sihek-phylogenetics

Papers — sihek / Todiramphus kingfishers

1. Andersen, Shult, Cibois, Thibault, Filardi & Moyle (2015)

“Rapid diversification and secondary sympatry in Australo-Pacific kingfishers (Aves: Alcedinidae: Todiramphus)” Royal Society Open Science 2(2):140375

• DOI: https://doi.org/10.1098/rsos.140375
• PMC (free, incl. PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448819/
• License: CC BY
• Local: 10.1098_rsos.140375.txt (full text)
• Why: source of the KP291* ND2 accessions; independently recovers the same sihek sister (T. recurvirostris) and the same paraphyly of T. cinnamominus, also with support they describe as equivocal.

2. Eliason, Hains, McCullough, Andersen & Hackett (2022)

“Genomic novelty within a ‘great speciator’ revealed by a high-quality reference genome of the collared kingfisher (Todiramphus chloris collaris)” G3: Genes|Genomes|Genetics 12(11):jkac260

• DOI: https://doi.org/10.1093/g3journal/jkac260
• PMC (free, incl. PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635628/
• License: CC BY
• Local: 10.1093_g3journal_jkac260.txt (full text)
• Why: the T. chloris reference genome (GCA_025345505.1) we are mapping sihek reads onto; scaffold N50 19 Mb, 96.6% BUSCO. Also a PSMC methods template.

3. Trask, Ferrie, Wang, Newland, Canessa, Moehrenschlager, Laut, Duenas & Ewen (2021)

“Multiple life-stage inbreeding depression impacts demography and extinction risk in an extinct-in-the-wild species” Scientific Reports 11:682

• DOI: https://doi.org/10.1038/s41598-020-79979-4
• Local: 10.1038_s41598-020-79979-4.pdf (PDF)
• Why: pedigree-based inbreeding depression in the sihek. The benchmark our genomic ROH estimate will be compared against.

4. McCullough, Eliason, Hackett, Myers & Andersen (2025) [PAYWALLED]

“Phylogenomics of a Genus of ‘Great Speciators’ Reveals Rampant Incomplete Lineage Sorting, Gene Flow, and Mitochondrial Discordance in Island Systems” Systematic Biology, published 18 Oct 2025

• DOI: https://doi.org/10.1093/sysbio/syaf075
• PubMed (abstract): https://pubmed.ncbi.nlm.nih.gov/41114641
• BioProject: PRJNA1174201
• Access: CLOSED. No PMC deposit, no repository copy, no preprint (checked Unpaywall, Semantic Scholar, PMC, CrossRef TDM, OpenAlex). Institutional access or an author reprint request (Michael Andersen, UNM) are the routes.
• Why: 20x WGS across all Todiramphus taxa; UCEs, BUSCOs, SNPs and mtDNA give no concordant topology. Explains why our ND2 sister node is weakly supported.