distinct larval stages (all male) and adult males and females of a hypermetamorphic insect ( Neodiprion lecontei ). We found that stage‐biased gene expression was most pronounced between larval and adult males, which is consistent with the ADH. However, even in the absence of a metamorphic transition, considerable stage‐biased expression was observed among morphologically and behaviourally distinct larval stages. Stage‐biased expression was also observed across ecologically relevant Gene Ontology categories and genes, highlighting the role of ecology in shaping patterns of gene expression. We also found that the magnitude and prevalence of stage‐biased expression far exceeded adult sex‐biased expression. Overall, our results highlight how the ADH can shed light on transcriptome‐wide patterns of gene expression in organisms with complex life cycles. For maximal insight, detailed knowledge of organismal ecology is also essential.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 4
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 9, No. 6 ( 2017-06-01), p. 1687-1698
    Type of Medium: Online Resource
    ISSN: 1759-6653
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
    detail.hit.zdb_id: 2495328-3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2017
    In:  BMC Evolutionary Biology Vol. 17, No. 1 ( 2017-12)
    In: BMC Evolutionary Biology, Springer Science and Business Media LLC, Vol. 17, No. 1 ( 2017-12)
    Type of Medium: Online Resource
    ISSN: 1471-2148
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2041493-6
    detail.hit.zdb_id: 3053924-9
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 6
    Online Resource
    Online Resource
    Wiley ; 2017
    In:  Annals of the New York Academy of Sciences Vol. 1389, No. 1 ( 2017-02), p. 186-212
    In: Annals of the New York Academy of Sciences, Wiley, Vol. 1389, No. 1 ( 2017-02), p. 186-212
    Abstract: Adaptation to different host taxa is a key driver of insect diversification. Herbivorous insects are classic models for ecological and evolutionary research, but it is recent advances in sequencing, statistics, and molecular technologies that have cleared the way for investigations into the proximate genetic mechanisms underlying host shifts. In this review, we discuss how genome‐scale data are revealing—at resolutions previously unimaginable—the genetic architecture of host‐use traits, the causal loci underlying host shifts, and the predictability of host‐use evolution. Collectively, these studies are providing novel insights into longstanding questions about host‐use evolution. On the basis of this synthesis, we suggest that different host‐use traits are likely to differ in their genetic architecture (number of causal loci and the nature of their genetic correlations) and genetic predictability (extent of gene or mutation reuse), indicating that any conclusions about the causes and consequences of host‐use evolution will depend heavily on which host‐use traits are investigated. To draw robust conclusions and identify general patterns in host‐use evolution, we argue that investigation of diverse host‐use traits and identification of causal genes and mutations should be the top priorities for future studies on the evolutionary genetics of host shifts.
    Type of Medium: Online Resource
    ISSN: 0077-8923 , 1749-6632
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2834079-6
    detail.hit.zdb_id: 211003-9
    detail.hit.zdb_id: 2071584-5
    SSG: 11
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 7
    In: Bioinformatics, Oxford University Press (OUP)
    Abstract: Single nucleotide polymorphism (SNP) markers are increasingly popular for population genomics and inferring ancestry for individuals of unknown origin. Because large SNP datasets are impractical for rapid and routine analysis, diagnostics rely on panels of highly informative markers. Strategies exist for selecting these markers, however, resources for efficiently evaluating their performance are limited for non-model systems. Results snpAIMeR is a user-friendly R package that evaluates the efficacy of genomic markers for the cluster assignment of unknown individuals. It is intended to help minimize panel size and genotyping effort by determining the informativeness of candidate diagnostic markers. Provided genotype data from individuals of known origin, it uses leave-one-out cross-validation to determine population assignment rates for individual markers and marker combinations. Availability snpAIMeR is available on CRAN (https://CRAN.R-project.org/package=snpAIMeR). Supplementary information Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 1468345-3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 8
    In: Evolutionary Applications, Wiley, Vol. 17, No. 3 ( 2024-03)
    Abstract: Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage‐based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species‐specific Genotyping‐in‐Thousands by sequencing (GT‐seq) panels. For laboratories involved in large‐scale genotyping efforts, diagnosing non‐target species and reassigning them to the appropriate monitoring program can be costly and time‐consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross‐species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species‐specific GT‐seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species‐informative amplicons (16) were newly identified from the four existing GT‐seq panels, thus demonstrating a low‐cost approach to species identification when using targeted sequencing methods. A species‐calling script was developed that is tailored for routine GT‐seq genotyping pipelines and automates the identification of non‐target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low‐frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost‐effective approach to species identification for genetic monitoring programs.
    Type of Medium: Online Resource
    ISSN: 1752-4571 , 1752-4571
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2024
    detail.hit.zdb_id: 2405496-3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...