Todd R. Disotell - US grants

This is a new Faculty Early Career Development Program grant (CAREER). The research plans of the P.I. center around the study of Old World monkey evolution from a molecular genetic perspective. Three major components of this plan are - 1) the search for genes which are most informative on the phylogenetic and evolutionary histories of the monkeys; 2) the analyses of such genes; and 3) the actual population genetics of these monkeys using mitochondrial and nuclear DNA markers. This is a very new and exciting area of genetic applications, and the investigator is well situated, in training and with facilities, to undertake the work. The instructional component of the proposal is especially strong and innovative. He will be bringing computer-aided instruction and hands-on laboaratory experience into the NYU curriculum. He is also developing auto-tutorial and self-paced labs and practicals for several classes. He has been particularly attuned and accessable to the minority student body at NYU, and this, in the inner city, is especially appropriate.

This laboratory project will test the conflicting hypotheses suggested by earlier studies of facial size and shape on the one hand, and DNA on the other, concerning whether the mangabey monkeys form either one related lineage or two. The hypotheses will be tested using DNA sequences of variable regions from three to four unlinked nuclear genes. This research will improve our understanding of the evolution of molecular and morphological characters in primate groups where molecular and morphological studies conflict in their interpretations, such as in the great apes and humans.

With National Science Foundation support Dr. Todd Disotell and his colleagues will purchase an ABI PRISM 310 Genetic Analyzer. This instrument is an automated system used for the sizing, sequencing and quantification of nucleic acids. The device integrates multicolor fluorescent labeling of nucleic acids with capillary electrophoresis to size and quantitate DNA molecules. Two of the advantages of using this technology to measure DNA include the use of polymers in capillary tubes rather than gels and the use of fluorescent dyes rather than radioactive isotopes for visualization. The instrument has a daily throughput of up to 4200 DNA bases when used for sequencing and is fully automated, so that once samples are prepared they are automatically loaded, run and analyzed without additional user input. This is a great advantage over manual techniques that need to be continuously monitored. The goal of the research is to understand the processes involved in the evolution of higher primate species and the instrument will be used to sequence multiple loci from large numbers of individuals from select primate species. In particular the researchers will focus on closely related Cercopithecines (guenons, macaques, mangabeys and mandrills) and on two species of baboons which interbreed in a hybrid zone. The project is especially interesting because it focuses on species that are just on the cusp of evolutionary separation and therefore the work will shed light on both the behavioral and biological mechanisms which serve to establish interspecific barriers. Intellectually the project falls at the borderline between population genetics and taxonomic analysis and serves to integrate concepts from both areas. Acquisition of this instrument will speed research in Dr. Disotell's lab and generate data of interest to many biologists and social scientists. It will also assist in the training of students in the NYU and other New York City university anthropology and biology departments.

With National Science Foundation support, Dr. Todd Disotell and his collaborators at New York University will purchase an ABI PRISM 377 system which consists of an electrophoresis and detection unit, a Power Macintosh computer and software for DNA sequencing analysis or PCR fragment sizing and quantification. The system will allow high throughput through the use of multicolored fluorescence technology, allowing multiplex electrophoreses by co-loading the products of multiple PCR or sequencing reactions in the same lane. To increase the efficiency of the group of utilizing scientists, a thermocycler (Perkin-Elmer Geneamp PCR System 9700) along with a microcentrifuge (Eppendorf 5400 Series) and microconcentrator (Savant DNA SpeedVac) will be acquired and housed with the ABI genetic analyzer. A Power Macintosh computer will allow data collected on the ABI genetic analyzer to be analyzed off-line, allowing the computer controlling the ABI machine to be dedicated to data collection. This instrumentation will greatly improve the efficiency of six research projects, pursued by a number of investigators. These include the study of 1. the genetic and developmental mechanisms of morphogenesis and the evolution of form in rhabditid nematodes; 2. genetics of organogenesis in the gonad of C. elegans; 3.primate molecular evolution and population genetics; 4. evolutionary genetics of cave adaptations in fish; unidentified proteins in fission yeast that interact with Ras G-proteins and microtubules; and 6. recognition of DNA structure by HMG proteins. The machine will also be used at both graduate and undergraduate levels and thus serve a valuable educational as well as research function.

