Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader

Flanagan, Ben A.; Krueger‐Hadfield, Stacy A.; Murren, Courtney J.; Nice, Chris C.; Strand, Allan E.; Sotka, Erik E.

doi:10.1111/mec.15854

Cited by 29 publications

(44 citation statements)

References 145 publications

(184 reference statements)

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“…2017a, Flanagan et al. 2021). One exception occurs in the invaded region of the Salish Sea in Washington state and British Columbia which was sourced by a mixture of northern and southern Japanese populations.…”

Section: The Invasion History Of Agarophyton Vermiculophyllummentioning

confidence: 99%

“…(2016, 2017a) and approximately 62,000 SNPs in Flanagan et al. (2021) found comparable levels of nuclear genetic diversity between native and non‐native regions, suggesting highly genetically diverse inocula, a highly diverse source population, multiple invasions, or some mix of the three processes. Multiple analyses definitively identified the Miyagi Prefecture (e.g., sites Soukanzan and Mangoku‐ura) as the main source of most of the Northern Hemisphere invasion (Figs.…”

Section: The Invasion History Of Agarophyton Vermiculophyllummentioning

confidence: 99%

“…2016, 2017a) and SNPs (Flanagan et al. 2021) suggests the mitochondrial bottleneck may largely be due to the spread of Haplotype 6 in the recolonization of higher latitudes following the last glacial maximum.…”

Section: The Invasion History Of Agarophyton Vermiculophyllummentioning

confidence: 99%

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Intraspecific diversity and genetic structure in the widespread macroalga Agarophyton vermiculophyllum

Krueger‐Hadfield

Byers

Bonthond

et al. 2021

Journal of Phycology

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Single‐gene markers, such as the mitochondrial cox1, microsatellites, and single‐nucleotide polymorphisms are powerful methods to describe diversity within and among taxonomic groups and characterize phylogeographic patterns. Large repositories of publicly‐available, molecular data can be combined to generate and evaluate evolutionary hypotheses for many species, including algae. In the case of biological invasions, the combination of different molecular markers has enabled the description of the geographic distribution of invasive lineages. Here, we review the phylogeography of the widespread invasive red macroalga Agarophyton vermiculophyllum (synonym Gracilaria vermiculophylla). The cox1 barcoding provided the first description of the invasion history and hinted at a strong genetic bottleneck during the invasion. Yet, more recent microsatellite and SNP genotyping has not found evidence for bottlenecks and instead suggested that genetically diverse inocula arose from a highly diverse source population, multiple invasions, or some mix of these processes. The bottleneck evident from cox1 barcoding likely reflects the dominance of one mitochondrial lineage, and one haplotype in particular, in the northern source populations in Japan. Recent cox1 sequencing of A. vermiculophyllum has illuminated the complexity of phylogeographic structure in its native range of the northwest Pacific Ocean. For example, the western coast of Honshu in the Sea of Japan displays spatial patterns of haplotypic diversity with multiple lineages found together at the same geographic site. By consolidating the genetic data of this species, we clarify the phylogenetic relationships of a well‐studied macroalga introduced to virtually every temperate estuary of the Northern Hemisphere.

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Section: The Invasion History Of Agarophyton Vermiculophyllummentioning

confidence: 99%

Section: The Invasion History Of Agarophyton Vermiculophyllummentioning

confidence: 99%

See 1 more Smart Citation

Intraspecific diversity and genetic structure in the widespread macroalga Agarophyton vermiculophyllum

Krueger‐Hadfield

Byers

Bonthond

et al. 2021

Journal of Phycology

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“…Despite such bottlenecks, loss of diversity measured by molecular markers does not necessarily reflect loss of quantitative trait variation (Dlugosch and Parker, 2008b;Estoup et al, 2016). A series of studies revealed that rapid phenotypic evolution facilitated the invasion of the widespread red macroalga Agarophyton vermiculophyllum despite the fact that the species experienced a severe genetic bottleneck and increased through clonal spreading (Krueger-Hadfield et al, 2016;Sotka et al, 2018;Flanagan et al, 2021). The European starling (Sturnus vulgaris) in North America was founded by only ∼180 individuals, but local populations seem to have evolved rapidly and now show the signature of only a moderate population bottleneck (Hofmeister et al, 2021).…”

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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“…[9]). Genetic bottlenecks can also contribute to performance by purging deleterious alleles, revealing beneficial cryptic variation or creating new beneficial interactions among genomic elements [3,[10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Epigenetics and the success of invasive plants

Mounger

Aïnouche

Bossdorf

et al. 2021

Phil. Trans. R. Soc. B

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Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of ‘genomic shock’ resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

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Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader

Cited by 29 publications

References 145 publications

Intraspecific diversity and genetic structure in the widespread macroalga Agarophyton vermiculophyllum

Intraspecific diversity and genetic structure in the widespread macroalga Agarophyton vermiculophyllum

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

Epigenetics and the success of invasive plants

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