ABSTRACT Understanding the processes that shape biological invasions is essential for predicting the spread and persistence of introduced species, yet these processes remain poorly resolved for many unintentionally introduced plants. We combined genome‐wide SNP data, demographic modeling, and climatic niche analyses to investigate the invasion of giant ragweed in South Korea. A total of 419 individuals from 35 introduced populations and 59 individuals from four native North American populations were analyzed. Introduced populations retained high genetic diversity and exhibited weak spatial structure, consistent with extensive human‐mediated dispersal. Approximate Bayesian Computation supported a recent invasion within the last ~70 years involving multiple introductions from genetically divergent sources, followed by rapid divergence and severe but transient demographic bottlenecks. Climatic niche analyses revealed substantial overlap between native and introduced ranges but pronounced niche unfilling, indicating that Ambrosia trifida has yet to occupy its full potential climatic niche in South Korea. Together, these results show that repeated introductions, admixture, and anthropogenic dispersal, rather than major climatic niche shifts, have shaped the contemporary invasion. Our findings highlight how integrating population genomics with niche analyses can resolve invasion processes and inform management of rapidly spreading invasive species.
ABSTRACT Lake whitefish Coregonus clupeaformis abundance has declined throughout most of the Laurentian Great Lakes in North America for two decades. Current management strategies in Lake Erie assume that there is a single stock of lake whitefish that spawns in the West Basin. There is documented lake whitefish spawning activity throughout the lake, leading to questions about locally adapted genetic stocks. Past research on lake whitefish genetic structure in Lake Erie has supported the single‐stock hypothesis, but these studies used only neutral genetic markers or contained a limited number of samples that were collected during the spawning season when stocks would be spatially isolated. Using a GT‐seq panel, we evaluate the genetic structure of lake whitefish collected from spawning shoals in the West, Central, and East basins of Lake Erie and compare these populations to lake whitefish from Lake Huron. We then investigate evidence of local adaptation and conduct demographic reconstruction using whole‐genome sequencing. Our goals were to conclusively quantify intra‐lake genetic structure in Lake Erie and determine whether spawning aggregations possess putatively adaptive variants that could be used for genetic stock identification at a sub‐lake level. Our analysis supported the single‐stock hypothesis in Lake Erie. However, Lake Erie stocks were distinct from neighboring Lake Huron. Whole‐genome analysis did not identify any strong evidence of adaptive loci differentiating stocks. Inference of historic effective population size suggests that declines in lake whitefish populations may have caused a genetic bottleneck. Combined, these results indicate that lake whitefish in Lake Erie may have experienced an Allee Effect after population declines, resulting in a loss of population structure and genetic diversity as spawning shoals were recolonized from a common source.
ABSTRACT The potato psyllid ( Bactericera cockerelli ) is a crop pest that serves as a vector for the bacterial pathogen Candidatus Liberibacter solanacearum (CLso), which causes disease in solanaceous and apiaceous crops. This psyllid species carries substantial haplotypic diversity based on mitochondrial cytochrome oxidase 1 (mtCOI) sequences, associated with strong geographic and temporal separation. Using mtCOI sequencing and genomic ddRADseq analysis of 111,587 SNPs across 590 individuals collected from native Solanaceae and cultivated crops at 50 geographically paired sites in California, we show that the previously described haplotype diversity in B. cockerelli may represent at least three genetically distinct cryptic species. These three lineages exhibited extremely high genomic F ST values across all 13 chromosomes and are strongly partitioned by the host plant. The Northwestern lineage is strictly associated with the native perennial Solanum umbelliferum , while the Western lineage is associated with solanaceous crops, and the Southwestern lineage moves between native and cultivated hosts in desert regions. Hybridization is also rare, suggesting reproductive isolation. SNP and divergence analyses for the obligate bacterial symbiont support conclusions of the host nuclear and mtCOI sequence analyses. We also detected five CLso variants in psyllid samples. The Northwestern lineage housed G, Sumb2, F and B variants, while the Western lineage housed only B and A variants. The largest diversity of CLso variants occurred in coastal regions where psyllid lineages overlap. Exploring the ecology and CLso associations of this potential cryptic species complex provides a foundation for improving biosecurity and management of potato psyllids and CLso pathogens.
ABSTRACT Shifts between population connectivity and isolation shape evolutionary divergence, but their effects remain underexplored in highly mobile taxa. Flying‐foxes ( Pteropus ) are a compelling model to study evolutionary divergence because of their rapid radiation in the island‐rich region of the Indo‐Australian Archipelago. Here, we investigate the population genetics of the highly mobile flying‐foxes Pteropus alecto , P. conspicillatus , P. poliocephalus , and P. scapulatus across large parts of their overlapping ranges in Australia, Indonesia, and New Guinea. Using reduced‐representation sequencing of 242 individuals, we examined the extent to which panmixia, isolation‐by‐distance, and hybridization are prevalent in these lineages. Phylogenetic, principal component, and demographic analyses indicated isolation‐by‐distance in P. alecto , including an unexpected east–west genetic split between Australian populations, whereas P. conspicillatus showed weak differentiation between Australia and New Guinea, and P. poliocephalus and P. scapulatus were panmictic across Australia. We further found evidence that infrequent hybridization and asymmetric gene flow, predominantly from P. conspicillatus to P. alecto , have shaped these recently diverged species. Although gene flow connected sampled populations along the geographic chain spanning Indonesia, Australia, and New Guinea, our results did not confirm the hypothesis that P. alecto and P. conspicillatus form a ring species. Rather, demographic analyses supported recent secondary contact during the last 14,848–35,856 years after a period of isolation between P. alecto and P. conspicillatus . Together, our findings indicate that long‐range connectivity and spatially heterogeneous restrictions on gene flow have shaped the evolution and diversification of flying‐foxes.
ABSTRACT Sustainable fisheries rely on balancing harvests with ecological impacts. Despite the importance of species' demographic profiles, many assessments forgo age due to methodological complexities. Developing non‐lethal methods for age determination can improve stock assessments to ensure future sustainability. Epigenetic signals, specifically DNA methylation, are dynamic and considered to be associated with decreasing genomic stability with age. Subsequently, the modelling of methylation percentages at CpG loci has been utilized to accurately predict chronological age in many organisms, including several fish species. We examined the influence of age (1–14 years), location (Texas versus Tennessee), and sex on DNA methylation patterns of members of the largemouth bass‐complex (LBc), consisting of largemouth bass ( Micropterus nigricans ), Florida bass ( Micropterus salmoides ), and their resulting hybrids, all recreational and commercially important species. As DNA methylation patterns are influenced by sex and environmental signals, we accounted for this when evaluating aging patterns in the LBc. Our results indicate global methylation patterns decrease with age, indicating potential genomic instability, and vary with sex and location. Non‐random changes also occur involving physiological pathways of diverse function. Accounting for this variability, aging clocks using single or regions of CpG loci were derived from 124 LBc samples and validated using sets of naïve ( n = 32) individuals, providing improved estimates over other non‐lethal aging methods. Our results reveal insights into dynamic methylome patterns in the LBc, and when accounting for variability, informative and accurate age estimations can be determined with non‐lethal molecular methods.
