Supporting data: Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers
Data files
May 16, 2024 version files 38.71 GB
Abstract
Sequence data in support of manuscript titled "Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers." This data was generated following a ddRAD sequencing protocol and used in phylogenomic studies to examine the evolutionary history of the eastern standing Phlox and evaluate hypotheses about if and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized.
README: Supporting Data: Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers
https://doi.org/10.5061/dryad.r2280gbmb
Sequence data from genome-wide ddRADseq of thirty-two described eastern standing Phlox taxa.
Description of the data and file structure
Individual_Sorted.tar.gz is a single tarball containing all ddRAD sequences from thirty-two described eastern standing Phlox taxa and outgroup taxa used in the phylogenomics study. These ddRAD sequence libraries were built as described in Goulet-Scott, Garner, and Hopkins, 2021.
These sequence libraries were sequenced paired-end. Within this folder you will find 240 zipped fastq files, with two zipped fastq files corresponding to one individual. The Forward sequence read ends in suffix R1_.fq.gz, and the Reverse sequence read ends in suffix R2_.fq.gz. The following table shows which individual each pair of data came from.
| Species and Individual ID | Forward FASTQ | Reverse FASTQ |
|---|---|---|
| Phlox amoena ; 1701_05 | P_amoena_1701_05_R1_.fq.gz | P_amoena_1701_05_R2_.fq.gz |
| Phlox amoena ; 1715_14 | P_amoena_1715_14_R1_.fq.gz | P_amoena_1715_14_R2_.fq.gz |
| Phlox amoena ; 1716_17 | P_amoena_1716_17_R1_.fq.gz | P_amoena_1716_17_R2_.fq.gz |
| Phlox amoena ; 1724_16 | P_amoena_1724_16_R1_.fq.gz | P_amoena_1724_16_R2_.fq.gz |
| Phlox amoena ; 1726_07 | P_amoena_1726_07_R1_.fq.gz | P_amoena_1726_07_R2_.fq.gz |
| Phlox amoena ; 1727_17 | P_amoena_1727_17_R1_.fq.gz | P_amoena_1727_17_R2_.fq.gz |
| Phlox amoena ; 1729_62 | P_amoena_1729_62_R1_.fq.gz | P_amoena_1729_62_R2_.fq.gz |
| Phlox amoena ; 1733_20 | P_amoena_1733_20_R1_.fq.gz | P_amoena_1733_20_R2_.fq.gz |
| Phlox amoena ; OPGC-3924 | P_amoena_OPGC-3924_R1_.fq.gz | P_amoena_OPGC-3924_R2_.fq.gz |
| Phlox amoena lighthipei ; 1703_12 | P_amoena_lig_1703_12_R1_.fq.gz | P_amoena_lig_1703_12_R2_.fq.gz |
| Phlox amoena lighthipei ; 1705_15 | P_amoena_lig_1705_15_R1_.fq.gz | P_amoena_lig_1705_15_R2_.fq.gz |
| Phlox amoena lighthipei ; 1707_04 | P_amoena_lig_1707_04_R1_.fq.gz | P_amoena_lig_1707_04_R2_.fq.gz |
| Phlox amplifolia ; OPGC-4072 | P_amplifolia_OPGC-4072_R1_.fq.gz | P_amplifolia_OPGC-4072_R2_.fq.gz |
