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141 results for “invasion genomics”

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zenodo36/100

Genome-wide association analysis identifies naturally segregating genetic variation associated with the rapid evolution of diapause in Aedes albopictus, an invasive vector mosquito.

The raw data for genotype calls, the output files from the genotype calls, the code to replicate the analysis, and the output of the analysis.

opencc-by-4.0Oct 2024View details →

dryad36/100

Data for: Population genomic insights into invasion success in the polyphagous agricultural pest, Halyomorpha halys

Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human-imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we use genome-wide polymorphisms derived from native, invasive, and intercepted samples and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys, to gain insights into population genomics processes that have promoted the successful global invasion of this polyphagous pest. Our analysis demonstrated that BMSB exhibits spatial structure but admixture rates are high among introduced populations, resulting in similar levels of genomic diversity across native and introduced populations. These spatial genomic patterns suggest a complex invasion scenario, potentially with multiple bridgehead events, posing a challenge for accurately assigning BMSB incursions to their source using reduced-representation genomic data. By associating allele frequencies with the invasion status of BMSB populations, we found significantly differentiated SNPs located in close proximity to genes for insecticide resistance and olfaction. Comparing variations in allele frequencies among populations for outlier SNPs suggests that BMSB invasion success has likely evolved from standing genetic variation. In addition to being a major nuisance of households, BMSB has caused significant economic losses to agriculture in recent years and continues to expand its range. Despite no record of BMSB insecticide resistance to date, our results show high capacity for potential evolution of such characters, highlighting the need for future sustainable and targeted management strategies.

opencc-zeroOct 2022View details →

dryad36/100

Chromosome-level genome assembly of Pterygoplichthys pardalis reveals its genetic basis of extensive invasion

The catfish, Pterygoplichthys pardalis, which belongs to the Loricariidae family, an invasive species which has caused huge damage to the ecological environment. However, the high-quality reference genome for the catfish has not yet been reported. In this study, we successfully assembled the first chromosome-level high-quality genome of P. pardalis using the data we produced from multiple sequencing platforms, which contains 26 chromosomes and with a scaffold N50 of 49.47 Mb. Different evaluation methods all indicate the high connectivity and accuracy of the P. pardalis genome we got. We predicated 23,859 protein-coding genes in the P. pardalis genome, and 22,169 (~92.92%) coding genes could be functionally annotated in public databases. Phylogenetic relationship analysis found P. pardalis was clustered with all the catfishes we used and diverged with them 132.5 million years ago. Besides, whole-genome collinearity analysis found that chromosome 6 of P. pardalis was aligned to two distinct chromosomes both for Ameiurus melas, Pangasianodon hypophthalmus and Ictalurus punctatus, indicating that there may have been a chromosomal fusion/fission event occurred. Furthermore, many immune-system-related genes were large-scale expanded in P. pardalis genome, which may make great contributions to their adaptive traits, even for the highly polluted environmental conditions, and successful invasion. Taken together, this study not only provides insights into the genetic basis of the successful invasion of P. pardalis, but also provides important data resources for comparative genomic analysis of P. pardalis in Siluriformes in the future.

opencc-zeroNov 2022View details →

dryad36/100

Investigating the effects of whole genome duplication on phenotypic plasticity: Implications for the invasion success of Giant Goldenrod (Solidago gigantea)

Polyploidy commonly occurs in invasive species and phenotypic plasticity (PP, the ability to alter one's phenotype in different environments), is predicted to be enhanced in polyploids and contribute to their invasive success. However, empirical support that increased PP is frequent in polyploids and/or confers invasive success is limited. Here, we investigated if polyploids are more pre-adapted to become invasive than diploids via the scaling of trait values and PP with ploidy-level, and if post-introduction selection has led to a divergence in trait values and PP responses between native- and non-native cytotypes. We grew diploid, tetraploid (from both native North American and non-native European ranges), and hexaploid Solidago gigantea in pots outside with low, medium, and high soil nitrogen and phosphorus (NP) amendments, and measured traits related to growth, asexual reproduction, physiology, and insects/pathogen resistance. We found little evidence to suggest that polyploidy and post-selection shaped mean trait and PP responses. To examine invasion dynamics, we compared diploids to tetraploids (as their introduction into Europe was more likely), and found that tetraploids had greater pathogen resistance, photosynthetic capacities, and water-use efficiencies and generally performed better under NP enrichments. Furthermore, tetraploids invested more into roots than shoots in low NP and into shoots than roots in high NP and this resource strategy is beneficial under variable NP conditions. Lastly, native-tetraploids exhibited greater plasticity in biomass accumulation, clonal-ramet production and water-use efficiency. Cumulatively, tetraploid S. gigantea possesses traits that might have pre-disposed and enabled them to become successful invaders. Our findings highlight that trait expression and invasive species dynamics are nuance while also providing insight into the invasion success and cyto-geographic patterning of S. gigantea that can be broadly applied to other invasive species with polyploid complexes.

opencc-zeroAug 2023View details →

dryad36/100

Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.

opencc-zeroSep 2023View details →

dryad36/100

Data for: Genomic signals of local adaptation across climatically heterogenous habitats in an invasive tropical fruit fly (Bactrocera tryoni)

Local adaptation plays a key role in the successful establishment of pest populations in new environments by enabling them to tolerate novel biotic and abiotic conditions experienced outside their native range. However, the genomic underpinnings of such adaptive responses remain unclear, especially for agriculturally important pests. We investigated population genomic signatures in the tropical/subtropical Queensland fruit fly, Bactrocera tryoni, which has an expanded range encompassing temperate and arid zones in Australia, and tropical zones in the Pacific Islands. Using reduced representation sequencing data from 28 populations, we detected allele frequency shifts associated with the native/invasive status of populations and identified environmental factors that have likely driven population differentiation. We also determined that precipitation, temperature, and geographic variables explain allelic shifts across the distribution range of B. tryoni. We found spatial heterogeneity in signatures of local adaptation across various climatic conditions in invaded areas. Specifically, disjunct invasive populations in the tropical Pacific Islands and arid zones of Australia were characterised by multiple significantly differentiated single nucleotide polymorphisms (SNPs), some of which were associated with genes with well-understood function in environmental stress (e.g., heat and desiccation) response. However, invasive populations in southeast Australian temperate zones showed higher gene flow with the native range and lacked a strong local adaptive signal. These results suggest that population connectivity with the native range has differentially affected local adaptive patterns in different invasive populations. Overall, our findings provide insights into the evolutionary underpinnings of invasion success of an important horticultural pest in climatically distinct environments.

opencc-zeroSep 2023View details →

dryad36/100