Big shells, bigger data: cohort analysis of Chesapeake Bay Crassostrea virginica reefs

Oysters in Virginia Chesapeake Bay oyster reefs are "age-truncated", possibly due to a combination of historical overfishing, disease epizootics, environmental degradation, and climate change. Research has suggested that oysters exhibit resilience to environmental stressors; however, that evidence is based on the current limited understanding of oyster lifespan. Until this paper, the Virginia Oyster Stock Assessment and Replenishment Archive (VOSARA), a spatially and temporally expansive dataset (222 reefs across 2003-2023) of shell lengths (SL, mm), had yet to be examined comprehensively in the context of resilience. We develop a novel method using Gaussian mixture modeling (GMM) to identify the age groups in each reef using yearly SL data and then link those age groups over time to identify cohorts and estimate their lifespan. Sixty-four reefs (29%) are deemed to have sufficient data (at least 300 oysters sampled for a minimum of 8 consecutive years) for this analysis. We fit univariate GMMs for each year ($t$) and reef ($r$) for each of the seven river strata ($R$) to estimate 1) the mean and standard deviation of SL for each $a_{Rrt}$th age group, and 2) the mixture percentage of each $a_{Rrt}$th age group. We link age groups across time to infer age cohorts by developing a mechanistic algorithm that prevents the shrinking of shell length when an $a_{Rrt}$th group becomes an ($a_{R,r,t+1}$)th group. Our method shows promise in identifying oyster cohorts and estimating lifespan solely using SL data. Our results show signals of resiliency in almost all river systems: oyster cohorts live longer and grow larger in the mid-to-late 2010s compared to the early 2000s.