Population genomics of the euryhaline teleost Poecilia latipinna

J. C B Nunez, T. P. Seale, M. A. Fraser, T. L. Burton, T. N. Fortson, D. Hoover, J. Travis, Marjorie F Oleksiak, Douglas L Crawford

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (p ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence.

Original languageEnglish (US)
Article numbere0137077
JournalPLoS One
Volume10
Issue number9
DOIs
StatePublished - Sep 3 2015

Fingerprint

Poecilia
Metagenomics
Salts
Sea level
Climate change
Microsatellite Repeats
Fish
Population
Isoenzymes
genetic variation
Conservation
genotyping
salt marshes
adaptive radiation
Wetlands
loci
population structure
Single Nucleotide Polymorphism
Genomics
Poecilia latipinna

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Nunez, J. C. B., Seale, T. P., Fraser, M. A., Burton, T. L., Fortson, T. N., Hoover, D., ... Crawford, D. L. (2015). Population genomics of the euryhaline teleost Poecilia latipinna. PLoS One, 10(9), [e0137077]. https://doi.org/10.1371/journal.pone.0137077

Population genomics of the euryhaline teleost Poecilia latipinna. / Nunez, J. C B; Seale, T. P.; Fraser, M. A.; Burton, T. L.; Fortson, T. N.; Hoover, D.; Travis, J.; Oleksiak, Marjorie F; Crawford, Douglas L.

In: PLoS One, Vol. 10, No. 9, e0137077, 03.09.2015.

Research output: Contribution to journalArticle

Nunez, JCB, Seale, TP, Fraser, MA, Burton, TL, Fortson, TN, Hoover, D, Travis, J, Oleksiak, MF & Crawford, DL 2015, 'Population genomics of the euryhaline teleost Poecilia latipinna', PLoS One, vol. 10, no. 9, e0137077. https://doi.org/10.1371/journal.pone.0137077
Nunez JCB, Seale TP, Fraser MA, Burton TL, Fortson TN, Hoover D et al. Population genomics of the euryhaline teleost Poecilia latipinna. PLoS One. 2015 Sep 3;10(9). e0137077. https://doi.org/10.1371/journal.pone.0137077
Nunez, J. C B ; Seale, T. P. ; Fraser, M. A. ; Burton, T. L. ; Fortson, T. N. ; Hoover, D. ; Travis, J. ; Oleksiak, Marjorie F ; Crawford, Douglas L. / Population genomics of the euryhaline teleost Poecilia latipinna. In: PLoS One. 2015 ; Vol. 10, No. 9.
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