Brian C. Verrelli

Evidence for balancing selection from nucleotide sequence analyses of human G6PD.

Glucose-6-phosphate dehydrogenase (G6PD) mutations that result in reduced enzyme activity have been implicated in malarial resistance and constitute one of the best examples of selection in the human genome. In the present study, we characterize the nucleotide diversity across a 5.2-kb region of G6PD in a sample of 160 Africans and 56 non-Africans, to determine how selection has shaped patterns of DNA variation at this gene. Our global sample of enzymatically normal B alleles and A, A-, and Med alleles with reduced enzyme activities reveals many previously uncharacterized silent-site polymorphisms. In comparison with the absence of amino acid divergence between human and chimpanzee G6PD sequences, we find that the number of G6PD amino acid polymorphisms in human populations is significantly high. Unlike many other G6PD-activity alleles with reduced activity, we find that the age of the A variant, which is common in Africa, may not be consistent with the recent emergence of severe malaria and therefore may have originally had a historically different adaptive function. Overall, our observations strongly support previous genotype-phenotype association studies that proposed that balancing selection maintains G6PD deficiencies within human populations. The present study demonstrates that nucleotide sequence analyses can reveal signatures of both historical and recent selection in the genome and may elucidate the impact that infectious disease has had during human evolution.

Numb regulates Notch1, but not Notch3, during myogenesis

In the vertebrate embryo, skeletal muscle is derived from the myotome of the somites. Notch1-3 demonstrate overlapping and distinct expression patterns in mouse somites. Notch1 and Notch2 have been shown to be inhibitors of skeletal myogenesis. The current data demonstrate that Notch3 also is an effective inhibitor of MyoD induced myogenesis. Numb, an adaptor protein that promotes Notch degradation by recruiting the E3 ubiquitin ligase, Itch, is limited in expression to dividing cells of the dorsal medial lip of the dermomyotome and the myotome itself. Here the specificity of the four protein isoforms of Numb for the Notch receptors was examined. In transcription and myogenic differentiation assays, Notch1 was consistently negatively regulated by all four Numb isoforms, and Notch3 was not a target for Numb. Notch2 however was variably affected. Subsequent analyses showed that unlike Notch1, that Notch3 was not polyubiquitinated, nor degraded when co-expressed in cells with Numb. These data provide the first observations that Notch receptors are variably affected by Numb and will be important for the interpretation of the function of Notch and Numb interactions during the development of many different cells and tissues.

Comparative Vertebrate Evolutionary Analyses of Type I Collagen: Potential of COL1a1 Gene Structure and Intron Variation for Common Bone-Related Diseases

Collagen type I alpha 1 (COL1a1), which encodes the primary subunit of type I collagen, the main structural and most abundant protein in vertebrates, harbors hundreds of mutations linked to human diseases like osteoporosis and osteogenesis imperfecta. Previous studies have attempted to predict the phenotypic severity associated with type I collagen mutations, yet an evolutionary analysis that compares historical and recent selective pressures, including across noncoding regions, has never been conducted. Here, we use a comparative genomic and species evolutionary analysis representing ∼450 My of vertebrate history to investigate functional constraints associated with both exons and introns of the >17-kb COL1a1 gene. We find that although the COL1a1 amino acid sequence is highly conserved, there are both spatial and temporal signatures of varying selective constraint across protein domains. Furthermore, sites of high evolutionary constraint significantly correlate with the location of disease-associated mutations, the latter of which also cluster with respect to specific severity classes typically categorized in clinical studies. Finally, we find that COL1a1 introns are significantly short in length with high GC content, patterns that are shared across highly diverged vertebrates, and which may be a signature of strong stabilizing selection for high COL1a1 gene expression. In conclusion, although previous studies focused on COL1a1 coding regions, the current results implicate introns as areas of high selective constraint and targets of bone-related phenotypic variation. From a broader perspective, our comparative evolutionary approach provides further resolution to models predicting mutations associated with bone-related function and disease severity.

Contrasting patterns of selective constraints in nuclear-encoded genes of the oxidative phosphorylation pathway in holometabolous insects and their possible role in hybrid breakdown in Nasonia

