Research Project: Genetics and Genomics of Introduced Species for Biological Control of Invasive Species

Location: Beneficial Insects Introduction Research Unit

2023 Annual Report

Objectives
Objective 1: Determine the genetic basis of the host ranges and climatic tolerances of pest herbivorous insects and parasitoids of these pests with a focus on using molecular genetic methods to elucidate factors responsible for the evolution of host specificity, to predict responses to climate change, and to develop methods for management of pest impacts. [NP304, C1, PS1A; C3, PS3A, 3B and 3C] Sub-objective 1.A – Determine genetic basis of differences in host specificity of aphid parasitoids. Sub-objective 1.B – Measure genetic variation in responses of parasitoids and their aphid hosts to different temperature regimes. Sub-objective 1.C – Develop and test mathematical models for impact of climate change on population dynamics and evolution of parasitoids and aphid hosts. Objective 2: Determine interactions between biological control, plant resistance, and aphid virulence in their effects on virulence frequencies. [NP304, C1, PS1A; C3, PS3A and 3B] Sub-objective 2.A – Measure interactions between resistance, virulence, and parasitoids in their effects on virulence frequencies. Sub-objective 2.B – Develop and test mathematical models of interactions between plants, aphids, and parasitoids in their effects on virulence frequencies. Objective 3: Determine molecular phylogenetic relationships, test host specificity, and introduce parasitoids for biological control of target aphids. [NP304, C1, PS1A; C3, PS3A and 3B] Sub-objective 3.A – Determine molecular phylogenetic relationships of parasitoids. Sub-objective 3.B – Test host specificity of parasitoids of pest aphids. Sub-objective 3.C – Introduce parasitoids against pest aphids. Sub-objective 3.D – Measure the impact of the introduced parasitoids on distribution and abundance target and non-target aphid species.

Approach
Hypotheses about genetic architecture of host specificity have two extremes: (a) few genes with large effects that interact additively; (b) many genes of small effects that interact epistatically. We will take two approaches to testing these hypotheses. In one approach, we will use hybridization of A. atriplicis and A. certus in the laboratory to map QTL affecting parasitism of D. noxia, a host for A. atriplicis and a non-host for A. certus. We will cross A. atriplicis into A. certus with multi-parent advanced generation intercrosses and inbreed the intercrosses to make recombinant inbred lines (RILs). We will genotype SNPs in the RILs, make a linkage map, measure parasitism of D. noxia by these lines, and map QTL affecting parasitism. In the other approach, we will map QTL involved in differences between lines of A. rhamni reared for >140 generations on R. padi versus control lines reared on A. glycines. We will cross and backcross these lines, make a linkage map based on SNPs, measure parasitism of R. padi by backcross females, and map QTL affecting parasitism. We will test whether genes that diverge in sequence and/or expression between RIL and backcross females are associated with QTL found above. We will do this by genotyping RIL and backcross females for alleles in divergent genes and integrating these genes onto the QTL maps. To find genes that diverge in sequence or expression between A. atriplicis and A. certus and between selection and control A. rhamni, we have sequenced and assembled their genomes and transcriptomes. We will test whether divergent genes associated with QTL are expressed in sensilla on antennae, ovipositor, or mouth partsby hybridizing probes for the genes in parasitoids and imaging whole-mounts microscopically. We will whether divergence in gene sequences or expression levels correlate with differences in host specificity, host acceptance, and host suitability among Aphelinus species. We will measure genetic variation in temperature responses of parasitoids and their hosts that could allow adaptation to new temperature regimes using isofemale lines. We will develop and test mathematical models for the impact of climate change on population dynamics and evolution of parasitoids and hosts. To test this whether parasitoids slow the increase in frequency of virulent aphid genotypes that can overcome host plant resistance, we will do within-generation to get parameter estimates and multi-generation experiments to test the effects of parasitoids on viruluence freqencies. We will also develop and test mathematical models of interactions between plants, aphids, and parasitoids in their effects on virulence frequencies. We will continue to determine molecular phylogenetic relationships of parasitoids in the genus Aphelinus. We will continue to test the host specificity of parasitoids of pest aphids, and we will introduce parasitoids with narrow host range and measure their impact on the distribution and abundance target and non-target aphid species.

