Spatiotemporal modelling of marine movement data using Template Model Builder (TMB)

Tracking of marine animals has increased exponentially in the past decade, and the resulting data could lead to an in-depth understanding of the causes and consequences of movement in the ocean. However, most common marine tracking systems are associated with large measurement errors. Accounting for these errors requires the use of hierarchical models, which are often difficult to fit to data. Using 3 case studies, we demonstrate that Template Model Builder (TMB), a new R package, is an accurate, efficient and flexible framework for modelling movement data. First, to demonstrate that TMB is as accurate but 30 times faster than bsam, a popular R package used to apply state-space models to Argos data, we modelled polar bear Ursus maritimus Argos data and compared the locations estimated by the models to GPS locations of these same bears. Second, to demonstrate how TMBs gain in efficiency and frequentist framework facilitate model comparison, we developed models with different error structures and compared them to find the most effective model for light-based geolocations of rhinoceros auklets Cerorhinca monocerata. Finally, to maximize efficiency through TMBs use of the Laplace approximation of the marginal likelihood, we modelled behavioural changes with continuous rather than discrete states. This new model directly accounts for the irregular sampling intervals characteristic of Fastloc-GPS data of grey seals Halichoerus grypus. Using real and simulated data, we show that TMB is a fast and powerful tool for modelling marine movement data. We discuss how TMBs potential reaches beyond marine movement studies.13 page(s

Geolocator tagging links distributions in the non-breeding season to population genetic structure in a sentinel North Pacific seabird.

We tested the hypothesis that segregation in wintering areas is associated with population differentiation in a sentinel North Pacific seabird, the rhinoceros auklet (Cerorhinca monocerata). We collected tissue samples for genetic analyses on five breeding colonies in the western Pacific Ocean (Japan) and on 13 colonies in the eastern Pacific Ocean (California to Alaska), and deployed light-level geolocator tags on 12 eastern Pacific colonies to delineate wintering areas. Geolocator tags were deployed previously on one colony in Japan. There was strong genetic differentiation between populations in the eastern vs. western Pacific Ocean, likely due to two factors. First, glaciation over the North Pacific in the late Pleistocene might have forced a southward range shift that historically isolated the eastern and western populations. And second, deep-ocean habitat along the northern continental shelf appears to act as a barrier to movement; abundant on both sides of the North Pacific, the rhinoceros auklet is virtually absent as a breeder in the Aleutian Islands and Bering Sea, and no tagged birds crossed the North Pacific in the non-breeding season. While genetic differentiation was strongest between the eastern vs. western Pacific, there was also extensive differentiation within both regional groups. In pairwise comparisons among the eastern Pacific colonies, the standardized measure of genetic differentiation (FꞌST) was negatively correlated with the extent of spatial overlap in wintering areas. That result supports the hypothesis that segregation in the non-breeding season is linked to genetic structure. Philopatry and a neritic foraging habit probably also contribute to the structuring. Widely distributed, vulnerable to anthropogenic stressors, and exhibiting extensive genetic structure, the rhinoceros auklet is fully indicative of the scope of the conservation challenges posed by seabirds

Genomic reconstruction of the SARS-CoV-2 epidemic in England

AbstractThe evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.</jats:p