Publications by authors named "Eleni L Petrou"

4 Publications

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Evidence for selection and spatially distinct patterns found in a putative zona pellucida gene in Pacific cod, and implications for management.

Ecol Evol 2021 Dec 30;11(23):16661-16679. Epub 2021 Nov 30.

School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA.

Genetic differentiation has been observed in marine species even when no obvious barriers to gene flow exist, and understanding such differentiation is essential for effective fisheries management. Highly differentiated outlier loci can provide information on how genetic variation might not only contribute to local adaptation but may also be affected by historical demographic events. A locus which aligned to a predicted zona pellucida sperm-binding protein 3 gene (ZP3) in Atlantic cod () was previously identified as the highest outlier based on in a RADseq study of Pacific cod () across the West Coast of North America. However, because of the limited length of the RAD sequence and restricted geographic area of sampling, no conclusion on the functional significance of the observed variation was possible. In other marine species, ZP3 is involved in reproductive isolation, local adaptation, and has neofunctionalized as an antifreeze gene, and so it may provide important insights in functional population structure of Pacific cod. Here, we sequenced a 544-bp region of ZP3 in 230 Pacific cod collected from throughout their geographic range. We observed striking patterns of spatial structuring of ZP3 haplotypes, with a sharp break near Kodiak, Alaska, USA where populations within ~200 km of each other are nearly fixed for different haplotypes, contrasting a pattern of isolation by distance at other genetic markers in this region ( = 0.003). Phylogenetic analysis of ZP3 haplotypes revealed that the more southern haplotypes appear to be ancestral, with the northern haplotype evolving more recently, potentially in response to a novel selective pressure as Pacific cod recolonized northern latitudes after glaciation. The sharp break in haplotype frequencies suggests strong selective pressures are operating on small spatial scales and illustrates that selection can create high divergence even in marine species with ample opportunities for gene flow.
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http://dx.doi.org/10.1002/ece3.8284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8668774PMC
December 2021

Functional genetic diversity in an exploited marine species and its relevance to fisheries management.

Proc Biol Sci 2021 02 24;288(1945):20202398. Epub 2021 Feb 24.

School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA.

The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring () across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particular , which influences the development of retinal photoreceptors in vertebrates. is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.
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http://dx.doi.org/10.1098/rspb.2020.2398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934995PMC
February 2021

Intraspecific DNA contamination distorts subtle population structure in a marine fish: Decontamination of herring samples before restriction-site associated sequencing and its effects on population genetic statistics.

Mol Ecol Resour 2019 Sep 17;19(5):1131-1143. Epub 2019 Jun 17.

School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington.

Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (a) the efficacy of bleach decontamination, (b) the effect of decontamination on RAD genotypes and (c) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and nonspawning (uncontaminated) herring. Samples were soaked for 10 min in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction site-associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data and can impact downstream analyses.
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http://dx.doi.org/10.1111/1755-0998.12978DOI Listing
September 2019

Environmental symbiont acquisition may not be the solution to warming seas for reef-building corals.

PLoS One 2010 Oct 7;5(10):e13258. Epub 2010 Oct 7.

Graduate Program in Evolution, Ecology and Behavior, Department of Geology, University at Buffalo, Buffalo, New York, United States of America.

Background: Coral reefs worldwide are in decline. Much of the mortality can be attributed to coral bleaching (loss of the coral's intracellular photosynthetic algal symbiont) associated with global warming. How corals will respond to increasing oceanic temperatures has been an area of extensive study and debate. Recovery after a bleaching event is dependent on regaining symbionts, but the source of repopulating symbionts is poorly understood. Possibilities include recovery from the proliferation of endogenous symbionts or recovery by uptake of exogenous stress-tolerant symbionts.

Methodology/principal Findings: To test one of these possibilities, the ability of corals to acquire exogenous symbionts, bleached colonies of Porites divaricata were exposed to symbiont types not normally found within this coral and symbiont acquisition was monitored. After three weeks exposure to exogenous symbionts, these novel symbionts were detected in some of the recovering corals, providing the first experimental evidence that scleractinian corals are capable of temporarily acquiring symbionts from the water column after bleaching. However, the acquisition was transient, indicating that the new symbioses were unstable. Only those symbiont types present before bleaching were stable upon recovery, demonstrating that recovery was from the resident in situ symbiont populations.

Conclusions/significance: These findings suggest that some corals do not have the ability to adjust to climate warming by acquiring and maintaining exogenous, more stress-tolerant symbionts. This has serious ramifications for the success of coral reefs and surrounding ecosystems and suggests that unless actions are taken to reverse it, climate change will lead to decreases in biodiversity and a loss of coral reefs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013258PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951366PMC
October 2010
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