S orientale S inexspectatum and S subsecundum 121112
S. orientale, S. inexspectatum and S. subsecundum 12/11/12
• The S. subsecundum results suggests that this species might have survived last glacial period in Beringia. It is of interest to explore whether this might be the case also for other peat mosses. • Flatberg (2005) suggested that S. inexspectatum is a homoploidal daughter species of S. subsecundum and S. orientale that could have survived in Beringia during last glacial period. • Both S. orientale and S. inexspectatum are two species with a mainly northern distribution that could have survived in Beringia during LGM. • We want to test whether S. inexspectatum is of hybrid origin of the two other species, and explore how likely it is that this species and S. orientale survived in Beringia.
Within population diversity in Alaskan populations of the three species.
Among species diversity fro Alaskan populations of the three species.
1) Hybrid origin? It is of interest to evaluate whether these taxa are different species, or whether they regularly interbreed. In particular, it is of interest to know whether plants from different taxa situated close to one another in space are more genetically similar than plants located further apart. The former would indicate rather regular mating on a a local scale, and possibly question whether these taxa are distinct species. I have tested for isolation-by-distance for plants within species and between species. It is clear from regression analyses that significant IBD exists within S. inexspectatum (blue diamonds, R 2=0. 01, P=0), within S. subsecundum (green triangles, R 2=0. 20, P=4. 82 x 10 -87), and also between the two taxa (red boxes, R 2<0. 01, P=1. 32 x 10 -6), the latter quite marginally, though. The slopes of S. inexspectatum and S. inexspectatum/S. subsecundum regression lines (uppermost and downmost lines above) are significantly different according to ANCOVA analysis (P<0. 0001). We cannot outrule that the two species mate locally, but the mating patterns are significantly different within and among taxa.
1) Hybrid origin? Same type of analyses comparing S. inexspectatum and S. orientale plants show significant IBD (green diamonds, R 2=0. 04, P=8. 65 x 10 -33), as do S. inexspectatum, but when comparing plant pairs from each of the two taxa there is a significant negative association between geographic and genetic distance (R 2=0. 01, P=7. 64 x 10 -37). This is so because some pairs of plants of the two taxa situated far away from one another are genetically similar, perhaps because the descendants of the original divergence in the two species today for some reason are geographically far away from one another.
1) Hybrid origin? Comparing population Fst with geographic distances between pairs of populations (following Rousset 1997) do not reveal a negative association between genetic and geographic distances, though, Even though the figure indicates a positive relationship between pairwise Fst and geographic distance, the regression line is marginally insignificant (P=0. 0522).
1) Hybrid origin? Ordination analysis indicate three distinct genetic clusters, even though this in itself may say little about eventual hybrid origin.
1) Hybrid origin? Structure analysis performed on distinct haplotypes within each of the three species shows that K=3 is the most likely number of clusters explaining the major genetic structure over taxa.
1) Hybrid origin? S. subsecundum S. orientale S. inexspectatum There is seemingly some admixture between the three taxa, but relatively little so. This does not support theory of hybrid origin of S. inexspectatum, since this should be reflected in significant sharing of genomic contents between S. inexspectatum and each of the two other taxa. For these three taxa, then, the most likely mode of speciation is classical divergent evolution.
1) No hybrid origin IMa analyses on S inexspectatum and S. subsecundum (20 random genotypes from each species) shows that expected time since divergence between the species in mutational units (time in years x mutation rate in years) is 0. 171 (95% CI: 0. 077 -0. 457, left graph), or 17, 100 years if assuming a yearly mutation rate of 10 -5. Migration rates between species has a highest probability at 0 in both directions.
1) No hybrid origin IMa analyses on S inexspectatum and S. orientale (20 random genotypes from each species) shows that here the expected time since divergence between the species in mutational units (time in years x mutation rate in years) is 0. 373 (95% CI: 0. 193 -1. 087, left graph), while migration from S. inexspectatum to S. orientale (m/u = 0. 42, blue graph) is higher than the other way (m/u = 0. 16, red graph). It therefore seems that introgression occurs between these species.
1) No hybrid origin IMa analyses on S subsecundum and S. orientale (20 random genotypes from each species) shows that here the expected time since divergence between the species in mutational units (time in years x mutation rate in years) is 0. 205 (95% CI: 0. 099 -0. 521, left graph). Migration rates between species has a highest probability at 0 in both directions.
1) No hybrid origin When comparing the most likely divergence times of the three species, it is clear that, again, the hybrid origin of S. inexspectatum is not supported. It is not possible based on these results to resolve the phylogenetic history of the species.
2) Survival in Beringia? S. subsecundum may have survived in Beringia. It is not possible to evaluate whether S. inexspectatum survived there, since we only have Alaskan samples of that species. However, when doing Structure analysis on Alaskan material, the most likely number of genetic clusters i K=1, which at least do not indicate that Alaska is a contact zone of any sort for S. inexspectatum. For S. orientale we have both Greenland, Asian and Alaskan samples, and by estimating time since divergence between major regions we can at least investigate whether populations in these regions are older than last glacial maximum, which should be the case if these lineages survived last glacial period up north as opposed to further south closer to the Asian popualtions that we study. Also, historical migration should not only be into Alaska (and not out of) if the plants have survived there for a very long period of time.
