DNA Analysis of a Large Collection of Shark Fins from a US Retail

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1 TITLE: DNA analysis of a large collection of shark fins from a US retail shop: species composition, 2 global extent of trade and conservation - a Technical Report from the Monterey Bay Aquarium a,1 a b,c 3 AUTHORS: Stephen R. Palumbi, Kristin M. Robinson, Kyle S. Van Houtan, Salvador J. b 4 Jorgensen a 5 AFFILIATIONS: Department of Biology, Hopkins Marine Station, Stanford University, Pacific b c 6 Grove, California 93950 USA; Monterey Bay Aquarium, Monterey, California 93940 USA; 7 Nicholas School of the Environment, 450 Research Drive, Durham, North Carolina 27708 USA. 1 8 Send correspondence to: [email protected], [email protected]

9 KEY WORDS: Shark finning, wildlife trafficking, IUU fishing, elasmobranchs

10 RUNNING HEAD: Shark fin forensics

11 WORD COUNT: 7,324

12 No. REFERENCES: 22

13 No. FIGURES: 3

14 No. TABLES: 3

19 ABSTRACT

20 We identified shark fins sampled across the entirety of a shark fin shop that had operated on the west 21 coast of the United States until 2014. From these specimens we obtained 963 species identifications 22 with Cytochrome oxidase (COI) sequencing and 1,720 identifications with control region (CR) 23 sequences. We found 36-39 distinct species with COI and 38-41 with CR. Of the species identified, 24 16-23 are currently listed as Endangered or Vulnerable on the IUCN Red List, an additional 2 are 25 considered data deficient, and 7 currently listed under CITES Appendix II. Of the 2.5 tonnes of fins 26 from this collection, we estimated 56-66% (CR or COI, respectively) come from CITES-listed species 27 or those the IUCN considers threatened or data deficient. Most of these species occur outside of the 28 United States EEZ, comprising a global set of species that is common in most fin surveys. The 29 principal target shark fishery in the United States (spiny dogfish; Squalus acanthias) has no fins in our 30 collection. Fins seen abundantly in our collection include pelagic species such as thresher, mako, 31 oceanic whitetip, silky, blue and hammerhead sharks, as in previous samples of the shark fin supply 32 chain. However, in addition, we see a large flood of blacktip, dusky, sandbar, and smalltail sharks that 33 are common in shallow coastal waters. This may indicate that the global market for shark fins takes 34 sharks from nearshore coastal zones, all over the world. Abundant species in the fin shop included 35 globally-distributed species such as scalloped hammerheads and shortfin mako sharks, but also 36 regionally-restricted species such as finetooth, blacknose, and Caribbean Reef sharks found only in the 37 western Atlantic or Caribbean. Specimens identified from rare species of particular conservation 38 concern included the wedgefish genus Rhyncobatus and the white shark. Both molecular markers 39 performed well in identifying most fins, achieving a similar degree of taxonomic certainty. The 40 universal primers for COI regularly amplified bacteria in wet fin samples, but the CR primers were 41 able to return shark sequences even from these degraded samples. However, the CR primers amplified 42 a second gene, likely a pseudogene, in some important and abundant species, and seriously 43 underestimated some species of high conversation concern such as the thresher sharks.

44 INTRODUCTION

45 Shark fins comprise a lucrative, extensive global market that leads to the death of 70-100 million 46 sharks a year (Worm et al., 2013), largely for the use of fin collagen (ceratotrichia) in shark fin soup. 47 A recent study estimates that the majority of shark fin harvests are unsustainable, illegal, and that the 48 volume traded has dramatically increased over the last decade (Sadovy de Mitcheson et al., 2018). 49 Extensive capture of ocean-going sharks in long-line and net fisheries has led to the global collapse of 50 many shark species (Baum et al., 2003; Nicholas K. Dulvy et al., 2008). However, the extent of the 51 shark fin trade suggests that many other species are being similarly affected (Fields et al., 2018; 52 Steinke et al., 2017). Recent assessments furthermore indicate some coastal shark populations have 53 declined nearly 90% in the last 50 years (Martin et al., 2016). Efforts to monitor impacts from trade 54 have been impeded, in part, by the extensive processing of fin products. Though some fins are traded 55 with skin on, and with many morphological features intact, many are traded with most features 56 removed, defying easy morphological-based cataloging.

57 Molecular tools have been used extensively to discover the identity of shark fin products in 58 trade, particularly by testing fins in large wholesale markets (Clarke, Magnussen, Abercrombie, 59 McAllister, & Shivji, 2006). Such tests have shown the widespread occurrence of ocean going sharks 60 such as blue sharks, oceanic white tip sharks, thresher sharks, hammerhead sharks and mako sharks. 61 But coastal species have increasingly been observed. Recently, effort has shifted to tests of retail 62 outlets that likely integrate supply chains over months or years (Cardeñosa et al., 2018; Feitosa et al., 63 2018; Fields et al., 2018). For example, Fields et al. (2018) surveyed 92 retail markets in Hong Kong 64 in 2014-2015 and processed 3,800 samples with a small piece of the COI gene, identifying them to the 65 species level. They found 59 species and 17 other groups that could not be well identified. Cardeñosa 66 et al. (2018) extended this survey to a total of 9,200 samples between 2014-2016 with 80% 67 identification rate totaling 82 species or complexes. Feitosa et al. (2018) surveyed several retail fish 68 markets in northern Brazil from 2014-2016, and from government inspections obtained in 2007, 69 identifying 17 mostly regional and coastally-distributed species from 427 fins. In other cases, reliance 70 on relatively small data sets [n =72 in (Steinke et al., 2017)] may not show the complete spectrum of 71 commercial species. Another issue is that short DNA sequences can sometimes fail to differentiate 72 closely related species. The balance between large sample numbers and a gene region sufficient to 73 determine species identity has been difficult to achieve. Another opportunity is to compare retail 74 outlets in Asia – especially at the heart of the fin trade in Hong Kong – with retail outlets in other parts 75 of the world that have different local shark fisheries and consumer demand.

76 Here we test 1,720 fins collected from a retail outlet on the west coast of the US that was 77 shuttered after shark fin sales were banned. We use sequences of the mitochondrial control region 78 (Giles, Riginos, Naylor, & Ovenden, 2016), compared to published data sources, to estimate the 79 identity of fins on the basis of sequence similarity and phylogenetic placement. For a subset of 961 80 fins, we also sequenced a region of the COI gene, giving us a comparative data set to test the ability of 81 these two gene regions to deliver accurate identifications. Both data sets gave very similar results, 82 showing the existence of up to 41 species in this retail collection. Detailed comparisons suggest that in 83 some species some putative control region sequences are likely to be nuclear pseudogenes. In other 84 samples, bacterial contamination renders COI amplification impossible but CR data appear robust.

86 METHODS

87 Sample collection

88 These data are free and open to the public, and were collected from fins provided by Jenny Giles in a 89 collaborative research program involving Dr. Giles, Steve Palumbi, and Sal Jorgenson focused on 90 genetic identification of shark market products at the Monterey Bay Aquarium and Stanford

91 University (Giles et al. submitted). The samples were derived from a larger collection of fins with a 92 range of physical conditions. Some fins occurred in a dried state, with skin attached (DR). Other dried 93 fins had their skin removed (DRR). Some fins were more processed –wet ceratotrichia from multiple 94 fins were pressed together in sheets (WC). Samples from disparate parts of each of these sheets were 95 punched out and individual ceratotrichia were processed. Representative fins from each separate box 96 or container were collected.

97 We used the IUCN Red List and CITES determinations to classify the conservation status of 98 the identified species. As per previous studies, we consider species listed as data deficient to be 99 threatened, as a central reason for being data poor is low population abundance, and most often when 100 data deficient species are eventually classified they become threatened (N K Dulvy et al., 2014; 101 Jenkins & Van Houtan, 2016).

102 DNA sequencing and alignment

103 DNA extractions were performed using NucleoSpin® Spin Columns (Macherey-Nagel). DNA was 104 amplified and sequenced using standard published methods. For COI amplifications, we used modified 105 Folmer COI primers [FishF1, FishF2, FishR1, FishR2 from (Ward, Zemlak, Innes, Last, & Hebert, 106 2005)], amplified with an extension temperature of 54°C, extension of 72°C, and denaturing of 94°C 107 for 60 seconds each. For the putative control region, 374-521 bp was amplified using the primers GwF 108 (5’-CTGCCCTTGGCTCCCAAAGC-3 )́ (Pardini et al., 2001) and 470r2 (5’- 109 GCCATTAAAGGGAACTAGRGGA-3 ),́ published in Giles et al. (2016).

110 Amplicons were treated with 0.75 units Exonuclease I and 1 unit Shrimp Alkaline Phosphatase (New 111 England Biolabs) per 8 microlitre of template, and were sequenced in one direction using the forward 112 PCR primer by Elim Biopharmaceuticals. Sequence data were aligned and ambiguities resolved 113 manually using CodonCodeAligner ver. 7.1.2 (CodonCode Corporation, Dedham, MA). Data sets of 114 cleaned sequences are in Appendix 1 (Master COI data file) and Appendix 2 (Master CR data file).

115 Constructing COI data base

116 All data used in analyses were derived from public data bases. We used the 1035 sequences of the COI 117 data base of Wong, Shivji, and Hanner (2009) to extract and download one or two individual COI 118 sequences from each of 75 shark species. We were unable to find a COI sequence of the large tooth 119 sawfish Pristis microdon, which appears in our Control Region data set (see below), although Pristis 120 zijsron is available (accession EU398989.1). Likewise, two recently described mitochondrial lineages 121 of the wedgefish genus Rhyncobatus (Giles et al., 2016) and the scoophead hammerhead Sphyra media 122 are available from control region sequences but not COI. Our final reference COI collection consists 123 of 177 sequences (sequences appended to Master COI data file, appendix 1).

124 Constructing the CR database

125 All data used in analyses were derived from public databases. We found 2876 sequences from 126 Genbank with mitochondrial control region sequences from Elasmobranchs (download Dec. 2017), 127 including 363 full mitochondrial genomes. From this set we chose one or two sequences from each 128 species. Because these were of variable length, we trimmed each sequence to the length between our 129 amplification primers (Giles et al., 2016). In addition, we collected representative control region 130 sequences from one representative product sample of each of the species that we found in our 131 Cytochrome oxidase survey. In total our reference data base has 122 sequences from 79 species 132 (sequences appended to Master CR data file, appendix 2).

