Why study a shrimp’s genes?
Shrimps are among the ocean’s most emblematic creatures, fast-moving, adaptable, and essential to coastal ecosystems. Because their larvae drift with currents for weeks, we often assume they form large, well-connected populations. But how connected are they, really?
This question inspired our study of the pink shrimp Farfantepenaeus brasiliensis, a key species for coastal fisheries from Florida to southern Brazil. Despite its wide distribution and economic importance, little was known about its evolutionary history. Could a single, high-dispersal species actually hide multiple genetic lineages shaped by subtle ocean forces?
A genomic lens on marine evolution
In our paper, published in Heredity, we used genomic and mitochondrial data to investigate how pink shrimp populations are structured along the western Atlantic. Our goal was to understand how evolution proceeds in species that appear highly connected.
Thousands of SNPs from ddRAD-seq data revealed two major genetic lineages (one northern, one southern) had have likely followed independent evolutionary paths for nearly two million years. And yet, these lineages still exchange genes occasionally. In other words, they are diverging while staying connected: a process known as divergence with gene flow.
From the continental shelf to the microscope
Fieldwork took us to Brazil’s continental shelf, where F. brasiliensis lives in shallow coastal waters close to the seafloor. Most samples came from trawl fishing operations, the same method used by commercial fleets that have long exploited this species. These productive areas are also among the most affected by overfishing, placing pressure on local shrimp stocks.
We sorted nets filled with fish and crustaceans, isolated the pink shrimps, and preserved tissues for genetic analyses. Many of the specimens used in this study were already deposited in crustacean collections, emphasizing the crucial role of scientific repositories in preserving biodiversity records and enabling integrative research like this.
In the lab, the work shifted from sea to sequence. Building ddRAD-seq libraries required precision and patience, but the resulting data revealed clear genetic differentiation between northern and southern populations. This pattern aligned with the Amazon–Orinoco Plume (AOP), a vast freshwater discharge that, while not a strict barrier, creates salinity gradients capable of shaping larval dispersal and limiting connectivity.
The Brazilian lineage also showed smaller effective population sizes (Ne), suggesting that historical fluctuations and long-term exploitation may have reduced its genetic diversity, a reminder that the ocean’s apparent continuity conceals complex evolutionary histories.
Currents, climate, and connection
To uncover how these lineages formed, we reconstructed their demographic history. Both expanded after the Last Glacial Maximum, when lower sea levels exposed new habitats. Later, as sea levels rose and currents shifted, populations became partially isolated again.
Interestingly, gene flow was asymmetric, stronger from south to north, consistent with the direction of the North Brazil Current, which flows along the same region influenced by the AOP. Seeing these patterns align between oceanography and genomics was deeply satisfying: the sea itself shaping the evolutionary fate of its inhabitants.
Science across borders
This project was built through collaboration between the University of São Paulo (USP) in Brazil and Florida International University (FIU) in the United States. We combined the field expertise of our Brazilian team with genomic and analytical expertise from FIU to capture the full picture of F. brasiliensis evolution.
Why it matters
Our results highlight that even in the open ocean, evolution can be subtle and complex. Marine species that appear continuous may actually be mosaics of distinct genetic units. For the pink shrimp, this discovery matters beyond evolutionary biology. Southern populations, especially those in Brazil, showed lower genetic diversity and smaller effective population sizes, making them more vulnerable to overfishing and environmental change. Recognizing these lineages as distinct management units is essential for conserving their evolutionary potential and ensuring sustainable fisheries.