Biology subjects

Paulose, J.

Publications and source records attributed to Paulose, J..

4 recordsLinked to original sources

bioRxiv2022

The influence of explicit local dynamics on range expansions driven by long-range dispersal

Range expansions are common in natural populations. They can take such forms as an invasive species spreading into a new habitat or a virus spreading from host to host during a pandemic. When the expanding species is capable of dispersing offspring over long distances, population growth is driven by rare but consequential long-range dispersal events that seed satellite colonies far from the densely occupied core of the population. These satellites accelerate growth by accessing unoccupied territory, and also act as reservoirs for maintaining neutral genetic variation present in the originating population, which would ordinarily be lost to drift. Prior theoretical studies of dispersal-driven expansions have shown that the sequential establishment of satellites causes initial genetic diversity to be either lost or maintained to a level determined by the breadth of the distribution of dispersal distances. If the tail of the distribution falls off faster than a critical threshold, diversity is steadily eroded over time; by contrast, broader distributions with a slower falloff allow some initial diversity to be maintained for arbitrarily long times. However, these studies used lattice-based models and assumed an instantaneous saturation of the local carrying capacity after the arrival of a founder. Real-world populations expand in continuous space with complex local dynamics, which potentially allow multiple pioneers to arrive and establish within the same local region. Here, we evaluate the impact of local dynamics on the population growth and the evolution of neutral diversity using a computational model of range expansions with long-range dispersal in continuous space, with explicit local dynamics that can be controlled by altering the mix of local and long-range dispersal events. We found that many qualitative features of population growth and neutral genetic diversity observed in lattice-based models are preserved under more complex local dynamics, but quantitative aspects such as the rate of population growth, the level of maintained diversity, and the rate of decay of diversity all depend strongly on the local dynamics. Besides identifying situations in which modeling the explicit local population dynamics becomes necessary to understand the population structure of jump-driven range expansions, our results show that local dynamics affects different features of the population in distinct ways, and can be more or less consequential depending on the degree and form of long-range dispersal as well as the scale at which the population structure is measured.

evolutionary biology↗

bioRxiv2019

From sectors to speckles: The impact of long range migration on gene surfing

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well-studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: depending on the tail of the dispersal distance distribution, diversity can either be preserved (i.e. many variants survive) or lost (i.e. one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.

evolutionary biology↗

bioRxiv2019

Sickle cell disease complications: prevalence and resource utilization

This study evaluated the prevalence rate of vaso-occlusive crisis (VOC) episodes, rates of uncomplicated and complicated VOC episodes, and the primary reasons for emergency room (ER) visits and inpatient admissions for sickle cell disease (SCD) patients. The Medicaid Analytic extracts database was used to identify adult SCD patients using claims from 01JUL2009-31DEC2012. The date of the first observed SCD claim was designated as the index date. Patients were required to have continuous medical and pharmacy benefits for [≥]6 months baseline and [≥]12 months follow-up period. Patient demographics, baseline clinical characteristics, the rate of uncomplicated and complicated VOC (VOC with concomitant SCD complications) episodes, and reasons for ER visits and inpatient stays were analyzed descriptively. A total of 8,521 patients were included in the analysis, with a median age of 30 years. The average follow-up period was 2.7 years. The rate of VOC episodes anytime in the follow-up was 3.31 in person-years. During the first-year follow-up period, an average of 2.79 VOC episodes were identified per SCD patients, with 1.06 VOC episodes treated in inpatient setting and 0.90 VOC episodes in ER without admission. A total of 76,154 VOC episodes were identified during the entire follow-up period for the overall SCD patients. Most of the VOC episodes (70.3% [n=53,523]) were uncomplicated episodes, and 29.7% were complicated episodes. Using primary diagnosis claims only, the most frequent complications during the VOC episode were infectious diseases (25.9%), fever (21.8%), and pulmonary disorders (16.2%). Among ER and hospitalizations related to VOC or SCD complication, ~85.0% had VOCs as the primary reason for admission; 15.0% had SCD complications as the primary reason. In summary, SCD and its related comorbidities and complications result in high acute health care utilization. In addition, VOC remains the primary reason for SCD patients ER visits and inpatient admissions.

epidemiology↗

bioRxiv2018

Spatial soft sweeps: patterns of adaptation in populations with long-range dispersal

Adaptation in extended populations often occurs through multiple independent mutations responding in parallel to a common selection pressure. As the mutations spread concurrently through the population, they leave behind characteristic patterns of polymorphism near selected loci--so-called soft sweeps--which remain visible after adaptation is complete. These patterns are well-understood in two limits of the spreading dynamics of beneficial mutations: the panmictic case with complete absence of spatial structure, and spreading via short-ranged or diffusive dispersal events, which tessellates space into distinct compact regions each descended from a unique mutation. However, spreading behaviour in most natural populations is not exclusively panmictic or diffusive, but incorporates both short-range and long-range dispersal events. Here, we characterize the spatial patterns of soft sweeps driven by dispersal events whose jump distances are broadly distributed, using lattice-based simulations and scaling arguments. We find that mutant clones adopt a distinctive structure consisting of compact cores surrounded by fragmented \"haloes\" which mingle with haloes from other clones. As long-range dispersal becomes more prominent, the progression from diffusive to panmictic behaviour is marked by two transitions separating regimes with differing relative sizes of halo to core. We analyze the implications of the core-halo structure for the statistics of soft sweep detection in small genomic samples from the population, and find opposing effects of long-range dispersal on the expected diversity in global samples compared to local samples from geographic subregions of the range. We also discuss consequences of the standing genetic variation induced by the soft sweep on future adaptation and mixing.

evolutionary biology↗