| Phlox bifida bifida ; BIF-04-09 | P_bifida_bifida_BIF-04-09_R1_.fq.gz | P_bifida_bifida_BIF-04-09_R2_.fq.gz |
| Phlox bifida bifida ; BIF-05-01 | P_bifida_bifida_BIF-05-01_R1_.fq.gz | P_bifida_bifida_BIF-05-01_R2_.fq.gz |
| Phlox bifida stellaria ; BIF-01-07 | P_bifida_stellaria_BIF-01-07_R1_.fq.gz | P_bifida_stellaria_BIF-01-07_R2_.fq.gz |
| Phlox buckleyi ; OPGC-4054 | P_buckleyi_OPGC-4054_R1_.fq.gz | P_buckleyi_OPGC-4054_R2_.fq.gz |
| Phlox carolina carolina ; OPGC-3602 | P_carolina_OPGC-3602_R1_.fq.gz | P_carolina_OPGC-3602_R2_.fq.gz |
| Phlox carolina alta ; OPGC-3611 | P_carolina_OPGC-3611_R1_.fq.gz | P_carolina_OPGC-3611_R2_.fq.gz |
| Phlox carolina alta ; OPGC-3614 | P_carolina_OPGC-3614_R1_.fq.gz | P_carolina_OPGC-3614_R2_.fq.gz |
| Phlox carolina angusta ; OPGC-3625 | P_carolina_OPGC-3625_R1_.fq.gz | P_carolina_OPGC-3625_R2_.fq.gz |
| Phlox carolina angusta ; OPGC-4059 | P_carolina_OPGC-4059_R1_.fq.gz | P_carolina_OPGC-4059_R2_.fq.gz |
| Phlox cuspidata ; 647-23-01 | P_cuspidata_allo_647-23-01_R1_.fq.gz | P_cuspidata_allo_647-23-01_R2_.fq.gz |
| Phlox cuspidata ; 648-27-01 | P_cuspidata_sym_N_Drum_648-27-01_R1_.fq.gz | P_cuspidata_sym_N_Drum_648-27-01_R2_.fq.gz |
| Phlox divaricata divaricata ; DIV_12_1905 | P_divaricata_DIV_12_1905_R1_.fq.gz | P_divaricata_DIV_12_1905_R2_.fq.gz |
| Phlox divaricata divaricata ; DIV_17_1908 | P_divaricata_DIV_17_1908_R1_.fq.gz | P_divaricata_DIV_17_1908_R2_.fq.gz |
| Phlox divaricata laphamii ; DIV_29_1924 | P_divaricata_DIV_29_1924_R1_.fq.gz | P_divaricata_DIV_29_1924_R2_.fq.gz |
| Phlox divaricata divaricata ; DIV_34_1908 | P_divaricata_DIV_34_1908_R1_.fq.gz | P_divaricata_DIV_34_1908_R2_.fq.gz |
| Phlox divaricata divaricata ; DIV_38_1910 | P_divaricata_DIV_38_1910_R1_.fq.gz | P_divaricata_DIV_38_1910_R2_.fq.gz |
| Phlox divaricata divaricata ; DIV-05-04 | P_divaricata_divaricata_DIV-05-04_R1_.fq.gz | P_divaricata_divaricata_DIV-05-04_R2_.fq.gz |
| Phlox divaricata divaricata ; DIV-16-17 | P_divaricata_divaricata_DIV-16-17_R1_.fq.gz | P_divaricata_divaricata_DIV-16-17_R2_.fq.gz |
| Phlox divaricata divaricata ; DIV-31-09 | P_divaricata_divaricata_DIV-31-09_R1_.fq.gz | P_divaricata_divaricata_DIV-31-09_R2_.fq.gz |
| Phlox divaricata divaricata ; DIV-32-16 | P_divaricata_divaricata_DIV-32-16_R1_.fq.gz | P_divaricata_divaricata_DIV-32-16_R2_.fq.gz |
| Phlox divaricata laphamii ; OPGC-3601 | P_divaricata_OPGC-3601_R1_.fq.gz | P_divaricata_OPGC-3601_R2_.fq.gz |
| Phlox divaricata divaricata ; OPGC-4099 | P_divaricata_divaricata_OPGC-4099_R1_.fq.gz | P_divaricata_divaricata_OPGC-4099_R2_.fq.gz |
