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Supplemental tables for 'Pan-microalgal dark proteome mapping via interpretable deep learning and synthetic chimeras'

Distinguishing genuine microbial proteins from contaminants remains a major bottleneck in genomics, particularly for environmental and non-model organisms where conventional homology-based tools are slow, resource-intensive, and leave large fractions of the "dark proteome" unclassified. LA4SR offers a scalable, interpretable framework that classifies algal and bacterial proteins directly from translated sequence data, achieving near-complete recall while accelerating inference by ~ 10,000-fold relative to BLASTP. By revealing that internal sequence features alone can drive robust classification, LA4SR bypasses the need for complete gene models or perfect annotations—opening new opportunities for analyzing complex microbial communities and metagenomes. Interpretability methods further link emergent amino acid signatures to evolutionary and ecological features, highlighting the potential of language models not only to accelerate genomics workflows but also to uncover new biological insights.   Table S1 | External spreadsheet. This spreadsheet contains LA4SR performance metrics, technical performance estimations, and BLAST results and runtimes of genomes comprising the algal training data. Table S2 | External spreadsheet. Captum attributions for 100 sequences each of algal and bacterial origin obtained using the LayerIntegratedGradients function. Table S3 | External spreadsheet. Influential motifs found with the DeepMotifMinerPro software introduced in this work (see Data S3). Table S4 | External spreadsheet. LA4SR and Diamond BLAST results for data from new assemblies from seen species (Fig. S7), contaminated assemblies from unseen genera (Fig. S7), and clean assemblies from unseen genera (Fig. 8). For the LA4SR results for genome assemblies from unseen genera, the genomes were published after the model was trained, and the genera shown were not included in the training dataset. Newly sequenced genomes uploaded to NCBI SRA accession SUB14799921.

Figure 4 in The first fossil spider cricket (Orthoptera: Gryllidae: Phalangopsinae): 20 million years of troglobiomorphosis or exaptation in the dark?

Figure 4. Cladogram of amphiacustine relationships (50% majority rule consensus tree of 28 equally parsimonious topologies: tree length, L = 29; consistency index, CI = 0.90; retention index, RI = 0.91). The percentage support for each node is given within an oval. Synapomorphies are indicated by numbers 1–20, and are explained in Table 2.

Figure 3 in The first fossil spider cricket (Orthoptera: Gryllidae: Phalangopsinae): 20 million years of troglobiomorphosis or exaptation in the dark?

Figure 3. Schematic reconstructions of the legs of Araneagryllus dylani gen. et sp. nov. showing the tibial armature and the distribution of the colour pattern. A, prothoracic leg. B, mesothoracic leg. C, metathoracic leg. Scale bar: 3 mm.

Figure 2 in The first fossil spider cricket (Orthoptera: Gryllidae: Phalangopsinae): 20 million years of troglobiomorphosis or exaptation in the dark?

Figure 2. Araneagryllus dylani gen. et sp. nov., camera lucida drawings of holotype AMNH DR-12-32. A, general habitus of specimen. Scale bar: 3 mm. B, left lateral view of head. Scale bar: 1 mm.

Figure 1 in The first fossil spider cricket (Orthoptera: Gryllidae: Phalangopsinae): 20 million years of troglobiomorphosis or exaptation in the dark?

Figure 1. Araneagryllus dylani gen. et sp. nov., photomicrograph of holotype AMNH DR-12-32. Scale bar: 3 mm.

Figure 5 in The first fossil spider cricket (Orthoptera: Gryllidae: Phalangopsinae): 20 million years of troglobiomorphosis or exaptation in the dark?

Figure 5. Phylogenetic inference assessment of Amphiacustina. Life histories are mapped onto the phylogeny in blue (strict troglobitic) and green (cavicolous/straminicolous epigean), and the distributions of the supposedly troglobiomorphic characters are shown on the right. Key: eyes large (+) or reduced (-); ocelli present (+) or absent/reduced (-); stridulatory apparatus (stridulum) present and functional (+) or absent/non-functional (-); auditory tympana present (+) or absent (-); in all cases, the ± symbol indicates polymorphism.

Fig. 4. 2B in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 4. 2B-PLS analysis of T. septentrionis. (A) Forewing size; (B) Forewing shape; (C) Hindwing size; and (D) Hindwing shape.