Progress Report
Wheat and barley are major crops in the US with annual revenues during the last decade of 9-19 billion dollars from 49-63 million acres planted. An invasive pest of these crops, the Russian wheat aphid, is seldom a pest in Eurasia, where parasitic wasps (parasitoids) and predators can limit its abundance. Parasitic wasps in the genus Aphelinus are among the most important Eurasian parasitoids of the Russian wheat aphid. Aphelinus hordei, a parasitoid of the Russian wheat aphid in Europe with a narrow host range, is a promising candidate for introduction. The North American Plant Protection approved a petition for its introduction, and APHIS-PPQ has approved a permit for field release in Colorado to control this pest. In spring 2023, an estimated 100,000 A. hordei were reared and shipped to Colorado State University for field release. Biological control by resident natural enemies may greatly diminish populations of the invasive soybean aphid on soybean. One such natural enemy is an accidentally introduced Asian parasitoid, Aphelinus certus. However, its impact may be limited by low parasitism early in the growing season, which may result from high overwintering mortality. In collaboration with University of Minnesota, thermocouple thermometry was used to measure the supercooling points of diapausing parasitoids, and parasitoid survival was assessed after exposure to ecologically relevant durations of low temperature. Aphelinus certus was freeze-intolerant with a median supercooling point of -28°C. When exposed to temperatures of 0°C for up to seven months, adults emerged only after durations greater than 60 days but survival decreased with durations greater than 150 days. In field experiments at sites from northern Minnesota to southern Iowa, survival was negatively correlated with increasing latitude and was greater for parasitoids placed on the ground than those 1 meter off the ground, probably because of the higher and more stable temperatures under snow. These results suggest that A. certus can overwinter in the region inhabited by soybean aphid but may experience substantial mortality even under ideal conditions. Climate change is predicted to bring warmer, drier winters to the North American Midwest, with decreased depth and duration of snow cover, which may further reduce overwintering survival (log 395241). In the simulations with mathematical models of the interaction between plant resistance in soybean and wheat, virulence of soybean aphid and Russian wheat aphid, and biological control with parasitoids in the genus Aphelinus, parasitoids reduced the abundances, and on wheat, the percent of virulent aphids. The impacts of parasitoids on virulent aphids were greater in southern locations than in northern locations, and the impacts on virulent aphids were greater on wheat than on soybean. Indeed, parasitoids actually increased the frequencies of virulent aphids on soybean when only susceptible plants were present, while reducing the abundance of all aphids. If one accepts that comparisons of population dynamics in southern versus northern locations indicate the likely effects of climate change in the northern locations, these results suggest that climate change would lead to decreased abundance and frequency of virulent aphids in northern locations (log 397791). During the last decade, the spotted-wing drosophila, Drosophila suzukii, has spread from eastern Asia to the Americas, Europe, and Africa. Divergence in genomic sequences and reproductive isolation were studied for cryptic species of Ganaspis near brasiliensis in five populations, two from China, two from Japan, and one from Canada, identified as the G1 versus G3 lineages based on differences in COI sequences. Genomes of these populations were assembled and annotated, and analyzed sequence divergence between them was estimated. Crosses were done between the G3 lineage from China and the G1 lineage from Japan to reproductive compatibility. The combined evidence of differences in the assemblies and annotations of the G1 and G3 lineages and their reproductive incompatibility shows they are different species. Genotyping-by-sequencing of reduced-representation libraries has ushered in an era where genome-wide data can be gotten for any species. Research on this topic in 28 papers published during the last two years was reviewed. These papers covered 33 species from 25 families and 11 orders. The majority of the papers were on population differences, including local adaptation and migration, but several were on genetic maps and their use in assembly scaffolding or analysis of quantitative trait loci, on the origin of incursions of pest insects, or on infection rates of a pathogen in a disease vector. Meta-analysis