More than 14 decades after the publication of "On the Origin of Species," the processes leading to the appearance and genetic stabilization of new, consistently distinct populations remains one of the least understood of evolutionary processes. While a variety of mechanisms may be associated with genetic isolation, attention recently has focussed upon genome-level features that are both rapidly-evolving and can drastically reduce the ability of their carriers to interbreed and produce viable hybrid offspring. A variety of recent evidence implicates transposable elements (TEs) in facilitating such reproductive isolation. TEs are small (100-10kb base pairs) genetic elements that have retained their ability to move about within genomes. Investigations conducted on organisms as diverse as fruit flies and wallabies suggest that there is a positive correlation between transposable element activity and sterility in inter-strain hybrids. In order to determine how TE-mediated barriers to inter-population hybridization might evolve, it is necessary to examine the behavior of such elements in fertile hybrids and their progeny in naturally occurring hybrid zones.

The goal of this project is to investigate the relationship between TE amplification and hybridity by testing for evidence of baboon endogenous virus (BaEV) transposition in a graded series of Old World Monkey hybrids in the papionin group. BaEV is an endogenous retrovirus that was once transmitted horizontally from individual to individual but now forms an integrated part of the vertically inherited genome of many Old World Monkeys. Retroviruses are one of the most complex TE forms, with large genomes that can generate copies through the intrinsically driven process of reverse transcription. This project will thus investigate the relationship between TE activity and reproductive isolation by testing BaEV amplification in papionin hybrids with varying degrees of hybrid ancestry.

The specific aims of the proposed research are: to determine the degree to which BaEV amplification is correlated with hybrid sterility; to determine the degree to which BaEV amplification increases in hybrid papionins with increased evolutionary distance between parental taxa; to detect novel BaEV integrations in individuals with known parentage that may be attributable to specific hybridization events; and to determine the extent of BaEV sequence variation in a wild primate population. These objectives will be accomplished by sampling a graded series of hybrid papionins reflecting different degrees of hybrid ancestry. These data will serve as a first step in determining the contribution of TEs to reproductive isolation in papionins.

This research addresses an open issue in the study of molecular evolution: The connection between organismal level features (e.g. weight, diet, behavior) and molecular traits (e.g. rate of DNA evolution, genome size, DNA variation within and between species). Specifically, how do differences in generation time, population size, metabolic rate, body size, the activity of natural selection, and species-specific differences in DNA replication accuracy affect the rate of DNA evolution? This project will add to scientific understanding by examining DNA evolutionary rate differences within a well-studied group of species.

The research will focus on the catarrhine primates, the mammalian group which includes humans, apes, and Old World monkeys, as they have significant and well-measured differences in life history variables, biology, and ecology. Furthermore, there is strong evidence for variation in the rate of DNA evolution within this group as there is evidence suggesting that humans and apes exhibit a slower rate of DNA evolution than the Old World monkeys.

Previous studies investigating variation in the rate of DNA evolution have examined a broad sample of DNA sequences, but in a limited set of distantly related species - for example, human, mouse, and cow. This research differs by sampling a set of 10 independent loci in an extensive sample of relatively closely related catarrhine primates. The loci were chosen to represent protein coding and non-coding (introns, pseudogenes and intergenic) sequences.

Ultimately, this project will contribute to the study of the how, when, and why of evolution, particularly as it pertains to primate and human evolution. The results may inform us as to:

-How are the modern day Old World monkey species related?
-When did the modern lineages of apes diverge?
-How and when did the colobine monkeys become anatomically specialized for leaf eating?
-When did the ancestors of humans become differentiated from the lineage ultimately leading to the
chimpanzee?

This is a doctoral dissertation improvement project integral to the co-investigator's graduate training. The research results will be published in a dissertation and scholarly papers, as well as presented at academic conferences. The DNA sequences obtained in the course of the study will be deposited in the publicly accessible GenBank database hosted by the National Center for Biotechnology Information (NCBI).

