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<h4>Genetic structure among regions</h4> <p> The mtDNA marker used here revealed strong genetic structure among northern, central and southern populations of <em>A. polyacanthus </em>on the GBR. This result is consistent with previous findings of strong allozyme structure between northern region bi-coloured and southern region black morphs of this species <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B59">59</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B60">60</a>] and indicates the presence of further strong structuring among bi-coloured morphs between northern and central regions. This pattern of genetic structure is consistent with large-scale water circulation patterns on the GBR, which are characterised by an offshore outer shelf bifurcation of the South Equatorial Current into a northern flowing Hiri and a southern flowing East Australian Currents around 16°S latitude <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B63">63</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B64">64</a>] positioned between the Northern and Central regions examined here. At smaller spatial scales this inflow generates complex continental shelf current patterns modulated by winds, tides and local reef matrix densities <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B65">65</a>]. Such cross-shelf currents differ among regions and are predominantly weaker and flow in an onshore direction in the northern region, are stronger and flow in an offshore direction in the central and southern regions of the GBR <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B65">65</a>]. The genetic structure of <em>A. polyacanthus </em>was consistent with these cross shelf current patterns. Continental shelf effects were detected in the northern but not in the central region and a higher abundance of individuals in a second divergent lineage was found on more inshore northern reefs (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F4">4</a>). Our analyses also indicate that the spatial structure among regions is best described by an isolation-by-distance model of dispersal in which genetic exchange is more likely among neighbouring locations than more distant ones (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F2">2</a>). While patterns of isolation-by-distance have been reported at large spatial scales in marine organisms [e.g. <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B66">66</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B67">67</a>]], our study reports one of very few examples of such dynamics at smaller spatial scales in a coral reef fish [see also <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B44">44</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B68">68</a>]] and suggests that a migration-drift equilibrium may be met at this spatial scale <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B8">8</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B69">69</a>]. </p> <h4>Genetic structure within regions</h4> <p> Strong genetic structure was evident within all three regions and was attributable to continental shelf position in the northern region (Table <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T2">2b</a>), however, no evidence of isolation-by-distance was found within any of the regions. These results are consistent with a departure from migration-drift equilibrium and a greater importance of genetic drift over migration in structuring this species at smaller spatial scales <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B8">8</a>]. It is possible, however, that reduced statistical power resulting from fewer reefs being compared within regions than between prevented the detection of isolation-by-distance within regions where it existed. A reduction in the number of reefs compared among regions to the number of reefs compared within regions detected a significant correlation between genetic and geographical distance. Although larger sample sizes within regions will be required to resolve this issue fully, this result indicates that our tests were powerful enough to detect isolation-by-distance even when fewer comparisons were included. Genetic differentiation among reefs within regions was comparable (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F3">3a – c</a>) and generally very high. For example, Lizard Island (LIZ) and North Direction Island (NDR) are separated by less than 10 km but have a <span>Φ</span><sub>ST </sub>value of 0.26 and Martin Reef (MAR) and Linnet Reef (LIN) are separated by less than 6 km and have a <span>Φ</span><sub>ST </sub>value of 0.33. Such differentiation is among the highest recorded for any coral reef fish at such small spatial scales [e.g. <a></a><a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B58">58</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B70">70</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B71">71</a>]] and is, despite obvious difficulties in comparing differentiation based on different molecular markers and taxa, comparable to values obtained for many direct-developing coral reef organisms at similar spatial scales <a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B45">45</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B47">47</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B48">48</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B57">57</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B72">72</a>-<a href="http://www.biomedcentral.com/1471-2148/8/248#B75">75</a>]. This finding suggests that the spatial patterns described by this study may be broadly applicable to many direct developing coral reef species. </p> <h4>Asymmetric migration and re-colonisation of reefs within regions</h4> <p> Despite the strong genetic structure of <em>A. polyacanthus </em>among reefs, our analyses indicated that migration rates were substantial and asymmetric in between 20 – 40% of comparisons. These patterns indicate a departure from the island model (which assumes equal migration rates among all populations) and add to a growing number of examples documenting asymmetric migration rates using genetic evidence [e.g. <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B32">32</a>]]. Variation in migration rates may affect the dynamics of meta-populations and spatial structure of species in several ways <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B22">22</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B26">26</a>]. If habitat patches differ in quality and local populations differ in size, migration from larger source populations into smaller sink populations may facilitate their long-term persistence by rescuing them from extinction <a></a><a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B24">24</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B26">26</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B27">27</a>]. If such dynamics are spatially and temporally persistent they should be identifiable by low genetic differentiation, and high and mostly uni-directional migration from sources to sinks. The strength of genetic differentiation was largely congruent with the Bayesian estimates of migration (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F3">3</a>) and insignificant or small pairwise <span>Φ</span><sub>ST </sub>values were often (e.g. DAY – LIZ; BRI – PIT; NDR – MAR; OTI – POL; SYK – POL) but not always (e.g. NDR – LIN) associated with asymmetric migration rates. The direction of migration however, did not identify any obvious sources or sinks in <em>A. polyacanthus </em>since most potential sinks (reefs that received a higher number of immigrants) also produced substantial numbers of emigrants as expected for potential source reefs (e.g. LIZ, TRU, POL, OTI: Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F3">3d – f</a>). The patterns uncovered here may indicate that migration at local scales is a stochastic process, although further sampling would be required to fully determine this. A second process by which asymmetric migration can affect the spatial structure of a meta-population is through the re-colonisation of extinct patches <a></a><a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B18">18</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B19">19</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B35">35</a>]. Asymmetric colonisation events from a single patch such as those observed among some reefs here (e.g. MYR to TRU; POL to OTI) could result in more genetic structure among more recently (re)-colonised patches through the effect of genetic drift associated with such founder effects, but then erase this structure over time as more migrants are received (propagule-pool model). The strength of fixation (<span>Φ</span><sub>ST</sub>) was greater between younger, more recently expanded populations compared to that found between reefs that expanded longer ago providing support for the colonisation model (Table <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T3">3</a>). This study therefore adds to only a handful of investigations that have explored, and largely supported, the predictions from such meta-population colonisation models [reviewed by <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B35">35</a>]]. This conclusion, however, is based on coalescence estimates with considerable variation and a small number of comparisons, and should, therefore, be interpreted with caution. It does imply, however, that population size reductions/extinctions and genetic bottlenecks/founder effects associated with re-colonisation of such reefs have the potential to increase the level of genetic structure in this meta-population, at least over relatively short evolutionary time scales. </p> <h4>Genetic diversities and historical population demography</h4> <p> Genetic diversities recorded here were generally high and comparable with those reported for other coral reef fishes using the same mitochondrial marker [e.g. <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B51">51</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B71">71</a>] but see <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B76">76</a>]] supporting the general observation of high genetic diversity in many coral reef fish species <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B50">50</a>]. Intra-specific variation in genetic diversities in <em>A. polyacanthus </em>was substantial both among reefs and regions and greater than those previously reported among reef fish populations separated by more than 17000 km <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B68">68</a>], or taxonomically distinct species from different environments <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B51">51</a>]. Our analyses also indicated consistent and substantial variation in historical population growth patterns of <em>A. polyacanthus </em>among reefs and regions on the GBR (Table <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T1">1</a>, <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T4">4</a>, <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T5">5</a>, Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F4">4</a> and <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F5">5</a>). The central and southern regions, and many (although not all) reefs within them, were characterised by population expansion indicated by mismatch analysis and neutrality indices. In particular, the southern region, located close to the species' southern border, was characterised by lower mitochondrial genetic diversity and population expansion rates 6 – 19 times greater than the central and northern regions. These lower genetic diversities and higher population expansion rates could be the result of either demographic or spatial range expansions. Spatial range expansion is particularly worth considering given the proximity of the sampled reefs in the southern region to the geographical range limit of <em>A. polyacanthus</em>. The genetic signatures of demographic and range expansion models can be very similar <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B77">77</a>] particularly when migration rates among sub-populations are high <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B78">78</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B79">79</a>]. When migration rates are low, spatially expanding populations may display multi-modal mismatch distributions, similar to those expected under constant population size models <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B78">78</a>]. While it is possible that both the central and southern regions represent a spatial range expansion of this species in a north to south direction along the GBR, we consider this unlikely for two reasons. First, the distribution of colour morphs