Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

- Fine-scale population structure and.
- evidence for local adaptation in Australian giant black tiger shrimp ( Penaeus monodon ) using SNP analysis.
- monodon populations..
- Conclusion: This study provides new insights on genetic population structure of Australian P.
- Full list of author information is available at the end of the article.
- monodon from Western Australia was a separate genetic stock with reduced a number of allelic due to colonisation by east coast P.
- monodon from Northern Territory separated into a discrete cluster while Queensland and Western Australia grouped with Thailand, Palau, PNG, Taiwan, Philippines, and Vietnam (Bac Lieu and Can Tho) in one cluster [34]..
- The main objective of this study is to resolve the population genetic structure of P.
- monodon genetic structure and local adaptation for management and conservation of Australian populations are discussed..
- Contrastingly, average private allelic richness (A PR ) and average MAF of polymorphic loci were slightly higher for Western Australia and 0.18) than for both northern Queensland (Bramston Beach, Etty Bay, and Townville.
- Among populations, Western Australia displayed the highest Ho and Av..
- values in all northern Queensland and Northern Terri- tory populations with the exception of Western Australia where average H O and H E values were similar (Table 2).
- Average F IS values for both northern Queens- land and Northern Territory sites were positive and ranged from 0.10 to 0.14, while average F IS value for Western Australia population was negative, but close to zero.
- Estimated N eLD varied across populations and ranged from 165.4 in Western Australia (95% CI to 24,121 in Bramston Beach (95% CI = 11, 024.
- with Western Australia and Etty Bay popula- tions having the lowest N eLD across all seven populations (Table 2)..
- Population differentiation and genetic structure.
- The individual density distribution of the first retained dis- criminant function indicated separation of north Queensland shrimp from those in the Northern Terri- tory and Western Australia groups (Fig.
- Not surprisingly, the most geographically separated sites (Nickol Bay in Western Australia and three north Queensland populations at approx.
- Differences among geograph- ically discrete populations accounted for only 4.2% of the total variance (p <.
- 0.01), while 0.2% of the total vari- ance (p <.
- Genetic structure based on outlier and neutral markers PCA analysis of all individuals for both neutral and outlier SNP separated Australian populations into the same three clusters as DAPC and Netview analyses (Western Australia separate from north Queensland and Northern Territory populations.
- Considering the 10,535 neutral SNPs, PC1 and PC2 explained 24.8 and 14.7% of the total genetic variance, respectively (Fig.
- Consider- ing the 89 outlier SNPs, PC1 and PC2 explained 5.8 and 1.0% of the total genetic variance, respectively (Fig.
- Western Australia population).
- In a simi- lar way, using 89 outlier loci, F ST values between north Queensland populations and Western Australia (F ST were in all cases higher than those between Table 2 Genetic diversity indices for the Penaeus monodon populations sampled.
- Table 3 Population differentiation estimates for Penaeus monodon populations sampled.
- 1 Population structure of 278 individuals of Penaeus monodon samples using 10,624 SNPs (BB: Bramston Beach, EB: Etty Bay, Townsville: TSV, Gulf of Carpentaria: GC, Joseph Bonaparte Gulf: JBG, Tiwi Island: TIW, and Nickol Bay: NKB).
- Northern Territory populations and Western Australia (F ST .
- Variance par- titioning based on neutral and outlier loci RDA models revealed that environmental effects explained 4.3 and 20.2% of genetic structure variation, while geographic location explained 12.9 and 2.8%, respect- ively.
- Protein translation of the remaining eight outlier SNPs demonstrated the following: 1) five contained synonymous and non- synonymous mutations in two and four reading frames, 2) two contained synonymous and non- synonymous mutations in one and five reading frames, and 3) one contained synonymous and non- synonymous mutations in zero and six reading frames, respectively (see Additional file 8).
- The 89 outlier SNPs on the intersections (shaded area) were retained for further analysis.
- Of note is that the Western Australia population.
- 4 Redundancy analysis on (a) 10,535 neutral loci and (b) 89 outlier SNPs allele frequencies in seven populations of Penaeus monodon in Australia.
- exhibited the lowest level of genetic variation of all assessed populations, which could be due to restricted gene flow between Western Australia and Northern Ter- ritory populations.
- monodon could be due to technical artefacts of the RADseq-based genotyping (i.e., null alleles) [41, 42] and/or sampling bias (i.e., Wahlund effect) [43, 44].
- In the Western Australia (Nickol Bay) population, het- erozygosity (i.e., H O and H E ) were equal or higher than other populations despite A R and PPL being slightly.
- This slight reduction in A R and PPL is most likely due to the smaller sample size in our study for the Western Australia population [46]..
- SNP genotyping of this Western Australia population re- vealed equal or higher heterozygosity, despite previous allozyme and microsatellite based demonstrations of re- duced heterozygosity and number of alleles in P.
- mono- don from the same Western Australia region [31, 47]..
- As such, based on the entire Western Australia SNP dataset encompassing 10,624 genome-wide SNPs, Western Australia P.
- Differences between our dataset and those using microsatellites, allozymes and mtDNA may simply be due to the level of genetic resolution of these markers when comparing allelic di- versity, where our high-resolution sampling captured more of the true genetic diversity within the P.
- monodon populations revealed relatively weak genetic structuring except for Western Australia which had the highest levels detected (Table 3).