133 BLAST searches

134 We compared all of our market COI sequences and CR sequences to the full NCBI BLAST data base 135 (in Jan 2018), and recorded the closest species match for each sample. Those species matches were

136 added to the sequence sample name in FASTA format for ease in comparing phylogenetic and 137 sequence distance results. (see appendix 1 and 2)

138 Comparing COI sequences phylogenetically

139 We added 961 COI sequences from individual fin or fin products to the 177 sequences reference set 140 and aligned them using the MAFFT server (Katoh & Standley, 2013). We aligned sequences with 141 default conditions and created a Neighbor-joining phylogenetic tree using Jukes-Cantor sequence 142 evolutionary parameters with bootstrap branch reliability scores. We inspected the resulting tree for 143 clades containing conspecific sequences from Genbank and that contained market sequences 144 determined to be closest to those same species by BLAST. We thus combine a phylogenetic clade- 145 based criterion with a sequence-distance BLAST criterion for assignment of COI sequences to species. 146 For crowded parts of the tree, particularly the genus Carcharhinus, we excluded all other sequences 147 and re-constructed the tree.

148 Comparing CR sequences phylogenetically

149 As a first step, we aligned all 1893 sequences plus 122 references using the MAFFT server. Because 150 control region sequences evolve so quickly, there were no conserved bases in the alignment on which 151 to build a well resolved tree. As a result, we constructed a UPGMA tree in MAFFT based on overall 152 genetic distances. This analysis identified four major clades, allowing us to split the data set. The first 153 clade included the lamnid sharks, and contained 423 sequences, including 346 sequences that 154 subsequently were determined to be pseudogenes. The Carcharhinus sharks consisted of 1044 155 sequences. The genus Spyrna contained 234 sequences, and finally, other Carchariniform sharks 156 consisted of 187 sequences. We re-aligned the sequences within these groups and rebuilt neighbor- 157 joining trees with bootstrap support. As in the analysis of the COI data set, we compared the 158 sequences within defined clades on these phylogenetic trees to their closest BLAST match in our 159 reference database. We also cross referenced the closest BLAST match of the COI sequence from the 160 same fin in 816 cases for which we have both data sets.

161 Assigning names to sequences

162 We determined species names three ways. First, we determined the best match between each of our 163 control region sequences to available databases. Second, we determined the best match of our COI 164 sequences to these databases. Third, we examined the relationship among sequences in our collection 165 and public reference sequences phylogenetically, looking for clusters of sequences that form species 166 groups. Those species groups were defined by diagnostic bases, by statistical reliability of branches 167 (bootstrap percentages), or by simple clustering. The strongest species names were defined by high 168 confidence identification (>97% match for CR and >99% for COI) for both genes and high confidence 169 phylogenetic clustering. For some fins we only had one DNA sequence, and so we relied on high % 170 match for that sequence and phylogenetic clustering.

171

172 RESULTS

173 Below, we detail the results of the dual analyses on COI and control region sequences. Each set of 174 results steps through a set of phylogenetic trees that show the relationship of each sequence we 175 collected to a reference set of sequences from public databases. The large format, full resolution trees 176 are included as figures.

177 COI sequences

178 In total we identified 963 fins as coming from 36-41 species. The uncertainty in species numbers is 179 because certain pairs of species are difficult to distinguish with COI data and some species have 180 multiple clades. Table 1 presents the summary results from COI and the control region. Also shown in 181 this table are the sample sizes for each region, and the phylogenetic criteria used to assign species 4

182 names to samples. The COI tree that we used is in a high definition pdf file in Figure 1A (all COI tree 183 w/ bootstraps). This figure can be expanded to examine any portion of the large, complex tree.

184 A taxonomic breakdown of the COI results shows that no market fins were derived from 185 dogfish (Squalus), catfish (Apristurus), carpet sharks (Nebrius), or Angel sharks (Squatina). Marketing 186 of dogfish fins is less likely because of their small size. However, dogfish make up the biggest shark 187 fishery in the U.S. and there have been calls for their fins to be exempted from state and national shark 188 fin bans.

189 Lamniform sharks

190 The lamnid market samples contain all three species of thresher sharks (Alopias), two species of mako 191 (Isurus), and the salmon shark (Lamna ditrops). COI clades have high bootstrap support (97%-99%) 192 across these species, except for A. superciliosus, the bigeye thresher, with bootstrap support of 55% 193 (Suppl. Fig 1A “all COI tree w bootstraps”). This species has the highest number of samples in our 194 COI data base (n=170), closely followed by Isurus onchyrhyncus, the shortfin mako shark (n=168). 195 DCA1-0004, which has a White Shark control region sequence is not in the COI data set.

196 Carcharhinoform sharks

197 Genus Carcharhinus. The largest number of congeneric species is in the genus Carcharhinus and is 198 reflected in the large number of market samples that cluster within this genus phylogenetically. Close 199 genetic ties among these species makes some identifications with COI difficult. However, there were a 200 number of cases where species formed well-supported clades in the bootstrap tree (Fig. 1B: 201 Carcharhinus COI tree w bootstraps). The Caribbean reef shark (C. perezii) is a common shark in the 202 Caribbean, and is represented here by a single COI sample in a clade defined by an 85% bootstrap. 203 Likewise, six sequences of C. leucas (bull shark) are defined by a 61% bootstrap value. This 204 Carcharhinus COI tree includes 14 other species clades with 41-93% bootstrap values and a total of 205 124 sequences (Table 1).

206 However, many other species of Carcharhinus are not well distinguishable by bootstrap 207 phylogenetic trees because they differ by few substitutions (Wong et al., 2009). In some cases, there 208 are diagnostic nucleotide substitutions that link sequences to certain species [(Wong et al., 2009), 209 Table 3]. For example, our bootstrap tree shows many market samples in a large undifferentiated set 210 representing reference sequences for C. falciformis, isodon, galapagensis and obscurus. Yet, C. 211 falciformis and C. isodon each have two diagnostic bases in the COI region, and C. galapagensis can 212 be distinguished from C. obscurus at two others. We used these diagnostic SNPs (listed in our Table 213 1) to provide species names and could then compare these names to the clades in the phylogenetic 214 analysis. As a result, a UPGMA tree shows a C. falciformis clade that corresponds largely to the 59 215 sequences that contain the C. falciformis diagnostic SNPs. Likewise, a C. isodon clade in the UPGMA 216 tree corresponds to the 15 sequences that show the diagnostic C. isodon SNPs. Diagnostic SNPs in 217 COI do not appear to exist to distinguish C. galapagensis and C. obscurus (Wong et al., 2009). 218 However, two SNPs define the COI clade that contains these two species and in our COI data set, we 219 observe 59 sequences. Another problematic species mixture is the sandbar and bignose sharks, C. 220 plumbeus and C. altimus. These cannot be distinguished by COI sequence alone and make up 17 221 sequences in our COI data base. For C. acronotus, we find two distinct sequence clades that BLAST to 222 this species at 96% or 100% identity (n=3, n=9, respectively). Whether the three sequences with lower 223 identity in a separate clade represent a different species will require further research. The widespread 224 blacktip reef shark (Carcharhinus limbatus) forms a UPGMA clade with 97 sequences. Less widely 225 distributed is the smalltail shark (C. porosus), found from the Gulf of Mexico to northern Brazil. 226 Despite its small size and restricted range, we found 33 sequences.

227 Hammerhead sharks

228 The hammerhead clade within the Carcharhinoformes is represented in our data set by six of the eight 229 named species. The local endemic Sphyrna gilberti (Quattro, Driggers III, Grady, Ulrich, & MA, 230 2013) is missing, possibly because there is no recorded COI sequence. S. zygaena is also missing from 231 our COI data, although this species occurs in the CR data set. S. lewini occurs in three separate clades. 232 Clade I, with ten sequences of Sphyrna lewini appears outside the main Sphyrna clade in the bootstrap 233 phylogeny. This group contains sequences only 96% identical to a second clade of S. lewini that 234 occurs more deeply imbedded in the Sphyrna clade. These two intraspecific clades have the same COI 235 amino acid sequence and differ at only silent sites. This group is also 100% identical to a number of S. 236 lewini sequences on Genbank. The second lewini clade has the most hammerhead sequences in our 237 sample (n=56) and also has several voucher reference sequences on Genbank with 100% identity. 238 These two clades may represent different species, but we will count them together in our data 239 summary.

240 The third S. lewini clade has no Genbank or BOLD reference sequences. Our sequences that 241 fall into this clade have 11 CR sequences that BLAST to S. corona rather than to S. lewini. As a result, 242 this third clade, is probably S. corona.

243 Other Carcharhiniform sharks

244 Within the family Carcharhinidae, but outside the genus Carcharhinus, several genera have defined 245 clades and are found in our collection. These include the tiger shark (Galeocerdo cuvier, n=6), and 246 two species of lemon sharks (Negaprion, n=6). Rhizopriodon species (sharpnose sharks) are extremely 247 similar in their COI sequences and our phylogenetic approach cannot distinguish R. porosus from 248 terraenovae for these 27 sequences. By contrast, R. lalandii and R. acutus appear to have slightly 249 different COI sequences but do not appear in the COI data set.

250 Outside the family Carcharhinidae, there are market samples from a number of Carchariniform 251 sharks in different families. The school shark, Galeorhinus galeus occurs in a small clade of eight 252 samples. Batch BLAST searches originally identified our G. galeus sequences as coming from C. 253 dussumieri or C. obscurus. However, a manual recheck shows 99-100% identity with the Wong et al. 254 (2009) sequences of G. galeus. Two market sequences were included in the clade that included the 255 genus Mustelus. A manual BLAST shows this sample to be 100% identical to M. lunulatus. The other 256 sequence was named by BLAST as M. canis, and is 100% identical to other M. canis in Genbank.