With National Science Foundation Support, Dr. Todd Disotell and his colleagues in the New York University Department of Anthropology will purchase an ABI 3730 DNA Analysis System and a BioRad iCycler iQ Real-Time PCR Detection System, along with support equipment. The key features of this instrumentation upgrade are the improvement in efficiency of data accumulation and an improvement in the kinds of evolutionary questions which can be addressed. The sequence analysis system is the latest generation high throughput capillary sequencer and genotyper, which will become the workhorse data acquisition instrument used in the group's laboratory's projects. It will permit accumulation of sequence data at five times the rate possible with the current equipment at less than half of the cost. The PCR detection system will be central to the laboratory's increasing use of ancient and degraded DNA recovered from archaeological materials, museum specimens, and biological detritus such as hair or feces. All of these sample types yield low quality and quantity DNA but clearly provide an unprecedented promise for addressing novel questions from such sources. Much of the support equipment will be used in a new facility being developed in the Anthropology Department's DNA Extraction Facility, including PCR work-station hoods and UV decontamination lighting.
Disotell's focus to date has been on catarrhine (Old World monkey and ape) systematics, population genetics, and conservation genetics. Di Fiore has similar interests and project involving New World monkeys. Jolly collaborates closely with Disotell in research involving population genetics and phylogeography of Old World monkeys, especially baboons. Di Fiore, Disotell, and Jolly also use molecular techniques to test and develop hypotheses about primate behavior, social and mating systems, and dispersal patterns. Anton will be bringing her expertise in modern human origins by supplying materials and hypotheses to be tested utilizing ancient DNA. This instrumenation will greatly facilitate all of the above research programs.
Numerous undergraduates and New York City area high school students carry out their honors research projects in the laboratory. Interns from the Departments of Anthropology and Biology at NYU, Howard Hughes Summer Research Fellows, Columbia University and CUNY graduate students who are members of the IGERT funded New York Consortium in Evolutionary Primatology (NYCEP), as well as foreign colleagues and their students train and do research projects in conjunction with the NYU faculty. Interns in the MA program in skeletal biology and forensics directed by Anton will also train and carry out research projects in the molecular facilities.
The data collected by this instrumentation and hypotheses being tested have a broader impact beyond the field of anthropology. The training of individuals from high school through the post-doctoral level is an equally important component of our research and academic program. The research carried out at NYU ties in with biomedical research (e.g. evolutionary biology of the SIV/HIV viruses and their host species) and applied conservation efforts (e.g. assessing genetic variation in highly endangered species such as lion tamarins in Brazil and chimpanzees and gorillas in West Africa).

Common baboons (Papio) comprise a series of geographically distinct forms or 'semi-species' that, while recognizably different from one another in appearance and behavior, are known to hybridize in the wild where their ranges meet. Papio is particularly useful in the study of the processes of divergence and reticulation that affect the evolution of closely-related, hybridizing species because baboons are the only primates for which we have detailed behavioral, genetic, and morphological data as well as long-term research in the dynamics of hybridization. In addition to this, studies of Papio can provide more direct insight into the evolution species, like early Homo, that occupy similar econiches. Baboons, like early Homo, are terrestrial, ecologically generalist primates that evolved in the savannas and woodlands of Pleistocene Africa. The climate-driven changes in these environments that affected the evolution of Papio may well have impacted Homo. However, baboons retain the genetic signature of the timing and geographic placement of these events that more recently evolved modern humans have lost.

Current knowledge of the evolution of Papio largely comes from studies of eastern African baboons. However, it is unclear if these eastern African baboons are representative of Papio as a whole. This study, therefore, will focus on the evolutionary relationships and patterns of gene flow among southern African forms, the yellow and chacma baboons, which come into physical contact with one another in central Zambia. The evolutionary relationships among populations of these two forms will be inferred from mitochondrial DNA sequence data, while genetic exchange between populations will be discerned using both mitochondrial DNA and an array of nuclear genomic microsatellite markers. Questions addressed by this research include: what are the relationships among populations of southern African baboons? Do these two forms hybridize, and if so, what pattern does the resulting gene flow take? Is this genetic exchange driven by the dispersal of males from their natal groups into other nearby groups, as in eastern Africa? Answers to these questions will help clarify the taxonomy of Papio, improve our understanding of the relationships among baboon species and the factors that have affected their evolution, and provide insight into how such processes may impact the evolution of similar primate species.

