...
Post A Reply
my profile
|
directory
login
|
register
|
search
|
faq
|
forum home
»
EgyptSearch Forums
»
Egyptology
»
What's the difference between genome-wide data and mitochondrial genomes?
» Post A Reply
Post A Reply
Login Name:
Password:
Message Icon:
Message:
HTML is not enabled.
UBB Code™ is enabled.
[QUOTE]Originally posted by xyyman: [QB] cont- Five-population simulations For a divergence time of 0.16 Ne generations, 25-STRP data sets were the first to show marked peakedness at K=5, though other values of K were still broadly supported (Figure 2a). 100 STRP data sets showed an average rescaled ΔK of 0.98 for K=5 (values of rescaled ΔK close to 1 suggest strong support for a particular number of populations), whereas other values of K received little support (Figure 2a). 35-SNP data sets showed a bias toward low K-values (Figure 2b).[b] Even 10 000-SNP data sets were less efficient at detecting five populations than 100 STRPs (Figure 2)[/b]. However, 1000-SNP data sets in which all loci were ascertained based on the criterion of minor allele frequency >0.1 were near perfect at detecting the correct value of K (Figure 2b). SNP haplotypes [b]15-SNP-haplotype data sets (θ=1, see Materials and methods) offered near identical performance to 15 STRP data sets in STRUCTURE analyses[/b]. Increasing marker number from 15 to 35 did less to improve the power of SNP haplotype data sets than STRP data sets (Figure 6a). The number of polymorphic loci comprising a simulated SNP haplotype varied from run to run. Time scale When a panmictic population splits into two isolated populations, all genetic diversity found within these daughter populations is initially descended from the parent population. Unless the daughter populations sample diversity from the parent population unevenly (due to a small parent population or other biological/ecological factors), [b]genetic data will fail to distinguish the daughter populations from one another for some period of post-divergence time.[/b] In other words, spatial but not genetic structure exists. As long as gene flow is limited, [b]genetic structure eventually arises through changes in allele frequencies due to drift and the emergence of derived alleles in one population[/b] or another. STRP loci in the parent population should show greater allelic diversity than [b]SNP loci,[/b] thereby providing greater opportunity for early genetic differentiation of the daughter populations due to random drift. In addition, the high rate of STRP mutation suggests private STRP variants should appear and accumulate more quickly than new SNPs. Our results support the general expectation that the greatest power gap between SNPs and STRPs is found when divergence times are small. For divergence times <0.24 Ne generations, detection of population structure with >0.95 power [b]requires 5–15 times as many SNPs as STRPs (Figure 1).[/b] If gene flow and other complicating factors are ignored, [b]the superior efficiency of STRP data decays rapidly[/b]as divergence time increases; marker choice becomes nearly irrelevant for divergence times >0.40 Ne generations. Indeed, <50 SNPs are needed to detect structure with >0.95 power for divergence times >0.32 Ne generations. For populations with small Ne and short generation time, 0.32 Ne generations represent a relatively small number of years. Even for non-model organisms, the development of 50 unlinked SNP markers is a realistic objective The exponential form of the SNP curves in Figure 1 suggests that [b]detection of such recent population structure may require very large (perhaps impossible) numbers of unlinked SNPs.[/b] This corroborates a recent empirical result in maize (Hamblin et al., 2007 Interestingly, while the[b] power of an individual SNP never approaches that of an individual STRP (Figure 3), multi-locus SNP and STRP data sets show roughly equal power[/b] for divergence times >0.3 Ne generations (Figure 1). This finding indicates that some[b] SNP loci [/b]outperform the average SNP by a large margin, [/QB][/QUOTE]
Instant Graemlins
Instant UBB Code™
What is UBB Code™?
Options
Disable Graemlins in this post.
*** Click here to review this topic. ***
Contact Us
|
EgyptSearch!
(c) 2015 EgyptSearch.com
Powered by UBB.classic™ 6.7.3