I am a biological anthropologist with a background in primate ecology. In a post-doc at the University of Washington, I acquired additional training in human demography, infectious disease epidemiology, and statistics. For the full picture, see a relatively recent version of my CV, posted here.

My current substantive research interests fall into four general headings:

I also maintain a number of more methodological research interests:

Demography and Infectious Disease

This is probably my primary current research area. I recently received a K01 Career Development Grant from the National Institute of Child Health and Human Development (NICHD) to study the consequences for infectious disease dynamics of changing demography (i.e., age-specific schedules of mortality, fertility, migration).

One area in which I have already done a fair bit of work is the effect of social structure on a variety of features of epidemic models. Specifically, Mark Handcock and I have investigated the effect of long-tailed marginal distributions of sexual contact networks on epidemic thresholds. We specified a number of competing stochastic models for network formation, estimated the resulting probability distributions using maximum likelihood, and chose the best-fitting models using likelihood-based model selection.

Most of the papers emerging from this work are rather terse and focused on the statistical estimation. For a more discursive treatment of the issues that motivated this work, see this CSSS working paper.

An exciting line of research, that also ties in themes in biodemography, is the interaction of infectious diseases such as tuberculosis and chronic diseases such as type II diabetes mellitus. Chronic diseases display age-specific patterns of expression that are frequently quite different from those of infectious diseases. As population structure and composition change, we should expect the distribution of chronic disease to change. What are the consequences of these shifts for patterns of infectious disease epidemiology? Can shifting chronic disease burdens contribute to the emergence or re-emergence of infectious diseases? What are the implications for control, particularly in resource-poor contexts?

I also have a strong interest in the demography of kinship and how this is affected by generalized AIDS epidemics. I have done some work calculating the frequencies of kin under a generalized AIDS epidemic using stable population theory (which includes writing software to calculate the various quantities -- see the Formal Demography section of my methodological section). I am also actively engaged in re-casting the problem using demographic microsimulation.

With the generous support of the Applera Foundation and the logistical expertise of IRiSS, I recently organized a conference at Stanford on the interactions between demography and infectious disease. Speakers discussed topics on the interaction of demographic processes such as changes in the size, distribution, and composition of populations with the epidemiology of HIV, tuberculosis, pandemic influenza, and malaria. Streaming video of the presentations is available from the conference website.

Selected Publications and Working Papers

Jones, J.H. and S. Helleringer. (2007) Statistical Models for Sexual Networks on Likoma Island, Malawi: Implications for Sexual Behavior and HIV Control. Paper presented at the 2007 Population Association of America Meetings, New York, NY.

Handcock, M.S. and J.H. Jones (2006) Interval estimates for epidemic thresholds in two-sex network models.Theoretical Population Biology. 70: 125-134. [PDF]

Handcock, M.S. and Jones, J.H. (2004) Likelihood-based inference for stochastic models of sexual network evolution.Theoretical Population Biology. 65: 413-422. [PDF]

Jones, J.H. and M.S. Handcock. (2003) Sexual contacts and epidemic thresholds. Nature. 423: 605-606. [PDF]

Jones, J.H. and M.S. Handcock. (2003) An assessment of preferential attachment as a mechanism for the growth of human sexual networks. Proceedings of the Royal Society of London, B. 270: 1123-1128. [PDF]

Handcock, M.S., J.H. Jones, M. Morris (2003) On 'Sexual contacts and epidemic thresholds,' models and inference for Sexual partnership distributions. University of Washington, Center for Statistics and the Social Sciences, Working Paper 31. [PDF]

Jones, J.H. (2006) The probability of maternal orphanhood under a generalized AIDS epidemic. Paper presented at the 2005 Population Association of America Meetings, Philadelphia, PA. Currently under revision for re-submission.

