Physical-Biological Interactions Paris' Lab

Connectivity Modeling System (CMS)

The CMS is a community modeling system, based on a stochastic, multi-scale Lagrangian framework. It is developed by Dr. Claire Paris and her team to study complex larval migrations and provide probability estimates of marine population connectivity. In addition, the CMS can also provide a Lagrangian descriptions of oceanic phenomena (advection, dispersion, retention) and can be used in a broad range of applications, from the dispersion and fate of pollutants to marine spatial conservation. The source code can be accessed at: CMS

The CMS has a stochastic biophysical algorithm coding for the dispersion of biotic and abiotic inertial particles. The biological modules are informed with empirical data, some of which are collected with a Lagrangian device that she pioneered, the ocean - Drifting In Situ Chamber (o-DISC), designed to track larval movement and investigate navigational cues.

This repository is to facilitate community contributions to the CMS suite of modules. Funding was provided by the National Science Foundation Biological Oceanography Program (OCE-1048697, OCE- 0928423, OCE-0825625) to C.B. Paris.

The manuscript by Paris et al. (2013, Environmental Modelling & Software) describing the CMS and its modules can be downloaded here.

The open-source code of the CMS is used worldwide for oceanographic and biological applications.


Figure 1

Figure 1. Particle trajectories within a freely evolving idealized Agulhas ring. The velocity fields for this release are obtained from the experiment described in Van Sebille and Van Leeuwen (2007). Four particle trajectories are shown here (panel a), all seeded in the core of the Agulhas ring. As the ring moves northwestward, the particles keep circulating around the ring centre, as can be seen in panels b-e which show snapshots of both the ring profile (colors) and the positions of the particles (black dots) every 100 days. The advection of the particles within the ring is expected behavior, because strong ocean eddies such as this Agulhas ring are capable of transporting water over large distances. A movie of a similar experiment using the same velocity data but more particles is available as supplementary material (downloadable from (Paris et al. 2012).

Figure 2

Figure 2 . Model evaluation for biotic particles: A) comparison of mean larval bicolor damselfish settlement (abundance per light-trap) and simulated settlement to the Florida Keys (Modified from Sponaugle et al. 2012). Connectivity Matrices; B) monthly probability of migration of larvae between the Florida Keys (UK=upper Keys, MK=middle Keys, LK=lower Keys, WK=western Keys), Mexico (ME), Cuba (CU), and the Bahamas (BA) from June to September of 2007 and 2008. Connectivity below and above diagonal line indicates downstream and upstream settlement, respectively. The magenta squares delineate the FKeys-HYCOM 1/100° (ca. 900 m resolution, nest 2) domain, overlapping the larger domain of the GoM-HYCOM 1/25° (ca. 3.7 km resolution, nest 1). The colorbar (natural logarithm scale) indicates the probability that particles released from sites represented along the y-axis settle to sites along the x-axis; the values along the diagonal represent self-recruitment, i.e. release and settlement sites are equal (Paris et al. 2012).