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

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

Detecting selection in the blue crab, Callinectes sapidus, using DNA sequence data from multiple nuclear protein-coding genes.

The identification of genes involved in the adaptive evolution of non-model organisms with uncharacterized genomes constitutes a major challenge. This study employed a rigorous and targeted candidate gene approach to test for positive selection on protein-coding genes of the blue crab, Callinectes sapidus. Four genes with putative roles in physiological adaptation to environmental stress were chosen as candidates. A fifth gene not expected to play a role in environmental adaptation was used as a control. Large samples (n>800) of DNA sequences from C. sapidus were used in tests of selective neutrality based on sequence polymorphisms. In combination with these, sequences from the congener C. similis were used in neutrality tests based on interspecific divergence. In multiple tests, significant departures from neutral expectations and indicative of positive selection were found for the candidate gene trehalose 6-phosphate synthase (tps). These departures could not be explained by any of the historical population expansion or bottleneck scenarios that were evaluated in coalescent simulations. Evidence was also found for balancing selection at ATP-synthase subunit 9 (atps) using a maximum likelihood version of the Hudson, Kreitmen, and Aguadé test, and positive selection favoring amino acid replacements within ATP/ADP translocase (ant) was detected using the McDonald-Kreitman test. In contrast, test statistics for the control gene, ribosomal protein L12 (rpl), which presumably has experienced the same demographic effects as the candidate loci, were not significantly different from neutral expectations and could readily be explained by demographic effects. Together, these findings demonstrate the utility of the candidate gene approach for investigating adaptation at the molecular level in a marine invertebrate for which extensive genomic resources are not available

Differential host mortality explains the effect of high temperature on the prevalence of a marine pathogen

<div><p>Infectious diseases threaten marine populations, and the extent of their impacts is often assessed by prevalence of infection (the proportion of infected individuals). Changes in prevalence are often attributed to altered rates of transmission, although the rates of birth, recovery, and mortality also determine prevalence. The parasitic dinoflagellate <i>Hematodinium perezi</i> causes a severe, often fatal disease in blue crabs. It has been speculated that decreases in prevalence associated with high temperatures result from lower rates of infection. We used field collections, environmental sensor data, and high-temperature exposure experiments to investigate the factors that change prevalence of infections in blue crab megalopae (post-larvae). These megalopae migrate from offshore waters, where temperatures are moderate, to marshes where temperatures may be extremely high. Within a few days of arriving in the marsh, the megalopae metamorphose into juvenile crabs. We found a strong negative association between prevalence of <i>Hematodinium</i> infection in megalopae and the cumulative time water temperatures in the marsh exceeded 34°C over the preceding two days. Temperatures this high are known to be lethal for blue crabs, suggesting that higher mortality of infected megalopae could be the cause of reduced prevalence. Experimental exposure of megalopae from the marsh to a temperature of 34°C resulted in higher mortality for infected than uninfected individuals, and decreased the prevalence of infection among survivors from 18% to 3%.</p></div

Tajima's <i>D</i>, Fay and Wu's <i>H</i>, Ewens-Watterson <i>EW</i>, and <i>DHEW</i> compound test results for <i>Callinectes sapidus</i>.

<p><i>D</i>, Tajima's <i>D</i>; <i>H</i>, Fay and Wu's <i>H</i>; <i>EW</i>, Ewens-Watterson <i>EW</i>; <i>DHEW(P)</i>, critical <i>P</i> for <i>DHEW</i> test. Significance of the <i>DHEW</i> test at nominal α = 0.01 is based on the p-values for <i>D</i> and <i>H</i> being less than <i>DHEW(P)</i> and the p-value of <i>EW</i> being greater than 1-<i>DHEW(P)</i>. Significance of the individual <i>EW</i> test is based on 1 minus the p-value of <i>EW</i>.</p><p>*<i>p</i><0.01, **<i>p</i><0.001.</p

GENE GENEALOGIES WITHIN THE ORGANISMAL PEDIGREES OF RANDOM-MATING POPULATIONS.

