Genomic Analyses Implicate the Amazon–Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab

Abstract

The Amazon–Orinoco plume (AOP) is the world’s largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP’s formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species.

Phylogeography of a Widely Distributed Atlantic Species: The Case of the Ghost Crab Ocypode quadrata (Fabricius, 1787) (Decapoda: Brachyura: Ocypodidae)

“…Possibly, USA and Mexican populations have been exposed to events of strong selective pressure and/or genetic drift, changing their size abruptly, which makes certain individuals more efficient in transmitting their genes than others [62,76]. Genetic structure and many mutational steps were also observed for Ilyoplax pusilla (De Haan, 1835) [77] and in the swimming crab Callinectes ornatus Ordway, 1863 [78]. These steps indicate modifications by transversions or transitions in the nitrogenous bases, in relation to the previous haplotype, increasing the genetic distance between them.…”

A temporal and spatial study of genetic structure in four species of bladed Bangiales (Rhodophyta) from the southeastern Pacific coast of Chile

“…River outflows can carry large amounts of sediments and freshwater and can influence physical and chemical characteristics of marine environments such as salinity, sea surface temperature, oxygen, and nutrient concentration. Freshwater outflow from large estuaries form plumes, characterized by low salinity and high turbidity, which can extend for dozens or even hundreds of kilometers into oceanic waters, having significant impacts on the dispersal of marine taxa (Peres et al, 2022; Wang et al, 2015). The average annual discharge of the Valdivia River is about 600 m 3 · s −1 , with peaks of almost 800 m 3 · s −1 during the austral winter (Dávila et al, 2002), which strongly affects turbidity and salinity, especially at the river's mouth (Huovinen et al, 2016; Pardo et al, 2011).…”

Genetic Variability and Genetic Differentiation of Populations in the Grooved Carpet Shell Clam (Ruditapes decussatus) Based on Intron Polymorphisms

“…A possible explanation for this inconsistency is just a higher isolation and lower effective size in these populations, which would result in the fact that distant populations would look alike just by chance. Another possible explanation is the effect of river plumes, which have been proposed as causes of genetic differentiation of populations located on both sides of the plume in some marine species due to the limitation of gene flow by means of restricting larval transport across the plume [41,42]. In this study, the plumes of rivers Minho, Douro, and Tejo (Figure 1b), which show some of the highest discharge rates among the Iberian rivers flowing to the Atlantic (340, 660, and 550 m 3 /s, respectively), could act as barriers to gene flow [43].…”