Browsing by Author "Herrera, James P"

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    Comparing transmission potential networks based on social network surveys, close contacts and environmental overlap in rural Madagascar.
    (Journal of the Royal Society, Interface, 2022-01-12) Kauffman, Kayla; Werner, Courtney S; Titcomb, Georgia; Pender, Michelle; Rabezara, Jean Yves; Herrera, James P; Shapiro, Julie Teresa; Solis, Alma; Soarimalala, Voahangy; Tortosa, Pablo; Kramer, Randall; Moody, James; Mucha, Peter J; Nunn, Charles
    Social and spatial network analysis is an important approach for investigating infectious disease transmission, especially for pathogens transmitted directly between individuals or via environmental reservoirs. Given the diversity of ways to construct networks, however, it remains unclear how well networks constructed from different data types effectively capture transmission potential. We used empirical networks from a population in rural Madagascar to compare social network survey and spatial data-based networks of the same individuals. Close contact and environmental pathogen transmission pathways were modelled with the spatial data. We found that naming social partners during the surveys predicted higher close-contact rates and the proportion of environmental overlap on the spatial data-based networks. The spatial networks captured many strong and weak connections that were missed using social network surveys alone. Across networks, we found weak correlations among centrality measures (a proxy for superspreading potential). We conclude that social network surveys provide important scaffolding for understanding disease transmission pathways but miss contact-specific heterogeneities revealed by spatial data. Our analyses also highlight that the superspreading potential of individuals may vary across transmission modes. We provide detailed methods to construct networks for close-contact transmission pathogens when not all individuals simultaneously wear GPS trackers.
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    Effects of land use, habitat characteristics, and small mammal community composition on Leptospira prevalence in northeast Madagascar.
    (PLoS neglected tropical diseases, 2020-12-31) Herrera, James P; Wickenkamp, Natalie R; Turpin, Magali; Baudino, Fiona; Tortosa, Pablo; Goodman, Steven M; Soarimalala, Voahangy; Ranaivoson, Tamby Nasaina; Nunn, Charles L
    Human activities can increase or decrease risks of acquiring a zoonotic disease, notably by affecting the composition and abundance of hosts. This study investigated the links between land use and infectious disease risk in northeast Madagascar, where human subsistence activities and population growth are encroaching on native habitats and the associated biota. We collected new data on pathogenic Leptospira, which are bacteria maintained in small mammal reservoirs. Transmission can occur through close contact, but most frequently through indirect contact with water contaminated by the urine of infected hosts. The probability of infection and prevalence was compared across a gradient of natural moist evergreen forest, nearby forest fragments, flooded rice and other types of agricultural fields, and in homes in a rural village. Using these data, we tested specific hypotheses for how land use alters ecological communities and influences disease transmission. The relative abundance and proportion of exotic species was highest in the anthropogenic habitats, while the relative abundance of native species was highest in the forested habitats. Prevalence of Leptospira was significantly higher in introduced compared to endemic species. Lastly, the probability of infection with Leptospira was highest in introduced small mammal species, and lower in forest fragments compared to other habitat types. Our results highlight how human land use affects the small mammal community composition and in turn disease dynamics. Introduced species likely transmit Leptospira to native species where they co-occur, and may displace the Leptospira species naturally occurring in Madagascar. The frequent spatial overlap of people and introduced species likely also has consequences for public health.
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    Food insecurity related to agricultural practices and household characteristics in rural communities of northeast Madagascar.
    (Food security, 2021-06-24) Herrera, James P; Rabezara, Jean Yves; Ravelomanantsoa, Ny Anjara Fifi; Metz, Miranda; France, Courtni; Owens, Ajilé; Pender, Michelle; Nunn, Charles L; Kramer, Randall A
    Ending hunger and alleviating poverty are key goals for a sustainable future. Food security is a constant challenge for agrarian communities in low-income countries, especially in Madagascar. We investigated agricultural practices, household characteristics, and food security in northeast Madagascar. We tested whether agricultural practices, demographics, and socioeconomics in rural populations were related to food security. Over 70% of respondents reported times during the last three years during which food for the household was insufficient, and the most frequently reported cause was small land size (57%). The probability of food insecurity decreased with increasing vanilla yield, rice yield, and land size. There was an interaction effect between land size and household size; larger families with smaller land holdings had higher food insecurity, while larger families with larger land had lower food insecurity. Other socioeconomic and agricultural variables were not significantly related to food insecurity, including material wealth, education, crop diversity, and livestock ownership. Our results highlight the high levels of food insecurity in these communities and point to interventions that would alleviate food stress. In particular, because current crop and livestock diversity were low, agricultural diversification could improve outputs and mitigate food insecurity. Development of sustainable agricultural intensification, including improving rice and vanilla cultivation to raise yields on small land areas, would likely have positive impacts on food security and alleviating poverty. Increasing market access and off-farm income, as well as improving policies related to land tenure could also play valuable roles in mitigating challenges in food security.

