Data from: Cross-platform compatibility of de novo-aligned SNPs in a non-model butterfly genus

High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in non-model systems. Using double-digest restriction site associated DNA sequencing, we sequenced a common set of 22 specimens from the butterfly genus Speyeria on two different Illumina platforms, using two variations of library preparation. We then used a de novo approach to bioinformatic locus assembly and SNP discovery for subsequent phylogenetic analyses. We found a high rate of locus recovery despite differences in library preparation and sequencing platforms, as well as overall high levels of data compatibility after data processing and filtering. These results provide the first application of NGS methods for phylogenetic reconstruction in Speyeria, and support the use and long-term viability of SNP genotyping applications in non-model systems

Diversification shifts in leafroller moths linked to continental colonization and the rise of angiosperms

International audienc

Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)

Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted re-sampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principle components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species’ genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research

Population genetic structure and assessment of allochronic divergence in the Macoun’s arctic butterfly (Oeneis macounii)

Patterns in the genetic variation of species can be used to infer their specific demographic and evolutionary history and provide insight into the general mechanisms underlying population divergence and speciation. The Macounâ s arctic butterfly (MA; Oeneis macounii [W. H. Edwards, 1885]) occurs across Canada and parts of the northern US in association with jack (Pinus banksiana Lamb.) and lodgepole (Pinus contorta Doug. ex Loud.) pine. MAâ s current distribution is highly fragmented, and the extent of reproductive isolation among allopatric populations is unknown. Furthermore, although MA is biennial, adults emerge every year in some populations. These populations presumably consist of two alternate-year cohorts, providing the opportunity for sympatric divergence via allochronic isolation. Using mitochondrial (mt) DNA and amplified fragment length polymorphism (AFLP) markers, we analyzed MAâ s genetic structure to determine the current and historical role of allopatric and allochronic isolation in MA population divergence. Both markers revealed high diversity and a low, but significant, degree of spatial structure and pattern of isolation by distance. Phylogeographic structure was generally absent, with low divergence among mtDNA haplotypes. MA likely exhibits low dispersal and gene flow among most allopatric populations; however, there was no evidence of differentiation resulting from allochronic isolation for sympatric cohorts.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Identification of genes and gene expression associated with dispersal capacity in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)

Dispersal flights by the mountain pine beetle have allowed range expansion and major damage to pine stands in western Canada. We asked what the genetic and transcriptional basis of mountain pine beetle dispersal capacity is. Using flight mills, RNA-seq and a targeted association study, we compared strong-flying, weak-flying, and non-flying female beetles from the recently colonized northern end of their range. Nearly 3,000 genes were differentially expressed between strong and weak flying beetles, while weak fliers and nonfliers did not significantly differ. The differentially expressed genes were mainly associated with lipid metabolism, muscle maintenance, oxidative stress response, detoxification, endocrine function, and flight behavior. Three variant loci, two in the coding region of genes, were significantly associated with flight capacity but these genes had no known functional link to flight. Several differentially expressed gene systems may be important for sustained flight, while other systems are downregulated during dispersal and likely to conserve energy before host colonization. The candidate genes and SNPs identified here will inform further studies and management of mountain pine beetle, as well as contribute to understanding the mechanisms of insect dispersal flights

What causes latitudinal gradients in species diversity? Evolutionary processes and ecological constraints on swallowtail biodiversity

Contact : [email protected] audienceThe latitudinal diversity gradient (LDG) is one of the most striking ecological patterns on our planet. Determining the evolutionary causes of this pattern remains a challenging task. To address this issue, previous LDG studies have usually relied on correlations between environmental variables and species richness, only considering evolutionary processes indirectly. Instead, we use a phylogenetically integrated approach to investigate the ecological and evolutionary processes responsible for the global LDG observed in swallowtail butterflies (Papilionidae). We find evidence for the diversification rate hypothesis with different diversification rates between two similarly aged tropical and temperate clades. We conclude that the LDG is caused by (1) climatically driven changes in both clades based on evidence of responses to cooling and warming events, and (2) distinct biogeographical histories constrained by tropical niche conservatism and niche evolution. This multidisciplinary approach provides new findings that allow better understanding of the factors that shape LDGs

