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Persistence and dispersal in a Southern Hemisphere glaciated landscape: the phylogeography of the spotted snow skink (Niveoscincus ocellatus) in Tasmania.

Cliff HB, Wapstra E, Burridge CP - BMC Evol. Biol. (2015)

Bottom Line: There was a high degree of mitochondrial haplotype diversity (96 unique haplotypes) and phylogeographic structure, where spatially distinct groups were associated with Tasmania's Northeast and a large area covering Southeast and Central Tasmania.Expansion in Central and Southeastern areas appears to have been more recent in both demographic and spatial contexts, than in Northeast Tasmania, which is consistent with inferences for other taxa of greater stability and persistence in Northeast Tasmania during the Last Glacial Maximum.These phylogeographic patterns indicate contrasting demographic histories of populations in close proximity to areas directly affected by glaciers in the Southern Hemisphere during the LGM.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia. hcliff11@gmail.com.

ABSTRACT

Background: The aim of this research was to identify the effects of Pleistocene climate change on the distribution of fauna in Tasmania, and contrast this with biotic responses in other temperate regions in the Northern and Southern Hemisphere that experienced glacial activity during this epoch. This was achieved by examining the phylogeographic patterns in a widely distributed Tasmanian endemic reptile, Niveoscincus ocellatus. 204 individuals from 29 populations across the distributional range of N. ocellatus were surveyed for variation at two mitochondrial genes (ND2, ND4), and two nuclear genes (β-globin, RPS8). Phylogenetic relationships were reconstructed using a range of methods (maximum parsimony, Bayesian inference and haplotype networks), and the demographic histories of populations were assessed (AMOVA, Tajima's D, Fu's Fs, mismatch distributions, extended Bayesian skyline plots, and relaxed random walk analyses).

Results: There was a high degree of mitochondrial haplotype diversity (96 unique haplotypes) and phylogeographic structure, where spatially distinct groups were associated with Tasmania's Northeast and a large area covering Southeast and Central Tasmania. Phylogeographic structure was also present within each major group, but the degree varied regionally, being highest in the Northeast. Only the Southeastern group had a signature of demographic expansion, occurring during the Pleistocene but post-dating the Last Glacial Maximum. In contrast, nuclear DNA had low levels of variation and a lack of phylogeographic structure, and further loci should be surveyed to corroborate the mitochondrial inferences.

Conclusions: The phylogeographic patterns of N. ocellatus indicate Pleistocene range and demographic expansion in N. ocellatus, particularly in the Southeast and Central areas of Tasmania. Expansion in Central and Southeastern areas appears to have been more recent in both demographic and spatial contexts, than in Northeast Tasmania, which is consistent with inferences for other taxa of greater stability and persistence in Northeast Tasmania during the Last Glacial Maximum. These phylogeographic patterns indicate contrasting demographic histories of populations in close proximity to areas directly affected by glaciers in the Southern Hemisphere during the LGM.

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TCS network for nuclear β-globin haplotypes from individuals of Niveoscincus ocellatus. Inferred haplotypes are indicated as bars on the links between haplotypes. Fill patterns indicate localities of individuals harbouring haplotypes with respect to the three mitochondrially-defined regions. Numbers correspond to explicit sampling localities of haplotypes as defined in Addtional file 1: Table S3
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Fig3: TCS network for nuclear β-globin haplotypes from individuals of Niveoscincus ocellatus. Inferred haplotypes are indicated as bars on the links between haplotypes. Fill patterns indicate localities of individuals harbouring haplotypes with respect to the three mitochondrially-defined regions. Numbers correspond to explicit sampling localities of haplotypes as defined in Addtional file 1: Table S3

Mentions: The TCS network for β-globin revealed limited phylogeographic structure and a lack of consistency with mtDNA relationships (Fig. 3). A common allele was observed in all three mitochondrially-defined regions, at 18 out of 27 localities where nuclear data were obtained. The only suggestion of geographic structuring was for alleles 13–35 (excluding 15, 16, and 31–34), which appear restricted to the western part of the island, and alleles 49–53 which were only observed at Lost Falls, Coles Bay, and Bicheno. During SAMOVA values of ΦCT had plateaued already at two groups, reflecting a western group (Mt Oakleigh, Lake St Clair, Lagoon of Islands, and Strathgordon) and the remainder. There was significant but weak population genetic structuring in the nuclear data when populations were grouped according to the inferred mtDNA groups (Table 1). However, in contrast to mtDNA, β-globin structure among populations, and among populations within groups, was more than an order of magnitude greater than that among groups (Table 1). Also in contrast to mtDNA, there was no suggestion of greater β-globin population genetic structuring in the Northeast than the Southeast. However, heterozygosity was higher in the Southeast than the Northeast, consistent with patterns of mtDNA haplotype diversity (Table 2).Fig. 3


Persistence and dispersal in a Southern Hemisphere glaciated landscape: the phylogeography of the spotted snow skink (Niveoscincus ocellatus) in Tasmania.

