Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies.

Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and summary-tree and SNP-based species-tree methods to infer a species tree for eastern North American Neodiprion species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that-except for three uncertain relationships-was robust to different strategies for analyzing whole-genome data. Nevertheless, underlying gene-tree discordance was high. To understand this genealogical variation, we used multiple linear regression to model site concordance factors estimated in 50-kb windows as a function of several genomic predictor variables. We found that site concordance factors tended to be higher in regions of the genome with more parsimony-informative sites, fewer singletons, less missing data, lower GC content, more genes, lower recombination rates, and lower D-statistics (less introgression). Together, these results suggest that incomplete lineage sorting, introgression, and genotyping error all shape the genomic landscape of gene-tree discordance in Neodiprion. More generally, our findings demonstrate how combining phylogenomic analysis with knowledge of local genomic features can reveal mechanisms that produce topological heterogeneity across genomes.

Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization.

Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.

When taxonomy and biological control researchers unite: Species delimitation of Eadya parasitoids (Braconidae) and consequences for classical biological control of invasive paropsine pests of Eucalyptus.

The invasive eucalyptus tortoise beetle, Paropsis charybdis, defoliates plantations of Eucalyptus nitens in New Zealand. Recent efforts to identify host specific biological control agents (parasitoids) from Tasmania, Australia, have focused on the larval parasitoid wasp, Eadya paropsidis (Braconidae), first described in 1978. In Tasmania, Eadya has been reared from Paropsisterna agricola (genus abbreviated Pst.), a smaller paropsine that feeds as a larva on juvenile rather than adult foliage of Eucalyptus nitens. To determine which of the many paropsine beetle hosts native to Tasmania are utilized by E. paropsidis, and to rule out the presence of cryptic species, a molecular phylogenetic approach was combined with host data from rearing experiments from multiple locations across six years. Sampling included 188 wasps and 94 beetles for molecular data alone. Two mitochondrial genes (COI and Cytb) and one nuclear gene (28S) were analyzed to assess the species limits in the parasitoid wasps. The mitochondrial genes were congruent in delimiting four separate phylogenetic species, all supported by morphological examinations of Eadya specimens collected throughout Tasmania. Eadya paropsidis was true to the type description, and was almost exclusively associated with P. tasmanica. A new cryptic species similar to E. paropsidis, Eadya sp. 3, was readily reared from Pst. agricola and P. charybdis from all sites and all years. Eadya sp. 3 represents the best candidate for biological control of P. charybdis and was determined as the species undergoing host range testing in New Zealand for its potential as a biological control agent. Another new species, Eadya sp. 1, was morphologically distinctive and attacked multiple hosts. The most common host was Pst. variicollis, but was also reared from Pst. nobilitata and Pst. selmani. Eadya sp. 1 may have potential for control against Pst. variicollis, a new incursion in New Zealand, and possibly Pst. selmani in Ireland. Our molecular data suggests that Pst. variicollis is in need of taxonomic revision and the geographic source of the beetle in New Zealand may not be Tasmania. Eadya sp. 2 was rarely collected and attacked P. aegrota elliotti and P. charybdis. Most species of Eadya present in Tasmania are not host specific to one beetle species alone, but demonstrate some host plasticity across the genera Paropsisterna and Paropsis. This study is an excellent example of collaborative phylogenetic and biological control research prior to the release of prospective biological control agents, and has important implications for the Eucalyptus industry worldwide.

Description of a new species of Euderus Haliday from the southeastern United States (Hymenoptera, Chalcidoidea, Eulophidae): the crypt-keeper wasp.

A new species of the genus Euderus Haliday, Euderus setsp. n., is described and illustrated from the southeastern United States, where it parasitizes the crypt gall wasp, Bassettia pallida Ashmead, 1896, on live oaks in the genus Quercus (subsection Virentes). This is the 1st species of the genus reported from the southeastern United States to parasitize cynipid gall wasps and the 3rd species of the genus reported to attack cynipids in North America. Modified sections of the identification keys to subgenera and species of Euderus (Yoshimoto, 1971) are included to integrate the new species.