257 Poor sequence reads

258 In addition to these 969 full length, high quality sequences, we obtained 149 sequences with poorer 259 read quality or shorter length. Phylogenetic analysis of these sequences using the same Genbank 260 reference libraries reveals a similar number and distribution of species as the higher quality sequences. 261 In particular, no species were seen in this set that had strong placement in species clades not included 262 in the previous analyses. Because these phylogenetic placements were in general more equivocal than 263 for the high quality sequence, we do not include them in our data summary. In addition, we produced 264 287 COI sequence reads that were such poor quality that they had lengths under 300 bp (n=144) or 265 between 300 and 500 bp (n=143). These sequences were not analyzed further.

266 Bacterial amplification of shark products

267 The final category of COI sequences is a set of 369 amplification products from fin samples that 268 BLAST to bacteria. Of these 244 are identified as Pseudomonas fluoresens, P. sp. or P. veronii (n=62, 269 174, 8 respectively). The rest are identified as generic bacteria, or in the genera Kangiella, 270 Oceanimonas, Ensifer, or Vibrio. Poor sequence quality reduced BLAST confidence in 97 sequences. 271 Most of these bacterial sequences (311 out of 369) are derived from wet ceratotrichia packaged to 272 allow rapid use in restaurants.

273

274 CR Sequences

275 BLAST searches of our CR sequences on Genbank find a >95% match to publicly available data for 276 1,528 of our sequences. Embedded in that number are 1,496 sequences with a >97% match. Left 277 behind are 346 without a reputable >95% match. The largest part of that group is a set of sequences 278 that show a maximum of 77-80% match to any control region sequence in the publicly available 279 control region data for sharks. Below we suggest that these are pseudogenes and conduct a separate 280 analysis to ascertain their value in fin identification.

281 For each clade in each of the phylogenetic trees (see methods), we counted the number of fin 282 CR sequences for which there was the same closest species match for CR and COI (CR=COI), the 283 number for which the two sequences did not match (CR<>COI), the number of samples for which we 284 did not have COI sequence (No COI), and the number of reference sequences from the database. In 285 total, we counted 1888 CR sequences, of which 496 matched the COI sequence, 320 did not match, 286 and 1072 had no COI sequence. The breakdown of these sequence matches by species is in Table 2.

287 Genera outside major clades

288 There are no sequences in our CR data set from the dogfish Squalus, or any sequences in this family, a 289 conclusion that matches our COI data set. In the wedgefish genus Rhyncobatus, we find four species 290 with high bootstrap support (n=6,4,1,1 respectively). This genus is undergoing taxonomic revision 291 (e.g. Giles et al. 2016) and the names of two of these species are not yet determined. The two fins that 292 are identified in the genus Mustelus in the COI data set were not sequenced as part of the CR data set, 293 and this genus does not appear in any other sample.

294 Carcharhiniformes

295 The large number of insertions and deletions in the CR data set interferes with bootstrap analysis 296 because there are few conserved sequence positions that can be included. However, a bootstrap tree 297 shows distinct clades including sequences identified by Genbank samples as the blue shark Prionace 298 glauca (bootstrap 100%, n=72), Rhizoprionodon porosus (bootstrap 89%, n=25), Negaprion acutidens 299 and N. brevirostris (bootstrap 49%, N=5,54, resp.), Galeocerdo cuvier (bootstrap 100%, n=15), and 300 Triaenodon obesus (bootstrap 100%, n=3). (See Fig 2. “Other genera CR tree”).

301 In addition, there are a large number of sequences that cluster in the genus Carcharhinus. To 302 improve tree resolution, these were grouped separately into a separate sequence file trimmed to 475 303 bases to match reference sequences, and run in MAFFT to produce a large UPGMA tree (Fig. 3 304 Carcharhinus CR tree). This improved tree still shows poor bootstrap resolution among most 305 Carcharhinus CR sequences. Nevertheless, within this tree, a series of clades defines a large number 306 of species and sequences. We assign a species name to fin sequences based on their inclusion in 307 distinct sequence clades named by reference samples from Genbank. Further confidence in these 308 clades and assignments comes from evaluating these assignments based on whether the CR 309 identification matches the COI identification. In a few cases, no Genbank sequence exists, and we 310 assign clade names based on COI assignments from the same fins. The following summarizes these 311 results from the bottom to the top of the tree.

312 C. porosus, the blacktip shark, occurs in several large clades of similar sequences (ca. 99% 313 identical, n =107 total). C. limbatus is the most abundant species and occurs in two major clades (n 314 =132, 127 respectively). Two representative sequences from those two clades DCA1_0172 and 315 DCA1_0173 are 98.6% identical, differing at 4 transitions and 2 transversions. By contrast, C. isodon 316 has one small clade of sequences (n=28), highly similar to control regions from whole mitochondrial 317 genomes for this species. A group of 19 sequences cluster together but show highest BLAST hits in 318 the 96-97% identity range for a variety of Carcharhinus species. The COI sequences of five of these 319 also show similarity to a large number of different species, never the same as the best CR BLAST hit. 320 It is not possible to determine what species these 19 sequences derive from these data.

321 For COI, C. plumbeus and C. altimus form a group that cannot be easily distinguished. 322 Although there are CR sequences for C. plumbeus in public data bases, there are currently no C. 323 altimus CR sequences. In our CR data set, C. plumbeus sequences make up a large clade (n=76). Two 324 of the sequences form a clade within this clade and have high affinity to COI C. altimus data (100%) 325 and lower affinity to C. plumbeus CR data (98-99%). Whether these two sequences represent C. 326 altimus (and the others represent C. plumbeus) will demand a series of positively identified individuals 327 sequenced for the control region.

328 A single sequence of C. brachyurus occurs in our data set, clusters well with the reference 329 sequence and has a COI sequence highly similar (100%) to C. brachyurus. In this clade is also a 330 subclade of C. brevipinna with 22 sequences. A large clade of sequences of C. obscurus occurs in 331 three subclades. Subclade 1 has four sequences with high similarity to the reference C. obscurus whole 332 mt genome. A second, large clade shows 98-99%% similarity to the first clade, with 109 sequences. A 333 third clade is a mixture of sequences with highest affinity to C. obscurus (n=16) or C. perezii (n=8). 334 One sequence in this third clade is 99% identical to C. perezii: this same fin has a 99% COI identity to 335 C. perezii. Whether this clade of 24 sequences actually represents C. perezii might require further 336 sampling. The species C. longimanus shows a single clade with 90 sequences, whereas C. 337 melanopterus occurs in a clade of 8. A clade of C. acronotus has 64 sequences, and C. leucas appears 338 with 18. The second most abundant species is C. falciformus (n=179) which occurs in a single clade in 339 our data set.

340 Last, there is a clade of 34 sequences that show no more than 94-96% identity to the closest 341 control region sequences in Genbank. Of the 12 fins with matching COI sequence, there is 100% 342 identity to C. amblyrhyncos in nine of them. (The three other fins have Alopias COI sequences.) There 343 is no C. amblyrhynchos CR sequence on Genbank, but we provisionally ascribe these 23 sequences to 344 C. amblyrhynchos based on their match to COI.

345 Hammerhead clade

346 The hammerhead group is represented by 234 sequences from the same species and clades as the COI 347 data set with the addition of four sequences from Sphyrna zygaena. Unlike the Carcharinids, bootstrap 348 values for hammerhead species assignments were high – ranging from 70-100% (Table 1). As in the 349 COI data set, there were two separate clades of control region sequences in S. lewini and a separate 350 clade for S. corona. There were 38 sequences of S. mokarran, two of which appeared in a related but 351 3-4% divergent clade. (Fig 4: Sphyrna CR tree).

352 Pseudogene sequences in Lamnid sharks

353 Our phylogenetic data and BLAST searches for the CR sequences show a virtual absence of Isurus or 354 A. pelagicus, despite the large occurrence of these taxa in the COI data set. Many CR sequences from 355 fins identified with COI in Isurus and Alopias are a poor match to vouchered CR sequences. For 356 example, sample DCA1-0745 has an Alopias pelagicus COI sequence (100% identical to 357 JN315429.1), but its CR sequence is only 75% identical to the control region sequence from the A. 358 pelagicus mtDNA genome sequence on Genbank (NC_022822.1). The closest match to the CR 359 sequence of DCA1-0745 is to a Lamnid shark in the genus Megachasma, at 77% identity. Overall, we 360 have 299 sequences that BLAST best to this genus at 77-81% identity.

361 To investigate this further, we generated a phylogenetic tree from control region sequences of 362 Lamnid species from Genbank including Isurus and Alopias (Fig. 5). Genbank sequences from full 363 mitochondrial genomes group together in this clade, along with sequences from other lamnid sharks 364 including two Isurus species, A. pelagicus and a large number of our market sequences from A. 365 superciliosus. (red labels in Figure 5). However, most of our market sample CR sequences from 366 lamnid sharks form a clade separate from the clade defined by vouchered whole mitochondrial 367 genomes. (upper, black labelled samples in Fig. 5). The other clade differs by about 20-24% and has

368 no voucher sequences from full mitochondrial genomes. Instead it has exclusively sequences we 369 generated with our CR primers from market samples. These include most of our market sequences 370 from I. onchyrhyncus, I. paucus, and Alopias pelagicus samples.

371 One overall explanation for these data is that our control region primers typically amplify a 372 different, but related, gene region in Isurus and most Alopias sharks. Because there are no duplicate 373 control region sequences in the Alopias full mt genome, this duplicate, related gene region is likely to 374 be a mitochondrial pseudogene (e.g., Bensasson, Zhang, Hartl, & Hewitt, 2001).

375 Species differences show lower divergence among pseudogenes

376 The clade of sequences from validated mitochondrial genomes differ between species more than do 377 our amplified fragments from the other clade. For example, nucleotide divergence of I. paucus and I. 378 oxyrhincus is 8% for Genbank mitochondrial CR sequences: transversions outnumber transitions 19 to 379 12. Between the I. paucus and I. oxyrhinucs sequences we amplified in the other clade, we find only 380 1.5% divergence (4 transitions and 3 transversions) along with 18 insertion/deletions. High divergence 381 in the validated mitochondrial clade is expected given the generally higher rate of molecular evolution 382 in mtDNA (Avise, 2012). By comparison, COI sequences from these same two I. paucus and I. 383 oxyrhinucs individuals differed at 12% of 631 sites, including 58 transitions and 17 transversions, 384 suggesting that the lower sequence clade in Figure 6 is evolving much like other mtDNA genes.

