Biology subjects

Brisson, D.

Publications and source records attributed to Brisson, D..

10 recordsLinked to original sources

bioRxiv2023

Modeling Tick Populations: An Ecological Test Case forGradient Boosted Trees

General linear models have been the foundational statistical framework used to discover the ecological processes that explain the distribution and abundance of natural populations. Analyses of the rapidly expanding cache of environmental and ecological data, however, require advanced statistical methods to contend with complexities inherent to extremely large natural data sets. Modern machine learning frameworks such as gradient boosted trees efficiently identify complex ecological relationships in massive data sets, which are expected to result in accurate predictions of the distribution and abundance of organisms in nature. However, rigorous assessments of the theoretical advantages of these methodologies on natural data sets are rare. Here we compare the abilities of gradient boosted and linear models to identify environmental features that explain observed variations in the distribution and abundance of blacklegged tick (Ixodes scapularis) populations in a data set collected across New York State over a ten-year period. The gradient boosted and linear models use similar environmental features to explain tick demography, although the gradient boosted models found non-linear relationships and interactions that are difficult to anticipate and often impractical to identify with a linear modeling framework. Further, the gradient boosted models predicted the distribution and abundance of ticks in years and areas beyond the training data with much greater accuracy than their linear model counterparts. The flexible gradient boosting framework also permitted additional model types that provide practical advantages for tick surveillance and public health. The results highlight the potential of gradient boosted models to discover novel ecological phenomena affecting pathogen demography and as a powerful public health tool to mitigate disease risks.

ecology↗

bioRxiv2022

A fast machine-learning-guided primer design pipeline for selective whole genome amplification

Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales - precisely the scales at which these processes occur - microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluate strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime from weeks to minutes. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluated the novel swga2.0 pipeline by designing primers sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.

genomics↗

bioRxiv2021

Host phenology can select for multiple stable parasite virulence strategies

Host phenology is an important driver of parasite transmission dynamics and evolution. Prior research has demonstrated that host phenology can drive monocyclic, obligate-killer parasites to evolve an intermediate virulence strategy where all parasites kill their host just before the season ends to limit the death of parasite progeny in the environment. The impact of host seasonality on parasites that are not constrained to a monocyclic life-cycle, however, cannot be inferred from these results. Here we present a mathematical model that demonstrates that many, but not all, seasonal host activity patterns support multiple evolutionarily stable parasite strategies (ESS), although these strategies cannot coexist in the same system. The specific monocyclic and polycyclic parasite evolutionarily stable strategies in each phenological pattern are interspersed with less-fit mono- and polycyclic strategies (evolutionary repellors). The ESS that dominates each system at equilibrium is a function of the strategy of the parasite introduced into the system. The results demonstrate that host phenology can, in theory, maintain diverse parasite strategies among isolated geographic locations.

evolutionary biology↗

bioRxiv2021

How host phenology impacts multi-season epidemic cycles

Parasite-host interactions can result in periodic population dynamics when parasites over-exploit host populations. The timing of host seasonal activity, or host phenology, determines the frequency and demographic impact of parasite-host interactions which may govern if the parasite can sufficiently over-exploit their hosts to drive population cycles. We describe a mathematical model of a monocyclic, obligate-killer parasite system with seasonal host activity to investigate the consequences of host phenology on host-parasite dynamics. The results suggest that parasites can reach the densities necessary to destabilize host dynamics and drive cycling in only some phenological scenarios, such as environments with short seasons and synchronous host emergence. Further, only parasite lineages that are sufficiently adapted to phenological scenarios with short seasons and synchronous host emergence can achieve the densities necessary to over-exploit hosts and produce population cycles. Host-parasite cycles can also generate an eco-evolutionary feedback that slows parasite adaptation to the phenological environment as rare advantageous phenotypes are driven to extinction when introduced in phases of the cycle where host populations are small and parasite populations are large. The results demonstrate that seasonal environments can drive population cycling in a restricted set of phenological patterns and provides further evidence that the rate of adaptive evolution depends on underlying ecological dynamics.