Using computer simulations, we generated and analyzed genetic distances among selectively neutral haplotypes transmitted through gene genealogies with random-mating organismal pedigrees. Constraints and possible biases on haplotype distances due to correlated ancestry were evaluated by comparing observed distributions of distances to those predicted from an inbreeding theory that assumes independence among haplotype pairs. Results suggest that: 1) mean time to common ancestry of neutral haplotypes can be a reasonably good predictor of evolutionary effective population size; 2) the nonindependence of haplotype paths of descent within a given gene genealogy typically produces significant departures from the theoretical probability distributions of haplotype distances; 3) frequency distributions of distances between haplotypes drawn from "replicate" organismal pedigrees or from multiple unlinked loci within an organismal pedigree exhibit very close agreement with the theory for independent haplotypes. These results are relevant to interpretations of current molecular data on genetic distances among nonrecombining haplotypes at either nuclear or cytoplasmic loci

Effect of temperature and salinity on prevalence of <i>H</i>. <i>perezi</i> in blue crab megalopae.

<p>(<i>A</i>) Hourly water temperature at Coastwide Reference Monitoring System (CRMS) station 0581 near the RWR marsh site (yellow), nearshore buoy 42051 (blue) and offshore buoy 42050 (green) for 40 days prior to collection of megalopae at RWR on Aug. 11, 2015. Red line indicates high-temperature threshold of 35°C, red-shaded area indicates 2-day period prior to megalopae collection. (<i>B</i>) Megalopae were collected from marshes at Rockefeller Wildlife Refuge (RWR), Freshwater City Locks (FWC), Louisiana Universities Marine Consortium (LUM), and Grand Isle Marine Laboratory (GIL). Temperature and salinity data from CRMS sites 0178 (at GIL), 0347 (at LUM), 0581 (at RWR) and 0633 (at FWC). Temperature data from buoys at stations 42050 (TABS F; green) and 42051 (TABS R; blue). (<i>C</i>) Prevalence, as percentage of megalopae from which a portion of the <i>H</i>. <i>perezi</i> 18S rRNA gene was PCR-amplified, plotted against temperature (°C) at collection time and location. (<i>D</i>) Prevalence plotted against salinity (ppt) at collection time and location. (<i>E</i>) Log-likelihoods and (<i>F</i>) slopes from logistic regression models that predict log odds ratio of infection from proportion of hourly marsh temperatures that exceeded each threshold, with variable threshold temperatures and time intervals. Increasing log-likelihood values (lighter color) indicate models with combinations of threshold temperature and time intervals with greater support. Steeper downward slopes (darker colors) indicate models in which thermal stress has a larger negative effect on prevalence of infection.</p

Comparison of complete and truncated isoforms of the 70 kDa heat shock protein family.

<p>(A) Protein structure of <i>E.coli</i> HSP70 (DNAK) chaperone (aa 1–605) complexed with ADP and substrate (PDB: 2KHO). (B) The truncated bovine HSC70 (aa 1–554) mutant E214A/D214B in post-ATP bound phase (PDB: 1YUW). The truncated form is missing a portion of the C-terminal α-helices, but retains the ATPase site within the nucleotide binding domain.</p

McDonald-Kreitman test results for <i>ant</i> and <i>tps.</i>

<p>McDonald-Kreitman tests for <i>ant</i> and <i>tps</i> using <i>C. sapidus</i> polymorphisms and fixed differences between <i>C. sapidus</i> and <i>C. similis</i>. Contingency tables for <i>atps</i>, <i>hsp</i>, and <i>rpl</i> could not be calculated because there were no fixed differences between <i>C. sapidus</i> and <i>C. similis</i>.</p><p>*<i>p</i><0.025.</p

ESTIMATION OF SINGLE GENERATION MIGRATION DISTANCES FROM GEOGRAPHIC VARIATION IN ANIMAL MITOCHONDRIAL DNA.

A new approach is introduced for the analysis of dispersal from the geographic distributions of mtDNA lineages. The method is based on the expected spatial distributions of lineages arising under a multigeneration random walk process. Unlike previous methods based on the predicted equilibria between genetic drift and gene flow, this approach is appropriate for non-equilibrium conditions, and yields an estimate of dispersal distance rather than dispersal rate. The theoretical basis for this method is examined, and an analysis of mtDNA restriction site data for Peromyscus maniculatus is presented as an example of how this approach can be applied to empirical data