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Genome-Wide Data for Effective Conservation of Manta and Devil Ray Species

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Genome-Wide Data for Effective Conservation of Manta and Devil Ray Species Genome-wide data for effective conservation of manta and devil ray species Supporting Information Supplementary Table 1: Sample information. We use species names assigned to samples at the time of collection, some now considered invalid (White et al. 2017). No. in No. in Sample codes Species Location Total COI ddRAD Dataset Datasets 0130, 0131, 0132, 0135, 0136, 0138 Manta alfredi D'Arros, Amirante Islands, Seychelles 6 6 6 0140, 0141, 0144, 0145, 0146, 0147, Manta alfredi Barefoot Channel, Yasawas Islands, Fiji 8 8 8 0148, 0149 0685, 0686 Manta alfredi Egmont, Chagos 2 2 2 0687, 0688 Manta alfredi Diego Garcia, Chagos 2 2 2 0731 Manta birostris Mirissa, Sri Lanka 1 1 1 0732, 0736 Manta birostris Negombo, Sri Lanka 2 1 2 0980a, 0981a, 0982a, 0983a, 0984a, Manta birostris Yucatan Northern tip, Mexico Caribbean 13 9 13 0985, 0986, 0987, 0988, 1239a, 1240a, 1241a, 1242a 1102, 1110, 1114, 1122 Manta birostris Jagna, Bohol landing site, Philippines 4 4 4 1168 Manta birostris Bahia de Banderas, Jalisco, Mexico Pacific 1 1 1 1327a, 1328b Manta birostris Flower Garden Banks National Marine Sanctuary, 2 2 2 Texas, USA 1 0684 Mobula eregoodootenkee Al Khor, Qatar 1 1 1 0696 Mobula eregoodootenkee Arabian Gulf, United Arab Emirates 1 1 1 0697 Mobula eregoodootenkee Fujeirah, United Arab Emirates 1 1 1 0810, 0813 Mobula eregoodootenkee Zinkwazi, South Africa 2 2 2 0873, 0874, 0886, 0888, 0891, 0900, Mobula hypostoma Sarasota, Florida 10 10 10 0924, 0929, 0933, 0938 0990, 0991, 0992, 0993 Mobula hypostoma Yucatan Northern tip, Mexico Caribbean 4 4 4 0003, 0024 Mobula japanica Jagna, Bohol landing site, Philippines 2 2 2 0219, 0229, 0234, 0283 Mobula japanica Negombo, Sri Lanka 4 4 4 0300, 0329, 0343 Mobula japanica Mirissa, Sri Lanka 3 3 3 0707, 0711 Mobula japanica Ras Al Khaimah, United Arab Emirates 2 2 2 0757, 0771, 0773 Mobula japanica Lome, Togo 3 3 3 0793 Mobula japanica Puerto Adolfo Lopez Mateos, Mexico Pacific 1 1 1 0853, 0862 Mobula japanica Karachi, Pakistan 2 2 2 0524 Mobula kuhlii Negombo, Sri Lanka 1 1 1 0582, 0677 Mobula kuhlii Durban, South Africa 2 2 2 0605 Mobula kuhlii Warner Beach, South Africa 1 1 1 0774, 0776, 0777, 0778 Mobula kuhlii Maumere, Indonesia 4 4 4 0101, 0104 Mobula mobular Gaza City Fishing Landing Site, Gaza, Palestine 2 2 2 2 0111, 0112 Mobula mobular Khanyounis Fishing Landing Site, Gaza, Palestine 2 2 2 0129 Mobula mobular Middle area fishing landing site, Gaza, Palestine 1 1 1 0816, 0821, 0824, 0827 Mobula munkiana El Pardito, Mexico Pacific 4 4 4 0830, 0833, 0840, 0843 Mobula munkiana Puerto Adolfo Lopez Mateos, Mexico Pacific 4 4 4 0844 Mobula munkiana Buena Vista Port of San Jose, Guatemala 1 1 1 1006, 1009, 1019 Mobula munkiana Peru 3 3 3 0943 Mobula rochebrunei Musee de la Mer, Goree, Senegal 1 0 0 0086 Mobula tarapacana Jagna, Bohol landing site, Philippines 1 1 1 0408, 0411 Mobula tarapacana Mirissa, Sri Lanka 2 2 2 0847 Mobula tarapacana Karachi, Pakistan 1 1 1 0159 Mobula thurstoni Jeddah Fish Market, Saudi Arabia 1 1 1 0712 Mobula thurstoni Fujeirah, United Arab Emirates 1 1 1 0780, 0782, 0783, 0784, 0785, 0786, Mobula thurstoni El Pardito, Mexico Pacific 7 7 7 0787 1366, 1367, 1368, 1369, 1370 Rhinoptera bonasus Sarasota, Florida, USA 5 0 5 Totals 121 110 120 a Samples identified as belonging to Mobula sp. 1 in our analyses b Likely hybrid (Manta birostris x Mobula sp. 1) 3 Supplementary Table 2: Information on two SNP matrices generated using ddRAD, p10 and p90. The number of SNPs in individual level matrices are given, with numbers of SNPs in species level matrices in brackets. Dataset Minimum Loci with Loci with Loci with >95% SNPs Missing individuals >2x SD <1/3x SD probability of Data possessing coverage coverage heterozygote a locus excess p10 10 1761 7661 24 7926 47% (7902) p90 90 789 0 0 1762 14% (1755) Supplementary Table 3: Details of SNP matrices used to run PCAs. Dataset p10 (7926 SNPs) was split into clades for ease of visualisation, resulting in sites unsampled within clades to drop out. Clade SNPs retained M. alfredi and M. birostris (including Mobula sp. 1) 5730 M. mobular (including samples identified as M. japanica) 5428 M. thurstoni and M. kuhlii (including samples identified as M. eregoodootenkee) 5384 M. hypostoma and M. munkiana 5063 4 Supplementary Table 4: Details of species delimitation models tested with Bayes Factor Delimitation (BFD*) within the first clade identified, the manta rays; Manta alfredi and Manta birostris, including individuals from sister clade Mobula japanica 0707, 0283, 0771 and 0024. MLE MLE SNPs (2logeBF) (2logeBF) Rank Description Rationale Reference retained - gamma - default prior 1/X prior 1 1746 -4941.58 -4946.44 Split M. alfredi into two species units in Monophyly of M. alfredi individuals in This study (-1063.58) (1054.72) Indian and Pacific Oceans. In addition, these ocean basins, and another species of manta ray is present distinguishability through PCA. M. in the Atlantic Ocean, sharing most birostris split hypothesised in several recent common ancestor with M. studies. birostris. 