Table 1.
Summary of Y-linked transfers
| Species | Transfer ID | Transfer type | Donor(s) | ω | Expression | Age (Ky) |
| D. mauritiana | Dmau_2L_6.65 | Ambig | Hrb27C | 1.02,Filt | NA | 673 [309,1885] |
| Dmau_2L_9.1 | Ambig | numb | nORF | NA | 460 [211,1287] | |
| Dmau_2L_12.3 | DNA | CG5787;Pih1D1 | Filt;Filt,Filt | NA | 609 [280,1706] | |
| Dmau_2L_15.71 | RNA | CG4455 | 1.38 | NA | 517 [237,1446] | |
| Dmau_2R_0.15* | DNA | NA | NA | NA | 429 [197,1201] | |
| Dmau_2R_4.35 | RNA | 14–3-3zeta | nORF | NA | 383 [176,1072] | |
| Dmau_2R_8.65 | DNA | L;ttv;LamC | nORF;nORF;0.14† | NA | 153(240) [70(110),429(672)] | |
| Dmau_2R_9.41* | RNA | SRPK | Filt | NA | 429 [197,1201] | |
| Dmau_2R_13.28 | DNA | CG7229 | Filt | NA | 80 [37,224] | |
| Dmau_2R_18.4 | RNA | CG3511 | 0.95 | NA | 147 [68,413] | |
| Dmau_2R_19.04 | DNA | NA | NA | NA | 305 [140,854] | |
| Dmau_3L_0.16 | RNA | CG13876 | 0.30 | NA | 158 [73,443] | |
| Dmau_3L_2.15 | DNA | NA | NA | NA | 98 [45,273] | |
| Dmau_3L_7.55 | DNA | CG7492;Ank2 | nORF;Filt | NA | 213 [98,597] | |
| Dmau_3L_22.2 | DNA | NA | NA | NA | 957 [439,2679] | |
| Dmau_3R_0.34* | DNA | NA | NA | NA | 380 [174,1064] | |
| Dmau_3R_1.23 | DNA | Nmdar1;dmau_PG00479 | nORF;nORF | NA | 282 [130,790] | |
| Dmau_3R_2.13 | DNA | NA | NA | NA | 28 [13,78] | |
| Dmau_3R_13.94 | DNA | Tctp | 0.14 | NA | 282 [129,790] | |
| Dmau_X_3.07 | DNA | CG16781;CG12206 | Filt,Filt;0.11† | NA | 683(778) [314(357),1913(2180)] | |
| Dmau_X_8.42* | Ambig | His3.3B | 2.83 | NA | 436 [200,1221] | |
| Dmau_X_20.09* | DNA | NA | NA | NA | 535 [246,1499] | |
| D. melanogaster | Dmel_2L_4.46 | DNA | Gs1l;RpL27A | nORF;nORF | NA | 45 [21,125] |
| Dmel_2L_12.86 | DNA | NA | NA | NA | 174 [80,487] | |
| Dmel_2L_19.94 | DNA | sick | nORF | NA | 559 [256,1564] | |
| Dmel_2L_22.75 | DNA | NA | NA | NA | 697 [320,1951] | |
| Dmel_2R_0.09 | DNA | NA | NA | NA | 624 [287,1748] | |
| Dmel_2R_0.57 | DNA | NA | NA | NA | 303 [139,848] | |
| Dmel_2R_2.32 | DNA | NA | NA | NA | 315 [145,883] | |
| Dmel_3L_23.41 | DNA | NA | NA | NA | 443 [203,1241] | |
| Dmel_3L_24.3 | DNA | NA | NA | NA | 343 [158,962] | |
| Dmel_3R_17.04 | Ambig | CR43975 | nORF | NA | 516 [237,1444] | |
| Dmel_3R_20.95 | DNA | vig2;Mocs2/CG42503;Clbn;Bili | 0.53;0.45;0.64;Filt | NA | 463(497) [213(391),1297(1391)] | |
| Dmel_X_12.65 | DNA | ade5;CG12717 | nORF;Filt | NA | 725 [333,2031] | |
| Dmel_X_12.66 | DNA | NA | NA | NA | 430 [197,1204] | |
| D. simulans | Dsim_2L_11.91 | DNA | bru1 | Filt | 2/11 [3] | 169 [77,472] |
| Dsim_2L_12.3 | DNA | CG5787;Pih1D1 | Filt;nORF | 14/17 [4.9];4/6 [1.2] | 813 [373,2275] | |
| Dsim_2L_15.71 | RNA | CG4455 | nORF | 22/22 [8.7] | 197 [90,551] | |
| Dsim_2L_19.34 | DNA | NA | NA | NA | 351 [161,983] | |
| Dsim_2R_0.06 | DNA | NA | NA | NA | 267 [122,747] | |
| Dsim_2R_4.35 | RNA | 14–3-3zeta | Filt | 0/2 [18.5] | 90 [41,252] | |