The principal energy generating system in animals is the oxidative phosphorylation (OXPHOS) pathway, which depends on the tight interaction of nuclear- and mitochondrial-encoded genes to function properly. Mitochondrial genes accumulate substitutions more quickly than nuclear genes, yet the impact of selection on mitochondrial genes is significantly reduced relative to nuclear genes because of the non-recombining nature of the mitochondrial genome and its predicted smaller effective population size. It has therefore been hypothesized that the nuclear-encoded genes of the OXPHOS pathway are under strong selective pressure to compensate for the accumulation of deleterious nucleotide substitutions in mitochondrial-encoded OXPHOS genes, a process known as compensatory co-adaptation. We evaluated this hypothesis by analyzing nuclear-encoded OXPHOS genes for signatures of positive selection as well as evolutionary constraints at amino acid sites. We considered OXPHOS genes of six holometabolous insects and their orthologs from three Nasonia parasitoid wasps, the hybrids of which suffer from an increased mortality rate caused by cytonuclear genic incompatibilities. Although nuclear OXPHOS genes are typically highly conserved, we found significant evidence for elevated amino acid divergence in 4 of the 59 studied nuclear-encoded OXPHOS genes. We also found that three of these four genes, as well as six other OXPHOS genes, contain amino acid substitutions between Nasonia species at evolutionarily constrained sites. It is possible that these genes account for the reported incompatibility in Nasonia hybrids and their characterization may lead to a better understanding of the role of positive selection in the genetics of speciation.

Haplotype Structure and Divergence at Human and Chimpanzee Serotonin Transporter and Receptor Genes: Implications for Behavioral Disorder Association Analyses

Genetic variation in the human serotonin system has long-been studied because of its functional consequences and links to various behavior-related disorders and it being routinely targeted in research and development for drug therapy. However, aside from clinical studies, little is known about this genetic diversity and how it differs within and between human populations with respect to haplotype structure, which can greatly impact phenotype association studies. In addition, no evolutionary approach among humans and other primates has examined how long- and short-term selective pressures explain existing serotonin variation. Here, we examine DNA sequence variation in natural population samples of 192 human and 40 chimpanzee chromosome sequences for the most commonly implicated approximately 38-kb serotonin transporter (SLC6A4) and approximately 63-kb serotonin 2A receptor (HTR2A) genes. Our comparative population genetic analyses find significant linkage disequilibrium associated with functionally relevant variants in humans, as well as geographic variation for these haplotypes, at both loci. In addition, although amino acid divergence is consistent with purifying selection, promoter and untranslated regions exhibit significantly high divergence in both species lineages. These evolutionary analyses imply that the serotonin system may have accumulated significant regulatory variation over both recent and ancient periods of time in both humans and chimpanzees. We discuss the implications of this variation for disease association studies and for the evolution of behavior-related phenotypes during the divergence of humans and our closest primate relatives.

Urban hubs of connectivity: contrasting patterns of gene flow within and among cities in the western black widow spider

As urbanization drastically alters the natural landscape and generates novel habitats within cities, the potential for changes to gene flow for urban-dwelling species increases. The western black widow spider (Latrodectus hesperus) is a medically relevant urban adapter pest species, for which we have previously identified population genetic signatures consistent with urbanization facilitating gene flow, likely due to human-mediated transport. Here, in an analysis of 1.9 million genome-wide SNPs, we contrast broad-scale geographical analyses of 10 urban and 11 non-urban locales with fine-scale within-city analyses including 30 urban locales across the western USA. These hierarchical datasets enable us to test hypotheses of how urbanization impacts multiple urban cities and their genetic connectivity at different spatial scales. Coupled fine-scale and broad-scale analyses reveal contrasting patterns of high and low genetic differentiation among locales within cities as a result of low and high genetic connectivity, respectively, of these cities to the overall population network. We discuss these results as they challenge the use of cities as replicates of urban eco-evolution, and have implications for conservation and human health in a rapidly growing urban habitat.

Urbanization as a facilitator of gene flow in a human health pest

Urban fragmentation can reduce gene flow that isolates populations, reduces genetic diversity and increases population differentiation, all of which have negative conservation implications. Alternatively, gene flow may actually be increased among urban areas consistent with an urban facilitation model. In fact, urban adapter pests are able to thrive in the urban environment and may be experiencing human‐mediated transport. Here, we used social network theory with a population genetic approach to investigate the impact of urbanization on genetic connectivity in the Western black widow spider, as an urban pest model of human health concern. We collected genomewide single nucleotide polymorphism variation from mitochondrial and nuclear double‐digest RAD (ddRAD) sequence data sets from 210 individuals sampled from 11 urban and 10 nonurban locales across its distribution of the Western United States. From urban and nonurban contrasts of population, phylogenetic, and network analyses, urban locales have higher within‐population genetic diversity, lower between‐population genetic differentiation and higher estimates of genetic connectivity. Social network analyses show that urban locales not only have more connections, but can act as hubs that drive connectivity among nonurban locales, which show signatures of historical isolation. These results are consistent with an urban facilitation model of gene flow and demonstrate the importance of sampling multiple cities and markers to identify the role that urbanization has had on larger spatial scales. As the urban landscape continues to grow, this approach will help determine what factors influence the spread and adaptation of pests, like the venomous black widow spider, in building policies for human and biodiversity health.