Disease Ecology

In 2007, I received a seed grant from the Woods Institute for the Environment Environmental Venture Projects Fund to initiate a project investigating the consequences for vector-borne disease transmission of land-use change (especially oil palm plantation development) in West Kalimantan, Indonesia. This study will form part of a larger project on the health and livelihoods of forest people in Borneo. I am collaborating with Lisa Curran of the Yale University School of Forestry and Environmental Sciences as well as a number of others scholars from a variety of institutions including the Santa Fe Institute, Duke University, and the Carnegie Institution of Washington, DC.

I see the primary challenges in the general area of disease ecology as (1) understanding the consequences for ecology, evolution and epidemic control of multi-host epidemics and (2) integrating the rich theory of community ecology into our understanding of infectious diseases. Along with Bill Durham, I co-teach a quite popular class entitled, Environmental Change and Emerging Infectious Disease.

Another, somewhat distinct, area in disease ecology is the interactions between different pathogens. There are a number of cases where co-morbid epidemics play a synergistic role, mutually amplifying their prevalence in human populations: TB and HIV, HIV and HSV-2 (or lots of other sexually transmitted infections). How does thinking about these diseases as parts of larger multi-pathogen systems help us design better interventions aimed at control and eradication?

Selected Publications and Working Papers

Jones, J.H. (2006) The co-evolutionary origins of the Human Immunodeficiency Virus. Working Paper. [PDF]

Jones, J.H. (2006) Wild bird culls are inefficient for control of avian influenza. Working Paper. [PDF]


"Biodemography" is pretty much a garbage-can term. It both means a lot and means different things to different people. I am interested in a number of problems in biodemography: (1) the evolution of mortality patterns, (2) nonhuman primate demography, (3) formal models of gene-culture coevolution, and, yes, (4) quantitative genetics.

I have undertaken a collaboration with colleagues at the University of Minnesota and the Jane Goodall Institute, analyzing the rich demographic record of the chimpanzees of the Gombe National Park, Tanzania.

We have one manuscript submitted on this topic and are working on the next. There are a lot of interesting and important questions just waiting to be answered with this data set. Along with Melissa Emery Thompson and a large group of collaborators, we just published a paper on patterns of reproductive senescence in wild chimpanzees. We have also been collaborating with Beatrice Hahn's group at the University of Alabama Birmingham on measuring the demographic impact of SIVcpz on the Gombe chimpanzees.

I have an interest in two-sex demography. In particular, I have been working on the implications of mortality crises on marriage markets and the consequences for household dynamics, patterns of parental investment and child welfare.

Selected Publications and Working Papers

Emery Thompson, M., J.H. Jones, A.E. Pusey, S. Brewer-Marsden, J. Goodall, D. Marsden, T. Matsuzawa, T. Nishida, V. Reynolds, Y. Sugiama, R.W. Wrangham. (2007) Aging and Fertility Patterns in Wild Chimpanzees Provide Insights into the Evolution of Menopause. Current Biology. 17(24): 2150-2156. [PDF]

Jones, J.H. and S.D. Jackman. 2008. Bayesian Hierarchical Hierarchical Mixture Models for High-Risk Births in California, 1968-2005. Paper Presented at the Population Association of America Annual Meetings, New Orleans, LA. 17 April 2008.

Jones, J.H. M.L. Wilson, J. Goodall, and A.E. Pusey (2006) Fertility patterns of the Gombe chimpanzees, 1964-2007. Submitted.

Jones, J.H. and B.D. Ferguson (forthcoming) The Marriage Squeeze in Colombia, 1973-2005: The Role of Excess Male Death. Social Biology.

Hilde, L.R. J.D. Hacker and J.H. Jones (2008) The Impact of the American Civil War on Post-War Marriage. Submitted

Ferguson, B.D., J.A. Restrepo, and J.H. Jones. (2008) Missing Men: The Direct Mortality Impacts of Firearm Violence in Colombia, 1979-2005. Paper Presented at the Population Association of America Annual Meetings, New Orleans, LA. 17 April 2008.

