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Data from: Patterns of genomic divergence and signals of selection in sympatric and allopatric northeastern Pacific and Sea of Cortez populations of the sargo (Anisotremus davidsonii) and longjaw mudsucker (Gillichthys mirabilis)

Citation

Garcia, Eric; Simison, Brian; Bernardi, Giacomo (2020), Data from: Patterns of genomic divergence and signals of selection in sympatric and allopatric northeastern Pacific and Sea of Cortez populations of the sargo (Anisotremus davidsonii) and longjaw mudsucker (Gillichthys mirabilis), Dryad, Dataset, https://doi.org/10.5061/dryad.gmsbcc2ht

Abstract

Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, USA, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. This dataset consists of demultiplexed sequence data from Sbf1 single digest RADseq analysis of poulations of both fish species throughout their distributions. 

Methods

This dataset consists of demultiplexed, and quality-filtered, 80-bp sequence data from Sbf1 single digest RADseq analysis and two illumina lanes. Demultiplexing was accomplished with custom perl scripts (Miller et al., 2012). See the publication  Garcia et al. "Patterns of Genomic Divergence and Signals of Selection in Sympatric and Allopatric Northeastern Pacific and Sea of Cortez populations of the Sargo (Anisotremus davidsonii) and Longjaw mudsucker (Gillichthys mirabilis)" at the Journal of Heredity for more details. 

Usage Notes

Notation for file names= [specie][individual][site/location]

Samples were collected from the following sites:

USA sites: ELK, Elkhorn Slough; GOL, Goleta Slough; CAS, Carpinteria Sough; CAL, southern California.

Mexico Sites: GNE, Guerrero Negro; BCS, Baja California Sur; ECO, Estero El Coyote; ELC, Estero La Choya; PC, Punta Choya; EMO, Estero Morua; ELP, Estero La Pinta; BK, Bahia Kino; BLA, Bahia de Los Angeles.

Funding

Consejo Nacional de Ciencia y Tecnología

UC Mexus

The Myers Trust

Friends of the Long Marine Lab