Fig. 7 in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 7. Forewing shape analysis. Mlp female (A) % of variance, (B) PC1, (C) PC2, (D) PC3. Mlp male (E) % of variance, (F) PC1, (G) PC2, (H) PC3. Wyn female (I) % of variance, (J) PC1, (K) PC2, (L) PC3. Wyn male (M) % of variance, (N) PC1, (O) PC2, (P) PC3.

Fig. 10 in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 10. FE-SEM image analysis of T. septentrionis. Forewing brown regions (A–F), and bluish-white regions (G–J) of T. septentrionis. Hindwing brown regions (K–Q), and bluish-white regions (R–T). FE-SEM image of the male pouch scale of T. septentrionis (U–X). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1. T in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 1. T. septentrionis forewing (A) with 25 landmarks; hindwing (B) with 18 landmarks. male pouch represented in white circle.

Fig. 9 in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 9. Morphospace analysis. (A) forewing PCs morphospace analysis, PC1 vs. PC2; (B) forewing CVs morphospace analysis; (C) hindwing PCs morphospace analysis, PC1 vs. PC2; (D) hindwing CVs morphospace analysis. Alphabet code used in image – first three letter code indicated as the collection site and fourth letter for sex (male or female). For eg: MlpF – Malappuram female.

Fig. 6 in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 6. Sexual wing asymmetry (male vs. female) of T. septentrionis wings validated by Discriminant function analysis (DFA). Forewing of T. septentrionis (A–D) and hindwing of T. septentrionis (E–H). Alphabet code used in image – first three letter code indicated as the collection site and fourth letter for sex (male or female). For eg: MlpF – Malappuram female.

Fig. 8 in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 8. Hindwing shape analysis. Mlp female (A) % of variance, (B) PC1, (C) PC2, (D) PC3. Mlp male (E) % of variance, (F) PC1, (G) PC2, (H) PC3. Wyn female (I) % of variance, (J) PC1, (K) PC2, (L) PC3. Wyn male (M) % of variance, (N) PC1, (O) PC2, (P) PC3.

Fig. 5 in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 5. Wing asymmetry (right or left) of T. septentrionis wings validated by Discriminant function analysis (DFA). Forewing of T. septentrionis (A–D) and hindwing of T. septentrionis (E–H). Alphabet code used in image – first three letter code indicated as the collection site and fourth letter for sex (male or female), fifth letter for wing side (right or left). For eg: MlpFR – Malappuram female right.

Fig. 2. 30 in High and lowland dependent wing phenotypic variation of the dark blue tiger butterfly, Tirumala septentrionis (Butler, 1874) (Lepidoptera: Nymphalidae) with FE-SEM wing scales nanomorphology

Fig. 2. 30 years mean climate data (A) Mlp region mean temperature, and precipitation; (B) Mean temperature of Mlp; (C) Wyn region mean temperature, and precipitation; (B) Mean temperature of Wyn.

Raw Economic Census data for full replication of Burlig and Preonas, "Out of the Darkness and Into the Light? Development Effects of Rural Electrification"

These raw data are intended to be copy-pasted into the folder "data/Economic Census" in Burlig and Preonas's replication archive

Raw SECC data (part 2) for full replication of Burlig and Preonas, "Out of the Darkness and Into the Light? Development Effects of Rural Electrification"

These raw data are intended to be coyp-pasted into the folder "data/secc data/secc_raw" in Burlig and Preonas's replication archive. This is 2 of 2 Zenodo uploads, each with 3 zipped folders. Together, all six files contain 58.9 GB of zipped raw data.

Raw SECC data (part 1) for full replication of Burlig and Preonas, "Out of the Darkness and Into the Light? Development Effects of Rural Electrification"

These raw data are intended to be copy-pasted into the folder “data/secc data/secc_raw” in Burlig and Preonas's replication archive. This is 1 of 2 Zenodo uploads, each with 3 zipped folders. Together, all six files contain 58.9 GB of zipped raw data.

Raw NSS data for full replication of Burlig and Preonas, "Out of the Darkness and Into the Light? Development Effects of Rural Electrification"

These raw data are intended to be copy-pasted into the folder "data/nss/raw" in Burlig and Preonas's replication archive