Exploitation of mitochondrial nad6 as a complementary marker for studying population variability in Lepidoptera

The applicability of mitochondrial nad6 sequences to studies of DNA and population variability in Lepidoptera was tested in four species of economically important moths and one of wild butterflies. The genetic information so obtained was compared to that of cox1 sequences for two species of Lepidoptera. nad6 primers appropriately amplified all the tested DNA targets, the generated data proving to be as informative and suitable in recovering population structures as that of cox1. The proposal is that, to obtain more robust results, this mitochondrial region can be complementarily used with other molecular sequences in studies of low level phylogeny and population genetics in Lepidoptera

Data from: Influence of historical land use and modern agricultural expansion on the spatial and ecological divergence of sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae) in Brazil

Human-mediated changes in landscapes can facilitate niche expansion and accelerate the adaptation of insect species. The interaction between the evolutionary history of the sugarcane borer, Diatraea saccharalis Fabricius, and historical and modern agricultural activity in Brazil shaped its spatial genetic structure, facilitating ecological divergence and incipient host-shifting. Based on microsatellite data, STRUCTURE analyses identified two (K=2) and three (K=3) significant genetic clusters that corresponded to: a) a strong signal of spatial genetic structure and, b) a cryptic signal of host differentiation. We inferred that K=2 reflects the footprint of agricultural activity, such as expansion of crop production (sugarcane and maize), unintentional dispersion of pests, and management practices. In contrast, K=3 indicated incipient host differentiation between larvae collected from sugarcane or maize. Our estimates of population size changes indicated that a historical bottleneck was associated with a reduction of sugarcane production ≈200 years ago. However, a more recent population expansion was detected (>1950’s), associated with agricultural expansion of large crop production into previously unfarmed land. Partial Mantel tests supported our hypothesis of incipient host-adaptation, and identified isolation-by-environment (e.g. host plant) in São Paulo and Minas Gerais states, where sugarcane has been traditionally produced in Brazil. The impact of agricultural production on D. saccharalis may continue, as the current population structure may hinder the efficacy of refuge plants in delaying insect resistance evolution to Bt toxin

Data from: Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)

We present the development of a genomic library using RADseq (restriction site associated DNA sequencing) protocol for marker discovery that can be applied on evolutionary studies of the sugarcane borer Diatraea saccharalis, an important South American insect pest. A RADtag protocol combined with Illumina paired-end sequencing allowed de novo discovery of 12 811 SNPs and a high-quality assembly of 122.8M paired-end reads from six individuals, representing 40 Gb of sequencing data. Approximately 1.7 Mb of the sugarcane borer genome distributed over 5289 minicontigs were obtained upon assembly of second reads from first reads RADtag loci where at least one SNP was discovered and genotyped. Minicontig lengths ranged from 200 to 611 bp and were used for functional annotation and microsatellite discovery. These markers will be used in future studies to understand gene flow and adaptation to host plants and control tactics

Genetic history, structure and gene flow among populations of Belgica antarctica, the only free-living insect in the western Antarctic Peninsula

Changes in climate and environment can impact the sustainability of populations and biodiversity. Understanding population genetic diversity in the past and present can help us better predict species' responses to future environmental change. Antarctica has experienced drastic environmental change which threatens its biodiversity. In this study, we characterized the phylogeography and population genetic structure of Belgica antarctica, a wingless midge that is endemic to the western Antarctic Peninsula. This insect has adaptive features to withstand extremes in temperature, salinity, humidity, anoxia and pH. Belgica antarctica is widespread on widely dispersed islands of ice-free habitat, but questions remain regarding its genetic history, diversity and gene flow. We created nuclear-based, single nucleotide polymorphism (SNP) markers and genotyped 229 individuals from 11 populations to examine historical and current population genetic patterns. Our results support recent divergence among populations on different islands within the last 1 Mya. Furthermore, despite a lack of wings, B. antarctica exhibited frequent migration among islands, perhaps via ocean currents or phoresy with Antarctic vertebrates (e.g. seabirds). The close link between the evolutionary history of B. antarctica and the region's environment and ecology emphasize the importance of understanding its population dynamics to predict its persistence under environmental change

All kmer=27 minicontigs

This file contains minicontigs assembled with all second reads we generated. Second reads correspond to reads generated from random sheared ends of a genomic fragment. Since reads with different start and endings position were generated from the same genomic regions it allows the assemble of minicontigs bigger than read size usually sequenced (bigger than ~80bp reads

Final SNP set.

This file contains the final SNP set (after several filtering steps detailed at manuscript) in .vcf and .fasta format. Fasta file contains ~80bp sequences of each RADtag loci. After alignment of each sequences from same loci, SNP of each sample can be accessed

Scripts and command line of each program used in this pipeline.

This file contains all necessary commands and scripts to reproduce the outputs uploaded here (SNP, minicontigs, microsatellites, repetitive element discovery and functional annotation

Repetitive elements identified with RepeatMasker.

This file contains a table of the identified repetitive elements (.tbl), a file with masked contigs and repetitive elements (.fasta format) and a file with contig ID, repetitive element ID and coordinates

Minicontigs associated with RADtag loci.

Minicontigs associated with RADseq loci in .fasta format

Blast2GO annotation file.

This .gff file contain the final annotation of minicontigs obtained using Blast2GO pipeline