Insights into invasive species from whole‐genome resequencing

North, Henry L.; McGaughran, Angela; Jiggins, Chris D.

doi:10.1111/mec.15999

Cited by 72 publications

(59 citation statements)

References 211 publications

(248 reference statements)

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“…For instance, a high-quality genome is useful for genome-wide scans of selection, trait association mapping, and timing invasion events (e.g. North et al 2021, DeGiorgio et al, 2016; Nielsen et al, 2005). With improved understanding and forecasting at each stage of the invasion process, managers can make decisions on invasions much more accurately than in the past (Bergeron et al 2019, Keriö et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

Ramachandran

Huebner

Daly

et al. 2021

Preprint

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The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12 Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.

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Section: Introductionmentioning

confidence: 99%

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

Ramachandran

Huebner

Daly

et al. 2021

Preprint

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“…Pest genomic databanks have become popular for answering questions around invasions and incursions (Chen et al, 2021;Gloria-Soria et al, 2018;Kelly et al, 2021;Popa-Báez et al, 2021;Schmidt et al, 2020Schmidt et al, , 2021Schmidt et al, , 2019Sherpa et al, 2019). The value provided by these databanks should continue to rise as costs of generating genome-scale data from large numbers of pests continue to decrease and as new genomic methods appropriate for pests are developed (North, McGaughran, & Jiggins, 2021). This study presents the use of two genomic databanks to solve emerging problems for biosecurity and human health, which concern new Australian incursions and invasions of the mosquitoes Ae.…”

Section: Discussionmentioning

confidence: 99%

Genomic databanks and targeted assays help characterise domestic mosquito incursions

Schmidt

Endersby‐Harshman

Kurucz

et al. 2022

Preprint

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Biosecurity strategies that aim to restrict the spread of invasive pests can profit greatly from knowledge of where new incursions have come from. This knowledge is often difficult to acquire, particularly for incursions that are detected outside their vessel of entry. Genomic databanks have shown recent efficacy for determining origins of individual incursions of pests such as mosquitoes and fruit flies, where genome-wide genetic variation in incursion samples is compared against variation in reference samples. This paper uses genomic databanks to trace and genetically characterise incursions of two species of mosquito (Aedes aegypti and Ae. albopictus) within Australia. We built an Ae. aegypti databank of samples from across its Australian range, and used this to trace a 2021 invasion of Tennant Creek, Northern Territory, to Townsville, Queensland. We used targeted assays to show the invasion did not carry a Wolbachia infection, but had similar mtDNA to wildtype Townsville samples, and thus concluded that the invasion was sourced from an uninfected area within or near Townsville, where the Wolbachia infection has been widespread since 2018. For Ae. albopictus, we traced incursions into the southern Torres Strait Islands from invaded islands, and show how origins of incursions collected in 2021 differed from those collected in 2019. Comparing patterns of genetic relatedness in both species indicated that Tennant Creek was likely invaded by mosquitoes from the same geographical location and are potentially all from the same family, whereas the Torres Strait incursions were all from distinct kinship groups. Our results highlight the value of repeated tracing over years and the utility of targeted assays to improve accuracy of inferences. The specificity of tracing to populations sampled >8 years previously suggest that genomic databanks can remain informative for tracing over years.

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“…This genetic variation might (i) stem from new mutations, or (ii) already segregate in the population as standing genetic variation, or (iii) come from gene exchange with other populations or species. Understanding the relative importance of these sources of adaptive variation has practical implications for conservation, biological control and infectious disease prevention (Harpak et al, 2021;North, McGaughran, & Jiggins, 2021;Pennings, 2012). We only have a few examples of convergent adaptation to ports but the most compelling example, in killifish (Fundulus sp.…”

Section: Parallel Adaptation In a Patchy Environment: Mutation Migrat...mentioning

confidence: 99%

Urban rendezvous along the seashore: Ports as Darwinian field labs for studying marine evolution in the Anthropocene

Touchard

Simon

Bierne

et al. 2022

Evolutionary Applications

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Humans have built ports on all the coasts of the world, allowing people to travel, exploit the sea, and develop trade. The proliferation of these artificial habitats and the associated maritime traffic are not predicted to fade in the coming decades. Ports share common characteristics: species find themselves in novel singular environments, with particular abiotic properties -e.g., pollutants, shading, protection from wave action-within novel communities in a melting-pot of invasive and native taxa. Here we discuss how this drives evolution, including setting-up of new connectivity hubs and gateways, adaptive responses to exposure to new chemicals or new biotic communities, and hybridization between lineages that would have never come into contact naturally. There are still important knowledge gaps however, such as the lack of experimental tests to distinguish adaptation from acclimation processes, the lack of studies to understand the putative threats of port lineages to natural populations, or to better understand the outcomes and fitness effects of anthropogenic hybridization. We thus call for further research examining "biological portuarization", defined as the repeated evolution of marine species in port-ecosystems under human-altered selective pressures. Furthermore, we argue that ports act as giant mesocosms often isolated from the open sea by seawalls and locks, and so provide replicated life-size evolutionary experiments essential to support predictive evolutionary sciences.

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Insights into invasive species from whole‐genome resequencing

Abstract: As an unintended consequence of global commerce and climate change, biodiversity is being redistributed at an unprecedented rate

Cited by 72 publications

References 211 publications

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

Genomic databanks and targeted assays help characterise domestic mosquito incursions

Urban rendezvous along the seashore: Ports as Darwinian field labs for studying marine evolution in the Anthropocene

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