Biology Faculty Researchhttps://scholarsbank.uoregon.edu/xmlui/handle/1794/179972024-03-28T22:49:42Z2024-03-28T22:49:42ZThe influence of explicit local dynamics on range expansions driven by long-range dispersalVilliger, NathanPaulose, Jaysonhttps://scholarsbank.uoregon.edu/xmlui/handle/1794/280692023-10-10T18:04:32Z2023-02-23T00:00:00ZThe influence of explicit local dynamics on range expansions driven by long-range dispersal
Villiger, Nathan; Paulose, Jayson
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.
22 pages
2023-02-23T00:00:00ZTrait biases in microbial reference genomesAlbright, SageLouca, Stilianoshttps://scholarsbank.uoregon.edu/xmlui/handle/1794/280482023-03-03T08:28:11Z2023-01-01T00:00:00ZTrait biases in microbial reference genomes
Albright, Sage; Louca, Stilianos
Common culturing techniques and priorities bias our discovery towards specific traits that may not
be representative of microbial diversity in nature. So far, these biases have not been systematically
examined. To address this gap, here we use 116,884 publicly available metagenome-assembled
genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample
of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database,
which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used
as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean,
soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the
conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire.
We find that the majority of examined genes are significantly biased for or against in RefSeq. Our
systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases
in reference genomes constitutes a resource for addressing these issues in the future.
17 pages
2023-01-01T00:00:00ZA generic hierarchical model of organic matter degradation and preservation in aquatic systemsShang, Haitaohttps://scholarsbank.uoregon.edu/xmlui/handle/1794/279272023-10-10T18:01:07Z2023-01-01T00:00:00ZA generic hierarchical model of organic matter degradation and preservation in aquatic systems
Shang, Haitao
Organic matter degradation and preservation are crucial components of Earth’s carbon cycle. Empirical and phenomenological models usually contain parameters determined by site-specific data and focus on different aspects of the decay and accretion characteristics. To investigate more fundamental mechanisms, this study suggests a hierarchical model that links microscopic physical quantities to macroscopic degradation and preservation patterns. This mechanistic model predicts several commonly observed phenomena, including the lognormal distribution of degradation rate constants, the recalcitrance-dependent sensitivity to temperature, the dependence of a heterogeneous organic-matter system’s persistence on its complexity, logarithmic-time decay, and power-law degradation behavior. The theoretical predictions of this model are consistent with the observational data from marine and lake environments. This hierarchical model may provide a step towards a fundamental theory of organic matter degradation and preservation in aquatic and other ecosystems.
10 pages
2023-01-01T00:00:00ZEpitope tag-specific differences in the detection of COSA-1 marked crossover sites in C. elegans spermatocytesCahoon, Cori K.Uebel, Celja J.Villeneuve, Anne M.Libuda, Diana E.https://scholarsbank.uoregon.edu/xmlui/handle/1794/279132023-10-10T17:35:34Z2023-01-06T00:00:00ZEpitope tag-specific differences in the detection of COSA-1 marked crossover sites in C. elegans spermatocytes
Cahoon, Cori K.; Uebel, Celja J.; Villeneuve, Anne M.; Libuda, Diana E.
Nascent crossover sites in C. elegans meiocytes can be cytologically detected using epitope-tagged versions of the pro-crossover protein COSA-1. In spermatocytes, differences exist between cytologically-detected and genetically-detected double crossover rates. Here, we examine nascent crossovers using both GFP- and OLLAS-tagged COSA-1. Similar to previous work, we find that most late pachytene spermatocytes display 5 COSA-1 foci, indicating one crossover per autosome bivalent. However, we detected more nuclei with >5 COSA-1 foci using OLLAS::COSA-1, reflecting some bivalents having 2 COSA-1 foci. These results demonstrate tag-specific differences in the detection of COSA-1 marked nascent crossovers in spermatocytes.
6 jpages
2023-01-06T00:00:00Z