385 True Lamnid mtDNA CR sequences in some species

386 The genus Isurus comprises a sizeable fraction of our COI data set, but there are only three sequences 387 from our CR data that BLAST highly and cluster phylogenetically to the available Isurus CR 388 sequences. Likewise, Alopias pelagicus is common in our COI data set but absent in the CR data set 389 despite a reference control region sequence from the complete mitochondrial genome of this species. 390 By contrast, we have 72 sequences of Alopias superciliosus that form a good clade with the control 391 region sequence from the mitochondrial genome of this species (lower clade in Figure 6). In addition 392 there are sequences from I. oxyrhincus (n =1), and I. paucus (n=2) in the clade of true CR sequences.

393 Two genes amplify from CR primers in some species

394 Multiple sequence products from individual fins can complicate identification. In our case, we 395 sometimes find sequences from different individuals of the same species in different clades: for 396 example, sequences from two I. oxyrhincus individuals identified as conspecifics by COI sequence 397 appear in different CR clades and differ by 21%. Likewise, phylogenetic trees of Alopias superciliosus 398 CR sequences from our fin sample suggest a mixture of valid control region sequences and pseudo-CR 399 data (Fig. 6, versus Fig. 7). Altogether, the phylogenetic tree shows 72 sequences of A. superciliosus 400 CR and 11 pseudoCR. The other two species, A. vulpinus and A. pelagicus have 1 and 7 pseudoCR 401 sequences, respectively. By contrast, Isurus oxyrhincus shows a large number of pseudoCR sequences 402 (296) and perhaps one true CR. The species I. paucus also is dominated by pseudoCR sequences 403 (n=9), with two valid CR.

404 Using pseudogenes in fin identifications

405 We can still use these pseudo-CR sequences in fin identification. First, we find fins that have been 406 identified as Isurus or Aolpias species by their COI sequences. Then we use the CR sequences from 407 these as references to identify species-specific clades of pseudo-CR sequences from other fins. 408 Effectively, this uses the COI identifications as a reference set of fins from which we derive species- 409 specific pseudo-CR data sets. This assignment identifies 305 sequences from I. oxyrhincus, 9 from I. 410 paucus, 14 from A. superciliosus, and 8 from A. pelagicus (Fig. 7). These pseudogene numbers are in 411 addition to the numbers of valid CR sequences: I. oxyrhincus =1, I. paucus =2, A. superciliosus =72, 412 and A. pelagicus =0. However, an analysis of both data sets, (Fig. 8 see below), suggests caution in

413 using CR sequences because species with these pseudogenes are seen in many fewer fins than 414 suggested by the COI data set.

415 Good CR amplifications for bacterial-laden samples

416 In our COI data set, 369 samples provided bacterial sequences. Of these, 284 amplified with our CR 417 primers, and 236 provided good CR sequence, demonstrating that these samples retained shark 418 mtDNA despite bacterial contamination. Most of these samples were from wet ceratotrichia 419 collections that had been stored at room temperature for weeks to months before processing. This 420 category of specimen is rare in shark fin samples. The species composition was similar to the 421 composition from the rest of the CR data set. Six samples BLASTed to Megachasma pelagios at low 422 similarity (80%), suggesting these were Lamnid sequences. Forty-eight sequences amplified the CR 423 region but did not return good sequence.

424 Comparison of CR and COI identities

425 In our data set of 1528 CR sequences with strong matches to Genbank, we also have COI data for 802. 426 Of these, 669 show a match between the species identities derived from the two different genes. 427 However, 133 show a high (>95%) match to a reference control region sequence but show a different 428 species match (also at high % identity) for COI. This mismatch calls into question these sequence 429 identifications. To resolve this, we re-sequenced a set of these mismatched samples for the 430 mitochondrial 16S gene or cytochrome b and found that the 16S species identity matches the COI 431 identity in about half the cases, and matches the CR identity in the other half. There are ten cases in 432 which a third species is discovered this way. As a result of the uncertainty that this causes in species 433 identifications, we have removed these sequences from our compilations.

434 Summary across all analyses

435 Table 2 compiles the species names derived from the CR data set, including cases where CR and COI 436 labels match, when they do not match, and when we do not have COI data. We then show the species 437 totals in Table 1, not including the cases where CR and COI sequences have high identity but do not 438 match.

439 Overall, we can identify 969 fin products by COI sequence as belonging to 38-41 species, 440 including 16-18 species of Carcharinus. We also identified 1,736 fins using control region sequences, 441 showing 41-43 species, including the vast majority of the species from the COI data set. Table 1 442 shows that the most common species are thresher sharks, mako sharks, hammerhead and blue sharks, 443 ocean species that have been seen widely in prior surveys of shark fin markets (e.g., Clarke et al., 444 2006). However, we also see a large number of samples and species of coastal requiem sharks in the 445 genus Carcharhinus, as well as a diverse collection of hammerheads in seven of eight named species. 446 The species targeted by the single biggest US shark fishery, spiny dogfish, does not appear among any 447 of our fin products.

448 The species list in our shop data sets (summarized in Table 1) include 14-20 vulnerable 449 species (IUCN Red list) and 3 endangered species. Six additional species the IUCN considers data 450 deficient, and 6 species are specifically regulated under CITES. Altogether, the vulnerable, 451 endangered and CITES species make up 36% of the species and 56% (CR) to 66% (COI) of the 452 individual fin products. Of the CITES listed species, only the whale shark, basking shark and 453 porbeagle (Lamna nasus) are not in our DNA sequence collection.

454 The Lamnid shark group and the hammerhead group have high fractions of vulnerable, 455 endangered or CITEs regulated species, and both have high frequency in our sample. Likewise, seven 456 of eight named hammerhead species are in our data set, including all five vulnerable, endangered or 457 CITES regulated species. Only the newly described endemic S. gilbert is not in our data set.

458 Yet our data also show a wide variety of sharks that have not yet caught conservation 459 attention, including a number of Carcharhinus species. We see 16-18 species of Carcharhinus sharks 460 with an average number of individuals per species of 21 and 48 for COI and CR, respectively. These 461 include widely ranging sharks such as the blacktip (C. limbatus), sandbar (C. plumbeus) and dusky 462 sharks (C. obscurus). But we also see large numbers of more restricted species such as the shorttail 463 shark (C. porosus) which lives in muddy estuaries in the western Atlantic, the blacknose (C. 464 acronotus), inhabiting sandy habitats in the same regions, and the sharpnosed sharks (genus 465 Rhizopionodon) found in Atlantic or Caribbean waters. Coastal sharks such as these are in contrast to 466 the oceanic, pelagic sharks that have been the focus of a large shark fin fishery and large shark fin 467 concern. Our data confirm that the diversity of coastal sharks is also a target of active shark finning.

468

469 DISCUSSION

470 Our data show a large variety of sharks with great taxonomic diversity across the retail market sample. 471 The COI data set provides identification of 36-39 species of sharks, including 17-19 Carcharhinus 472 species, from 963 fin products. Likewise, the Control Region data set shows 38-41 species, including 473 the vast majority of the species from the COI data set.

474 These species represent a large fraction of the known endangered, vulnerable or data deficient 475 sharks in the world: more than 20 species in those categories occur in our data set. Moreover, 56-66% 476 of the fins in our data set derive from these categories of sharks, largely because of the preponderance 477 of thresher, mako and hammerhead sharks in the sample.

478 Our data bolster several recent retail market surveys that have also concluded that the shark fin 479 market is highly diverse and highly endangered (Cardeñosa et al., 2018; Feitosa et al., 2018; Fields et 480 al., 2018; Steinke et al., 2017). Steinke et al. (2017) found 20 species in 72 shark samples from 481 Vancouver, Canada. Fields et al. (2018) found 59 species and 17 higher taxonomic groups when they 482 monitored 3,952 samples from Hong Kong retail shops from 2014-2015. Similarly, Cardeñosa et al. 483 (2018) found 82 species and species complexes in Hong Kong among small fin discards in 2016. 484 Feitosa et al. (2018) found 17 predominantly nearshore species from 427 fin samples collected in 485 northeastern Brazil. In these cases, and the samples reported here, some similarities emerge. All 486 samples show a large number of endangered and threatened species. Thresher, hammerhead and mako 487 sharks are abundant (especially Alopias superciliosus, Sphyrna lewini, and Isurus oxyrhincus). 488 Abundant Carcharhinus samples include C. falciformis, C. limbatus, and C. longimanus, though there 489 is a wide variety of other Carcharhinus species – generally at low and variable abundance - in the 490 larger samples.

491 There are also some striking differences. The Alopias/Isurus group dominates the small 492 Steinke sample (Table 1). The Alopias/Isurus group is also abundant in our sample, dominated by A. 493 superciliosus and I. oxyrhincus. Yet in the Hong Kong shops sampled by Fields et al. (2018) and 494 Cardeñosa et al. (2018), this group is a minor component. By contrast, the Fields et al. (2018) and 495 Cardeñosa et al. (2018) samples are dominated by blue sharks, a single species in the Carcharhinidae 496 that makes up nearly half their samples. Blue sharks occur in our sample, and in Steinke et al. (2017), 497 at about 2-10%. Blue sharks also dominated the earlier sample of Clarke et al. (2006) from the Hong 498 Kong wholesale market, prompting Fields et al. (2018) to ask how blue sharks could maintain their 499 market presence at such a high level for so long. The relatively lower number of blue shark fins in 500 retail markets on the US west coast may partially answer this question if there is a strong regional 501 difference in market availability of this species. No blue sharks occur in the Brazil samples, which is 502 dominated by regional sharpnose and Carcharhinus species (Feitosa et al., 2018).