| Phlox divaricata laphamii ; DIV-03-05 | P_divaricata_laphamii_DIV-03-05_R1_.fq.gz | P_divaricata_laphamii_DIV-03-05_R2_.fq.gz |
| Phlox divaricata laphamii ; DIV-18-29 | P_divaricata_laphamii_DIV-18-29_R1_.fq.gz | P_divaricata_laphamii_DIV-18-29_R2_.fq.gz |
| Phlox divaricata laphamii ; DIV-19-21 | P_divaricata_laphamii_DIV-19-21_R1_.fq.gz | P_divaricata_laphamii_DIV-19-21_R2_.fq.gz |
| Phlox divaricata laphamii ; DIV-24-12 | P_divaricata_laphamii_DIV-24-12_R1_.fq.gz | P_divaricata_laphamii_DIV-24-12_R2_.fq.gz |
| Phlox divaricata laphamii ; OPGC-3931 | P_divaricata_laphamii_OPGC-3931_R1_.fq.gz | P_divaricata_laphamii_OPGC-3931_R2_.fq.gz |
| Phlox divaricata laphamii ; OPGC-3935 | P_divaricata_laphamii_OPGC-3935_R1_.fq.gz | P_divaricata_laphamii_OPGC-3935_R2_.fq.gz |
| Phlox divaricata laphamii ; OPGC-3941 | P_divaricata_laphamii_OPGC-3941_R1_.fq.gz | P_divaricata_laphamii_OPGC-3941_R2_.fq.gz |
| Phlox divaricata laphamii ; OPGC-3945 | P_divaricata_laphamii_OPGC-3945_R1_.fq.gz | P_divaricata_laphamii_OPGC-3945_R2_.fq.gz |
| Phlox divaricata laphamii ; OPGC-4179 | P_divaricata_laphamii_OPGC-4179_R1_.fq.gz | P_divaricata_laphamii_OPGC-4179_R2_.fq.gz |
| Phlox divaricata laphamii ; OPGC-4186 | P_divaricata_laphamii_OPGC-4186_R1_.fq.gz | P_divaricata_laphamii_OPGC-4186_R2_.fq.gz |
| Phlox drummondii ; 528-E583 | P_drummondii_528-E583_R1_.fq.gz | P_drummondii_528-E583_R2_.fq.gz |
| Phlox drummondii ; 617-22-1 | P_drummondii_617-22-1_R1_.fq.gz | P_drummondii_617-22-1_R2_.fq.gz |
| Phlox drummondii ; 620-9-1 | P_drummondii_620-9-1_R1_.fq.gz | P_drummondii_620-9-1_R2_.fq.gz |
| Phlox drummondii ; 622-8-2 | P_drummondii_622-8-2_R1_.fq.gz | P_drummondii_622-8-2_R2_.fq.gz |
| Phlox drummondii ; 633-9-2 | P_drummondii_633-9-2_R1_.fq.gz | P_drummondii_633-9-2_R2_.fq.gz |
| Phlox drummondii ; 695-15-2 | P_drummondii_695-15-2_R1_.fq.gz | P_drummondii_695-15-2_R2_.fq.gz |
| Phlox drummondii ; 502-E35 | P_drummondii_allo_NW_502-E35_R1_.fq.gz | P_drummondii_allo_NW_502-E35_R2_.fq.gz |
| Phlox drummondii ; 636-G-1 | P_drummondii_allo_S_636-G-1_6_R1_.fq.gz | P_drummondii_allo_S_636-G-1_6_R2_.fq.gz |
| Phlox drummondii ; 508-3-801 | P_drummondii_sym_Roe_508-3-801_R1_.fq.gz | P_drummondii_sym_Roe_508-3-801_R2_.fq.gz |
| Phlox floridana ; OPGC-3933 | P_floridana_OPGC-3933_R1_.fq.gz | P_floridana_OPGC-3933_R2_.fq.gz |
| Phlox glaberrima glaberrima ; 1702-05 | P_glaberrima_1702-05_6_R1_.fq.gz | P_glaberrima_1702-05_6_R2_.fq.gz |
| Phlox glaberrima glaberrima ; 1706-05 | P_glaberrima_1706-05_R1_.fq.gz | P_glaberrima_1706-05_R2_.fq.gz |
