Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader.
Ontology highlight
ABSTRACT:
SUBMITTER: Jaspers C
PROVIDER: S-EPMC8713979 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The identification of native sources and vectors of introduced species informs their ecological and evolutionary history and may guide policies that seek to prevent future introductions. Population genetics provides a powerful set of tools to identify origins and vectors. However, these tools can mislead when the native range is poorly sampled or few molecular markers are used. Here, we traced the introduction of the Asian seaweed Gracilaria vermiculophylla (Rhodophyta) into estuaries in coastal western North America, the eastern United States, Europe, and northwestern Africa by genotyping more than 2,500 thalli from 37 native and 53 non-native sites at mitochondrial cox1 and 10 nuclear microsatellite loci. Overall, greater than 90% of introduced thalli had a genetic signature similar to thalli sampled from the coastline of northeastern Japan, strongly indicating this region served as the principal source of the invasion. Notably, northeastern Japan exported the vast majority of the oyster Crassostrea gigas during the 20th century. The preponderance of evidence suggests G. vermiculophylla may have been inadvertently introduced with C. gigas shipments and that northeastern Japan is a common source region for estuarine invaders. Each invaded coastline reflected a complex mix of direct introductions from Japan and secondary introductions from other invaded coastlines. The spread of G. vermiculophylla along each coastline was likely facilitated by aquaculture, fishing, and boating activities. Our ability to document a source region was enabled by a robust sampling of locations and loci that previous studies lacked and strong phylogeographic structure along native coastlines.
| S-EPMC5478068 | biostudies-literature
Project description:Despite the increasing number of species invasions, the factors driving invasiveness are still under debate. This is particularly the case for "invisible" invasions by aquatic microbial species. Since in many cases only a few individuals or propagules enter a new habitat, their genetic variation is low and might limit their invasion success, known as the genetic bottleneck. Thus, a key question is, how genetic identity and diversity of invading species influences their invasion success and, subsequently, affect the resident community. We conducted invader-addition experiments using genetically different strains of the globally invasive, aquatic cyanobacterium Raphidiopsis raciborskii (formerly: Cylindrospermopsis raciborskii) to determine the role of invader identity and genetic diversity (strain richness) at four levels of herbivory. We tested the invasion success of solitary single strain invasions against the invader genetic diversity, which was experimentally increased up to ten strains (multi-strain populations). By using amplicon sequencing we determined the strain-specific invasion success in the multi-strain treatments and compared those with the success of these strains in the single-strain treatments. Furthermore, we tested for the invasion success under different herbivore pressures. We showed that high grazing pressure by a generalist herbivore prevented invasion, whereas a specialist herbivore enabled coexistence of consumer and invader. We found a weak effect of diversity on invasion success only under highly competitive conditions. When invasions were successful, the magnitude of this success was strain-specific and consistent among invasions performed with single-strain or multi-strain populations. A strain-specific effect was also observed on the resident phytoplankton community composition, highlighting the strong role of invader genetic identity. Our results point to a strong effect of the genetic identity on the invasion success under low predation pressure. The genetic diversity of the invader population, however, had little effect on invasion success in our study, in contrast to most previous findings. Instead, it is the interaction between the consumer abundance and type together with the strain identity of the invader that defined invasion success. This study underlines the importance of strain choice in invasion research and in ecological studies in general.
| S-EPMC7370804 | biostudies-literature
Project description:Marine bacterioplanktons are thought to play a vital role in Southern Ocean ecology and ecosystem function, as they do in other ocean systems. However, our understanding of phylogenetic diversity, genome-enabled capabilities and specific adaptations to this persistently cold environment is limited. Bacterioplankton community composition shifts significantly over the annual cycle as sea ice melts and phytoplankton bloom. Microbial diversity in sea ice is better known than that of the plankton, where culture collections do not appear to represent organisms detected with molecular surveys. Broad phylogenetic groupings of Antarctic bacterioplankton such as the marine group I Crenarchaeota, alpha-Proteobacteria (Roseobacter-related and SAR-11 clusters), gamma-Proteobacteria (both cultivated and uncultivated groups) and Bacteriodetes-affiliated organisms in Southern Ocean waters are in common with other ocean systems. Antarctic SSU rRNA gene phylotypes are typically affiliated with other polar sequences. Some species such as Polaribacter irgensii and currently uncultivated gamma-Proteobacteria (Ant4D3 and Ant10A4) may flourish in Antarctic waters, though further studies are needed to address diversity on a larger scale. Insights from initial genomics studies on both cultivated organisms and genomes accessed through shotgun cloning of environmental samples suggest that there are many unique features of these organisms that facilitate survival in high-latitude, persistently cold environments.