ecology↗

bioRxiv2021

Host phenology drives the evolution of intermediate parasite virulence

AO_SCPLOWBSTRACTC_SCPLOWThe traditional mechanistic trade-offs resulting in a negative correlation between transmission and virulence are the foundation of nearly all current theory on the evolution of parasite virulence. Several ecological factors have been shown to modulate the optimal virulence strategies predicted from mechanistic trade-off models, but these ecological factors have not yet been shown to be sufficient to explain the intermediate virulence strategies observed in any natural system. The timing of seasonal activity, or phenology, is a common factor that influences the types and impact of many ecological interactions but is difficult to incorporate into virulence evolution studies. We develop a mathematical model of a disease system with seasonal host activity to study the evolutionary consequences of host phenology on the virulence of obligate-killer parasite. Results from this model demonstrated that seasonal host activity is sufficient to drive the evolution of intermediate parasite virulence in some types of natural disease systems, even when a traditional mechanistic trade-off between transmission and virulence is not assumed in the modeling framework. The optimal virulence strategy in these systems can be determined by both the duration of the host activity period as well as the variation in the host emergence timing. Parasites with low virulence strategies are favored in environments with long host activity periods and in environments in which hosts emerge synchronously. The results demonstrate that host phenology can be sufficient to select for intermediate optimal virulence strategies, providing an alternative mechanism to account for virulence evolution in some natural systems.

evolutionary biology↗

bioRxiv2019

The role of host phenology for parasite transmission

Phenology is a fundamental determinant of species distributions, abundances, and interactions. In host-parasite interactions, host phenology can affect parasite fitness due to the temporal constraints it imposes on host contact rates. However, it remains unclear how parasite transmission is shaped by the wide range of phenological patterns observed in nature. We develop a mathematical model of the Lyme disease system to study the consequences of differential tick developmental-stage phenology for the transmission of B. burgdorferi. Incorporating seasonal tick activity can increase B. burgdorferi fitness compared to continuous tick activity but can also prevent transmission completely. B. burgdorferi fitness is greatest when the activity period of the infectious nymphal stage slightly precedes the larval activity period. Surprisingly, B. burgdorferi is eradicated if the larval activity period begins long after the end of nymphal activity due to a feedback with mouse population dynamics. These results highlight the importance of phenology, a common driver of species interactions, for the fitness of a parasite.

ecology↗

bioRxiv2019

Dispersal patterns of Trypanosoma cruzi in Arequipa, Peru

Anthropogenic environmental alterations such as urbanization can threaten native populations as well as create novel environments that allow human pests and pathogens to thrive. As the number and size of urban environments increase globally, it is more important than ever to understand the dispersal dynamics of hosts, vectors and pathogens of zoonotic disease systems. For example, a protozoan parasite and the causative agent of Chagas disease in humans, Trypanosoma cruzi, recently colonized and spread through the city of Arequipa, Peru. We used population genomic and phylogenomic tools to analyze whole genomes of 123 T. cruzi isolates collected throughout Arequipa to determine patterns of T. cruzi dispersal. The data show significant population genetic structure within city blocks-parasites in the same block tend to be very closely related - but no population structure among blocks within districts - parasites in neighboring blocks are no more closely related to one another than to parasites in distant districts. These data suggest that T. cruzi dispersal within a block occurs regularly and that occasional long-range dispersal events allow the establishment of new T. cruzi populations in distant blocks. Movement of domestic animals may be the primary mechanism of inter-block and inter-district T. cruzi dispersal. Author SummaryUrbanization creates environments that are ideal for some human pests and pathogens. As the number and size of urban environments increases globally, it is becoming vital to understand how human disease-causing pathogens, their vectors, and their non-human hosts disperse through urban landscapes. Here we study a population of Trypanosoma cruzi - the protozoan parasite and causative agent of Chagas disease in humans - that recently colonized the city of Arequipa, Peru. We use population genomic and phylogenomic tools to understand how this parasite population dispersed through the city to achieve its current distribution and abundance. We show that T. cruzi collected from the same city block tend to be very closely related, while those from neighboring blocks are often as distantly related as those from blocks in distant districts. The data suggest that vectors facilitate frequent within-block dispersal of the parasite, while domestic animal movement may facilitate the relatively infrequent inter-block and interdistrict dispersal.