| Phlox glaberrima triflora ; OPGC-3442 | P_glaberrima_OPGC-3442_6_R1_.fq.gz | P_glaberrima_OPGC-3442_6_R2_.fq.gz |
| Phlox glaberrima triflora ; OPGC-3586 | P_glaberrima_OPGC-3586_R1_.fq.gz | P_glaberrima_OPGC-3586_R2_.fq.gz |
| Phlox glaberrima triflora ; OPGC-3594 | P_glaberrima_OPGC-3594_R1_.fq.gz | P_glaberrima_OPGC-3594_R2_.fq.gz |
| Phlox glaberrima interior ; GLA-01-44 | P_glaberrima_interior_GLA-01-44_R1_.fq.gz | P_glaberrima_interior_GLA-01-44_R2_.fq.gz |
| Phlox glaberrima interior ; GLA-02-05 | P_glaberrima_interior_GLA-02-05_R1_.fq.gz | P_glaberrima_interior_GLA-02-05_R2_.fq.gz |
| Phlox glaberrima interior ; GLA_03_19 | P_glaberrima_interior_GLA_03_19_R1_.fq.gz | P_glaberrima_interior_GLA_03_19_R2_.fq.gz |
| Phlox glaberrima interior ; GLA_10_1927 | P_glaberrima_interior_GLA_10_1927_R1_.fq.gz | P_glaberrima_interior_GLA_10_1927_R2_.fq.gz |
| Phlox glaberrima interior ; GLA_21_1907 | P_glaberrima_interior_GLA_21_1907_R1_.fq.gz | P_glaberrima_interior_GLA_21_1907_R2_.fq.gz |
| Phlox maculata maculata ; MAC-01-09 | P_maculata_MAC-01-09_R1_.fq.gz | P_maculata_MAC-01-09_R2_.fq.gz |
| Phlox maculata pyramidalis ; MAC_03_1912 | P_maculata_MAC_03_1912_R1_.fq.gz | P_maculata_MAC_03_1912_R2_.fq.gz |
| Phlox maculata maculata ; OPGC-3456 | P_maculata_OPGC-3456_R1_.fq.gz | P_maculata_OPGC-3456_R2_.fq.gz |
| Phlox maculata maculata ; OPGC-3599 | P_maculata_OPGC-3599_R1_.fq.gz | P_maculata_OPGC-3599_R2_.fq.gz |
| Phlox maculata maculata ; OPGC-4074 | P_maculata_OPGC-4074_R1_.fq.gz | P_maculata_OPGC-4074_R2_.fq.gz |
| Phlox ovata ; OPGC-4037 | P_ovata_OPGC-4037_R1_.fq.gz | P_ovata_OPGC-4037_R2_.fq.gz |
| Phlox ovata ; OPGC-4042 | P_ovata_OPGC-4042_R1_.fq.gz | P_ovata_OPGC-4042_R2_.fq.gz |
| Phlox paniculata ; PAN-01-02 | P_paniculata_PAN-01-02_6_R1_.fq.gz | P_paniculata_PAN-01-02_6_R2_.fq.gz |
| Phlox paniculata ; PAN_03_05 | P_paniculata_PAN_03_05_R1_.fq.gz | P_paniculata_PAN_03_05_R2_.fq.gz |
| Phlox paniculata ; PAN_04_1904 | P_paniculata_PAN_04_1904_R1_.fq.gz | P_paniculata_PAN_04_1904_R2_.fq.gz |
| Phlox paniculata ; PAN_05_1901 | P_paniculata_PAN_05_1901_R1_.fq.gz | P_paniculata_PAN_05_1901_R2_.fq.gz |
| Phlox paniculata ; PAN_07_1913 | P_paniculata_PAN_07_1913_R1_.fq.gz | P_paniculata_PAN_07_1913_R2_.fq.gz |
| Phlox pilosa deamii ; 1719_18 | P_pil_deam_1719_18_R1_.fq.gz | P_pil_deam_1719_18_R2_.fq.gz |
| Phlox pilosa deamii ; 1720_07 | P_pil_deam_1720_07_R1_.fq.gz | P_pil_deam_1720_07_R2_.fq.gz |
