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Table 1 The phylogenetic distribution of HGT genes. The number and percentage of foreign genes unique to species, sister species pairs, the genus Rotaria and shared between Rotaria and Adineta, based on two ortholog assignment methods: 1) reciprocal BLAST and 2) Markov clusters. The unbracketed numbers show presence/absence in transcriptomes. The bracketed numbers are adjusted for false negative rates estimated from BLAST matches to the R. magnacalcarata genome (see Methods)

From: Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats

Ortholog method Species Unique to species Sister species Rotaria Rotaria + Adineta Total
   Number Percentage (%) Number Percentage (%) Number Percentage (%) Number Percentage (%)  
Method 1: Reciprocal BLAST mag 76 (53) 13.1 (6.7) 27 (37) 4.6 (4.7) 154 (351) 26.5 (43.9) 324 (356) 55.8 (44.7) 581 (798)
soc 127 (94) 22.1 (12.3) 27 (37) 4.7 (4.9) 128 (309) 22.3 (40.5) 293 (322) 51 (42.3) 575 (763)
sor 350 (263) 29.6 (18.8) 222 (308) 18.8 (22) 129 (294) 10.9 (21) 483 (531) 40.8 (38.1) 1,184 (1,396)
tar 497 (364) 37 (23.3) 222 (308) 16.5 (19.7) 155 (374) 11.5 (23.9) 469 (516) 34.9 (33) 1,343 (1,561)
Method 2: Markov clusters mag 67 (46) 6.1 (3.5) 53 (53) 4.8 (4) 305 (489) 27.9 (37) 668 (735) 61.1 (55.6) 1,093 (1,322)
soc 126 (90) 11.8 (7.2) 53 (53) 5 (4.2) 271 (422) 25.4 (34) 617 (679) 57.8 (54.6) 1,067 (1,244)
sor 280 (201) 17.3 (11.3) 248 (247) 15.3 (13.9) 263 (421) 16.3 (23.7) 827 (910) 51.1 (51.1) 1,618 (1,779)
tar 303 (211) 17.9 (11.3) 248 (247) 14.6 (13.3) 321 (500) 18.9 (26.9) 823 (905) 48.6 (48.6) 1,695 (1,863)
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