Doctor of Philosophy, Rockefeller University (2010)
Marcus Feldman, Postdoctoral Faculty Sponsor
Worldwide patterns of genetic variation are driven by human demographic history. Here, we test whether this demographic history has left similar signatures on phonemes-sound units that distinguish meaning between words in languages-to those it has left on genes. We analyze, jointly and in parallel, phoneme inventories from 2,082 worldwide languages and microsatellite polymorphisms from 246 worldwide populations. On a global scale, both genetic distance and phonemic distance between populations are significantly correlated with geographic distance. Geographically close language pairs share significantly more phonemes than distant language pairs, whether or not the languages are closely related. The regional geographic axes of greatest phonemic differentiation correspond to axes of genetic differentiation, suggesting that there is a relationship between human dispersal and linguistic variation. However, the geographic distribution of phoneme inventory sizes does not follow the predictions of a serial founder effect during human expansion out of Africa. Furthermore, although geographically isolated populations lose genetic diversity via genetic drift, phonemes are not subject to drift in the same way: within a given geographic radius, languages that are relatively isolated exhibit more variance in number of phonemes than languages with many neighbors. This finding suggests that relatively isolated languages are more susceptible to phonemic change than languages with many neighbors. Within a language family, phoneme evolution along genetic, geographic, or cognate-based linguistic trees predicts similar ancestral phoneme states to those predicted from ancient sources. More genetic sampling could further elucidate the relative roles of vertical and horizontal transmission in phoneme evolution.
View details for DOI 10.1073/pnas.1424033112
View details for PubMedID 25605893
Niche construction is the process by which organisms can alter the ecological environment for themselves, their descendants, and other species. As a result of niche construction, differences in selection pressures may be inherited across generations. Homophily, the tendency of like phenotypes to mate or preferentially associate, influences the evolutionary dynamics of these systems. Here we develop a model that includes selection and homophily as independent culturally transmitted traits that influence the fitness and mate choice determined by another focal cultural trait. We study the joint dynamics of a focal set of beliefs, a behavior that can differentially influence the fitness of those with certain beliefs, and a preference for partnering based on similar beliefs. Cultural transmission, selection, and homophily interact to produce complex evolutionary dynamics, including oscillations, stable polymorphisms of all cultural phenotypes, and simultaneous stability of oscillation and fixation, which have not previously been observed in models of cultural evolution or gene-culture interactions. We discuss applications of this model to the interaction of beliefs and behaviors regarding education, contraception, and animal domestication.
View details for DOI 10.1073/pnas.1400824111
View details for PubMedID 25024189
Human populations vary demographically with population sizes ranging from small groups of hunter-gatherers with less than fifty individuals to vast cities containing many millions. Here we investigate how the cultural transmission of traits affecting survival, fertility, or both can influence the birth rate, age structure, and asymptotic growth rate of a population. We show that the strong spread of such a trait can lead to a demographic transition, similar to that experienced in Europe in the late 19th and early 20th centuries, without using ecological or economic optimizing models. We also show that the spread of a cultural trait that increases fertility, but not survival, can cause demographic change similar to the 'Neolithic demographic transition': a period of increased population growth that is thought to have accompanied the transition from hunter-gatherer to agricultural lifestyles. We investigate the roles of vertical, oblique, and horizontal learning of such a trait in this transition and find that compared to vertical learning alone, horizontal and oblique learning can accelerate the trait's spread, lead to faster population growth, and increase its equilibrium frequency.
View details for DOI 10.1016/j.tpb.2013.06.006
View details for Web of Science ID 000324508700007
The molecular chaperone Hsp90 is essential in eukaryotes, in which it facilitates the folding of developmental regulators and signal transduction proteins known as Hsp90 clients. In contrast, Hsp90 is not essential in bacteria, and a broad characterization of its molecular and organismal function is lacking. To enable such characterization, we used a genome-scale phylogenetic analysis to identify genes that co-evolve with bacterial Hsp90. We find that genes whose gain and loss were coordinated with Hsp90 throughout bacterial evolution tended to function in flagellar assembly, chemotaxis, and bacterial secretion, suggesting that Hsp90 may aid assembly of protein complexes. To add to the limited set of known bacterial Hsp90 clients, we further developed a statistical method to predict putative clients. We validated our predictions by demonstrating that the flagellar protein FliN and the chemotaxis kinase CheA behaved as Hsp90 clients in Escherichia coli, confirming the predicted role of Hsp90 in chemotaxis and flagellar assembly. Furthermore, normal Hsp90 function is important for wild-type motility and/or chemotaxis in E. coli. This novel function of bacterial Hsp90 agreed with our subsequent finding that Hsp90 is associated with a preference for multiple habitats and may therefore face a complex selection regime. Taken together, our results reveal previously unknown functions of bacterial Hsp90 and open avenues for future experimental exploration by implicating Hsp90 in the assembly of membrane protein complexes and adaptation to novel environments.
View details for DOI 10.1371/journal.pgen.1003631
View details for Web of Science ID 000322321100033
View details for PubMedID 23874229
Niche construction is a process through which organisms modify their environment and, as a result, alter the selection pressures on themselves and other species. In cultural niche construction, one or more cultural traits can influence the evolution of other cultural or biological traits by affecting the social environment in which the latter traits may evolve. Cultural niche construction may include either gene-culture or culture-culture interactions. Here we develop a model of this process and suggest some applications of this model. We examine the interactions between cultural transmission, selection, and assorting, paying particular attention to the complexities that arise when selection and assorting are both present, in which case stable polymorphisms of all cultural phenotypes are possible. We compare our model to a recent model for the joint evolution of religion and fertility and discuss other potential applications of cultural niche construction theory, including the evolution and maintenance of large-scale human conflict and the relationship between sex ratio bias and marriage customs. The evolutionary framework we introduce begins to address complexities that arise in the quantitative analysis of multiple interacting cultural traits.
View details for DOI 10.1371/journal.pone.0042744
View details for Web of Science ID 000307500800020
View details for PubMedID 22905167
Long-term influenza evolution has been well studied, but the patterns of sequence diversity within seasons are less clear. H3N2 influenza genomes sampled from New York State over ten years indicated intraseasonal changes in evolutionary dynamics. Using the mean Hamming distance of a set of amino acid or nucleotide sequences as an indicator of its diversity, we found that influenza sequence diversity was significantly higher during the early epidemic period than later in the influenza season. Diversity was lowest during the peak of the epidemic, most likely due to the high prevalence of a single dominant amino acid sequence or very few dominant sequences during the peak epidemic period, corresponding with rapid expansion of the viral population. The frequency and duration of dominant sequences varied by influenza protein, but all proteins had an abundance of one distinct sequence during the peak epidemic period. In New York State from 1995 to 2005, high sequence diversity during the early epidemic suggested that seasonal antigenic drift could have occurred primarily in this period, followed by a clonal expansion of typically one clade during the peak of the epidemic, possibly indicating a shift to neutral drift or purifying selection.
View details for DOI 10.1371/journal.pone.0008544
View details for Web of Science ID 000273225000009
View details for PubMedID 20049091
View details for DOI 10.1007/978-4-431-54511-8_13