Scanning the human genome for “signatures” of positive selection: Transformative opportunities and ethical obligations
Abstract: The relationship history of evolutionary anthropology and genetics is complex. At best, genetics is a beautifully integrative part of the discipline. Yet this integration has also been fraught, with punctuated, disruptive challenges to dogma, periodic reluctance by some members of the field to embrace results from analyses of genetic data, and occasional over-assertions of genetic definitiveness by geneticists. At worst, evolutionary genetics has been a tool for reinforcing racism and colonialism. While a number of genetics/genomics papers have disproportionately impacted evolutionary anthropology, here we highlight the 2002 presentation of an elegantly powerful approach for identifying “signatures” of past positive selection from haplotype-based patterns of genetic variation. Together with technological advances in genotyping methods, this article transformed our field by facilitating genome-wide “scans” for signatures of past positive selection in human populations. This approach helped researchers test longstanding evolutionary anthropology hypotheses while simultaneously providing opportunities to develop entirely new ones. Genome-wide scans for signatures of positive selection have since been conducted in diverse worldwide populations, with striking findings of local adaptation and convergent evolution. Yet there are ethical considerations with respect to the ubiquity of these studies and the cross-application of the genome-wide scan approach to existing datasets, which we also discuss.
Factors influencing taxonomic unevenness in scientific research: a mixed-methods case study of non-human primate genomic sequence data generation
Abstract: Scholars have noted major disparities in the extent of scientific research conducted among taxonomic groups. Such trends may cascade if future scientists gravitate towards study species with more data and resources already available. As new technologies emerge, do research studies employing these technologies continue these disparities? Here, using non-human primates as a case study, we identified disparities in massively parallel genomic sequencing data and conducted interviews with scientists who produced these data to learn their motivations when selecting study species. We tested whether variables including publication history and conservation status were significantly correlated with publicly available sequence data in the NCBI Sequence Read Archive (SRA). Of the 179.6 terabases (Tb) of sequence data in SRA for 519 non-human primate species, 135 Tb (approx. 75%) were from only five species: rhesus macaques, olive baboons, green monkeys, chimpanzees and crab-eating macaques. The strongest predictors of the amount of genomic data were the total number of non-medical publications (linear regression; r2 = 0.37; p = 6.15 × 10−12) and number of medical publications (r2 = 0.27; p = 9.27 × 10−9). In a generalized linear model, the number of non-medical publications (p = 0.00064) and closer phylogenetic distance to humans (p = 0.024) were the most predictive of the amount of genomic sequence data. We interviewed 33 authors of genomic data-producing publications and analysed their responses using grounded theory. Consistent with our quantitative results, authors mentioned their choice of species was motivated by sample accessibility, prior published work and relevance to human medicine. Our mixed-methods approach helped identify and contextualize some of the driving factors behind species-uneven patterns of scientific research, which can now be considered by funding agencies, scientific societies and research teams aiming to align their broader goals with future data generation efforts.
Culture, behavior and health
Abstract: Cultural behaviors have important implications for human health. Culture, a socially transmitted system of shared knowledge, beliefs and/or practices that varies across groups, and individuals within those groups, has been a critical mode of adaptation throughout the history of our species. Socioeconomic status, gender, religion and moral values all play into how individuals experience, conceptualize and react to their world, and therefore general understandings of cultural groups are insufficient for grasping a patient’s unique experience with health and illnesses. Additionally, structural inequalities and political economy play a critical, and often overlooked, role in health and disease. Understanding how behaviors are rooted in an individual’s unique cultural experience and as a response to social pressures can better equip medical professionals with the context, skills and empathy necessary for holistic care.
Healthcare providers can improve individual outcomes by thoroughly factoring in life experiences as part of understanding an individual’s health and treating their illnesses. The use of a ‘mini-ethnography’ can help healthcare providers understand how identity, interpretation of illness and the moral values of patients factor into building a trusting relationship that considers the patient’s life experiences into treatment plans. The image on the left summarizes this approach.
Evolution of floral traits and impact of reproductive mode on diversification in the phlox family (Polemoniaceae)
Abstract: Pollinator-mediated selection is a major driver of evolution in flowering plants, contributing to the vast diversity of floral features. Despite long-standing interest in floral variation and the evolution of pollination syndromes in Polemoniaceae, the evolution of floral traits and known pollinators has not been investigated in an explicit phylogenetic context. Here we explore macroevolutionary patterns of both pollinator specificity and three floral traits long considered important determinants of pollinator attraction across the most comprehensive species-level phylogenetic tree yet produced for the family. The presence of floral chlorophyll is reconstructed as the ancestral character state of the family, even though the presence of floral anthocyanins is the most prevalent floral pigment in extant taxa. Mean corolla length and width of the opening of the floral tube are correlated, and both appear to vary with pollinator type. The evolution of pollination systems appears labile, with multiple gains and losses of selfing and conflicting implications for patterns of diversification. Explicit testing of diversification models rejects the hypothesis that selfing is an evolutionary dead-end. This study begins to disentangle the individual components that comprise pollination syndromes and lays the foundation for future work on the genetic mechanisms that control each trait.