DOI: 10.6084/m9.figshare.22921697.v2
title: Supplementary Tables for the manuscript, <strong>Quantitative trait loci underlying a speciation phenotype.</strong>

description: <strong>Table S1 | </strong>Summary of scaffolds associated with <em>L. kohalensis </em>x <em>L. paranigra </em>pulse rate QTL across studies. Column headers are defined as follows; <em>scaffold</em>: scaffold identity, <em>size</em>: size (in bp) of scaffold, <em>LG</em>: linkage group on which the scaffold falls, <em>start_position</em>: genomic location of start of scaffold, <em>end_position</em>: genomic location of end of scaffold, <em>id_source</em>: study in which the scaffold has been identified, <em>peak_location_reanalysis</em>: location (in cM) of given QTL peak in present study, <em>scaffold_type_reanalysis</em>: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in present study, <em>peak_location_finemap</em>: location (in cM) of given QTL in Xu & Shaw 2019, <em>scaffold_type_reanalysis</em>: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in Xu & Shaw 2019. <strong>Table S2 | </strong>Annotations and genomic locations of <em>L. kohalensis </em>transcripts (reciprocal best BLAST hits only). Column headers are defined as follows; <em>transcript: </em>transcript identifier, <em>scaffold</em>: scaffold to which the transcript maps, <em>start: </em>genomic location of start of transcript, <em>stop</em>: genomic location of end of transcript, <em>direction</em>: indicator of which direction the transcript is transcribed in, <em>Entry_Name</em>: Uniprot ID assigned to transcript, <em>Protein_Name</em>: Protein name associated with Uniprot_ID, <em>Gene_Name</em>: Gene names associated with Uniprot_ID, <em>Gene_Ontology_IDs</em>: GO IDs associated with Uniprot_ID, <em>pident</em>: percentage of identical matches, <em>length: </em>length (in bp) of sequence overlap, <em>mismatch</em>: number of mismatches, <em>gapopen</em>: number of gap openings, <em>qstart</em>: start of alignment in query, <em>qend</em>: end of alignment in query, <em>sstart:</em> start of alignment in subject, <em>send</em>: end of alignment in subject, <em>evalue</em>: expect value, <em>bitscore</em>: bit score. <strong>Table S3 | </strong>Annotations and genomic locations of <em>L. paranigra </em>transcripts (reciprocal best BLAST hits only). Column headers are defined as follows; <em>transcript: </em>transcript identifier, <em>scaffold</em>: scaffold to which the transcript maps, <em>start: </em>genomic location of start of transcript, <em>stop</em>: genomic location of end of transcript, <em>direction</em>: indicator of which direction the transcript is transcribed in, <em>Entry_Name</em>: Uniprot ID assigned to transcript, <em>Protein_Name</em>: Protein name associated with Uniprot_ID, <em>Gene_Name</em>: Gene names associated with Uniprot_ID, <em>Gene_Ontology_IDs</em>: GO IDs associated with Uniprot_ID, <em>pident</em>: percentage of identical matches, <em>length: </em>length (in bp) of sequence overlap, <em>mismatch</em>: number of mismatches, <em>gapopen</em>: number of gap openings, <em>qstart</em>: start of alignment in query, <em>qend</em>: end of alignment in query, <em>sstart:</em> start of alignment in subject, <em>send</em>: end of alignment in subject, <em>evalue</em>: expect value, <em>bitscore</em>: bit score. <strong>Table S4 | </strong>Annotations and genomic locations of <em>L. kohalensis </em>transcripts (all BLAST hits). Column headers are defined as follows; <em>transcript: </em>transcript identifier, <em>scaffold</em>: scaffold to which the transcript maps, <em>start: </em>genomic location of start of transcript, <em>stop</em>: genomic location of end of transcript, <em>direction</em>: indicator of which direction the transcript is transcribed in, <em>Entry_Name</em>: Uniprot ID assigned to transcript, <em>Protein_Name</em>: Protein name associated with Uniprot_ID, <em>Gene_Name</em>: Gene names associated with Uniprot_ID, <em>Gene_Ontology_IDs</em>: GO IDs associated with Uniprot_ID, <em>pident</em>: percentage of identical matches, <em>length: </em>length (in bp) of sequence overlap, <em>mismatch</em>: number of mismatches, <em>gapopen</em>: number of gap openings, <em>qstart</em>: start of alignment in query, <em>qend</em>: end of alignment in query, <em>sstart:</em> start of alignment in subject, <em>send</em>: end of alignment in subject, <em>evalue</em>: expect value, <em>bitscore</em>: bit score. <strong>Table S5 | </strong>Annotations and genomic locations of <em>L. paranigra </em>transcripts (all BLAST hits). Column headers are defined as follows; <em>transcript: </em>transcript identifier, <em>scaffold</em>: scaffold to which the transcript maps, <em>start: </em>genomic location of start of