Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader

Priorities for improving predictions of vessel-mediated marine invasions

Nonindigenous marine species are impacting the integrity of marine ecosystems worldwide. The invasion rate is increasing, and vessel traffic, the most significant human-assisted transport pathway for marine organisms, is predicted to double by 2050. The ability to predict the transfer of marine species by international and domestic maritime traffic is needed to develop cost-effective proactive and reactive interventions that minimise introduction, establishment and spread of invasive species. However, despite several decades of research into vessel-mediated species transfers, some important knowledge gaps remain, leading to significant uncertainty in model predictions, often limiting their use in decision making and management planning. In this review, we discuss the sequential ecological process underlying human-assisted biological invasions and adapt it in a marine context. This process includes five successive stages: entrainment, transport, introduction, establishment, and the subsequent spread. We describe the factors that influence an organism's progression through these stages in the context of maritime vessel movements and identify key knowledge gaps that limit our ability to quantify the rate at which organisms successfully pass through these stages. We then highlight research priorities that will address these knowledge gaps and improve our capability to manage biosecurity risks at local, national and international scales. We identified four major data and knowledge gaps: (1) quantitative rates of entrainment of organisms by vessels; (2) the movement patterns of vessel types lacking maritime location devices; (3) quantifying the release (introduction) of organisms as a function of vessel behaviour (e.g. time spent at port); and (4) the influence of a species' life history on establishment success, for a given magnitude of propagule pressure. We discuss these four research priorities and how they can be addressed in collaboration with industry partners and stakeholders to improve our ability to predict and manage vessel-mediated biosecurity risks over the coming decades.

Climatic and soil characteristics account for the genetic structure of the invasive cactus moth Cactoblastis cactorum, in its native range in Argentina

Background

Knowledge of the physical and environmental conditions that may limit the migration of invasive species is crucial to assess the potential for expansion outside their native ranges. The cactus moth, Cactoblastis cactorum, is native to South America (Argentina, Paraguay, Uruguay and Brazil) and has been introduced and invaded the Caribbean and southern United States, among other regions. In North America there is an ongoing process of range expansion threatening cacti biodiversity of the genus Opuntia and the commercial profits of domesticated Opuntia ficus-indica.

Methods

To further understand what influences the distribution and genetic structure of this otherwise important threat to native and managed ecosystems, in the present study we combined ecological niche modeling and population genetic analyses to identify potential environmental barriers in the native region of Argentina. Samples were collected on the host with the wider distribution range, O. ficus-indica.

Results

Significant genetic structure was detected using 10 nuclear microsatellites and 24 sampling sites. At least six genetic groups delimited by mountain ranges, salt flats and wetlands were mainly located to the west of the Dry Chaco ecoregion. Niche modeling supports that this region has high environmental suitability where the upper soil temperature and humidity, soil carbon content and precipitation were the main environmental factors that explain the presence of the moth. Environmental filters such as the upper soil layer may be critical for pupal survival and consequently for the establishment of populations in new habitats, whereas the presence of available hosts is a necessary conditions for insect survival, upper soil and climatic characteristics will determine the opportunities for a successful establishment.

Managing the risk of biological invasions

The large environmental impacts and enormous economic costs caused by biological invasions provide a strong impetus for managing invasion risks. Understanding the factors driving the invasion process and their consequences will raise awareness of invasions among the general public, stakeholders, and policymakers and inform effective management strategies. The identification of priority species and introduction pathways and sites and the development of national capabilities for prevention and preparedness, early detection, monitoring, and rapid response will reduce the impacts of invasive species in terms of effectiveness and cost efficiency.

Stronger evidence for genetic ancestry than environmental conditions in shaping the evolution of a complex signalling trait during biological invasion

Introductions of invasive species to new environments often result in rapid rates of trait evolution. While in some cases these evolutionary transitions are adaptive and driven by natural selection, they can also result from patterns of genetic and phenotypic variation associated with the invasion history. Here, we examined the brown anole (Anolis sagrei), a widespread invasive lizard for which genetic data have helped trace the sources of non-native populations. We focused on the dewlap, a complex signalling trait known to be subject to multiple selective pressures. We measured dewlap reflectance, pattern and size in 30 non-native populations across the southeastern United States. As well, we quantified environmental variables known to influence dewlap signal effectiveness, such as canopy openness. Further, we used genome-wide data to estimate genetic ancestry, perform association mapping and test for signatures of selection. We found that among-population variation in dewlap characteristics was best explained by genetic ancestry. This result was supported by genome-wide association mapping, which identified several ancestry-specific loci associated with dewlap traits. Despite the strong imprint of this aspect of the invasion history on dewlap variation, we also detected significant relationships between dewlap traits and local environmental conditions. However, we found limited evidence that dewlap-associated genetic variants have been subject to selection. Our study emphasizes the importance of genetic ancestry and admixture in shaping phenotypes during biological invasion, while leaving the role of selection unresolved, likely due to the polygenic genetic architecture of dewlaps and selection acting on many genes of small effect.

