Data · dataset · 2023
Supporting data: The fasta file and partition file generated by aligning the mined RAD loci from the Falco biarmicus whole genome to the variable RAD loci in our RADseq analysis of Falco cherrug.
Listed in Debreceni Egyetem Adattár
To explicitly root our phylogenetic tree, we mined our RAD loci’s homologous genomic bits from the publicly available reference genome of Falco peregrinus (assembly: GCA_001887755) and Falco biarmicus (assembly: GCA_023638135).
Description
These are explicit outgroup samples for the phylogenetic analyses of relationships between populations of Falco cherrug and Falco rusticolus. F. peregrinus is a distant outgroup, whereas F. biarmicus is a close outgroup from the Hierofalcon group.
The RAD loci sequences with observed heterozygosity of < 0.05 and zero missingness (i.e. present in all individuals) were recovered with Stacks, and then checked for polymorphic sites. Loci containing at least one polymorphic site (n = 422) were subject to consensus sequence generation using the EMBOSS tool consambig. Loci sequences were matched against the reference genome of Falco biarmicus using blastn v. 2.5.0 with an expected e-value of 1e-25.
Read the rest (1 more)
The genomic region with the highest score was retained and aligned with RAD loci sequences using MUSCLE v. 3.8. Alignments of loci were concatenated with AMAS.py. The resulting fasta and partition files were used in this dataset's downstream analyses, where we used F. peregrinus as the outgroup sample.
Links
Where it is published
- Dataverse dataset page adattar.unideb.hu/dataset.xhtml?persistentId=doi%3A10.48428%2FADATTAR%2FUUXM4D ↗
landing page · from adattar unideb hu
- DOI doi.org/10.48428/adattar/uuxm4d ↗
DOI / persistent id · from adattar unideb hu
Catalogue records · 1
- Dataverse API adattar.unideb.hu/api/datasets/:persistentId/?persistentId=doi%3A10.48428%2FADAT… ↗
metadata API · from adattar unideb hu
Topics
- Stated by source
- Medicine, Health and Life Sciences
- From keywords
- Engineering · Humanities · Life Sciences · Medicine & Health · Social Science
- Inferred from text
- Phylogeny and comparative analysis 78%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Debreceni Egyetem Adattár | doi:10.48428/ADATTAR/UUXM4D | 10 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:field:310410 | enrichment · adattar unideb hu | taxonomy-embedding@1.0.0 | title+keywords+description (78%) |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:humanities | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:social-science | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| created_date | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | |
| description | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /description |
| publication_date | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | |
| title | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /name |
| updated_date | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | |
| version_label | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 |