Amplicon sequencing of 42 nuclear loci supports directional gene flow between South Pacific populations of a hydrothermal vent limpet.

Sophie Plouviez,Joseph E Neigel,F A Bastiaan Von Meijenfeldt,Abigail Leavitt Labella,David W Weisrock,Bernard Ball,Cindy L Van Dover

doi:10.1002/ece3.5235

Abstract

In the past few decades, population genetics and phylogeographic studies have improved our knowledge of connectivity and population demography in marine environments. Studies of deep‐sea hydrothermal vent populations have identified barriers to gene flow, hybrid zones, and demographic events, such as historical population expansions and contractions. These deep‐sea studies, however, used few loci, which limit the amount of information they provided for coalescent analysis and thus our ability to confidently test complex population dynamics scenarios.In this study, we investigated population structure, demographic history, and gene flow directionality among four Western Pacific hydrothermal vent populations of the vent limpet Lepetodrilus aff. schrolli. These vent sites are located in the Manus and Lau back‐arc basins, currently of great interest for deep‐sea mineral extraction. A total of 42 loci were sequenced from each individual using high‐throughput amplicon sequencing. Amplicon sequences were analyzed using both genetic variant clustering methods and evolutionary coalescent approaches. Like most previously investigated vent species in the South Pacific, L. aff. schrolli showed no genetic structure within basins but significant differentiation between basins. We inferred significant directional gene flow from Manus Basin to Lau Basin, with low to no gene flow in the opposite direction. This study is one of the very few marine population studies using >10 loci for coalescent analysis and serves as a guide for future marine population studies.

Highlights

Genetic homogeneity and panmixia were once assumed to be characteristic of marine species with planktonic larvae capable of dispersal over long distances (Scheltema, 1986)
We investigated population structure, demographic history, and gene flow directionality among four Western Pacific hydrothermal vent populations of the vent limpet Lepetodrilus aff. schrolli
Population subdivision can result from barriers to dispersal that include oceanic currents (Baums, Miller, & Hellberg, 2005; Thornhill, Mahon, Norenburg, & Halanych, 2008), geomorphology (Won, Young, Lutz, & Vrijenhoek, 2003), and vicariance events like the rising of the Isthmus of Panama (Bermingham & Lessios, 1993; Cunningham & Collins, 1994), or by persisting for long periods of time across a given area (Cunningham & Collins, 1998; Wright, 1951)

Summary

| INTRODUCTION

Genetic homogeneity and panmixia were once assumed to be characteristic of marine species with planktonic larvae capable of dispersal over long distances (Scheltema, 1986). In the other species studied (snails, shrimp, mussels, barnacles), no within‐basin population structure was detected in Manus, North Fiji, or Lau Basins (Kyuno et al, 2009; Plouviez et al, 2013; Suzuki et al, 2006; Thaler et al, 2014, 2011). Genetic differentiation between Manus and North Fiji basins (Figure 2) has been detected using COI in three species, Ifremeria nautilei snails, Bathymodiolus mussel species, and Chorocaris sp. Unlike previous population studies in the region that used COI and microsatellite loci, we assessed the potential for genetic structure and restricted gene flow between basins using over 15 kb of aligned DNA sequences from 42 single‐copy intronic and exonic loci sampled from 93 individuals collected in the Manus and Lau Basins.

| MATERIALS AND METHODS

Findings

| DISCUSSION