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Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10-14 times, and that the orb web evolved at least three times. In fact, these findings principally result from inappropriate phylogenetic methodology, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e. not absent) web architectures. “Absence” of webs is simply inapplicable data. To be analyzed properly by character optimization algorithms, it must be coded as “?” or “-” because these codes, and these alone, are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (dropping even one taxon affects taxon sampling and results), and mistakes in spider natural history. In sum, methodological error: 1) causes character optimization algorithms to produce illogical results, and 2) does not distinguish absence from secondary loss. Proper methodology and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ~5-7 times, not gained 10-14 times. The orb web, specifically, may be homologous (originated only once) although lost 2-6 times.
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Supplemental Figure 1. Ace character state reconstruction of Fernandez et al. 2018 data set
Preferred 'ace' ancestral state reconstruction of web types using Fernandez et al. 2018 coding scheme (Table S1) but including Pararchaea. Optimization correctly shows four, rather than three independent origins of the orb web.
Supplemental Figure 3. Optimization of Fernandez et al. 2018 data set with non foraging silk-lined burrows and no foraging webs treated as a single character
Optimization of Fernandez et al. 2018 data set with non foraging silk-lined burrows and no foraging webs treated as a single character; spiders are unequivocally primitively webless under this scenario based on an ER model (AICc = 375.491).
Supplemental Figure 4. Ancestral state reconstruction of foraging webs - character states corrected and no foraging webs treated as missing/inapplicable
Preferred ancestral state reconstruction of web types using a corrected character coding scheme (Table S1, modified from Blackledge et al. 2009), the ER model in corHMM, and with webless taxa treated as inapplicable (-); tree modified as ultrametric; AICc = 222.8629. This hypothesis implies a single ancient origin of the orb web; spiders primitively use webs for foraging.
Supplemental Figure 5. Ancestral state reconstruction of web types using Fernandez et al. 2018 character uncorrected scoring scheme with no foraging webs scored as missing/inapplicable
An analysis of F&al’s matrix using corHMM with an ER model that includes Pararchaea, only further modified by changing “no foraging web” to missing/inapplicable optimizes irregular ground and aerial sheets as the ancestral web architectures with four independent origins of the orb web.