DOI: 10.5061/dryad.1jwstqjxx
title: Genomic and geographic diversification of a “great-speciator” (Rhipidura rufifrons)

description: The radiation of so-called “great speciators” represents a paradox among
 the myriad avian radiations endemic to the southwest Pacific. In such
 radiations, lineages otherwise capable of dispersing across vast distances
 of open ocean differentiate rapidly and frequently across relatively short
 geographic barriers. Here, we evaluate the phylogeography of the Rufous
 Fantail (Rhipidura rufifrons). Although a presumed “great-speciator”, no
 formal investigations across its range have been performed. Moreover, the
 delimitation of lineages within R. rufifrons, and the
 biogeographic implications of those relationships remain unresolved. To
 investigate whether R. rufifrons represents a great speciator, we
 identified thousands of single-nucleotide polymorphisms for 89
 individuals, representing 19 described taxa. Analyses recovered seven
 divergent lineages and evidence of gene flow between geographically
 isolated populations. We also found plumage differences to be a poor proxy
 for evolutionary relationships. Given the relatively recent divergence
 dates for the clade (1.35–2.31 mya), rapid phenotypic differentiation, and
 evidence for multiple independent lineages within the species complex, we
 determine that R. rufifrons possesses the characteristics of a great
 speciator.
description: The following line is the only processing that has occurred for
 these data and was completed within the STACKS2 pipeline
 process_radtags -p ./raw_manthey-data/ -b ./barcodes_key -o
 ./stacks_manthey/ -i gzfastq -e ndeI -c -q -r -E phred33
description: # Genomic and geographic diversification of a “great-speciator” (Rhipidura
 rufifrons) Dataset DOI: [10.5061/dryad.1jwstqjxx](10.5061/dryad.1jwstqjxx)
 ## Description of the data and file structure #### File name:
 Rhip_ruf_fq-files.zip These data were generated by the authors of the
 "Genomic and geographic diversification of a great-speciator
 (*Rhipidura rufifrons*)" project. The .fq file names all include the
 museum accession number, and additional information for each sample can be
 found in Table 2 of the manuscript. These data were generated from a
 single digest RAD-seq protocol (Miller et al. 2007). The raw reads have
 only undergone the process_radtags (demultiplexing) command within the
 STACKS 2 pipeline. process_radtags -p ./input_file_location/ -b
 ./barcode_key_file -o ./output_directory/ -i gzfastq -e ndeI -c -q -r -E
 phred33 Museum Codes: KUNHM–University of Kansas Natural History Museum,
 AMNH-American Museum of Natural History, ANWC–Australian National Wildlife
 Collection, CAS–California Academy of Sciences, BPBM–Bernice P Bishop
 Museum, UWBM–University of Washington Burke Museum, WAM–Western Australia
 Museum R. = *Rhipidura* r. = *rufifrons* d. = *dryas* The raw data files
 will all contain the "tissue #" in their name, which in all
 cases will be after the last underscore. Raw folder changed naming
 conventions for many reasons (multiple researchers, multiple sequencing
 runs, etc); however, in all cases, the museum/tissue number is used in the
 name, and this is how samples should be tracked. Species Tissue # Museum
 *R. r. intermedia* B31321 ANWC *R. r. intermedia* B31559 ANWC *R. r.
 intermedia* B43019 ANWC *R. r. intermedia* B57118 ANWC *R. r. intermedia*
 B57131 ANWC *R. r. intermedia* B57199 ANWC *R. r. intermedia* B56097 ANWC
 *R. r. intermedia* B56405 ANWC *R. r. rufifrons* B44315 ANWC *R. r.
 rufifrons* B46863 ANWC *R. r. rufifrons* B49720 ANWC *R. r. louisiadensis*
 97870 CAS *R. r. louisiadensis* 97887 CAS *R. r. louisiadensis* 97970 CAS
 *R. r. louisiadensis* 184548 BPBM *R. r. louisiadensis* 96782 CAS *R. r.
 louisiadensis* 96783 CAS *R. r. louisiadensis* 96785 CAS *R. r. agilis*
 19407 KUNHM *R. r. agilis* 19408 KUNHM *R. r. agilis* 19417 KUNHM *R. r.
 saipanensis* 22578 KUNHM *R. r. saipanensis* 22588 KUNHM *R. r.
 saipanensis* 22597 KUNHM *R. r. saipanensis* 22601 KUNHM *R. r. ugiensis*
 15928 KUNHM *R. r. ugiensis* M007 U of Miami *R. r. ugiensis* M008 U of
 Miami *R. r. kuperi* M105 U of Miami *R. r. kuperi* M106 U of Miami *R. r.
 kuperi* M109 U of Miami *R. r. russata* M112 U of Miami *R. r. russata*
 M113 U of Miami *R. r. russata* 12828 KUNHM *R. r. russata* 12832 KUNHM
 *R. r. russata* 13547 KUNHM *R. r. russata* 15915 KUNHM *R. r. granti*
 32098 KUNHM *R. r. granti* 32104 KUNHM *R. r. granti* 33777 KUNHM *R. r.
 granti* 33786 KUNHM *R. r. granti* 33791 KUNHM *R. r. granti* 33862 KUNHM
 *R. r. granti* 33910 KUNHM *R. r. granti* 33919 KUNHM *R. r. granti*
 Bu66046 UWBM *R. r. granti* Bu66083 UWBM *R. r. brunnea* 32766 KUNHM *R.
 r. brunnea* 32767 KUNHM *R. r. brunnea* 32779 KUNHM *R. r. brunnea* 32783
 KUNHM *R. r. brunnea* 32791 KUNHM *R. r. commoda* 5282 KUNHM *R. r.
 commoda* Bu63074 UWBM *R. r. commoda* Bu63198 UWBM *R. r. commoda* Bu58811
 UWBM *R. r. commoda* Bu60315 UWBM *R. r. commoda* 32061 KUNHM *R. r.
 commoda* 32066 KUNHM *R. r. rufofronta* 15904 KUNHM *R. r. rufofronta*
 15910 KUNHM *R. r. rufofronta* 32807 KUNHM *R. r. rufofronta* 32809 KUNHM
 *R. r. rufofronta* 32810 KUNHM *R. r. rufofronta* 32823 KUNHM *R. r.
 rufofronta* 32854 KUNHM *R. r. rufofronta* Bu60248 UWBM *R. d. dryas*
 B57249 ANWC *R. d. dryas* 22743 KUNHM *R. d. dryas* B29495 ANWC *R. d.
 dryas* B29660 ANWC *R. d. dryas* B29869 ANWC *R. d. dryas* B32683 ANWC *R.
 d. dryas* B33738 ANWC *R. d. dryas* B48642 ANWC *R. d. dryas* B55074 ANWC
 *R. d. semicollaris* 22704 WAM *R. d. semicollaris* 23563 WAM *R. d.
 semicollaris* 23884 WAM *R. d. semicollaris* 24442 WAM *R. d.
 semicollaris* 24503 WAM *R. d. squamata* 24890 WAM *R. d. sumbensis* 22842
 WAM *R. teysmanni* DOT12566 AMNH *R. lepida* 23628 KUNHM *R. lepida* 23660
 KUNHM *R. lepida* 23623 KUNHM *R. dahli* 5305 KUNHM *R. dahli* 5313 KUNHM