Genomic and Transcriptomic Differentiation of Independent Invasions of the Pacific Oyster Crassostrea gigas

Wegner, K. Mathias; Lokmer, Ana; John, Uwe

doi:10.3389/fevo.2020.567049

Cited by 3 publications

(1 citation statement)

References 65 publications

(90 reference statements)

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“…In a rare comparison of sequence variation and expression variation, a study of two independent invasions of the Pacific Oyster (Crassostrea gigas) into the North Sea found little overlap between differentially expressed genes and outlier loci. This suggested that differential gene expression did not necessarily correlate with changes in allele frequencies (Wegner et al, 2020). However, as is common in ecological genomics, this study suffered from limited annotation of the transcriptome and limited coverage of the genome (using reduced representation RADseq).…”

Section: Discoveries and Limitations Of Genomic Studies Of Diverse Invasive Speciesmentioning

confidence: 99%

The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again

et al. 2021

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The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.

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Section: Discoveries and Limitations Of Genomic Studies Of Diverse Invasive Speciesmentioning

confidence: 99%

The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again

et al. 2021

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Climate change impacts on a sedimentary coast—a regional synthesis from genes to ecosystems

Buschbaum,

Shama,

Amorim

et al. 2024

Mar. Biodivers.

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Climate change effects on coastal ecosystems vary on large spatial scales, but can also be highly site dependent at the regional level. The Wadden Sea in the south-eastern North Sea is warming faster than many other temperate coastal areas, with surface seawater temperature increasing by almost 2 °C over the last 60 years, nearly double the global ocean mean increase. Climate warming is accompanied by rising sea levels, which have increased by approximately 2 mm yr−1 over the last 120 years. For this sedimentary coast, the predicted acceleration of sea-level rise will have profound effects on tidal dynamics and bathymetry in the area. This paper synthesises studies of the effects of ocean warming and sea level rise in the northern Wadden Sea, largely based on research conducted at the Wadden Sea Station Sylt of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research. An increasing rate of sea level rise above a critical threshold will lead to coastal erosion and changes in sediment composition, and may cause the transition from a tidal to lagoon-like environment as tidal flats submerge. This involves changes to coastal morphology, and the decline of important habitats such as muddy tidal flats, salt marshes and seagrass meadows, as well as their ecological services (e.g. carbon sequestration). Ocean warming affects plankton dynamics and phenology, as well as benthic community structure by hampering cold-adapted but facilitating warm-adapted species. The latter consist mostly of introduced non-native species originating from warmer coasts, with some epibenthic species acting as ecosystem engineers that create novel habitats on the tidal flats. Warming also changes interactions between species by decoupling existing predator–prey dynamics, as well as forming new interactions in which mass mortalities caused by parasites and pathogens can play an understudied but essential role. However, Wadden Sea organisms can adapt to changing abiotic and biotic parameters via genetic adaptation and phenotypic plasticity, which can also be inherited across generations (transgenerational plasticity), enabling faster plastic responses to future conditions. Important research advances have been made using next-generation molecular tools (-omics), mesocosm experiments simulating future climate scenarios, modelling approaches (ecological network analysis), and internet-based technologies for data collection and archiving. By synthesising these climate change impacts on multiple levels of physical and biological organisation in the northern Wadden Sea, we reveal knowledge gaps that need to be addressed by future investigations and comparative studies in other regions in order to implement management, mitigation and restoration strategies to preserve the uniqueness of this ecosystem of global importance.

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Can Transcriptomics Elucidate the Role of Regulation in Invasion Success?

Vaughan,

Dhami

2024

Molecular Ecology

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When a species invades a novel environment, it must bridge the environment–phenotype mismatch in its new range to persist. Contemporary invasion biology research has focused on the role that trait variation and adaptation, and their underlying genomic factors, play in a species' adaptive potential, and thus facilitating invasion. Empirical studies have provided valuable insights into phenotypes that persist and arise in novel environments, coupled with ‘omics tools that further the understanding of the contributions of genomic architecture in species establishment. Particularly, the use of transcriptomics to explore the role of plasticity in the initial stages of an invasion is growing. Here, we assess the role of various mechanisms relating to regulation and functional adaptation (often measured via the transcriptome) that support trait‐specific plasticity in invasive species, allowing phenotypic variability without directly altering genomic diversity. First, we present a comprehensive review of the studies utilising transcriptomics in invasion biology. Second, we collate the evidence for and against the role of a range of regulatory processes in contributing to invasive species plasticity. Finally, we pose open questions in invasion biology where the use of transcriptome data may be valuable, as well as discuss the methodological limitations.

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Genomic and Transcriptomic Differentiation of Independent Invasions of the Pacific Oyster Crassostrea gigas

Cited by 3 publications

References 65 publications

The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again

The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again

Climate change impacts on a sedimentary coast—a regional synthesis from genes to ecosystems

Can Transcriptomics Elucidate the Role of Regulation in Invasion Success?

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