| Phlox pilosa deamii ; 1721_09 | P_pil_deam_1721_09_R1_.fq.gz | P_pil_deam_1721_09_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1704_01 | P_pilosa_1704_01_R1_.fq.gz | P_pilosa_1704_01_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1708_08 | P_pilosa_1708_08_R1_.fq.gz | P_pilosa_1708_08_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1710_13 | P_pilosa_1710_13_R1_.fq.gz | P_pilosa_1710_13_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1712_01 | P_pilosa_1712_01_R1_.fq.gz | P_pilosa_1712_01_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1713_08 | P_pilosa_1713_08_R1_.fq.gz | P_pilosa_1713_08_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1714_07 | P_pilosa_1714_07_R1_.fq.gz | P_pilosa_1714_07_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1718_20 | P_pilosa_1718_20_R1_.fq.gz | P_pilosa_1718_20_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1722_12 | P_pilosa_1722_12_R1_.fq.gz | P_pilosa_1722_12_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1728_07 | P_pilosa_1728_07_R1_.fq.gz | P_pilosa_1728_07_R2_.fq.gz |
| Phlox pilosa pilosa South ; 1729_22 | P_pilosa_1729_22_R1_.fq.gz | P_pilosa_1729_22_R2_.fq.gz |
| Phlox pilosa pilosa North ; PIL_6_1983 | P_pilosa_PIL_06_1983_R1_.fq.gz | P_pilosa_PIL_06_1983_R2_.fq.gz |
| Phlox pilosa pilosa North ; PIL_9_1929 | P_pilosa_PIL_09_1929_R1_.fq.gz | P_pilosa_PIL_09_1929_R2_.fq.gz |
| Phlox pilosa pilosa North ; PIL_10_1955 | P_pilosa_PIL_10_1955_R1_.fq.gz | P_pilosa_PIL_10_1955_R2_.fq.gz |
| Phlox pilosa pilosa North ; PIL_11_1924 | P_pilosa_PIL_11_1924_R1_.fq.gz | P_pilosa_PIL_11_1924_R2_.fq.gz |
| Phlox pilosa detonsa ; OPGC-3929 | P_pilosa_detonsa_OPGC-3929_R1_.fq.gz | P_pilosa_detonsa_OPGC-3929_R2_.fq.gz |
| Phlox pilosa fulgida ; OPGC-3624 | P_pilosa_fulgida_OPGC-3624_R1_.fq.gz | P_pilosa_fulgida_OPGC-3624_R2_.fq.gz |
| Phlox pilosa fulgida ; PIL-02-01 | P_pilosa_fulgida_PIL-02-01_R1_.fq.gz | P_pilosa_fulgida_PIL-02-01_R2_.fq.gz |
| Phlox pilosa fulgida ; PIL-04-03 | P_pilosa_fulgida_PIL-04-03_R1_.fq.gz | P_pilosa_fulgida_PIL-04-03_R2_.fq.gz |
| Phlox villosissima latisepala ; OPGC-3962 | P_pilosa_latisepala_OPGC-3962_R1_.fq.gz | P_pilosa_latisepala_OPGC-3962_R2_.fq.gz |
| Phlox villosissima latisepala ; OPGC-3963 | P_pilosa_latisepala_OPGC-3963_R1_.fq.gz | P_pilosa_latisepala_OPGC-3963_R2_.fq.gz |
| Phlox pilosa ozarkana ; OPGC-4024 | P_pilosa_ozarkana_OPGC-4024_R1_.fq.gz | P_pilosa_ozarkana_OPGC-4024_R2_.fq.gz |
| Phlox pilosa pilosa South ; 538L | P_pilosa_pilosa_538L_R1_.fq.gz | P_pilosa_pilosa_538L_R2_.fq.gz |
| Phlox pilosa pilosa South ; OPGC-3952 | P_pilosa_pilosa_OPGC-3952_R1_.fq.gz | P_pilosa_pilosa_OPGC-3952_R2_.fq.gz |
| Phlox pilosa pilosa South ; OPGC-3954 | P_pilosa_pilosa_OPGC-3954_R1_.fq.gz | P_pilosa_pilosa_OPGC-3954_R2_.fq.gz |