showed that less than 16 percent, and most often, less than 1 percent of the genome was implicated in local adaptation and that the number of adaptive loci correlated with genetic divergence among populations. Neither library type nor alignment method affected the number of SNP or adaptive loci or pairwise genetic divergence between populations. The amount of genetic divergence did not vary with the numbers of populations, number of insects, number of SNP (single-nucleotide polymorphic) loci, or number of adaptive loci. However, genetic divergence did correlate with the number of adaptive loci, suggesting that local adaptation was associated with greater overall genetic divergence between populations. The number of species in a taxonomic group depends on speciation and extinction rates. The superfamily Chalcidoidea has undergone extensive radiation, and contains >22,000 described species. Evidence about speciation in 40 studies of chalcidoids was reviewed. These studies involved several hundred species in 9 of the 50 chalcidoid families, most of which are parasitoids of other insects, although some are pollinators or herbivores. The evidence about speciation includes differences in host specificity, courtship and mating, morphology, and post-mating incompatibility. Much of the evidence is circumstantial, involving differences in host specificity or correlations between evolutionary trees of parasitoids and hosts, and with the exception of Nasonia species, there has been little work on the genetics of speciation. Although bacterial infections can cause current reproductive incompatibilities between species, it is unlikely that such infections were involved in the initial speciation process. On the other hand, the evidence concerning early learning as a first step in ecological speciation is compelling. The genomes of Aphelinus maculatus a parasitoid of Phorodon cannabis on Cannabis sativa (hemp) in New York and Aphelinus near varipes a parasitoid of Aphis ruborum on Fragaria × ananassa (strawberry) in Mississippi were assembled. Assembly statistics for A. maculatus were size = 577 megabases, N50 (length of shortest contig to include 50% of assembly) = 1.6 megabases, L50 (number of contigs that include 50 percent of genome) = 94, percent BUSCO genes in hymenopteran gene set = 91%. There was less than 1 percent bacterial contamination in the assembly, but the assembly captured the complete genome of the bacterial endosymbiont, Wolbachia. Assembly statistics for Aphelinus near varipes were size = 349 megabases, N50 = 0.28 megabases, L50 = 373, percent BUSCO genes in hymenopteran gene set = 89%. There was less than 1 percent bacterial contamination in the assembly, but the assembly captured the complete genome of the bacterial endosymbiont, Wolbachia. Aphelinus rhamni was selected during 3256 generations for increased parasitism of Rhopalosiphum padi, a sub-optimal, low-preference host species, by rearing the parasitoid on this aphid. Then selection and control lines were crossed and backcrossed to produce 843 backcross females that are being phenotyped for parasitism on R. padi and genotyped at many loci across the genome. These data will provide a detailed genetic map of the quantitative trait loci involved in increased parasitism of R. padi. To go along with this genetic map, the genome A. rhamni is being resequenced on the PacBio HiFi platform. Furthermore, the OmniC protocol has been used to create contiguity markers and these have been sequenced on the Illumina platform to provider markers for improved scaffolding. Host specificities of Aphelinus abdominalis from Acyrthosiphon pisum in the Netherlands, Aphelinus daucicola from Delaware on Aphis helianthi, Aphelinus near varipes from Aphis craccivora in Hungary, and Aphelinus nigritus from Melanaphis sacchari in Texas were measured for multiple aphid species in seven genera and two tribes (Acyrthrosiphum pisum, Aphis craccivora, Aphis glycines, Aphis gossypii, Aphis helianthi , Diuraphis noxia, Melanaphis sacchari, Myzus persicae, Rhopalosiphum maidis, Rhopalosiphum padi, Schizaphis graminum).

Accomplishments

Review Publications
Hopper, K.R. 2023. Modeling the effects climate change, plant resistance, herbivore virulence, and parasitism on the population dynamics of aphids and parasitoids in wheat and soybean. Ecological Modelling. 481. https://doi.org/10.1016/j.ecolmodel.2023.110376.
Stenoien, C.M., Christianson, L., Welch, K., Dregni, J., Hopper, K.R., Heimpel, G.E. 2023. Cold tolerance and overwintering survival of Aphelinus certus (Hymenoptera: Aphelinidae), a parasitoid of the soybean aphid (Hemiptera: Aphididae) in North America. Bulletin of Entomological Research. 1-13. https://doi.org/10.1017/S0007485323000196.