2) Survival in Beringia? The most likely number of clusters explaining genetic structuring within S. orientale Alaskan populations is K=1. The delta. K method indicates K=2 to be most likely (above), since it cannot be used to evaluate the likelihood of K=1, but that results in all individuals having very close to 1/2 of their genomes belonging to each of the clusters, which does not seem to be very likely. If assuming K=6 (cf peak in delta. K above), then all individuals’ genomes are divided into 6 almost exactly equal groups (each containing 16. 7% of the total genome).
Within populatiton diversity in S. orientale populations in Greenland, Alaska and Asia (pop sizes 5 or more). Average diversity is pretty much equal in Alaska and Asian populations.
2) Survival in Beringia? Within region diversity in S. orientale populations in Greenland, Alaska and Asia when populations are merged. Again, diversity seems quite similar in Asia and Alaska. Number of private alleles are higher in Alaska populations compared to those in other regions, though, with average private alleles being 3. 25 in Alaskan populations, compared to 1. 67 in Asian populations and 0. 92 in Greenland populations. Nei’d unbiased genetic diversity between regions are shown below. Greenland is more similar to Asia than Alaska.
2) Survival in Beringia? The most likely number of clusters explaining genetic structuring within all sampled S. orientale populations is K=2. Below is a figure showing differences in genetic composition of the three studied regions when assuming K=2. Alaska is to the left, Asia in the middle, and Greenland genotypes are shown to the right in the figure. There is no clear indication from this that Alaska might be some sort of «contact zone» . Alaska Asia Greenland
Structure pies with relative sizes (areas) equivalent to estimated 2 Nu within regions from mean of Migrate runs. All indiduals sampled within regions are used in the analysis. Scaled number of migrants (M=2 Nm where N is effective size of recipient population) are shown as arrows with widths equivalent to estimated M values between regions.
Structure pies with relative sizes (areas) equivalent to estimated 2 Nu within regions from mean of Migrate runs. All indiduals sampled within regions are used in the analysis. Scaled migration rates (M=m/u) are shown as arrows with widths equivalent to estimated M values between regions.
2) Survival in Beringia? IMa analyses on Alaskan, Asian and Greenland plants of S. orientale (20 random genotypes from each region). The chains have problems in mixing well, and the results might be seriously biased. The divergence between the regions (in mutational units) is reflected in Nei’s genetic distances which also are smaller for Asia-Greenland than AK-Greenland.
2) Survival in Beringia? IMa analyses on Alaskan, Asian and Greenland plants of S. orientale also indicates that migration (measured by scaled migration rate m/u) has been occurring from Greenland to Alaska(left graph), from Asia to Greenland (middle graph), and between Alaska and Asia in both directions (right graph), but seemingly more from Asia to Alaska than the other way around. Again, these estimates must be viewed as uncertain, at least for the time being.
2) Survival in Beringia? One way of testing whether divergence time estimates from IMa seems reasonable is to perform ABC analyses (as for S. subsecundum previously). Again, I have used DIY-ABC where I cannot model migration, so that divergence time estimates must be treated as minimum estimates. Based on preliminaryt IMa results and Nei’s genetic distance, I assume that Alaska diverged from Asia/Greenland clades before Greenland Asia clades split, as shown in the scenario that I have used in the ABC simulations above. The three regions are characterized by three different effective sizes, Greenland Asia split t 1 years ago, while Alaska and Asia split t 2 years ago. Altogether 2 mill simulations are used, and results are based on the 10, 000 simulations most similar to the observed data set in terms of Fst, gene diversity and number of alleles.
2) Survival in Beringia? I have assumed effective sizes of Alaska and Asia to be between 1, 000 and 100, 000 individuals each, while effective size in Greenland is set between 1 and 1, 000. I have assumed t 1 to be between 1 and 100, 000 years while t 2 is set between 1 and 200, 000 years (when t 2>t 1), and individual locus mutation rates are assumed to be between 10 -4 and 10 -6 for individuals loci, and average mutation rate across loci is also assumed to be within this range. Modal mutation rate per year over all loci is found to be 4. 76 x 10 -5(fig. above).
2) Survival in Beringia? When assuming this mutation rate, then modal values of estimated divergence times becomes t 1=9, 450 yrs (2, 570 -83, 200) for divergence between Asia and Greenland, and t 2=24, 000 yrs (9, 180 -169, 000).
2) Survival in Beringia? When comparing the results, it is interesting to note that ABC simulations get somewhat higher estimates of divergence times than IMa even though migration is not taken into account in the simulations. If we assume the estimated mutation rate is correct, then divergence times for Greenland Asia will be before LGM for both approaches, while if we assume a somewhat lowermutation rate, then IMa suggest rather recent divergence between Greenland Asia. Alaska and Asia seem to have diverged after LGM if we assume a relatively high mutation rate, then Asian and Alaskan lineages seem to have coalesced after LGM.
• S. inexspectatum is not a homoploid hybrid og S. subsecundum and S. oruentale. • It is difficult to conclude anything certain about Beringian survival based on this, I think, since it is difficult to get good estimates of coalescence times and migration rates. It is interesting, though, to note that the highest number of private alleles is found in Alaska, and that ABC methods indicate that divergence between Alaska lineages and the others should have occurred before LGM, based on different mutation rate estimates.
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