| S-EPMC2443171 | biostudies-literature
Project description:In the United States, policy initiatives aimed at increasing sources of renewable energy are advancing bioenergy production, especially in the Midwest region, where agricultural landscapes dominate. While policy directives are focused on renewable fuel production, biodiversity and ecosystem services will be impacted by the land-use changes required to meet production targets. Using data from field observations, we developed empirical models for predicting abundance, diversity, and community composition of flower-visiting bees based on land cover. We used these models to explore how bees might respond under two contrasting bioenergy scenarios: annual bioenergy crop production and perennial grassland bioenergy production. In the two scenarios, 600,000 ha of marginal annual crop land or marginal grassland were converted to perennial grassland or annual row crop bioenergy production, respectively. Model projections indicate that expansion of annual bioenergy crop production at this scale will reduce bee abundance by 0 to 71%, and bee diversity by 0 to 28%, depending on location. In contrast, converting annual crops on marginal soil to perennial grasslands could increase bee abundance from 0 to 600% and increase bee diversity between 0 and 53%. Our analysis of bee community composition suggested a similar pattern, with bee communities becoming less diverse under annual bioenergy crop production, whereas bee composition transitioned towards a more diverse community dominated by wild bees under perennial bioenergy crop production. Models, like those employed here, suggest that bioenergy policies have important consequences for pollinator conservation.
| S-EPMC4217732 | biostudies-other
Project description:Invasive species often evolve rapidly following introduction despite genetic bottlenecks that may result from small numbers of founders; however, some invasions may not fit this "genetic paradox". The invasive cane toad (Rhinella marina) displays high phenotypic variation across its introduced Australian range. Here, we used three genome-wide datasets to characterize their population structure and genetic diversity. We found that toads form three genetic clusters: 1) native range toads, 2) toads from the source population in Hawaii and long-established areas near introduction sites in Australia, and 3) toads from more recently established northern Australian sites. Although we find an overall reduction in genetic diversity following introduction, we do not see this reduction in loci putatively under selection, suggesting that genetic diversity may have been maintained at ecologically relevant traits, or that mutation rates were high enough to maintain adaptive potential. Nonetheless, toads encounter novel environmental challenges in Australia, and the transition between genetic clusters occurs at a point along the invasion transect where temperature rises and rainfall decreases. We identify environmentally associated loci known to be involved in resistance to heat and dehydration. This study highlights that natural selection occurs rapidly and plays a vital role in shaping the structure of invasive populations.
| S-EPMC6901984 | biostudies-literature
Project description:The introduced oriental shrimp Palaemon macrodactylus has recently become widespread in temperate estuaries worldwide. However, this recent worldwide spread outside of its native range arises after a previous introduction to the US Pacific coast, where it was restricted for more than 30 years. Using a phylogeographic approach, the present work investigates the genetic history of the invasion of this decapod worldwide. Japan acted as the main native source area for worldwide introduced populations, but other native areas (likely South Korea and China) may act as source populations as well. The recently introduced European and NW Atlantic populations result from colonization from both Japan and an unknown area of the native range, although colonization from the NE Pacific could not be ruled out. Most introduced populations had higher haplotypic diversity than most native populations. P. macrodactylus has a strong potential to become one of the most widespread introduced species and may become the dominant estuarine shrimp in Europe. The ecological and economic consequences of this invasion remain to be thoroughly evaluated.
| S-EPMC5376162 | biostudies-literature
Project description:BACKGROUND: Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit. RESULTS: Extensive sampling in Africa, Australasia and South America revealed the existence of "nested" levels of cryptic diversity, in which at least five distinct species can be further subdivided into smaller-scale genetic lineages. The ranges of several evolutionary units are limited by well-documented biogeographic disjunctions. Evidence for both cryptic native diversity and the existence of invasive populations allows us to considerably refine our view of the native versus introduced status of the evolutionary units within Pyura stolonifera in the different coastal communities they dominate. CONCLUSIONS: This study illustrates the degree of taxonomic complexity that can exist within widespread species for which there is little taxonomic expertise, and it highlights the challenges involved in distinguishing between indigenous and introduced populations. The fact that multiple genetic lineages can be native to a single geographic region indicates that it is imperative to obtain samples from as many different habitat types and biotic zones as possible when attempting to identify the source region of a putative invader. "Nested" cryptic diversity, and the difficulties in correctly identifying invasive species that arise from it, represent a major challenge for managing biodiversity.