503 Comparison across genes and methods

504 There is strong evidence from these data that the CR and COI generally produce data equivalently well 505 for most sharks, but that using CR primers specifically underestimates thresher shark abundance. The 506 number of shark fins in our COI data set for each species is highly correlated to the number of fins we 2 507 find with our CR primers (r =0.91, Fig. 8). However there are two strong outliers. For both Alopias 508 superciliosus and A. pelagicus the number of fins observed with CR primers, even taking in to account 509 the fins identified with pseudo-gene CR sequences - falls far below the line relating COI and CR 510 results (Fig. 8).

511 These outliers are because Alopias fins defined by COI sequences frequently fail to show Alopias CR 512 sequences: 48 of the 208 Alopias fins with COI sequences have CR sequences with high identity to a 513 different species, all C. falciformis, C. obscurus, and C. longimanus (see Table 3). These CR 514 sequences are not Alopias pseudo-genes. Our hypothesis is that these CR identifications are incorrect, 515 and derive from failure of the CR primers to easily amplify Alopias CR regions, amplifying common 516 Carcharhinus species DNA as lab contaminants.

517 The lowest red point in Figure 8 represents very different identification rates for COI and CR for A. 518 pelagicus: COI data show 38 fins for this species out of a total of 963 fins, but we find only 8 out of 519 1736 CR sequences. Lab records show that failure rate of CR amplifications of fins that have a A. 520 pelagicus COI sequences is high. We searched for a possible explanation for this underrepresentation 521 and found that the reverse primer from (Giles et al., 2016) does not match A. pelagicus at four of 22 522 positions, making it a poor amplification tool (Fig. 9). The match to A. superciliosus is better: 21 of 22 523 bases match. But the 3’ end base, the most crucial one for the polymerase chain reaction, does not 524 match. This may make this primer less valuable for this species as well.

525 Conservation status

526 Our data confirm the strong abundance of endangered, vulnerable and CITES listed shark species in 527 retail fin markets. As in previous surveys, we find about half the fins come from species of 528 conservation concern. This consistency is particularly important because it spans very different types 529 of retail markets, in Hong Kong and the US west coast, imbedded in very different fisheries cultures 530 and retail markets. In particular, the US has made strong strides in recent years in regulating fisheries, 531 and returning overfished stocks to sustainability (Barner et al., 2015). Yet the shark markets in the US 532 and Hong Kong remain quite similar in the presence of protected species. This suggests that fisheries 533 policy improvements in the US have not penetrated the fin trade, and that highly regulated US 534 fisheries do not contribute much to the retail fin market. This suggestion is supported by lack of fins 535 from the biggest US shark fishery, spiny dogfish (squalus acanthias), both in the US west coast and 536 Hong Kong retail fin market (Cardeñosa et al., 2018; Feitosa et al., 2018; Fields et al., 2018; Steinke et 537 al., 2017).

538 There have been a series of other questions asked of the global shark fishery, notably about the 539 persistence of some abundant fins on the global market from the same species for over a decade 540 (Davidson, Krawchuk, & Dulvy, 2016; Fields et al., 2018). For example, blue sharks were a dominant 541 feature of the Hong Kong market as shown in (Clarke et al., 2006), and again a decade later 542 (Cardeñosa et al., 2018; Fields et al., 2018). Such dominance of a global market by a single species 543 might suggest higher sustainability for this species than thought originally. However, our data show 544 many fewer blue sharks, in contrast to nearly 50% of the samples being blue sharks in the Hong Kong 545 retail market (Cardeñosa et al., 2018; Fields et al., 2018), we show no more that 4% in our survey. 546 Likewise, bull sharks and sickle fin lemon sharks are at a much higher percentage in the Hong Kong 547 market than in the US west coast. By contrast, our data show a higher abundance of bigeye thresher 548 and the Atlantic smalltail sharks than seen in Hong Kong. These differences suggest that a single 549 market can provide an incomplete picture of the global trade and call for more coordinated fin testing 550 at high levels of sampling.

551

552 ACKNOWLEDGMENTS 553 J. Giles provided assistance with data collection, technical issues, and laboratory supervision. 554 555 FUNDING 556 This research was supported through generous contributions to the Monterey Bay Aquarium. 557 558 COMPETING INTERESTS 559 The authors declare there are no competing interests. Stephen Palumbi is an employee of Stanford 560 University. Salvador Jorgensen and Kyle Van Houtan are employees of the Monterey Bay Aquarium. 561 562 AUTHOR CONTRIBUTIONS 563 SP oversaw data collection experiments, analyzed the data, contributed reagents/materials/analysis 564 tools, and prepared figures and tables. 565 566 KR collected data and performed lab work. 567 568 SP, SJ, KV, KR conceived and designed the experiments, authored or reviewed drafts of the paper, 569 and approved the final draft. 570 571 DATA AVAILABILITY 572 All data and supplemental files are available open-access via the Open Science Framework, available 573 at https://osf.io/9d65y/ and through the following DOI:10.17605/OSF.IO/9D65Y. 574 575 SUPLLEMENTAL INFORMATION 576 Supplemental information for this article can be found online. 577

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633 Table 1: COI and CR sequences identifications for this study, compared to recently published studies.

TAXON FAMILY GENUS SPECIES COMMON MBA MBA STIENKE FIELDS FEITOSA IUCN CITES GROUP NAME NAME NAME NAME COI CR COI COI COI STATUS STATUS thresher sharks Alopiidae Alopias pelagicus pelagic thresher shark 38 8 12 19 -- VU II thresher sharks Alopiidae Alopias superciliosus bigeye thresher shark 170 95 8 37 -- VU II thresher sharks Alopiidae Alopias vulpinus common thresher shark 1 1 1 2 -- VU II lamnid sharks Lamnidae Isurus paucus longfin mako shark 12 11 3 4 -- VU -- lamnid sharks Lamnidae Isurus oxyrinchus shortfin mako shark 168 306 8 133 -- VU -- lamnid sharks Lamnidae Lamna ditropis salmon shark 1 1 3 17 -- LC -- lamnid sharks Lamnidae Lamna nasus porbeagle shark -- 0 5 6 -- VU II lamnid sharks Lamnidae Carcharodon carcharias white shark 0 1 ------VU II ground sharks Triakidae Mustelus canis dusky smooth-hound 1 -- -- 3 8 NT -- ground sharks Triakidae Mustelus lunulatus sicklefin smooth-hound 1 -- 1 17 -- LC -- ground sharks Triakidae Mustelus mustelus common smooth-hound ------10 -- VU -- ground sharks Triakidae Mustelus mosis Arabian smooth-hound ------12 -- DD -- ground sharks Triakidae Mustelus higmani smalleye smooth-hound 0 0 0 0 8 LC -- requiem sharks Carcharhinidae Galeorhinus galeus school shark 8 -- -- 19 -- VU -- requiem sharks Carcharhinidae Rhizoprionodon porosus/terraenovae Caribbean sharpnose shark 27 27 1 17 142 LC -- requiem sharks Carcharhinidae Rhizoprionodon acutus milk shark -- -- 3 66 -- LC -- requiem sharks Carcharhinidae Rhizoprionodon longurio Pacific sharpnose shark ------7 -- DD -- requiem sharks Carcharhinidae Rhizoprionodon lalandii Brazilian sharpnose shark 0 0 0 0 1 DD -- carpet sharks Ginglymostomatidae Ginglymostoma cirratum nurse shark 0 0 0 0 14 DD -- hammerheads Sphyrnidae Sphyrna zygaena smooth hammerhead 0 4 -- 165 -- VU II hammerheads Sphyrnidae Sphyrna mokarran great hammerhead 10 38 2 41 40 EN II hammerheads Sphyrnidae Sphyrna tiburo bonnethead 11 11 -- 3 12 LC -- hammerheads Sphyrnidae Sphyrna corona scalloped bonnethead 11 6 -- 0.01 -- NT -- hammerheads Sphyrnidae Sphyrna lewini clade 1 scalloped hammerhead 10 24 7 0 18 EN II hammerheads Sphyrnidae Sphyrna lewini clade 2 scalloped hammerhead 56 92 -- 196 -- EN II hammerheads Sphyrnidae Sphyrna media scoophead 4 5 -- 0.01 -- DD -- hammerheads Sphyrnidae Sphyrna tudes smalleye hammerhead 20 38 -- 0.01 10 VU -- requiem sharks Carcharhinidae Triaenodon obesus whitetip reef shark 4 2 -- 1 -- NT -- requiem sharks Carcharhinidae Prionace glauca blue shark 42 72 7 1632 -- NT -- requiem sharks Carcharhinidae Galeocerdo cuvier tiger shark 6 15 -- 16 12 NT -- requiem sharks Carcharhinidae Negaprion acutidens sicklefin lemon shark 3 5 1 29 -- VU -- requiem sharks Carcharhinidae Negaprion brevirostris lemon shark 3 54 -- 5 -- NT -- ground sharks Hemigaleidae Hemipristis elongata snaggletooth shark -- 0 -- 5 -- VU -- requiem sharks Carcharhinidae Lamiopsis temminckii broadfin shark -- 0 -- 4 -- EN -- requiem sharks Carcharhinidae Carcharhinus amblyrhynchos grey reef shark 8 34 1 15 -- NT -- requiem sharks Carcharhinidae Carcharhinus signatus night shark 1 1 -- 0 -- VU -- requiem sharks Carcharhinidae Carcharhinus brevipinna spinner shark 12 22 1 55 -- NT -- requiem sharks Carcharhinidae Carcharhinus brachyurus copper shark 1 1 -- 13 -- NT -- requiem sharks Carcharhinidae Carcharhinus melanopterus I blacktip reef shark 4 8 -- 2 -- NT -- requiem sharks Carcharhinidae Carcharhinus longimanus oceanic whitetip shark 26 64 -- 48 -- VU II requiem sharks Carcharhinidae Carcharhinus melanopterus II blacktip reef shark 3 0 -- 0 -- NT -- requiem sharks Carcharhinidae Carcharhinus leucas bull shark 6 18 -- 87 17 NT -- requiem sharks Carcharhinidae Carcharhinus perezii Caribbean reef shark 1 20 -- 0.01 -- NT -- requiem sharks Carcharhinidae Carcharhinus falciformis silky shark 59 127 -- 483 11 NT II requiem sharks Carcharhinidae Carcharhinus isodon finetooth shark 15 18 -- 6 -- LC -- requiem sharks Carcharhinidae Carcharhinus galapagensis=obscurus Galapagos/Dusky 59 87 1 42 -- VU -- requiem sharks Carcharhinidae Carcharhinus acronotus blacknose shark 12 61 -- 9 68 NT -- requiem sharks Carcharhinidae Carcharhinus plumbeus=altimus Sandbar/Bignose 19 72 -- 11 -- VU -- requiem sharks Carcharhinidae Carcharhinus limbatus blacktip shark 97 254 1 219 9 NT -- requiem sharks Carcharhinidae Carcharhinus porosus smalltail shark 33 105 -- 2 42 DD -- requiem sharks Carcharhinidae Carcharhinus amboinensis pigeye shark ------54 -- DD -- requiem sharks Carcharhinidae Carcharhinus leiodon smoothtooth shark -- -- 2 -- -- VU -- requiem sharks Carcharhinidae Carcharhinus dussumieri whitecheek shark ------14 -- NT -- requiem sharks Carcharhinidae Carcharhinus sorrah spot-tail shark ------50 -- NT -- requiem sharks Carcharhinidae Carcharhinus albimarginatus silvertip shark ------5 -- VU -- requiem sharks Carcharhinidae Carcharhinus macloti hardnose shark ------6 -- NT -- requiem sharks Carcharhinidae Isogomphodon oxyrhynchus daggernose shark 0 0 0 0 14 CR -- requiem sharks Carcharhinidae ------0 0 -- 114 -- NT -- dogfishes Squalidae Squalus -- dogfishes ------19 -- DD -- dogfishes Squalidae Squalus brevirostris/megalops shortnose spurdog 0 0 0 0 1 DD -- squaliform sharks Centrophoridae Deania profundorum arrowhead dogfish ------4 -- LC -- squaliform sharks Dalatiidae Dalatias licha kitefin shark ------53 -- NT -- chimaeras Callorhinchidae Callorhinchus -- elephantfish ------27 -- LC -- carpet sharks Hemiscylliidae Chiloscyllium -- bamboo sharks ------21 -- NT -- chimaeras Chimaeridae Hydrolagus -- chimaeras ------14 -- LC -- whale shark Rhincodontidae Rhincodon typus whale shark -- -- 4 -- -- EN II wedgefishes Rhinidae Rhyncobatus [ Gulf species ] unk wedgefish -- 1 ------VU -- wedgefishes Rhinidae Rhynchobatus laevis smoothnose wedgefish -- 4 ------VU -- wedgefishes Rhinidae Rhynchobatus australiae whitespotted wedgefish -- 6 -- 26 -- VU -- wedgefishes Rhinidae Rhynchobatus djiddensis giant guitarfish -- 1 ------VU -- 634 -- Mixed rare 17 rare species ------26 ------15