transcript, <em>stop</em>: genomic location of end of transcript, <em>direction</em>: indicator of which direction the transcript is transcribed in, <em>Entry_Name</em>: Uniprot ID assigned to transcript, <em>Protein_Name</em>: Protein name associated with Uniprot_ID, <em>Gene_Name</em>: Gene names associated with Uniprot_ID, <em>Gene_Ontology_IDs</em>: GO IDs associated with Uniprot_ID, <em>pident</em>: percentage of identical matches, <em>length: </em>length (in bp) of sequence overlap, <em>mismatch</em>: number of mismatches, <em>gapopen</em>: number of gap openings, <em>qstart</em>: start of alignment in query, <em>qend</em>: end of alignment in query, <em>sstart:</em> start of alignment in subject, <em>send</em>: end of alignment in subject, <em>evalue</em>: expect value, <em>bitscore</em>: bit score. <strong>Table S6 | </strong>Annotations, genomic locations, and QTL associations of <em>L. kohalensis </em>transcripts expressed on QTL scaffolds. Column headers are defined as follows; <em>scaffold</em>: scaffold identity, <em>transcript: </em>transcript identifier, <em>start: </em>genomic location of start of transcript, <em>stop</em>: genomic location of end of transcript, <em>direction</em>: indicator of which direction the transcript is transcribed in, <em>Entry_Name</em>: Uniprot ID assigned to transcript, <em>Protein_Name</em>: Protein name associated with Uniprot_ID, <em>Gene_Name</em>: Gene names associated with Uniprot_ID,<em> pident</em>: percentage of identical matches, <em>length: </em>length (in bp) of sequence overlap, <em>mismatch</em>: number of mismatches, <em>gapopen</em>: number of gap openings, <em>qstart</em>: start of alignment in query, <em>qend</em>: end of alignment in query, <em>sstart:</em> start of alignment in subject, <em>send</em>: end of alignment in subject, <em>evalue</em>: expect value, <em>bitscore</em>: bit score, <em>size</em>: size (in bp) of scaffold, <em>LG</em>: linkage group on which the scaffold falls, <em>start_position</em>: genomic location of start of scaffold, <em>end_position</em>: genomic location of end of scaffold, <em>id_source</em>: study in which the scaffold has been identified, <em>peak_location_reanalysis</em>: location (in cM) of given QTL peak in present study, <em>scaffold_type_reanalysis</em>: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in present study, <em>peak_location_finemap</em>: location (in cM) of given QTL in Xu & Shaw 2019, <em>scaffold_type_reanalysis</em>: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in Xu & Shaw 2019. <strong>Table S7 | </strong>Annotations, genomic locations, and QTL associations of <em>L. paranigra </em>transcripts expressed on QTL scaffolds. Column headers are defined as follows; <em>scaffold</em>: scaffold identity, <em>transcript: </em>transcript identifier, <em>start: </em>genomic location of start of transcript, <em>stop</em>: genomic location of end of transcript, <em>direction</em>: indicator of which direction the transcript is transcribed in, <em>Entry_Name</em>: Uniprot ID assigned to transcript, <em>Protein_Name</em>: Protein name associated with Uniprot_ID, <em>Gene_Name</em>: Gene names associated with Uniprot_ID,<em> pident</em>: percentage of identical matches, <em>length: </em>length (in bp) of sequence overlap, <em>mismatch</em>: number of mismatches, <em>gapopen</em>: number of gap openings, <em>qstart</em>: start of alignment in query, <em>qend</em>: end of alignment in query, <em>sstart:</em> start of alignment in subject, <em>send</em>: end of alignment in subject, <em>evalue</em>: expect value, <em>bitscore</em>: bit score, <em>size</em>: size (in bp) of scaffold, <em>LG</em>: linkage group on which the scaffold falls, <em>start_position</em>: genomic location of start of scaffold, <em>end_position</em>: genomic location of end of scaffold, <em>id_source</em>: study in which the scaffold has been identified, <em>peak_location_reanalysis</em>: location (in cM) of given QTL peak in present study, <em>scaffold_type_reanalysis</em>: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in present study, <em>peak_location_finemap</em>: location (in cM) of given QTL in Xu & Shaw 2019, <em>scaffold_type_reanalysis</em>: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in Xu & Shaw 2019. <strong>Table S8 | </strong>Genes associated with enriched GO terms in pulse rate QTL. Column headers are defined as follows; <em>Go Term:</em> Gene Ontology term, <em>Species: </em>species from which the reads came, <em>Transcript: </em>Transcript ID, <em>Uniprot ID</em>: Uniprot code associated with transcript, <em>Protein </em>Name: Protein name associated with Uniprot ID, <em>scaffold</em>: scaffold identity,<em> LG</em>: linkage group on which the scaffold falls.