Reviewing Introduction Histories, Pathways, Invasiveness, and Impact of Non-Indigenous Species in Danish Marine Waters

Non-indigenous species (NIS) are of concern for biodiversity conservation and ecosystem functioning. We present an updated list of NIS, including cryptogenic species, from Danish marine waters containing 123 species. Benthic invertebrates (36%) and phytoplankton (28%) dominate the list, but fish (15%) and macroalgae (13%) are also important. The Limfjord in Northern Jutland emerges as a hotspot for the introduction of NIS. Data from multiple sources were included, i.e., the National Monitoring Program (NOVANA), the National Fish Atlas project, the citizen science project Arter.dk, research articles, and annual national reports of the ICES working group ITMO. Forty-six NIS species were subject to expert judging using a modified Harmonia protocol; 19 were found to fulfil the four selected criteria identifying a species as being ‘invasive’. Additionally, 38 species, not yet recorded in Danish waters, were evaluated using the same method, and 31 were found to fulfil the ‘invasive’ criteria. For nine selected species, introduction history, distribution maps, and time-series diagrams are presented. Our data document that the national monitoring efforts should be expanded to record macrozooplankton, coastal fish, and mobile epibenthic species. Furthermore, the national data repository, Arter.dk, should be expanded to enable more detailed documentation of new NIS records.

Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation

Despite extensive research on agricultural pests, our knowledge about their evolutionary history is often limited. A mechanistic understanding of the demographic changes and modes of adaptation remains an important goal, as it improves our understanding of organismal responses to environmental change and our ability to sustainably manage pest populations. Emerging genomic datasets now allow for characterization of demographic and adaptive processes, but face limits when they are drawn from contemporary samples, especially in the context of strong demographic change, repeated selection, or adaptation involving modest shifts in allele frequency at many loci. Temporal sampling, however, can improve our ability to reconstruct evolutionary events. Here, we leverage museum samples to examine whether population genomic diversity and structure has changed over time, and to identify genomic regions that appear to be under selection. We focus on the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say 1824; Coleoptera: Chrysomelidae), which is widely regarded as a super-pest due to its rapid, and repeated, evolution to insecticides. By combining whole genome resequencing data from 78 museum samples with modern sampling, we demonstrate that CPB expanded rapidly in the 19th century, leading to a reduction in diversity and limited genetic structure from the Midwest to Northeast United States. Temporal genome scans provide extensive evidence for selection acting in resistant field populations in Wisconsin and New York, including numerous known insecticide resistance genes. We also validate these results by showing that known selective sweeps in modern populations are identified by our genome scan. Perhaps most importantly, temporal analysis indicates selection on standing genetic variation, as we find evidence for parallel evolution in the two geographical regions. Parallel evolution involves a range of phenotypic traits not previously identified as under selection in CPB, such as reproductive and morphological functional pathways that might be important for adaptation to agricultural habitats.

Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA

The Asian tiger mosquito (Aedes albopictus) arrived in the USA in the 1980’s and rapidly spread throughout eastern USA within a decade. The predicted northern edge of its overwintering distribution on the East Coast of the USA roughly falls across New York, Connecticut, and Massachusetts, where the species has been recorded as early as 2000. It is unclear whether Ae. albopictus populations have become established and survive the cold winters in these areas or are recolonized every year. We genotyped and analyzed populations of Ae. albopictus from the northeast USA using 15 microsatellite markers and compared them with other populations across the country and to representatives of the major global genetic clades to investigate their connectivity and stability. Founder effects or bottlenecks were rare at the northern range of the Ae. albopictus distribution in the northeastern USA, with populations displaying high levels of genetic diversity and connectivity along the East Coast. There is no evidence of population turnover in Connecticut during the course of three consecutive years, with consistent genetic structure throughout this period. Overall, these results support the presence of established populations of Ae. albopictus in New York, Connecticut, and Massachusetts, successfully overwintering and migrating in large numbers. Given the stability and interconnectedness of these populations, Ae. albopictus has the potential to continue to proliferate and expand its range northward under mean warming conditions of climate change. Efforts to control Ae. albopictus in these areas should thus focus on vector suppression rather than eradication strategies, as local populations have become firmly established and are expected to reemerge every summer.