635 Table 2: Comparison of best BLAST or phylogenetic identification for CR and COI gene sequences. 636 CR=COI represents the number of fins that showed the same identification for both genes. CR<>COI 637 represents fins with identifications that do not match. No COI represents fins for which there is no 638 COI sequence. Refs is the number of reference sequences from Genbank in the phylogeneytic clades 639 defining species. 640 Table 2: Clade and BLAST identification of CR sequences compared to COI total without Clade CR=COI CR<>COI No COI CR<>COI Refs Notes Taxon totals Lamnid A. superciliosus 39 0 33 72 2 A. pelagicus 0 0 0 0 1 I.oxyrhincus 1 0 0 1 0 I. paucus 0 0 2 2 3 L. ditropis 1 0 0 1 1 Carcharodon carcharias 0 0 1 1 1 77 Hammerheads S. lewini 46 2 70 116 2 S. tudes 19 0 19 38 2 S. media 0 4 5 5 1 4 all tudes S. tiburo 7 0 4 11 3 refs in diff clade S. corona 0 10 6 6 1 10 all lewini S. mokarran 9 0 29 38 2 S. zygaena 0 0 4 4 2 234 Charchariacea C. porosus 28 2 77 105 0 C. limbatus clade 1 20 0 112 132 0 C. limbatus clade 2 74 5 48 122 1 wrong ref! C. isodon 11 10 7 18 6 C. noname 2 1 3 15 16 0 C. plumbeus 14 4 58 72 4 C. brachyurus 1 0 0 1 0 C. brevipinna 12 0 10 22 2 C. obscurus clade 1 0 1 3 3 0 C. obscurus clade 2 51 25 33 84 2 C. obscurus clade 3 0 4 20 20 1 perezii? C. longimanus 26 26 38 64 2 C. melanopterus 7 0 1 8 2 C. acronotus 11 3 50 61 2 C. falciformis 32 52 95 127 2 C. noname 1 0 2 0 0 3 C. amblyrhyncus 23 0 11 34 0 C. leucas 6 0 12 18 3 1044 439 153 763 1202 51 1355 Rhyncobatus Rhynchobatus australiae 0 0 6 6 3 Rhynchobatus cf. 0 0 4 4 2 Rhynchobatus Gulf 0 0 1 1 1 Rhynchobatus Red Sea 0 0 1 1 1 Other genera P. glauca 13 0 59 72 1

Rhizopriodon porosus 23 0 2 25 1 Rhizopriodon terraenovae 1 0 1 2 1

Negaprion brevirostis 3 0 51 54 2 Negaprion acutidens 3 0 2 5 2 Triaenodon obesus 2 0 0 2 1 Galeocero cuvier 5 0 10 15 2

Pseudogene sequences (BLAST to Megamouth) I. oxyrinchus 135 161 296 I. paucus 6 3 9 A.superciliosus 3 8 2 13 A.pelagicus 0 6 1 7 A. vulpinus 0 1 0 1

Pseudogene sequences BLAST to Alopias A. pelagicus 1 1 I. oxyrynchus 0 6 3 9 86 % bootstrap A. superciliosus 3 0 0 3

Pseudogene sequences BLAST to P. kamoharai A. superciliosus 0 5 2 7 0 All pseudogenes 7 167 172 346 0 346 0 641 496 167 1072 1568 68 1735 1389 642

643 Table 3: Fins with high fidelity COI sequence identifications (left column) that have different CR 644 identifications, mostly to three species of common Carcharhinus sharks. 645 646 Table 3: Fins with high fidelity CR identifications that have different COI identifications Identity of CR sequence: 647 COI identity: Total C.falciformis CR C.longimanus CR C.obscurus CR other 648 All 133 57 28 25 23 649 Alopias COI 48 15 16 17 0 650 Galeocerdo COI 8 1 2 2 3 Isurus 34 33 1 0 0 651 Prionace 17 2 9 6 0 652 0ther 26 6 0 0 20 653 654

655 FIGURE LEGENDS

656 Figure 1A: All COI tree with bootstraps. All phylogenetic trees are expandable jpg files. Each shows 657 our market samples labeled as ‘DCA’ plus a sample number, followed by the best BLAST search of 658 the COI sequence from that sample, where available, then the best BLAST search of the CR sequence 659 from that sample. 660 661 Figure 1B: Carcharhinus COI tree with bootstraps. 662 663 Figure 2: Other genera CR tree 664 665 Figure 3: Carcharhinus CR tree 666 667 Figure 4: Sphyrna CR tree. 668 669 Figure 5: Unexpected amplification of pseudogenes. The figure shows phylogenetic relationships 670 among mitochondrial control region sequences (red labels) from Genbank and sequences from MBAq 671 fins derived from our control region primers (black labels). The top black-labelled cluster of sequences 672 from Alopias and Isurus species are 20-25% divergent from known mitochondrial sequences from the 673 same species. These black-labelled sequences are probably mitochondrial pseudogenes, sequences 674 originally from the mitochondria that were passed into the nucleus long ago and no longer function. 675 One exception is a set of Alopias superciliosus sequences from our data set that appear to be valid 676 control region sequences. 677 678 Figure 6: Lamnid CR sequence tree. Sequences that amplify with CR primer and that cluster with CR 679 sequences from whole mitochondrial genomes are shown in the lower clade, suggesting that these 680 sequences are from true Control Regions section of mtDNA. The upper clade, starting with 681 DCA_0857 are CR amplified sequences that are highly divergent, suggesting they are pseudogene 682 sequences. 683 684 Figure 7: Numerous sequences amplified with CR primers from lamnid sharks that form a clade 685 separate from the clade defined by vouchered whole mitochondrial genomes. These sequences have 686 only a best match of 70-80% match to M. pelagios or P. kamoharai or C. Taurus, and group together 687 with the putative pseudogene sequences in the upper clades of Figures 5 and 6. We use the species 688 identification of a subset of these fins based on COI to define species clades, and use membership of a 689 fin in one of these clades to assign the species name to that fin. For example, the first sequence at the 690 top of this tree (DCA1_0566) came from a fin with a COI sequence with a 99% match to A. pelagicus. 691 Another fin (DCA1_2250) is in this pseudo-CR sequence clade but has no COI sequence. We can use 692 the presence of DCA1_2250 in this clade as good evidence that it is a fin from A. pelagicus as well.

693 Figure 8: Good correlation between the number of fins seen for each species based on COI data (x- 694 axis) compared to the control region (CR) data (y-axis). Two exceptions (red dots) are two species of 695 Alopias, which appear to be underestimated with CR primers compared to COI primers.