Role of Caribbean Islands in the diversification and biogeography of Neotropical Heraclides swallowtails

International audienceNumerous hypotheses on the evolution of Neotropical biodiversity have stimulated research to provide a better understandingof diversity dynamics and distribution patterns of the region. However, few studies integrate molecular and morphological datawith complete sampling of a Neotropical group, and so there has been little synthesis of the multiple processes governing biodi-versity through space and time. Here, a total-evidence phylogenetic approach is used to reconstruct the evolutionary history ofthe butterfly subgenusHeraclides. We used DNA sequences for two mitochondrial genes and one nuclear gene and coded 133morphological characters of larvae and adults. A robust and well-resolved phylogeny was obtained using several analyticalapproaches, while molecular dating and biogeographical analyses indicated an early Miocene origin (22 Mya) in the CaribbeanIslands. We inferred six independent dispersal events from the Caribbean to the mainland, and three from the mainland to theCaribbean, and we suggest that cooling climates with decreasing sea levels may have contributed to these events. The time-cali-brated tree is best explained by a museum model of diversity in which both speciation and extinction rates remained constantthrough time. By assessing both continental and fine-scale biodiversity patterns, this study provides new findings, for instancethat islands may act as source of diversity rather than as a sink, to explain spatio-temporal macroevolutionary processes withinthe Neotropical region

The contribution of genetics and genomics to understanding the ecology of the mountain pine beetle system

Environmental change is altering forest insect dynamics worldwide. As these systems change, they pose significant ecological, social and economic risk through, for example, the loss of valuable habitat, green space and timber. Our understanding of such systems is often limited by the complexity of multiple interacting taxa. Thus, studies assessing the ecology, physiology and genomics of each key organism in such systems is increasingly important for developing appropriate management strategies. Here we summarize the genetic and genomic contributions made by the TRIA project â a long-term study of the mountain pine beetle system encompassing beetle, fungi and pine. Contributions include genetic and genomic resources for species identification, sex determination, detection of selection, functional genetic analysis, mating system confirmation, hybrid stability tests and integrated genetic studies of multiple taxa. These resources and subsequent findings have accelerated our understanding of the mountain pine beetle system, facilitating improved management strategies (e.g. enhancements to stand susceptibility indices and predictive models) and highlighting mechanisms for promoting resilient forests. Further, work from the TRIA project serves as a model for the increasing number and severity of invasive and native forest insect outbreaks globally (e.g. Dutch elm and thousand cankers disease).The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Convergent herbivory on conifers by Choristoneura moths after boreal forest formation

International audienceMitogenomes are useful markers for phylogenetic studies across a range of taxonomic levels. Here, we focus on mitogenome variation across the tortricid moth genus Choristoneura and particularly the spruce budworm (Choristoneura fumiferana) species complex, a notorious pest group of North American conifer forests. Phylogenetic relationships of Tortricidae, representing two subfamilies, four tribes and nine genera, were analyzed using 21 mitogenomes. These included six newly-sequenced mitogenomes for species in the spruce budworm complex plus three additional Choristoneura species and 12 previously published mitogenomes from other tortricids and one from the Cossidae. We evaluated the phylogenetic informativeness of the mitogenomes and reconstructed a time-calibrated tree with fossil and secondary calibrations. We found that tortricid mitogenomes had conserved protein and ribosomal regions, and analysis of all protein-coding plus ribosomal genes together provided an efficient marker at any taxonomic rank. The time-calibrated phylogeny showed evolutionary convergence of conifer feeding within Choristoneura, with two independent lineages, the Nearctic spruce budworm complex and the Palearctics pecies Choristoneura murinana, both shifting onto conifers about 11 million years ago from angiosperms. These two host-plant shifts both occurred after the formation of boreal forest in the late Miocene. Haplotype diversification within the spruce budworm complex occurred in the last 4 million years, and is probably linked to the initial cooling cycles of the Northern Hemisphere in the Pliocene