Cliff HB, Wapstra E, Burridge CP - BMC Evol. Biol. (2015)

TCS network for nuclear β-globin haplotypes from individuals of Niveoscincus ocellatus. Inferred haplotypes are indicated as bars on the links between haplotypes. Fill patterns indicate localities of individuals harbouring haplotypes with respect to the three mitochondrially-defined regions. Numbers correspond to explicit sampling localities of haplotypes as defined in Addtional file 1: Table S3
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4482293&req=5

Fig3: TCS network for nuclear β-globin haplotypes from individuals of Niveoscincus ocellatus. Inferred haplotypes are indicated as bars on the links between haplotypes. Fill patterns indicate localities of individuals harbouring haplotypes with respect to the three mitochondrially-defined regions. Numbers correspond to explicit sampling localities of haplotypes as defined in Addtional file 1: Table S3
Mentions: The TCS network for β-globin revealed limited phylogeographic structure and a lack of consistency with mtDNA relationships (Fig. 3). A common allele was observed in all three mitochondrially-defined regions, at 18 out of 27 localities where nuclear data were obtained. The only suggestion of geographic structuring was for alleles 13–35 (excluding 15, 16, and 31–34), which appear restricted to the western part of the island, and alleles 49–53 which were only observed at Lost Falls, Coles Bay, and Bicheno. During SAMOVA values of ΦCT had plateaued already at two groups, reflecting a western group (Mt Oakleigh, Lake St Clair, Lagoon of Islands, and Strathgordon) and the remainder. There was significant but weak population genetic structuring in the nuclear data when populations were grouped according to the inferred mtDNA groups (Table 1). However, in contrast to mtDNA, β-globin structure among populations, and among populations within groups, was more than an order of magnitude greater than that among groups (Table 1). Also in contrast to mtDNA, there was no suggestion of greater β-globin population genetic structuring in the Northeast than the Southeast. However, heterozygosity was higher in the Southeast than the Northeast, consistent with patterns of mtDNA haplotype diversity (Table 2).Fig. 3

Bottom Line: There was a high degree of mitochondrial haplotype diversity (96 unique haplotypes) and phylogeographic structure, where spatially distinct groups were associated with Tasmania's Northeast and a large area covering Southeast and Central Tasmania.Expansion in Central and Southeastern areas appears to have been more recent in both demographic and spatial contexts, than in Northeast Tasmania, which is consistent with inferences for other taxa of greater stability and persistence in Northeast Tasmania during the Last Glacial Maximum.These phylogeographic patterns indicate contrasting demographic histories of populations in close proximity to areas directly affected by glaciers in the Southern Hemisphere during the LGM.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia. hcliff11@gmail.com.

ABSTRACT

Background: The aim of this research was to identify the effects of Pleistocene climate change on the distribution of fauna in Tasmania, and contrast this with biotic responses in other temperate regions in the Northern and Southern Hemisphere that experienced glacial activity during this epoch. This was achieved by examining the phylogeographic patterns in a widely distributed Tasmanian endemic reptile, Niveoscincus ocellatus. 204 individuals from 29 populations across the distributional range of N. ocellatus were surveyed for variation at two mitochondrial genes (ND2, ND4), and two nuclear genes (β-globin, RPS8). Phylogenetic relationships were reconstructed using a range of methods (maximum parsimony, Bayesian inference and haplotype networks), and the demographic histories of populations were assessed (AMOVA, Tajima's D, Fu's Fs, mismatch distributions, extended Bayesian skyline plots, and relaxed random walk analyses).

Results: There was a high degree of mitochondrial haplotype diversity (96 unique haplotypes) and phylogeographic structure, where spatially distinct groups were associated with Tasmania's Northeast and a large area covering Southeast and Central Tasmania. Phylogeographic structure was also present within each major group, but the degree varied regionally, being highest in the Northeast. Only the Southeastern group had a signature of demographic expansion, occurring during the Pleistocene but post-dating the Last Glacial Maximum. In contrast, nuclear DNA had low levels of variation and a lack of phylogeographic structure, and further loci should be surveyed to corroborate the mitochondrial inferences.

Conclusions: The phylogeographic patterns of N. ocellatus indicate Pleistocene range and demographic expansion in N. ocellatus, particularly in the Southeast and Central areas of Tasmania. Expansion in Central and Southeastern areas appears to have been more recent in both demographic and spatial contexts, than in Northeast Tasmania, which is consistent with inferences for other taxa of greater stability and persistence in Northeast Tasmania during the Last Glacial Maximum. These phylogeographic patterns indicate contrasting demographic histories of populations in close proximity to areas directly affected by glaciers in the Southern Hemisphere during the LGM.

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