| | DOI: 10.1111/mec.15204 ORIGINAL ARTICLE A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius Baocheng Guo1,2 | Bohao Fang3 | Takahito Shikano3| Paolo Momigliano3 | Cui Wang3| Alexandra Kravchenko4| Juha Merilä3 1 Abstract - - 2 Pungitius - 3 - 4 Pungitius Correspondence - - Pungitius - Funding information Pungitius - Pungitius - KEYWORDS 4046| © 2019 John Wiley & Sons Ltd wileyonlinelibrary.com/journal/mec Molecular Ecology. 2019;28:4046–4064. GUO et al. | | sensu Pungitius- - Pungitius- - - Pungitius - - - - - - - - Pungitius- - - - - - Gasterosteus aculeatus Gasterosteus - PungitiusP. platygasterP. hellenicus - - Pungitius | GUO et al. 60°N 130°E1140°E 150°E 60°E PS-RU-BOL PP-RU-BLS 50°N PS-RU-TAN PP-RU-GOR PP-JP-ROK(OM) PT-RU-VLA PT-RU-VLA PS-RU-PRE PK-RU-NRI PS-RU-TAN PK-RU-NRI PS-RU-PRE PP-RU-GOR PS-RU-BOL 40°N PP-JP-ROK(OM) 0250 500 km 180°E 150° W E 150° 120° W E 120° 90° E W 90° 60°W E 60° 30°W 30°E 0° 75°N 60°N P. pungitius P. laevis 45°N P. platygaster P. sinensis PH-GR-SPE P. tymensis P. hellenicus 0 1,000 2,000 km 30°N P. kaibarae Sample site Pungitius Pungitius Pungitius - Pungitius - - - GUO et al. | fastqc | fastx | - Pungitius - Pungitius pungitiusP. lae- visP. platygasterP. hellenicusP. sinensisP. tymensis and P. kaibarae - P. bussei and P. stenurus- - P. polyakovi bwa mem samtools - P. pungitius samtools and bcftools vcftools P. occidentalis - - P. laevis Gasterosteus aculeatus- G. wheatlandiCulaea incon- in C. inconstansG. wheatlandi stans Apeltes quadracus - - - Pungitius - | r p = 4.12 × 10 preparation and sequencing Pstr - p = 4.09 × 10 - Pst de novo - pyrad - - - - Dpyrad pyrad | - - rp < 2.2 × 10 | GUO et al. (a) (b) Gasterosteus aculeatus GA-US-ALA Gasterosteus aculeatus 100 GW-US-MAI-02 100 Gasterosteus wheatlandi GW-US-MAI-01 B AQ-US-MAI-02 100 AQ-US-MAI-01 Apeltes quadracus CI-CA-GUE-02 100 Culaea inconstans CI-CA-GUE-01 Gasterosteus wheatlandi PS-RU-TAN-01 100 PS-RU-TAN-02 100 PS-RU-BOL-02 100 100 PS-RU-BOL-01 PP-JP-NAK-02[FW] SINENSIS-CLADE 100 100 PP-JP-NAK-01[FW] Pungitius sinensis 96 PP-JP-YON-01[FW] 100 PP-JP-YON-02[FW] Culaea inconstans 95 PS-CN-LIU-01 100 100 PS-CN-LIU-02 100 PS-RU-PRE-02 100 Pungitius kaibarae 100 PS-RU-PRE-01 100 PS-RU-KIE-01 100 PS-RU-KIE-02 PK-RU-NRI-01 100 PK-RU-NRI-02 100 Pungitius tymensis Pungitius sinensis PP-JP-ROK-02[OM] 100 PP-JP-ROK-01[OM] SINENSIS-CLADE 100 PT-JP-MOT-02 A 100 PT-JP-MOT-01 100 100 PT-RU-VLA-01 100 Pungitius hellenicus PT-RU-VLA-02 100 PH-GR-SPE-02 PH-GR-SPE-01 Pungitius kaibarae 100 PR-GR-LOU-01 100 PR-GR-LOU-02 PL-FR-ANT-01[II] 100 Pungitius platygaster PL-FR-ANT-02[II] 100 100 PL-FR-NOH-02[I] 100 PUNGITIUS-CLADE PL-FR-NOH-01[I] 100 PL-FR-YON-01[III] Pungitius tymensis 100 PL-FR-YON-02[III] Pungitius laevis 100 PP-CA-TEM-02 100 PP-CA-TEM-01 PP-CA-FLO-01 NA 100 C PP-CA-FLO-02 100 PP-RU-BLS-01 100 PP-RU-BLS-02 100 PP-JP-BIW-02[BW] Pungitius platygaster 100 100 PP-JP-BIW-01[BW] 100 FE PP-RU-GOR-02 100 PP-RU-GOR-01 PP-RU-LEN-01 PUNGITIUS-CLADE 100 100 PP-RU-LEN-02 PP-RU-USH-01 100 PP-RU-UNG-01 91 Pungitius hellenicus PP-FI-HEL-01 100 PP-FI-HEL-02 78 53 PP-SE-BYN-02 100 EE PP-SE-BYN-01 Pungitius pungitius 100 PP-FI-RYT-02 DISTRIBUTION 100 PP-FI-RYT-01 100 100 PP-RU-LEV-02 100 PP-RU-LEV-01 Pungitius laevis PP-SE-FIS-02 100 PP-SE-FIS-01 100 PP-NO-STO-01 PP-NO-UGE-01 95 100 PP-NO-UGE-02 81 100 PP-FR-MAR-01 WE PP-FR-MAR-02 Pungitius pungitius PP-UK-HAR-01 100 DISTRIBUTION 100 PP-UK-HAR-02 56 PP-BE-MAL-02 0.03 97 20 15 10 50 PP-BE-MAL-01 MIOCENE PLIOCENE Mya PLEISTOCENE P. pungitius P.