    Supplementary information

    The online version contains supplementary material available at 10.1007/s12571-021-01179-3.
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    Predictions of primate-parasite coextinction.
    (Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2021-11) Herrera, James P; Moody, James; Nunn, Charles L
    Future biodiversity loss threatens the integrity of complex ecological associations, including among hosts and parasites. Almost half of primate species are threatened with extinction, and the loss of threatened hosts could negatively impact parasite associations and ecosystem functions. If endangered hosts are highly connected in host-parasite networks, then future host extinctions will also drive parasite extinctions, destabilizing ecological networks. If threatened hosts are not highly connected, however, then network structure should not be greatly affected by the loss of threatened hosts. Networks with high connectance, modularity, nestedness and robustness are more resilient to perturbations such as the loss of interactions than sparse, nonmodular and non-nested networks. We analysed the interaction network involving 213 primates and 763 parasites and removed threatened primates (114 species) to simulate the effects of extinction. Our analyses revealed that connections to 23% of primate parasites (176 species) may be lost if threatened primates go extinct. In addition, measures of network structure were affected, but in varying ways because threatened hosts have fewer parasite interactions than non-threatened hosts. These results reveal that host extinctions will perturb the host-parasite network and potentially lead to secondary extinctions of parasites. The ecological consequences of these extinctions remain unclear. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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    Primate diversification inferred from phylogenies and fossils.
    (Evolution; international journal of organic evolution, 2017-12) Herrera, James P
    Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses.
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    Testing the adaptive radiation hypothesis for the lemurs of Madagascar.
    (Royal Society open science, 2017-01-18) Herrera, James P
    Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an 'early burst' of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the 'early burst' signal of adaptive radiation may have been eroded by extinction.
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    The changing ecology of primate parasites: Insights from wild-captive comparisons.
    (American journal of primatology, 2019-07-02) Herrera, James P; Chakraborty, Debapriyo; Rushmore, Julie; Altizer, Sonia; Nunn, Charles
    Host movements, including migrations or range expansions, are known to influence parasite communities. Transitions to captivity-a rarely studied yet widespread human-driven host movement-can also change parasite communities, in some cases leading to pathogen spillover among wildlife species, or between wildlife and human hosts. We compared parasite species richness between wild and captive populations of 22 primate species, including macro- (helminths and arthropods) and micro-parasites (viruses, protozoa, bacteria, and fungi). We predicted that captive primates would have only a subset of their native parasite community, and would possess fewer parasites with complex life cycles requiring intermediate hosts or vectors. We further predicted that captive primates would have parasites transmitted by close contact and environmentally-including those shared with humans and other animals, such as commensals and pests. We found that the composition of primate parasite communities shifted in captive populations, especially because of turnover (parasites detected in captivity but not reported in the wild), but with some evidence of nestedness (holdovers from the wild). Because of the high degree of turnover, we found no significant difference in overall parasite richness between captive and wild primates. Vector-borne parasites were less likely to be found in captivity, whereas parasites transmitted through either close or non-close contact, including through fecal-oral transmission, were more likely to be newly detected in captivity. These findings identify parasites that require monitoring in captivity and raise concerns about the introduction of novel parasites to potentially susceptible wildlife populations during reintroduction programs.