Jones, J.H. and Ferguson. (2007) The Consequences of Sex-Ratio Imbalances n Dyadic Power within Colombian Households. Paper presented at the American Anthropological Association Annual Meeting, Washington DC. 30 November 2007. (Paper in preparation for submission to Human Nature)

Life History Theory

Life history theory is the topic that led me to demography. I maintain an active interest in understanding the evolution of human life histories, and in particular the following questions: What factors favored the evolution of childhood, a developmental stage arguably unique to humans? What is the optimal response to risk in an organism that is already long-lived and slow-reproducing? What are the selective benefits of extended post-reproductive survival? How are human populations "regulated"?

Some of the papers that represent this interest have taken an extended back-burner because of displacement by more recently emerging interests (particularly those that have payed the bills!). The big danger when you let work sit around for a long time is that you run the risk of changing your mind. I have indeed done this on a couple issues, but think that thinking has at least reached a fairly stable local equilibrium.

Jones, J.H. (forthcoming) Demography. In Human Evolutionary Biology, Muehlenbein, M, ed. Cambridge University Press.

Jones, J.H. and R. Bliege Bird. (2008) The marginal valuation of fertility. Paper to be presented.

Jones, J.H. and S. Tuljapurkar. (2007) Risk Management and the Evolution of Biparental Care. Working Paper.

Jones, J.H. (2005) Fetal programming: adaptive life history tactics or making the best of a bad start? American Journal of Human Biology. 17(1): 22-33. [PDF]

Jones, J.H. (2006) The shape of human life histories: Understanding the force of selection on the human life cycle. Working Paper.

Jones, J.H. (2006) Pair-bonding and the human life history problem. Working Paper.

Formal Demography

Along with Shripad Tuljapurkar, I run an NIH-funded on formal demography. From the computer labs that I developed for the workshop, I have put together an R package for doing demographic calculations. It is, of course, free and openly available to all researchers. Some of the functionality included in demogR includes:

The package is described in a recent paper in the Journal of Statistical Software:

Jones, J.H. (2007) demogR: A Package for the Construction and Analysis of Age-structured Demographic Models in R. Journal of Statistical Software. 22(10): 1-28.

Demographic Microsimulation

One of the major goals of my Career Grant is to develop microsimulation approaches to studying the dynamics of of infectious disease in populations with changing demography. In particular, I will use demographic microsimulation, in concert with traditional mathematical/stochastic analysis, to investigate the causal chain leading from demographic rates to social structure to epidemiological outcome.

Microsimulation can be used to address lots of problems. For example, I received a small grant from the Stanford Office of Technology Licensing with Rebecca Bleige Bird and, Doug Bird to use microsimulation to explore the relationships between human demography, burning practices, and grassland biodiversity in Western Australia. We are using agent-based modeling with the RePast simulation platform to test the hypothesis that aboriginal burning increases grassland biodiversity. This project uses an extensive dataset base on measurements from remote sensing to provide a habitat classification against which to compare our simulations. Based on the work the work supported by the OTL grant, we have just submitted a large NSF grant to expand both the empirical base (ethnographic, ecological, and remote sensing data) and simulations.


Most of my current statistical work is involved with teaching. However, I am working on a couple applications of Bayesian methodology to address some problems in human biology and demography. These are some of the substantive issues we deal with in the class that I co-teach with Simon Jackman on Applied Bayesian Analysis. More later...

Jones, J.H. and S.D. Jackman. 2008. Bayesian Hierarchical Hierarchical Mixture Models for High-Risk Births in California, 1968-2005. Paper Presented at the Population Association of America Annual Meetings, New Orleans, LA. 17 April 2008.

Spatial Methods

I have a growing interest in spatial methods. For now, here is a link to a page with resources for spatial anthropology, mostly open-source software like GRASS and R. This page also contains links to some notes on statistical things like regression diagnositcs and maximum likelihood estimation in R. More later...