Brian R. Johnson

Despite the advantages associated with social living, one of the main costs of sociality is an increased exposure to pathogens. For honey bees, these costs are artificially inflated in the unnatural and densely crowded apiary environments common to commercial operations. Modern beekeeping practices have not only exacerbated these problems but have also led to the introduction of novel parasites. One newly introduced parasite of honey bees is Nosema ceranae, a unicellular, spore-forming gut parasite that has achieved a cosmopolitan distribution in recent decades. N. ceranae is widely considered a dangerous pathogen for both individual bees and colonies as a whole. The parasite can infect every member of the honey bee colony; however, it remains to be understood whether there are asymmetrical contributions to spreading N. ceranae spores by particular castes. Here, we test the long-held suspicion that honey bee drones may be important for driving pathogen transmission between colonies in modern apiary settings. Although we find sparse evidence that N. ceranae infection causes enhanced transmission by changing drone or worker behavior, we do confirm that infected drones drift at high rates and are accepted by foreign colonies. Our results thus present a grim picture for enhanced diseases transmission by males in crowded apiaries.

Free will is a question that has interested scientists and philosophers for centuries. It is a staple of discussion in some academic fields and is a lively topic in the popular press and social media. In the present paper, I present a simple argument for free will as an emergent property of intelligent life. In short, the consensus view in physics is that quantum mechanics is inherently probabilistic and processes such as radioactive decay are truly random. Following this, there are quantum random number generators that can be used to inform probabilistic decision making in computers, and in ourselves if we desire. A conditional decision (I will do x with 90% probability) that references a quantum number generator is not deterministic and the future that follows is therefore not determined. To put it into the context of the famous thought experiment, if one could go back in time and redo such decisions, they would not stay the same. The ability to link randomness in the quantum realm to conditional probabilistic action at the macroscopic level is argued to be one of the many cases of radical emergences that must proceed from the evolution of intelligent life with significant technological advancement.

The idea that race is a purely social construct appears to have achieved almost universal acceptance within academia. However, this consensus is artificial and maintained by a taboo on the subject of race, particularly in the biological sciences. Here, I argue that the common-sense view that race has a biological basis but is unimportant for traits such as intelligence or character best fits the scientific data. I start by showing that most past biological discussions of race have focused on the wrong concepts. Specifically, population structure at the genomic level is irrelevant to most notions of race, which stress functional differences in a handful of traits. I therefore argue that the concept of ecotype, which is associated with local adaptation of a handful of traits in a highly connected network of populations, is the best descriptor of human races. I then explain the relationship between the social construction of race and its biological basis. The essential point here is that race is socially constructed from real biological variation. I conclude with a brief discussion of scientific racism, which I argue is better labeled pseudoscientific racism. I posit that stifling discussion of race by biologists has been counterproductive and misguided. When scientists refuse to refute the racist spin doctoring of biological data that is central to scientific racism, it gives the public the notion that the data are not on their side. Moreover, ideologically driven positions, such as races do not exist, erode public confidence in the scientific community.

Many social and environmental variables can affect the interactions among individuals in an insect colony that fundamentally structure its social organization. Along with important attributes such as age and caste, immunity-related factors such as the performance of sanitary tasks or exposure to a pathogen can also influence an individual’s social interactions and their place in the resulting social network. Most work on this subject has supported the hypothesis that health-compromised individuals will exhibit altered social or spatial behavior that presumably limits the spread of infection. Here, we test this hypothesis using honey bee workers recently involved in hygienic behavior, an important set of sanitary tasks in which unhealthy brood are uncapped and then removed from the colony. Using static social networks, we quantify the interaction patterns of workers recently involved in hygienic tasks and compare their network centrality to non-hygienic workers. Using dynamic networks, we analyze the capability of hygienic workers to spread a potential infection throughout the colony. We find no substantial differences in how connected hygienic workers are in the network, and we show that hygienic workers would spread a novel infection throughout the colony to the same extent as non-hygienic workers. Our results suggest that experience with certain sanitary tasks may not necessarily produce rapid changes in social behavior. This work highlights the importance of considering the benefits of remaining socially integrated in important information networks and the temporal limitations for how quickly organized immune responses can occur in response to potential infections.

