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Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation.

Dierickx EG, Shultz AJ, Sato F, Hiraoka T, Edwards SV - Evol Appl (2015)

Bottom Line: Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions.Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4%.These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified.

View Article: PubMed Central - PubMed

Affiliation: Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University Cambridge, MA, USA ; Department of Zoology, University of Cambridge Cambridge, UK.

ABSTRACT
Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data set of 9760 loci containing 3455 single nucleotide polymorphisms yielded estimates of genetic diversity and gene flow that were generally robust across seven different filtering and sampling protocols and suggest a low level of genomic variation (θ per site = ∼0.00002-0.00028), with estimates of effective population size (N e = ∼500-15 881) falling far below current census size. Genetic differentiation was small but detectable between Japan and Hawaii (F ST ≈ 0.038-0.049), with no F ST outliers. Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4%. These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified.

No MeSH data available.


Related in: MedlinePlus

(A) STRUCTURE plots for Black-footed Albatross using RADseq data set 2 (see Table1). Models with K = 3–5 were the most highly supported and consistently suggest two clusters corresponding to Hawaii and Japan, albeit differentiated in only a small portion of the genome. (B) Discriminant analysis of principal component (DAPC) plot based on data set 1 indicating that Hawaiian individuals from Tern and from Midway group together, but not with individuals from Izu-Torishima in Japan.
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fig05: (A) STRUCTURE plots for Black-footed Albatross using RADseq data set 2 (see Table1). Models with K = 3–5 were the most highly supported and consistently suggest two clusters corresponding to Hawaii and Japan, albeit differentiated in only a small portion of the genome. (B) Discriminant analysis of principal component (DAPC) plot based on data set 1 indicating that Hawaiian individuals from Tern and from Midway group together, but not with individuals from Izu-Torishima in Japan.

Mentions: Here, we report the STRUCTURE results for data set 2 (1 SNP per locus), because STRUCTURE can be sensitive to linked loci. The results of the other six data sets were qualitatively similar. The log-likelihood of the model was very similar across K = 1–5 (not shown), but maximized at K = 3 clusters, whereas K = 5 was favoured by the Delta K test (Earl and vonHoldt 2012; Fig.5A). Models with K = 3, 4 or 5 showed evidence of two major clusters dividing Japan and Hawaii, albeit for a small portion of the genome (Fig.5A). Despite the high amount of shared SNP variation genome-wide between Izu-Torishima and the Hawaiian islands, STRUCTURE detected more differentiation between Japan and Hawaii than between the two Hawaiian islands (Fig.5A).


Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation.

Dierickx EG, Shultz AJ, Sato F, Hiraoka T, Edwards SV - Evol Appl (2015)

(A) STRUCTURE plots for Black-footed Albatross using RADseq data set 2 (see Table1). Models with K = 3–5 were the most highly supported and consistently suggest two clusters corresponding to Hawaii and Japan, albeit differentiated in only a small portion of the genome. (B) Discriminant analysis of principal component (DAPC) plot based on data set 1 indicating that Hawaiian individuals from Tern and from Midway group together, but not with individuals from Izu-Torishima in Japan.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4516419&req=5

fig05: (A) STRUCTURE plots for Black-footed Albatross using RADseq data set 2 (see Table1). Models with K = 3–5 were the most highly supported and consistently suggest two clusters corresponding to Hawaii and Japan, albeit differentiated in only a small portion of the genome. (B) Discriminant analysis of principal component (DAPC) plot based on data set 1 indicating that Hawaiian individuals from Tern and from Midway group together, but not with individuals from Izu-Torishima in Japan.
Mentions: Here, we report the STRUCTURE results for data set 2 (1 SNP per locus), because STRUCTURE can be sensitive to linked loci. The results of the other six data sets were qualitatively similar. The log-likelihood of the model was very similar across K = 1–5 (not shown), but maximized at K = 3 clusters, whereas K = 5 was favoured by the Delta K test (Earl and vonHoldt 2012; Fig.5A). Models with K = 3, 4 or 5 showed evidence of two major clusters dividing Japan and Hawaii, albeit for a small portion of the genome (Fig.5A). Despite the high amount of shared SNP variation genome-wide between Izu-Torishima and the Hawaiian islands, STRUCTURE detected more differentiation between Japan and Hawaii than between the two Hawaiian islands (Fig.5A).

Bottom Line: Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions.Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4%.These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified.

View Article: PubMed Central - PubMed

Affiliation: Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University Cambridge, MA, USA ; Department of Zoology, University of Cambridge Cambridge, UK.

ABSTRACT
Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data set of 9760 loci containing 3455 single nucleotide polymorphisms yielded estimates of genetic diversity and gene flow that were generally robust across seven different filtering and sampling protocols and suggest a low level of genomic variation (θ per site = ∼0.00002-0.00028), with estimates of effective population size (N e = ∼500-15 881) falling far below current census size. Genetic differentiation was small but detectable between Japan and Hawaii (F ST ≈ 0.038-0.049), with no F ST outliers. Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4%. These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified.

No MeSH data available.


Related in: MedlinePlus