696 Figure 9: Mismatch between our reverse Control Region primer and the mitochondrial sequence of 697 Alopias pelagicus may explain the strong underestimate of this species in our CR data set. The reverse 698 CR primer is shown as the reverse complement of the synthesized reverse primer to correspond to the 699 published sequence.

bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not 12/28/2017certified by peer review) is the author/funder, who has granted bioRxiv a licensePhylo.io to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Zoom:

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418_DCA1_1034Carcharhinus_falciformis 0 395_DCA1_1090Carcharhinus_falciformis 0 389_DCA1_1772Carcharhinus_falciformis 0 412_DCA1_1292Carcharhinus_falciformis 0 245_DCA1_0552Carcharhinus_falciformis 0 226_DCA1_1971Carcharhinus_falciformis 0 1033_ESHKC125-07_Carcharhinus_falciformisQWX 0 359_DCA1_1475Carcharhinus_acronotus 0 251_DCA1_2821Carcharhinus_isodon 0 430_DCA1_1431Carcharhinus_isodon 0 435_DCA1_1289Carcharhinus_isodon 0 1084_ESHKC065-07_Carcharhinus_acronotusQWX 0 303_DCA1_0542Carcharhinus_obscurus 0 318_DCA1_0860Carcharhinus_obscurus 0 315_DCA1_0572Carcharhinus_obscurus 0 324_DCA1_1962Carcharhinus_obscurus 0 524_DCA1_0678Carcharhinus_obscurus 0 311_DCA1_0747Carcharhinus_obscurus 0 325_DCA1_0767Carcharhinus_obscurus 0 538_DCA1_1774Carcharhinus_obscurus 0 547_DCA1_0450Carcharhinus_obscurus 0 313_DCA1_0799Carcharhinus_obscurus 0 422_DCA1_1749Carcharhinus_galapagensis 0 1007_FJ519095_1_Carcharhinus_galapagensis 0 528_DCA1_1763Carcharhinus_obscurus 0 558_DCA1_1480Carcharhinus_plumbeus 0 554_DCA1_0164Carcharhinus_plumbeus 0 365_DCA1_0690Carcharhinus_altimus 0 1087_ESHKC097-07_Carcharhinus_altimusQWX 0 962_Carcharhinus_acronotus 0 790_DCA1_0526Prionace_glauca 0 796_DCA1_0754Prionace_glauca 0 767_DCA1_0541Prionace_glauca 0 772_DCA1_0594Prionace_glauca 0 989_Prionace_glauca 0 782_DCA1_2164Prionace_glauca 0 788_DCA1_0650Prionace_glauca 0 766_DCA1_0887Prionace_glauca 0 1106_ESHKD010-07_Prionace_glaucaQWX 210_DCA1_2155Carcharhinus_acronotus 517_DCA1_1319Carcharhinus_melanopterus 414_DCA1_1335Carcharhinus_falciformis 516_DCA1_1350Carcharhinus_melanopterus 2 390_DCA1_1470Carcharhinus_falciformis 0 43 1015_ESHKC081-07_Carcharhinus_amboinensisQWX 0 1089_ESHKC078-07_Carcharhinus_amboinensisQWX 0 230_DCA1_1963Carcharhinus_falciformis 0 240_DCA1_1953Carcharhinus_falciformis 0 397_DCA1_1494Carcharhinus_falciformis 0 403_DCA1_1163Carcharhinus_falciformis 0 243_DCA1_0740Carcharhinus_falciformis 0 419_DCA1_1400Carcharhinus_falciformis 0 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317_DCA1_0538Carcharhinus_obscurus 0 323_DCA1_0774Carcharhinus_obscurus 0 312_DCA1_0782Carcharhinus_obscurus 0 328_DCA1_0781Carcharhinus_obscurus 0 541_DCA1_0524Carcharhinus_obscurus 0 531_DCA1_1142Carcharhinus_obscurus 0 533_DCA1_0670Carcharhinus_obscurus 0 329_DCA1_0796Carcharhinus_obscurus 0 322_DCA1_0730Carcharhinus_obscurus 0 310_DCA1_0598Carcharhinus_obscurus 0 309_DCA1_0842Carcharhinus_obscurus 0 523_DCA1_0653Carcharhinus_obscurus 0 1009_ESHKC062-07_Carcharhinus_acronotusQWX 0 434_DCA1_1121Carcharhinus_isodon 0 429_DCA1_1442Carcharhinus_isodon 0 361_DCA1_1455Carcharhinus_acronotus 0 214_DCA1_2728Carcharhinus_acronotus 0 387_DCA1_1132Carcharhinus_falciformis 0 224_DCA1_2783Carcharhinus_falciformis 0 244_DCA1_0536Carcharhinus_falciformis 0 405_DCA1_1286Carcharhinus_falciformis 0 394_DCA1_1751Carcharhinus_falciformis 0 406_DCA1_1050Carcharhinus_falciformis 0 417_DCA1_1032Carcharhinus_falciformis 0 242_DCA1_0809Carcharhinus_falciformis 0 228_DCA1_0743Carcharhinus_falciformis 2 399_DCA1_1495Carcharhinus_falciformis 5 237_DCA1_1964Carcharhinus_falciformis 392_DCA1_1489Carcharhinus_falciformis 222_DCA1_2747Carcharhinus_falciformis 43 43 220_DCA1_2798Carcharhinus_brevipinna 43 372_DCA1_1021Carcharhinus_brevipinna 43 373_DCA1_1088Carcharhinus_brevipinna 43 374_DCA1_1115Carcharhinus_brevipinna 43 375_DCA1_1080Carcharhinus_brevipinna 8 43 376_DCA1_1027Carcharhinus_brevipinna 43 377_DCA1_1149Carcharhinus_brevipinna 43 378_DCA1_1381Carcharhinus_brevipinna 20 379_DCA1_1478Carcharhinus_brevipinna 20 380_DCA1_1302Carcharhinus_brevipinna 20 1018_ESHKC032-07_Carcharhinus_brevipinnaQWX 20 1092_ESHKC033-07_Carcharhinus_brevipinnaQWX 20 221_DCA1_1969Carcharhinus_brevipinna 966_Carcharhinus_brevipinna 371_DCA1_0320Carcharhinus_brevipinna 72 72 216_DCA1_1432Carcharhinus_amblyrhynchos 72 218_DCA1_0565Carcharhinus_amblyrhynchos 0 72 219_DCA1_0599Carcharhinus_amblyrhynchos 72 964_Carcharhinus_amblyrhynchos 72 368_DCA1_1464Carcharhinus_amblyrhynchos 72 367_DCA1_1073Carcharhinus_amblyrhynchos 72 369_DCA1_1294Carcharhinus_amblyrhynchos 72 217_DCA1_0909Carcharhinus_amblyrhynchos 72 366_DCA1_1504Carcharhinus_amblyrhynchos 1014_EGRYR012-07_Carcharhinus_amblyrhynchosQWX 4 1088_EGRYR006-07_Carcharhinus_amblyrhynchosQWX 91 1031_ESHKC169-07_Carcharhinus_dussumieriQWX 1100_ESHKC170-07_Carcharhinus_dussumieriQWX 64 1004_FJ519530_1_Sphyrna_zygaena 65 1082_EWHHS024-06_Sphyrna_zygaenaQWX 1 1145_EWHHS005-06_Sphyrna_zygaenaQWX 76 76 861_DCA1_2640Sphyrna_mokarran 76 862_DCA1_2600Sphyrna_mokarran 76 863_DCA1_2639Sphyrna_mokarran 76 865_DCA1_2306Sphyrna_mokarran 15 76 866_DCA1_2383Sphyrna_mokarran 76 867_DCA1_1972Sphyrna_mokarran 76 1001_JN989316_1_Sphyrna_mokarran 76 1054_EWHHS068-06_Sphyrna_mokarranQWX 76 1120_EWHHS093-06_Sphyrna_mokarranQWX 76 945_DCA1_0239Sphyrna_mokarran 77 946_DCA1_1786Sphyrna_mokarran 864_DCA1_2675Sphyrna_mokarran 944_DCA1_1982Sphyrna_mokarran 41 41 370_DCA1_1037Carcharhinus_brachyurus 41 965_Carcharhinus_brachyurus 9 1017_ESHKC142-07_Carcharhinus_brachyurusQWX 7 1091_ESHKC141-07_Carcharhinus_brachyurusQWX 1006_GQ227288_1_Carcharhinus_dussumieri 335_DCA1_2146Carcharhinus_porosus 97 97 835_DCA1_1014Sphyrna_lewini 97 999_Sphyrna_lewini 97 836_DCA1_1015Sphyrna_lewini 97 912_DCA1_1412Sphyrna_lewini 97 926_DCA1_1120Sphyrna_lewini 97 929_DCA1_1307Sphyrna_lewini 97 843_DCA1_1068Sphyrna_lewini 97 911_DCA1_1133Sphyrna_lewini 97 859_DCA1_1016Sphyrna_lewini 97 914_DCA1_1147Sphyrna_lewini 97 917_DCA1_1362Sphyrna_lewini 97 837_DCA1_1446Sphyrna_lewini 97 838_DCA1_1417Sphyrna_lewini 97 841_DCA1_1416Sphyrna_lewini 97 845_DCA1_1413Sphyrna_lewini 97 924_DCA1_1051Sphyrna_lewini 97 928_DCA1_1190Sphyrna_lewini 97 933_DCA1_1129Sphyrna_lewini 97 935_DCA1_1427Sphyrna_lewini 97 936_DCA1_1118Sphyrna_lewini 97 937_DCA1_1397Sphyrna_lewini 97 938_DCA1_1405Sphyrna_lewini 97 939_DCA1_1436Sphyrna_lewini 97 930_DCA1_1054Sphyrna_lewini 97 931_DCA1_1459Sphyrna_lewini 97 932_DCA1_1418Sphyrna_lewini 97 904_DCA1_1092Sphyrna_lewini 97 901_DCA1_1161Sphyrna_lewini 97 902_DCA1_1183Sphyrna_lewini 97 908_DCA1_1500Sphyrna_lewini 97 897_DCA1_1514Sphyrna_lewini 97 898_DCA1_1020Sphyrna_lewini 97 899_DCA1_1038Sphyrna_lewini 97 900_DCA1_1217Sphyrna_lewini 97 840_DCA1_1040Sphyrna_lewini 97 919_DCA1_1139Sphyrna_lewini 97 920_DCA1_1291Sphyrna_lewini 97 921_DCA1_1352Sphyrna_lewini 97 846_DCA1_1437Sphyrna_lewini 97 922_DCA1_1162Sphyrna_lewini 97 918_DCA1_1320Sphyrna_lewini 97 913_DCA1_1376Sphyrna_lewini 97 842_DCA1_1069Sphyrna_lewini 97 849_DCA1_1030Sphyrna_lewini 97 907_DCA1_1184Sphyrna_lewini 97 896_DCA1_1318Sphyrna_lewini 97 894_DCA1_1099Sphyrna_lewini 97 839_DCA1_1010Sphyrna_lewini 97 847_DCA1_1064Sphyrna_lewini 97 943_DCA1_1135Sphyrna_lewini 97 844_DCA1_1451Sphyrna_lewini 97 848_DCA1_1461Sphyrna_lewini 97 942_DCA1_1349Sphyrna_lewini 97 941_DCA1_1305Sphyrna_lewini 66 915_DCA1_1131Sphyrna_lewini 75 1048_EWHHS006-06_Sphyrna_lewiniQWX 895_DCA1_1467Sphyrna_lewini 1114_EWHHS059-06_Sphyrna_lewiniQWX 87 903_DCA1_1084Sphyrna_lewini 7 57 906_DCA1_1083Sphyrna_lewini 916_DCA1_1311Sphyrna_lewini 64 64 905_DCA1_1022Sphyrna_lewini 64 909_DCA1_1103Sphyrna_lewini 664 910_DCA1_1425Sphyrna_lewini 64 925_DCA1_1134Sphyrna_lewini 64 927_DCA1_1171Sphyrna_lewini 64 934_DCA1_1392Sphyrna_lewini 64 998_Sphyrna_corona_DCA1_1392 940_DCA1_1379Sphyrna_lewini 923_DCA1_1315Sphyrna_lewini 81 1016_EWHHS163-06_Eusphyra_blochiiQWX 1090_EWHHS164-06_Eusphyra_blochiiQWX 26 868_DCA1_1086Sphyrna_tiburo 26 869_DCA1_2739Sphyrna_tiburo 26 1140_EWHHS147-06_Sphyrna_tiburoQWX 26 1002_Sphyrna_tiburo 10 26 949_DCA1_1394Sphyrna_tiburo 26 950_DCA1_1407Sphyrna_tiburo 4 26 948_DCA1_1398Sphyrna_tiburo 26 951_DCA1_1391Sphyrna_tiburo 50 952_DCA1_1123Sphyrna_tiburo 50 953_DCA1_1343Sphyrna_tiburo 50 947_DCA1_1178Sphyrna_tiburo 89 870_DCA1_2829Sphyrna_tiburo 954_DCA1_2741Sphyrna_tiburo 1076_EWHHS133-06_Sphyrna_tiburoQWX 11 83 83 871_DCA1_2205Sphyrna_tudes 83 1000_Sphyrna_mediaDCA1_2205 83 872_DCA1_2708Sphyrna_tudes 873_DCA1_2825Sphyrna_tudes 874_DCA1_2738Sphyrna_tudes 51 51 875_DCA1_2606Sphyrna_tudes 51 1003_Sphyrna_tudes 12 51 876_DCA1_2618Sphyrna_tudes 51 878_DCA1_2619Sphyrna_tudes 51 877_DCA1_2742Sphyrna_tudes 51 879_DCA1_2715Sphyrna_tudes 51 880_DCA1_2716Sphyrna_tudes 51 881_DCA1_2717Sphyrna_tudes 51 882_DCA1_2720Sphyrna_tudes 51 883_DCA1_2721Sphyrna_tudes 51 884_DCA1_2743Sphyrna_tudes 51 885_DCA1_2750Sphyrna_tudes 51 886_DCA1_2709Sphyrna_tudes 51 887_DCA1_2714Sphyrna_tudes 51 888_DCA1_2718Sphyrna_tudes 51 889_DCA1_2719Sphyrna_tudes 51 890_DCA1_2745Sphyrna_tudes 51 891_DCA1_2710Sphyrna_tudes 76 892_DCA1_2711Sphyrna_tudes 893_DCA1_1944Sphyrna_tudes 1078_EWHHS123-06_Sphyrna_tudesQWX 45 807_DCA1_2152Rhizopriondon_porosus 45 88 1046_ESHKD070-07_Rhizoprionodon_lalandiiQWX 44 1112_ESHKD072-07_Rhizoprionodon_lalandiiQWX 44 994_Rhizoprionodon_porosus 44 813_DCA1_0847Rhizoprionodon_porosus 44 820_DCA1_2758Rhizoprionodon_porosus 44 830_DCA1_1094Rhizoprionodon_porosus 44 822_DCA1_1965Rhizoprionodon_porosus 44 826_DCA1_1977Rhizoprionodon_porosus 44 809_DCA1_2803Rhizoprionodon_porosus 44 821_DCA1_2830Rhizoprionodon_porosus 44 810_DCA1_2756Rhizoprionodon_porosus 44 811_DCA1_2768Rhizoprionodon_porosus 44 812_DCA1_2823Rhizoprionodon_porosus 44 814_DCA1_2723Rhizoprionodon_porosus 44 815_DCA1_2725Rhizoprionodon_porosus 44 816_DCA1_2760Rhizoprionodon_porosus 44 817_DCA1_2784Rhizoprionodon_porosus 44 818_DCA1_2807Rhizoprionodon_porosus 44 819_DCA1_2826Rhizoprionodon_porosus 44 823_DCA1_2759Rhizoprionodon_porosus 44 824_DCA1_2757Rhizoprionodon_porosus 44 825_DCA1_2801Rhizoprionodon_porosus 44 808_DCA1_2734Rhizoprionodon_porosus 44 833_DCA1_1430Rhizoprionodon_terraenovae 44 995_Rhizoprionodon_terraenovae 44 829_DCA1_1085Rhizoprionodon_porosus 44 831_DCA1_2621Rhizoprionodon_porosus 44 832_DCA1_2748Rhizoprionodon_porosus 44 834_DCA1_2755Rhizoprionodon_terraenovae 44 828_DCA1_1093Rhizoprionodon_porosus 44 1064_ESHKD059-07_Rhizoprionodon_porosusQWX 52 1130_ESHKD058-07_Rhizoprionodon_porosusQWX 23 1075_ESHKD044-07_Rhizoprionodon_terraenovaeQWX 1139_ESHKD053-07_Rhizoprionodon_terraenovaeQWX 1011_ESHKD100-07_Rhizoprionodon_acutusQWX 32 982_KY176593_1_Glaucostegus_cemiculus 33 96 996_JN108019_1_Rhynchobatus_australiae 38 997_Rhynchobatus_laevis/palpebratus 991_KR003773_1_Rhina_ancylostoma 990_EU398989_1_Pristis_zijsron 993_KF564313_1_Rhinobatos_rhinobatos