Taxonomically restricted genes are increasingly understood to play major roles in evolution. However, a significant body of work has taken issue with the notion of widespread “novel” genes and argued that such genes have homologs in distant clades that can be found with either sufficiently powerful alignment techniques, or by using synteny to find their ancestral sequences. Here, we argue that such work is misguided. Moreover, we argue that the whole notion of genetic assignment of function (and annotation) based on historical origin violates the levels of analysis distinction between origin and current utility. The evolutionary history of a gene is so often not reflective of its current utility that naming genes based on the function of their homologs is bad practice. This is nowhere more apparent than in the case of genes that have changed so radically from their ancestors that they bear no similarity to them at the sequence or protein folding levels. We coin the term, overwriting, for this process in which selection creates novel genes by retaining the structure of a gene only (intron, exon, promoter positions), but nothing else, and argue for a general importance for this process.

There is considerable variation in the mean IQ scores of human racial groups. Such group differences may be caused by genetic or environmental effects. Here we review and refute the claims of those who argue that mean IQ differences are the result of genetic effects, a claim which has seen a resurgence in recent years. We begin with data that question the notion that races vary in IQ and real-world achievement in a manner supporting a racial hierarchy. First, minorities of different genetic ancestry have comparable IQ and achievement levels in the US. Second, worldwide, we often see gaps as large as between White and Black Americans within single racial groups. Third, the Black-White achievement gap is entirely due to sex specific differences in achievement. There are, however, no sex specific mean differences in IQ. With respect to the magnitude of racial achievement gaps, they are well within the range of effects caused by socioeconomic factors, particularly those related to education. Further, when IQ tests do not reference past knowledge (particularly vocabulary), the IQ gap disappears. We then review work showing that mixed race persons do not typically show intermediate IQ, a key prediction of the genetic hypothesis. Finally, we review the three extant transracial adoption studies, which do not provide any support for a genetic explanation for group level differences in IQ. In sum, there is nothing about the nature of racial IQ gaps that suggests a genetic explanation, and the experimental work does not support a genetic explanation.

Genes limited to particular clades, taxonomically restricted genes (TRGs), are common in all sequenced genomes. TRGs have recently become associated with the evolution of novelty, as numerous studies across the tree of life have now linked expression of TRGs with novel phenotypes. However, TRGs that underlie ancient lineage specific traits have been largely omitted from discussions of the general importance of TRGs. Here it is argued that when all TRGs are considered, it is apparent that TRGs are fundamental to biology and evolution and likely play many complementary roles to the better understood toolkit genes. Genes underlying photosynthesis and skeletons, for example, are examples of commonplace fundamental TRGs. Essentially, although basic cell biology has a highly conserved genetic basis across the tree of life, most major clades also have lineage specific traits central to their biology and these traits are often based on TRGs. In short, toolkit genes underlie what is conserved across organisms, while TRGs define in many cases what is unique. An appreciation of the importance of TRGs will improve our understanding of evolution by triggering the study of neglected topics in which TRGs are of paramount importance.

The origin of the insect odorant receptor (OR) gene family has been hypothesized to have coincided with the evolution of terrestriality in insects. Missbach et al. (2014) suggested that ORs instead evolved with an ancestral OR co-receptor (Orco) after the origin of terrestriality and the OR/Orco system is an adaptation to winged flight in insects. We investigated genomes of the Collembola, Diplura, Archaeognatha, Zygentoma, Odonata, and Ephemeroptera, and find ORs present in all insect genomes but absent from lineages predating the evolution of insects. Orco is absent only in the ancestrally wingless insect lineage Archaeognatha. Our new genome sequence of the zygentoman firebrat Thermobia domestica reveals a full OR/Orco system. We conclude that ORs evolved before winged flight, perhaps as an adaptation to terrestriality, representing a key evolutionary novelty in the ancestor of all insects, and hence a molecular synapomorphy for the Class Insecta.

Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata, an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components.

Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata , an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components. Data availability: The Medauroidea extradentata genome assembly, Med v1.0, is available for download via NCBI (Bioproject: PRJNA369247). The genome, annotation files, and official gene set Mext_OGS_v1.0 are also available at the i5k NAL workspace ( https://i5k.nal.usda.gov/medauroidea-extradentata ) and at github ( https://github.com/pbrec/medauroidea_genome_resources ). The genomic raw reads are available via NCBI SRA: SRR6383867 and the raw transcriptomic reads are available at NCBI SRA: SRR6383868, SRR6383869.