Table 1 Details of all polymorphic loci, including frequency of the most common allele across all silver eel (SE) and glass eel (GE) samples
From: Signatures of natural selection between life cycle stages separated by metamorphosis in European eel
Locus | Gene | Ireland | Iceland | Spain | |||
|---|---|---|---|---|---|---|---|
SE | GE | SE | GE | SE | GE | ||
40S_S18_1401 | 40s ribosomal protein s18 | 0.829 | 0.846 | 0.828 | 0.807 | 0.838 | 0.750 |
60S_L10A_21874 | 60s ribosomal protein L10a | 0.846 | 0.782 | 0.776 | 0.839 | 0.775 | 0.779 |
ACT_A3B_8646 | Actinin alpha 3b | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
ACTB_21752 | Beta-actin | 0.788 | 0.808 | 0.906 | 0.862 | 0.863 | 0.886 |
ACYL_13914 | Acyl carrier protein | 0.750 | 0.776 | 0.758 | 0.823 | 0.738 | 0.826 |
ADH_3 | Alcohol dehydrogenase class-3 | 0.737 | 0.859 | 0.733 | 0.690 | 0.795 | 0.761 |
ADSS_L1_15447 | Adenylosuccinate synthetase isozyme 1 | 1.000 | 0.987 | 1.000 | 0.984 | 1.000 | 1.000 |
ALD_R | Aldose reductase | 0.759 | 0.838 | --- | 0.537 | 0.859 | 0.936 |
ALDH_2_16634 | Aldehyde dehydrogenase 2 | 0.638 | 0.763 | 0.600 | 0.550 | 0.688 | 0.682 |
ANK_R_13478 | Ankyrin repeat domain-comtaining protein 1 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
ANN_A11_16176 | Annexin A11 | 0.897 | 0.923 | 0.807 | 0.919 | 0.900 | 0.852 |
ANX_2_249 | Annexin A2-A | 0.987 | 0.949 | 1.000 | 0.983 | 0.975 | 1.000 |
ARF_4_18099 | ADP-ribsylation factor 4 | 0.987 | 1.000 | 0.969 | 0.983 | 0.988 | 0.977 |
ATP_BC_259 | ATP-bindincasette sub-family A member 1 | 1.000 | 1.000 | 1.000 | 1.000 | 0.988 | 0.989 |
BPNT_1_18778 | 3'(5'),5'-biphosphate nucleotidase 1 | 0.971 | 1.000 | 0.985 | 1.000 | 1.000 | 1.000 |
CLIC_5_10148 | Chloride intracellular channel 5 | 0.568 | 0.487 | 0.521 | 0.492 | 0.521 | 0.492 |
COI_17591 | Cytochrome oxidase subunit I | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
COP_9_18132 | 266S protease regulatory subunit 7 | 0.950 | 0.962 | 0.968 | 0.968 | 0.988 | 0.966 |
CSDE_1_11069 | Cold shock domain-containing protein E1 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
CSDE_1_19713 | Cold shock domain-containing protein E1 | 0.950 | 1.000 | 0.968 | 0.983 | 0.963 | 0.977 |
CST_21113 | Cystatin precursor | 0.782 | 0.597 | 0.726 | 0.661 | 0.775 | 0.750 |
CYT_BC1_9061 | Cytochrome b-c1 complex subunit 2 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
EF_1G_4796 | Translation elongation factor 1 gamma | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
EF2_10494 | Translation elongation factor 2 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
EIF_3F_341 | Translation elongation factor 3 subunit F | 0.872 | 0.892 | 0.967 | 0.967 | 0.910 | 0.932 |
EIF_3J_11587 | Translation elongation factor 3 subunit J | 0.963 | 0.974 | 0.940 | 0.968 | 0.950 | 0.930 |
FER_H_20955 | Ferritin heavy subunit | 0.988 | 1.000 | 1.000 | 0.983 | 1.000 | 1.000 |
FGB_47 | Fibrinogen Beta Chain | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
GAPDH_20355 | Glyceraldehyde-3-phoshpate dehydrogenase | 0.962 | 0.962 | 0.969 | 0.589 | 0.974 | 1.000 |
GDE1_2508 | Glycerophosphochlorine phosphodiesterase | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
GOG_B1_15792 | Golgin sub-family B member 1 | 0.987 | 0.987 | 0.970 | 0.968 | 1.000 | 0.966 |
GPX_4_19607 | Glutathione peroxidase 4 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
HMG_T_9973 | High mobility group-T protein | 0.988 | 0.988 | 1.000 | 0.984 | 0.988 | 0.966 |
HSP_90A_15666 | Heat shock protein 90 alpha | 0.988 | 0.949 | 0.984 | 0.968 | 0.988 | 0.977 |
HSP_90B_21100 | Heat shock protein 90 beta | 0.895 | 0.949 | 0.966 | 0.984 | 1.000 | 1.000 |
HSPE_1_17854 | 10 kDa heat shock protein | 1.000 | 1.000 | 1.000 | 0.984 | 1.000 | 1.000 |
IF_RF2_19747 | Interferon regulatory factor 2 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
