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Hi, my name is Jorge Assis. I’m a Data Scientist, Marine Ecologist, Climate Change Analyst, R and Python Developer based in Portugal [github.com/jorgeassis]
© OCEANA / Juan Cuetos

Keywords: Marine Protected Areas; Biodiversity connectivity

Marine Protected Areas (MPAs) are key tools for ocean resource management and conservation. They prevent marine biodiversity declines and increase the resilience of ecosystems by protecting critical habitats and spawning biomass, as well as by supplying propagule and adult spillover to adjacent unprotected areas. To enhance the protection benefits, networks of individual MPAs operating synergistically are increasingly preferred over single MPAs, as they comprehensively protect whole species, across the spectrum of marine biodiversity. …


Sea ice generates as seawater freezes, and because it is less dense than sea water, it floats throughout the surface of the ocean. Sea ice covers approximately 12% of the world’s oceans, and much of it is enclosed within the polar ice packs: the Arctic ice pack (Arctic Ocean) and the Antarctic ice pack (Southern Ocean). Polar ice packs experience significant yearly cycling linked to annual seasons, a natural process upon dependes global marine ecosystems. According to ongoing measurements, both summer ice thickness and extent are in a dramatic decline.

Here are a few lines of R code to produce…


iNaturalist is a global platform where naturalists, citizen scientists, and biologists post their observations with photographs. Observations can be curated by the network of users to provide valuable open data to scientific research projects, conservation agencies and the general public. In particular, the data has been used to describe the global distribution of species, address niche-based questions, support biodiversity and ecosystem-based conservation, and to understand correlations between anthropogenic pressures and population extinctions.

Data may be accessed via its website, mobile application or API. Here I provide some line of python code to automatically download multiple records from iNaturalist using the…


Species distribution models (SDM; for review and definition see, e.g., Peterson et al., 2011) are a dominant paradigm to quantify the relationship between environmental dynamics and several manifestations of species biogeography. These statistical approaches pushed an emerging body of research describing the global distribution of species, addressing niche-based questions, supporting biodiversity conservation and ecosystem-based management, as well as infering the likely anthropogenic pressures leading to population turnover and extinction.

Spatial autocorrelation (SA) is a common challenge while modelling the distribution and abundance of species. This phenomenon, likely present in most ecological datasets, denotes the situation where the values of variables…


The major cause of global sea-level change is the exchange of water between ice and ocean during ice ages. The Last Glacial Maximum (LGM) was the most recent period with ice sheets at their greatest extent (maximum coverage between 26,500 and 19,000 years ago).

Massive ice sheets covered much of Northern Europe, North America and Asia and significantly affected global climate with increasing drought and desertification. Sea levels dropped about 120 meters (about 410 feet) when compared to today. This lead to exposed continental shelves, joined land masses and extensive coastal plains.

Here are a few lines of R code…


Genetic diversity estimation per site or group of sites can be biased due to unbalanced sampling designs. There is an expected relationship between the number of sampled individuals in a single population and genetic diversity (e.g., as allelic richness; the total number of alleles).

To overcome the issue, standardized allelic richness and standardized number of private alleles can be determined to the smallest number of individuals within sites or group of sites under multiple randomizations.

The sites or groups of sites with higher standardized genetic diversity than the global mean can be also assessed by testing the proportion of randomizations…


The availability of high-resolution global environmental datasets is crucial to model the relationship between the occurrence or abundance of species and their natural environment. For terrestrial environments, WorldClim has served this purpose since the early 2000s, significantly improving the application in the fields of ecology, biogeography, conservation biology and evolution.

Equivalent data for the marine realm only became available in 2012, with the pioneer initiative Bio-ORACLE providing data for several ecologically relevant variables. A new update of this dataset includes the most recent Intergovernmental Panel on Climate Change (IPCC) scenarios and new present-day variables like sea ice thickness, dissolved iron…


Photo by Jonatan Pie on Unsplash

The glacial and interglacial cycles of the Quaternary were particularly important in shaping the distribution of marine species, with range expansions and contractions responding to climate oscillations.

The Last Glacial Maximum was one of the most extreme periods of the Quaternary, resulting in severe reductions in the northern distribution of cold-temperate species, due to the advance of massive ice sheets. As climate conditions ameliorated throughout the Holocene, persisting populations (within refugia) or in extended southern ranges, gradually recolonized northward regions.

Climate-driven range shifts can leave distinct footprints on the genetic diversity levels of populations. Particularly, regions where populations persisted for…


Unlike measuring pairwise terrestrial distances, marine distances need to account for landmasses, which cannot be crossed. Marine distances are a crucial predictor in genetics to build isolation by distance models. These measure gene frequencies variation under increasing geographic distances.

When marine distances are plotted against pairwise genetic differentation levels, a linear relationship is expected. Here I provide a straightforward R script to determine minimum marine distances.

How it works?

A high-resolution polygon representing global landmasses is converted into an infinite resistance surface. …


Populations occurring along low latitude ranges are expected to retain high and unique genetic diversity because they persisted throughout the last glacial period and until our times. However, recent climate change is producing range shifts at the edge of distributions, where changes on the limiting niche of species is leading to the extinction of many populations of distinct species. Such processes may erode the genetic diversity of populations, a process that prevails over past historical effects and with potential consequences on reducing future adaptive capacity.

Using a kelp species (Saccorhiza polyschides) as a model, we tested if a decline in…

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