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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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Bayesian inference tree for Niveoscincus ocellatus based on 1420 bp of ND2 and ND4 mitochondrial DNA sequence. Branch lengths are scaled relative to the scale bar. Posterior probabilities >0.95 are indicated by the black dots, with values at key nodes also specified above branches at nodes. Bootstrap values from parsimony analysis, where they exceeded 70 %, are also listed below branches. Numbers in parentheses indicate the number of individuals from a site exhibiting that haplotype. The branch leading to the outgroup N. greeni was truncated to aid visualisation, and likewise that leading to N. pretiosus was removed. Grey boxes highlight regionally monophyletic areas within the major clades
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Fig2: Bayesian inference tree for Niveoscincus ocellatus based on 1420 bp of ND2 and ND4 mitochondrial DNA sequence. Branch lengths are scaled relative to the scale bar. Posterior probabilities >0.95 are indicated by the black dots, with values at key nodes also specified above branches at nodes. Bootstrap values from parsimony analysis, where they exceeded 70 %, are also listed below branches. Numbers in parentheses indicate the number of individuals from a site exhibiting that haplotype. The branch leading to the outgroup N. greeni was truncated to aid visualisation, and likewise that leading to N. pretiosus was removed. Grey boxes highlight regionally monophyletic areas within the major clades

Mentions: A total of 95 unique haplotypes were identified from the 204 N. ocellatus sampled, with 183 (12.9 %) of 1420 characters variable and 147 (10.4 %) parsimony-informative. Tree topologies were very similar between maximum parsimony and Bayesian tree-building methods, only differing in relationships at shallow phylogenetic levels, while the composition of major clades were consistent across analyses; therefore only the Bayesian inference tree is presented (Fig. 2; parsimony tree Additional file 1: Figure S1). Four major clades are evident: a ‘Northeastern’ clade, a ‘Southeastern’ clade, a ‘Northwestern’ clade, and a clade of three Lake Mackenzie haplotypes (Fig. 2). The relationships among these four clades were uncertain and received low topological support, but with the exception of the three Lake Mackenzie haplotypes each clade received posterior probability greater than 0.95. The topology obtained from BEAST analysis using a coalescent tree prior and a strict, externally calibrated, molecular clock was compatible with that described above, and suggests that the major lineages diverged during the last 2 Myr (Additional file 1: Figure S2).Fig. 2


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)

Bayesian inference tree for Niveoscincus ocellatus based on 1420 bp of ND2 and ND4 mitochondrial DNA sequence. Branch lengths are scaled relative to the scale bar. Posterior probabilities >0.95 are indicated by the black dots, with values at key nodes also specified above branches at nodes. Bootstrap values from parsimony analysis, where they exceeded 70 %, are also listed below branches. Numbers in parentheses indicate the number of individuals from a site exhibiting that haplotype. The branch leading to the outgroup N. greeni was truncated to aid visualisation, and likewise that leading to N. pretiosus was removed. Grey boxes highlight regionally monophyletic areas within the major clades
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Bayesian inference tree for Niveoscincus ocellatus based on 1420 bp of ND2 and ND4 mitochondrial DNA sequence. Branch lengths are scaled relative to the scale bar. Posterior probabilities >0.95 are indicated by the black dots, with values at key nodes also specified above branches at nodes. Bootstrap values from parsimony analysis, where they exceeded 70 %, are also listed below branches. Numbers in parentheses indicate the number of individuals from a site exhibiting that haplotype. The branch leading to the outgroup N. greeni was truncated to aid visualisation, and likewise that leading to N. pretiosus was removed. Grey boxes highlight regionally monophyletic areas within the major clades
Mentions: A total of 95 unique haplotypes were identified from the 204 N. ocellatus sampled, with 183 (12.9 %) of 1420 characters variable and 147 (10.4 %) parsimony-informative. Tree topologies were very similar between maximum parsimony and Bayesian tree-building methods, only differing in relationships at shallow phylogenetic levels, while the composition of major clades were consistent across analyses; therefore only the Bayesian inference tree is presented (Fig. 2; parsimony tree Additional file 1: Figure S1). Four major clades are evident: a ‘Northeastern’ clade, a ‘Southeastern’ clade, a ‘Northwestern’ clade, and a clade of three Lake Mackenzie haplotypes (Fig. 2). The relationships among these four clades were uncertain and received low topological support, but with the exception of the three Lake Mackenzie haplotypes each clade received posterior probability greater than 0.95. The topology obtained from BEAST analysis using a coalescent tree prior and a strict, externally calibrated, molecular clock was compatible with that described above, and suggests that the major lineages diverged during the last 2 Myr (Additional file 1: Figure S2).Fig. 2

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.

Show MeSH