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From ∼1500 positively identified taxa, we targeted a subset of 100 taxa commonly found in marine environments.
We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species.
Figure 1A shows the agreement between γ and tree deviation for completely sampled 100 taxa trees.
Agreement between significant γ and tree deviation ranged between 40% for 20 taxa trees to 20% for 100 taxa trees.
Incomplete lineage sampling increased agreement between γ and tree deviation (52% agreement for 20 taxa trees at 50% taxon sampling to 28% agreement for 100 taxa trees at 50% taxon sampling).
To examine the power of γ to detect a known rate decrease, 50000 trees containing 100 taxa were simulated with an initial high rate followed by a slower rate using the program Phylogen v1.1 [15].
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The 173 taxa and 580 characters used therein (Supplementary Note 1) were supplemented with a further 138 taxa and 173 characters (Supplementary Note 2); the total data set consists of 311 taxa and 753 characters.
From the 410 taxa identified, 303 taxa were common enough for multivariate analyses.
Over the same period, phytoplankton diversity declined from 52 taxa in 59 samples to 42 taxa in 74 samples.
A phylogenetic analysis was conducted using 24 taxa and 59 morphological characters (Supplementary Tables 5–6.
However, at the alpha scale, urban ponds supported lower faunal diversity (mean: 22 taxa) than floodplain (mean: 32 taxa) or arable ponds (mean: 30 taxa).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com