The Two Sides of the Mediterranean: Population Genomics of the Black Sea Urchin Arbacia lixula (Linnaeus, 1758) in a Warming Sea

Abstract

Global environmental changes may have a profound impact on ecosystems. In this context, it is crucial to gather biological and ecological information of the main species in marine communities to predict and mitigate potential effects of shifts in their distribution, abundance, and interactions. Using genotyping by sequencing (GBS), we assessed the genetic structure of a keystone species in the Mediterranean shallow littoral ecosystems, the black sea urchin Arbacia lixula. This bioengineer species can shape their communities due to its grazing activity and it is experiencing an ongoing expansion with increasing temperatures. The population genomic analyses on 5,241 loci sequenced in 240 individuals from 11 Mediterranean sampled populations revealed that all populations were diverse and showed significant departure from equilibrium. Albeit genetic differentiation was in general shallow, a significant break separated the western and eastern Mediterranean populations, a break not detected in previous studies with less resolutive markers. Notably, no clear effect of the Almería-Oran front, an important break in the Atlanto-Mediterranean transition, could be detected among the western basin populations, where only a slight differentiation of the two northernmost populations was found. Despite the generally low levels of genetic differentiation found, we identified candidate regions for local adaptation by combining different genomic analysis with environmental data. Salinity, rather than temperature, seemed to be an important driver of genetic structure in A. lixula. Overall, from a population genomics standpoint, there is ample scope for A. lixula to continue thriving and adapting in the warming Mediterranean.

Evaluating restriction enzyme selection for genome reduction in conservation genomics

“…We analyzed published population genomics data of two fish (Actinopterygii: Symphodus ocellatus, Symphodus tinca ) and two sea urchins (Echinoidea: Paracentrotus lividus and Arbacia lixula ) (Carreras et al, 2020, 2021; Torrado et al, 2020). Genomic loci for the four species were obtained by GBS using enzymes for genome reduction.…”

“…Population genomic studies published in different taxa are of particular interest since they allow the evaluation of the effect of the genomic technique used (Carreras et al, 2020, 2021; Torrado, Carreras, Raventos, Macpherson, & Pascual, 2020). Carreras et al studied the genetic structure of the two species of sea urchins cohabiting in the Mediterranean Sea: the edible sea urchin Paracentrotus lividus (2020) and the black sea urchin Arbacia lixula (2021).…”

“…Here, we aim to test whether GBS data obtained using different restriction enzymes and species results in differential enrichment of genomic regions, functionalities or in both aspects, in total and candidate loci. To do so, we analyzed published data from four species (Carreras et al, 2020, 2021; Torrado et al, 2020), two endemic fish species obtained with the EcoT22I enzyme ( S. ocellatus and S. tinca ), and two ecosystem building sea urchins with the ApekI enzyme ( P. lividus and A. lixula ). We used the fasta files of all loci genotyped in the corresponding population genomic studies.…”

“…In both species, Carreras et al identified some degree of population structure and candidate loci for adaptation associated with salinity and different temperature variables. They mapped the small fraction of loci under selection, showing that numerous candidate loci were located in exonic regions, suggesting that candidate loci could be enriched at exonic regions (Carreras et al, 2020(Carreras et al, , 2021. The two endemic fishes from the Mediterranean sea Symphodus ocellatus and Symphodus tinca inhabit algal-covered rocky substrates and sea-grass beds like Posidonia oceanica (Macpherson, Gordoa, & Garcıá-Rubies, 2002).…”

Sex-Specific Transcriptomic Differences in the Immune Cells of a Key Atlantic-Mediterranean Sea Urchin

“…Given this projection, an enhancing number of studies are using A. lixula as a model to investigate its genetic variation and adaptation patterns (Wangensteen et al, 2012;Pérez-Portela et al, 2019;Carreras et al, 2021), trophic ecology (Wangensteen et al, 2011), biological cycles (Wangensteen et al, 2013a) and responses to future climatic conditions and stressors (e.g. Pérez-Portela et al, 2020a).…”