and lineages within colour morphs were confined to regions. If north-to-south range expansion were occurring in this species, we would have expected colonisation of both northern lineages in the central region and colonisation of black and white lineages in the southern region. This was not the case (see Additional file <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/suppl/S2">2</a>). Second, we did not sample any multi-modal mismatch distributions in the central and southern regions as expected in spatially expanding species with relatively low migration rates (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F4">4</a>). The demographic expansion model therefore appears a more parsimonious explanation for our results, although further sampling in the southern region would be required before these hypotheses can be definitively distinguished. In all, this suggests that genetic bottlenecks and founder effects arising through colonisation of new or extinct sub-populations may affect the meta-population dynamics towards the edges of a species' geographic range to a greater extent than within more centrally located regions <a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B42">42</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B43">43</a>]. </p> <div> <div> <blockquote> <p> <strong>Additional file 2.</strong> Tree of unique haplotypes. The phylogenetic structure of <em>A. polyacanthus </em>was explored using Bayesian inference implemented in MrBayes 3.0B4 <a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B107">107</a>]. The analysis included 92 unique haplotypes found in the 283 individuals discussed above, 10 black morph individuals from Great Keppel Island (23°10S; 150°57E) and three black and white morph individuals from the Solomon Islands (9°24S; 160°32E). The analysis was performed using a Markov Chain Monte Carlo search with four chains for one million generations. Trees were sampled every 100 generations and the first 100,000 generations were discarded as burn-in. The tree was out-group rooted using two closely related species, <em>Amphiprion melanopus </em>and <em>A. akindynos</em>. Credibility values were obtained from a majority rule consensus tree of the last 2000 trees and values greater than 90% are indicated on the major nodes of the tree. </p> <p> Format: PDF Size: 529KB <a href="http://www.biomedcentral.com/content/supplementary/1471-2148-8-248-s2.pdf">Download file</a> </p> </blockquote> <p> <a href="http://www.adobe.com/products/acrobat/readstep.html"><br></a> </p> </div> </div> <p> There were substantial differences in the mismatch distributions and population growth rates among reefs within regions (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F4">4</a>, <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F5">5</a>, Table <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T4">4</a>). Most reefs had comparably high genetic diversities (Table <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T1">1</a>), low population expansion rates, and times that were significantly different from 0 (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F5">5</a>). This provides evidence for constant population size and was further supported by mismatch analysis for four of these reefs (YON, MYR, BRO, POL). Three reefs Trunk (TRU), One Tree Island (OTI) and Sykes Reef (SYK) were characterised by low genetic diversities (Table <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T1">1</a>), uni-modal, left-skewed mismatch distributions (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F4">4</a>), high population growth rates and expansion times that could not be distinguished from 0 (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F5">5</a>) all consistent with population expansion. Mismatch analysis indicated population expansion in a further three reefs (BRI, ORP, PIT) from the central region. In concert, these results provide evidence for recent population bottlenecks and/or local extinctions on these reefs. Four reefs in the northern region (NDR, LIZ, LIN, MAR) had very high nucleotide diversities and bimodal mismatch distributions that were most likely the result of constant population sizes (as indicated by mismatch analysis for LIN, Table <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/table/T4">4</a>) and the presence of approximately equal numbers of individuals from two differentiated lineages at these locations (Figure <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/figure/F4">4</a>, Additional file <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/suppl/S2">2</a>). The presence and maintenance of two or more divergent lineages across relatively small spatial scales is emerging as a feature of many coral reef organisms <a></a><a></a><a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B51">51</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B80">80</a>-<a href="http://www.biomedcentral.com/1471-2148/8/248#B82">82</a>]. The dynamic history of coral reefs associated with sea-level fluctuations from the mid Miocene to the end of the Pleistocene has been implicated as the major evolutionary force promoting divergence and subsequent coalescence in species with high dispersal potential [e.g. <a></a><a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B51">51</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B76">76</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B82">82</a>]]. Because of the limited dispersal potential of <em>A. polyacanthus</em>, deep genetic divergences may evolve among locations in the absence of sea-level fluctuations and significant genetic structure has previously been found between GBR, Coral Sea and Melanesian populations of this species [<a></a><a></a>[<a href="http://www.biomedcentral.com/1471-2148/8/248#B57">57</a>,<a href="http://www.biomedcentral.com/1471-2148/8/248#B60">60</a>], Additional file <a></a><a href="http://www.biomedcentral.com/1471-2148/8/248/suppl/S2">2</a>]. It is therefore likely that colonisation events from these locations may be the source of the second lineage prominent on the inshore northern reefs highlighting the potential for long distance dispersal in this brooding species. The absence of this second lineage from several northern, all central and southern reefs, however, indicates that this is likely to be a rare and/or recent event. </p>
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