| Dsim_2R_9.41* | RNA | SRPK | Filt | 25/29 [575.6] | 204 [94,573] | |
| Dsim_3L_7.55 | DNA | CG7492;Ank2 | nORF;0.63,0.62 | 8/9 [11.2];32/36 [6.6] | 383 [176,1072] | |
| Dsim_3L_10.87 | RNA | Sod | 0.09† | 1/8 [10.4] | 182(477) [84(219),509(1335)] | |
| Dsim_3L_22.2* | DNA | NA | NA | NA | 408 [187,1142] | |
| Dsim_3R_4.18 | DNA | NA | NA | NA | 161 [74,452] | |
| Dsim_3R_12.73 | DNA | NA | NA | NA | 96 [44,269] | |
| Dsim_3R_13.94* | DNA | Tctp | nORF | 0/30 [17.4] | 197 [90,551] | |
| Dsim_X_7.6 | RNA | Sdt | Filt | 11/30 [2.3] | 374 [172,1047] | |
| Dsim_X_15.22 | RNA | Cyp1 | 0.78 | 0/18 [4.5] | 222 [102,623] | |
| Dsim_X_20.2 | DNA | CG17450/CG32819/CG32820 | Filt | 0/8 [19.5] | 268 [123,750] |
A total of 45 unique Y-linked transfers were detected, arising either as retrocopies (RNA), as DNA translocations (DNA), or via an undetermined mode (Ambig). Twenty-five of the Y-linked transfers harbored at least one gene—i.e., were GeTYs [donor gene names in donor(s) column]—with six GeTYs being shared between species (italicized rows). In all columns, GeTYs comprising several genes have each gene name separated by semicolons, with those having identical gene models being separated by a forward slash. Purifying selection was detected for three GeTYs (ω column; genes having more than one detected ORF being further delineated by a comma), whereas others showed evidence of degeneration (ω column; nORF = no ORF; Filt = Y-linked or donor CDS lacked either a start or stop codon, contained an inactivating mutation, or >10% Y-linked codons were missing in donor alignment; Dataset S6). Two publicly available testes-specific RNA-Seq datasets (23, 24) revealed weak evidence for Y-linked GeTY expression, with most GeTYs having low relative expression (i.e., the fraction of diagnostic exonic sites where the Y-linked allele contributed >1% of the total coverage for that site; fraction shown in expression column) and low absolute expression (i.e., mean coverage of Y-linked alleles mapping to diagnostic exonic sites; values in square brackets in expression column). Point estimates of transfer times revealed evolutionarily recent origins, with the oldest transfer arising around 1 Mya (see age column; error margins in square brackets, age estimates for putatively functional genes after correcting for purifying selection shown in standard parentheses; Dataset S7). For some Y-linked transfers, multiple haplotypes were detected in male-specific short read data suggesting that these transfers likely underwent subsequent duplication on the Y chromosome, with GeTY Dsim_2R_9.41 also showing signs of an additional autosomal/X-linked duplication. Age and expression estimates may be unreliable for these Y-linked transfers.
Putative duplicated transfers.
Postmultiple testing correction significance (q < 0.05).