| Phlox pilosa pilosa North ; OPGC-4183 | P_pilosa_pilosa_OPGC-4183_R1_.fq.gz | P_pilosa_pilosa_OPGC-4183_R2_.fq.gz |
| Phlox pilosa pilosa North ; PIL-03-01 | P_pilosa_pilosa_PIL-03-01_R1_.fq.gz | P_pilosa_pilosa_PIL-03-01_R2_.fq.gz |
| Phlox villosissima villosissima ; OPGC-3965 | P_pilosa_ripara_OPGC-3965_R1_.fq.gz | P_pilosa_ripara_OPGC-3965_R2_.fq.gz |
| Phlox pilosa sangamonensis ; SAN-01-10 | P_pilosa_sangamonensis_SAN-01-10_R1_.fq.gz | P_pilosa_sangamonensis_SAN-01-10_R2_.fq.gz |
| Phlox pilosa sangamonensis ; SAN-02-04 | P_pilosa_sangamonensis_SAN-02-04_R1_.fq.gz | P_pilosa_sangamonensis_SAN-02-04_R2_.fq.gz |
| Phlox pilosa sangamonensis ; SAN-03-07 | P_pilosa_sangamonensis_SAN-03-07_R1_.fq.gz | P_pilosa_sangamonensis_SAN-03-07_R2_.fq.gz |
| Phlox pilosa argillacea ; PIL_20_1915 | P_pilosa_white_PIL_20_1915_R1_.fq.gz | P_pilosa_white_PIL_20_1915_R2_.fq.gz |
| Phlox pilosa argillacea ; PIL_21_1926 | P_pilosa_white_PIL_21_1926_R1_.fq.gz | P_pilosa_white_PIL_21_1926_R2_.fq.gz |
| Phlox pilosa argillacea ; PIL_22_1923 | P_pilosa_white_PIL_22_1923_R1_.fq.gz | P_pilosa_white_PIL_22_1923_R2_.fq.gz |
| Phlox pulchra ; OPGC-3620 | P_pulchra_OPGC-3620_R1_.fq.gz | P_pulchra_OPGC-3620_R2_.fq.gz |
| Phlox roemariana ; 511-N-813 | P_roemariana_allo_511-N-813_R1_.fq.gz | P_roemariana_allo_511-N-813_R2_.fq.gz |
| Phlox roemariana ; 641-32-TO | P_roemariana_allo_S_641-32-TO_R1_.fq.gz | P_roemariana_allo_S_641-32-TO_R2_.fq.gz |
| Phlox roemariana ; 600 | P_roemariana_sym_Drum_600_R1_.fq.gz | P_roemariana_sym_Drum_600_R2_.fq.gz |
| Phlox stolonifera ; OPGC-4080 | P_stolonifera_OPGC-4080_R1_.fq.gz | P_stolonifera_OPGC-4080_R2_.fq.gz |
| Phlox stolonifera ; OPGC-4100 | P_stolonifera_OPGC-4100_R1_.fq.gz | P_stolonifera_OPGC-4100_R2_.fq.gz |
| Phlox stubulata ; OPGC-4030 | P_subulata_OPGC-4030_R1_.fq.gz | P_subulata_OPGC-4030_R2_.fq.gz |
Sharing/Access Information:
All sequence data can also be found on NCBI at https://www.ncbi.nlm.nih.gov/sra/PRJNA1109731
References:
Goulet-Scott, Benjamin E., Austin G. Garner, and Robin Hopkins. "Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses." Evolution 75.7 (2021): 1699-1710.
Methods
We extracted genomic DNA from bud tissue, processed this DNA into double-digest restriction-site-associated digestion (ddRAD) sequencing libraries, and paired-end sequenced the libraries as described in Goulet-Scott et al., 2021. Resulting sequence data was demultiplexed by individual following Goulet-Scott et al., 2021.
Goulet-Scott, Benjamin E., Austin G. Garner, and Robin Hopkins. "Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses." Evolution 75.7 (2021): 1699-1710.