2 1749 -5085.46 -5086.94 In addition to M. alfredi and M. Hypothesised in several studies. Some Marshall et al. 2009; (-775.82) (-773.72) birostris, a third species of manta ray is showing divergence on phylogenetic Hinojosa-Alvarez et al. present in the Atlantic Ocean, sharing trees following this pattern 2016; this study most recent common ancestor with M. birostris. 3 1748 -5332.41 -5335.11 Split M. alfredi into two species units in Monophyly of M. alfredi individuals This study (-281.92) (-277.38) Indian and Pacific Oceans, but recognise based on these ocean basins, and a single species within the M. birostris distinguishability through PCA. complex Potential hybridisation between M. birostris groups. 5 4 1750 -5339.87 -5341.8 Split M. birostris based entirely on To assess whether all M. birostris Marshall et al. 2009 (-267) (-264) geography (Atlantic/Gulf of Mexico individuals sampled in the Atlantic individuals a separate species unit). could be considered a distinct species Single species within M. alfredi. from M. birostris sampled elsewhere 5 1751 -5473.37 -5473.8 Null model and current arrangement – Current taxonomic arrangement Marshall et al. 2009; (Null) (Null) two species of manta ray: M. alfredi Kashiwagi et al. 2012 and M. birostris 6 1754 -7348.39 -7350.44 Random assignment of individuals into To assess relative support for other (3750.04) (3753.28) two species units models. 7 1754 -7360.08 -7359.33 Single species of manta ray (lump M. Similar levels of sequence divergence White et al. 2017 (3773.42) (3771.06) alfredi and M. birostris) as species that have previously been lumped based on said low sequence divergence 8 1760 -11864.6 -11864.51 Lump M. japanica with M. birostris. M. To assess evidence for interaction (12782.46) (12781.42) alfredi distinct from higher up the tree. 6 Supplementary Table 5: Details of species delimitation models tested with Bayes Factor Delimitation (BFD*) within the second clade identified; Mobula mobular and Mobula japanica, including Manta alfredi individuals 0135, 0131, 0685 and 0146. MLE MLE SNPs (2logeBF) (2logeBF) Rank Description Rationale Reference retained - gamma - default prior 1/X prior 1 1752 -5390.81 -5391.65 M. japanica and M. mobular are distinct Taxonomy recognised prior to revision Notarbartolo di Sciara, (-119.58) (-118.44) species units, where the latter is by White et al. 2017 1987; Bustamante et restricted to the Mediterranean Sea. al. 2016; Adnet et al, 2012 2 1755 -5390.93 -5393.24 Split individuals into Atlantic (including Distinguishability of these two groups This study (-119.34) (-115.26) Mediterranean) and Indo-Pacific through PCA species units 3 1755 -5424.82 -5426.71 Random assignment of individuals into To assess relative support for other (-51.56) (-48.32) two species units models. 4 1757 -5450.6 -5450.87 Null model and current arrangement - Current taxonomic arrangement White et al. 2017; (Null) (Null) M. japanica is a junior synonym of M. Poortvliet et al. 2015 mobular, recognising a single species 5 1759 -9150.56 -9153.48 Lump M. alfredi with M. mobular (as To assess evidence for interaction (7399.92) (7405.22) formerly recognised; not including from higher up the tree. specimens formerly attributed to M. japanica) 7 Supplementary Table 6: Details of species delimitation models tested with Bayes Factor Delimitation (BFD*) within the third clade identified; Mobula thurstoni, Mobula kuhlii and Mobula eregoodootenkee, including Mobula hypostoma individuals 0874, 0933, 0924 and 0992. MLE MLE SNPs (2logeBF) (2logeBF) Rank Description Rationale Reference retained - gamma - default prior 1/X prior 1 1710 -3160.68 -3159.35 Split M. kuhlii into two species units in Monophyly of M. kuhlii individuals This study (-1263.8) (-1270) East and West Indian Ocean, and based on geographical location recognise M. thurstoni and M. sampled, and distinguishability eregoodootenkee through PCA. Monophyly and distinguishability of M. thurstoni and M. eregoodootenkee 2 1717 -3289.06 -3291.85 M. eregoodootenkee, M. kuhlii and M. Taxonomy recognised prior to revision Notarbartolo di Sciara, (-1007.04) (-1005) thurstoni are distinct species by White et al. 2017 1987 3 1731 -3792.58 -3794.35 Null model and current arrangement – Current taxonomic arrangement White et al. 2017 (Null) (Null) M. eregoodootenkee is a junior synonym of M. kuhlii. M. thurstoni is distinct 4 1756 -5679.77 -5683.06 Random assignment of individuals to 3 To assess relative support for other (3774.38) (3777.42) species units models. 5 1759 -5818.44 -5816.29 Single species within this clade (lump For completeness (4051.72) (4043.88) M.
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