evolutionary biology↗

bioRxiv2019

Immigration and establishment of urban Trypanosoma cruzi populations

Changing environmental conditions, including those caused by human activities, reshape biological communities through both loss of native species and establishment of non-native species in the altered habitats. Dynamic interactions with the abiotic environment impact both immigration and initial establishment of non-native species into these altered habitats. The repeated emergence of disease systems in urban areas worldwide highlights the importance of understanding how dynamic migratory processes affect the current and future distribution and abundance of pathogens in urban environments. In this study, we examine the pattern of invasion of Trypanosoma cruzi--the causative agent of human Chagas disease--in the city of Arequipa, Peru. Phylogenetic analyses of 136 T. cruzi isolates from Arequipa and other South American locations suggest that only one T. cruzi immigrant established a population in Arequipa as all T. cruzi isolated from vectors in Arequipa form a recent monophyletic group within the broader South American phylogeny. We discuss several hypotheses that may explain the limited number of established T. cruzi lineages despite multiple introductions of the parasite.\n\nAuthor SummaryHuman-associated pests and pathogens, who benefit from the abundance of humans and human-associated hosts or vectors, commonly invade environments altered by human activities. As the number and size of human-disturbed environments increase, so does the importance of identifying ecological and environmental factors that affect the probability that disease systems immigrate to, subsequently establish populations in, urban environments. We examined the number and timing of immigration and establishment events of Trypanosoma cruzi, the causative agent of Chagas disease, in a currently endemic area. Phylogenetic analyses of 136 T. cruzi isolates suggests that the current population descended from a single, recent immigration event. We discuss historical and ecological hypotheses that can explain the limited T. cruzi diversity in this region.

evolutionary biology↗

bioRxiv2017

Placenta DNA Methylation Adaptation to Maternal Glucose Tolerance in Pregnancy

Maternal hyperglycemia during pregnancy is associated with fetal growth and adverse perinatal and developmental outcomes. Placental epigenetic maladaptation may underlie these associations. We performed an epigenome-wide association study of term placentas and prenatal maternal glucose response 2-hour post oral glucose challenge at 24-30 weeks of gestation among 448 mother-infant pairs. Maternal glucose levels post-load were strongly associated with lower DNA methylation of 4 CpGs (FDR q<0.05) within the Phosphodiesterase 4B gene (PDE4B). Additionally, three other CpGs were differentially methylated relative to maternal glucose response within the TNFRSF1B; LDLR; and BLM genes (FDR q<0.05). Methylation levels correlated with expression in placental tissue for all 4 CpG sites in PDE4B (rs: 0.26-0.35, P<0.01), LDLR (rs: 0.22, P=0.03) and at TNFRSF1B (rs: -0.25, P=0.01). Our study provides evidence that maternal glucose response during pregnancy is associated with DNA methylation of genes within the placenta that are partially under epigenetic control.

genomics↗

bioRxiv2017

Negative frequency-dependent selection is frequently confounding

This preprint has been reviewed and recommended by Peer Community in Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100024). The existence of persistent genetic variation within natural populations presents an evolutionary problem as natural selection and genetic drift tend to erode genetic diversity. Models of balancing selection were developed to account for the high and sometimes extreme levels of polymorphism found in many natural populations. Negative frequency-dependent selection may be the most powerful selective force maintaining balanced natural polymorphisms but it is also commonly misinterpreted. The aim of this review is to clarify the processes underlying negative frequency-dependent selection, describe classes of natural polymorphisms that can and cannot result from these processes, and discuss observational and experimental data that can aid in accurately identifying the processes that generated or are maintain diversity in nature. Finally, I consider the importance of accurately describing the processes affecting genetic diversity within populations as it relates to research progress.

evolutionary biology↗