- However, this finding contrasts the F ST values observed between Western Australia and Northern Territory (0.116) and Queensland .
- As such, the significantly different genetic composition between Western Australia and all other populations may reflect the effects of restricted gene flow and genetic drift, which is not surprising for P.
- Regardless of the exact cause, these results suggest that there is a restriction in gene flow between geographically disparate Australian P.
- One possible ex- planation for this genetic structure is the presence of biogeographic barriers between eastern, northern, and Western Australia that caused restricted gene flow be- tween P.
- monodon populations.
- Upwelling of deep cold water along the north-western Australian coastline, which has existed since the Late Miocene period, is one biogeographical barrier known to prevent gene flow be- tween Western Australia and other Australian regions [54].
- monodon populations appear to be driven by the presence of biogeographic barriers between eastern, northern, and Western Australia that effectively limited or prevented gene flow over evolu- tionary timescales..
- Evidence for local adaptation.
- Moreover, the observed levels of gen- etic structure based on these 89 outlier SNPs agreed with the genetic structure observed when all 10,535 neu- tral SNPs were considered..
- Analysis of population structure based on 89 outlier SNPs using PCA presented a similar spatial pattern as to PCA based on 10,535 neutral SNPs in the form of three groups:.
- north Queensland, Northern Territory, and Western Australia (Nickol Bay).
- however, determination of the exact cause requires further investiga- tion.
- These outlier-based analyses suggest that key environmental factors (see Results) and geographic distance, synergistically or independently, contributed to the generation of the 89 outlier SNPs ob- served among Australian P.
- In Australia, sea surface temperatures have become significantly warmer between 1950 and 2007 along north-eastern and north-western tropical coasts by 0.12 °C and 0.11 °C per decade, respectively [70], while sea surface temperature in south-western Australia has risen by 0.026 to 0.034 °C per year between 1985 and 2004 [71].
- monodon populations and the potential functional genomics implications of the identified 89 outlier SNPs..
- Only 11 of these 89 outlier SNPs matched P.
- monodon should be managed as three separate stocks: north Queensland, Northern Territory, and Western Australia.
- greater divergence in the Western Australia population..
- This study suggests that both geographical distance and environmental factors interact to influence the genetic structure of Australian P.
- Analysis of population structure using both neutral (n = 10,535) and outlier (n = 89) SNPs suggest that Australian P.
- monodon populations have likely undergone local adaptation to region-specific thermal regimes.
- Statistical significance of each variance com- ponent was assessed using 1000 permutations for each of the following hierarchical comparisons: 1) among groups, 2) among populations within groups, and 3) within populations.
- Additional file 9).
- To test the significance of the final RDA model, the vegan function anova.cca was run with 999 permuta- tions then outlier SNPs were identified on each of.
- Additional file 1.
- Additional file 2.
- Additional file 3.
- Additional file 4.
- Additional file 5.
- Additional file 6.
- Population differentiation estimates for Penaeus monodon populations sampled using neutral and outlier loci.
- Additional file 7.
- Additional file 8.
- Additional file 9.
- Marine environmental variables (n = 23) for each of the seven geographically discrete sampling locations as determined using location-specific latitude and longitude..
- AMOVA: Analysis of molecular variance.
- Identifying environmental factors associated with the genetic structure of the New Zealand scallop: linking seascape genetics and ecophysiological tolerance.
- Population structure of the giant tiger prawn Penaeus monodon in Australian waters, determined using microsatellite markers.
- In: Proceedings of the First International Conference on the Culture of Penaeid Prawns/Shrimps, 4- 7 December 1984, Iloilo City, Philippines: Aquaculture Department, Southeast Asian Fisheries Development Center.
- Genetic structure of Penaeus monodon in Australia: concordant results from mtDNA and allozymes.
- Mitochondrial DNA variation in Indo-Pacific populations of the giant tiger prawn, Penaeus monodon.
- Estimating F-statistics for the analysis of population structure.
- RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic.
- A parallel population genomic and hydrodynamic approach to fishery management of highly-dispersive marine invertebrates: the case of the Fijian black-lip pearl oyster Pinctada margaritifera.
- Population structure of the giant tiger shrimp Penaeus monodon in Bangladesh based on variation in microsatellites and immune- related genes.
- Population genetic structure in penaeid prawns.
- Population genetic structure of Pacific white shrimp (Litopenaeus vannamei) from Mexico to Panama:.
- Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).
- Regional patterns of genetic structure among Australian populations of the mud crab, Scylla serrata (Crustacea:.
- Population genetic structure of the brown tiger prawn, Penaeus esculentus, in tropical northern Australia.
- Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes.
- Local adaptation in marine invertebrates.
- Huerlimann R, Wade NM, Gordon L, Montenegro JD, Goodall J, McWilliam S, Tinning M, Siemering K, Giardina E, Donovan D: De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome.
- Transcriptomic response to low salinity stress in gills of the Pacific white shrimp, Litopenaeus vannamei.
- Systematics and biogeography of the genus Donax (Bivalvia: Donacidae) in eastern North America.
- inbreedR: an R package for the analysis of inbreeding based on genetic markers.
- analysis of ecological data:.
- Jombart T: adegenet: a R package for the multivariate analysis of genetic markers

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