| S-EPMC3146881 | biostudies-other
Project description:The global spread of invasive species may be facilitated by adaptation to the practices that humans use to manage those species. For example, marine invertebrates that adapt to metal-based antifouling biocides on ship hulls may be more likely to be introduced to and establish in metal-polluted environments. We tested this idea by studying clonal variation in tolerance to, and ability to recover from, exposure to copper in a widespread invasive marine bryozoan, Watersipora subtorquata. We cloned colonies of this organism to independently test multiple environments in a genotype by environment design, and then created a genetic variance-covariance matrix. Genotypes were exposed to a gradient of copper concentrations and growth measured during exposure and after a recovery period. There was a significant genotype × environment interaction in growth during exposure and recovery. We found clonal variation in tolerance and ability to recover from exposure to copper, with growth during exposure apparently trading off against growth after exposure. A weak genetic correlation between growth during and after exposure further indicated that they are separate traits. Overall, the genetic variation within this population indicates that there is considerable potential for adaptation to copper, but this comes at a cost to growth in unpolluted environments.
| S-EPMC3402204 | biostudies-literature
Project description:Documenting ecological patterns across spatially, temporally and taxonomically diverse ecological communities is necessary for a general understanding of the processes shaping biodiversity. A major gap in our understanding remains the comparison of diversity patterns across a broad spectrum of evolutionarily and functionally diverse organisms, particularly in the marine realm. Here, we aim to narrow this gap by comparing the diversity patterns of free-living microbes and macro-invertebrates across a natural experiment provided by the marine lakes of Palau: geographically discrete and environmentally heterogeneous bodies of seawater with comparable geological and climatic history, and a similar regional species pool. We find contrasting patterns of ?-diversity but remarkably similar patterns of ?-diversity between microbial and macro-invertebrate communities among lakes. Pairwise dissimilarities in community composition among lakes are positively correlated between microbes and macro-invertebrates, and influenced to a similar degree by marked gradients in oxygen concentration and salinity. Our findings indicate that a shared spatio-temporal and environmental context may result in parallel patterns of ?-diversity in microbes and macro-invertebrates, in spite of key trait differences between these organisms. This raises the possibility that parallel processes also influence transitions among regional biota across the tree of life, at least in the marine realm.
| S-EPMC6790787 | biostudies-literature
Project description:Bacteriophages (phages) have been proposed as alternative therapeutics for the treatment of multidrug-resistant bacterial infections. However, there are major gaps in our understanding of the molecular events in bacterial cells that control how bacteria respond to phage predation. Using the model organism Enterococcus faecalis, we used two distinct genomic approaches, namely, transposon library screening and RNA sequencing, to investigate the interaction of E. faecalis with a virulent phage. We discovered that a transcription factor encoding a LytR family response regulator controls the expression of enterococcal polysaccharide antigen (epa) genes that are involved in phage infection and bacterial fitness. In addition, we discovered that DNA mismatch repair mutants rapidly evolve phage adsorption deficiencies, underpinning a molecular basis for epa mutation during phage infection. Transcriptomic profiling of phage-infected E. faecalis revealed broad transcriptional changes influencing viral replication and progeny burst size. We also demonstrate that phage infection alters the expression of bacterial genes associated with intra- and interbacterial interactions, including genes involved in quorum sensing and polymicrobial competition. Together, our results suggest that phage predation has the potential to influence complex microbial behavior and may dictate how bacteria respond to external environmental stimuli. These responses could have collateral effects (positive or negative) on microbial communities, such as the host microbiota, during phage therapy.IMPORTANCE We lack fundamental understanding of how phage infection influences bacterial gene expression and, consequently, how bacterial responses to phage infection affect the assembly of polymicrobial communities. Using parallel genomic approaches, we have discovered novel transcriptional regulators and metabolic genes that influence phage infection. The integration of whole-genome transcriptomic profiling during phage infection has revealed the differential regulation of genes important for group behaviors and polymicrobial interactions. Our work suggests that therapeutic phages could more broadly influence bacterial community composition outside their intended host targets.
| S-EPMC7064774 | biostudies-literature