SVG (data:image/svg+xml;base64, PHN2ZyB3aWR0aD0iNzUwIiBoZWlnaHQ9Ijc2MiIgdmVyc2lvbj0iMS4xIiB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC

Dessimoz Lab (../gotodessimozlab.html) https://mafft.cbrc.jp/alignment/server/spool/_phyloio.171229031330463.html 1/1 bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not 2/26/2018certified by peer review) is the author/funder, who has granted bioRxiv a licensePhylo.io to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Zoom:

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SVG (data:image/svg+xml;base64, PHN2ZyB3aWR0aD0iMTAwMCIgaGVpZ2h0PSI5MjEuMjUiIHZlcnNpb249IjEuMSIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj48ZyB0cmFuc2Zvcm09InRyYW5zbGF0ZSg0

Dessimoz Lab (../gotodessimozlab.html) https://mafft.cbrc.jp/alignment/server/spool/_phyloio.18022705212877.html 1/2 bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not 2/14/2018certified by peer review) is the author/funder, who has granted bioRxiv a licensePhylo.io to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license.

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306_KT879785_1Rhynchobatus_springeriWX 307_KT879758_1Rhynchobatus_immaculatusWX 308_GQ980006_1Pristis_microdonWX 309_GQ980007_1Pristis_microdonWX 310_GQ980007_1_Pristis_microdon_WX 311_GQ980008_1Pristis_zijsronWX 312_GQ980009_1Pristis_zijsronWX + 313_GQ980009_1_Pristis_zijsron_WX SVG (data:image/svg xml;base64, 314_KC610069_2Zapteryx_exasperataWX 315_KC610071_2Zapteryx_exasperataWX PHN2ZyB3aWR0aD0iMTAwMCIgaGVpZ2h0PSI5MjEuMjUiIHZlcnNpb249IjEuMSIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3Jn

Dessimoz Lab (../gotodessimozlab.html) https://mafft.cbrc.jp/alignment/server/spool/_phyloio.180215025728187.html 1/1 bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not 2/13/2018certified by peer review) is the author/funder, who has granted bioRxiv a licensePhylo.io to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Zoom:

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SVG (data:image/svg+xml;base64, PHN2ZyB3aWR0aD0iODYxLjExMTE0NTAxOTUzMTIiIGhlaWdodD0iODUzLjMzMzM3NDAyMzQzNzUiIHZlcnNpb249IjEuM

Dessimoz Lab (../gotodessimozlab.html) https://mafft.cbrc.jp/alignment/server/spool/_phyloio.18021404262509.html# 1/1 bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not 2/14/2018certified by peer review) is the author/funder, who has granted bioRxiv a licensePhylo.io to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Zoom:

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Dessimoz Lab (../gotodessimozlab.html) https://mafft.cbrc.jp/alignment/server/spool/_phyloio.18021502344066.html 1/1 bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license.

bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not 2/15/2018certified by peer review) is the author/funder, who has granted bioRxiv a licensePhylo.io to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Zoom:

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Dessimoz Lab (../gotodessimozlab.html) https://mafft.cbrc.jp/alignment/server/spool/_phyloio.180216022311540.html 1/1 bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not 2/11/2018certified by peer review) is the author/funder, who has granted bioRxiv a licensePhylo.io to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 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SVG (data:image/svg+xml;base64, PHN2ZyB3aWR0aD0iMTIwNC40NDQ0NTgwMDc4MTI1IiBoZWlnaHQ9IjgyMy4zMzMzNzQwMjM0Mzc1IiB2ZXJzaW9uPSI

Dessimoz Lab (../gotodessimozlab.html) https://mafft.cbrc.jp/alignment/server/spool/_phyloio.180212014817637.html 1/1 bioRxiv preprint doi: https://doi.org/10.1101/433847; this version posted October 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license.

Figure 8

350 R² = 0.9086 300

250 all other genera

200 genus Alopias

150 species with CR 100

50 Number of fins identified to the same 0 0 50 100 150 200 Number of fins identified to a particular species with COI

Figure 9