Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.

The hypothesis that pelagic larval duration (PLD) influences range size in marine species with a benthic adult stage and a pelagic larval period is intuitively attractive; yet, studies conducted to date have failed to support it. A possibility for the lack of a relationship between PLD and range size may stem from the failure of past studies to account for the effect of species evolutionary ages, which may add to the dispersal capabilities of species. However, if dispersal over ecological (i.e. PLD) and across evolutionary (i.e. species evolutionary age) time scales continues to show no effect on range size then an outstanding question is why? Here we collected data on PLD, evolutionary ages and range sizes of seven tropical fish families (five families were reef‐associated and two have dwell demersal habitats) to explore the independent and interactive effects of PLD and evolutionary age on range size. Separate analyses on each family showed that even after controlling for evolutionary age, PLD has an insignificant or a very small effect on range size. To shed light on why dispersal has such a limited effect on range size, we developed a global ocean circulation model to quantify the connectivity among tropical reefs relative to the potential dispersal conferred by PLD. We found that although there are several areas of great isolation in the tropical oceans, most reef habitats are within the reach of most species given their PLDs. These results suggest that the lack of habitat isolation can potentially render the constraining effect of dispersal on range size insignificant and explain why dispersal does not relate to range size in reef fishes.

The abundance of nuclear plastid DNA-like sequences (NUPTs) in nuclear genomes can vary immensely; however, the forces responsible for this variation are poorly understood. “The limited transfer window hypothesis” predicts that species with only one plastid per cell will have fewer NUPTs than those with many plastids per cell, but a lack of genome sequence data from monoplastidic species has made this hypothesis difficult to test. Here, by analyzing newly available genome sequences from diverse mono- and polyplastidic taxa, we show that the hypothesis holds. On average, the polyplastidic species we studied had 80 times more NUPTs than those that were monoplastidic. Moreover, NUPT content was positively related to nuclear genome size, indicating that in addition to plastid number, NUPTs are influenced by the forces controlling the expansion and contraction of noncoding nuclear DNA. These findings are consistent with data on nuclear DNAs of mitochondrial origin (NUMTs), suggesting that similar processes govern the abundance of both NUPTs and NUMTs.

Plant breeders face multiple global challenges that affect food security, productivity, accessibility, and nutritional quality. One major challenge for plant breeders is developing environmentally resilient crop cultivars in response to rapid shifts in cultivation conditions and resources due to climate change. Plant breeders rely on different crop genetic resources, breeding tools, and methods to incorporate genetic diversity into commercialized cultivars. Breeders use genetic diversity to develop new cultivars with improved agronomics, such as higher yield, biotic and abiotic stress tolerance, and to improve the nutritional quality of foods for a growing world population. Plant breeders perform the essential task of strategic integration of new genetic diversity while preserving important economic traits of individual crops such as relative maturity (maize, Zea mays L.), fruit type (tomato, Lycopersicon esculentum Mill.), plant type (lettuce Lactuca sativa L.), and habitat type (canola, Brassica napus L.) that are highly specialized for specific consumer preferences or market needs. This review provides an industry perspective on how genetic diversity is incorporated for crop improvement by (a) using a real-life example to highlight the vast amount of genetic diversity that exists in plants, (b) providing a conceptual example to illustrate strategic challenges a breeder faces while incorporating diversity, (c) describing how and why it can a decade or more to incorporate diversity into commercialized cultivars, even when advanced tools and technologies are used, and (d) sharing factors that plant breeders consider when applying various tools, including genome editing, at different stages of plant breeding.

Genetic diversity is shaped by the interaction of drift and selection, but the details of this interaction are not well understood. The impact of genetic drift in a population is largely determined by its demographic history, typically summarized by its long-term effective population size (Ne). Rapidly changing population demographics complicate this relationship, however. To better understand how changing demography impacts selection, we used whole-genome sequencing data to investigate patterns of linked selection in domesticated and wild maize (teosinte). We produce the first whole-genome estimate of the demography of maize domestication, showing that maize was reduced to approximately 5% the population size of teosinte before it experienced rapid expansion post-domestication to population sizes much larger than its ancestor. Evaluation of patterns of nucleotide diversity in and near genes shows little evidence of selection on beneficial amino acid substitutions, and that the domestication bottleneck led to a decline in the efficiency of purifying selection in maize. Young alleles, however, show evidence of much stronger purifying selection in maize, reflecting the much larger effective size of present day populations. Our results demonstrate that recent demographic change-a hall-mark of many species including both humans and crops-can have immediate and wide-ranging impacts on diversity that conflict with expectations based on long-term Ne alone.