Baboons are commonly used in biomedical, behavioral, and genetic research. An accurate understanding of the evolutionary relationships among these important model organisms is necessary for such studies. This project will provide scientific training opportunities for the co-PI and undergraduate students. It will also promote professional contact and collaboration between scientists in the United States and Zambia, which has not been a traditional geographical focus of research by biological anthropologists.

Human beings carry evidence of much of their history as a species in patterns of DNA variation in their genomes. Anthropologists have used patterns of genetic variation in human populations to infer past human migrations and divergences between populations. Genetic data also have been used to distinguish between natural selection, human behavior, and random events, as influences on human evolution at the molecular level.

However, patterns that are apparently indicative of evolutionary forces may instead be artifacts of biases towards the inclusion of particular types of genetic variants in a study. Biases can be introduced during the discovery of testable genetic variants or during the design of databases or gene chips. In this project, the researchers will examine the extent to which biases in the design of current public databases of human genetic variation (i.e. HapMap) and the latest tools for gathering genetic data (gene chips or microarrays) affect results of molecular anthropology studies. They ask whether or not pre-made gene chips and genetic databases widely used by the medical community for gene mapping are appropriate for inferring population history and human evolution, within what types of populations significant effects of bias would be expected, and the nature and consequences of such bias.

As an example, this research will use predominantly Southeast Asian populations which were underrepresented in the original studies of the human genome and development of current gene mapping technologies. Saliva samples will be collected from individuals as a source of DNA from a minimum of four ethnic minorities (Akha, Lisu, Lahu, Hmong, or Karen), commonly referred to as Hill Tribes, residing in Northern Thailand. These populations are of interest because they are known to have complex migratory histories throughout Asia, and individuals are unlikely to marry outside of their ethnicity. DNA from other Asian and non-Asian majority populations is already available for use in this study. Genetic variation within and between each population will be measured, and this information will be compiled to create artificial simulated populations with which to test hypotheses, which will help the researchers to understand actual observations better. Results will then be analyzed for evidence of known kinds of evolutionary events for each group of genetic variants. Comparison of the results will show what types of biases have significant affects on such inferences, and allow for a more comprehensive genetic characterization of the populations under study.

The broader impacts of this study include describing the extent to which the accuracy of scientists' views of human dispersal and population history may be affected by biases in widely-available genotyping tools and databases originally designed for gene mapping. This project will also facilitate international (Thailand and United States), interdisciplinary (Anthropology, Psychiatry, and Genetics), and institutional (New York University Graduate School of Arts and Sciences and Yale University School of Medicine) collaborations. Both samples and data collected for this study will be used for graduate student training of American and Thai researchers, with the intent to continue this international collaboration in the future.

Viruses have been part of the primate environment for tens of thousands to millions of years and differences in primate susceptibility to viral infection and disease suggests that some species are better adapted to co-exist with certain viruses.? One of the best-known examples of this is variation in primate susceptibility to simian (or human) immunodeficiency viruses (SIV/HIV) and AIDS-like diseases.? Despite a high level of genetic similarity among primate species, the same viruses that have been known to cause AIDS in humans (SIV/HIV) are generally non-pathogenic in most naturally infected non-human primates.? This research hypothesizes that there is key variation in the primate innate immune system that leads to the observed variation in susceptibility.

In order to determine if specific innate immune system genes contribute to SIV/HIV pathogenicity in primates, the protein-coding regions of ten genes involved in one of two viral recognition pathways (TLR7/ssRNA induced signaling pathway and RIG-I/dsRNA induced signaling pathway) will be sequenced in 18 primate species.? Species were chosen to represent taxa with varying degrees of relatedness and susceptibility to SIV/HIV infection and AIDS-like diseases.

There are three main objectives to this research.? Objective 1 is to test for signs of adaptation by comparing immune system gene trees to species phylogenies.? Objective 2 is to test for signs of adaptation by looking for signatures of positive and negative selection across loci and species. Objective 3 is to test the functional significance of these adaptations by mapping variable amino acids to particular binding domains on the translated protein.

