Adaptation of pest species to laboratory conditions and selection for resistance to toxins in the laboratory are expected to cause inbreeding and genetic bottlenecks that reduce genetic variation. Heliothis virescens, a major cotton pest, has been colonized in the laboratory many times, and a few laboratory colonies have been selected for Bt resistance. We developed 350 bp Double-Digest Restriction-site Associated DNA-sequencing (ddRAD-seq) molecular markers to examine and compare changes in genetic variation associated with laboratory adaptation, artificial selection, and inbreeding in this non-model insect species. We found that allelic and nucleotide diversity declined dramatically in laboratory-reared H. virescens as compared with field-collected populations. The declines were primarily due to the loss of low frequency alleles present in field-collected H. virescens. A further, albeit modest decline in genetic diversity was observed in a Bt-selected population. The greatest decline was seen in H. virescens that were sib-mated for 10 generations, where more than 80% of loci were fixed for a single allele. To determine which regions of the genome were resistant to fixation in our sib-mated and Bt-selected lines, we generated a dense intraspecific linkage map containing 3 PCR-based, and 659 ddRAD-seq markers. Markers that retained polymorphism were observed in small clusters spread over multiple linkage groups. These markers are likely associated with genomic regions under balancing selection, thus preventing fixation of deleterious alleles.

The conservation of threatened species must be underpinned by phylogeographic knowledge in order to be effective. This need is epitomised by the freshwater fish Carassius carassius, which has recently undergone drastic declines across much of its European range. Restriction Site Associated DNA sequencing (RADseq) is being increasingly used for such phylogeographic questions, however RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. Such tradeoffs have predominantly been addressed using simulated data. Here we compare the results generated from microsatellites and RADseq to the phylogeography of C. carassius, to add real-data-informed perspectives to this important debate. These datasets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns; showing the existence of two previously unidentified C. carassius lineages in Europe. These lineages have been isolated for approximately 2.2-2.3 M years, and should arguably be considered as separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with Approximate Bayesian Computation to show that the postglacial colonisation routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology.

Projection analysis is a useful tool for understanding the relationship of two populations. It compares a test genome to a set of genomes from a reference population. The projection’s shape depends on the historical relationship of the test genome’s population to the reference population. Here, we explore the effects on the projection when ancient samples are included in the analysis. First, we conduct a series of simulations in which the ancient sample is directly ancestral to a present-day population (one-population model) or the ancient sample is ancestral to a sister population that diverged before the time of sampling (two-population model). We find that there are characteristic differences between the projections for the one-population and two-population models, which indicate that the projection can be used to determine whether a test genome is directly ancestral to a present day population or not. Second, we compute projections for several published ancient genomes. We compare three Neanderthals, the Denisovan and three ancient human genomes to European, Han Chinese and Yoruba reference panels. We use a previously constructed demographic model and insert these seven ancient genomes and assess how well the observed projections are recovered.

Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data is available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data. Here we outline a simple solution to increase the overlap while avoiding potential the biases introduced by imputing data. If some external topological or taxonomic information is available, this can be used to maximize the overlap between the data and the phylogeny. We develop an algorithm that replaces a species lacking data with a species that has data. This swap can be made because for those two species, all phylogenetic relationships are exactly equivalent. We have implemented our method in a new R package phyndr, which will allow researchers to apply our algorithm to empirical data sets. It is relatively efficient such that taxon swaps can be quickly computed, even for large trees. To facilitate the use of taxonomic knowledge we created a separate data package taxonlookup; it contains a curated, versioned taxonomic lookup for land plants and is interoperable with phyndr. Emerging online databases and statistical advances are making it possible for researchers to investigate evolutionary questions at unprecedented scales. However, in this effort species mismatch among data sources will increasingly be a problem; evolutionary informatics tools, such as phyndr and taxonlookup, can help alleviate this issue.

Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through genetic drift. Loss of genome-wide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genome-wide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genome-wide variation was estimated as a proxy for evolutionary potential using more than 10,000 SNP markers generated by ddRAD-Seq. We found that genome-wide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genome-wide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine evolutionary potential along an urban-to-rural gradient and quantify urbanization as a driver of population genomics patterns.

Pseudomonas syringae pv. phaseolicola (Pph) is a significant bacterial pathogen of agricultural crops, and phage φ6 and other members of the dsRNA virus family Cystoviridae undergo lytic (virulent) infection of Pph, using the type IV pilus as the initial site of cellular attachment. Despite the popularity of Pph/phage φ6 as a model system in evolutionary biology, Pph resistance to phage φ6 remains poorly characterized. To investigate differences between phage φ6 resistant Pph strains, we examined genomic and gene expression variation among three bacterial genotypes that differ in the number of type IV pili expressed per cell: ordinary (wild-type), non-piliated, and super-piliated. Genome sequencing of non-piliated and super-piliated Pph identified few mutations that separate these genotypes from wild type Pph – and none present in genes known to be directly involved in type IV pilus expression. Expression analysis revealed that 81.1% of GO terms up-regulated in the non-piliated strain were down-regulated in the super-piliated strain. This differential expression is particularly prevalent in genes associated with respiration — specifically genes in the tricarboxylic acid cycle (TCA) cycle, aerobic respiration, and acetyl-CoA metabolism. The expression patterns of the TCA pathway appear to be generally up and down-regulated, in non-piliated and super-piliated Pph respectively. As pilus retraction is mediated by an ATP motor, loss of retraction ability might lead to a lower energy draw on the bacterial cell, leading to a different energy balance than wild type. The lower metabolic rate of the super-piliated strain is potentially a result of its loss of ability to retract.

Annelida represents a large and morphologically diverse group of bilaterian organisms. The recently published polychaete and leech genome sequences revealed an equally dynamic range of diversity at the genomic level. The availability of more annelid genomes will allow for the identification of evolutionary genomic events that helped shape the annelid lineage and better understand the diversity within the group. We sequenced and assembled the genome of the common earthworm, Eisenia fetida. As a first pass at understanding the diversity within the group, we classified 440 earthworm homeoboxes and compared them to those of the leech Helobdella robusta and the polychaete Capitella teleta. We inferred many gene expansions occurring in the lineage connecting the most recent common ancestor (MRCA) of Capitella and Eisenia to the Eisenia/Helobdella MRCA. Likewise, the lineage leading from the Eisenia/Helobdella MRCA to the leech Helobdella robusta has experienced substantial gains and losses. However, the lineage leading from Eisenia/Helobdella MRCA to E. fetida is characterized by extraordinary levels of homeobox gain. The evolutionary dynamics observed in the homeoboxes of these lineages are very likely to be generalizable to all genes. These genome expansions and losses have likely contributed to the remarkable biology exhibited in this group. These results provide a new perspective from which to understand the diversity within these lineages, show the utility of sub-draft genome assemblies for understanding genomic evolution, and provide a critical resource from which the biology of these animals can be studied. The genome data can be accessed through the Eisenia fetida Genome Portal: http://ryanlab.whitney.ufl.edu/genomes/Efet/

Variation is the spice of life or, in the case of evolution, variation is the necessary material on which selection can act to enable adaptation. Karyotypic variation in ploidy (the number of homologous chromosome sets) and aneuploidy (imbalance in the number of chromosomes) are fundamentally different than other types of genomic variants. Karyotypic variation emerges through different molecular mechanisms than other mutational events, and unlike mutations that alter the genome at the base pair level, rapid reversion to the wild type chromosome number is often possible. Although karyotypic variation has long been noted and discussed by biologists, interest in the importance of karyotypic variants in evolutionary processes has spiked in recent years, and much remains to be discovered about how karyotypic variants are produced and subsequently selected.