JAM_3_13916 | Junctional adhesion molecule 3b | 0.938 | 0.885 | 0.984 | 0.952 | 0.950 | 0.893 |
KRT_13_20618 | Keratin | 0.808 | 0.795 | 0.821 | 0.783 | 0.800 | 0.796 |
KRT_A_15738 | Keratin alpha-like | 0.975 | 1.000 | 0.952 | 0.984 | 0.960 | 0.988 |
LBL_L2_20921 | No hit | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
LDH_B_9441 | Lactase dehydrogenase B | 1.000 | 1.000 | 0.952 | 0.950 | 1.000 | 1.000 |
MDH_1393 | Malate dehydrogenase | 0.449 | 0.592 | 0.567 | 0.603 | 0.615 | 0.476 |
MYH_14857 | Superfast myosin heavy chain | 0.514 | 0.473 | 0.500 | 0.516 | 0.425 | 0.489 |
NADH_4_21742 | NADH dehydrogenase subunit 4 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
NADH_5_17101 | NADH dehydrogenase subunit 5 | 0.974 | 1.000 | 1.000 | 1.000 | 1.000 | 0.977 |
NADH1_10_21119 | NADH dehydrogenase 1 alpha subunit 10 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
NCP_2_15547 | Nucleolar complex protein 2 | 0.974 | 0.934 | 1.000 | 0.967 | 0.962 | 0.932 |
NEX_19953 | Nexilin | 0.592 | 0.608 | 0.485 | 0.567 | 0.577 | 0.523 |
NGD_21138 | Neuroguidin | 0.795 | 0.842 | 0.906 | 0.758 | 0.825 | 0.852 |
NRAP_1541 | Nebulin-related anchoring protein | 1.000 | 0.987 | 0.984 | 1.000 | 0.988 | 0.989 |
PA2G4_2600 | Proliferation associated protein 2G4 | 0.663 | 0.645 | 0.652 | 0.550 | 0.575 | 0.580 |
PFN_15113 | Profilin-2 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
PGD_18096 | 6-phosphogluconate dehydrogenase | 0.987 | 0.961 | 0.969 | 0.967 | 0.988 | 0.966 |
PGI_1 | Phosphoglucose isomerase-1 | 0.800 | 0.797 | 0.742 | 0.750 | 0.675 | 0.807 |
PGI_2 | Phosphoglucose isomerase-2 | 0.552 | 0.566 | 0.553 | 0.500 | 0.625 | 0.556 |
PGK_1_11454 | Phosphoglycerate kinase 1 | 0.947 | 0.961 | 0.909 | 0.903 | 0.975 | 0.939 |
PRP_40_16504 | Pre-mRNA-processing factor 40 homolog A | 0.829 | 0.842 | 0.833 | 0.903 | 0.846 | 0.845 |
PSA_4_21534 | Proteasome subunit alpha type-4 | 0.513 | 0.434 | 0.550 | 0.550 | 0.590 | 0.432 |
PSME_1_21196 | Proteasome activator | 0.719 | 0.583 | - | 0.621 | 0.625 | 0.667 |
RFC_3_18186 | Replication factor C subunit 3 | 0.763 | 0.776 | 0.773 | 0.717 | 0.800 | 0.784 |
RTF_1_21288 | RNA polymerase-associated protein RTF1 | 0.756 | 0.724 | 0.900 | 0.758 | 0.846 | 0.750 |
SDH_O | Sorbitol dehydrogenase | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
SLC_25A5_19808 | ADP/ATP translocase 2 | 1.000 | 1.000 | 0.967 | 0.984 | 1.000 | 1.000 |
SM_22_6449 | Transgelin | 0.963 | 0.934 | 0.946 | 0.952 | 0.950 | 0.955 |
SN4_TDR_374 | Taphylococcal nuclease domain-containing protein | 0.962 | 0.910 | 0.919 | 0.862 | 0.888 | 0.909 |
TENT_02_11046 | No hit | 0.744 | 0.711 | 0.739 | 0.774 | 0.713 | 0.784 |
TENT_03_12589 | Collagen type XXVIII alpha 1 a | 0.949 | 0.987 | 1.000 | 0.968 | 0.988 | 0.966 |
TENT_05_19704 | No hit | 1.000 | 0.987 | 0.968 | 0.983 | 1.000 | 1.000 |
TENT_06_16512 | Protein Phosphatase regulatory subunit | 0.603 | 0.581 | 0.600 | 0.533 | 0.575 | 0.625 |
TENT_07_21161 | No hit | 0.419 | 0.368 | 0.348 | 0.397 | 0.350 | 0.286 |
TNNT_2E_20968 | Troponin T2e | 0.949 | 0.885 | 0.913 | 0.875 | 0.838 | 0.895 |
TRIM_35_8416 | Tripartite motif-contaning protein 35 | 0.692 | 0.658 | 0.750 | 0.629 | 0.641 | 0.698 |
TTN_B_20952 | Titin b | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
TUB_A_19211 | Tubulin alpha 2 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
UBI_A52_5049 | Ubiquitin A-52 ribosomal protein fusion product 1 | 0.987 | 0.974 | 0.967 | 0.917 | 1.000 | 0.989 |
UGP_2_2128 | UDP-glucose pyrophosphorylase 2 | 0.671 | 0.541 | 0.531 | 0.690 | 0.663 | 0.546 |
UGP_A_2307 | Glycerol-3-phosphate transporter subunit | 0.671 | 0.603 | 0.600 | 0.613 | 0.600 | 0.636 |
UNA_SINE2_16912 | Eel Short interspersed elements | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
ZETA_15177 | Tyr 3-monooxygenase | 0.739 | 0.865 | 0.810 | 0.783 | 0.756 | 0.852 |