This research will further our understanding of the evolution of the primate immune system and determine if variation in theses genes contribute to variation in a primate species? ability to co-exist with SIV infection.? More generally, the project will serve as a model for understanding molecular co-adaptation by examining interactions between an organism?s innate immune system and viruses and may be useful for biomedical research attempting to combat HIV/AIDS in humans by providing potential targets for drug development.?

This doctoral dissertation improvement project will serve as the co-investigator?s thesis research and result in her being trained in state-of-the-art molecular, analytical, and bioinformatics techniques. This research will be published as a dissertation and in scholarly papers, as well as presented at academic conferences.? Sequences generated as part of this research will be annotated and submitted to GenBank.

African papionin monkeys (baboons, macaques, and mangabeys) are morphologically diverse and live in a wide variety of habitats. They provide an excellent model for studying the processes and patterns of primate and human evolution. To understand how different features have evolved and if they have evolved more than once, an accurate phylogeny needs to be inferred. To best infer such a phylogeny, multiple independent molecular sequences or markers need to be analyzed. To this end, a large comparative multilocus dataset of several thousand to over ten thousand base pairs of mitochondrial and nuclear (X chromosomal, Y chromosomal, autosomal) DNA will be sequenced in a variety of African papionins. Additionally, 40 Alu insertions will be genotyped. These markers have proven extremely powerful in evolutionary analyses as their shared presence in a genomic location is a strong indicator of relationship. This study will concentrate on the mangabeys (genera Cercocebus and Lophocebus) including the two most recently discovered species C. sanjei and "Lophocebus" kipunji. Preliminary analyses suggest that there is a complex evolutionary history within the Cercocebus/Mandrillus clade with the long faced large bodied mandrills and drills perhaps being more closely related to some of the smaller bodied short faced species of Cercocebus than these species are to other members of their own genus. Similarly, the relationships amongst gelada and other baboons to the species of Lophocebus may be equally complex. The goal of this project is to generate a robust phylogeny of the African papionins in order to allow better inferences of how similar morphological features such as body size and shape of the skull have evolved independently multiple times as well as their overall evolutionary history and development.

Broader impacts of this study will include the training of several graduate, undergraduate, and even high school students in the latest molecular laboratory techniques and the increasingly important analytical methods used to understand molecular data. These Old World primates are also critical in understanding the evolution of SIV/HIV and other pathogens. Having a robust phylogeny will allow researchers to infer patterns of host-switching and co-evolution with such pathogens. Almost all of these African primates are critically endangered and the data collected in this study will allow for the better delineation of groups in dire need of conservation.

This project will contribute to a better understanding of the cryptic diversity within dwarf galagos in Eastern Africa, integrating genetic, morphological and bio-acoustic data. This study will strive to 1) describe the genetic relationship within and among currently recognized dwarf galago species and, 2) test the importance of vocal communication in maintaining reproductive isolation between cryptic species. The project will yield the most comprehensive molecular assessment of galagid evolutionary relationships undertaken to date and will help elucidate likely causes of diversification and speciation among cryptic primates. From a conservation perspective, it will contribute to understand the diversity of nocturnal galagids in Eastern Africa, which is crucial for developing effective conservation and management programs. The study also promotes international collaboration at many levels.

Understanding and describing biological diversity is one of the main goals for biologists. This task, however, is particularly challenging when speciation is not always accompanied by noticeable morphological change. An appreciation of such cryptic species is not only important for better understanding biological diversity, but it may also affect our ability to explore models and patterns of speciation. Nocturnal dwarf galagos (Galagoides) are among the most morphologically cryptic of all primates and their evolutionary history is one of the most longstanding problems in primatology. Given the lack of morphological differentiation, galago species have been mostly described based on their advertisement calls. Within galagids, acoustic communication plays a critical role and vocal signals are used to maintain contact with other members of the same species and to attract mates. Species cohesiveness is therefore likely to be maintained by non-visual recognition systems, and advertisement calls have been suggested to play a critical role in reproductive isolation. The lack of genetic data, however, has not allowed testing of whether specific differences in vocal signals can really contribute to species cohesion, and whether "vocal species" are actually genetically distinct.