Speciation of pelagic zooplankton: Invisible boundaries can drive isolation of oceanic ctenophores

The study of evolution and speciation in non-model systems provides us with an opportunity to expand our understanding of biodiversity in nature. Connectivity studies generally focus on species with obvious boundaries to gene flow, but in open-ocean environments, such boundaries are difficult to identify. Due to the lack of obvious boundaries, speciation and population subdivision in the pelagic environment remain largely unexplained. Comb jellies (Phylum Ctenophora) are mostly planktonic gelatinous invertebrates, many of which are considered to have freely interbreeding distributions worldwide. It is thought that the lobate ctenophore Bolinopsis infundibulum is distributed throughout cooler northern latitudes and B. vitrea warmer. Here, we examined the global population structure for species of Bolinopsis with genetic and morphological data. We found distinct evolutionary patterns within the genus, where B. infundibulum had a broad distribution from northern Pacific to Atlantic waters despite many physical barriers, while other species were geographically segregated despite few barriers. Divergent patterns of speciation within the genus suggest that oceanic currents, sea-level, and geological changes over time can act as either barriers or aids to dispersal in the pelagic environment. Further, we used population genomic data to examine evolution in the open ocean of a distinct lineage of Bolinopsis ctenophores from the North Eastern Pacific. Genetic information and morphological observations validated this as a separate species, Bolinopsis microptera, which was previously described but has recently been called B. infundibulum. We found that populations of B. microptera from California were in cytonuclear discordance, which indicates a secondary contact zone for previously isolated populations. Discordance at this scale is rare, especially in a continuous setting.

Multigenerational laboratory culture of pelagic ctenophores and CRISPR-Cas9 genome editing in the lobate Mnemiopsis leidyi

Despite long-standing experimental interest in ctenophores due to their unique biology, ecological influence and evolutionary status, previous work has largely been constrained by the periodic seasonal availability of wild-caught animals and difficulty in reliably closing the life cycle. To address this problem, we have developed straightforward protocols that can be easily implemented to establish long-term multigenerational cultures for biological experimentation in the laboratory. In this protocol, we describe the continuous culture of the Atlantic lobate ctenophore Mnemiopsis leidyi. A rapid 3-week egg-to-egg generation time makes Mnemiopsis suitable for a wide range of experimental genetic, cellular, embryological, physiological, developmental, ecological and evolutionary studies. We provide recommendations for general husbandry to close the life cycle of Mnemiopsis in the laboratory, including feeding requirements, light-induced spawning, collection of embryos and rearing of juveniles to adults. These protocols have been successfully applied to maintain long-term multigenerational cultures of several species of pelagic ctenophores, and can be utilized by laboratories lacking easy access to the ocean. We also provide protocols for targeted genome editing via microinjection with CRISPR-Cas9 that can be completed within ~2 weeks, including single-guide RNA synthesis, early embryo microinjection, phenotype assessment and sequence validation of genome edits. These protocols provide a foundation for using Mnemiopsis as a model organism for functional genomic analyses in ctenophores.

Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader

Invasion rates have increased in the past 100 y irrespective of international conventions. What characterizes a successful invasion event? And how does genetic diversity translate into invasion success? Employing a whole-genome perspective using one of the most successful marine invasive species world-wide as a model, we resolve temporal invasion dynamics during independent invasion events in Eurasia. We reveal complex regionally independent invasion histories including cases of recurrent translocations, time-limited translocations, and stepping-stone range expansions with severe bottlenecks within the same species. Irrespective of these different invasion dynamics, which lead to contrasting patterns of genetic diversity, all nonindigenous populations are similarly successful. This illustrates that genetic diversity, per se, is not necessarily the driving force behind invasion success. Other factors such as propagule pressure and repeated introductions are an important contribution to facilitate successful invasions. This calls into question the dominant paradigm of the genetic paradox of invasions, i.e., the successful establishment of nonindigenous populations with low levels of genetic diversity.