In the 'arms race' against pathogens, having less common immune genes can be advantageous. Infectious agents may have evolved to evade the defenses of the more common varieties, making organisms with rare variants more likely to survive. In primates, like all vertebrates, many proteins essential to the immune system are encoded by the Major Histocompatibility Complex (MHC), which is involved in resistance to pathogens such as HIV and tuberculosis. The advantage of having rare forms has made the MHC gene complex one of the most diverse regions in the human genome. Recently, researchers found that at least one variant of the MHC entered the human gene pool when the ancestors of some modern humans interbred with an extinct hominin. The novel form's rarity may have facilitated the introduction and spread of the MHC variant through the population.

To better understand the effects of hybridization on MHC, this research by doctoral student Christina Bergey (New York University), under the guidance of Dr. Todd Disotell, focuses on a natural experiment in which two species of baboons successfully interbreed in Ethiopia. Using the latest DNA sequencing techniques, MHC loci are genetically typed and thousands of neutral markers from individuals across the hybrid zone are utilized to test whether MHC alleles are able to transfer and spread widely throughout the parental population. The Ethiopian baboon hybrid zone offers an ideal opportunity to explore the influence of selection and hybridization on MHC diversity in an appropriate primate model.

The study increases our understanding of hybridization, a phenomenon that has affected our lineage numerous times. It also provides evolutionary context to primate MHC variation, which has behavioral, immunological, and biomedical importance. DNA sequences are deposited in publicly available databases and all software is made freely available online and released under open source licenses. Since increasing public understanding of evolution is an essential goal of anthropological research, new forms of outreach to publicize the results also are employed in the conduct of the project.

The goal of this collaborative research is to use genomic data to address fundamental questions about the evolution of primates. The investigators will sequence the genomes of the roughly 36 anthropoid (monkey and ape) genera for which little or no genomic data are available. Comparisons of the genomes of different but closely related organisms can yield many insights into their biology, such as which areas of the genome affect traits of biological importance, and when important branching events occurred in the primate tree of life. Studies of monkey and ape genomes also provide comparative data for understanding what is unique about the human genome. This research will result in a freely accessible anthropoid primate genomic database and will facilitate the training of graduate, undergraduate, and high school students, including students from New York City public schools, in state-of-the-art bioinformatics as well as molecular laboratory techniques.

Identifying patterns of variation in DNA substitutions and understanding their causes is a central goal of comparative genetics. Genomic regions that depart from 'baseline' neutral rates of molecular evolution may have biological function and therefore influence adaptive phenotypes. The power of many comparative analyses improves when more species from major branches of the tree of life are included. Up to now, relatively few monkey species have been the target of large-scale sequencing efforts. The researchers will use a combination of short-read and long-molecule DNA sequencing to obtain genomic sequences of ~36 anthropoid genera and then combine these with the 12 that are already sequenced. With this large comparative dataset, the researchers will 1) infer the best possible primate tree, including estimates of the timing of splits among major branches; 2) determine which life history traits such as generation length cause variations in the rate of genomic evolution among monkey, ape, and human lineages; and 3) scan for areas of the genome of major branches of the anthropoid tree that might be of functional significance.

This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2).

Both humans and non-human primates have evolved defensive adaptations against malaria via changes in the genome. This doctoral dissertation research uses comparative primate data to advance knowledge about the co-evolution of primates and malaria or similar parasites, including how malaria has impacted the evolution of the primate immune system and identification of genetic mechanisms underlying the immune response to blood stage malaria. The project outcomes may inform public health relevant research on the human response to malaria. The project also supports outreach efforts that focus on increasing participation of underrepresented groups in STEM research through K-12 outreach and computational genomic capacity building.

Using a comparative functional and evolutionary genomics approach, the researchers identify primate genes and pathways that are differentially expressed in response to malaria infection, including those with species-specific involvement in malaria response. The researchers also identify signatures of malaria-imposed changes across primate genomes. The study outcomes can advance understanding of how the primate immune system has evolved in response to this host-pathogen arms race. The analysis uses an innovative approach to investigate primate malaria response in natural transmission systems. This study can help to determine which malaria responses arose through the host-pathogen coevolutionary arms race as well as explore how human and primate evolution has been impacted by the selection pressure of malaria.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.